Soybean is a globally important legume crop that provides a primary source of high-quality vegetable protein and oil. Seed protein and oil content are two valuable quality traits controlled by multiple genes in soybean. In this study, the restricted two-stage multi-locus genome-wide association analysis (RTM-GWAS) procedure was performed to dissect the genetic architecture of seed protein and oil content in a diverse panel of 279 soybean accessions from the Yangtze and Huaihe River Valleys in China. We identified 26 quantitative trait loci (QTLs) for seed protein content and 23 for seed oil content, including five associated with both traits. Among these, 39 QTLs corresponded to previously reported QTLs, whereas 10 loci were novel. As reported previously, the QTL on chromosome 20 was associated with both seed protein and oil content. This QTL exhibited opposing effects on these traits and contributed the most to phenotype variation. From the detected QTLs, 55 and 51 candidate genes were identified for seed protein and oil content, respectively. Among these genes, eight may be promising candidate genes for improving soybean nutritional quality. These results will facilitate marker-assisted selective breeding for soybean protein and oil content traits.

Plant photosynthesis is mainly dependent on leaf color, and this has an impact on yield. Mutants lacking in chlorophyll have been analyzed to gain insight into the genetic processes involved in photosynthesis, chloroplast development, and chlorophyll metabolism. A yellow-to-lethal mutant, ytl, was selected from the M₆ generation of the ⁶⁰Coγ ray irradiation-treated soybean cultivar Nannong 1138-2. The mutant exhibited reduced chlorophyll content, with the thylakoid structure disrupted. Segregation of the cross between Williams 82 (W82) and ytl indicated that a recessive allele controlled yellow-to-lethal traits. The bulked-segregant analysis (BSA)-Seq method performed preliminary mapping, followed by simple sequence repeat (SSR) marker validation and further mapping. The candidate gene was mapped to a 418 Kb region containing 53 genes. High-throughput sequencing and first-generation sequencing results showed a two bp deletion in the second exon of Glyma.08g106500, leading to a frameshift mutation in ytl. As a promising candidate gene, Glyma.08g106500 encoded a chloroplast-localized pentatricopeptide repeat (PPR) domain-containing protein involved in the assembly of chloroplast proteins. These results will contribute to cloning the mutant ytl gene and provide insight into the regulatory processes controlling photosynthesis and chloroplast development and growth in soybean.

Deciphering the genetic basis underlying agronomic traits is of importance for soybean improvement. However, covariation, modulated by genetic correlations between complicated traits via hub QTLs, commonly affects the efficiency and accuracy of soybean improvement. The goals of soybean improvement have nearly all focused on agronomic traits, including yield, plant type traits, and seed-related traits especially. To decipher the hub QTLs of yield, plant type, and seed, nine pertinent traits of an F₂ population (181 plants) derived from a cross between KeXin No.03 and JiDou 17, which were different in multiple traits such as plant height, seed protein, and 100-seed weight, were investigated with a high-density genetic map covering 2708.63 cM. A highly significant negative phenotypic correlation (−0.95) was found between seed protein (Pro) and seed oil (Oil). A total of 35 final QTLs after combining the ones closely linked physically were identified for eight traits explaining from 0.10% to 24.63% of the phenotypic variance explained (PVE) using composite interval mapping (CIM) and inclusive composite interval mapping (ICIM) procedures, and 13 QTLs were novel genes. A genomic region on chromosome 14 (qPro14, qOil14.2, and qSw14) was associated with three seed-related traits based on the relationship within and among the three trait modules. In addition, four genomic regions were detected as hub QTLs which linked to the seed-related module and plant-type model, including the E loci (E1 and E2). From the QTL results, 31 candidate genes were annotated, including the verified genes E1, E2, and QNE1, and they were grouped into three categories of biological processes. These results illustrate the genetic architecture as correlations among various soybean traits, and the hub QTLs should provide insights into the genetic improvement of complex traits in soybean.

As an important branch of the lipoxygenase (LOX) metabolism pathway, hydroperoxide lyase (HPL) is involved in regulating plant development and defense responses. However, the upstream regulatory mechanism of HPL remains unclear in soybean. In the present study, by analyzing the upstream promoter region of the GmHPL gene, cis-elements such as MYB motifs, G-box motifs, ERE motifs and W-box motifs were predicted, which were related to the stress response. Yeast one-hybrid was employed and two transcription factors were identified, GmERF36 and GmILR3. The orthologs of ERF36 and ILR3 in Arabidopsis were involved in pathogen stress. A dual-luciferase reporter assay verified the yeast one-hybrid results and indicated that GmERF36 and GmILR3 suppressed the expression of the GmHPL protein. The qRT-PCR results indicated that GmHPL and GmERF36 initially displayed inverse expression patterns within 24 h after Colletotrichum truncatum treatment (GmERF36 was upregulated while GmHPL was downregulated); then, both of them were upregulated before decreasing. The results indicated that the response of GmHPL to pathogen stress partially depended on GmERF36. Our study gives rise to new insights into the upstream regulatory network of the GmHPL gene.

Seed oil content is one of the primary breeding objectives in soybean. However, the genetic basis of seed oil content remains largely unexplored. In this study, we employed a recombinant inbred line (RIL) population consisting of 201 lines derived from a cross between Feidong and Guanyun, to identify quantitative trait loci (QTLs) for seed oil content in soybean under five environments. High broad-sense heritability (92.34%) indicates a substantial genetic contribution to phenotypic variation in this population and set of environments. A high-density genetic map containing 11,220 SNP markers was constructed, spanning 2507.62 cM, with an average distance of 0.22 cM between markers. By jointly using five QTL mapping methods, a total of 24 QTLs for seed oil content were identified, including eight stable QTLs detected in at least three environments and seven QTLs identified by all five methods. Out of these QTLs, qOil-5-4, qOil-9-2 and qOil-10-3 were considered as the major and stable QTLs. Within these three major and stable QTL intervals, except that Glyma.05g244100 (GmMFT/GmST05) is an experimentally validated gene, the other six genes that were highly expressed during seed development stages were identified as putative candidate genes requiring further validation. In conclusion, the major stable QTLs and candidate genes identified in this study facilitate the dissection of the genetic architecture underlying seed oil content and hold great potential for application in developing new high-oil soybean cultivars after further fine mapping and validation in independent genetic backgrounds.