Dissecting the Genetic Basis of Resistance to Soybean Cyst Nematode Combining Linkage and Association Mapping

Abstract

A set of 585 informative single-nucleotide polymorphism (SNP) loci was used to genotype both a panel of diverse accessions and a set of recombinant inbred lines (RILs) bred from the cross Zhongpin03-5373 (ZP; resistant to SCN)  Zhonghuang13 (ZH; susceptible). The SNP loci are mostly sited within genic sequence in regions of the soybean [Glycine max (L.) Merr.] genome thought to harbor genes determining resistance to the soybean cyst nematode (SCN, Heterodera glycines Ichinohe). The three strongest quantitative trait nucleotides (QTNs) identified by association mapping (AM) involved the genes Glyma18 g02590 (a component of the multigene locus rhg1-b), Glyma11 g35820 and Glyma11 g35810 (an rhg1-b paralog), as well as some other loci with smaller effects. The linkage mapping (LM) analysis performed using the RILs revealed two putative quantitative trait loci (QTL): one mapping to rhg1-b and the other to an rhg1-b paralog; both of these loci were also identified by AM. The former locus explained 25.5% of the phenotypic variance for SCN resistance and the latter 5.8%. In combination, the two major loci acted nonadditively, providing a high level of SCN resistance.

Genome-Wide Association Analysis Pinpoints Additional Major Genomic Regions Conferring Resistance to Soybean Cyst Nematode (Heterodera glycines Ichinohe)

“…This region overlapped or located closely with previously reported QTL, which were identified from PI 438489B (27.7–32.4 Mb); PI 90763 (32.4–34.1 Mb); PI 404198A (33.6–34.1 Mb); and PI 437654 (29.7–32.2 Mb) (Yue et al, 2001; Guo et al, 2005, 2006; Wu et al, 2009). This region is also close to the regions identified in a previous GWAS study for SCN resistance by Li et al (2016). Of these eight SNPs, ss715610417, ss715610420, and ss715610421 were located in the same haplotype block containing Glyma.11g234500 (GmSNAP11 ), which belonged to same SNAP family with Glyma.18g02590 (GmSNAP18 ), which is one of the Rhg1 genes (Cook et al, 2012).…”

Genome wide association study discovers genomic regions involved in resistance to soybean cyst nematode (Heterodera glycines) in common bean

“…Since the distribution of FI values was continuous, the most likely genetic basis of resistance in common bean is quantitative in nature. Likewise, many studies conducted on soybean also indicated a complex genetic architecture of SCN resistance [35, 36]. Many of the highly resistant accessions in the common bean core collection could be used in breeding programs to start introgression of resistance into elite/adapted germplasm and commercial cultivars.…”

“…Since SCN resistance loci in soybean are already known, we focused the search for candidate genes in common bean genomic regions based on previous information available in soybean. In soybean, linkage mapping and association analysis studies enabled the identification of rhg1 on chromosome 18 in Peking, PI88788, PI209332, and PI437654, while a second locus, Rhg4 on chromosome 8, was found in Peking, PI209332, and PI437654 [11, 12, 36]. Fine mapping of the rhg1 locus on chromosome 18 confirmed that the copy number variation of a genomic segment spanning three genes (Glyma.18g02580, Glyma.18g02590 and Glyma.18g02610 within a 31 kb rhg1-b region of PI88788) was required to confer resistance [11].…”

Genome-wide association study and genomic selection for tolerance of soybean biomass to soybean cyst nematode infestation

“…GWAS has been shown to be successful in studies investigating the genetics of SCN in soybean [48]. Li et al [49] mapped a 6-Mb region of chromosome 15 to be associated with SCN. In this report, this region has been narrowed to a less than 2-Mb region.…”