Summary: Stem lodging resistance plays a critical role in maintaining soybean yield stability, yet the molecular mechanisms governing stem development and lodging tolerance remain poorly understood. Here, we report the characterization of lodging‐related mutant 3 (lrm3), a weak‐stemmed soybean line exhibiting increased lodging susceptibility. Molecular cloning revealed that LRM3 encodes a U‐box E3 ubiquitin ligase that physically interacts with the transcription factor MYB6, targeting it for 26S proteasome‐mediated degradation. Transcriptomic and chromatin immunoprecipitation analyses demonstrated that MYB6 binds directly to the promoter regions of PHENYLALANINE AMMONIA‐LYASE (PAL) genes, repressing their transcriptional activity and consequently reducing lignin biosynthesis and secondary cell wall deposition in stems. Population genetic analysis identified three major LRM3 haplotypes, with Haplotype 1 preferentially retained in landraces and modern cultivars, suggesting artificial selection during domestication. Collectively, our findings elucidate a previously uncharacterized regulatory mechanism integrating ubiquitin‐mediated proteolysis and phenylpropanoid metabolism to enhance stem mechanical strength. This study provides novel genetic insights and molecular tools for improving lodging resistance in soybean breeding programs.

The UNUSUAL FLORAL ORGANS (UFO) gene is an essential regulatory factor of class B genes and plays a vital role in the process of inflorescence primordial and flower primordial development. We investigated the role of UFO genes in soybean to better understand the development of floral organs through gene cloning, expression analysis, and gene knockout. In situ hybridization demonstrated predominant expression of the GmUFO1 gene in the flower primordium. Phenotypic observation of GmUFO1 knockout mutant lines (Gmufo1) showed obvious alteration in floral organ number and shape, and mosaic organ formation. In contrast, GmUFO2 knockout mutant lines (Gmufo2) showed no obvious difference in floral organs. However, the GmUFO1 and GmUFO2 double knockout lines (Gmufo1ufo2) showed a more severe mutant phenotype than the Gmufo1 lines. Gene expression analysis also showed differences in the expression of major ABC function genes in the knockout lines. Based on the phenotypic and expression analysis, our results suggest the major role of GmUFO1 in the regulation of flower organ formation in soybean and that GmUFO2 does not have any direct effect, but it might have an interaction role with GmUFO1 in the regulation of flower development. In conclusion, the present study identified UFO genes in soybean and improved our understanding of floral development that could be useful for flower design in hybrid soybean breeding.

The UNUSUAL FLORAL ORGANS (UFO) gene is an essential regulatory factor of class B genes and plays a vital role in the process of inflorescence primordial and flower primordial development. The role of UFO genes in soybean was investigated to better understand the development of floral organs through gene cloning, expression analysis, and gene knockout. There are two copies of UFO genes in soybean and in situ hybridization, which have demonstrated similar expression patterns of the GmUFO1 and GmUFO2 genes in the flower primordium. The phenotypic observation of GmUFO1 knockout mutant lines (Gmufo1) showed an obvious alteration in the floral organ number and shape and mosaic organ formation. By contrast, GmUFO2 knockout mutant lines (Gmufo2) showed no obvious difference in the floral organs. However, the GmUFO1 and GmUFO2 double knockout lines (Gmufo1ufo2) showed more mosaic organs than the Gmufo1 lines, in addition to the alteration in the organ number and shape. Gene expression analysis also showed differences in the expression of major ABC function genes in the knockout lines. Based on the phenotypic and expression analysis, our results suggest the major role of GmUFO1 in the regulation of flower organ formation in soybeans and that GmUFO2 does not have any direct effect but might have an interaction role with GmUFO1 in the regulation of flower development. In conclusion, the present study identified UFO genes in soybean and improved our understanding of floral development, which could be useful for flower designs in hybrid soybean breeding.

Alkaline stress is one of the major abiotic constraints that limits plant growth and development. However, the genetic basis underlying alkaline tolerance in soybean [Glycine max (L.) Merr.] remains largely unexplored. In this study, an integrated genomic analysis approach was employed to elucidate the genetic architecture of alkaline tolerance in a diverse panel of 326 soybean cultivars. Through association mapping, we detected 28 single nucleotide polymorphisms (SNPs) significantly associated with alkaline tolerance. By examining the genomic distances around these significant SNPs, five genomic regions were characterized as stable quantitative trait loci (QTLs), which were designated as qAT1, qAT4, qAT14, qAT18, and qAT20. These QTLs are reported here for the first time in soybean. Seventeen putative candidate genes were identified within the physical intervals of these QTLs. Haplotype analysis indicated that four of these candidate genes exhibited significant allele variation associated with alkaline tolerance-related traits, and the haplotype alleles for these four genes varied in number from two to four. The findings of this study may have important implications for soybean breeding programs aimed at enhancing alkaline tolerance.

Alkaline stress is one of the major abiotic constraints limiting the plant growth and development. The alkaline tolerance in crop plants is a complex trait regulated by many genes. The genetic basis of alkaline tolerance is largely unknown in soybean. In this study, an integrated strategy of genomic analysis was utilized to elucidate the genetic architecture of alkaline tolerance across the panel of 326 diverse soybean cultivars. Our study revealed 28 SNPs was significantly associated with alkaline tolerance through association mapping using seven GWAS models. By considering the detection of SNPs in multiple environments and GWAS models, the genomic regions of five consistent SNPs were depicted as stable QTLs viz., qAT1, qAT4, qAT14, qAT18 and qAT20. All these five alkaline tolerance QTLs are reported for the first time. By using the in silico analysis, we detected 17 genes within physical intervals of five QTLs as putative candidates. Haplotype alleles of four candidate genes showed significant differences in the regulation of alkaline tolerance-related traits varying from two to four regulating alkaline tolerance from lowest to highest through moderate levels. The outcome of the current investigation can be used in soybean breeding programs for producing cultivars with enhanced alkaline tolerance.