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

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Abstract

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.

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Acknowledgements

We thank Mr. Hanwen Zhang (hywenzhang@henceedu.com) at Hence Education Ltd., Vancouver, Canada, for improving the language within the manuscript.

Funding

This work was supported by National Natural Science Foundation of China (32070557 and 31871242), and Huazhong Agricultural University Scientific & Technological Self-Innovation Foundation (2014RC020).

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Authors and Affiliations

  1. Crop Information Center, College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070, China

    Xu Han, Zhuo-Ran Xu, Chun-Yu Han & Yuan-Ming Zhang

  2. Institute of Crop Germplasm and Biotechnology, Jiangsu Academy of Agricultural Sciences, Nanjing, 210014, China

    Ling Zhou

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Contributions

YMZ designed this experiment. XH, ZRX, LZ, and CYH performed field experiments and real data analysis. XH wrote the draft, and YMZ and XH revised the manuscript. All authors reviewed the manuscript.

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Correspondence to Yuan-Ming Zhang.

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Supplementary Information

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Supplementary Figure 1.

Frequency distributions for first (a) and full (b) flowering time and plant height (c) in 286 soybean accessions. NJ: Nanjing; WH: Wuhan; EZ: Ezhou. 2011 in NJ2011 indicates year. Mean ± standard deviation is showed. (PDF 2205 KB)

Supplementary Figure 2.

Validation of QTNs for first flowering time using phenotypic differences between elite and alternative alleles of each QTN. These QTNs include MM7502, MM15510, MM19192, MM25031, MM25114, MM25599, MM28606, MM30687, MM33259, MM46206, MM47999, MM48293, MM51539, MM51663, MM53568, MM53674, MM54137, MM55040, MM56754, MM57775, MM57851, MM58369, MM65212, MM67058, MM82865, MM85086, MM87394, MM92726, MM92745, MM93630, and MM102840. Error bar represents standard deviation. E1: Nanjing (2011); E2: Nanjing (2012); E5: Ezhou (2017); E6: Wuhan (2017). (PDF 525 KB)

Supplementary Figure 3.

Validation of QTNs for full flowering time using phenotypic differences between elite and alternative alleles of each QTN. These QTNs include MM5544, MM7502, MM9632, MM12021, MM14978, MM16560, MM19352, MM19374, MM20918, MM25114, MM25129, MM27076, MM32189, MM33259, MM35045, MM48293, MM51539, MM51663, MM53674, MM54137, MM55040, MM56090, MM57775, MM62301, MM62964, MM65212, MM67680, MM71416, MM72971, MM82865, MM86837, MM87394, MM92726, MM92745, MM93630, and MM99199. Error bar represents standard deviation. E1: Nanjing (2011); E2: Nanjing (2012); E5: Ezhou (2017); E6: Wuhan (2017). (PDF 537 KB)

Supplementary Figure 4.

Validation of QTNs for plant height using phenotypic differences between elite and alternative alleles of each QTN. These QTNs include MM93, MM10723, MM12824, MM14428, MM30756, MM37383, MM41287, MM45845, MM45847, MM54781, MM56083, MM63977, MM65389, MM66997, MM68942, MM77907, MM89741, MM89777, MM90929, MM95579, and MM95591. Error bar represents standard deviation. E3: Wuhan (2014); E4: Wuhan (2015); E5: Ezhou (2017); E6: Wuhan (2017). (PDF 423 KB)

Supplementary Figure 5.

The expressional levels (FPKM) of potential candidate genes for flowering time (a) and plant height (b) in 9 soybean tissues. (PDF 1117 KB)

Supplementary file 6 (PDF 473 KB)

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Han, X., Xu, ZR., Zhou, L. et al. Identification of QTNs and their candidate genes for flowering time and plant height in soybean using multi-locus genome-wide association studies. Mol Breeding 41, 39 (2021). https://doi.org/10.1007/s11032-021-01230-3

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