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Soybean [Glycine max (L.) Merr.] is widely planted in the world, and provides most of the plant protein and oil for humans. Fresh pod and seed are the basic harvested organs in vegetable soybean production, and are important characteristics in vegetable variety registration and product export. To dissect the genetic basis of fresh pod and seed, one RIL population was analyzed for eight related traits under four environments. Eight QTL clusters were detected on seven chromosomes with phenotypic variation explained (PVE) 5.28–17.30% under multiple environments or conferring diverse traits, and six were demonstrated by BLUP values. One pleiotropism QTL on chromosome 20 with PVEs 8.92–17.30% was linked with fresh pod weight, fresh seed weight, length and area under multiple environments, and was verified by BLUP values with PVEs 12.07–16.81%. Moreover, significant phenotype differences between favorable and unfavorable alleles demonstrated these linkage QTLs. The significant correlations of QTL markers for fresh pod length and large-pod phenotype (pod length ≥ 4.5 cm, the criterion for vegetable variety registration and product export) were identified, which provided selection markers for large-pod identification. Further analysis showed that the large-pod RIL parent “C813” possessed six favorable alleles of linked QTLs, and the elite line “L-63” possessed all of the eight favorable alleles, which presented the best phenotypes in the population. Based on these, the candidate genes were identified to present different expressions between RIL parents at different pod developmental-stages. Thus, these QTLs and candidate genes provided novel insights into the genetic basis for vegetable soybean fresh pod and seed in breeding program.

Soybean is a major oil crop in the world, and fatty acids are the predominant components for oil bio-synthesis and catabolism metabolisms and also are the most important energy resources for organisms. In view of this, two recombinant inbred line (RIL) populations (ZL-RIL and ZQ-RIL) and one natural population were evaluated for five individual seed fatty acid contents (palmitic acid, stearic acid, oleic acid, linoleic acid, and linolenic acid) under four different environments, simultaneously. In total, sixteen additive QTL clusters were identified in ZL-RIL population, and fifteen were stably expressed across multiple environments or had pleiotropic effects on various fatty acid contents. Furthermore, five and five of these 16 QTL clusters were verified in ZQ-RIL population and natural population, respectively. Among these consistent and stable QTL clusters, one QTL cluster controlling fatty acid on chromosome 5 with pleiotropic effect was identified under all of the environments in ZL-RIL and ZQ-RIL populations and also was validated in the natural population. Meanwhile, another stable QTL cluster was detected on chromosome 9 with pleiotropic effect under multiple environments in ZL-RIL population and was further verified by the natural population. More importantly, some causal genes, such as the genes on chromosome 9, involving in the fatty acid catabolism process were found in these stable QTL clusters, and some of them, such as Gm09G042000, Gm09G041500, and Gm09G047200 on chromosome 9, showed different expressions in ZL-RIL parents (Zheng92116 and Liaodou14) based on the transcriptome sequencing analysis at different seed developmental stages. Thus, the study results provided insights into the genetic basis and molecular markers for regulating seed fatty acid contents in soybean breeding program. SUPPLEMENTARY INFORMATION: The online version contains supplementary material available at 10.1007/s11032-021-01227-y.