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Breeding approaches for Improved Nutritional Quality
and Nutraceutical properties in Vegetable crops
Presented By
NARAYANA SWAMY G
Ph.D. Ist Year Roll No: 11919
Division of Vegetable crops
ICAR- Indian Institute of Horticultural Research, Bengaluru-560 089
Content
Introduction
Nutritional quality and Coloured
Vegetables
Nutraceuticals-Properties
Breeding approaches- improved
nutrition quality
Case studies
Conclusion
2
INTRODUCTION
 About 2500 years ago, Hippocrates, the father of modern
medicine, conceptualized the relation between the use of
appropriate foods for health and their therapeutic benefits
 He promulgated that ‘’let food be your medicine and medicine be
your food’’
2500 years ago
 The improper diet and unbalanced nutrition are the major reasons of
malnutrition of about 3 billion people in our world (Kumari M. et al., 2020).
 According to global hunger index India ranks 94 among 107 countries
in 2020 with a serious issue of child wasting (IFPRI,2020)
 India is home to 46.6 million stunted children which is one third of world's
total. (Global Nutrition Report, 2018).
Aim: Lay stress on the importance of
child nutrition and how kids can
benefit from a nourishing diet right
from birth..
8 March 2018
Quality improvement of
crop plants is a
significant component
in nutritional and food
security
Food
security
All people, at all
times, have physical,
social, and economic
access to sufficient,
safe and nutritious
food’ (World Food
Summit, 1996).
Consumption and
physiological uses of
adequate quantities of
safe and nutritious food
by every member of the
household to support
an active, productive
and healthy life (Sidhu
and Rao, 2010)
Nutritional
Security
Quality defined as the “degree of excellence or superiority” (Kader
et al., 1985).
Quality includes flavour, colour, shape, size, degree of damage,
nutrient levels and traits that permit greater perceived food safety or
environmental sustainability.
Nutritional value is used to provide good-balanced ratio of the
fundamental nutrients like carbohydrates, fat, protein, minerals, and
vitamin in items of food or diet.
Nutritional Quality of Vegetables
Nutritional quality describes the inherent biological or health value of
produce including the ratio of beneficial to harmful substances, taste,
fragrance, freshness, and shelf-life that govern consumer behaviour.
Traditional
component
Organic
Acid
Protines
Lipid &
Fatty
acids
Carbohydrate
s
Dietary
fibre
Vitamins
Vicente et al.(2009)
Quality attributes of Vegetables
Intrinsic quality attributes Extrinsic quality attributes
- Inherent to the product itself
- Provide stimuli to consumers and eventual
quality perceptions
Linked to the production method but
not a property of the food itself
 Like pesticides, eco-and animal
friendliness, packaging materials,
processing technology.
Sensory attributes
(Classical aspects)
 Flavour
 Taste
 Appearance
 Colour
 Texture
 Smell
Health attributes
• Major nutrients
• Amino acids
• Vitamins
• Dietary minerals
• Antioxidants
(Influence purchasing policy of some
consumers)
Carotenoids : Lycopene, Lutein, -carotene
Polyphenolics : Flavonoids, Flavones, Anthocyanin
Glucosinolate :Sulphoraphane, Indole-3-Carbinol
Thiosulphides : Alliin, Methiin, Ethiin
Dietary fiber : Lignin, Pectin, Cellulose
Miscellaneous : Selenium, Phytosterol, Saponins
Behara et al. (2019)
Type of traits Description Examples
Morphological Appearance of
the produce
Fruit size,
shape, colour
Organoleptic Palatability of
the produce
Taste, aroma,
juiciness,
softness
Nutritional Value of the produce
for human or animal
nutrition
Protein content, oil
content, vitamin
content, mineral
content
Consumer
preference
Increases the
marketability of the
produce
Keeping quality,
storability
Various quality traits (Debnath and Guha , 2015)
Vegetables are bulky source of
micronutrients and their ‘compound
matrix’ is effective in supply of diverse
elements to the body
Globally, the Food and Agriculture Organization (FAO) recommends for intake of 400 g
vegetables per day in order to boost the consumption
Behera and Singh,2019
Important source of dietary
minerals and vitamins and
contribute to fight against
micronutrient malnutrition
The health benefiting
compounds act as antioxidants
in human body and play role in
homeostasis balance
They contribute functionally
active secondary metabolites
which have preventive role
against various health ailments.
Why we need to emphasis on nutritional security through vegetables?
The 5 A Day campaign is based on advice
from the World Health Organization (WHO),
which recommends eating a minimum of
400 g of fruit and vegetables a day to lower
the risk of serious health problems, such as
heart disease, stroke and some types of
cancer.
Red vegetables
help to fight
cancer, reduce
the risk of
diabetes and
heart disease,
improve skin
quality.
Orange and
yellow
vegetables
improve
immune
function, reduce
the risk of heart
disease,
promote eye
health
Green
vegetables boost
the immune
system, help
detoxify the
body, restore
energy and
vitality.
fight Cancer
and unwanted
inflammation,
protects cell
from damage,
boosts memory
Protect Against
certain cancers,
keep bones
strong, reduces
the risk of heart
ailment, lowers
cholesterol
 Natural Pigments like chlorophyll, anthocyanin, carotenoids make vegetables colourful.
 Dark and intensively coloured vegetable usually contain more chemically active
antioxident pigments than pale crops.
 Eating a mix of different coloured vegetables nourish our body with a range nutritive
compounds.
Coloured Vegetables
Lycopene,
quercetin
and
Hesperidin
Chlorophyll,
fiber, lutein,
zeaxanthin,
calcium, folate,
vitamin C and
beta carotene
Lutein,
zeaxanthin,
resveratrol,
Anthocyanin,
fiber,
flavonoids
Beta-glucans
and lignans
Beta-
carotene,
zeaxanthin,
flavonoids Rai et al.( 2012)
Natural Nutraceuticals
Nutraceutical is a combination of the words “nutrition” and “pharmaceuticals,” are any
substance that is a food or a part of a food and provides medical or health benefits,
including the prevention and treatment of diseases.(Rai et al., 2012)
The term "Nutraceutical" was coined by Dr Stephen DE Felice in 1989.
A nutraceutical is demonstrated to have a physiological benefit or provide
protection against chronic disease through antioxidant activity (Gupta et al., 2013)
Vegetables are functional foods nutraceuticals because they provide minerals
and nutrients which are health promoting and a major source of biologically active
nutraceuticals.
Nutraceuticals: the concept
 The term of “Nutraceutical” is applied
for mainly to ingredient (rather than
complete product). Finished product
referred as functional foods or
fortified foods.
Important nutraceuticals in plants (inner whorl) & their role in human health
(outer whorl)
Nutraceuticals
Singh et al., 2020
Neutraceutical properties in Vegetables
Chemical compounds Plant source Properties
Allicin (organosulfur
compound)
Garlic, onion, parsnip Antifungal; antibacterial; antioxidant; used to
treat arteriosclerosis
Apigenin Cabbage, celery, lettuce 4’,5,7-trihydroxyflavone is a flavone that is the
aglycone of several glycosides
Beta carotene Carrots, pumpkins, sweet
potatoes, winter squash,
broccoli, spinach and kale
Anti aging; anti cancerous; improve lung
function; reduce complications associated with
diabetes
Betanin Beets, chard Natural colourant used in icecreams
Capsaicin or trans-8-
methyl-N-vanillyl-5
nonenamide
Red chilli Used for pain relief topically and as a digestive
aid when taken internally; antioxidant;
antiallergic
Caffeic acids Carrot Inhibitor of the lipoxygenase enzyme that forms
leukotrienes from arachidonic acid
Tocopherol Broccoli, carrot, celery,
onion
It is a fat-soluble antioxidant that stops the
production of reactive oxygen species formed
when fat undergoes oxidation
Plant Glucosamine Lettuce, peas, cabbage Chondroitin and glucosamine are part of normal
cartilage and act as a cushion between the joints
Tocopherol Broccoli, carrot, celery,
onion
It is a fat-soluble antioxidant that stops the
production of reactive oxygen species formed
when fat undergoes oxidation
Plant Glucosamine Lettuce, peas, cabbage Chondroitin and glucosamine are part of normal
cartilage and act as a cushion between the joints
Luteoline Cauliflower, celery ,
sweet pepper
A carotenoid which shows eye benefits
Sulphoraphane Broccoli Used against breast cancer
Phytosterol Germinated corn Lower cholesterol absorption in the digestive
tract thereby lowering overall cholesterol level in
the bloodstream
Proanthocyanin Red cabbage, egg plant Help in urinary tract infections by inhibiting
adhesion of microorganisms like E. coli to the
urinary tract wall
Zeaxanthin Carrot , celery, kale,
lettuce
Used for eye health and in age related
mascular degeneration
Rai et al.( 2012)
Carotenoids- Lycopene, Lutein, β-carotene
Glucosinolate- Sulphoraphane, Indole-3-carbinol
Polyphenolics- Flavonoids, Flavones, anthocyanin
Thiosulphides- Allin, Methiin, Ethiin
Indoles: Indole-3-carbinol (I3C) and indole 3-acetonitrile (I3A)
Phytochemicals in Vegetables
Phytochemicals or phytoceuticals present in plant foods like
vegetables which neutralize harmful free radicals generated in the body
and have protective or disease preventive characteristics.
 These are secondary metabolites and formed due to the enzymatic
resections of primary metabolites (amino acids, sugars, vitamins etc.)
There are over 900 phytochemicals found in foods, one serving of a
fruit or vegetable may have as many as 100 different phytochemicals
Breeding objectives for improved nutrition quality
 To enhance productivity to meet the ever increasing food requirement of people.
 Conventional breeding in conjunction with molecular biology will make it possible to
get vegetable varieties enriched with nutraceuticals and edible colors suitable for
fresh market as well as industry.
 High yielding and dietary micronutrients rich variety development.
 Enrichment of nutraceuticals need special attention.
 Wider adaptability, rich in dietary nutrients and antioxidants.
 Crop specific breeding.
 Good in organoleptic scores, high portion of edible parts, high acceptance among
consumers.
