Londrina State University (UEL), Celso Garcia Cid Road, km 380, Londrina, PR, Brazil.
Department of Plant Agriculture, University of Guelph, Guelph, ON, N1G 2V7, Canada.
Theor Appl Genet. 2021 Mar;134(3):777-792. doi: 10.1007/s00122-020-03723-9. Epub 2021 Jan 19.
A locus on chromosome 13, containing multiple TIR-NB-LRR genes and SNPs associated with M. javanica resistance, was identified using a combination of GWAS, resequencing, genetic mapping and expression profiling. Meloidogyne javanica, a root-knot nematode, is an important problem in soybean-growing areas, leading to severe yield losses. Some accessions have been identified carrying resistance loci to this nematode. In this study, a set of 317 soybean accessions was characterized for resistance to M. javanica. A genome-wide association study was performed using SNPs from genotyping-by-sequencing, and a region of 29.2 kb on chromosome 13 was identified. An analysis of haplotypes showed that SNPs were able to discriminate between susceptible and resistant accessions, with 25 accessions sharing the haplotype associated with resistance. Furthermore, five accessions that exhibited resistance without carrying this haplotype may carry different loci conferring resistance to M. javanica. We also conducted the screening of the SNPs in the USDA soybean germplasm, revealing that several soybean accessions previously reported as resistant to other nematodes also shared the resistance haplotype on chromosome 13. Two SNP-based TaqMan® assays were developed and validated in two panels of soybean cultivars and in biparental populations. In silico analysis of the region associated with resistance identified the occurrence of genes with structural similarity with classical major resistance genes (NBS-LRR genes). Specifically, several nonsynonymous SNPs were observed in Glyma.13g194800 and Glyma.13g194900. The expression profile of these candidate genes demonstrated that the two gene models were up-regulated in the resistance source PI 505,099 after nematode infection. Overall, the SNPs associated with resistance and the genes identified constitute an important tool for introgression of resistance to the root-knot nematode by marker-assisted selection in soybean breeding programs.
利用 GWAS、重测序、遗传图谱和表达谱分析相结合的方法，在 13 号染色体上鉴定出一个包含多个 TIR-NB-LRR 基因和与 M. javanica 抗性相关的 SNPs 的基因座。根结线虫 M. javanica 是大豆种植区的一个重要问题，导致严重的产量损失。已经确定了一些携带这种线虫抗性的品系。在这项研究中，对 317 个大豆品系进行了对 M. javanica 的抗性鉴定。利用测序的 SNP 进行了全基因组关联研究，鉴定出 13 号染色体上的 29.2 kb 区域。对单倍型的分析表明，SNP 能够区分敏感和抗性品系，25 个品系共享与抗性相关的单倍型。此外，五个表现出抗性而不携带该单倍型的品系可能携带不同的基因座，赋予其对 M. javanica 的抗性。我们还对 USDA 大豆种质资源中的 SNPs 进行了筛选，结果表明，几个以前被报道对其他线虫具有抗性的大豆品系也在 13 号染色体上共享了抗性单倍型。开发并验证了两个基于 SNP 的 TaqMan®检测方法，在两个大豆品种群体和双亲群体中进行了验证。对与抗性相关的区域的计算机分析确定了具有与经典主要抗性基因（NBS-LRR 基因）结构相似的基因的存在。具体来说，在 Glyma.13g194800 和 Glyma.13g194900 中观察到几个非同义 SNP。这些候选基因的表达谱表明，在感病源 PI 505,099 被线虫感染后，这两个基因模型上调。总的来说，与抗性相关的 SNP 和鉴定出的基因构成了大豆抗根结线虫的标记辅助选择在大豆育种计划中进行基因导入的重要工具。
