A framework for gene mapping in wheat demonstrated using the Yr7 yellow rust resistance gene

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 asso...

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Bibliographic Details
Published in:PloS one 2020-04, Vol.15 (4), p.e0231157-e0231157
Main Authors: Gardiner, Laura-Jayne, Bansept-Basler, Pauline, El-Soda, Mohamed, Hall, Anthony, O'Sullivan, Donal M
Format: Article
Language:English
Subjects:
Biology and Life Sciences
Chromosomes
Disease resistance
Gene mapping
Genes
Genomes
Haplotypes
Homology
Infections
Mapping
Nucleotide sequence
Pathogens
Plant resistance
Population
Quantitative trait loci
Recombination
Research and Analysis Methods
Single-nucleotide polymorphism
Stripe rust
Wheat
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Summary: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.
ISSN:1932-6203
1932-6203
DOI:10.1371/journal.pone.0231157