Behera et al., 2019 & Singh et al., 2020
Crops Wild relatives/ accessions/ landraces/ varieties Nutrients
Tomato
S. pimpinellifolium, Caro Red (Rugers x S. hirsutum) Vitamin A
High pigment mutants (hp), Crimpson (og), Pusa Rohini Lycopene
Caro Rich, F-7045, VRT-35, CGT, VRT-5 Beta carotene
S. pennellii, IL12-4 Ascorbic acid
S. chilense and atroviolacium (atv) from S. cheesmaniae Anthocyanin
Chilli C. annuum var. IC: 119262(CA2), Bayadaggi kaddi Ascorbic acid
Paprika KTPL-19 Capsanthin
Cucumber Xishuangbanna gourd Beta carotene
Muskmelon Honey dew32 Ascorbic acid
Spine gourd Momordica dioca Protein
M. chochinchinenesis Lycopene
Bitter gourd DRAR-1, DVBTH-5 Beta carotene
Sweet potato Resisto, Zambezi, Chiwoko Beta carotene
Cassava UMUCASS 44, UMUCASS 45 and UMUCASS 46 Vitamin A
Broccoli Brassica villosa Glucosinolates
Natural resources rich in quality traits useful for breeding
Singh et al.,2020
Crop Varieties Nutraceuticals
Tomato Pusa Rohini 4.5 mg/100g fw Lycopene
Brinjal
Pusa Safed Baingan, 31.21
mg/100 g fw
Pusa Hara Baingan 1, 33.5
mg/100 g fw
Pusa Shyamla, 48.2 mg/100g
fw
Phenolics
Phenolics
Anthocyanin
Bitter gourd Pusa Aushadhi, 6.51 mg/100 g
fw
Pusa Rasdhar, 4.3 mg/100 g fw
Phenolics
Onion Pusa Madhvi, 101.2 mg/100g
fw
Pusa Ridhi, 107.42 mg/100g fw
Pusa Soumya, 74.6 mg/100g fw
Quercetin
Carrot Pusa Yamdagini, 7.55 mg/100g
fw
Beta-carotene
Pusa Rudhira, 386 mg/100g fw Lycopene
Pusa Asita, 339 mg/100g fw Anthocyanin
Pusa Rudhira, 45.15 mg/100g Phenols
Beetroot Crosby, 17.15 mg/g dm Anthocyanin (Sawicki
et al., 2016)
Red cabbage Primero 109 mg/100g fw Anthocyanin
(Ahmadian et
al.,2014)
Cauliflower Pusa Sharad, 23.94 μ mol/ 100 g fw
Pusa Beta Kesari 1, 8-10ppm
Sinigrin
Beta carotene
Purple
Cauliflower
Graffiti, 375 mg/100g fw Anthocyanin (Chiu
et al., 2010)
Broccoli Green broccoli, 15.2-59.3 μ mol/100
g fw
Purple broccoli ,26.3 μ mol/100 g fw
Glucosinolates
Bathua Pusa Green, 7.6 mg/100g dw Iron
Palak All Green, 16.2 mg/100g dw Iron
Amaranth Pusa Kirti, 38.5 mg/100g dw Iron
Methi Pusa Early Bunching, 17.2 mg/100g
dw
Iron
Sag sarson PusaSag -1, 16.3 mg/100g dw Iron
Sweet Potato Bhu Sona , 14.0 mg /100g
Bhu Krishna , dry matter (24-25.5%),
starch(19.5%), total sugar(1.9-2.2%)
Sree kanaka, 90.0 mg /100g
β-carotene
Anthocyanin
Tapioca Sree Visakham, 466 IU/100g Carotene
Palam Kanchan
Novel genotypes/ breeding lines identified for nutrition
Carotene Rich Tomato
Carotene rich Cherry tomato
Carotene rich cauliflower
Pusa Asita
Cole Crops
Root Vegetable Crops
Solanaceous Vegetable Crops
Palam Vichitra
Pusa Gulabi Pusa Jamuni
Anthocyanin Rich Tomato
Important gene for quality traits
Crop Nutrients Gene
Tomato Lycopene High pigment (1,2,3) hp
ySAMdc; spe-2
β-carotene Green flesh (gf)
Yellow (r)
Tangerine (t)
Lutein cry-2
Carotenoids Phytoene synthase (Psy-1)
Anthocyanin Anthocyanin fruit (Aft)
Aubergine (Abg)
Atroviolacium(atv)
Tocopherol hmgr-1
Folate GCH-1
Kaempherol LC and C1
High flavonols chi-a
Chilli Capsaicinoids C
Delta gene Reddish - orange
colour
Ogc gene -Crimson colour
Apricot gene – yellowish pink
colour
Anthocyanin (Aft) Gene – purple
colour
r gene -yellow colour (Yellow
flesh)
Crop Nutrients Gene
Chilli β-carotene B; bc
Anthocyanin (Immature
fruit)
A/F
Potato Protein AmA1
β-carotene Or, Crt-B
Phytoene Dxs
Sweet potato High protein Asp-1
Anthocyanin IbMYB1
Cauliflower β-carotene Or
Anthocyanin Pr
Cabbage Anthocyanin MYB
Lettuce Folate Gch1
Iron Pfe
Ascorbate Gul oxidase
Cucumber β-carotene Ore
Singh et al. (2015)
Purple (Pr) gene mutation in cauliflower
confers an abnormal pattern of anthocyanin
accumulation (Chiu et al., 2010)
The Orange (Or) gene mutation in cauliflower
confers the accumulation of high levels of -
carotene in various tissues normally devoid of
carotenoids.(Lu et al., 2006)
High pigment (hp-1) mutation, known to
increase flavonoids in tomato fruits.(Sapir et al.,
2008)
26
Breeding approaches for improved nutritional quality
Conventional breeding
approach:
 Selection
 Hybridization
 Mutation
 Polyploidy breeding
 Soma clonal variation
Biotechnological
approach
1.Molecular Breeding:
 Development
and deployment
of molecular markers
 Marker Assisted
selection
 QTLs associated
with quality traits
2.SNPs discovery
3.Genome sequencing
and transcriptome
analysis
4.Transgenic approach
5.RNA interference
6.Targeted genome
editing.
Most of the colour varieties are developed by this method
Selected on the basis of phenotypic characters
Pusa Kulfi
high lutein
Pusa asita
High anthocyanin
SELECTION
27
Pusa Rudhira
(High lycopene)
Pusa Meghali
(High β-carotene)
Pusa Vristi
(Lycopene:
405µg /100g)
Pusa Payasa
High β-Carotene)
Chinese Red
(Lycopene)
Pusa Mridula
(Lycopene)
Pusa Gulabi
(Anthocyanin)
Carotene
content
(11.27
mg%)
ESRao et
al., IIHR.
Pusa Rohini (Lycopene)
Pusa Uphar (Lycopene)
28
Arka Abhir
(Capsanthin)
Punjab lal
(Capsanthin)
HYBRIDIZATION
• Crossing between two genetically dissimilar parents. It is the best method for
crop improvement in cross pollinated crops.
• Two genetically superior divergent parents are selected and crosses were made
to develop superior cultivars.
 US pickling cucumber (‘Addis’) × XIS (Cucumis
sativus var. xishuangbannanesis Qi et Yuan) High β-carotene inbred line (S4),
‘EOM 402-10’, was developed. Cuevas et al., Euphytica (2010).
Pusa
Nayanajyoti
(High β-Carotene)
Pusa Vasuda
(Lycopene)
Kuroda
( β-Carotene)
Oxheart
(Lycopene+An
thocyanin)
 Tomato (High Beta carotene)
Lycopersicon esculentum x Lycopersicon hirsutum and
Lycopersicon esculentum x Lycopersicon hirsutum f glabratum –
(Kalloo, 1988).
 Tomato Caro red (Provitamin -A rich tomato variety)
Common Tomato (Solanum esculentum Mill) x Wild Tomato species,
(Solanum hirsutum Humb.). (M. L. Tomes (1958)
INTERSPECIFIC HYBRIDIZATION
Crosses were made between two different species of the same genus known as
Interspecific hybridization.
 U.S. pickling cucumber lines (Cucumis sativus L. var. sativus) x
(C. sativus L. var. xishuangbannanesis Qi et Yuan- Orange-fruited
Xishuangbannan cucumber lines ) (Simon and Navazio, 1997)
Soma clonal variation is defined as genetic or epigenetic changes that arise in vitro between
clonal regenerants and their corresponding donor plants.
Leva et al., (2017): Encyclopedia of Applied Plant Sciences (2nd edition) 2: 468-473
Chromosomal rearrangements are an important source of this variation.
A cultivar of sweet potato ‘Scarlet’ having higher yield and disease resistance
characteristics similar to their parent but also have darker and more stable skin colour
SOMACLONAL VARIATION
(Moyer and Collins, 1983)
MUTAGENESIS
Species Mutant gene Phenotype References
Tomato r (yellow flesh) Yellow fruit colour Fray and Grierson,1993
delta Orange fruit colour Ronen et al.,1999
tangerine Orange fruit colour Isaacson et al.,2002
Beta Orange fruit colour Ronen et al.,2000
hp-1 Flavanoids Rajasree et al., 2021
Pepper y (yellow) Yellow fruit colour Lefebvre et al., 1998
c2 Yellow fruit colour Thorup et al., 2000
POLYPLOIDY BREEDING
Cucumis melo inbred M01-3 (2n=24) by colchicine.
Tetraploid muskmelon- rich in soluble solid, soluble sugar and
vitamin C contents (Zhang et al. 2010)
Triploid and tetraploid watermelon- increased range of lycopene
than diploid (Liu et al. 2010)
Auto-tetraploid cultivar of fenugreek- larger leaf area and larger
productivity concerning seed number, pod number than diploids
and rich in K, Na, Ca and P (Peiman Zandi et al., 2017)
 Polyploids can be induced due to aberration in cell division.
 This can be used to enhance nutraceuticals and colors
Need of biotechnological intervention for nutritional quality improvement
 Crop improvement relies on modulating the genes and genomic regions
underlying key traits, either directly or indirectly
 Identification of robust and tightly linked molecular markers for target
traits.
 Intensification of crop improvement programmes using biotechnological
and breeding interventions had resulted in the trait discovery and release
of improved varieties
 Molecular techniques are helpful in improving bioavailability of the target
compounds, their biosynthesis in plant species/tissues where these
compounds are not naturally produced, over-expression of transgenes
and removal of anti-nutritional factors.
Development and deployment of molecular markers
Crop Trait Marker Reference
Brassica 2-propenyl glucosinolate
content
ISSR Marker Ripley and Roslinsky.
(2005)
B. villosa High glucosinolate
content
OI12-F02 (QTL 2)
(Micro satellite marker)
Sarikamis et al. (2006)
Cauliflower â-carotene AFLP markers linked to
“Or” gene
Li and Garvin (2003)
Chinese cabbage β-carotene accumulation SCAR markers linked to
“or” gene
Zhang
et al. (2008)
Carrot β- Carotene AFLP marker linked to Y2
loci
Santos and Simon (2002)
Cucumber Endocarp carotene
content
SSR marker on LG-3 Bo et al. (2011)
Broad bean Increased protein content
and reduced fibre content
zt 2 gene specific SCAR
marker
Gutierrez et al. (2008)
Molecular markers are used to study linkage with gene responsible for high nutraceuticals and edible
colours using mapping population.
These markers enabled the development of high-density genetic maps useful for mapping of target genes
and utilize them in crop breeding.
Molecular markers are also employed for the detection of genetic variation associated with valuable
nutrient traits among cultivars in a species and facilitate the identification of appropriate parents for
molecular breeding.( Singh et al., 2020)
Molecular Breeding and Marker Assisted selection
Introgression of ‘Or’ gene into Indian
cauliflower leads to development of β-
carotene (8-20 ppm) rich cauliflower
variety Pusa Beta Kesari VitA-1
(Kalia et al., 2018).
Introgression of β-carotene quantity
controlling gene ‘ Ore’ in cultivated
cucumber linked to seven SSR
markers on linkage group 3
(Bo et al., 2011).
QTLs associated with Nutritional quality traits
The analysis of quantitative trait locus (QTL) is a statistical approach that correlates the
phenotypic measurements with the genotypic data to evaluate the genetic basis of
variations among complex traits.
In vegetables, QTLs were mostly identified for a variety of nutritional quality related trait.
QTL analysis of fruit antioxidants in tomato using L. pennellii introgression lines
detected a total of 20 QTL including five for TACW, six for ascorbic acid, and nine for
total phenolics (Rousseaux et al. ,2005)
Just et al. (2009) performed QTL analysis for pigment content on a carotenoid
biosynthesis and found that Y and Y2 loci on linkage groups 2 and 5 respectively,
control much variation for carotenoid accumulation in carrot roots.
Iorizzo et al. (2019) identified a region in chromosome 3 with co-localized QTL for all
anthocyanin pigments of the carrot root
Example
Crop Trait Mapping
Population
QTLs/ Genes Chromosomes References
Maskmelon
Soluable sugar
content
RIL 6 QTLs;
SSCQU8.3
8,9,10 Pereira et al.(2018)
Total carotene in
flesh
RIL 1Q; CARQU9.1 9 Pereira et al.(2018)
Orange flesh
colour
F3 CmOr gene 9 Tzuri et al .(2015)
Vitamin-C 2QTL Sinclair et al. (2004)
Tomato
Lycopene content
RIL 2 QTl (lyc7.1 ,
lyc12.1,)
7,12 Ashrafi et al. (2012)
BC1S1 8 Q 1,4,5,6,7,10,12 Chen et al.(1999)
BC3 5 Q 2,3,5,8,12 Fulton et al.(2000)
RIL 2 Q 4,11 Rousseaux et al.
(2005)
ILs 2 Q 3,6 Foolad et al.( 2000)
Phenolic content ILs 9 Q 3,5,6,7,8,9 Foolad et al.(2000)
Brinjal
Anthocyanin
- fap10.1 - De Jong et al.(2004)
F2 26 QTLs 2,5,6,8,10 Barchi et al. (2011)
Beetroot Sucrose content - 13QTL - Trebbi et al.(2005)
Carrot β-carotene & δ-
carotene
- 8QTL &4QTL - Santos and Simon
(2002)
SNPs discovery
The SNPs are the predominant and mostly used markers in plant genetic analysis.
