Plant height (PH) and the number of nodes on the main stem (NN) serve as major plant architecture traits affecting soybean seed yield. Although many quantitative trait loci for the two traits have been reported, their genetic controls at different developmental stages in soybeans remain unclear. Here, 368 soybean breeding lines were genotyped using 62,423 single nucleotide polymorphism (SNP) markers and phenotyped for the two traits at three different developmental stages over two locations in order to identify their quantitative trait nucleotides (QTNs) using compressed mixed linear model (CMLM) and multi-locus random-SNP-effect mixed linear model (mrMLM) approaches. As a result, 11 and 13 QTNs were found by CMLM to be associated with PH and NN, respectively. Among these QTNs, 8, 3, and 4 for PH and 6, 6, and 8 for NN were found at the three stages, and 3 and 6 were repeatedly detected for PH and NN. In addition, 34 and 30 QTNs were found by mrMLM to be associated with PH and NN, respectively. Among these QTNs, 11, 13, and 16 for PH and 11, 15, and 8 for NN were found at the three stages. A majority of these QTNs overlapped with the previously reported loci. Moreover, one QTN within the known E2 locus for flowering time was detected for the two traits at all three stages, and another that overlapped with the Dt1 locus for stem growth habit was also identified for the two traits at the mature stage. This may explain the highly significant correlation between the two traits. Our findings provide evidence for mixed major plus polygenes inheritance for dynamic traits and an extended understanding of their genetic architecture for molecular dissection and breeding utilization in soybeans.

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The colour of plant organs is a useful trait in crop breeding. The pod colours of soybeans primarily include black, brown and tan types, which are controlled by two classical genetic loci, L1 and L2. Most wild soybeans have black pods, which reflect a possible role in adaptation to the natural environment. Here, an improved chromosome segment substitution line (CSSL) population SojaCSSLP3 was established to identify the L1 gene. The segment on the 19th chromosome represented by the SSR marker Satt313 was found to link with locus L1. The region was further delimited three times with increased SSR and InDel markers using a population derived from a heterozygous plant of CSSL124 from SojaCSSLP3. The L1 gene was finally located in a 184.43-kb region between SSR_19p09 and Indel_19P7. Thirteen putative genes in this region were analysed with qRT-PCR. The expression level of Glyma19 g27460, which is a member of the SANT superfamily with a MYB DNA-binding domain, was significantly upregulated in black pods and was recognized to be the most likely candidate for the L1 gene.