Use of modern tomato breeding germplasm for deciphering the genetic control of agronomical traits by Genome Wide Association study

Autor: Nicolas Samson, Julien Bonnet, Stéphane Grenier, Mathilde Causse, Guillaume Bauchet, Laurent Grivet
Přispěvatelé: Unité de recherche Génétique et amélioration des fruits et légumes (GALF), Institut National de la Recherche Agronomique (INRA), Syngenta France, Boyce Thompson Institute Cornell, Ithaca College, Génétique et Amélioration des Fruits et Légumes (GAFL)
Jazyk: angličtina
Rok vydání: 2017
Předmět:
0106 biological sciences
0301 basic medicine
Germplasm
Linkage disequilibrium
haplotype
Genome-wide association study
tomato
germoplasme
01 natural sciences
Linkage Disequilibrium
tomate
Gene Frequency
Solanum lycopersicum
déséquilibre de liaison
2. Zero hunger
Genetics
Chromosome Mapping
food and beverages
General Medicine
genêtic variation
Phenotype
diversité génétique
architecture génétique
genome wide association study (GWAS)
caractère de sélection
Biotechnology
DNA
Plant
Genotype
Quantitative Trait Loci
introgression
Outcrossing
Quantitative trait locus
Biology
Polymorphism
Single Nucleotide
03 medical and health sciences
congruence moléculaire
[SDV.BV]Life Sciences [q-bio]/Vegetal Biology
Genetic Association Studies
Genetic association
Genetic diversity
matériel génétique
Genetic architecture
Plant Breeding
030104 developmental biology
Haplotypes
Agronomy and Crop Science
seed collections
contrôle génétique
010606 plant biology & botany
Zdroj: TAG Theoretical and Applied Genetics
TAG Theoretical and Applied Genetics, Springer Verlag, 2017, 130 (5), pp.875-889 ⟨10.1007/s00122-017-2857-9⟩
TAG Theoretical and Applied Genetics, Springer Verlag, 2017, 130 (5), pp.875-889. ⟨10.1007/s00122-017-2857-9⟩
ISSN: 0040-5752
1432-2242
DOI: 10.1007/s00122-017-2857-9⟩
Popis: A panel of 300 tomato accessions including breeding materials was built and characterized with >11,000 SNP. A population structure in six subgroups was identified. Strong heterogeneity in linkage disequilibrium and recombination landscape among groups and chromosomes was shown. GWAS identified several associations for fruit weight, earliness and plant growth. Genome-wide association studies (GWAS) have become a method of choice in quantitative trait dissection. First limited to highly polymorphic and outcrossing species, it is now applied in horticultural crops, notably in tomato. Until now GWAS in tomato has been performed on panels of heirloom and wild accessions. Using modern breeding materials would be of direct interest for breeding purpose. To implement GWAS on a large panel of 300 tomato accessions including 168 breeding lines, this study assessed the genetic diversity and linkage disequilibrium decay and revealed the population structure and performed GWA experiment. Genetic diversity and population structure analyses were based on molecular markers (>11,000 SNP) covering the whole genome. Six genetic subgroups were revealed and associated to traits of agronomical interest, such as fruit weight and disease resistance. Estimates of linkage disequilibrium highlighted the heterogeneity of its decay among genetic subgroups. Haplotype definition allowed a fine characterization of the groups and their recombination landscape revealing the patterns of admixture along the genome. Selection footprints showed results in congruence with introgressions. Taken together, all these elements refined our knowledge of the genetic material included in this panel and allowed the identification of several associations for fruit weight, plant growth and earliness, deciphering the genetic architecture of these complex traits and identifying several new loci useful for tomato breeding.
Databáze: OpenAIRE
Externí odkaz: