Seed size and shape are important characteristics in soybean breeding, whereas the genetic basis are still unknown, which constrains the improvement of related traits. In view of this, one recombinant inbred line population was assessed for six related traits under four environments. In total, 10 QTLs controlling the related traits were identified, and five were detected across at least two environments, which located on chromosomes 2, 4, 6, 13, and 16 with phenotypic variation explained (PVE) 3.6% to 9.4%. Among them, qSS-02 and qSS-16 were identified to control four and five related traits with pleiotropic effects on chromosomes 2 and 16 across three and two environments, respectively. Meanwhile, qSS-04 was detected to control all of the six related traits on chromosome 4 under four environments with PVEs 4.5% to 9.4%. Furthermore, the candidate genes, that is, Glyma.04G055100 (big grain protein) and Glyma.13G068500 (cytochrome P450), were screened out for their different expressions between population parents at different seed growth and developmental stages. Thus, these results could provide novel insights for the genetic basis of seed size and shape in soybean.

Soybean provides irreplaceable protein and oil. Pods and seeds are essential soybean harvested organs. To illustrate the genetic basis of pod‐ and seed‐related traits, a natural population was assessed for eight related traits under four environments. In all, 15 associated SNPs were identified across multiple environments or controlling various traits, and 11 were verified through BLUP. Two SNPs on chromosome 15 were associated with six traits across multiple environments. Two SNPs on chromosome 2 were also associated with six traits under multiple environments. Significant phenotype differences between favourable and unfavourable alleles/haplotypes under four environments were detected. Significant association of pod length SNP and large‐pod phenotype (pod length ≥4.5 cm) was detected. The genetic basis of elite germplasms was analysed, and ‘Chuxiu’ possessed all of the 15 favourable alleles with best phenotype. Some candidate genes participating in cell wall structural remodelling, gibberellin and ethylene pathways were selected with different expressions in pod developmental stages. These results provided novel insights into genetic basis and molecular markers/candidate genes for soybean fresh pod and seed genetic improvement.

Seed coat cracking (SCC) is a major factor that affects seed appearance quality, pathogen infection, humility absorption and seed storage in soybean. In view of this, a recombinant inbred line (RIL) population and a natural population were genotyped by SoySNP6K and were evaluated for type-I SCC percentage. Eight QTLs were identified on six chromosomes with phenotypic variation explanations ranging from 3.46% to 34.71% in RIL population. Twenty-three SNPs associated with cracking percentage were identified on eight chromosomes in natural population. More importantly, the association SNP ss715593768 in natural population was the left marker of qSCC-C2-1 in RIL population, which were detected across all of the environments and BLUP values. Two genes, Glyma.06G197300 and Glyma.06G202100, were proposed in this QTL region. These two genes showed differential expressions at seed developmental stages between RIL parents in the seed transcriptome sequencing and quantitative reverse transcription-polymerase chain reaction (qRT-PCR) analysis, and also showed differential expressions between two germplasms with different cracking percentage in natural population. Thus, the results provide novel insight into the genetic basis and molecular improvement of SCC in soybean.

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