The SNPs have become choice markers in modern breeding programme due to their
abundance, stability, amenability to automation, and cost effectiveness (Ganal et al.
,2009).
GBS is also in use for generating genome-wide markers have been used in mapping
QTLs in pumpkin (Zhang et al. ,2015).
Crop Quality trait Reference
Tomato fruit metabolic traits Viquez-Zamora et al. (2013)
Carrot carotenoid biosynthesis Jourdan et al. (2015)
Muskmelon fruit traits Chang et al.( 2016)
Chilli capsaicinoids Nimmakayala et al. (2016)
Genome sequencing :
• Whole genome sequencing serves as the basis for finding genome-
wide analysis of genetic variation
• With the advent of NGS technologies, the sequencing of complete
genome or transcriptome of a species/genotype has become
possible within a few hours
Transcriptome Sequencing:
 Transcriptome sequencing, also called RNA sequencing, refers to
the sequencing of cDNA to get information about a sample’s
total RNA content at a given time in a given condition under
study. This requires the conversion of mRNA into cDNA before the
sequencing reaction.
 Transcriptomic analysis has been used in a number of vegetable
crops for understanding the quality related traits.
 Transcriptome sequencing is done either by first-generation
Sanger sequencing or by high throughput NGS approaches
less representatives of commercial growth condition.
•Transcriptomic changes occurring during the browning of fresh-
cut fruits
•11 genes from five gene families (i.e., PPO, PAL, POD, CAT, and
SOD) were identified as potentially associated with enzymatic
browning . (Zhu et al.,2017)
Luffa
cultivar
‘Fusi-3’
Pea
Spinach
•The presence of r or rb or bsg genes results into accumulation of
low level of starch and a high level of sucrose.
•Mutant alleles at three loci r , rb , and bsg affect starch and sugar
synthesis (Harrison et al.,2000).
~320,000 high-quality SNPs were identified and indicated that
Spinacia turkestanica was more closely related to the
cultivated S. oleracea than S. tetrandra (Xu et al.,2015)
Transgenic Approach
Genetic engineering enabled vegetable breeders to incorporate desired transgenes into
elite cultivars, thereby improving their value, nutritional quality and other health
benefits. (Singh et al., 2020)
Romer et al.( 2000)
developed
transgenic tomato
to enhance the
carotenoid content
and profile of
tomato fruit which
increase in β-
carotene content
about threefold, up
to 45% of the total
carotenoid content
in cultivar “Ailsa
Cray”
To increase the
overall protein
content of
potato
(Chakraborty et
al., 2010)
expressed the
AmA1 gene from
Amaranthus
seed albumin in
potato tubers.
The transgenic
potato lines
called “Protato”
had 48%
increased
protein content
Lettuce
expressing the
deregulated
Arabidopsis
H+/Ca2+
transporter
sCAX1 (cation
exchanger 1)
contained 25–
32% more
calcium than
controls (Park
et al., 2009)
A transgene
construct
pSG766A used
to increase
expression of
isopentenyl
transferase (key
enzyme for
cytokinin
synthesis) in
broccoli. (Chen
et al.,2009)
cyanide-free
transgenic
cultivars of
cassava can be
promising
option to
provide safe
cassava
(Siritunga and
Sayre,2003)
Transgenics with enhanced nutritional quality
Crops Trait Gene References
Potato Beta carotene phytoene synthase
(CrtB), phytoene desaturase (CrtI)
and lycopene betacyclase
(CrtY) from Erwinia
Diretto et al.( 2007)
Potato Vit-C and Vit-E StVTCIA and Al-HPT Bulley et al.(2011); Elizabath et
al.(2011)
Potato Ca Scaxl, Cax2b Park et al.(2005); Kim et al.( 2006)
Potato Starch ShSV, PsGTP, AfNTTI
Amylose (ssn,ssm, SBEI,SBEII)
Fernandez et al.( 2009); Zang et al.
(2008)
Potato Total protien AmA1 Chakraborty et al.(2010)
Sweet potato Increased carotenoids IbOr-Ins -
Tomato Enhanced carotenoid
content
bacterial carotenoid gene (crtI)
encoding for phytoene desaturase
-
Tomato Suppression of PG to
delay fruit ripening
Antisense construct based on
pTOM6 for polygalactronase enzyme
-
RNA interference in vegetables for quality traits
Crops Traits Reference
Tomato
Increasing antioxidants Niggeweg et al. (2004)
Increasing carotenoid and flavonoid content suppression of
DET1 expression
Williams et al.(2004)
Extending shelf-life by blocking the expression of ACC oxidase
gene and two ripening specific N-glycoprotein modifying
enzymes
Meli et al. (2010)
reduction in polygalacturonase activity leading to delayed fruit
ripening
Sheehy et al. (1988
Targeting ripening gene using chimeric RNAiACS construct also
resulted into delayed ripening of fruits up to 45 days (
Gupta et al., (2013)
Onion Suppression of the lachrymatory factor synthase gene Eady et al. (2008)
Carrot
Development of Dau c 1.01 and Dau c 1.02-silenced transgenic
carrot plants show reduced allergenicity
Peters et al. (2011)
reduction in storage root thickness and colour Moreno et al. (2013)
The RNA silencing is a novel gene regulatory mechanism that limits the transcript level by
either suppressing transcription (TGS) or by activating a sequence- specific RNA degradation
process (PTGS/RNA interference) (Agrawal et al., 2003)
 RNAi has been successfully utilized in vegetables for improving important traits like
modifcation of plant architecture, improvement in fruit quality in terms of high β-carotene
and lycopene content, enhanced shelf life
Targeted genome editing
 TGE facilitates targeted and stable editing of DNA using
engineered nucleases including meganucleases, ZFNs, TALENs
and CRISPR/Cas9 nucleases.
 CRISPR/Cas9 has been more popular because of its ease of use
compared to other genome editing technologies (Das et al.,
2019)
 CRISPR/Cas9 has shown immense potential for crop
improvement and several traits ranging from nutritional, and
others have been enhanced (Jaganathan et al., 2018)
 Li et al. (2018) reported about 5.1-fold increase in lycopene
content in tomato fruit through genome editing.
 Xu et al.( 2019) reported long shelf life in tomato through
genome editing.
Species Genome
editing tool
Targeted gene Gene function or
phenotype
Reference
Solanaum
lycopersicum
CRISPR PETALA2a (AP2a),
NON-RIPENING (NOR)
Fruit development and
ripening
Wang et al.(2019)
Solanaum
lycopersicum
CRISPR Psy1 and CrtR-b2 Carotenoid metabolism D’Ambrosio et al.(2018)
Solanaum
lycopersicum
CRISPR Carotenoid isomerase
and Psy1
Carotenoid metabolism Dahan-Meir et al.(2018)
Solanaum
lycopersicum
CRISPR SGR1, Blc, LCY-E, LCY-
B1, LCY-B2
Increased lycopene
content
Li et al.(2018)
Solanaum
lycopersicum
CRISPR SlMYB12 Pink tomato fruit color Deng et al.(2018)
Solanaum
lycopersicum
CRISPR MPK20 sugar metabolism Chen et al.(2018)
Solanaum tuberosum CRISPR BSS1 Starch biosynthesis Andersson et al.(2018)
Solanaum tuberosum CRISPR GBSS Starch quality Andersson et al. (2017).
Solanaum tuberosum CRISPR StALS1 Starch quality (Butler et al., 2016)
Solanaum tuberosum CRISPR SBE1 and StvacINV22 Sugar metabolism Ma et al.,2017
Use of CRISPR/Cas9 technology to improve quality trait
Potato
•To increase the overall protein content of potato
(Chakraborty et al., 2010) expressed the AmA1
gene from Amaranthus seed albumin in potato
tubers. The transgenic potato lines called
“Protato” had 48% increased protein content
Tomato
• Fruits of Arka Vikas were modified by fruit
specific expression of two transcription
factors Ros1 and Del . Avg. anthocyanin
content of transgenic fruits were 70-100
folds higher than that of the control fruits
( Maligeppagol et al.,2013)
Tomato
Biofortification of vegetable crops
•It is a process of enrichment of health beneficial dietary nutrients in crop through
conventional and molecular breeding, genetic and agronomic measures.
•Biotechnological tools have opened up the possibilities to introduce genes responsible for
the biosynthesis of micronutrients.
Transformation of tomato with the Petunia chi-a
gene encoding chalcone isomerase resulted
transgenic tomato lines produced an increase of
up to 78 fold in fruit peel flavonols, mainly due
to an accumulation of rutin (Muir Shelagh et al,
2001).
Achievements in bio-fortified
nutraceuticals in some vegetables
Crop Biofortified element /mineral/
Vitamin
Tomato Chlorogenic acid, flavonoids,
anthocyanin, stilben, Folate,
phytoene ,β- carotene ,lycopene,
provitamin A
Onion &
Broccoli
Selenium
Lettuce Iron
Carrot Calcium
Radish Selenium
Brassica
spp.
Selenium
Parulekar et al.(2019)
•Pusa Beta Kesari 1 first biofortified variety through pure line
selection
•Contain high beta carotene (8.0 to 10.0 ppm)
•High β-carotene (14.0 mg/100g) & 27 – 29% dry matter
•Total sugars 2-2.4% and Recommended for cultivation in
Odisha (Yadav et al. ,2017)
• High anthocyanin (90mg/100g), Dry matter: 24.0-25.5% and
Starch: 19.5% Total sugar: 1.9-2.2%
• Recommended for cultivation in Odisha
•Tubers with dark orange flesh colour and
very high beta carotene
Carotene content in tubers is 466 IU/100gm
Biofortified Varieties Developed in India
Okra: Kashi Lalima
Anthocyanin 3.0mg/100g
Zinc: 49.7ppm (3.3%) higher
French bean: Kashi Baigani
Anthocyanin: 7.0mg/100g
Red Radish: Kashi Lohit
Anthocyanin : 39.9µg/g F.W
Black carrot: Kashi Krishna
Anthocyanin (275-300mg/100g)
Red carrot: Kashi Arun
Lycopene: 7.50mg/100g FW
Beta-carotene: 3.7mg/100g FW.
Yam: Sree Neelima
Anthocyanin rich
Sl
No.
Title of the Research Article Year of
Publication
Journal Name
1 Color-related chlorophyll and
carotenoid concentrations of
Chinese kale can be altered
through CRISPR/Cas9 targeted
editing of the carotenoid isomerase
gene BoaCRTISO
Oct.,
2020
Horticulture
Research
2 Hybridization in Peppers
(Capsicum spp.) to Improve the
Volatile Composition in Fully Ripe
Fruits: The Effects of Parent
Combinations and Fruit Tissues
May
2020
Agronomy
8.60 (NAAS)
3 Enhancement of Chlorogenic
Content of the Eggplant Fruit with
Eggplant Hydroxycinnamoyl CoA-
Quinate Transferase Gene via Novel
Agroinfiltration Protocol
Nov.,
2020
Pharmacognosy
Magazine
7.31 (NAAS)
2020
Objective :
The purpose of this present study was to perform targeted editing of BoaCRTISO gene
using the CRISPR/Cas9 system to change the colour and pigment concentrations of
Chinese kale
2020
Case study -1
CASE STUDY 1
Sun et al., 2020
Introduction
Carotenoid isomerase (CRTISO), an enzyme that acts before the
bifurcation point in the carotenoid biosynthetic pathway, is responsible
for catalyzing the conversion of lycopene precursors to lycopene(Yuan
et al.,2015)
Recently, a CRISPR/Cas9 gene editing system in Chinese kale was
established( Sun et al.,2018) and used it to demonstrate functional
differences among members of the PDS family, which are important
genes involved in the carotenoid biosynthetic pathway (Sun et al., 2019)
The present study was done to perform targeted editing of
BoaCRTISO using the CRISPR/Cas9 system to change the colour and
pigment concentrations of Chinese kale.
Materials and Methods
•Plasmid construction:
 Target site AGG (exon 11) is PAM, CRTISO CRISPR F/R –obtained by removing AGG.
