This document discusses the use of molecular markers in fruit crop breeding. It begins by explaining how molecular markers like RFLPs, AFLPs, RAPDs, ISSRs, SSRs, and SNPs can be used in marker-assisted selection to improve the efficiency of breeding programs through early trait assessment, selection of complex traits, and distinguishing hybrids from parental lines. It then provides examples of studies using ISSR and SSR markers in citrus and peach breeding. The document concludes by summarizing achievements in various fruit crops using different molecular marker techniques and outlining ongoing research projects at PAU utilizing biotechnology approaches like marker-assisted breeding.

1. M K SAINI
Presented by:
Mandeep Kaur
L-2018-A-35-D
PhD Fruit Science
Marker assisted Selection (MAS)
in fruit crops
Presented to:
Dr H S Dhaliwal
Dr Monika Gupta
Dr Rachna Arora

2. M K SAINI
Molecular Markers
• Conventional plant breeding - Time consuming.
• Breeding and releasing an improved variety is often difficult task.
• Molecular markers - Novel approach to improve strategies in plant breeding.
• Molecular markers are genes or particular segments of DNA that are representative
of differences at DNA level.
• Molecular Markers - Improves Efficiency of Breeding Programs
.
– MAS
– Marker assisted gene pyramiding: Resistance breeding
– Construction of linkage maps & QTL mapping
– Assessment of genetic variability
– Characterization of germplasm
– Varietal identification
Belete (2018) Ethiopia

3. M K SAINI
3
Non-PCR based markers
RFLPs
MOLECULAR MARKERS IN FRUIT CROPS
PCR based markers
AFLPs
RAPDs
ISSRs
SSRs
Functional markers
SCARs
SSC8
SCF27
GSLP1
Sequenced based markers
SNP

4. M K SAINI
Marker - assisted Selection (MAS)
• Marker-assisted selection or marker aided selection (MAS)
• It is an indirect method of selection whereby a phenotype is selected based on a
marker (morphological, biochemical or DNA/RNA variation) associated to a trait
of interest rather than on the trait itself (Jiang 2013).
• Marker - assisted selection for conventional breeding: WHY ?
– Early assessment of traits
– Precise selection of the complex traits
– Traits with low heritability
– Difficult traits (eg - abiotic stresses)
– Distinction between homo & heterozygotes
– No question of biosafety and bioethics

5. M K SAINI
Identification of zygotic and nucellar seedlings in
citrus interspecific crosses by ISSR markers
• Polyembryony => Breeding problem.
• Objective => Hybrid populations for scion breeding.
• Maternal parent- Yashar (Y)
• Pollen parent- Page (P), Marrs (M), Hamlin (H), Changsha (Ch) and Ponkan (Po).
• 227 plantlets- 67 hybrid and 160 nucellar seedlings
White arrowheads - confirmed polymorphic markers in N1, N4, N9 and N10 for pollen parent.
Non confirmed polymorphism N5, N6, N7 and N8
Golein et al (2017) Iran
Fig: Primers amplication on page

6. M K SAINI
Identification of zygotic and nucellar seedlings
by simple sequence repeats markers
• Rough Lemon => Highly susceptible to Phytophthora root rot.
• Rough Lemon (Citrus jambhiri Lush.) –> Female parent.
• X-639 Citrandarin (X; Cleopatra mandarin × Trifoliate orange) –> Male parent.
• After embryo rescue, only hybrid seedlings from RL X crosses were screened.
Fig: PAGE gel showing PCR amplification using DNAs from seedling of RL X
Yellow labeled zygotic seedlings with bifoliate and trifoliate leaves
Singh et al (2020) PAU, Ludhiana

7. M K SAINI
Hybridity confirmation of low chill peach
(Prunus persica) hybrids using SSR markers
Tab: Hybridity confirmation by SSR polymorphic markers
Devi et al (2018) PAU, Ludhiana
• Small genome size (265 Mb) => Breeding constraint.
• Objective => To widen varietal range with improved fruit quality.
• Shan-i-Punjab, Tropic Sweet => Female
• Florda Prince, Flordaglo and Prabhat => Male
• 22 SSR markers - Hybridity confirmation.
• Only six markers - Test the hybridity of F1 seedling.

