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A biparental soybean population of 364 recombinant inbred lines (RILs) derived from Zhongdou 41 × ZYD 02.878 was used to identify quantitative trait loci (QTL) associated with hundred-seed weight (100-SW), pod length (PL), and pod width (PW). 100-SW, PL, and PW showed moderate correlations among one another, and 100-SW was correlated most strongly with PW (0.64–0.74). Respectively 74, 70, 75 and 19 QTL accounting for 38.7%–78.8% of total phenotypic variance were identified by inclusive composite interval mapping, restricted two-stage multi-locus genome-wide association analysis, 3 variance-component multi-locus random-SNP-effect mixed linear model analysis, and conditional genome-wide association analysis. Of these QTL, 189 were novel, and 24 were detected by multiple methods. Six loci were associated with 100-SW, PL, and PW and may be pleiotropic loci. A total of 284 candidate genes were identified in colocalizing QTL regions, including the verified gene Seed thickness 1 (ST1). Eleven genes with functions involved in pectin biosynthesis, phytohormone, ubiquitin-protein, and photosynthesis pathways were prioritized by examining single nucleotide polymorphism (SNP) variation, calculating genetic differentiation index, and inquiring gene expression. The prediction accuracies of genomic selection (GS) for 100-SW, PL, and PW based on single trait-associated markers reached 0.82, 0.76, and 0.86 respectively, but selection index (SI)-assisted GS strategy did not increase GS efficiency and inclusion of trait-associated markers as fixed effects reduced prediction accuracy. These results shed light on the genetic basis of 100-SW, PL, and PW and provide GS models for these traits with potential application in breeding programs.

Drought is one of the primary abiotic stress factors affecting the yield, growth, and development of soybeans. In extreme cases, drought can reduce yield by more than 50%. The seedling stage is an important determinant of soybean growth: the number and vigor of seedlings will affect growth and yield at harvest. Therefore, it is important to study the drought resistance of soybean seedlings. In this study, a recombinant inbred line (RIL) population comprising 234 F6:10 lines (derived from Zhonghuang 35 × Jindou 21) and a panel of 259 soybean accessions was subjected to drought conditions to identify the effects on phenotypic traits under these conditions. Using a genetic map constructed by single nucleotide polymorphism (SNPs) markers, 18 quantitative trait loci (QTL) on 7 soybean chromosomes were identified in two environments. This included 9 QTL clusters identified in the RIL population. Fifty-three QTL were identified in 19 soybean chromosomes by genome-wide association analysis (GWAS) in the panel of accessions, including 69 significant SNPs (−log10 (P) ≥ 3.97). A combination of the two populations revealed that two SNPs (−log10 (P) ≥ 3.0) fell within two of the QTL (qPH7-4 and qPH7-6) confidence intervals. We not only re-located several previously reported drought-resistance genes in soybean and other crops but also identified several non-synonymous stress-related mutation site differences between the two parents, involving Glyma.07g093000, Glyma.07g093200, Glyma.07g094100 and Glyma.07g094200. One previously unreported new gene related to drought stress, Glyma.07g094200, was found by regional association analysis. The significant SNP CHR7-17619 (G/T) was within an exon of the Glyma.07g094200 gene. In the RIL population, the DSP value of the “T” allele of CHR7-17619 was significantly (P

Drought stress is an important factor affecting soybean yield. Improving drought tolerance of soybean varieties can increase yield and yield stability when the stress occurs. Identifying QTL related to drought tolerance using molecular marker-assisted selection is able to facilitate the development of drought-tolerant soybean varieties. In this study, we used a high-yielding and drought-sensitive cultivar ‘Zhonghuang 35’ and a drought-tolerant cultivar ‘Jindou 21’ to establish F6:9 recombinant inbred lines. We constructed a high-density genetic map using specific locus amplified fragment sequencing (SLAF-Seq) technology. The genetic map contained 8078 SLAF markers distributing across 20 soybean chromosomes with a total genetic distance of 3780.98 cM and an average genetic distance of 0.59 cM between adjacent markers. Two treatments (irrigation and drought) were used in the field tests, the Additive-Inclusive Composite Interval Mapping (ICIM-ADD) was used to call QTL, and plant height and seed weight per plant were used as the indicators of drought tolerance. We identified a total of 23 QTL related to drought tolerance. Among them, seven QTL (qPH2, qPH6, qPH7, qPH17, qPH19-1, qPH19-2, and qPH19-3) on chromosomes 2, 6, 7, 17, and 19 were related to plant height, and five QTL (qSWPP2, qSWPP6, qSWPP13, qSWPP17, and qSWPP19) on chromosomes 2, 6, 13, 17, and 19 were related to seed weight and could be considered as the major QTL. In addition, three common QTL (qPH6/qSWPP6, qPH17/qSWPP17, and qPH19-3/qSWPP19) for both plant height and seed weight per plant were located in the same genomic regions on the same chromosomes. Three (qPH2, qPH17, and qPH19-2) and four novel QTL (qSWPP2, qSWPP13, qSWPP17, and qSWPP19) were identified for plant height and seed weight per plant, respectively. Two pairs of QTL (qPH2/qSWPP2 and qPH17/qSWPP17) were also common for both plant height and seed weight per plant. These QTL and closely linked SLAF markers could be used to accelerate breeding for drought tolerant cultivars via MAS.