Identification of Candidate Genes Controlling Soybean Cyst Nematode Resistance in “Handou 10” Based on Genome and Transcriptome Analyzes

He Wei,Jinying Li,Chenfang Lei,Shiwei Wang,Qijian Song,Weiguo Lu,Haichao Li,Jinshe Wang,Yongkang Wu,Hui Zhang,Yun Lian

doi:10.3389/fpls.2022.860034

He Wei, Jinying Li + Show 9 more

Open Access

https://doi.org/10.3389/fpls.2022.860034

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Abstract

Soybean cyst nematode (SCN; Heterodera glycines Ichinohe) is a highly destructive pathogen for soybean production worldwide. The use of resistant varieties is the most effective way of 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 are unknown. An F2:8 recombinant inbred line (RIL) population derived from a cross between Zheng 9525 (susceptible) and Handou 10 was developed and its resistance to SCN HG type 2.5.7 (race 1) and 1.2.5.7 (race 2) was identified. We identified seven quantitative trait loci (QTLs) with additive effects. Among these, three QTLs on Chromosomes 7, 8, and 18 were resistant to both races. These QTLs could explain 1.91–7.73% of the phenotypic variation of SCN’s female index. The QTLs on chromosomes 8 and 18 have already been reported and were most likely overlapped with rhg1 and Rhg4 loci, respectively. However, the QTL on chromosome 7 was novel. Candidate genes for the three QTLs were predicted through genes functional analysis and transcriptome analysis of infected roots of Handou 10 vs. Zheng 9525. Transcriptome analysis performed also indicated that the plant–pathogen interaction played an important role in the SCN resistance for Handou 10. The information will facilitate SCN–resistant gene cloning, and the novel resistant gene will be a source for improving soybeans’ resistance to SCN.

Highlights

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is a devastating pest affecting soybean (Glycine max [L.] Merr.) production worldwide (Riggs, 1977; Koenning and Wrather, 2010; Tylka and Marett, 2014; Mitchum, 2016; Miraeiz et al, 2020; Peng et al, 2021)
A recombinant inbred line (RIL) mapping population of 392 F2:8 lines was developed by single seed descent (SSD) from the cross between Zheng 9525 and Handou 10
Plastic cups (Ø 6 cm × h 12 cm) were filled with soil infected by SCN [HG types 2.5.7, 1.2.5.7, and 1.2.3.5.6.7], respectively

Summary

Introduction

Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is a devastating pest affecting soybean (Glycine max [L.] Merr.) production worldwide (Riggs, 1977; Koenning and Wrather, 2010; Tylka and Marett, 2014; Mitchum, 2016; Miraeiz et al, 2020; Peng et al, 2021). SCN has caused approximately 36% of yield losses in the total soybean production from 1996–2014 in the United States (Kim et al, 2016). A highly virulent of SCN has been observed in China (Lian et al, 2019). SCN is a soil-borne pathogen and pest management is difficult. SCN management includes crop rotation, pesticide application, biological control, Genes for Soybean Resistance pest-resistant varieties, etc.; breeding for resistant varieties is the most effective method (Usovsky et al, 2021). As in Missouri in the United States, the dominant race in the Huanghuai Valley in China is race 2, which was evolved from race 1 (Lu et al, 2006; Mitchum et al, 2007; Lian et al, 2016; Howland et al, 2018). Race 2 was used to screen new varieties for SCN resistance in the Huanghuai Valley, most varieties were susceptible to SCN race 2.1

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