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

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-bysequencing 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.

Novel stripe rust all‐stage resistance loci identified in a worldwide collection of durum wheat using genome‐wide association mapping

“…Several Yr genes are known to be located on chromosome arm 2BL including Yr5 , Yr7 , Yr43 , Yr44, Yr53 , and YrSP (P. Zhang et al., 2009; Xu et al., 2013; McGrann et al., 2014; Feng et al., 2015; Marchal et al., 2018). However, QYrdu .2B is distal to Yr5 (flanked by the marker barc349 at 404 Mb), Yr7 (at the pericentromeric region) (Gardiner et al., 2020), Yr44 and Yr53 (both close to the SSR marker wmc441 at 589 Mb), and YrSP (close to the SSR marker wmc332 at 726 Mb and wmc441 at 589 Mb). Yr43 (distal to the SSR marker wmc149 at 763 Mb) is the closest designated gene to QYrdu.2B in this study.…”

Impacts of aphid herbivory on mycorrhizal growth responses across three cultivars of wheat

“…Winter wheat varieties such as cv. Avalon, which undergo foundational stages during winter before yielding in the early summer, may be rendered more susceptible to aphid infestation by climate change; warmer temperatures could shorten R. padi generation times (Finlay & Luck, 2011) and see them spend more time on crops over winter, meaning greater emphasis on breeding for defence traits of winter wheat varieties is now needed (Bass et al, 2006;Gardiner et al, 2020).…”

“…In contrast, cv. Avalon hosted the greatest number of aphids and is considered susceptible to wheat diseases like yellow stripe rust (Gardiner et al, 2020). Bird cherry-oat aphids are hostalternating, meaning they over-winter on a primary host plant (Prunus padus) before colonising their secondary hosts (grasses) in spring (Blackman & Eastop, 2000).…”

Combining a New Exome Capture Panel With an Effective varBScore Algorithm Accelerates BSA-Based Gene Cloning in Wheat

“…Yr7 is a major Yellow stripe rust (YR) resistance gene that is identified in wheat. Gardiner et al (2020) firstly used a To test the varBScore algorithm, we download the BSA data set of Yr7 (https://www.ebi.ac.uk/ena, study PRJEB36010) and then analyzed the data by using the varBScore algorithm, which showed a very distinct peak on chromosome 2B along each chromosomal pseudomolecule (Figure 2A). Further analysis showed that the highest scoring points were located on the regions (586,775,469-88,621,811 bp, 655,257,794-658,193,278 bp, and 680,759,276-682,847,904 bp) of chromosome2B ( Figure 2B), and the third peak region was close to the candidate region.…”