Tran Dung T, Steketee Clinton J, Boehm Jeffrey D, Noe James, Li Zenglu
Institute of Plant Breeding, Genetics and Genomics and Department of Crop and Soil Sciences, University of Georgia, Athens, GA, United States.
Department of Plant Pathology, University of Georgia, Athens, GA, United States.
Front Plant Sci. 2019 Apr 10;10:401. doi: 10.3389/fpls.2019.00401. eCollection 2019.
Soybean cyst nematode ( Ichinohe) (SCN) is the most destructive pest affecting soybeans [ (L.) Merr.] in the U.S. To date, only two major SCN resistance alleles, and , identified in PI 88788 () and Peking (), residing on chromosomes (Chr) 18 and 8, respectively, have been widely used to develop SCN resistant cultivars in the U.S. Thus, some SCN populations have evolved to overcome the PI 88788 and Peking derived resistance, making it a priority for breeders to identify new alleles and sources of SCN resistance. Toward that end, 461 soybean accessions from various origins were screened using a greenhouse SCN bioassay and genotyped with Illumina SoySNP50K iSelect BeadChips and three KASP SNP markers developed at the and loci to perform a genome-wide association study (GWAS) and a haplotype analysis at the and loci. In total, 35,820 SNPs were used for GWAS, which identified 12 SNPs at four genomic regions on Chrs 7, 8, 10, and 18 that were significantly associated with SCN resistance ( < 0.001). Of those, three SNPs were located at and , and 24 predicted genes were found near the significant SNPs on Chrs 7 and 10. KASP SNP genotyping results of the 462 accessions at the and loci identified 30 that carried PI 88788-type resistance, 50 that carried Peking-type resistance, and 58 that carried neither the Peking-type nor the PI 88788-type resistance alleles, indicating they may possess novel SCN resistance alleles. By using two subsets of SNPs near the and loci obtained from SoySNP iSelect BeadChips, a haplotype analysis of 461 accessions grouped those 58 accessions differently from the accessions carrying Peking or PI 88788 derived resistance, thereby validating the genotyping results at and . The significant SNPs, candidate genes, and newly characterized SCN resistant accessions will be beneficial for the development of DNA markers to be used for marker-assisted breeding and developing soybean cultivars carrying novel sources of SCN resistance.
大豆胞囊线虫（猪野）（SCN）是影响美国大豆[（L.）Merr.]的最具破坏性的害虫。迄今为止，仅在PI 88788（）和北京（）中分别位于第18号和第8号染色体上鉴定出的两个主要SCN抗性等位基因，已在美国广泛用于培育抗SCN品种。因此，一些SCN种群已经进化以克服源自PI 88788和北京的抗性，这使得育种者优先识别新的等位基因和SCN抗性来源。为此，使用温室SCN生物测定法对来自不同来源的461份大豆种质进行了筛选，并使用Illumina SoySNP50K iSelect BeadChips以及在和位点开发的三个KASP SNP标记进行基因分型，以在和位点进行全基因组关联研究（GWAS）和单倍型分析。总共35,820个SNP用于GWAS，其在第7、8、10和18号染色体的四个基因组区域鉴定出12个与SCN抗性显著相关的SNP（<0.001）。其中，三个SNP位于和，并且在第7和10号染色体上的显著SNP附近发现了24个预测基因。462份种质在和位点的KASP SNP基因分型结果鉴定出30份携带PI 88788型抗性，50份携带北京型抗性，58份既不携带北京型也不携带PI 88788型抗性等位基因，表明它们可能拥有新的SCN抗性等位基因。通过使用从SoySNP iSelect BeadChips获得的和位点附近的两个SNP子集，对461份种质进行单倍型分析，将这58份种质与携带北京或PI 88788衍生抗性的种质进行了不同分组，从而验证了在和位点的基因分型结果。显著的SNP、候选基因以及新鉴定的抗SCN种质将有利于开发用于标记辅助育种的DNA标记以及培育携带新的SCN抗性来源的大豆品种。
