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 high-confidence 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 fine-mapping. We expect that the proposed strategy of intensive data mining coupled with validation will significantly influence research in plant genetics and breeding.

中文翻译：

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外显子组关联分析为目前小麦育种（Triticum aestivum L.）使用的叶锈病（Puccinia triticina）抗性基因提供了线索。

抗性育种对于持续控制小麦（Triticum aestivum L.）的叶锈病（Puccinia triticina）至关重要，而直接针对功能性变体的目标是有效进行标记辅助选择和基于地图的克隆的圣杯。我们评估了外显子组关联分析在1574个单交及其133个亲本的大型杂交小麦群体中的叶锈严重程度的极限和前景。经过插补和质量控制后，外显子组测序显示202 875个单核苷酸多态性（SNP），覆盖了高可信注释基因空间的19.7％。我们进行了密集的数据挖掘，发现了对应于50个不同基因座的2171个SNP的显着关联。其中一些关联定位在已知的抗性基因Lr21，Lr34-B，Lr1和Lr10附近，而其他相关的基因组区域（例如1A和3D染色体上的基因组区域）则包含了几个可能与抗性有关的注释基因。通过独立种群进行的验证有助于缩小应该通过精细定位靶向的假定抗性基因的范围。我们预计，密集数据挖掘与验证相结合的拟议策略将对植物遗传学和育种研究产生重大影响。