 Adding 5’ end- ATTG , 3’ end-AAAC
•Agrobacterium-mediated transformation
The explants were infected with the Agrobacterium strain GV3101, co cultivated with
Agrobacterium in MS media and hygromycin B were transferred to tissue culture bottles
that contained the subculture media
•Detection of mutations
To evaluate mutations introduced into the CRISPR/ Cas9 transgenic plants, the genomic
DNA of each positive transgenic shoot was amplified using the specific primers CRTISO-
CRISPR-test-F/R
•Colour measurements
Three positions on the leaves and the bolting stems of each mutant were randomly
selected, and the L*, a*, and b* colour values were obtained
•Chlorophyll and carotenoid assays
HPLC analysis of the carotenoids and chlorophyll was carried out
•RNA extraction and qPCR expression analysis
The expression levels of genes encoding carotenoid-degrading enzymes and chlorophyll
biosynthesizing- and degrading-enzymes were calculated based on the respective
expression levels of the respective genes in WT bolting stems.
Result
Vector Map and Analysis of BoaCRTISO
mutations
CRISPR/Cas9-induced mutations in Chinese kale. (Target sequence-blue, PAM sequence
(NGG)-red, mutated bases-red and asterisks-spacing between bases.
WT wild-type plant, M # number of mutants, i # number of base insertions, r #
number of base replacements.
Twenty-three hygromycin-resistant plants were obtained from ~2000 explants.
The target expression cassette was transferred into 16 lines out of 23 and the transgenic
efficiency was 69.57%.
Mutation pattern and efficiency were studied(fig-a and fig-b and mutation frequency Fig C)
The biallelic mutant M1 and the homozygous mutants M3, M6, and M16 were selected for
subsequent studies.
Colour of crtiso mutants
Marked differences in color were
observed between the crtiso mutants and
WT plants.
The leaves and bolting stems of the four
tested mutants were yellow, with M6
being the most yellow
The variation in chromatic parameters in the leaves and bolting stems of the four mutants was
consistent
the values of L* and b* were significantly higher than those of WT plants,
while the values of a* were significantly lower.
Pigment concentrations of crtiso mutants
•The total carotenoid and chlorophyll concentrations in the mutants were significantly lower than
those in the WT plants
•All pigments in the M6 leaves significantly decreased by more than 20% compared with those in the
WT leaves
•The concentrations of most pigments in the leaves of M1, M3, and M16 were also significantly lower
than those in the WT leaves, although the differences in violaxanthin, β-carotene, and neoxanthin
were not significant
Carotenoid- and chlorophyll-related gene expression levels in crtiso mutants
•In WT plants, the expression levels of carotenoid biosynthesis-related genes in the leaves
were substantially higher than those in bolting stems.
•The genes with highest and lowest expression levels in the leaves were ZEP1 and NXS
respectively.
•The genes with the highest and lowest expression levels in the bolting stems were ZEP2 and
VDE respectively,
•After the targeted editing, the CRTISO gene expression in the leaves of the crtiso mutants
was consistently downregulated and led to reduced expression of most carotenoid
biosynthesis-related genes in the leaves and bolting stems
Expression levels of genes related to carotenoid biosynthesis and degradation
B
L
L
B
Expression levels of genes related to chlorophyll biosynthesis and degradation
•The expression levels of chlorophyll biosynthesis related genes in the leaves and bolting
stems of crtiso mutants were generally downregulated
•However, some chlorophyll biosynthesis-related genes were upregulated. These genes
included ALAD and ChlI in M1 leaves; ALAD, ChlI, and CS in M3 leaves; and ChlI in M6
bolting stems
ALAD in M1 leaves
ChlI in M1 leaves
Schematic diagram of the
results of this study.
Blue genes were down regulated
in the mutants,
Red genes were upregulated in
the mutants,
Black genes did not change
significantly in terms of their
expression.
The down arrow next to a pigment
indicates a decrease in its content.
⊥ indicates suppression.
59
The inhibition of BoaCRTISO gene
expression in the crtiso mutants
led to the downregulation of
expression levels of carotenoid and
chlorophyll biosynthesis-related
genes, as well as carotenoid and
chlorophyll contents, which led to
the yellowing of the crtiso mutants.
•In this study, the carotenoid isomerase gene from Chinese kale (BoaCRTISO)
was targeted and edited using the CRISPR/Cas9 system and Agrobacterium-
mediated stable transformation.
•CRISPR/Cas9 system was used to edit the BoaCRTISO gene of Chinese kale,
resulting in the production of 13 mutants of the biallelic, homozygous,
heterozygous, and chimeric types.
•BoaCRTISO was knocked down rather than knocked out in this study
•The expression level of the CCD1 gene was also significantly reduced, which
may be a response to the decrease in the expression levels of carotenoid
biosynthesis genes.
•Inhibition of CRTISO expression affected both the carotenoid and chlorophyll
pathways, leading to decreased carotenoid and chlorophyll concentrations and
creating a new yellow color of Chinese kale, with improved market prospects.
•The CRISPR/Cas9 system is therefore a promising technique for crop quality
improvement
Inference
CASE
STUDY 2
Peris et al., 2020
Objectives
(i) To study the inheritance of the volatile fractions in peppers.
(ii) To assess the opportunity of developing new combinations of
volatiles by hybridization.
Introduction
Capsicum peppers (Capsicum spp.), especially C. annuum L., are one of
the most important vegetables and spices in the world and their fruits are
used in a range of food dishes, to provide aroma and flavor.
Pungency has been largely studied, while studies on the volatile fraction are
more recent and less diverse.
More than 200 varietal types have been reported, which greatly vary in
their external traits and also in their organoleptic and functional
properties [Patel, K et al., 2016]. Among them, C. annuum is the most
economically important species and is phylogenetically related to C. chinense
and C. frutescens [Dias et al., 2019)
A diverse profile of volatiles including terpenoids, esters, alkanes, and
several aldehydes and alcohols, was found among the evaluated accessions
of chilli.
Hybridization provided higher amounts of total volatiles and a more
complex composition, particularly in the pericarp.
The present study was designed to study the inheritance of the volatile
fractions in peppers and to determine if they can be improved by breeding
strategies.
Materials and Methods
10 Capsicum accessions
(8 C. annuum and 2 C.
chinense),
1. Planting material
6 C. annuum × C. annuum (Intra specific hybridization) & 3 C. annuum× C. chinense (Inter
specific hybridization) hybrids between accessions.
2.Preparation of Samples and Extraction of Volatiles
 10 plants/ accession, 2 samples (1 pericarp and 1 placental tissues).
 Pericarp subsamples: mixing 2 g of fresh weight from the pericarp (free of placental tissues
and septa) and finely cut into 3 × 3 mm pieces and immediately transferred into a 20 mL
sealed crimp cap headspace vial. Placental subsamples: 2 g of placenta and seeds.
3. Extraction of the Volatile Fraction (HS-PME)
 Headspace-solid-phase microextraction (HS-SPME) was used to
isolate the volatile compounds [9,21].
 SPME(divinylbenzene/carboxen/polydimethylsiloxane,
DVB/CAR/PDMS, 50/30 µm) (Supelco, Bellefonte, PA, USA) were
used to perform the extraction from the HS.
 The fiber was exposed to the headspace of the sample vials for 40
min at 40 ◦C to allow adsorption of volatiles.
 The fiber was thermally desorbed at 250 ◦C for 30 s in splitless
mode in the gas chromatograph injection port, using a splitless
inlet liner of 0.75 mm ID. Purge flow was maintained at 50 mL
min−1 and purge time was 1 min.
 In order to ensure that there was no cross-contamination from
previous samples, the fiber was always reconditioned for 30 min at
250 ◦C in the injection port of another gas chromatograph
4. Analysis of Volatiles
Volatile fraction was analyzed by gas chromatography–
mass spectrometry (GC–MS),
RESULTS
The highest amount of total volatile fractions and number of volatile compounds was found in
Capsicum annuum accessions Chile Arbol followed by Cayenne, Pasilla Bajio, Serrano and
Capsicum chinense accession PI 152225.
Individual volatiles in placental tissues were more in Serrano (Terpenoids 429.79 %), PI
152225 (Esters 341.38 % and Alkanes 583.37 %). Highest amount of volatiles in placental
tissues was found in hybrid accessions Cayenne x Serrano (2327. 611 % Intra specific
hybridization).
Figure 2. Heatmap hierarchical cluster analysis
of the volatiles identified in the hybrid
accessions studied (Intra and Inter specific
Hybridization), corresponding to the pericarp
(Pe) and placental (Pl) tissues. Accession and
volatile abbreviations correspond to those
indicated in Tables 1 and 2, respectively.
Figure 1. Heatmap hierarchical
cluster analysis of the volatiles
identified in the parent accessions
studied, corresponding to the
pericarp (Pe) and placental (Pl)
tissues. Accession and volatile
abbreviations correspond to those
indicated in Tables 1 and 2,
respectively.
Accumulation of Volatiles in Fruit Tissues
(Placenta and Pericarp) abundant in
accessions ‘Cayenne’, ‘Chile Serrano’ and
PI152225 and hybrid accessions i.e.
Cayenne×Serrano and Arbol×Serrano
Inference:
 There are ample opportunities to improve the aroma-related compounds in fully ripe
Capsicum peppers by hybridization, both qualitatively and quantitatively.
 Most hybrids showed more complex volatile profiles than those of their corresponding
parents as a result of the confluence of volatiles from both parent lines, with cases of
intermediate inheritance or transgressive inheritance, and also, but to a lesser
extent, to the appearance of new compounds, presumably due to genetic
complementation.
 Thus, breeders can plan sets of hybrid combinations using parents with complementary
volatile fractions, and then perform final selections of those hybrids with the most
desirable flavors and aromas based on organoleptic tests.
 In general, placental tissues were quantitatively richer in volatile compounds,
which is of special interest for breeding the aroma and flavor of varieties where the
whole fruit is used in culinary applications.
CASE STUDY 3
Kaushik et al., 2020
Objectives
 To establish and standardize an efficient agroinfiltration protocol for the eggplant fruit
for enhancing Phenolics.
 To determine the function of Egg plant SmHQT (eggplant hydroxycinnamoyl
CoA-quinate transferase).
Introduction
Among vegetables, phenolic acids, for example, chlorogenic acid, is present in larger
quantities in the eggplant (Solanum melongena L.). For the production of chlorogenic
acid in the eggplant hydroxycinnamoyl CoA-quinate transferase (SmHQT), is a central
enzyme that catalyzes the reaction to the chlorogenic acid production.
Materials and Methods
a. Construct used for the
agroinfiltration assay .
Genomic DNA-extracted-from the Fruits-
Amplified for the SmHQT
Agroinfiltration GUS bearing vector
pCAMBIA1304 Adgene
pBS+ Vector pBS+ SmHQT digested
HindIII/BamH1
Cloning pUC cloning vector
Sub cloning pBIN19 Add gene
Sub culture LB broth (5 ml) – 2 ml syringe was
injected into the Eggplant fruits at 10-15 spots
Plant material: Arka Shirish – Green colour
Brinjal variety.
In silico cis-regulating elements map and
interactome analysis
Results
Figure 1: Protein-protein interaction networks SmHQT
controlling high chlorogenic biosynthesis pathway in
eggplant using Arabidopsis databases. Their
interactions were analysed online using STRING
database
(https://string-db.org/) In this study, nine potential protein
interaction networks (TT4, CYP98A3, 4CL3, 4CL1, C4H, IRX4,
4CL2, LysoPL2, and CCOAMT) were identified for HQT gene.
Fig 2 comparison of
fruit slices after
following the X-Gluc
staining procedure
with the control fruit
slices are above.
Figure 3: The high performance liquid
chromatography results of agroinfiltrated
versus control fruits in three independent
fruits on different plants.
A. tumefaciens GV3101
strain was used and
transformed to, GUS
bearing vector with
SmHQT was transiently
expressed in eggplant
fruit
Agroinfiltrated fruits
Control
Figure 4: Differential gene
expression level (quantitative reverse
transcription polymerase chain
reaction) of six candidate genes of
the chlorogenic pathway is
represented with respect to control
plant fruit. The expression was
analysed at one day and 3 days after
infection.
Inference:
 Due to the overexpression of the SmHQT gene, higher chlorogenic content was exhibited by
the eggplant fruits, which was validated by HPLC.
 The chlorogenic acid content after following the agroinfiltration procedure was more two
times in the agroinfiltrated fruit.
