Quantitative trait loci (QTLs) identified so far in soybean were mainly derived in the final stage of plant development, which did not apply to the exploitation of genetic effects that were expressed during a specific developmental stage. Thus, the aim of this study was to identify conditional QTLs associated with yield traits at a specific developmental interval of soybean plant. The 143 recombinant inbred lines developed from the cross of soybean cultivars 'Charleston' and 'Dongnong 594' were used for the developmental QTLs analysis of pod number in the main stem and plant height by composite interval mapping method combined with mixed genetic model. The results indicated that the number and type of QTLs and their genetic effects for the two agronomic traits were different in a series of measuring stages. A total of 10 unconditional QTLs in 6 linkage groups and 5 conditional QTLs in 3 linkage groups were identified for the pod number of the main stem, while 13 unconditional QTLs in 7 linkage groups and 12 conditional QTLs in 6 linkage groups were identified for plant height. Many QTLs that were detected in the early stages were different from those detected at the later stages. Some QTLs existed only at one stage and others existed across two or three stages. Five marker intervals (satt509-satt251, sat_099-sat_113, sat_113-OPAW19_4, satt457-OPC10_85, sat_095-OPBA08_5) were proven to be associated both with the development of pod number in the main stem and the development of plant height. The present study suggested that the development of pods and plant height in soybean were governed by time-dependent gene expression.

Pod number is an important factor that influences yield in soybean. Here, we used two associated recombinant inbred line (RIL) soybean populations, RIL3613 (containing 134 lines derived from Dongnong L13 × Heihe 36) and RIL6013 (composed of 156 individuals from Dongnong L13 × Henong 60), to identify quantitative trait loci (QTLs) regulating the vertical distribution and quantity of seeds and seed pods. The numbers of pods were quantified in the upper, middle, and lower sections of the plant, as well as in the plants as a whole, and QTLs regulating these spatial traits were mapped using an inclusive complete interval mapping method. A total of 21 and 26 QTLs controlling pod-number-related traits were detected in RIL3613 and RIL6013, respectively, which explained 1.25–11.6698% and 0.0001–7.91% of the phenotypic variation. A total of 34 QTLs were verified by comparison with previous research, were identified in both populations, or were found to regulate multiple traits, indicating their authenticity. These results enhance our understanding of the vertical distribution of pod-number-related traits and support molecular breeding for seed yield.

Hundred-seed weight (HSW) is an important measure of yield and a useful indicator to monitor the inheritance of quantitative traits affected by genotype and environmental conditions. To identify quantitative trait nucleotides (QTNs) and mine genes useful for breeding high-yielding and high-quality soybean ( Glycine max ) cultivars, we conducted a multilocus genome-wide association study (GWAS) on HSW of soybean based on phenotypic data from 20 different environments and genotypic data for 109,676 single-nucleotide polymorphisms (SNPs) in 144 four-way recombinant inbred lines. Using five multilocus GWAS methods, we identified 118 QTNs controlling HSW. Among these, 31 common QTNs were detected by various methods or across multiple environments. Pathway analysis identified three potential candidate genes associated with HSW in soybean. We used allele information to study the common QTNs in 20 large-seed and 20 small-seed lines and identified a higher percentage of superior alleles in the large-seed lines than in small-seed lines. These observations will contribute to construct the gene networks controlling HSW in soybean, which can improve the genetic understanding of HSW, and provide assistance for molecular breeding of soybean large-seed varieties.

Protein content (PC), an important trait in soybean (Glycine max) breeding, is controlled by multiple genes with relatively small effects. To identify the quantitative trait nucleotides (QTNs) controlling PC, we conducted a multi-locus genome-wide association study (GWAS) for PC in 144 four-way recombinant inbred lines (FW-RILs). All the FW-RILs were phenotyped for PC in 20 environments, including four locations over 4 years with different experimental treatments. Meanwhile, all the FW-RILs were genotyped using SoySNP660k BeadChip, producing genotype data for 109,676 non-redundant single-nucleotide polymorphisms. A total of 129 significant QTNs were identified by five multi-locus GWAS methods. Based on the 22 common QTNs detected by multiple GWAS methods or in multiple environments, pathway analysis identified 8 potential candidate genes that are likely to be involved in protein synthesis and metabolism in soybean seeds. Using superior allele information for 22 common QTNs in 22 elite and 7 inferior lines, we found higher superior allele percentages in the elite lines and lower percentages in the inferior lines. These findings will contribute to the discovery of the polygenic networks controlling PC in soybean, increase our understanding of the genetic foundation and regulation of PC, and be useful for molecular breeding of high-protein soybean varieties.

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