The discovery of novel SNPs associated with group A soyasaponin biosynthesis from Korea soybean core collection

Lee, Sang-Beom; Lee, Kwang-Sik; Kim, Sujeong; Kim, Dool-Yi; Seo, Mi-Suk; Jeong, Soon‐Chun; Moon, Jung‐Kyung; Park, Soo-Kwon; Choi, Mansoo

doi:10.1016/j.ygeno.2022.110432

Cited by 4 publications

(4 citation statements)

References 29 publications

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“…After filtering, a total of 542,422 high-quality SNPs were obtained from the re-sequencing data of the soybean core collection. Population structure analysis was performed using the high-quality SNPs, and based on the reference results of the 180K SNP analysis of the core soybean collection by ( Lee et al., 2022 ), the optimal value for K was determined to be 4 ( Figure 6A ). The resulting clusters were labeled as Subpopulation (SP)-I, SP -II, SP-III, and SP-IV, comprising 105, 158, 101, and 51 resources, respectively.…”

Section: Resultsmentioning

confidence: 99%

Genome-wide analysis of KIX gene family for organ size regulation in soybean (Glycine max L.)

Park,

Moon,

Park

et al. 2023

Front. Plant Sci.

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The KIX domain, conserved among various nuclear and co-activator factors, acts as a binding site that interacts with other transcriptional activators and co-activators, playing a crucial role in gene expression regulation. In plants, the KIX domain is involved in plant hormone signaling, stress response regulation, cell cycle control, and differentiation, indicating its potential relevance to crop productivity. This study aims to identify and characterize KIX domains within the soybean (Glycine max L.) genome to predict their potential role in improving crop productivity. The conservation and evolutionary history of the KIX domains were explored in 59 plant species, confirming the presence of the KIX domains in diverse plants. Specifically, 13 KIX domains were identified within the soybean genome and classified into four main groups, namely GmKIX8/9, GmMED15, GmHAC, and GmRECQL, through sequence alignment, structural analysis, and phylogenetic tree construction. Association analysis was performed between KIX domain haplotypes and soybean seed-related agronomic traits using re-sequencing data from a core collection of 422 accessions. The results revealed correlations between SNP variations observed in GmKIX8-3 and GmMED15-4 and soybean seed phenotypic traits. Additionally, transcriptome analysis confirmed significant expression of the KIX domains during the early stages of soybean seed development. This study provides the first characterization of the structural, expression, genomic haplotype, and molecular features of the KIX domain in soybean, offering a foundation for functional analysis of the KIX domain in soybean and other plants.

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Section: Resultsmentioning

confidence: 99%

Genome-wide analysis of KIX gene family for organ size regulation in soybean (Glycine max L.)

Park,

Moon,

Park

et al. 2023

Front. Plant Sci.

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“…Vuong et al [ 47 ] genotyped 553 soybean plants using SoySNP50K and revealed 14 QTLs containing 60 SNPs associated with the resistance to the soybean cyst nematode through a GWAS. Lee et al [ 48 ] genotyped 430 soybean lines from a core collection using the 180K AXIOM® SoyaSNP array and determined that 14 novel SNPs responsible for soya-saponin biosynthesis are closely related to Glyma.07g524600 through a GWAS. Hu et al [ 49 ] identified qPDH1 as a pod dehiscence-related QTL that includes Glyma09g06290 (bHLH transcription factor) on chromosome 16 using 211 soybean accessions and the NAJU 355K SoySNP array.…”

Section: Introductionmentioning

confidence: 99%

“…Hu et al [ 49 ] identified qPDH1 as a pod dehiscence-related QTL that includes Glyma09g06290 (bHLH transcription factor) on chromosome 16 using 211 soybean accessions and the NAJU 355K SoySNP array. Li et al [ 48 ] performed a GWAS and combined the results with QTL mapping data and identified candidate genes ( E2 , GmPRR3b , and GmVIP5 ) associated with the flowering time and the circadian clock in 265 soybean landraces using SoySNP618K.…”

Section: Introductionmentioning

confidence: 99%

QTL mapping reveals key factors related to the isoflavone contents and agronomic traits of soybean (Glycine max)