 To identify the optimal target for increasing chlorogenic pathway flux post‐SmHQT activity,
expression patterns were analyzed with qRT-PCR, and the results showed the changes in
the expression level of the other chlorogenic acid pathway genes.
 Furthermore, the cis regulating elements and protein-protein interaction (PPI) analyses
supported the HPLC results.
Quantitative gene expression analysis
Nutritional Qualities and associated health benefits of vegetable crops is becoming
important criteria for their increase in consumers diet.
In this respect, breeding programmes for improving the content of nutrients complex
quality traits and shelf life in vegetables are becoming more important for breeders.
Molecular breeding and genetic manipulation have emerged as the two most potent
technologies which have the potential to attain quality improvement for the coming
years
Advances in NGS technology have enabled the incorporation of genomics with various
disciplines of crop breeding
The key gene or genes regulating a molecular pathway are being genetically engineered
or edited to develop phenotypically improved crop lines
Conclusion
I
S
T
H
A
N
K
Y
O
U

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BREEDING FOR IMPROVED NUTRITION QUALITY AND NUTRACEUTICALS PROPERTIES IN VEGETABLE CROPS

  • 1. Breeding approaches for Improved Nutritional Quality and Nutraceutical properties in Vegetable crops Presented By NARAYANA SWAMY G Ph.D. Ist Year Roll No: 11919 Division of Vegetable crops ICAR- Indian Institute of Horticultural Research, Bengaluru-560 089
  • 2. Content Introduction Nutritional quality and Coloured Vegetables Nutraceuticals-Properties Breeding approaches- improved nutrition quality Case studies Conclusion 2
  • 3. INTRODUCTION  About 2500 years ago, Hippocrates, the father of modern medicine, conceptualized the relation between the use of appropriate foods for health and their therapeutic benefits  He promulgated that ‘’let food be your medicine and medicine be your food’’
  • 5.  The improper diet and unbalanced nutrition are the major reasons of malnutrition of about 3 billion people in our world (Kumari M. et al., 2020).  According to global hunger index India ranks 94 among 107 countries in 2020 with a serious issue of child wasting (IFPRI,2020)  India is home to 46.6 million stunted children which is one third of world's total. (Global Nutrition Report, 2018).
  • 6. Aim: Lay stress on the importance of child nutrition and how kids can benefit from a nourishing diet right from birth.. 8 March 2018
  • 7. Quality improvement of crop plants is a significant component in nutritional and food security Food security All people, at all times, have physical, social, and economic access to sufficient, safe and nutritious food’ (World Food Summit, 1996). Consumption and physiological uses of adequate quantities of safe and nutritious food by every member of the household to support an active, productive and healthy life (Sidhu and Rao, 2010) Nutritional Security Quality defined as the “degree of excellence or superiority” (Kader et al., 1985). Quality includes flavour, colour, shape, size, degree of damage, nutrient levels and traits that permit greater perceived food safety or environmental sustainability. Nutritional value is used to provide good-balanced ratio of the fundamental nutrients like carbohydrates, fat, protein, minerals, and vitamin in items of food or diet.
  • 8. Nutritional Quality of Vegetables Nutritional quality describes the inherent biological or health value of produce including the ratio of beneficial to harmful substances, taste, fragrance, freshness, and shelf-life that govern consumer behaviour. Traditional component Organic Acid Protines Lipid & Fatty acids Carbohydrate s Dietary fibre Vitamins Vicente et al.(2009)
  • 9. Quality attributes of Vegetables Intrinsic quality attributes Extrinsic quality attributes - Inherent to the product itself - Provide stimuli to consumers and eventual quality perceptions Linked to the production method but not a property of the food itself  Like pesticides, eco-and animal friendliness, packaging materials, processing technology. Sensory attributes (Classical aspects)  Flavour  Taste  Appearance  Colour  Texture  Smell Health attributes • Major nutrients • Amino acids • Vitamins • Dietary minerals • Antioxidants (Influence purchasing policy of some consumers) Carotenoids : Lycopene, Lutein, -carotene Polyphenolics : Flavonoids, Flavones, Anthocyanin Glucosinolate :Sulphoraphane, Indole-3-Carbinol Thiosulphides : Alliin, Methiin, Ethiin Dietary fiber : Lignin, Pectin, Cellulose Miscellaneous : Selenium, Phytosterol, Saponins Behara et al. (2019) Type of traits Description Examples Morphological Appearance of the produce Fruit size, shape, colour Organoleptic Palatability of the produce Taste, aroma, juiciness, softness Nutritional Value of the produce for human or animal nutrition Protein content, oil content, vitamin content, mineral content Consumer preference Increases the marketability of the produce Keeping quality, storability Various quality traits (Debnath and Guha , 2015)
  • 10. Vegetables are bulky source of micronutrients and their ‘compound matrix’ is effective in supply of diverse elements to the body Globally, the Food and Agriculture Organization (FAO) recommends for intake of 400 g vegetables per day in order to boost the consumption Behera and Singh,2019 Important source of dietary minerals and vitamins and contribute to fight against micronutrient malnutrition The health benefiting compounds act as antioxidants in human body and play role in homeostasis balance They contribute functionally active secondary metabolites which have preventive role against various health ailments. Why we need to emphasis on nutritional security through vegetables? The 5 A Day campaign is based on advice from the World Health Organization (WHO), which recommends eating a minimum of 400 g of fruit and vegetables a day to lower the risk of serious health problems, such as heart disease, stroke and some types of cancer.
  • 11. Red vegetables help to fight cancer, reduce the risk of diabetes and heart disease, improve skin quality. Orange and yellow vegetables improve immune function, reduce the risk of heart disease, promote eye health Green vegetables boost the immune system, help detoxify the body, restore energy and vitality. fight Cancer and unwanted inflammation, protects cell from damage, boosts memory Protect Against certain cancers, keep bones strong, reduces the risk of heart ailment, lowers cholesterol  Natural Pigments like chlorophyll, anthocyanin, carotenoids make vegetables colourful.  Dark and intensively coloured vegetable usually contain more chemically active antioxident pigments than pale crops.  Eating a mix of different coloured vegetables nourish our body with a range nutritive compounds. Coloured Vegetables Lycopene, quercetin and Hesperidin Chlorophyll, fiber, lutein, zeaxanthin, calcium, folate, vitamin C and beta carotene Lutein, zeaxanthin, resveratrol, Anthocyanin, fiber, flavonoids Beta-glucans and lignans Beta- carotene, zeaxanthin, flavonoids Rai et al.( 2012)
  • 12. Natural Nutraceuticals Nutraceutical is a combination of the words “nutrition” and “pharmaceuticals,” are any substance that is a food or a part of a food and provides medical or health benefits, including the prevention and treatment of diseases.(Rai et al., 2012) The term "Nutraceutical" was coined by Dr Stephen DE Felice in 1989. A nutraceutical is demonstrated to have a physiological benefit or provide protection against chronic disease through antioxidant activity (Gupta et al., 2013) Vegetables are functional foods nutraceuticals because they provide minerals and nutrients which are health promoting and a major source of biologically active nutraceuticals. Nutraceuticals: the concept  The term of “Nutraceutical” is applied for mainly to ingredient (rather than complete product). Finished product referred as functional foods or fortified foods.
  • 13. Important nutraceuticals in plants (inner whorl) & their role in human health (outer whorl) Nutraceuticals Singh et al., 2020
  • 14. Neutraceutical properties in Vegetables Chemical compounds Plant source Properties Allicin (organosulfur compound) Garlic, onion, parsnip Antifungal; antibacterial; antioxidant; used to treat arteriosclerosis Apigenin Cabbage, celery, lettuce 4’,5,7-trihydroxyflavone is a flavone that is the aglycone of several glycosides Beta carotene Carrots, pumpkins, sweet potatoes, winter squash, broccoli, spinach and kale Anti aging; anti cancerous; improve lung function; reduce complications associated with diabetes Betanin Beets, chard Natural colourant used in icecreams Capsaicin or trans-8- methyl-N-vanillyl-5 nonenamide Red chilli Used for pain relief topically and as a digestive aid when taken internally; antioxidant; antiallergic Caffeic acids Carrot Inhibitor of the lipoxygenase enzyme that forms leukotrienes from arachidonic acid Tocopherol Broccoli, carrot, celery, onion It is a fat-soluble antioxidant that stops the production of reactive oxygen species formed when fat undergoes oxidation Plant Glucosamine Lettuce, peas, cabbage Chondroitin and glucosamine are part of normal cartilage and act as a cushion between the joints
  • 15. Tocopherol Broccoli, carrot, celery, onion It is a fat-soluble antioxidant that stops the production of reactive oxygen species formed when fat undergoes oxidation Plant Glucosamine Lettuce, peas, cabbage Chondroitin and glucosamine are part of normal cartilage and act as a cushion between the joints Luteoline Cauliflower, celery , sweet pepper A carotenoid which shows eye benefits Sulphoraphane Broccoli Used against breast cancer Phytosterol Germinated corn Lower cholesterol absorption in the digestive tract thereby lowering overall cholesterol level in the bloodstream Proanthocyanin Red cabbage, egg plant Help in urinary tract infections by inhibiting adhesion of microorganisms like E. coli to the urinary tract wall Zeaxanthin Carrot , celery, kale, lettuce Used for eye health and in age related mascular degeneration Rai et al.( 2012)
  • 16. Carotenoids- Lycopene, Lutein, β-carotene Glucosinolate- Sulphoraphane, Indole-3-carbinol Polyphenolics- Flavonoids, Flavones, anthocyanin Thiosulphides- Allin, Methiin, Ethiin Indoles: Indole-3-carbinol (I3C) and indole 3-acetonitrile (I3A) Phytochemicals in Vegetables Phytochemicals or phytoceuticals present in plant foods like vegetables which neutralize harmful free radicals generated in the body and have protective or disease preventive characteristics.  These are secondary metabolites and formed due to the enzymatic resections of primary metabolites (amino acids, sugars, vitamins etc.) There are over 900 phytochemicals found in foods, one serving of a fruit or vegetable may have as many as 100 different phytochemicals
  • 17. Breeding objectives for improved nutrition quality  To enhance productivity to meet the ever increasing food requirement of people.  Conventional breeding in conjunction with molecular biology will make it possible to get vegetable varieties enriched with nutraceuticals and edible colors suitable for fresh market as well as industry.  High yielding and dietary micronutrients rich variety development.  Enrichment of nutraceuticals need special attention.  Wider adaptability, rich in dietary nutrients and antioxidants.  Crop specific breeding.  Good in organoleptic scores, high portion of edible parts, high acceptance among consumers. Behera et al., 2019 & Singh et al., 2020
  • 18. Crops Wild relatives/ accessions/ landraces/ varieties Nutrients Tomato S. pimpinellifolium, Caro Red (Rugers x S. hirsutum) Vitamin A High pigment mutants (hp), Crimpson (og), Pusa Rohini Lycopene Caro Rich, F-7045, VRT-35, CGT, VRT-5 Beta carotene S. pennellii, IL12-4 Ascorbic acid S. chilense and atroviolacium (atv) from S. cheesmaniae Anthocyanin Chilli C. annuum var. IC: 119262(CA2), Bayadaggi kaddi Ascorbic acid Paprika KTPL-19 Capsanthin Cucumber Xishuangbanna gourd Beta carotene Muskmelon Honey dew32 Ascorbic acid Spine gourd Momordica dioca Protein M. chochinchinenesis Lycopene Bitter gourd DRAR-1, DVBTH-5 Beta carotene Sweet potato Resisto, Zambezi, Chiwoko Beta carotene Cassava UMUCASS 44, UMUCASS 45 and UMUCASS 46 Vitamin A Broccoli Brassica villosa Glucosinolates Natural resources rich in quality traits useful for breeding Singh et al.,2020
