Fruit Science related ppt. in which you easily find out that which molecular marker is suitable for various traits and quality

2. Banda University of Agriculture & Technology, Banda (U.P)-210001
TOPIC: MARKER ASSISTED SELECTION(MAS) IN FRUIT CROPS
 Name : Aadarsh Pandey
 I’D No. : 2369
 M.Sc (Hort.) Fruit Science
 FSC-591 Master’s
Seminar
 Sybmitted to : Dr.Akhilesh Srivastava
 Head & Professor, Department of Fruit
Science, BUAT, Banda

3. CONTENTS
INTRODUCTION
MARKERS AND ITS TYPES
STEPS INVOLVED IN MARKER ASSISTED SELECTION (MAS) IN
FRUIT CROPS
BASIC PROCEDURE OF MARKER ASSISTED-SELECTION
ADVANTAGES & DISADVANTAGES OF MAS
CASE STUDIES IN FRUITS CROPS
CONCLUSION
BIBLIOGRAPHY

4. Morphological Marker- In plant breeding, marker that are related to
variation in shape, size colour & surface of various plant parts.
 Biochemical Marker- Marker that are related to variation in protein and
amino acid banding pattern are known as biochemical marker. A gene encodes
a protein that can be extracted and observed ;for example, isozyme and storage
protein
DNA Marker- A gene or other fragment of DNA whose location in the
genome is known. A genetic marker is a known DNA sequence.
MARKER AND ITS TYPE

5. MOLECULAR MARKERS
Molecular marker are particular segments of DNA that are demonstrative of
diffrences at DNA level.
Molecular markers increase the efficiency of Breeding Programme.
Molecular marker are found at specific locations of the genome.
Molecular marker technologies offer such a possibility by adopting a wide range of
novel approaches to improving strategies in plant breeding.
Breeding a new variety takes between several years and even the release of an
improved variety cannot be guaranteed.

6. MOLECULAR MARKERS IN FRUIT CROPS
NON-PCR based markers/
Hybridization based
markers
PCR-based markers Sequenced based
markers
RFLPs
AFLPS
RAPDS
ISSRS
SSRS
SNP

7.  Restriction Fragment length Polymorphism(RFLP)- It refers to variation found in the
length of DNA fragments generated by specific restriction endonuclease enzymes. RFLP
is a first type of DNA markers developed to distinguish individuals at the DNA level.
This technique was developed before the discovery of Polymerase Chain
Reaction(PCR).
 Amplified Fragment Length Polymorphism(AFLP)- AFLP can be performed using
very small DNA samples (typically 0.2-2.5 µg per individual). This technique was
originally known as selective restriction fragment amplification.
 Random Amplified Polymorphic DNA(RAPD)- It refers to polymorphism found
within a species in the randomly amplified DNA generated by restriction endonuclease
enzyme. RAPDs are PCR based DNA markers.

8. Inter-Simple Sequence Repeats Marker(ISSR)- ISSRs are semi-arbitrary markers amplified
by PCR in the presence of one primer complementary to a target micro-satellite. Amplification
in presence of non- anchored primers also has been called microsatellite-primed PCR, or MP-
PCR. Such amplification does not require genome sequence information and leads to multi-
locus and highly polymorphic patterns.
Single Sequence Repeats(SSR)- SSR or Microsatellites are tandemly repeated mono-, di, tri,
tetra, Penta, and hexa-nucleotide motifs. SSR length polymorphism are caused by differences in
the number of repeats.
Single Nucleotide Polymorphism(SNP)-The variation which are found at a single nucleotide
position are known as single nucleotide polymorphisms or SNP. Such variation due to sub-
situation, deletion or insertion. This type of polymorphism have two alleles and also called bi-
allelic loci. This is most common class of DNA polymorphism.

9. INTRODUCTION
• Marker -assisted breeding (MAB), also called molecular-assisted
breeding(MAB) , is the application of molecular biotechnologies,
specifically DNA markers , in combination with linkage maps and
genomics , to alter and improve plant or animal traits on the basis of
phenotypic assays (Jiang 2013).
• MAS is a process in which a marker is used for indirect selection of a
genetic determinant or determinants of a trait of interest, i.e.
productivity, and/or quality (Prabhu et al., 2009).

10. STEPS INVOLVED IN MARKER ASSISTED SELECTION IN FRUIT CROPS

11. Application
MAS is applicable for genetic improvement of plants as well as animals and in plants.
 It is equally applicable in both self-pollinated and cross pollinated species.
The marker aided selection consists of five important steps, viz:
 Selection of parents,
 Development of breeding population,
 Isolation of DNA from each plant,
 Scoring RFLPs
 Correlation with morphological traits.

