Abstract
BackgroundFrost is a limiting abiotic stress for the winter pea crop (Pisum sativum L.) and identifying the genetic determinants of frost tolerance is a major issue to breed varieties for cold northern areas. Quantitative trait loci (QTLs) have previously been detected from bi-parental mapping populations, giving an overview of the genome regions governing this trait. The recent development of high-throughput genotyping tools for pea brings the opportunity to undertake genetic association studies in order to capture a higher allelic diversity within large collections of genetic resources as well as to refine the localization of the causal polymorphisms thanks to the high marker density. In this study, a genome-wide association study (GWAS) was performed using a set of 365 pea accessions. Phenotyping was carried out by scoring frost damages in the field and in controlled conditions. The association mapping collection was also genotyped using an Illumina Infinium® BeadChip, which allowed to collect data for 11,366 single nucleotide polymorphism (SNP) markers.ResultsGWAS identified 62 SNPs significantly associated with frost tolerance and distributed over six of the seven pea linkage groups (LGs). These results confirmed 3 QTLs that were already mapped in multiple environments on LG III, V and VI with bi-parental populations. They also allowed to identify one locus, on LG II, which has not been detected yet and two loci, on LGs I and VII, which have formerly been detected in only one environment. Fifty candidate genes corresponding to annotated significant SNPs, or SNPs in strong linkage disequilibrium with the formers, were found to underlie the frost damage (FD)-related loci detected by GWAS. Additionally, the analyses allowed to define favorable haplotypes of markers for the FD-related loci and their corresponding accessions within the association mapping collection.ConclusionsThis study led to identify FD-related loci as well as corresponding favorable haplotypes of markers and representative pea accessions that might to be used in winter pea breeding programs. Among the candidate genes highlighted at the identified FD-related loci, the results also encourage further attention to the presence of C-repeat Binding Factors (CBF) as potential genetic determinants of the frost tolerance locus on LG VI.
Highlights
Frost is a limiting abiotic stress for the winter pea crop (Pisum sativum L.) and identifying the genetic determinants of frost tolerance is a major issue to breed varieties for cold northern areas
The distribution of the estimate of the linkage disequilibrium (LD, r2) along to the genetic position for each linkage group as well as for the whole genome is presented in Additional file 5
Among the remaining 590 genes, we focused on gene families pointed as candidates in previous studies, i.e. C-repeat Binding Factors (CBF)/ Dehydration-Responsive ElementBinding (DREB) genes, genes coding for brassinosteroid receptors, genes implied in the production of gibberellin and genes implied in the synthesis of soluble sugars
Summary
Frost is a limiting abiotic stress for the winter pea crop (Pisum sativum L.) and identifying the genetic determinants of frost tolerance is a major issue to breed varieties for cold northern areas. In addition to the economic importance of pea seeds, pea crops have beneficial environmental impacts, mainly due to their ability to fix atmospheric nitrogen. They do not need nitrogen fertilizers and help reducing N2O emissions [3]. Winter peas are being developed in order to obtain higher and more stable yields. They are limited by freezing temperatures during the winter time and the development of winter pea genotypes able to overcome freezing periods is desirable
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