15 peach germplasm structure verde ignazio slide 0

15 peach germplasm structure verde ignazio

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1. Genetic structure of European peach germplasm. Molecular markers as tools to manage practical issues in germplasm collections Ignazio Verde CRA - Fruit Tree Research Center Rome ItalyYOUR LOGO 2. Agriculture and genetic diversity Crop Domestication and Diversification Loss of genetic diversityDiversity Selection of elite genotypes with favorable traits Reduction in population size (Bottleneck)Doebley et al. 2006 CellYOUR LOGO 3. Germplasm Collection as a tool for preserving genetic diversity of crops Collect: FAO reported 1.300 genbanks all over the world with over 6 million accessions for all crops and wild relatives Manage: Fruit trees, large size, redundancy (only 2030% on average are unique), phenotyping and genotyping Exploit individuation of favorable alleles (GWAS) for breeding and crop improvementYOUR LOGO 4. Population Structure: concept Structure or stratification: systematic difference in allele frequencies between subpopulations within a population. The whole population is stratified in 2 or more subpopulations with different allele frequencies Long term isolation (e.g. Eastern vs. Western pool) Breeding for particular traits (e.g. Peach vs. Nectarine)b) Structured populationa) Unstructured population Bamshad et al 2004 Nat Rev GenetYOUR LOGO 5. Peach genetic diversity: a brief historyCenter of origin ~ 100 BC XVI century ~ 3,000 BCYOUR LOGO 6. Type of molecular markers: SSRs Simple Sequence Repeats or microsatellite Short motif (CA, ACA etc) repeated in tandem Codominant and single locus High variability (many alleles at one locus) MW A Low level of massive analysisBhighAllele 1 Allele 2 Allele 3 lowYOUR LOGOHeter.Homo 7. Type of molecular markers: SNPs SNPs: Single Nucleotide Polymorphism Bi-allelic (less variable) and codominant Most abundant markers within the genome Highthroughput analysis (Arrays, Genotype by Sequence) Sample 1Sample 2 YOUR LOGO 8. Molecular marker as a tool for managing and exploiting germplasm collections Genetic diversity N. alleles, allele frequencies, heterozygosity, nucleotide diversity, individuate redundancy or synonymies Population structure systematic difference in allele frequencies between subpopulations within a population Association Studies (GWAS) Individuate chromosome regions and associated markers controlling important agronomic traits YOUR LOGO 9. 234 western accessions with 50 SSRs Observed Heterozygosity Ho = 0.34; Expected He = 0.46 Stratification of western germplasm based on fruit traits (peach/nectarine, melting/non-melting) Individuated several duplicates or closely related genotypesYOUR LOGO 10. 11 peach accession (Eastern vs Western) Whole genome set of SNPs (1 million) Historical bottlenecks and loss of genetic diversity = nucleotide diversityYOUR LOGO 11. FruitBreedomics: Markers and Germplasm Collections Genome wide SNP markers (IPSC 9k SNP array, Verde et al.2012) 8144 SNPs distributed among the 8 peach chromosomes. 4271 polymorphic SNPs on 1540 accessions 1240 unique peach accessions (6 germplasm collections): Italy (2 collections UNIMI and CRA, 468 accessions) Spain (1 collection IRTA, 298 accessions) France (2 collections Avignon and Bordeaux, 279 accessions) China (1 collection China, 195 accessions) Individuated about 300 duplicated or closely related genotypes (identity > 98%) YOUR LOGO 12. FB Results: Genetic Diversity and Population Structure Genetic diversity: Expected Heterozygosity (He): 0.286 (0.03 - 0.68) Observed Heterozygosity (Ho): 0.39 (0.055 - 0.5) Population structure: 3 subpopulations optimal Estearn (58), Western Breeding (352), Western Landraces (165) 665 accessions were admixed. Further stratification: Nectarines YOUR LOGO 13. Core Collection: concepts Chose a subset of samples that represent the whole collection diversity (number of alleles) Bypass the limitations posed by huge collections Reduce redundancy and duplications (synonymies)YOUR LOGO 14. Core collections: practical issues Genetic Diversity, genetic relationship (duplicates and closely related accessions) and Structure of the collection Passport data, geographic, genetic (pedigree), phenotype, molecular data (SSRs, SNPs) Strategy Maximization strategy (M Strategies) focused on the alleles Minimum number of samples maximum number of alleles M-Core. Es. 141 individuals in grape catch 86% of the diversity of the whole of 1,771 samples Nested Genetic Core Collections (G-Core): different cores obtained by increasing the number of accessions (es 12, 24, 48, 92) catching 58, 73, 83 and 100% of the diversity, respectivelyYOUR LOGO 15. Conclusions and perspectives Germplasm collections are valuable tools for Genetic Association Studies: Individuate useful alleles within the collections Identify diagnostic markers associated to traits of interest Availability of molecular tools for Marker Assisted BreedingYOUR LOGO 16. YOUR LOGO


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