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Soybean is one main source of dietary protein; therefore, improving protein content is an important objective in breeding programs. There is a significant negative correlation between protein and oil content, which influenced mapping quantitative trait locus (QTL) and quantitative trait nucleotides for these two traits. In this study, a linkage map was created with 2232 single-nucleotide polymorphism markers for the four-way recombinant inbred line (FW-RIL) population derived from the cross (Kenfeng 14 × Kenfeng 15) × (Heinong 48 × Kenfeng 19), and then conditional and unconditional QTL analyses were carried out by inclusive complete interval mapping based on the phenotypic data of protein and oil content collected in 10 different environments. As shown in the results of linkage analysis, a total of 85 QTL have been detected. We have performed association analysis using 109,676 markers after quality filtering for FW-RIL, and the results have shown that a total of 60 QTNs were detected. We have performed association analysis using 63,306 markers after quality filtering for resource population, and the results have shown that a total of 123 QTNs were detected. We have combined linkage and association analysis, and there are six QTNs verified by FW-RIL and resource population. We have performed pathway analysis on the genes in these six QTN attenuation regions, and the result shows that a total of four candidate genes are related to the synthesis or metabolism of soybean protein. These findings will facilitate marker-assisted selection and molecular breeding of soybean.

Plant height (PH) is an important trait in soybean, as taller plants may have higher yields but may also be at risk for lodging. Many genes act jointly to influence PH throughout development. To map the quantitative trait loci (QTL) controlling PH, we used the unconditional variable method (UVM) and conditional variable method (CVM) to analyze PH data for a four-way recombinant inbred line (FW-RIL) population derived from the cross of (Kenfeng14 × Kenfeng15) × (Heinong48 × Kenfeng19). We identified 7, 8, 16, 19, 15, 27, 17, 27, 22, and 24 QTL associated with PH at 10 developmental stages, respectively. These QTL mapped to 95 genomic regions. Among these QTL, 9 were detected using UVM and CVM, and 89 and 66 were only detected by UVM or CVM, respectively. In total, 36 QTL controlling PH were detected at multiple developmental stages and these made unequal contributions to genetic variation throughout development. Among 19 novel regions discovered in our study, 7 could explain over 10% of the phenotypic variation and contained only one single QTL. The unconditional and conditional QTL detected here could be used in molecular design breeding across the whole developmental procedure., Competing Interests: The authors have declared that no competing interests exist.

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.

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.