Kim,

Seo,

Lee

et al. 2023

BMC Plant Biol

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Background Soybean is a valuable source of edible protein and oil, as well as secondary metabolites that can be used in food products, cosmetics, and medicines. However, because soybean isoflavone content is a quantitative trait influenced by polygenes and environmental interactions, its genetic basis remains unclear. Results This study was conducted to identify causal quantitative trait loci (QTLs) associated with soybean isoflavone contents. A mutant-based F2 population (190 individuals) was created by crossing the Korean cultivar Hwanggeum with low isoflavone contents (1,558 µg g−1) and the soybean mutant DB-088 with high isoflavone contents (6,393 µg g−1). A linkage map (3,049 cM) with an average chromosome length of 152 cM was constructed using the 180K AXIOM® SoyaSNP array. Thirteen QTLs related to agronomic traits were mapped to chromosomes 2, 3, 11, 13, 19, and 20, whereas 29 QTLs associated with isoflavone contents were mapped to chromosomes 1, 3, 8, 11, 14, 15, and 17. Notably, the qMGLI11, qMGNI11, qADZI11, and qTI11, which located Gm11_9877690 to Gm11_9955924 interval on chromosome 11, contributed to the high isoflavone contents and explained 11.9% to 20.1% of the phenotypic variation. This QTL region included four candidate genes, encoding β-glucosidases 13, 14, 17–1, and 17–2. We observed significant differences in the expression levels of these genes at various seed developmental stages. Candidate genes within the causal QTLs were functionally characterized based on enriched GO terms and KEGG pathways, as well as the results of a co-expression network analysis. A correlation analysis indicated that certain agronomic traits (e.g., days to flowering, days to maturity, and plant height) are positively correlated with isoflavone content. Conclusions Herein, we reported that the major QTL associated with isoflavone contents was located in the interval from Gm11_9877690 to Gm11_9955924 (78 kb) on chromosome 11. Four β-glucosidase genes were identified that may be involved in high isoflavone contents of soybean DB-088. Thus, the mutant alleles from soybean DB-088 may be useful for marker-assisted selection in developing soybean lines with high isoflavone contents and superior agronomic traits.

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“…In Korea, a 180K Axiom ® Soya SNP array has been developed from more than 4 million high-quality SNPs identified from the resequencing of 16 Korean and 31 Chinese genetic resources [34]. This array has been used in the structural analysis of genetic diversity [35] and in association analysis for various traits, such as the flowering time, ultraviolet B resistance, and the soyasaponin biosynthesis of soybean [36][37][38]. The purpose of this study was to investigate the genetic diversity of soybean using high-density SNP chip data from 203 wild soybean accessions and to detect candidate genes for major agricultural traits that can affect soybean yield using GWAS analysis.…”

Section: Introductionmentioning

confidence: 99%

Genome-Wide Association Study for Agronomic Traits in Wild Soybean (Glycine soja)

et al. 2023

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The agronomic traits of soybean are important because they are directly or indirectly related to its yield. Cultivated soybean (Glycine max (L.) Merr) has lost genetic diversity during domestication and selective breeding. However, wild soybean (G. soja) represents a useful breeding material because it has a diverse gene pool. In this study, a total of 96,432 single-nucleotide polymorphisms (SNPs) across 203 wild soybean accessions from the 180K Axiom® Soya SNP array were employed in the association analysis. Wild soybean accessions were divided into four clusters based on their genetic distance using ADMIXTURE, principal component analysis, and neighbor-joining clusters. The linkage disequilibrium decayed rapidly in wild soybean. A genome-wide association study was conducted for days to flowering (DtF), days to maturity (DtM), the number of pods (NoP), and the 100-seed weight (100SW), which are major agronomic traits for wild soybean accessions. A total of 22 significant SNPs were found to be associated with DtF, DtM, and the 100SW. Based on the detected SNP markers, Glyma.12g210400, a gene related to DtF, Glyma.17g115300, a gene related to DtM, and Glyma.14g140200, a gene related to the 100SW, were selected as candidate genes. The SNP markers related to agronomic traits identified in this study are expected to help improve the quality of soybean cultivars through selective breeding.

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The discovery of novel SNPs associated with group A soyasaponin biosynthesis from Korea soybean core collection

Cited by 4 publications

References 29 publications

Genome-wide analysis of KIX gene family for organ size regulation in soybean (Glycine max L.)

Genome-wide analysis of KIX gene family for organ size regulation in soybean (Glycine max L.)

QTL mapping reveals key factors related to the isoflavone contents and agronomic traits of soybean (Glycine max)

Genome-Wide Association Study for Agronomic Traits in Wild Soybean (Glycine soja)

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