Whole‐genome re‐sequencing reveals the impact of the interaction of copy number variants of the rhg1 and Rhg4 genes on broad‐based resistance to soybean cyst nematode

• DOI: 10.1111/pbi.13086
• Publication Date: 2019-01-28T12:06:33Z
• Authors: Gunvant B. Patil; Naoufal Lakhssassi; Jinrong Wan; Li Song; Zhou Zhou; Mariola Klepadlo; Tri D. Vuong; Adrian O. Stec; Sondus S. Kahil; Vincent Colantonio; Babu Valliyodan; J. Hollis Rice; Sarbottam Piya; Tarek Hewezi; Robert M. Stupar; Khalid Meksem; Henry T. Nguyen
• Keywords: Soybean cyst nematode; Epistasis; SNP

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