Development of SNP markers and haplotype analysis of the candidate gene for rhg1, which confers resistance to soybean cyst nematode in soybean

Li, Yinghui; Zhang, Chen; Smulders, M.J.M.; Ma, Zhong‐Qi; Liu, Zhangxiong; Nan, Haiyang; Chang, Ru-Zhen; Qiu, Lijuan

doi:10.1007/s11032-009-9272-0

Cited by 29 publications

(22 citation statements)

References 40 publications

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“…Compared to the findings in rhg1 reported by Li et al (2009), who identified 37 SNPs and 5 InDels among 8 resistant G. max genotypes, we identified 70 SNPs and 8 InDels, among which 32 SNP loci were shared. For Rhg4, however, we only identified 9 SNPs, which was less than the 31 SNPs among 76 G. max genotypes found in the same sequence region by Yuan et al (2012).…”

Section: Dna Polymorphism Among 23 G Soja Resistant Accessionscontrasting

confidence: 53%

“…a Glycine max resistant cultivar is underlined. Among domesticated soybean collections, the haplotypes 689 C-757 C in rhg1 and 1724 C-1760 C-2120 T-2387 G in Rhg4 were found to be predominant, and were considered to be SCN resistance-associated haplotypes (Yuan 2007;Li et al 2009). For wild soybeans, we found that, except for ZYD01185, 22 accessions possessed either one of the resistanceassociated haplotypes or both.…”

Section: Haplotypes Of G Soja Accessions and G Max Resistant Accessmentioning

confidence: 76%

“…Two SNPs (689 C/A and 757 C/T) at rhg1, four SNPs (1724 C/A, 1760 C/T, 2120 T/A, and 2387 G/A) at Rhg4, and two SNPs (389 G/C and 1165 T/A) at SHMT were previously found to be associated with SCN resistance by Li et al (2009), Yuan (2007, and Liu et al (2012), respectively. Haplotypes formed by these SNPs among 31 G. soja and G. max resistant accessions were investigated.…”

Section: Haplotypes Of G Soja Accessions and G Max Resistant Accessmentioning

confidence: 96%

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Genetic diversity of rhg1 and Rhg4 loci in wild soybeans resistant to soybean cyst nematode race 3

et al. 2016

Genet. Mol. Res.

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ABSTRACT. Over-utilization of germplasms that are resistant to the soybean cyst nematode (SCN) in soybean breeding programs can lead to genetic vulnerability in resistant cultivars. Resistant wild soybean (Glycine soja) is considered an invaluable gene source for increasing the genetic diversity of SCN resistance. In this study, we genotyped 23 G. soja accessions that are resistant to SCN race 3 for polymorphisms in the resistance genes, rhg1, Rhg4, and SHMT, and investigated their genetic relationship with eight Glycine max resistant cultivars. We identified 89 single nucleotide polymorphisms (SNPs) and 11 DNA insertion-deletions (InDels), of which 70 SNPs and 8 InDels were found in rhg1, 9 SNPs were found in Rhg4, and 10 SNPs and 3 InDels were found in SHMT. Nucleotide diversity was π = 0.00238 and θ = 0.00235, and haplotype diversity was 1.000. A phylogenetic tree comprising four clusters was constructed using sequence variations of the 23 G. soja and 8 G. max resistant accessions. Five G. soja accessions in subcluster A2, and four G. soja accessions in cluster B were genetically distant from G. max genotypes. Eight resistance-associated SNPs in the three resistance genes formed nine haplotypes in total. G. soja resistant accessions had different haplotypes (H2, H4, H5, H6, H7, and H8) compared with those of G. max (H1, H3, and H9). These results provide vital information on the use of wild soybeans for broadening the genetic base of SCN resistance.

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Section: Dna Polymorphism Among 23 G Soja Resistant Accessionscontrasting

confidence: 53%

Section: Haplotypes Of G Soja Accessions and G Max Resistant Accessmentioning

confidence: 76%

Section: Haplotypes Of G Soja Accessions and G Max Resistant Accessmentioning

confidence: 96%

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Genetic diversity of rhg1 and Rhg4 loci in wild soybeans resistant to soybean cyst nematode race 3

et al. 2016

Genet. Mol. Res.

