Evolution and selection of Rhg1, a copy-number variant nematode-resistance locus

The soybean cyst nematode (SCN) resistance locus Rhg1 is a tandem repeat of a 31.2 kb unit of the soybean genome. Each 31.2-kb unit contains four genes. One allele of Rhg1, Rhg1-b, is responsible for protecting most US soybean production from SCN. Whole-genome sequencing was performed, and PCR assays were developed to investigate allelic variation in sequence and copy number of the Rhg1 locus across a population of soybean germplasm accessions. Four distinct sequences of the 31.2-kb repeat unit were identified, and some Rhg1 alleles carry up to three different types of repeat unit. The total number of copies of the repeat varies from 1 to 10 per haploid genome. Both copy number and sequence of the repeat correlate with the resistance phenotype, and the Rhg1 locus shows strong signatures of selection. Significant linkage disequilibrium in the genome outside the boundaries of the repeat allowed the Rhg1 genotype to be inferred using high-density single nucleotide polymorphism genotyping o...大豆孢囊线虫（Soybean Cyst Nematode, SCN）抗性位点Rhg1是大豆基因组中一段31.2 kb单元的串联重复序列。每个31.2 kb的重复单元包含4个基因。Rhg1的一个等位基因Rhg1-b可使美国绝大多数大豆种植免受SCN侵染。本研究对一组大豆种质资源群体开展全基因组测序，并开发聚合酶链反应（Polymerase Chain Reaction, PCR）检测技术，以探究Rhg1位点在序列与拷贝数层面的等位基因变异情况。本研究共鉴定出4种不同的31.2 kb重复单元序列，部分Rhg1等位基因可携带至多3种不同类型的重复单元。单倍体基因组中该重复序列的总拷贝数范围为1至10。重复序列的拷贝数与序列均与抗性表型显著相关，且Rhg1位点呈现出强烈的选择印记。重复序列边界之外的基因组区域存在显著连锁不平衡，因此可通过高密度单核苷酸多态性（Single Nucleotide Polymorphism, SNP）基因分型技术推断Rhg1基因型……