Identification of QTNs and their candidate genes for flowering time and plant height in soybean using multi-locus genome-wide association studies

Flowering time (FT) and plant height (PH) are important agronomic traits in soybean. However, their genetic foundations are not fully understood. Thus, in this study, a total of 106,013 single nucleotide polymorphisms in 286 soybean accessions were used to associate with the first and full FT (FT1 and FT2) and PH in 4 environments and their BLUP values using 6 multi-locus genome-wide association study methods. As a result, 38, 43, and 27 stable quantitative trait nucleotides (QTNs) were identified, respectively, for FT1, FT2, and PH across at least 3 methods and/or environments. Among these QTNs for FT1, FT2, and PH, 31, 36, and 21 were found to have significant phenotype differences across 2 alleles; 22, 18, and 13 were consistent with the corresponding loci in previous studies; 13 and 8 genes, with more than average expression level, around 64 FT and 27 PH QTNs were predicted as their corresponding candidate genes. Among these candidate genes, GmPRR3b, and GmGIa for FT, and GmTFL1b for PH were known, while some were new, e.g., GmPHYA4, GmVRN5, GmFPA, and GmSPA1 for FT, and Glyma.02g300200, GmFPA, and Glyma.13g339800 for PH. All the validated QTNs were used to design the best cross-combinations in 2 FT directions. In each FT direction, the best 5 cross-combinations were predicted, such as Heihe 54 × Qincha 1 for early FT, and Yingdejiadou × Wuhuabayuehuang for late FT. This study provides solid foundations for genetic basis, molecular biology, and breeding by design of soybean FT and PH.