Natural variation in GmSW6 regulates seed weight and quality in soybean.

Genome-Wide Identification of the Soybean UMAMIT Family and Functional Analysis of GmUMAMIT118 in Improving Seed Protein Content

Seed protein content, oil content, and yield are key agronomic traits that determine the economic value of soybean. For decades, soybean has served as a leading source of plant protein for human and animal nutrition due to its high protein concentration. Manipulating amino acid transporters to regulate the direction of nitrogen allocation represents a promising strategy for improving seed protein content. Multiple studies have employed this strategy by targeting amino acid importers. Recently, the Usually Multiple Amino acids Move In and Out Transporter (UMAMIT) family has been characterized as amino acid exporters; nevertheless, their role in regulating the seed protein content of soybean has not yet been investigated. In this study, we identified 120 soybean UMAMIT genes via a genome-wide search and designated them according to chromosomal location. Phylogenetic analysis grouped these genes into 10 clades (A–J). Whole-genome duplication (WGD)/segmental duplication served as the main driver of the GmUMAMIT family expansion, followed by tandem duplication. By integrating transcriptome data with QTL/GWAS loci, we identified twelve candidate genes associated with seed protein content and verified their expression patterns during seed development via qPCR. One candidate gene, GmUMAMIT118, was selected and overexpressed in Arabidopsis thaliana, resulting in transgenic lines with significantly higher seed protein content and yield. Collectively, these results provided a comprehensive overview of the soybean UMAMIT family and offered a preliminary exploration of its role in improving seed protein content.

GWAS-based identification of GmKASII and its interaction with GmFATA1B reveals their role in soybean oil composition and accumulation.

Soybean (Glycine max L.) is a major oilseed crop worldwide, and its seed oil quality is largely determined by fatty acid composition. Although the enzymatic framework of plant fatty acid biosynthesis has been extensively characterized, the molecular mechanisms that regulate fatty acid partitioning and seed oil accumulation are not fully understood. In this study, genome-wide association analysis of soybean seed oil content identified GmKASII as a candidate gene underlying natural variation in seed oil accumulation, which was further supported by expression analysis and functional SNP characterization. Genetic manipulation of GmKASII significantly altered soybean seed oil accumulation and fatty acid composition. GmKASII overexpression increased seed oil content and promoted the accumulation of specific C18 fatty acids, including stearic acid (C18:0) and linoleic acid (C18:2), whereas gmkasII knockout reduced seed oil content and resulted in increased palmitic acid (C16:0) and decreased C18:0 levels. Protein-protein interaction assays, including yeast two-hybrid, luciferase complementation, and co-immunoprecipitation analyses, demonstrated that GmKASII physically interacts with acyl-ACP thioesterase GmFATA1B, suggesting a potential functional connection between fatty acid chain elongation and acyl-ACP hydrolysis pathways. Transient expression analysis in tobacco further suggested that co-expression of GmKASII and GmFATA1B influences fatty acid composition in a heterologous system. Collectively, these findings demonstrate that GmKASII plays an important role in regulating plastidial fatty acid flux and seed oil biosynthesis, and reveal a potential regulatory connection between fatty acid elongation and acyl-ACP release pathways in soybean.

Characterization of GmNPF genes prioritizes candidate genes for soybean yield and protein improvement

Nitrate uptake and translocation are crucial for plant growth and development, with Nitrate Transporter 1/Peptide Transporter family (NRTs) being critical in mediating nitrogen supply. Soybean ( Glycine max ) has been a major source of plant-based protein globally, and it requires high amounts of nitrogen to support the plant’s development and protein accumulation in seeds. However, genes accounting for nitrogen uptake and usage have yet to be systematically identified. This study focuses on the characterization of Nitrate Transporter 1/Peptide Transporter family ( NPF ) genes belonging to the NRTs in soybean. In total, 126 GmNPF genes were identified in the soybean genome, and they exhibit evolutionary conservation and functional diversity based on the analysis of protein physicochemical properties, chromosomal localization, phylogenetic relationship, synteny correlation, conserved domain, motif, gene structure and cis-acting element prediction. Additionally, spatiotemporal expression specificity analyses revealed that several GmNPFs are potentially important in root, stem, leaf and seed. In addition, we also identified a set of GmNPF genes inducible by low nitrogen stress or being regulated by POWR1 and SWEET10a/b ( SWEET39 ), two major high protein QTL genes in soybean, suggesting their participation in nitrogen absorption and seed protein deposition in soybean. Importantly, we also identified six GmNPFs showing contrasting allelic frequencies between cultivated and wild soybean, and the allelic variation was tightly associated with the variation in protein levels in cultivated soybean. The study uncovers a set of candidate genes with great potential in improving soybean protein and yield via enhanced nitrogen uptake and utilization.

Functional Characterization of GmRD22 Modulating Nitrogenase Activity in Soybean with Transcriptomic Comparison Between Two Genotypes

The findings suggest that GmRD22 has undergone directional selection during soybean domestication and improvement, and offer new insights into the genetic control of SNF and establish promising targets for breeding soybean varieties with improved nitrogen fixation efficiency.

GWAS-based identification of a candidate gene and development of a predictive KASP marker for seed protein and oil contents in soybean

Dissecting the genetic basis underlying drought tolerance at different development stages in soybean

Introduction Soybean is an indispensable crop supplying protein and oil for humans and animals, and playing an essential role in global food security. Drought represses soybean seed germination, reducing biomass accumulation and even inhibiting yield. Methods In order to dissect the genetic components underlying soybean drought tolerance during different development stage, a natural population containing 140 accessions was employed to evaluate seven drought tolerance-related traits under water-welled and drought stress conditions. Subsequently, genome-wide association study (GWAS) was conducted based on 150K single nucleotide polymorphism (SNP) markers of “Zhongdouxin-1”. And the drought tolerance coefficient of seven different traits were analyzed with seven GWAS models. Results A total of 1807 significant SNPs were detected across 20 chromosome, including 569 SNPs for germination stage, and 1242 SNPs for seedling stage. Of 569 SNPs identified in germination stage, 354 SNPs on chromosomes 2, 7, 13, 14, and 17 accounting for 62.21%. Among 1242 SNPs found in seedling stage, 869 SNPs on chromosomes 11, 14, 15, 17 and 18 accounting for 69.97%. Moreover, among 1807 significant SNPs, 163 SNPs exhibited pleiotropic effects, of which 23 were located in exon, 21 in intron, 12 in 5’UTR or 3’UTR and 11 in upstream or downstream. Furthermore, 249 stable SNPs were detected by more than four GWAS models. According to these stable SNPs, RNA expression levels and gene annotations, four causal genes (Glyma.02G080200, Glyma.11G056200, Glyma.12G188900, and Glyma.18G110200) conferring soybean drought tolerance were detected, which participated in ethylene stimulus response, water deprivation response, and proteolysis. Discussion Collectively, 249 stable SNPs, 163 pleiotropic SNPs and four candidate genes identified in present study provided promising molecular resources and reliable foundation for drought resistance improvement and marker-assisted selective breeding in soybean.