Genetic loci and candidate genes of symbiotic nitrogen fixation–related characteristics revealed by a genome-wide association study in soybean

Huo, Xiaobo; Li, Xihuan; Du, Hui; Kong, Youbin; Tian, Rui; Li, Wenlong; Zhang, Caiying

doi:10.1007/s11032-019-1022-3

Cited by 12 publications

(12 citation statements)

References 41 publications

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“…Similarly, GWAS enabled the identification of several SNPs associated with Ndfa under different environments in soybean (Dhanapal et al, 2015). This approach identified 11 SNF-related characteristics linked to 20 SNP loci on eight chromosomes in soybean (Huo et al, 2019). Among these, three SNP loci located on chromosome Gm17 were associated with the shoot N concentration while two SNP loci in the adjacent region were linked to high nodule numbers and nodule fresh and dry weights.…”

Section: Snf-associated Qtls and Snpsmentioning

confidence: 99%

Rhizobial–Host Interactions and Symbiotic Nitrogen Fixation in Legume Crops Toward Agriculture Sustainability

2021

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Symbiotic nitrogen fixation (SNF) process makes legume crops self-sufficient in nitrogen (N) in sharp contrast to cereal crops that require an external input by N-fertilizers. Since the latter process in cereal crops results in a huge quantity of greenhouse gas emission, the legume production systems are considered efficient and important for sustainable agriculture and climate preservation. Despite benefits of SNF, and the fact that chemical N-fertilizers cause N-pollution of the ecosystems, the focus on improving SNF efficiency in legumes did not become a breeder’s priority. The size and stability of heritable effects under different environment conditions weigh significantly on any trait useful in breeding strategies. Here we review the challenges and progress made toward decoding the heritable components of SNF, which is considerably more complex than other crop allelic traits since the process involves genetic elements of both the host and the symbiotic rhizobial species. SNF-efficient rhizobial species designed based on the genetics of the host and its symbiotic partner face the test of a unique microbiome for its success and productivity. The progress made thus far in commercial legume crops with relevance to the dynamics of host–rhizobia interaction, environmental impact on rhizobial performance challenges, and what collectively determines the SNF efficiency under field conditions are also reviewed here.

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Section: Snf-associated Qtls and Snpsmentioning

confidence: 99%

Rhizobial–Host Interactions and Symbiotic Nitrogen Fixation in Legume Crops Toward Agriculture Sustainability

2021

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“…Huo et al . (2019) identified five SNP loci on chromosome 17, which were associated with shoot nitrogen concentrations under different environments, and led to the identification of two candidate genes (Glyma17g16400 and Glyma17g15600), which were further verified by gene expression analysis. The assay has also been used for other applications.…”

Section: Discussionmentioning

confidence: 96%

“…The BARCSoySNP6K assay has been applied in various genetic research, e.g., it has been used to construct linkage maps (Lee et al ., 2015), identify QTL/genes controlling a number of traits such as sudden death syndrome resistance (Wen et al ., 2014; Lightfoot et al ., 2018), aphid resistance (Bhusal et al ., 2017; Zhang et al ., 2017), charcoal rot resistance (Vinholes et al ., 2019), Phytophthora sojae , Pythium irregulare and Fusarium graminearum resistance (Stasko et al ., 2016; Million et al ., 2019), salt tolerance (Do et al ., 2018), waterlogging (Ye et al ., 2018), iron deficiency chlorosis (Merry et al ., 2019), nitrogen fixation (Huo et al ., 2019), growth period (Liu et al ., 2016), seed isoflavone content (Li et al ., 2018), oil and fatty acids (Priolli et al ., 2019), protein content (Nascimento et al ., 2018) and yield (Ye et al ., 2018). These studied not only confirmed previously identified QTL but also resulted in the discovery of new QTL, candidate genes or pathways controlling these traits.…”