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“…Possible roles include contributions to additive resistance; contributions to resistance in other resistance types (e.g PI88788 and Toyohazu; R types 2 and 3) or contributions to the resistance to other Hg types (Nelsen et al 2003;Li et al 2009). Unlikely, in view of the susceptibility of segregation events within the interval from the RLK to Satt309 in both PI evolution and NIL segregation, is the hypothesis that the linked genes are factors necessary in susceptible genotypes for SCN parasitism.…”

Section: Discussionmentioning

confidence: 99%

Recombination suppression at the dominant Rhg1/Rfs2 locus underlying soybean resistance to the cyst nematode

et al. 2011

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Host resistance to "yellow dwarf" or "moonlight" disease cause by any population (Hg type) of Heterodera glycines I., the soybean cyst nematode (SCN), requires a functional allele at rhg1. The host resistance encoded appears to mimic an apoptotic response in the giant cells formed at the nematode feeding site about 24-48 h after nematode feeding commences. Little is known about how the host response to infection is mediated but a linked set of 3 genes has been identified within the rhg1 locus. This study aimed to identify the role of the genes within the locus that includes a receptor-like kinase (RLK), a laccase and an ion antiporter. Used were near isogeneic lines (NILs) that contrasted at their rhg1 alleles, gene-based markers, and a new Hg type 0 and new recombination events. A syntenic gene cluster on Lg B1 was found. The effectiveness of SNP probes from the RLK for distinguishing homolog sequence variants on LgB1 from alleles at the rhg1 locus on LgG was shown. The resistant allele of the rhg1 locus was shown to be dominant in NILs. None of the recombination events were within the cluster of the three candidate genes. Finally, rhg1 was shown to reduce the plant root development. A model for rhg1 as a dominant multi-gene resistance locus based on the developmental control was inferred.

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“…Therefore the robust marker-phenotype associations are required for successful MAS. Soybean SNP and SRR markers are often more robust and with higher resolution to detect a specific allele in the population (Coryell et al, 1999;Zhu et al, 2003;Hyten et al, 2008;Li et al, 2009;Hyten et al, 2010). Even one marker alone can be extremely effective in screening breeding populations.…”

Section: Mas and Qtl Cloningmentioning

confidence: 99%

Current development and application of soybean genomics

Zhao

et al. 2011

Front. Biol.

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Soybean (Glycine max), an important domesticated species originated in China, constitutes a major source of edible oils and high-quality plant proteins worldwide. In spite of its complex genome as a consequence of an ancient tetraploidilization, platforms for map-based genomics, sequence-based genomics, comparative genomics and functional genomics have been well developed in the last decade, thus rich repertoires of genomic tools and resources are available, which have been influencing the soybean genetic improvement. Here we mainly review the progresses of soybean (including its wild relative Glycine soja) genomics and its impetus for soybean breeding, and raise the major biological questions needing to be addressed. Genetic maps, physical maps, QTL and EST mapping have been so well achieved that the marker assisted selection and positional cloning in soybean is feasible and even routine. Whole genome sequencing and transcriptomic analyses provide a large collection of molecular markers and predicted genes, which are instrumental to comparative genomics and functional genomics. Comparative genomics has started to reveal the evolution of soybean genome and the molecular basis of soybean domestication process. Microarrays resources, mutagenesis and efficient transformation systems become essential components of soybean functional genomics. Furthermore, phenotypic functional genomics via both forward and reverse genetic approaches has inferred functions of many genes involved in plant and seed development, in response to abiotic stresses, functioning in plant-pathogenic microbe interactions, and controlling the oil and protein content of seed. These achievements have paved the way for generation of transgenic or genetically modified (GM) soybean crops.

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Development of SNP markers and haplotype analysis of the candidate gene for rhg1, which confers resistance to soybean cyst nematode in soybean

Cited by 29 publications

References 40 publications

Genetic diversity of rhg1 and Rhg4 loci in wild soybeans resistant to soybean cyst nematode race 3

Genetic diversity of rhg1 and Rhg4 loci in wild soybeans resistant to soybean cyst nematode race 3

Recombination suppression at the dominant Rhg1/Rfs2 locus underlying soybean resistance to the cyst nematode

Current development and application of soybean genomics

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