Whole genome re‐sequencing reveals the impact of the interaction of copy number variants of the rhg‐1 and Rhg4 genes on broad‐ased resistance to soybean cyst nematode

First author: Gunvant B. Patil; Affiliations: University of Missouri (密苏里大学): Columbia, USA

Corresponding author: Henry T. Nguyen

Soybean cyst nematode (SCN; 大豆胞囊线虫病) is the most devastating (毁灭性的) plant‐parasitic nematode (线虫). Most commercial soybean varieties with SCN resistance are derived from PI88788. Resistance derived from PI88788 is breaking down due to narrow genetic background and SCN population shift. PI88788 requires mainly the rhg1‐ locus, while ‘Peking’ requires rhg1‐a and Rhg4 for SCN resistance. In the present study, whole‐genome sequencing of 106 soybean lines was used to define the Rhg haplotypes and investigate their responses to the SCN HG‐Types. The analysis showed a comprehensive profile of SNPs and copy number variations (CNV) at these loci. CNV of rhg1 (GmSNAP18) only contributed towards resistance in lines derived from PI88788 and “Cloud”. At least 5.6 copies of the PI88788‐ ype rhg1 were required to confer SCN resistance, regardless of the Rhg4 (GmSHMT08) haplotype. However, when the GmSNAP18 copies dropped below 5.6, a “Peking”‐ ype GmSHMT08 haplotype was required to ensure SCN resistance. This points to a novel mechanism of epistasis between GmSNAP18 and GmSHMT08 involving minimum requirements for copy number. The presence of more Rhg4 copies confers resistance to multiple SCN races. Moreover, transcript abundance of the GmSHMT08 in root tissue correlates with more copies of the Rhg4 locus, reinforcing SCN resistance. Finally, haplotype analysis of the GmSHMT08 and GmSNAP18 promoters inferred additional levels of the resistance mechanism. This is the first report revealing the genetic basis of broad‐ased resistance to SCN and providing new insight into epistasis, haplotype‐compatibility, CNV, promoter variation, and its impact on broad‐ased disease resistance in plants.

大豆胞囊线虫病SCN是植物中最具毁灭性的寄生线虫。大多数商业大豆品种中的SCN抗性都来自于PI88788。来自于PI88788的抗性正由于狭窄的遗传背景和SCN群体漂变逐渐消失。PI88788主要依赖于rhg1‐位点，而“Peking”品种则需要rhg1‐a和Rhg4来保持SCN抗性。本文的研究对106个大豆株系进行了重测序研究，鉴定了Rhg单倍型，并研究了其对于HG类型SCN的响应。作者绘制了这些位点上的SNP和拷贝数变异CNV的综合概况。rhg1的CNV仅仅在来自于PI88788和“Cloud”品种的株系中作用于SCN抗性。不管是否存在Rhg4单倍型，大豆植株至少需要5.6个PI88788类型的rhg1赋予植株SCN抗性。然而，当GmSNAP18拷贝数低于5.6个时，大豆植株至少需要一个“Peking”类的GmSHMT08单倍型来赋予植株SCN抗性。这说明了GmSNAP18和GmSHMT08之间存在一个新的上位性机制，该机制需要一个最低的拷贝数。Rhg4的拷贝数越多，会赋予大豆植株对更多类型SCN的抗性。此外，根中GmSHMT08的转录本富集与更多的Rhg4位点拷贝相关，能够增强大豆植株的SCN抗性。最终，GmSHMT08和GmSNAP18的启动子单倍型分析显示存在另外的抗性调控机制。本文是第一次报道大豆对于SCN广谱抗性的遗传学基础，并揭示了上位性、单倍型组合、CNV和启动子变异对于植物广谱抗性的影响。

通讯：Henry T. Nguyen (http://soybeangenomics.missouri.edu/personnel/nguyenbio.htm)

个人简介：1977年，宾夕法尼亚州立大学，作物学学士；1978年，宾夕法尼亚州立大学，农艺学硕士；1982年，密苏里大学，农艺学博士。

研究方向：植物非生物胁迫抗性的分子遗传学和功能基因组学研究；基因组学和生物技术在作物改良中的应用。

doi: https://doi.org/10.1111/pbi.13086

Journal: Plant Biotechnology Journal

First Published: January 28, 2019