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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

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Agriculture and genetic diversity

Crop Domestication and Diversification• Loss of genetic diversity– Selection of elite genotypes with favorable traits – Reduction in population size (Bottleneck)

Doebley et al. 2006 Cell

Div

ersi

ty

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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 20-30% on average are unique), phenotyping and genotyping

• Exploit individuation of favorable alleles (GWAS) for breeding and crop improvement

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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)

a) Unstructuredpopulation

b) Structured population

Bamshad et al 2004 Nat Rev Genet

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Peach genetic diversity: a brief history

Center oforigin

~ 3,000 BC

XVI century~ 100 BC

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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)– Low level of massive analysis MW BA

high

low

Allele 1

Allele 2

Allele 3

Heter.

Homo

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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

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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

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– 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

melting

Peachesmelting

Nectarinesnon-melting

Peaches

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– 11 peach accession (Eastern vs Western)– Whole genome set of SNPs ( 1 million)∼– Historical bottlenecks and loss of genetic diversity

Π = nucleotide diversity

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FruitBreedomics: Markers andGermplasm 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%)

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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

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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)

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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

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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

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Thank you for yourattention