Marker assisted selection in fruit crops

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

1. 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

2. 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

3. 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

4. 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.

5. MOLECULAR MARKERS IN FRUIT CROPS NON-PCR based markers/ Hybridization based markers PCR-based markers Sequenced based markers RFLPs AFLP S RAPD S ISSR S SSR S SNP

6. 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.

7. 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.

8. 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).

9. STEPS INVOLVED IN MARKER ASSISTED SELECTION IN FRUIT CROPS

10. Application MAS is applicable for genetic improvement of plants as well as animals and i n plants . I t 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.

11. BASIC PROCEDURE OF MARKER ASSISTED SELECTION( MAS)

12. 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.

13. 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)

14. 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)

15. 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

16. 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.

17. 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.

18. 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

19. 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.

20. 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,

21. 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)

22. 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)

23. 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

24. 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.