Deciphering the genetic basis of resistance to soybean cyst nematode combining IBD and association mapping

Abstract

Key message IBD analysis clarified the dynamics of chromosomal recombination during the ZP pedigree breeding process and identified ten genomic regions resistant to SCN race3 combining association mapping. Abstract Soybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most devastating pathogens for soybean production worldwide. The cultivar Zhongpin03-5373 (ZP), derived from SCN-resistant progenitor parents, Peking, PI 437654 and Huipizhi Heidou, is an elite line with high resistance to SCN race3. In the current study, a pedigree variation map was generated for ZP and its ten progenitors using 3,025,264 high-quality SNPs identified from an average of 16.2 × re-sequencing for each genome. Through identity by decent (IBD) tracking, we showed the dynamic change of genome and detected important IBD fragments, which revealed the comprehensively artificial selection of important traits during ZP breeding process. A total of 2,353 IBD fragments related to SCN resistance including SCN-resistant genes rhg1, rhg4 and NSFRAN07 were identified based on the resistant-related genetic paths. Moreover, 23 genomic regions underlying resistance to SCN race3 were identified by genome-wide association study (GWAS) in 481 re-sequenced cultivated soybeans. Ten common loci were found by both IBD tracking and GWAS analysis. Haplotype analysis of 16 potential candidate genes suggested a causative SNP (C/T, − 1065) located in the promoter of Glyma.08G096500 and encoding a predicted TIFY5b-related protein on chr8 was highly correlated with SCN race3 resistance. Our results more thoroughly elucidated the dynamics of genomic fragments during ZP pedigree breeding and the genetic basis of SCN resistance, which will provide useful information for gene cloning and the development of resistant soybean cultivars using a marker-assisted selection approach.

Nemacounter: A user-friendly software to accurately phenotype SCN cysts

“…New sources of resistance to cyst nematodes can be discovered through both classical and reverse genetic screening methods. Forward screening techniques, such as Genome-Wide Association Studies (GWAS) and Quantitative Trait Loci (QTL) analysis, are potent tools for identifying genes that confer resistance to pathogens [7][8][9] . The effectiveness of GWAS and QTL analysis is heavily dependent on the precision of infection measurements 10 .…”

Cataloging SCN resistance loci in North American public soybean breeding programs

“…Genome-wide association studies (GWASs) are an efficient complementary approach to QTL mapping, which allow the determination of marker–trait associations in genetically unstructured accession panels ( Zhu et al., 2008 ). In soybeans, GWASs have been successfully employed to validate Rhg1 and Rhg4 SCN resistance loci ( Han et al., 2015 ; Vuong et al., 2015 ; Tran et al., 2019 ; Tian et al., 2023 ). Further, quantitative trait nucleotides (QTNs) on chromosomes 18 and 19 have been identified in Glycine soja accessions for resistance to HG 2.5.7 (Race 5) using a GWAS ( Zhang et al., 2016 ).…”

“…Investigations into resistance for HG 0 (Race 3) using a GWAS have identified QTNs on chromosomes 7 and 10 ( Tran et al., 2019 ). A recent study using a GWAS identified Rhg1 , Rhg2 , GmNSF RAN07 , and a QTN on chromosome 7 for resistance to HG 0 ( Tian et al., 2023 ). These studies demonstrate the effectiveness of GWASs in identifying marker–trait associations for complex traits such as SCN resistance.…”