15 peach germplasm structure verde ignazio

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15 peach germplasm structure verde ignazio

  1. 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 Italy YOUR LOGO
  2. 2. Agriculture and genetic diversity Crop Domestication and Diversification • Loss of genetic diversity Diversity – Selection of elite genotypes with favorable traits – Reduction in population size (Bottleneck) Doebley et al. 2006 Cell YOUR LOGO
  3. 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 improvement YOUR LOGO
  4. 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 population a) Unstructured population Bamshad et al 2004 Nat Rev Genet YOUR LOGO
  5. 5. Peach genetic diversity: a brief history Center of origin ~ 100 BC XVI century ~ 3,000 BC YOUR LOGO
  6. 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 analysis B high Allele 1 Allele 2 Allele 3 low YOUR LOGO Heter. Homo
  7. 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 1 Sample 2 YOUR LOGO
  8. 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. 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 genotypes YOUR LOGO
  10. 10. – 11 peach accession (Eastern vs Western) – Whole genome set of SNPs (∼1 million) – Historical bottlenecks and loss of genetic diversity Π = nucleotide diversity YOUR LOGO
  11. 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. 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. 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. 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, respectively YOUR LOGO
  15. 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 Breeding YOUR LOGO
  16. 16. YOUR LOGO

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