The ‘PI 438489B’ by ‘Hamilton’ SNP-Based Genetic Linkage Map of Soybean [Glycine max (L.) Merr.] Identified Quantitative Trait Loci that Underlie Seedling SDS Resistance

Abstract

Soybeans [Glycine max (L.) Merr.] are susceptible to many diseases including fungal diseases such as soybean sudden death syndrome (SDS). Several studies reported SDS resistance quantitative trait loci (QTL) on the soybean genome using different recombinant inbred line (RIL) populations and low density genetic linkage maps. High density exclusively single nucleotide polymorphisms-based (SNP-based) maps were not yet reported in soybean. The objectives of this study were (1) to construct a high density SNP-based genetic linkage map of soybean using the ‘PI438489B’ by ‘Hamilton’ (PIxH, n=50) recombinant inbred line population, and (2) to map QTL for SDS resistance using this high-density reliable genetic SNP-based map. The PI438489B by Hamilton high-density SNP-based genetic map was a high density map composed of 31 LGs, 648 SNPs, and covered 1,524.7 cM with an average of 2.37 cM between two adjacent SNP markers. Fourteen significant QTL were identified for SDS resistance using interval mapping (IM) and composite interval mapping (CIM) with LOD scores that ranged between 2.6 and 5.0. Twelve QTL were identified for foliar disease severity (FDS) and three QTL for root rot severity (RRS) of which one QTL underlain both FDS and RRS. The fourteen QTL were mapped onto ten separate chromosomes of the soybean genome. Seven of the intervals encompassing the QTL had been identified previously (on LGs C1, C2, D1b, G, L, N and O) associated with resistance to SDS but seven were novel (LGs A2 (2), B1, C2, D1a, D1b and O). We constructed the first PI438489B by Hamilton exclusively SNP-Based map and identified fourteen QTL that underlie SDS resistance including both resistances to foliar and root rot symptoms caused by Fusarium virguliforme infection. The QTL discovered here for SDS resistance could be useful to include in breeding programs in developing soybean cultivars resistant to SDS.

Genome‐wide association and epistasis studies unravel the genetic architecture of sudden death syndrome resistance in soybean

“…In comparison with the alternative allele, the desired allele of this locus may reduce the disease severity by 10% (Figure a). An SDS resistance QTL has been previously reported at this genomic region (Abdelmajid et al ., ). Further analysis pinpointed ss715584189_T_C to the coding region of stress‐induced receptor‐like kinase gene 1 ( SIK1 ) (Figure b and Table ).…”

Genome-wide association mapping of partial resistance to Phytophthora sojae in soybean plant introductions from the Republic of Korea

“…The current study along with previous QTL mapping studies have identified 33 genetic regions on 18 chromosomes with QTL for partial resistance to P. sojae [ 33 , 39 – 50 , 52 , 56 , 61 ]. Of the 33 regions, four are coincident with Rps -genes [ 9 , 10 , 12 , 15 , 63 ] five are coincident with QTL for resistance to Sudden Death Syndrome [ 89 – 93 ], root disease caused by members of the fungus Fusarium viguliforme , 11 are coincident with QTL/genes for resistance to Soybean Cyst Nematode [ 94 – 103 ], and 11 are coincident with QTL for resistance to the necrotrophic fungal pathogen S. sclerotiorum causing Sclerotinia stem rot [ 59 , 62 , 104 , 105 ]. The coincidence of QTL for partial resistance to P. sojae with QTL and R -genes for resistance to pathogens with varied lifestyles provides evidence that partial resistance is likely conferred through a variety of different mechanisms.…”

Genome-Wide Association Study Reveals Novel Loci for SC7 Resistance in a Soybean Mutant Panel

“…In the vicinity of these identified SNPs, there were some QTLs reported to response to biotic stress. For example, SCN 19-1, SCN 19-2, SCN 19-4, SCN 33-7, SCN 44-5, SCN 18-1 , and SCN 37-1 have been reported to resistant to soybean cyst nematode ( Yue et al, 2001 ; Guo et al, 2006 ; Vuong et al, 2010 ; Jiao et al, 2015 ); SDS 13-1 was associated with resistant to soybean fungi disease sudden death syndrome (SDS) ( Abdelmajid et al, 2012 ); Japanese beetle resistance 1-4 was associated with herbivory pest Japanese beetles resistance ( Yesudas et al, 2010 ); Phytoph 5-3 was related to Phytophthora sojae infection ( Wu et al, 2011 ); Rag 3-2 associated with aphid resistance( Zhang et al, 2009 ); Asian Soybean Rust 2-4 resisted to fungal pathogen Phakopsora pachyrhizi ( Harris et al, 2015 ); Peanut root-knot nematode 2-2 was associated with resistance to peanut root-knot nematode in soybean ( Tamulonis et al, 1997 ).…”