Seed-flooding stress is one of the major abiotic constraints severely affecting soybean yield and quality. Understanding the molecular mechanism and genetic basis underlying seed-flooding tolerance will be of greatly importance in soybean breeding. However, very limited information is available about the genetic basis of seed-flooding tolerance in soybean. The present study performed Genome-Wide Association Study (GWAS) to identify the quantitative trait nucleotides (QTNs) associated with three seed-flooding tolerance related traits, viz., germination rate (GR), normal seedling rate (NSR) and electric conductivity (EC), using a panel of 347 soybean lines and the genotypic data of 60,109 SNPs with MAF > 0.05. A total of 25 and 21 QTNs associated with all three traits were identified via mixed linear model (MLM) and multi-locus random-SNP-effect mixed linear model (mrMLM) in three different environments (JP14, HY15, and Combined). Among these QTNs, three major QTNs, viz., QTN13, qNSR-10 and qEC-7-2, were identified through both methods MLM and mrMLM. Interestingly, QTN13 located on Chr.13 has been consistently identified to be associated with all three studied traits in both methods and multiple environments. Within the 1.0 Mb physical interval surrounding the QTN13, nine candidate genes were screened for their involvement in seed-flooding tolerance based on gene annotation information and available literature. Based on the qRT-PCR and sequence analysis, only one gene designated as GmSFT (Glyma.13g248000) displayed significantly higher expression level in all tolerant genotypes compared to sensitive ones under flooding treatment, as well as revealed nonsynonymous mutation in tolerant genotypes, leading to amino acid change in the protein. Additionally, subcellular localization showed that GmSFT was localized in the nucleus and cell membrane. Hence, GmSFT was considered as the most likely candidate gene for seed-flooding tolerance in soybean. In conclusion, the findings of the present study not only increase our knowledge of the genetic control of seed-flooding tolerance in soybean, but will also be of great utility in marker-assisted selection and gene cloning to elucidate the mechanisms of seed-flooding tolerance.

Bacterial leaf pustule (BLP), caused by Xanthornonas axonopodis pv. glycines (Xag), is a worldwide disease of soybean, particularly in warm and humid regions. To date, little is known about the underlying molecular mechanisms of BLP resistance. The only single recessive resistance gene rxp has not been functionally identified yet, even though the genotypes carrying the gene have been widely used for BLP resistance breeding. Using a linkage mapping in a recombinant inbred line (RIL) population against the Xag strain Chinese C5, we identified that quantitative trait locus (QTL) qrxp–17–2 accounted for 74.33% of the total phenotypic variations. We also identified two minor QTLs, qrxp–05–1 and qrxp–17–1, that accounted for 7.26% and 22.26% of the total phenotypic variations, respectively, for the first time. Using a genome-wide association study (GWAS) in 476 cultivars of a soybean breeding germplasm population, we identified a total of 38 quantitative trait nucleotides (QTNs) on chromosomes (Chr) 5, 7, 8, 9,15, 17, 19, and 20 under artificial infection with C5, and 34 QTNs on Chr 4, 5, 6, 9, 13, 16, 17, 18, and 20 under natural morbidity condition. Taken together, three QTLs and 11 stable QTNs were detected in both linkage mapping and GWAS analysis, and located in three genomic regions with the major genomic region containing qrxp_17_2. Real-time RT-PCR analysis of the relative expression levels of five potential candidate genes in the resistant soybean cultivar W82 following Xag treatment showed that of Glyma.17G086300, which is located in qrxp–17–2, significantly increased in W82 at 24 and 72 h post-inoculation (hpi) when compared to that in the susceptible cultivar Jack. These results indicate that Glyma.17G086300 is a potential candidate gene for rxp and the QTLs and QTNs identified in this study will be useful for marker development for the breeding of Xag-resistant soybean cultivars.

Ubiquitin/proteasome-mediated proteolysis (UPP) plays a crucial role in almost all aspects of plant growth and development, proteasome subunit RPN10 mediates ubiquitination substrate recognition in the UPP process. The recognition pathway of ubiquitinated UPP substrate is different in different species, which indicates that the mechanism and function of RPN10 are different in different species. However, the homologous ZmRPN10 in maize has not been studied. In this study, the changing of leaf angle and gene expression in leaves in maize wild-type B73 and mutant rpn10 under exogenous brassinosteroids (BRs) were investigated. The regulation effect of BR on the leaf angle of rpn10 was significantly stronger than that of B73. Transcriptome analysis showed that among the differentially expressed genes, CRE1, A-ARR and SnRK2 were significantly up-regulated, and PP2C, BRI1 AUX/IAA, JAZ and MYC2 were significantly down-regulated. This study revealed the regulation mechanism of ZmRPN10 on maize leaf angle and provided a promising gene resource for maize breeding.

Mulching practices have demonstrated the potential to increase crop yields and resource utilization efficiency. However, the response of different crops with various growth stages to different mulching practices remains unclear, particularly in the rainfed agroecosystem. Therefore, a two-year field experiment (2013–2015) of different crops (wheat, maize, and potato) was conducted to evaluate the effects of three different mulching treatments: straw strip mulching (SM), plastic film mulching (PM), and conventional planting without mulching as the control (CK), on soil moisture and temperature, evapotranspiration (ET), water use efficiency (WUE), crop yield and economic benefits on the Loess Plateau. The results indicated that both mulching practices significantly increased the soil water content (SM: 4.3% and PM: 3.6%) compared to CK. However, the effects on soil temperature varied between mulching practices, PM increased soil temperature by 4.9% compared to CK, while SM decreased it by 6.3%. The improved soil hydrothermal conditions, characterized by favorable temperatures and higher soil water status would lead to a higher crop daily growth rate (5.3–49.8%), as well as greater dry matter accumulation (4.7–36.7%). Furthermore, mulching practice (SM and PM) has a significant influence on crop yield and its components of various crops, as well as WUE. The mean grain yield of SM and PM was, respectively, increased by 11.4% and 27.1% for winter wheat, compared to CK, 1.8% and 24.3% for spring maize, and 23.0% and 13.9% for potato, respectively. Compared to CK, PM yielded a higher net economic benefit and WUE for winter wheat and spring maize, while SM presented the best economic benefit and WUE for potato. In conclusion, a comprehensive analysis of crop yield, economic benefits, and resource utilization efficiency suggests that straw strip mulching for potato is a more sustainable environmentally friendly mulching practice, recommended for rainfed farming systems on the Loess Plateau and areas with similar climatic conditions.

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.

Soybean pod-related traits are important for seed development, yield formation, and cultivar evaluation. However, conventional measurements are inefficient and have limited ability to characterize complex pod features such as curvature, local enlargement, and continuous color variation. In this study, mature pod images of 187 cultivated soybean accessions collected across two successive years were analyzed using a deep learning-assisted image phenotyping approach. Eight pod-related traits related to size, morphology, and color were extracted from pod images. A genome-wide association study (GWAS) was performed using 61,541 high-quality SNP markers to dissect the genetic basis of these image-derived pod traits. A total of 16 stable loci associated with pod size, morphology, and color traits were identified across 11 chromosomes. Among these loci, eight were not reported in the previous image-based soybean pod GWAS study. Based on SoyBase gene annotation and Gene Ontology biological process information, 32 biologically relevant candidate gene records were prioritized within the corresponding candidate genomic intervals, while pod-related expression profiles and SoyBase association information were used as supporting evidence for candidate gene evaluation. These findings indicate that refined image-derived traits can provide complementary genetic information beyond conventional pod measurements and offer additional opportunities for dissecting soybean pod development, morphology, and mature pod color variation.