Quantitative Trait Loci (QTL) that Underlie SCN Resistance in Soybean [Glycine max (L.) Merr.] PI438489B by ‘Hamilton’ Recombinant Inbred Line (RIL) Population

Kassem, My Abdelmajid; Ramos, Laura; Hyten, David L.; Bond, Jason P.; Arelli, Prakash R.; Njiti, V. N.; Cianzio, Silvia R.; Kantartzi, Stella K.; Meksem, Khalid

doi:10.5147/ajpb.v1i3.111

Cited by 10 publications

(8 citation statements)

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“…The precisely identifying and positioning of QTL are crucial for successful MAS. Up to now, many QTL associated with SCN resistance have been effectively tagged with different molecular marker systems, including SSR, RAPD, RFLP and SNP [ 12 , 14 , 19 , 46 – 48 ]. However, no sequencing based mapping like GWAS for QTL or genes underlying the resistance to SCN has been reported so far.…”

Section: Discussionmentioning

confidence: 99%

Genetic characteristics of soybean resistance to HG type 0 and HG type 1.2.3.5.7 of the cyst nematode analyzed by genome-wide association mapping

et al. 2015

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BackgroundSoybean cyst nematode (SCN, Heterodera glycines Ichinohe) is one of the most fatal pests of soybean (Glycine max (L.) Merr.) worldwide and causes huge loss of soybean yield each year. Multiple sources of resistance are urgently needed for effective management of SCN via the development of resistant cultivars. The aim of the present study was to investigate the genetic architecture of resistance to SCN HG Type 0 (race 3) and HG Type 1.2.3.5.7 (race 4) in landraces and released elite soybean cultivars mostly from China.ResultsA total of 440 diverse soybean landraces and elite cultivars were screened for resistance to SCN HG Type 0 and HG Type 1.2.3.5.7. Exactly 131 new sources of SCN resistance were identified. Lines were genotyped by SNP markers detected by the Specific Locus Amplified Fragment Sequencing (SLAF-seq) approach. A total of 36,976 SNPs were identified with minor allele frequencies (MAF) > 4 % that were present in 97 % of all the genotypes. Genome-wide association mapping showed that a total of 19 association signals were significantly related to the resistance for the two HG Types. Of the 19 association signals, eight signals overlapped with reported QTL including Rhg1 and Rhg4 genes. Another eight were located in the linked regions encompassing known QTL. Three QTL were found that were not previously reported. The average value of female index (FI) of soybean accessions with resistant alleles was significantly lower than those with susceptible alleles for each peak SNP. Disease resistance proteins with leucine rich regions, cytochrome P450s, protein kinases, zinc finger domain proteins, RING domain proteins, MYB and WRKY transcription activation families were identified. Such proteins may participate in the resistant reaction to SCN and were frequently found in the tightly linked genomic regions of the peak SNPs.ConclusionsGWAS extended understanding of the genetic architecture of SCN resistance in multiple genetic backgrounds. Nineteen association signals were obtained for the resistance to the two Hg Types of SCN. The multiple beneficial alleles from resistant germplasm sources will be useful for the breeding of cultivars with improved resistance to SCN. Analysis of genes near association signals may facilitate the recognition of the causal gene(s) underlying SCN resistances.Electronic supplementary materialThe online version of this article (doi:10.1186/s12864-015-1800-1) contains supplementary material, which is available to authorized users.

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Section: Discussionmentioning

confidence: 99%

Genetic characteristics of soybean resistance to HG type 0 and HG type 1.2.3.5.7 of the cyst nematode analyzed by genome-wide association mapping

et al. 2015

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“…An early study by Anand and Raoarelli ( 1989 ) indicated that at least one gene controls soybean resistance to HG 2.5.7. Thus far, at least 22 QTLs distributed on 10 chromosomes (1, 5, 6, 8, 10, 11, 15, 18, 19, and 20) have been associated with resistance to HG 2.5.7 (race 5; Yue et al, 2001a , b ; Guo et al, 2006a , b ; Wu et al, 2009 ; Vuong et al, 2010 ; Abdelmajid et al, 2014 ). Among these QTLs, genomic regions either containing or adjacent to the rhg1 locus on chromosome 18 have repeatedly been identified using different resistant soybean sources (Yue et al, 2001a ; Guo et al, 2006a , b ; Wu et al, 2009 ), suggesting the presence of highly important genes in this region that confer HG 2.5.7 resistance.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Study of Resistance to Soybean Cyst Nematode (Heterodera glycines) HG Type 2.5.7 in Wild Soybean (Glycine soja)

Zhang

Davis

et al. 2016

Front. Plant Sci.

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Soybean cyst nematode (SCN) is the most destructive soybean pest worldwide. Host plant resistance is the most environmentally friendly and cost-effective way of mitigating SCN damage to soybeans. However, overuse of the resistant soybean [Glycine max (L.) Merr.] cultivars from limited genetic resources has resulted in SCN race shifts in many soybean-growing areas. Thus, exploration of novel sources of SCN resistance and dissection of the genetic basis are urgently needed. In this study, we screened 235 wild soybean (Glycine soja Sieb. & Zucc.) accessions to identify genotypes resistant to SCN HG Type 2.5.7 (race 5), a less investigated type but is prevalent in the southeastern US. We also dissected the genetic basis of SCN resistance using a genome-wide association study with SNPs genotyped by SoySNP50k iSelect BeadChip. In total, 43 resistant accessions (female index < 30) were identified, with 10 SNPs being significantly associated with SCN HG 2.5.7 resistance in this wild species. Furthermore, four significant SNPs were localized to linked regions of the known quantitative trait locus (QTL) rhg1 on chromosome 18. The other four SNPs on chromosome 18 and two SNPs on chromosome 19 are novel. Genes encoding disease resistance-related proteins with a leucine-rich region, a mitogen-activated protein kinase (MAPK) on chromosome 18, and a MYB transcription factor on chromosome 19 were identified as promising candidate genes. The identified SNPs and candidate genes will benefit future marker-assisted breeding and dissection of the molecular mechanisms underlying the soybean-SCN interaction.

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“…SCN_7_1 is an important QTL to SCN resistance for Handou 10. Some QTLs ( Webb et al, 1995 ; Ferreira et al, 2011 ; Abdelmajid et al, 2014 ; Chang et al, 2016 ; Vuong et al, 2015 ; Li et al, 2016 ) related to SCN resistance on chromosome 7 were reported at www.soybase.org . The physical location of SCN_7_1 was basically the same as the marker php02301a mapped in PI437654 ( Webb et al, 1995 ), but far from the QTLs detected by other researchers (see Footnote 2).…”

Section: Discussionmentioning

confidence: 99%

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

Lian

et al. 2022

Front. Plant Sci.

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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.

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Quantitative Trait Loci (QTL) that Underlie SCN Resistance in Soybean [Glycine max (L.) Merr.] PI438489B by ‘Hamilton’ Recombinant Inbred Line (RIL) Population

Cited by 10 publications

References 46 publications

Genetic characteristics of soybean resistance to HG type 0 and HG type 1.2.3.5.7 of the cyst nematode analyzed by genome-wide association mapping

Genetic characteristics of soybean resistance to HG type 0 and HG type 1.2.3.5.7 of the cyst nematode analyzed by genome-wide association mapping

Genome-Wide Association Study of Resistance to Soybean Cyst Nematode (Heterodera glycines) HG Type 2.5.7 in Wild Soybean (Glycine soja)

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

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