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Genome‐wide association mapping of QTLs implied in potato virus Y population sizes in pepper: evidence for widespread resistance QTL pyramiding
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Genome‐wide association mapping of QTLs implied in potato virus Y population sizes in pepper: evidence for widespread resistance QTL pyramiding
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Genome‐wide association mapping of QTLs implied in potato virus Y population sizes in pepper: evidence for widespread resistance QTL pyramiding
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Journal Article
Genome‐wide association mapping of QTLs implied in potato virus Y population sizes in pepper: evidence for widespread resistance QTL pyramiding
2020
Overview
Summary
In this study, we looked for genetic factors in the pepper (Capsicum annuum) germplasm that control the number of potato virus Y (PVY) particles entering the plant (i.e. effective population size at inoculation) and the PVY accumulation at the systemic level (i.e. census population size). Using genotyping‐by‐sequencing (GBS) in a core collection of 256 pepper accessions, we obtained 10 307 single nucleotide polymorphisms (SNPs) covering the whole genome. Genome‐wide association studies (GWAS) detected seven SNPs significantly associated with the virus population size at inoculation and/or systemic level on chromosomes 4, 6, 9 and 12. Two SNPs on chromosome 4 associated with both PVY population sizes map closely to the major resistance gene pvr2 encoding the eukaryotic initiation factor 4E. No obvious candidates for resistance were identified in the confidence intervals for the other chromosomes. SNPs detected on chromosomes 6 and 12 colocalized with resistance quantitative trait loci (QTLs) previously identified with a biparental population. These results show the efficiency of GBS and GWAS in C. annuum, indicate highly consistent results between GWAS and classical QTL mapping, and suggest that resistance QTLs identified with a biparental population are representative of a much larger collection of pepper accessions. Moreover, the resistance alleles at these different loci were more frequently combined than expected by chance in the core collection, indicating widespread pyramiding of resistance QTLs and widespread combination of resistance QTLs and major effect genes. Such pyramiding may increase resistance efficiency and/or durability.
Publisher
John Wiley & Sons, Inc,Wiley,Blackwell,John Wiley and Sons Inc
Subject
/ alleles
/ Biologie végétale (sciences végétales, sylviculture, mycologie...)
/ Capsicum
/ Eukaryotic Initiation Factor-4E
/ Genes
/ Genome-wide association studies
/ Genome-Wide Association Study
/ Genomes
/ Genomics
/ Genotype
/ loci
/ Mapping
/ Original
/ pepper
/ Peppers
/ Phytobiology (plant sciences, forestry, mycology...)
/ Phytopathology and phytopharmacy
/ Polymorphism, Single Nucleotide
/ Potatoes
/ Single nucleotide polymorphisms
/ Single-nucleotide polymorphism
/ Viruses