  • 19. Crop Varieties Nutraceuticals Tomato Pusa Rohini 4.5 mg/100g fw Lycopene Brinjal Pusa Safed Baingan, 31.21 mg/100 g fw Pusa Hara Baingan 1, 33.5 mg/100 g fw Pusa Shyamla, 48.2 mg/100g fw Phenolics Phenolics Anthocyanin Bitter gourd Pusa Aushadhi, 6.51 mg/100 g fw Pusa Rasdhar, 4.3 mg/100 g fw Phenolics Onion Pusa Madhvi, 101.2 mg/100g fw Pusa Ridhi, 107.42 mg/100g fw Pusa Soumya, 74.6 mg/100g fw Quercetin Carrot Pusa Yamdagini, 7.55 mg/100g fw Beta-carotene Pusa Rudhira, 386 mg/100g fw Lycopene Pusa Asita, 339 mg/100g fw Anthocyanin Pusa Rudhira, 45.15 mg/100g Phenols Beetroot Crosby, 17.15 mg/g dm Anthocyanin (Sawicki et al., 2016)
  • 20. Red cabbage Primero 109 mg/100g fw Anthocyanin (Ahmadian et al.,2014) Cauliflower Pusa Sharad, 23.94 μ mol/ 100 g fw Pusa Beta Kesari 1, 8-10ppm Sinigrin Beta carotene Purple Cauliflower Graffiti, 375 mg/100g fw Anthocyanin (Chiu et al., 2010) Broccoli Green broccoli, 15.2-59.3 μ mol/100 g fw Purple broccoli ,26.3 μ mol/100 g fw Glucosinolates Bathua Pusa Green, 7.6 mg/100g dw Iron Palak All Green, 16.2 mg/100g dw Iron Amaranth Pusa Kirti, 38.5 mg/100g dw Iron Methi Pusa Early Bunching, 17.2 mg/100g dw Iron Sag sarson PusaSag -1, 16.3 mg/100g dw Iron Sweet Potato Bhu Sona , 14.0 mg /100g Bhu Krishna , dry matter (24-25.5%), starch(19.5%), total sugar(1.9-2.2%) Sree kanaka, 90.0 mg /100g β-carotene Anthocyanin Tapioca Sree Visakham, 466 IU/100g Carotene
  • 21. Palam Kanchan Novel genotypes/ breeding lines identified for nutrition Carotene Rich Tomato Carotene rich Cherry tomato Carotene rich cauliflower Pusa Asita Cole Crops Root Vegetable Crops Solanaceous Vegetable Crops Palam Vichitra Pusa Gulabi Pusa Jamuni Anthocyanin Rich Tomato
  • 22. Important gene for quality traits Crop Nutrients Gene Tomato Lycopene High pigment (1,2,3) hp ySAMdc; spe-2 β-carotene Green flesh (gf) Yellow (r) Tangerine (t) Lutein cry-2 Carotenoids Phytoene synthase (Psy-1) Anthocyanin Anthocyanin fruit (Aft) Aubergine (Abg) Atroviolacium(atv) Tocopherol hmgr-1 Folate GCH-1 Kaempherol LC and C1 High flavonols chi-a Chilli Capsaicinoids C
  • 23. Delta gene Reddish - orange colour Ogc gene -Crimson colour Apricot gene – yellowish pink colour Anthocyanin (Aft) Gene – purple colour r gene -yellow colour (Yellow flesh)
  • 24. Crop Nutrients Gene Chilli β-carotene B; bc Anthocyanin (Immature fruit) A/F Potato Protein AmA1 β-carotene Or, Crt-B Phytoene Dxs Sweet potato High protein Asp-1 Anthocyanin IbMYB1 Cauliflower β-carotene Or Anthocyanin Pr Cabbage Anthocyanin MYB Lettuce Folate Gch1 Iron Pfe Ascorbate Gul oxidase Cucumber β-carotene Ore Singh et al. (2015)
  • 25. Purple (Pr) gene mutation in cauliflower confers an abnormal pattern of anthocyanin accumulation (Chiu et al., 2010) The Orange (Or) gene mutation in cauliflower confers the accumulation of high levels of - carotene in various tissues normally devoid of carotenoids.(Lu et al., 2006) High pigment (hp-1) mutation, known to increase flavonoids in tomato fruits.(Sapir et al., 2008)
  • 26. 26 Breeding approaches for improved nutritional quality Conventional breeding approach:  Selection  Hybridization  Mutation  Polyploidy breeding  Soma clonal variation Biotechnological approach 1.Molecular Breeding:  Development and deployment of molecular markers  Marker Assisted selection  QTLs associated with quality traits 2.SNPs discovery 3.Genome sequencing and transcriptome analysis 4.Transgenic approach 5.RNA interference 6.Targeted genome editing.
  • 27. Most of the colour varieties are developed by this method Selected on the basis of phenotypic characters Pusa Kulfi high lutein Pusa asita High anthocyanin SELECTION 27 Pusa Rudhira (High lycopene) Pusa Meghali (High β-carotene) Pusa Vristi (Lycopene: 405µg /100g) Pusa Payasa High β-Carotene) Chinese Red (Lycopene) Pusa Mridula (Lycopene) Pusa Gulabi (Anthocyanin) Carotene content (11.27 mg%) ESRao et al., IIHR.
  • 28. Pusa Rohini (Lycopene) Pusa Uphar (Lycopene) 28 Arka Abhir (Capsanthin) Punjab lal (Capsanthin)
  • 29. HYBRIDIZATION • Crossing between two genetically dissimilar parents. It is the best method for crop improvement in cross pollinated crops. • Two genetically superior divergent parents are selected and crosses were made to develop superior cultivars.  US pickling cucumber (‘Addis’) × XIS (Cucumis sativus var. xishuangbannanesis Qi et Yuan) High β-carotene inbred line (S4), ‘EOM 402-10’, was developed. Cuevas et al., Euphytica (2010). Pusa Nayanajyoti (High β-Carotene) Pusa Vasuda (Lycopene) Kuroda ( β-Carotene) Oxheart (Lycopene+An thocyanin)
  • 30.  Tomato (High Beta carotene) Lycopersicon esculentum x Lycopersicon hirsutum and Lycopersicon esculentum x Lycopersicon hirsutum f glabratum – (Kalloo, 1988).  Tomato Caro red (Provitamin -A rich tomato variety) Common Tomato (Solanum esculentum Mill) x Wild Tomato species, (Solanum hirsutum Humb.). (M. L. Tomes (1958) INTERSPECIFIC HYBRIDIZATION Crosses were made between two different species of the same genus known as Interspecific hybridization.  U.S. pickling cucumber lines (Cucumis sativus L. var. sativus) x (C. sativus L. var. xishuangbannanesis Qi et Yuan- Orange-fruited Xishuangbannan cucumber lines ) (Simon and Navazio, 1997)
  • 31. Soma clonal variation is defined as genetic or epigenetic changes that arise in vitro between clonal regenerants and their corresponding donor plants. Leva et al., (2017): Encyclopedia of Applied Plant Sciences (2nd edition) 2: 468-473 Chromosomal rearrangements are an important source of this variation. A cultivar of sweet potato ‘Scarlet’ having higher yield and disease resistance characteristics similar to their parent but also have darker and more stable skin colour SOMACLONAL VARIATION (Moyer and Collins, 1983) MUTAGENESIS Species Mutant gene Phenotype References Tomato r (yellow flesh) Yellow fruit colour Fray and Grierson,1993 delta Orange fruit colour Ronen et al.,1999 tangerine Orange fruit colour Isaacson et al.,2002 Beta Orange fruit colour Ronen et al.,2000 hp-1 Flavanoids Rajasree et al., 2021 Pepper y (yellow) Yellow fruit colour Lefebvre et al., 1998 c2 Yellow fruit colour Thorup et al., 2000
  • 32. POLYPLOIDY BREEDING Cucumis melo inbred M01-3 (2n=24) by colchicine. Tetraploid muskmelon- rich in soluble solid, soluble sugar and vitamin C contents (Zhang et al. 2010) Triploid and tetraploid watermelon- increased range of lycopene than diploid (Liu et al. 2010) Auto-tetraploid cultivar of fenugreek- larger leaf area and larger productivity concerning seed number, pod number than diploids and rich in K, Na, Ca and P (Peiman Zandi et al., 2017)  Polyploids can be induced due to aberration in cell division.  This can be used to enhance nutraceuticals and colors
  • 33. Need of biotechnological intervention for nutritional quality improvement  Crop improvement relies on modulating the genes and genomic regions underlying key traits, either directly or indirectly  Identification of robust and tightly linked molecular markers for target traits.  Intensification of crop improvement programmes using biotechnological and breeding interventions had resulted in the trait discovery and release of improved varieties  Molecular techniques are helpful in improving bioavailability of the target compounds, their biosynthesis in plant species/tissues where these compounds are not naturally produced, over-expression of transgenes and removal of anti-nutritional factors.
  • 34. Development and deployment of molecular markers Crop Trait Marker Reference Brassica 2-propenyl glucosinolate content ISSR Marker Ripley and Roslinsky. (2005) B. villosa High glucosinolate content OI12-F02 (QTL 2) (Micro satellite marker) Sarikamis et al. (2006) Cauliflower â-carotene AFLP markers linked to “Or” gene Li and Garvin (2003) Chinese cabbage β-carotene accumulation SCAR markers linked to “or” gene Zhang et al. (2008) Carrot β- Carotene AFLP marker linked to Y2 loci Santos and Simon (2002) Cucumber Endocarp carotene content SSR marker on LG-3 Bo et al. (2011) Broad bean Increased protein content and reduced fibre content zt 2 gene specific SCAR marker Gutierrez et al. (2008) Molecular markers are used to study linkage with gene responsible for high nutraceuticals and edible colours using mapping population. These markers enabled the development of high-density genetic maps useful for mapping of target genes and utilize them in crop breeding. Molecular markers are also employed for the detection of genetic variation associated with valuable nutrient traits among cultivars in a species and facilitate the identification of appropriate parents for molecular breeding.( Singh et al., 2020)
  • 35. Molecular Breeding and Marker Assisted selection Introgression of ‘Or’ gene into Indian cauliflower leads to development of β- carotene (8-20 ppm) rich cauliflower variety Pusa Beta Kesari VitA-1 (Kalia et al., 2018). Introgression of β-carotene quantity controlling gene ‘ Ore’ in cultivated cucumber linked to seven SSR markers on linkage group 3 (Bo et al., 2011).
  • 36. QTLs associated with Nutritional quality traits The analysis of quantitative trait locus (QTL) is a statistical approach that correlates the phenotypic measurements with the genotypic data to evaluate the genetic basis of variations among complex traits. In vegetables, QTLs were mostly identified for a variety of nutritional quality related trait. QTL analysis of fruit antioxidants in tomato using L. pennellii introgression lines detected a total of 20 QTL including five for TACW, six for ascorbic acid, and nine for total phenolics (Rousseaux et al. ,2005) Just et al. (2009) performed QTL analysis for pigment content on a carotenoid biosynthesis and found that Y and Y2 loci on linkage groups 2 and 5 respectively, control much variation for carotenoid accumulation in carrot roots. Iorizzo et al. (2019) identified a region in chromosome 3 with co-localized QTL for all anthocyanin pigments of the carrot root Example
  • 37. Crop Trait Mapping Population QTLs/ Genes Chromosomes References Maskmelon Soluable sugar content RIL 6 QTLs; SSCQU8.3 8,9,10 Pereira et al.(2018) Total carotene in flesh RIL 1Q; CARQU9.1 9 Pereira et al.(2018) Orange flesh colour F3 CmOr gene 9 Tzuri et al .(2015) Vitamin-C 2QTL Sinclair et al. (2004) Tomato Lycopene content RIL 2 QTl (lyc7.1 , lyc12.1,) 7,12 Ashrafi et al. (2012) BC1S1 8 Q 1,4,5,6,7,10,12 Chen et al.(1999) BC3 5 Q 2,3,5,8,12 Fulton et al.(2000) RIL 2 Q 4,11 Rousseaux et al. (2005) ILs 2 Q 3,6 Foolad et al.( 2000) Phenolic content ILs 9 Q 3,5,6,7,8,9 Foolad et al.(2000) Brinjal Anthocyanin - fap10.1 - De Jong et al.(2004) F2 26 QTLs 2,5,6,8,10 Barchi et al. (2011) Beetroot Sucrose content - 13QTL - Trebbi et al.(2005) Carrot β-carotene & δ- carotene - 8QTL &4QTL - Santos and Simon (2002)
  • 38. SNPs discovery The SNPs are the predominant and mostly used markers in plant genetic analysis. The SNPs have become choice markers in modern breeding programme due to their abundance, stability, amenability to automation, and cost effectiveness (Ganal et al. ,2009). GBS is also in use for generating genome-wide markers have been used in mapping QTLs in pumpkin (Zhang et al. ,2015). Crop Quality trait Reference Tomato fruit metabolic traits Viquez-Zamora et al. (2013) Carrot carotenoid biosynthesis Jourdan et al. (2015) Muskmelon fruit traits Chang et al.( 2016) Chilli capsaicinoids Nimmakayala et al. (2016)
  • 39. Genome sequencing : • Whole genome sequencing serves as the basis for finding genome- wide analysis of genetic variation • With the advent of NGS technologies, the sequencing of complete genome or transcriptome of a species/genotype has become possible within a few hours Transcriptome Sequencing:  Transcriptome sequencing, also called RNA sequencing, refers to the sequencing of cDNA to get information about a sample’s total RNA content at a given time in a given condition under study. This requires the conversion of mRNA into cDNA before the sequencing reaction.  Transcriptomic analysis has been used in a number of vegetable crops for understanding the quality related traits.  Transcriptome sequencing is done either by first-generation Sanger sequencing or by high throughput NGS approaches less representatives of commercial growth condition.