12. BASIC PROCEDURE OF MARKER ASSISTED SELECTION( MAS)

13. ADVANTAGES OF MAS
 Accuracy: The accuracy of MAS, is very high because molecular markers are
not affected by environmental conditions. It is very effective even with the
characters having low heritability.
Rapid Method: MAS is a rapid method of crop improvement. It takes 3-5 years
for developing a new cultivar against 10-15 years taken by the conventional
method of breeding.
Non-transgenic Product: MAS leads to development of non-transgenic cultivars
which are acceptable to everybody. In other words, it does not involve transgene.
Hence there is no question of gene silencing.

14. ADVANTAGES OF MAS
• Identification of Recessive Alleles: MAS permits identification of recessive
alleles even in heterozygous condition and thus speeds up the progress of crop
improvement programs. In other words, it is equally effective for the genetic
improvement of recessive characters.
• Early Detection of Traits: MAS permits early detection of traits that are
expressed late in the life of plant. For example characters such as grain or fruit
quality, flower color, male sterility, photoperiod sensitivity that express late in the
life of a plant can be screened in the seedling stage. In other words, DNA tested at
seedling stage can through light about the trait which are expressed later on.
SOURCE:-(Biology discussion.com)

15. DISADVANTAGES OF MAS
 MAS is a costly method. It requires well equipped laboratory viz. expensive
equipment’s, glassware and chemicals.
 MAS requires well trained manpower for handling of sophisticated equipment,
isolation of DNA molecule and study of DNA markers.
 The detection of various linked DNA markers (AFLP, RFLP, RAPD, SSR etc.) is
a difficult, laborious and time consuming task.
 It has been reported that MAS may become less efficient than phenotypic
selection in the long terms.
SOURCE:-(Biology discussion.com)

16. IDENTIFICATION OF ZYGOTIC AND NUCELLAR SEEDLING IN CITRUS
INTERSPECIFIC CROSSES BY ISSR MARKERS
 Major problems found in Citrus breeding program is undesirable nucellar poly-
embryogenesis.
 Maternal parent- Yashar(Y)
 Paternal parent- Page(P), Mars(M), Hamlin(H), Changsha (C),and Ponkan
(Po).
Objective:- To generate hybrid seedlings for scion breeding.
 227 plantlets, 67 hybrid 160 nucellar seedlings

17. White arrowheads- Confirmed polymorphic markers N1, N4, N9 and N10, specific for
pollen progenitor (Page). Not been confirmed polymorphisms N5, N6, N7 and N8.
Different Banding Pattern of DNA showed in Figure.

18. Hybridity confirmation of low chill peach (Prunus persica) hybrids using SSR marker
 Maternal Parents- Shan-e-Punjab & Tropic Sweet.
 Paternal Parent- Florida Prince ,Flordaglo & Prabhat.
 22 SSR marker taken for hybridity confirmation.
 Among of 22 markers only 6 markers were able to test the hybridity of F1-
Seedlings.
 Objective- To widen the varietal range with improved fruits quality.

19. Hybrid NO. Pedigree Result Markers(s)
H-1 Shan-e-Punjab × Florida Prince Hybridity confirmed CPPCT-030
CPPCT-022
H-2 Shan-e-Punjab × Flordaglo Hybridity confirmed CPPCT-030
CPPCT-022
MA020a
H-3 Shan-e-Punjab × Prabhat Hybridity confirmed CPPCT-030
MA023a
MA020a
H-4 Tropic Sweet × Florida Prince Hybridity confirmed CPPCT-030
MA015a
UDP96-005
H-5 Tropic Sweet × Flordaglo Hybridity confirmed CPPCT-030
MA020a
H-6 Tropic Sweet × Prabhat Hybridity confirmed CPPCT-030
MA015a

20. Achievements made in breeding of fruit crops through molecular approaches
FRUITS WORK DONE MARKERS TYPE
Pomegranate Gene mapping and gene relationship RAPDs, SSRs, and SNPs
Citrus Identification of hybrids, phylogenetic
studies and association of genome
mapping to detect various QTLs
RFLPs, RAPDs, AFLPs, SSRs, SNPs.
Mango Identification of hybrids and cultivars AFLPs, RAPDs, SSRs .
Banana Genetic variability and phylogenetic
studies
RAPDs, SSRs.
Grapes Sex expression, identification of
seedless parents, identification of
QTLs association with downy mildew
resistance
AFLPs, RAPDs, SSRs, SNPs.
Guava Genetic diversity and evaluation of
genetic variants
RAPDs and SSRs
Date palm Phylogenetic relationship and genetic
variability
RAPDs, SSRs.