8. M K SAINI
Identification of seedless trait using seedless
functional molecular marker SCF27-2000
Zhu et al (2019) China
Detection of seedless marker in Hybrids of Ruby Seedless × 00-1-5
• Objective => New cold-resistant seedless grapes for the colder regions.
• Embryo abortion of Seedless female parent => Breeding problem.
• 00-1-5 (V. vinifera × V. amurensis) = cold-resistant, seeded hybrid.

9. M K SAINI
Fruits name Markers type Work done References
Citrus RFLPs, RAPDs, AFLPs, SSRs,
ISSRs, SNPs and DArTs
Identification of hybrids, phylogenetic studies and
association of genome mapping to detect various QTLs
Ahmed et al (2017)
Imai et al (2018)
Mango AFLPs, RAPDs, SSRs and
ISSRs
Identification of hybrids and cultivars Imai et al (2018)
Banana RAPDs, SSRs and ISSRs Genetic variability and phylogenetic studies Curtolo et al (2018)
Apple RFLPs, RAPDs, SSRs, ISSRs,
SCARs, SNPs and DArTs
Genetic variability, identification of QTLs controlling flesh
mealiness, construction of genome map of woolly aphid
and detect resistance genes, development of high-
density molecular marker map, GWAS applications in
QTLs analysis and MYB10 gene linked with a locus
responsible for red flesh and foliage. ACS and ACO, two
genes detected for ethylene production by using gene
specific markers positioned on a molecular marker
linkage map
Bus et al (2008)
Chagne et al (2007)
Costa et al (2005)
Grapes AFLPs, RAPDs, SSRs, ISSRs,
SNPs, SCC8, SCF27 and
GSLP1
Sex expression, identification of seedless parents,
identification of QTLs association with downy mildew
resistance
Li et al (2015)
Rao et al (2017)
Pear AFLPs, RAPDs, SSRs, SNPs,
ISSRs, PPACS 2 and BGA 35
Genetic variability, relationship among cultivars and
development of a high-density genetic linkage map in
pear (Pyrus communis × Pyrus pyrifolia)
Costa et al (2005)
Kalkisim et al (2016)
Guava RAPDs and SSRs Genetic diversity and evaluation of genetic variants Pessanha et al (2011)
Pineapple RFLPs, RAPDs, SSRs and ISSRs Genetic diversity Wang et al (2017)
India jujube AFLPs, RAPDs and ISSRs Genetic diversity and relationship among cultivars Baranski et al (2012)
Peach RAPDs, AFLPs, SSRs, SRAPs
and SSAPs
Species diversity and identification of brown rot causing
genes, i. e., MAT1-1 and MAT1-2
Pérez et al (2020)
Jiao et al (2014)
Strawberry RAPDs, SNPs, SSRs and
SCARs
DNA fingerprinting, identification of genes, i.e., Hsp70,
LOC101295509 and LOC101311180.
Ahmad et al (2020)
Achievements made in breeding of fruit crops through molecular approaches

10. M K SAINI
Research Projects in PAU
• Mapping of phytophthora resistance in intergeneric rootstock population
and development of improved rootstocks in citrus (2019-2022).
• Genetic improvement of Kinnow mandarin for fruit quality, biotic and
abiotic stress tolerance.
• Whole genome and transcriptome sequence based SSR and SNP markers
development in guava (Psidium guajava L.) for linkage mapping and trait
association (2018-2022).
• Isolation, Cloning & Characterization of Antifungal Genes from Potent
Strains of Trichoderma for Resistance to Phytophthora in Rough Lemon.
• Rapid production of virus free Daisy tangerine on Carizzo rootstock by in
vitro shoot tip grafting.
• Standardization of in vitro clonal multiplication protocol for nematode
resistant prunus rootstock ‘Flordaguard’.
Source - https://www.pau.edu

11. M K SAINI
Conclusion & Future Prospects
• Biotechnology has brought great opportunities and
prospects for overcoming problems of conventional
breeding.
• However, biotechnology as transgenic breeding or genetic
manipulation cannot replace conventional breeding but it is
and only is a supplementary addition to conventional
breeding.
• Therefore, integration of biotechnology into conventional
breeding programs will be an optimistic strategy for fruit
crop improvement in the future.

12. M K SAINI