Section: Discussionmentioning

confidence: 99%

Soybean BARCSoySNP6K: An assay for soybean genetics and breeding research

et al. 2020

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The limited number of recombinant events in recombinant inbred lines suggests that for a biparental population with a limited number of recombinant inbred lines, it is unnecessary to genotype the lines with many markers. For genomic prediction and selection, previous studies have demonstrated that only 1000-2000 genome-wide common markers across all lines/accessions are needed to reach maximum efficiency of genomic prediction in populations. Evaluation of too many markers will not only increase the cost but also generate redundant information. We developed a soybean (Glycine max) assay, BARCSoySNP6K, containing 6000 markers, which were carefully chosen from the SoySNP50K assay based on their position in the soybean genome and haplotype block, polymorphism among accessions and genotyping quality. The assay includes 5000 single nucleotide polymorphisms (SNPs) from euchromatic and 1000 from heterochromatic regions. The percentage of SNPs with minor allele frequency >0.10 was 95% and 91% in the euchromatic and heterochromatic regions, respectively. Analysis of progeny from two large families genotyped with SoySNP50K versus BARCSoySNP6K showed that the position of the common markers and number of unique bins along linkage maps were consistent based on the SNPs genotyped with the two assays; however, the rate of redundant markers was dramatically reduced with the BARCSoySNP6K. The BARC-SoySNP6K assay is proven as an excellent tool for detecting quantitative trait loci, genomic selection and assessing genetic relationships. The assay is commercialized by Illumina Inc. and being used by soybean breeders and geneticists and the list of SNPs in the assay is an ideal resource for SNP genotyping by targeted amplicon sequencing.

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“…Then the genome‐wide association analysis of SNPs and fresh pod‐ and seed‐related traits was conducted using the MLM (mixed linear model) model in the GAPIT software of R language statistical program. The P value was set 0.001 as the Type I error significant threshold according to our previous study (Huo et al., 2019).…”

Section: Methodsmentioning

confidence: 99%

“…The genotypes of 269 germplasms in the natural population were analysed by the SoySNP6K in our previous study (Huo et al., 2019), and the population structure and linkage disequilibrium (LD) decay analysis were conducted as our previous description (Huo et al., 2019). Then the genome‐wide association analysis of SNPs and fresh pod‐ and seed‐related traits was conducted using the MLM (mixed linear model) model in the GAPIT software of R language statistical program.…”

Section: Methodsmentioning

confidence: 99%

Stable pleiotropic loci and candidate genes for fresh pod‐ and seed‐related characteristics across multiple environments in soybean (Glycine max)

et al. 2021

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Soybean provides irreplaceable protein and oil. Pods and seeds are essential soybean harvested organs. To illustrate the genetic basis of pod‐ and seed‐related traits, a natural population was assessed for eight related traits under four environments. In all, 15 associated SNPs were identified across multiple environments or controlling various traits, and 11 were verified through BLUP. Two SNPs on chromosome 15 were associated with six traits across multiple environments. Two SNPs on chromosome 2 were also associated with six traits under multiple environments. Significant phenotype differences between favourable and unfavourable alleles/haplotypes under four environments were detected. Significant association of pod length SNP and large‐pod phenotype (pod length ≥4.5 cm) was detected. The genetic basis of elite germplasms was analysed, and ‘Chuxiu’ possessed all of the 15 favourable alleles with best phenotype. Some candidate genes participating in cell wall structural remodelling, gibberellin and ethylene pathways were selected with different expressions in pod developmental stages. These results provided novel insights into genetic basis and molecular markers/candidate genes for soybean fresh pod and seed genetic improvement.

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Genetic loci and candidate genes of symbiotic nitrogen fixation–related characteristics revealed by a genome-wide association study in soybean

Cited by 12 publications

References 41 publications

Rhizobial–Host Interactions and Symbiotic Nitrogen Fixation in Legume Crops Toward Agriculture Sustainability

Rhizobial–Host Interactions and Symbiotic Nitrogen Fixation in Legume Crops Toward Agriculture Sustainability

Soybean BARCSoySNP6K: An assay for soybean genetics and breeding research

Stable pleiotropic loci and candidate genes for fresh pod‐ and seed‐related characteristics across multiple environments in soybean (Glycine max)

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