Abstract
We used three approaches to map the yellow rust resistance gene Yr7 and identify associated SNPs in wheat. First, we used a traditional QTL mapping approach using a double haploid (DH) population and mapped Yr7 to a low-recombination region of chromosome 2B. To fine map the QTL, we then used an association mapping panel. Both populations were SNP array genotyped allowing alignment of QTL and genome-wide association scans based on common segregating SNPs. Analysis of the association panel spanning the QTL interval, narrowed the interval down to a single haplotype block. Finally, we used mapping-by-sequencing of resistant and susceptible DH bulks to identify a candidate gene in the interval showing high homology to a previously suggested Yr7 candidate and to populate the Yr7 interval with a higher density of polymorphisms. We highlight the power of combining mapping-by-sequencing, delivering a complete list of gene-based segregating polymorphisms in the interval with the high recombination, low LD precision of the association mapping panel. Our mapping-by-sequencing methodology is applicable to any trait and our results validate the approach in wheat, where with a near complete reference genome sequence, we are able to define a small interval containing the causative gene.
Highlights
Yellow stripe rust (YR) caused by Puccinia striiformis is one of the most damaging diseases of wheat with 88% of the world’s wheat production susceptible to infection [1, 2, 3]
Screening of the Avalon x Cadenza (AxC) double haploid (DH) population with Puccinia striiformis (Pst) isolate 08/21 in a seedling test revealed a bimodal distribution of infection scores, following an approximately 1:1 segregation ratio–the expected inheritance pattern for a single, major gene (S2 Table)
The already large confidence interval, though it spans just 10% of the genetic length of chromosome 2B, contains ~50% of all 2B AxC SNPs and is likely to span an enormous physical interval characterized by low recombination rates, which poses a major challenge for the fine mapping of Yr7
Summary
Yellow stripe rust (YR) caused by Puccinia striiformis is one of the most damaging diseases of wheat with 88% of the world’s wheat production susceptible to infection [1, 2, 3]. Identifying new YR resistance genes and their associated molecular makers is of great interest in breeding programs using marker assisted selection [4, 5]. Two major YR resistance genes, Yr5 and Yr7, were identified in wheat and mapped to the long arm of chromosome 2B [6, 7]. Intercrossing Yr5 and Yr7 near-isogenic lines (NILs) in the genetic background of Avocet S (AVS) revealed distinct segregation patterns for each gene, indicating probable allelism. This hypothesis was confirmed by a recent study which showed that Yr5 and Yr7 are distinct.
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