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Vegetable soybeans are one of the most important vegetable types in East Asia. The yield of vegetable soybeans is considerably influenced by the size of their pods. To facilitate the understanding of the genetic basis of the pod length and width in vegetable soybeans, we conducted a genome-wide association study (GWAS) and transcriptome sequencing. Four quantitative trait loci, namely, qGPoL1, qGPoL2, qGPoW1, and qGPoW2, were mapped via GWAS analysis. Through the integration of gene function annotation, transcriptome sequencing, and expression pattern analysis, we identified Glyma.06G255000 and Glyma.13G007000 as the key determinants of the pod length and width in vegetable soybeans, respectively. Furthermore, two kompetitive allele-specific polymerase chain reaction (KASP) markers, namely, S06-42138365 (A/T) and S13_628331 (A/T), were developed and effectively validated in 27 vegetable soybean accessions. Overall, our research identified genes that regulate the pod length and width and determined KASP markers for molecular marker-assisted selection breeding. These findings have crucial implications for the improvement of soybean crops and can contribute to the development of efficient breeding strategies. [ABSTRACT FROM AUTHOR]

The determination of the soybean branch number plays a pivotal role in plant morphogenesis and yield components. This polygenic trait is subject to environmental influences, and despite its significance, the genetic mechanisms governing the soybean branching number remain incompletely understood. To unravel these mechanisms, we conducted a comprehensive investigation employing a genome-wide association study (GWAS) and bulked sample analysis (BSA). The GWAS revealed 18 SNPs associated with the soybean branch number, among which qGBN3 on chromosome 2 emerged as a consistently detected locus across two years, utilizing different models. In parallel, a BSA was executed using an F2 population derived from contrasting cultivars, Wandou35 (low branching number) and Ruidou1 (high branching number). The BSA results pinpointed a significant quantitative trait locus (QTL), designated as qBBN1, located on chromosome 2 by four distinct methods. Importantly, both the GWAS and BSA methods concurred in co-locating qGBN3 and qBBN1. In the co-located region, 15 candidate genes were identified. Through gene annotation and RT-qPCR analysis, we predicted that Glyma.02G125200 and Glyma.02G125600 are candidate genes regulating the soybean branch number. These findings significantly enhance our comprehension of the genetic intricacies regulating the branch number in soybeans, offering promising candidate genes and materials for subsequent investigations aimed at augmenting the soybean yield. This research represents a crucial step toward unlocking the full potential of soybean cultivation through targeted genetic interventions. [ABSTRACT FROM AUTHOR]

Iron is a crucial nutrient for biological functions in plants. High-pH and calcareous soil is a major stress causing iron deficiency chlorosis (IDC) symptoms and yield losses in crops. Use of calcareous soil-tolerance genetic resources is the most effective preventative method to combat the effects of high-pH and calcareous soils. A previous study using a mungbean recombinant inbred line (RIL) population of the cross Kamphaeg Saen 2 (KPS2; IDC susceptible) × NM-10–12 identified a major quantitative trait locus (QTL), qIDC3.1 , which controls resistance and explains more than 40% of IDC variation. In this study, we fine-mapped qIDC3.1 and identified an underlying candidate gene. A genome wide association analysis (GWAS) using 162 mungbean accessions identified single nucleotide polymorphisms (SNPs) on chromosome 6; several SNPs were associated with soil plant analysis development (SPAD) values and IDC visual scores of mungbeans planted on calcareous soil, respectively. These SNPs corresponded to qIDC3.1. Using the same RIL population as in the previous study and an advanced backcross population developed from KPS2 and IDC-resistant inbred line RIL82, qIDC3.1 was further confirmed and fine-mapped to an interval of 217 kilobases harboring five predicted genes, including LOC106764181 (VrYSL3), which encodes a yellow stripe1-like-3 (YSL3) protein, YSL3 is involved in iron deficiency resistance. Gene expression analysis revealed that VrYSL3 was highly expressed in mungbean roots. In calcareous soil, expression of VrYSL3 was significantly up-regulated, and it was more obviously upregulated in the roots of RIL82, than in those of KPS2. Sequence comparison of VrYSL3 between the RIL82 and KPS2 revealed four SNPs that result in amino acid changes in the VrYSL3 protein and a 20-bp insertion/deletion in the promoter where a cis-regulatory element resides. Transgenic Arabidopsis thaliana plants overexpressing VrYSL3 showed enhanced iron and zinc contents in the leaves. Taken together, these results indicate that VrYSL3 is a strong candidate gene responsible for calcareous soil resistance in mungbean. [Display omitted] • Fine mapping and GWAS suggested VrYSL3 controls resistance to iron-deficiency chlorosis in mungbean. • VrYSL3 sequence alignment revealed polymorphisms causing amino acid changes in VrYSL3 protein. • YSL3 is involved in iron acquisition by monocots. However, our finding suggests that YSL3 is also used by dicots. [ABSTRACT FROM AUTHOR]

• This study conducted GWAS on salt tolerance related traits in mungbean, and mined seven significant QTLs associated with survival rate under salt treatment. • The candidate gene VrFRO8 was evidenced by comparative genomics, transcriptome analysis and RT-qPCR analysis. The expression level of VrFRO8 , was significantly up-regulated after salt treatment compared with the control group. • We inferred the correlation between VrFRO8 , iron ion and SOD under salt stress. VrFRO8 might reduce SOD contents by influence Fe2+/Fe3+ ratio under the damage of salt stress. • 188 genes in the salt-stress signal transduction pathway were also identified in this study using the comparative genomics and transcriptomics analysis. Mungbean (Vigna radiata (L.) R. Wilczek) is an important legume crop of Asia. Salt concentrations typically causes major yield reductions in mungbean. Although the biochemical and genetic basis of salt tolerance-related gene are well studied in Arabidopsis and soybean, limited information concerning the salt tolerance-related genes in mungbean. To address this issue, we mined salt tolerance related genes using the survival rate trait and 160,1405 SNPs in 112 mungbean accessions. As a result, VrFRO8 significantly associated with salt-stress were identified in the GWAS analysis. The candidate gene VrFRO8 was evidenced by comparative genomics, transcriptome and RT-qPCR analysis. The expression level of VrFRO8 was significantly up-regulated (P-value = 0.001) after salt treatment compared with the control group. Moreover, 188 genes and 158 transcription factors related to salt-stress signal transduction pathway were mined, and 18 genes (18/188) had higher expression level in the salt-tolerant varieties than salt-sensitive varieties. And, the function of VrFRO8 was predicted in mungbean, the protein interaction between VrFRO8 and seven related-genes were found by molecular structure analysis. VrFRO8 might reduce SOD contents by influence Fe2+/Fe3+ ratio under the damage of salt stress. This study used multi-omics data to mine a key genes significantly associated with salt tolerance, and constructed a VrFRO8- related PPI network for salt tolerance, which would lay a solid foundation for further molecular biology research of VrFRO8 and mungbean breeding. [ABSTRACT FROM AUTHOR]