  • 40. •Transcriptomic changes occurring during the browning of fresh- cut fruits •11 genes from five gene families (i.e., PPO, PAL, POD, CAT, and SOD) were identified as potentially associated with enzymatic browning . (Zhu et al.,2017) Luffa cultivar ‘Fusi-3’ Pea Spinach •The presence of r or rb or bsg genes results into accumulation of low level of starch and a high level of sucrose. •Mutant alleles at three loci r , rb , and bsg affect starch and sugar synthesis (Harrison et al.,2000). ~320,000 high-quality SNPs were identified and indicated that Spinacia turkestanica was more closely related to the cultivated S. oleracea than S. tetrandra (Xu et al.,2015)
  • 41. Transgenic Approach Genetic engineering enabled vegetable breeders to incorporate desired transgenes into elite cultivars, thereby improving their value, nutritional quality and other health benefits. (Singh et al., 2020) Romer et al.( 2000) developed transgenic tomato to enhance the carotenoid content and profile of tomato fruit which increase in β- carotene content about threefold, up to 45% of the total carotenoid content in cultivar “Ailsa Cray” To increase the overall protein content of potato (Chakraborty et al., 2010) expressed the AmA1 gene from Amaranthus seed albumin in potato tubers. The transgenic potato lines called “Protato” had 48% increased protein content Lettuce expressing the deregulated Arabidopsis H+/Ca2+ transporter sCAX1 (cation exchanger 1) contained 25– 32% more calcium than controls (Park et al., 2009) A transgene construct pSG766A used to increase expression of isopentenyl transferase (key enzyme for cytokinin synthesis) in broccoli. (Chen et al.,2009) cyanide-free transgenic cultivars of cassava can be promising option to provide safe cassava (Siritunga and Sayre,2003)
  • 42. Transgenics with enhanced nutritional quality Crops Trait Gene References Potato Beta carotene phytoene synthase (CrtB), phytoene desaturase (CrtI) and lycopene betacyclase (CrtY) from Erwinia Diretto et al.( 2007) Potato Vit-C and Vit-E StVTCIA and Al-HPT Bulley et al.(2011); Elizabath et al.(2011) Potato Ca Scaxl, Cax2b Park et al.(2005); Kim et al.( 2006) Potato Starch ShSV, PsGTP, AfNTTI Amylose (ssn,ssm, SBEI,SBEII) Fernandez et al.( 2009); Zang et al. (2008) Potato Total protien AmA1 Chakraborty et al.(2010) Sweet potato Increased carotenoids IbOr-Ins - Tomato Enhanced carotenoid content bacterial carotenoid gene (crtI) encoding for phytoene desaturase - Tomato Suppression of PG to delay fruit ripening Antisense construct based on pTOM6 for polygalactronase enzyme -
  • 43. RNA interference in vegetables for quality traits Crops Traits Reference Tomato Increasing antioxidants Niggeweg et al. (2004) Increasing carotenoid and flavonoid content suppression of DET1 expression Williams et al.(2004) Extending shelf-life by blocking the expression of ACC oxidase gene and two ripening specific N-glycoprotein modifying enzymes Meli et al. (2010) reduction in polygalacturonase activity leading to delayed fruit ripening Sheehy et al. (1988 Targeting ripening gene using chimeric RNAiACS construct also resulted into delayed ripening of fruits up to 45 days ( Gupta et al., (2013) Onion Suppression of the lachrymatory factor synthase gene Eady et al. (2008) Carrot Development of Dau c 1.01 and Dau c 1.02-silenced transgenic carrot plants show reduced allergenicity Peters et al. (2011) reduction in storage root thickness and colour Moreno et al. (2013) The RNA silencing is a novel gene regulatory mechanism that limits the transcript level by either suppressing transcription (TGS) or by activating a sequence- specific RNA degradation process (PTGS/RNA interference) (Agrawal et al., 2003)  RNAi has been successfully utilized in vegetables for improving important traits like modifcation of plant architecture, improvement in fruit quality in terms of high β-carotene and lycopene content, enhanced shelf life
  • 44. Targeted genome editing  TGE facilitates targeted and stable editing of DNA using engineered nucleases including meganucleases, ZFNs, TALENs and CRISPR/Cas9 nucleases.  CRISPR/Cas9 has been more popular because of its ease of use compared to other genome editing technologies (Das et al., 2019)  CRISPR/Cas9 has shown immense potential for crop improvement and several traits ranging from nutritional, and others have been enhanced (Jaganathan et al., 2018)  Li et al. (2018) reported about 5.1-fold increase in lycopene content in tomato fruit through genome editing.  Xu et al.( 2019) reported long shelf life in tomato through genome editing.
  • 45. Species Genome editing tool Targeted gene Gene function or phenotype Reference Solanaum lycopersicum CRISPR PETALA2a (AP2a), NON-RIPENING (NOR) Fruit development and ripening Wang et al.(2019) Solanaum lycopersicum CRISPR Psy1 and CrtR-b2 Carotenoid metabolism D’Ambrosio et al.(2018) Solanaum lycopersicum CRISPR Carotenoid isomerase and Psy1 Carotenoid metabolism Dahan-Meir et al.(2018) Solanaum lycopersicum CRISPR SGR1, Blc, LCY-E, LCY- B1, LCY-B2 Increased lycopene content Li et al.(2018) Solanaum lycopersicum CRISPR SlMYB12 Pink tomato fruit color Deng et al.(2018) Solanaum lycopersicum CRISPR MPK20 sugar metabolism Chen et al.(2018) Solanaum tuberosum CRISPR BSS1 Starch biosynthesis Andersson et al.(2018) Solanaum tuberosum CRISPR GBSS Starch quality Andersson et al. (2017). Solanaum tuberosum CRISPR StALS1 Starch quality (Butler et al., 2016) Solanaum tuberosum CRISPR SBE1 and StvacINV22 Sugar metabolism Ma et al.,2017 Use of CRISPR/Cas9 technology to improve quality trait
  • 46. Potato •To increase the overall protein content of potato (Chakraborty et al., 2010) expressed the AmA1 gene from Amaranthus seed albumin in potato tubers. The transgenic potato lines called “Protato” had 48% increased protein content Tomato • Fruits of Arka Vikas were modified by fruit specific expression of two transcription factors Ros1 and Del . Avg. anthocyanin content of transgenic fruits were 70-100 folds higher than that of the control fruits ( Maligeppagol et al.,2013) Tomato Biofortification of vegetable crops •It is a process of enrichment of health beneficial dietary nutrients in crop through conventional and molecular breeding, genetic and agronomic measures. •Biotechnological tools have opened up the possibilities to introduce genes responsible for the biosynthesis of micronutrients. Transformation of tomato with the Petunia chi-a gene encoding chalcone isomerase resulted transgenic tomato lines produced an increase of up to 78 fold in fruit peel flavonols, mainly due to an accumulation of rutin (Muir Shelagh et al, 2001). Achievements in bio-fortified nutraceuticals in some vegetables Crop Biofortified element /mineral/ Vitamin Tomato Chlorogenic acid, flavonoids, anthocyanin, stilben, Folate, phytoene ,β- carotene ,lycopene, provitamin A Onion & Broccoli Selenium Lettuce Iron Carrot Calcium Radish Selenium Brassica spp. Selenium Parulekar et al.(2019)
  • 47.
  • 48. •Pusa Beta Kesari 1 first biofortified variety through pure line selection •Contain high beta carotene (8.0 to 10.0 ppm) •High β-carotene (14.0 mg/100g) & 27 – 29% dry matter •Total sugars 2-2.4% and Recommended for cultivation in Odisha (Yadav et al. ,2017) • High anthocyanin (90mg/100g), Dry matter: 24.0-25.5% and Starch: 19.5% Total sugar: 1.9-2.2% • Recommended for cultivation in Odisha •Tubers with dark orange flesh colour and very high beta carotene Carotene content in tubers is 466 IU/100gm Biofortified Varieties Developed in India
  • 49. Okra: Kashi Lalima Anthocyanin 3.0mg/100g Zinc: 49.7ppm (3.3%) higher French bean: Kashi Baigani Anthocyanin: 7.0mg/100g Red Radish: Kashi Lohit Anthocyanin : 39.9µg/g F.W Black carrot: Kashi Krishna Anthocyanin (275-300mg/100g) Red carrot: Kashi Arun Lycopene: 7.50mg/100g FW Beta-carotene: 3.7mg/100g FW. Yam: Sree Neelima Anthocyanin rich
  • 50. Sl No. Title of the Research Article Year of Publication Journal Name 1 Color-related chlorophyll and carotenoid concentrations of Chinese kale can be altered through CRISPR/Cas9 targeted editing of the carotenoid isomerase gene BoaCRTISO Oct., 2020 Horticulture Research 2 Hybridization in Peppers (Capsicum spp.) to Improve the Volatile Composition in Fully Ripe Fruits: The Effects of Parent Combinations and Fruit Tissues May 2020 Agronomy 8.60 (NAAS) 3 Enhancement of Chlorogenic Content of the Eggplant Fruit with Eggplant Hydroxycinnamoyl CoA- Quinate Transferase Gene via Novel Agroinfiltration Protocol Nov., 2020 Pharmacognosy Magazine 7.31 (NAAS)
  • 51. 2020 Objective : The purpose of this present study was to perform targeted editing of BoaCRTISO gene using the CRISPR/Cas9 system to change the colour and pigment concentrations of Chinese kale 2020 Case study -1 CASE STUDY 1 Sun et al., 2020
  • 52. Introduction Carotenoid isomerase (CRTISO), an enzyme that acts before the bifurcation point in the carotenoid biosynthetic pathway, is responsible for catalyzing the conversion of lycopene precursors to lycopene(Yuan et al.,2015) Recently, a CRISPR/Cas9 gene editing system in Chinese kale was established( Sun et al.,2018) and used it to demonstrate functional differences among members of the PDS family, which are important genes involved in the carotenoid biosynthetic pathway (Sun et al., 2019) The present study was done to perform targeted editing of BoaCRTISO using the CRISPR/Cas9 system to change the colour and pigment concentrations of Chinese kale.
  • 53. Materials and Methods •Plasmid construction:  Target site AGG (exon 11) is PAM, CRTISO CRISPR F/R –obtained by removing AGG.  Adding 5’ end- ATTG , 3’ end-AAAC •Agrobacterium-mediated transformation The explants were infected with the Agrobacterium strain GV3101, co cultivated with Agrobacterium in MS media and hygromycin B were transferred to tissue culture bottles that contained the subculture media •Detection of mutations To evaluate mutations introduced into the CRISPR/ Cas9 transgenic plants, the genomic DNA of each positive transgenic shoot was amplified using the specific primers CRTISO- CRISPR-test-F/R •Colour measurements Three positions on the leaves and the bolting stems of each mutant were randomly selected, and the L*, a*, and b* colour values were obtained •Chlorophyll and carotenoid assays HPLC analysis of the carotenoids and chlorophyll was carried out •RNA extraction and qPCR expression analysis The expression levels of genes encoding carotenoid-degrading enzymes and chlorophyll biosynthesizing- and degrading-enzymes were calculated based on the respective expression levels of the respective genes in WT bolting stems.
