Identification of hub genes regulating isoflavone accumulation in soybean seeds via GWAS and WGCNA approaches

Abstract

IntroductionIsoflavones are the secondary metabolites synthesized by the phenylpropanoid biosynthesis pathway in soybean that benefits human and plant health.MethodsIn this study, we have profiled seed isoflavone content by HPLC in 1551 soybean accessions grown in Beijing and Hainan for two consecutive years (2017 and 2018) and in Anhui for one year (2017).ResultsA broad range of phenotypic variations was observed for individual and total isoflavone (TIF) content. The TIF content ranged from 677.25 to 5823.29 µg g-1 in the soybean natural population. Using a genome-wide association study (GWAS) based on 6,149,599 single nucleotide polymorphisms (SNPs), we identified 11,704 SNPs significantly associated with isoflavone contents; 75% of them were located within previously reported QTL regions for isoflavone. Two significant regions on chromosomes 5 and 11 were associated with TIF and malonylglycitin across more than 3 environments. Furthermore, the WGCNA identified eight key modules: black, blue, brown, green, magenta, pink, purple, and turquoise. Of the eight co-expressed modules, brown (r = 0.68***), magenta (r = 0.64***), and green (r = 0.51**) showed a significant positive association with TIF, as well as with individual isoflavone contents. By combining the gene significance, functional annotation, and enrichment analysis information, four hub genes Glyma.11G108100, Glyma.11G107100, Glyma.11G106900, and Glyma.11G109100 encoding, basic-leucine zipper (bZIP) transcription factor, MYB4 transcription factor, early responsive to dehydration, and PLATZ transcription factor respectively were identified in brown and green modules. The allelic variation in Glyma.11G108100 significantly influenced individual and TIF accumulation.DiscussionThe present study demonstrated that the GWAS approach, combined with WGCNA, could efficiently identify isoflavone candidate genes in the natural soybean population.

Cytochrome GmGLY1 is Involved in the Biosynthesis of Glycitein in Soybean

“…Hap3 accessions (with high GLC) tended to be distributed in the southern region, while Hap2 accessions (with low GLC) tended to be distributed in the northern region. The geographic distribution of GLC in the different haplotypes was consistent with the malonylglycitin content in a previous study …”

“…The geographic distribution of GLC in the different haplotypes was consistent with the malonylglycitin content in a previous study. 18 4. DISCUSSION 4.1.…”

“…The combination of GWAS and WGCNA has been successfully applied to identify the genes responsible for isoflavone biosynthesis in soybean. 18 In this study, we conducted a GWAS using 211 soybean germplasms across five environments. Our objectives were to (i) identify genomic regions and candidate genes involved in isoflavone biosynthesis, (ii) validate the function of the candidate genes, and (iii) identify favorable haplotypes associated with seed isoflavones based on SNPs in the candidate genes.…”

“…Genes assigned to the same module may have similar expression patterns and functions; thus, WGCNA is an effective method for narrowing the range of candidate genes. The combination of GWAS and WGCNA has been successfully applied to identify the genes responsible for isoflavone biosynthesis in soybean …”

Genome-Wide Association Study Reveals Influence of Cell-specific Gene Networks on Soybean Root System Architecture

“…Weighted gene co-expression network analysis (WGCNA) has been applied to predict tissue-specific networks, identify networks related to lateral root and nodule formation, and identify the regulatory components of flooding tolerance (Jhan et al 2023; Smita et al 2020; Juexin Wang et al 2019). GCN approaches using RNA-seq have been successfully applied to various crops, including soybean (Azam et al 2023; Yao et al 2023; Gao et al 2018). Identifying network components representing sub-networks connected by central connecting genes could offer valuable insights into their regulatory roles for both plant and other development-related traits (Ko and Brandizzi 2020; X.…”