Identification of candidate genes controlling soybean cyst nematode resistance in ‘Handou 10’ based on genomic and transcriptome analyses

Authors: WEI, H - Henan Academy Of Agricultural Science; ZHANG, H - Henan Academy Of Agricultural Science; LIANG, Y - Henan Academy Of Agricultural Science; LI, J - Henan Academy Of Agricultural Science; LI, H - Henan Academy Of Agricultural Science; Song, Qijian; WU, Y - Henan Academy Of Agricultural Science; LEI, C - Henan Academy Of Agricultural Science; WANG, S - Henan Academy Of Agricultural Science; WANG, J - Henan Academy Of Agricultural Science; LU, W - Henan Academy Of Agricultural Science

Submitted to: Frontiers in Plant Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/21/2022
Publication Date: 3/15/2022
Citation: Wei, H., Zhang, H.Y., Liang, Y., Li, J.Y., Li, H.C., Song, Q., Wu, Y., Lei, C.F., Wang, S.W., Wang, J.S., Lu, W.G. 2022. Identification of candidate genes controlling soybean cyst nematode resistance in ‘Handou 10’ based on genomic and transcriptome analyses. Frontiers in Plant Science. 13. Article 860034. https://doi.org/10.3389/fpls.2022.860034.
DOI: https://doi.org/10.3389/fpls.2022.860034

Interpretive Summary: Soybean cyst nematode (SCN) is a devastating soil-borne pathogen pest affecting soybean and common bean production worldwide. In heavily infested fields, it can cause >30% yield loss especially in drought years. Pest management is difficult and breeding for resistant varieties is the most effective. In the United States, resistance to SCN in most elite cultivars is derived from a soybean known known as PI88788, which can be overcome by a change of SCN races. Thus, it is vital to identify new sources of SCN resistance to broaden the genetic basis. A Chinese elite cultivar ‘Handou 10’ was found to be resistant to SCN races in multi-year field testing, however genes underlying the SCN resistance in the variety were unknown. Researchers at ARS and Henan Academy of Agricultural Science in China analyzed the resistance to SCN races in a population derived from this cultivar and identified three major genomic regions that were associated with the resistance. Two of these genomic regions were previously reported, but the third one was novel. We identified genes that appear to control this new source of resistance. The study provided useful information and genetic resources for scientists to improve soybean SCN resistance.

Technical Abstract: Soybean cyst nematode (SCN; Heterodera glycines Ichninohe) is a highly destructive pathogen for soybean production worldwide. The use of resistant varieties is the most effective way for preventing yield loss. Handou 10 is a commercial soybean variety with desirable agronomic traits and SCN resistance, however genes underlying the SCN resistance in the variety is unknown. A F2:8 recombinant inbred line (RIL) population derived from a cross between Zheng 9525 (susceptible) and Handou 10 was developed, analysis of the resistance to SCN HG Type 2.5.7 (race 1) and 1.2.5.7 (race 2) in the population identified seven QTL with additive effects. Among these, three QTL on Chromosome 7, 8 and 18 were resistant to both races. These QTL could explain 1.91 to 7.73% of the phenotypic variation of SCN female index. The QTL on Chromosome 8 and 18 have already been reported and were most likely overlapped rhg1 and Rhg4 locus, respectively, however, the QTL on Chromosome 7 was novel. Candidate genes for the three QTL were predicted through gene functional analysis and transcriptome analysis of infected roots of Handou 10 vs. Zheng 9525. The information will facilitate SCN resistant gene cloning and the novel resistance gene will be a source to improve soybean SCN resistance.