Published on February 28, 2014
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
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
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
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
Peach genetic diversity: a brief history Center of origin ~ 100 BC XVI century ~ 3,000 BC YOUR LOGO
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
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
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
– 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
– 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
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
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
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
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
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
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