Exome association analysis sheds light onto leaf rust (Puccinia triticina) resistance genes currently used in wheat breeding (Triticum aestivum L.)

Abstract

Resistance breeding is crucial for a sustainable control of leaf rust (Puccinia triticina) in wheat (Triticum aestivum L.) while directly targeting functional variants is the Holy Grail for efficient marker-assisted selection and map-based cloning. We assessed the limits and prospects of exome association analysis for severity of leaf rust in a large hybrid wheat population of 1574 single-crosses plus their 133 parents. After imputation and quality control, exome sequencing revealed 202 875 single-nucleotide polymorphisms (SNPs) covering 19.7% of the highconfidence annotated gene space. We performed intensive data mining and found significant associations for 2171 SNPs corresponding to 50 different loci. Some of these associations mapped in the proximity of the already known resistance genes Lr21, Lr34-B, Lr1 and Lr10, while other associated genomic regions, such as those on chromosomes 1A and 3D, harboured several annotated genes putatively involved in resistance. Validation with an independent population helped to narrow down the list of putative resistance genes that should be targeted by finemapping. We expect that the proposed strategy of intensive data mining coupled with validation will significantly influence research in plant genetics and breeding.1396

A catalogue of resistance gene homologs and a chromosome-scale reference sequence support resistance gene mapping in winter wheat

“…Common to all approaches was a peak towards the distal end of the long arm of chromosome 4A. This association had been reported before by Liu et al (2020a), who analyzed 133 genotypes and 1,574 of their hybrid offspring by exome sequencing. The GWAS peak was co-located with a 26 Mb region of high sequence divergence between Chinese Spring and Attraktion (Figure 5), which we attribute to an alien introgression, possibly originating from T. dicoccoides (Przewieslik-Allen et al, 2021).…”

A catalogue of resistance gene homologs and a chromosome‐scale reference sequence support resistance gene mapping in winter wheat

“…This association had been reported before by Liu et al . (2020a), who analysed 133 genotypes and 1574 of their hybrid offspring by exome sequencing. The GWAS peak was co‐located with a 26 Mb region of high sequence divergence between Chinese Spring and Attraktion (Figure 5), indicative of the presence of an alien introgression.…”

Unlocking big data doubled the accuracy in predicting the grain yield in hybrid wheat

“…Second, marker density needs to be adjusted to the population size ( 16 ). Considering the genetic relatedness between lines, the genome size of wheat, and the sizes of the individual populations, marker density does not represent a major limiting factor for genome-wide prediction studies of individual datasets ( 22 ), as sufficient marker coverage of more than 10,000 single-nucleotide polymorphisms (SNPs) can be achieved by using high-density SNP chips, genotyping-by-sequencing, or exome capture sequencing ( 23 , 24 ). Third, the integrated analyses of phenotypic data pose problems because of their unbalanced and often noisy structure: The individual experimental series usually lack proper links across experimental series and/or environments.…”