  • 54. Result Vector Map and Analysis of BoaCRTISO mutations CRISPR/Cas9-induced mutations in Chinese kale. (Target sequence-blue, PAM sequence (NGG)-red, mutated bases-red and asterisks-spacing between bases. WT wild-type plant, M # number of mutants, i # number of base insertions, r # number of base replacements. Twenty-three hygromycin-resistant plants were obtained from ~2000 explants. The target expression cassette was transferred into 16 lines out of 23 and the transgenic efficiency was 69.57%. Mutation pattern and efficiency were studied(fig-a and fig-b and mutation frequency Fig C) The biallelic mutant M1 and the homozygous mutants M3, M6, and M16 were selected for subsequent studies.
  • 55. Colour of crtiso mutants Marked differences in color were observed between the crtiso mutants and WT plants. The leaves and bolting stems of the four tested mutants were yellow, with M6 being the most yellow The variation in chromatic parameters in the leaves and bolting stems of the four mutants was consistent the values of L* and b* were significantly higher than those of WT plants, while the values of a* were significantly lower.
  • 56. Pigment concentrations of crtiso mutants •The total carotenoid and chlorophyll concentrations in the mutants were significantly lower than those in the WT plants •All pigments in the M6 leaves significantly decreased by more than 20% compared with those in the WT leaves •The concentrations of most pigments in the leaves of M1, M3, and M16 were also significantly lower than those in the WT leaves, although the differences in violaxanthin, β-carotene, and neoxanthin were not significant
  • 57. Carotenoid- and chlorophyll-related gene expression levels in crtiso mutants •In WT plants, the expression levels of carotenoid biosynthesis-related genes in the leaves were substantially higher than those in bolting stems. •The genes with highest and lowest expression levels in the leaves were ZEP1 and NXS respectively. •The genes with the highest and lowest expression levels in the bolting stems were ZEP2 and VDE respectively, •After the targeted editing, the CRTISO gene expression in the leaves of the crtiso mutants was consistently downregulated and led to reduced expression of most carotenoid biosynthesis-related genes in the leaves and bolting stems Expression levels of genes related to carotenoid biosynthesis and degradation B L L B
  • 58. Expression levels of genes related to chlorophyll biosynthesis and degradation •The expression levels of chlorophyll biosynthesis related genes in the leaves and bolting stems of crtiso mutants were generally downregulated •However, some chlorophyll biosynthesis-related genes were upregulated. These genes included ALAD and ChlI in M1 leaves; ALAD, ChlI, and CS in M3 leaves; and ChlI in M6 bolting stems ALAD in M1 leaves ChlI in M1 leaves
  • 59. Schematic diagram of the results of this study. Blue genes were down regulated in the mutants, Red genes were upregulated in the mutants, Black genes did not change significantly in terms of their expression. The down arrow next to a pigment indicates a decrease in its content. ⊥ indicates suppression. 59 The inhibition of BoaCRTISO gene expression in the crtiso mutants led to the downregulation of expression levels of carotenoid and chlorophyll biosynthesis-related genes, as well as carotenoid and chlorophyll contents, which led to the yellowing of the crtiso mutants.
  • 60. •In this study, the carotenoid isomerase gene from Chinese kale (BoaCRTISO) was targeted and edited using the CRISPR/Cas9 system and Agrobacterium- mediated stable transformation. •CRISPR/Cas9 system was used to edit the BoaCRTISO gene of Chinese kale, resulting in the production of 13 mutants of the biallelic, homozygous, heterozygous, and chimeric types. •BoaCRTISO was knocked down rather than knocked out in this study •The expression level of the CCD1 gene was also significantly reduced, which may be a response to the decrease in the expression levels of carotenoid biosynthesis genes. •Inhibition of CRTISO expression affected both the carotenoid and chlorophyll pathways, leading to decreased carotenoid and chlorophyll concentrations and creating a new yellow color of Chinese kale, with improved market prospects. •The CRISPR/Cas9 system is therefore a promising technique for crop quality improvement Inference
  • 61. CASE STUDY 2 Peris et al., 2020 Objectives (i) To study the inheritance of the volatile fractions in peppers. (ii) To assess the opportunity of developing new combinations of volatiles by hybridization.
  • 62. Introduction Capsicum peppers (Capsicum spp.), especially C. annuum L., are one of the most important vegetables and spices in the world and their fruits are used in a range of food dishes, to provide aroma and flavor. Pungency has been largely studied, while studies on the volatile fraction are more recent and less diverse. More than 200 varietal types have been reported, which greatly vary in their external traits and also in their organoleptic and functional properties [Patel, K et al., 2016]. Among them, C. annuum is the most economically important species and is phylogenetically related to C. chinense and C. frutescens [Dias et al., 2019) A diverse profile of volatiles including terpenoids, esters, alkanes, and several aldehydes and alcohols, was found among the evaluated accessions of chilli. Hybridization provided higher amounts of total volatiles and a more complex composition, particularly in the pericarp. The present study was designed to study the inheritance of the volatile fractions in peppers and to determine if they can be improved by breeding strategies.
  • 63. Materials and Methods 10 Capsicum accessions (8 C. annuum and 2 C. chinense), 1. Planting material 6 C. annuum × C. annuum (Intra specific hybridization) & 3 C. annuum× C. chinense (Inter specific hybridization) hybrids between accessions. 2.Preparation of Samples and Extraction of Volatiles  10 plants/ accession, 2 samples (1 pericarp and 1 placental tissues).  Pericarp subsamples: mixing 2 g of fresh weight from the pericarp (free of placental tissues and septa) and finely cut into 3 × 3 mm pieces and immediately transferred into a 20 mL sealed crimp cap headspace vial. Placental subsamples: 2 g of placenta and seeds.
  • 64. 3. Extraction of the Volatile Fraction (HS-PME)  Headspace-solid-phase microextraction (HS-SPME) was used to isolate the volatile compounds [9,21].  SPME(divinylbenzene/carboxen/polydimethylsiloxane, DVB/CAR/PDMS, 50/30 µm) (Supelco, Bellefonte, PA, USA) were used to perform the extraction from the HS.  The fiber was exposed to the headspace of the sample vials for 40 min at 40 ◦C to allow adsorption of volatiles.  The fiber was thermally desorbed at 250 ◦C for 30 s in splitless mode in the gas chromatograph injection port, using a splitless inlet liner of 0.75 mm ID. Purge flow was maintained at 50 mL min−1 and purge time was 1 min.  In order to ensure that there was no cross-contamination from previous samples, the fiber was always reconditioned for 30 min at 250 ◦C in the injection port of another gas chromatograph 4. Analysis of Volatiles Volatile fraction was analyzed by gas chromatography– mass spectrometry (GC–MS),
  • 65.
  • 66. RESULTS The highest amount of total volatile fractions and number of volatile compounds was found in Capsicum annuum accessions Chile Arbol followed by Cayenne, Pasilla Bajio, Serrano and Capsicum chinense accession PI 152225.
  • 67. Individual volatiles in placental tissues were more in Serrano (Terpenoids 429.79 %), PI 152225 (Esters 341.38 % and Alkanes 583.37 %). Highest amount of volatiles in placental tissues was found in hybrid accessions Cayenne x Serrano (2327. 611 % Intra specific hybridization).
  • 68. Figure 2. Heatmap hierarchical cluster analysis of the volatiles identified in the hybrid accessions studied (Intra and Inter specific Hybridization), corresponding to the pericarp (Pe) and placental (Pl) tissues. Accession and volatile abbreviations correspond to those indicated in Tables 1 and 2, respectively. Figure 1. Heatmap hierarchical cluster analysis of the volatiles identified in the parent accessions studied, corresponding to the pericarp (Pe) and placental (Pl) tissues. Accession and volatile abbreviations correspond to those indicated in Tables 1 and 2, respectively. Accumulation of Volatiles in Fruit Tissues (Placenta and Pericarp) abundant in accessions ‘Cayenne’, ‘Chile Serrano’ and PI152225 and hybrid accessions i.e. Cayenne×Serrano and Arbol×Serrano
  • 69. Inference:  There are ample opportunities to improve the aroma-related compounds in fully ripe Capsicum peppers by hybridization, both qualitatively and quantitatively.  Most hybrids showed more complex volatile profiles than those of their corresponding parents as a result of the confluence of volatiles from both parent lines, with cases of intermediate inheritance or transgressive inheritance, and also, but to a lesser extent, to the appearance of new compounds, presumably due to genetic complementation.  Thus, breeders can plan sets of hybrid combinations using parents with complementary volatile fractions, and then perform final selections of those hybrids with the most desirable flavors and aromas based on organoleptic tests.  In general, placental tissues were quantitatively richer in volatile compounds, which is of special interest for breeding the aroma and flavor of varieties where the whole fruit is used in culinary applications.
  • 70. CASE STUDY 3 Kaushik et al., 2020 Objectives  To establish and standardize an efficient agroinfiltration protocol for the eggplant fruit for enhancing Phenolics.  To determine the function of Egg plant SmHQT (eggplant hydroxycinnamoyl CoA-quinate transferase). Introduction Among vegetables, phenolic acids, for example, chlorogenic acid, is present in larger quantities in the eggplant (Solanum melongena L.). For the production of chlorogenic acid in the eggplant hydroxycinnamoyl CoA-quinate transferase (SmHQT), is a central enzyme that catalyzes the reaction to the chlorogenic acid production.
  • 71. Materials and Methods a. Construct used for the agroinfiltration assay . Genomic DNA-extracted-from the Fruits- Amplified for the SmHQT Agroinfiltration GUS bearing vector pCAMBIA1304 Adgene pBS+ Vector pBS+ SmHQT digested HindIII/BamH1 Cloning pUC cloning vector Sub cloning pBIN19 Add gene Sub culture LB broth (5 ml) – 2 ml syringe was injected into the Eggplant fruits at 10-15 spots Plant material: Arka Shirish – Green colour Brinjal variety. In silico cis-regulating elements map and interactome analysis
  • 72. Results Figure 1: Protein-protein interaction networks SmHQT controlling high chlorogenic biosynthesis pathway in eggplant using Arabidopsis databases. Their interactions were analysed online using STRING database (https://string-db.org/) In this study, nine potential protein interaction networks (TT4, CYP98A3, 4CL3, 4CL1, C4H, IRX4, 4CL2, LysoPL2, and CCOAMT) were identified for HQT gene. Fig 2 comparison of fruit slices after following the X-Gluc staining procedure with the control fruit slices are above. Figure 3: The high performance liquid chromatography results of agroinfiltrated versus control fruits in three independent fruits on different plants. A. tumefaciens GV3101 strain was used and transformed to, GUS bearing vector with SmHQT was transiently expressed in eggplant fruit Agroinfiltrated fruits Control
  • 73. Figure 4: Differential gene expression level (quantitative reverse transcription polymerase chain reaction) of six candidate genes of the chlorogenic pathway is represented with respect to control plant fruit. The expression was analysed at one day and 3 days after infection. Inference:  Due to the overexpression of the SmHQT gene, higher chlorogenic content was exhibited by the eggplant fruits, which was validated by HPLC.  The chlorogenic acid content after following the agroinfiltration procedure was more two times in the agroinfiltrated fruit.  To identify the optimal target for increasing chlorogenic pathway flux post‐SmHQT activity, expression patterns were analyzed with qRT-PCR, and the results showed the changes in the expression level of the other chlorogenic acid pathway genes.  Furthermore, the cis regulating elements and protein-protein interaction (PPI) analyses supported the HPLC results. Quantitative gene expression analysis
  • 74. Nutritional Qualities and associated health benefits of vegetable crops is becoming important criteria for their increase in consumers diet. In this respect, breeding programmes for improving the content of nutrients complex quality traits and shelf life in vegetables are becoming more important for breeders. Molecular breeding and genetic manipulation have emerged as the two most potent technologies which have the potential to attain quality improvement for the coming years Advances in NGS technology have enabled the incorporation of genomics with various disciplines of crop breeding The key gene or genes regulating a molecular pathway are being genetically engineered or edited to develop phenotypically improved crop lines Conclusion