Nested Association Mapping of Stem Rust Resistance in Wheat Using Genotyping by Sequencing

We combined the recently developed genotyping by sequencing (GBS) method with joint mapping (also known as nested association mapping) to dissect and understand the genetic architecture controlling stem rust resistance in wheat (Triticum aestivum). Ten stem rust resistant wheat varieties were crossed to the susceptible line LMPG-6 to generate F6 recombinant inbred lines. The recombinant inbred line populations were phenotyped in Kenya, South Africa, and St. Paul, Minnesota, USA. By joint mapping of the 10 populations, we identified 59 minor and medium-effect QTL (explained phenotypic variance range of 1% – 20%) on 20 chromosomes that contributed towards adult plant resistance to North American Pgt races as well as the highly virulent Ug99 race group. Fifteen of the 59 QTL were detected in multiple environments. No epistatic relationship was detected among the QTL. While these numerous small- to medium-effect QTL are shared among the families, the founder parents were found to have different allelic effects for the QTL. Fourteen QTL identified by joint mapping were also detected in single-population mapping. As these QTL were mapped using SNP markers with known locations on the physical chromosomes, the genomic regions identified with QTL could be explored more in depth to discover candidate genes for stem rust resistance. The use of GBS-derived de novo SNPs in mapping resistance to stem rust shown in this study could be used as a model to conduct similar marker-trait association studies in other plant species.

本研究融合了近期开发的基因分型测序（GBS）技术与联合图谱构建（亦称嵌套关联图谱构建）方法，旨在解析并深入理解控制小麦（Triticum aestivum）抗条锈病的遗传结构。通过将十个抗条锈病的小麦品种与感病品种LMPG-6杂交，生成了F6重组自交系。这些重组自交系群体在肯尼亚、南非和美国的圣保罗进行了表型分析。通过联合图谱构建这十个群体，我们在20条染色体上识别出59个具有小至中等效应的QTL（解释的表型变异范围为1%至20%），这些QTL对于抗北美Pgt菌系以及高度致病性的Ug99菌系群体中的抗病性起到了重要作用。在多个环境中检测到了59个QTL中的15个。未在QTL之间发现上位效应关系。尽管这些众多的小至中等效应QTL在家族间共享，但发现奠基亲本对QTL的等位基因效应存在差异。通过联合图谱构建识别出的14个QTL在单一群体图谱构建中也得到了检测。由于这些QTL是通过具有已知物理染色体位置的SNP标记进行图谱构建的，因此，携带QTL的基因组区域可以进一步深入研究，以发现抗条锈病的候选基因。本研究中利用GBS衍生的从头SNP进行条锈病抗性图谱构建的方法，可作为在其他植物物种中开展类似标记-性状关联研究的范例。