21. FRUITS WORK DONE MARKERS TYPE
Olive DNA fingerprinting and genetic relationships. AFLPs, RAPDs, SSRs and SNPs
Pineapple Genetic diversity. RFLPs, RAPDs, SSRs and ISSRs
Chinese jujube RFLPs, RAPDs, SSRs and ISSRs SSRS
Indian jujube Genetic diversity and relationship among
cultivars.
AFLPs, RAPDs and ISSRs
Peach Species diversity and identification of brown rot
causing genes, i. e., MAT1-1 and MAT1-2
RAPDs, AFLPs, SSRs, SRAPs and SSAPs
Strawberry DNA fingerprinting, identification of genes, i.e.,
Hsp70, LOC101295509 and LOC101311180
involved in heat tolerance.
RAPDs, SNPs, SSRs and SCARs,

22. DNA Markers for Genetic Diversity Assessment in Fruit Crops
FRUIT MARKER TYPE REFERENCE
APPLE AFLP, RAPDs Coart et al. (2003); Botez et al. (2009); Sestras et al.
(2009)
BANANA RAPDs Brown et al. (2009)
CITRUS RFLPs Durham et al. (1992)
GRAPES RFLP, SSR Bourquin et al. (1993)
CASHEW RAPD, SSR Thimmappaiah et al. (2009)
PEAR SSR, AFLP Sisko et al. (2009)

23. DNA marker for varietal identification
FRUIT MARKER TYPE REFERENCE
RAPSBERRY RAPD Parent et al. (1993)
APPLE RAPD Koller et al. (1993)
GRAPES
CULTIVAR
SSR Thomas et al. (1995)
GRAPES
ROOTSTOCKS
RAPD Hong Xu et al. (1995)
LEMON RAPD Deng et al. (1995)
MANGO RAPD Schnell et al. (1995)

24. • Biotechnology has brought great opportunities and propects for overcoming
problems of conventional breeding.
• However, biotechnology or transgenic breeding or genetic manipulation
cannot replace conventional breeding but it is & 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
CONCLUSION AND FUTURE PROPECTS

25. BIBLIOGRAPHY
Jiang GL (2013) Molecular markers and marker-assisted breeding in plants. In: Andersen SB, editor. Plant
breeding from laboratories to fields. Rijeka: In Tech Pp. 45-83
Prabhu A. S., Filippi M. C., Silva G. B., Silva-Lobo V. L., Morais O. P. (2009). An unprecedented outbreak of
rice blast on a newly released cultivar BRS Colosso in Brazil, in Advances in Genetics, Genomics and
Control of Rice Blast, eds Wang G. L., Valent B. (Dordrecht: Springer Science; ), 257–267.
Joshi, S. P., P. K. Ranjekar and V. S. Gupta (1999). Molecular markers in plant genome analysis. Curr. Sci.
77:230-40.
Bhat, Z. A., DHILLON, W. S., Rashid, R., Bhat, J. A., Dar, W. A., & Ganaie, M. Y. (2010). The role of
molecular markers in improvement of fruit crops. Notulae Scientia Biologicae, 2(2), 22-30.
Thakur, R., Singh, V., & Banerjee, D. (2023). Use of Molecular Marker in Fruit crops for their traits and
Genetical Diversity Analysis. In E3S Web of Conferences (Vol. 453, p. 01020). EDP Sciences.
Golein, B., Fifaei, R., & Ghasemi, M. (2011). Identification of zygotic and nucellar seedlings in citrus
interspecific crosses by inter simple sequence repeats (ISSR) markers. African Journal of
Biotechnology, 10(82), 18965-18970.
Devi, I. N. D. I. R. A., Singh, H., & Thakur, A. N. I. R. U. D. H. (2018). Morphological characterization and
hybridity confirmation of low chill peach (Prunus persica ) hybrids using SSR markers. Indian
Journal of Agricultural Sciences, 88(6), 889-94.
Hasan, N., Choudhary, S., Naaz, N., Sharma, N., & Laskar, R. A. (2021). Recent advancements in molecular
marker-assisted selection and applications in plant breeding programmes. Journal of Genetic
Engineering and Biotechnology, 19(1), 1-26.