Yandang Liu

Background: Copper transporters (COPTs) are essential for maintaining copper homeostasis in plants, a process critical for growth, development, and stress adaptation. However, the soybean GmCOPT family remains poorly characterized. Methods: In this study, we performed a genome-wide identification of COPT genes in soybean (Glycine max), conducted phylogenetic, collinearity, and evolutionary analyses, predicted protein motifs, structures, and promoter cis-regulatory elements, and analyzed the expression profiles of the GmCOPT family. Results: We identified ten GmCOPT genes. Phylogenetic analysis of COPT proteins across five plant species revealed that soybean COPTs are more closely related to those from Medicago truncatula. Collinearity analysis suggested that segmental duplication is the primary driver of GmCOPT family expansion, and all duplicated gene pairs exhibited Ka/Ks ratios below 1, indicating purifying selection. Expression profiling revealed tissue-preferential patterns among GmCOPT genes. The presence of ABRE, MBS, and LTR cis-acting regulatory elements in the promoter regions of GmCOPTs suggests their potential involvement in abiotic stress responses. RT-qPCR validation demonstrated that GmCOPT genes responded differentially to salt stress in soybean roots and leaves, with some significantly repressed and others markedly induced. Notably, GmCOPT7 and GmCOPT8 were significantly induced in both tissues in response to salt stress. Conclusions: These findings suggest that GmCOPT genes have undergone duplication-driven expansion and functional diversification, with different expression patterns and salt-inducible responses. This work provides candidate genes for future functional investigations into the roles of GmCOPT genes in abiotic stress tolerance in soybean.

First pod height (FPH) is a critical agronomic trait in soybean because it directly affects mechanized harvesting efficiency and harvestable yield. Pods below the cutter-bar height are left uncollected, leading to direct seed loss. However, the genetic architecture underlying FPH remains largely underexplored. Here, we conducted a genome-wide association study (GWAS) on FPH data using 386 soybean accessions evaluated across three environments, together with best linear unbiased prediction (BLUP) values. Phenotypic analysis showed that cultivated soybean exhibited significantly greater FPH than wild accessions, consistent with selection for improved harvestability during domestication. Using two GWAS methods, RTM-GWAS and EMMAX, we identified seven stable (detected by the same method at least three times) quantitative trait nucleotides/loci (QTNs/QTLs) significantly associated with FPH. By integrating sequence variation, gene expression, and functional description, we identified GmAIR9 (corresponding to Glyma.09G084300/SoyZH13_09G078900), which encodes a microtubule-associated protein preferentially expressed in stems, as a candidate gene for further investigation. Haplotype analysis of GmAIR9 revealed that haplotype H3 was associated with low FPH and was detected exclusively in wild soybean accessions, whereas haplotype H1 was associated with increased FPH. Moreover, the frequency of H1 increased from 50.00% in wild soybeans to 71.03% in landraces and 83.47% in improved cultivars. These findings provide valuable genetic resources and promising candidate loci for future validation and breeding applications to optimize FPH and improve the suitability of soybean cultivars for mechanized harvesting.