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Acta Agronomica Sinica ›› 2022, Vol. 48 ›› Issue (3): 635-643.doi: 10.3724/SP.J.1006.2022.14008


Identification of QTLs and candidate genes for 100-seed weight trait using PyBSASeq algorithm in soybean

WANG Juan1(), ZHANG Yan-Wei2, JIAO Zhu-Jin1, LIU Pan-Pan1, CHANG Wei1,*()   

  1. 1School of Life Science and Agricultural Engineering, Nanyang Normal University, Nanyang 473061, Henan, China
    2Crop Research Institute, Shandong Academy of Agricultural Sciences, Jinan 250100, Shandong, China
  • Received:2021-01-18 Accepted:2021-04-26 Online:2022-03-12 Published:2021-06-04
  • Contact: CHANG Wei E-mail:252576027@qq.com;weichang0@126.com
  • Supported by:
    Science and Technology Project of Henan Province(192102110125);Youth Foundation Project of Nanyang Normal University(QN2016003)


The PyBSASeq algorithm, based on quantifying the enrichment of likely trait-associated SNPs in a chromosomal interval, was proved more suitable for genetic analysis of complex quantitative traits in bulked segregant analysis. In this study, to identify the loci and candidate genes of 100-seed weight (SW) in soybean using the PyBSASeq algorithm, 149 RILs derived from the hybrid of ‘Huapidou’ and ‘Qihuang 26’ were used as materials. As a result, 11 candidate regions closely associated with SW were identified by mining the 100-grain weight related loci of soybean, which were located on chromosomes 1, 2, 4, 7, 9, 14, and 16, respectively. Among these regions, qSW4-1, qSW9-1, qSW9-2, and qSW7-1 were consistent with the QTLs for 100-seed weight reported previously, and a total of 218 coding genes were included in the candidate regions. Among these genes, Glyma.02G075000 and Glyma.04G082500 were predicted to be candidate genes using gene expressional and haplotype analysis. Bioinformatics analysis showed that the candidate genes were mainly involved in sugar transport and biosynthesis of Vitamin E. The results will be helpful to elucidate the genetic mechanism of seed weight regulation in soybean and provide a reference for the study of quantitative trait based on BSA-Seq method.

Key words: soybean, 100-seed weight, PyBSASeq, SLAF-Seq

Fig. 1

Distribution histogram for 100-seed weight of the RIL population and parents"

Table 1

Summary of sSNP related to 100-seed weight trait in soybean"

Numbers of QTLs
Total number of SNP
Range of P-value
1 9 57 15.79 1.16×10-4-6.71×10-3
2 7 408 1.72 3.07×10-3-5.99×10-3
4 33 233 14.16 1.57×10-3-9.36×10-3
7 41 163 25.15 9.51×10-4-8.03×10-3
9 8 136 5.88 1.45×10-3-8.13×10-3
14 73 170 42.94 9.29×10-5-8.74×10-3
16 10 239 4.18 6.71×10-4-8.46×10-3
总数Total 181 5110 3.54 9.29×10-5-9.36×10-3

Fig. 2

QTL mapping for 100-seed weight in soybean using PyBSASeq method"

Table 2

Summary of QTLs related to 100-seed weight trait in soybean"

QTL 染色体
Confidence interval (bp)
N_s/N_t 阈值
qSW1-1 1 3353593-4295069 0.80 0.20 Marker4145223/4003887 1.16×10-3
qSW2-1 2 6277409-6795574 0.46 0.15 Marker6292178/6353955 3.07×10-3
qSW4-1[39,40] 4 6745068-7489088 0.84 0.13 Marker6412385/6990477 1.57×10-3
qSW7-1[41,42,43] 7 7022337-13703737 1.00 0.33 Marker5915595/8069918 9.51×10-4
qSW7-2 7 36784876-38304878 1.00 0.10 Marker5871955/37004467 1.82×10-3
qSW9-1[13] 9 13567640-13932246 0.67 0.33 Marker4706727/13932246 1.45×10-3
qSW9-2[44,45,46] 9 44196936-44232803 0.60 0.20 Marker4584679/44196936 2.06×10-3
qSW9-3 9 47099980-47940126 1.00 0.33 Marker4755711/47109866 3.11×10-3
qSW14-1 14 8672359-12688053 1.00 0.09 Marker5172395/11147027 2.93×10-4
qSW14-2 14 41729998-42423216 1.00 0.13 Marker5029131/41946443 9.29×10-5
qSW16-1 16 33408123-35629720 0.83 0.17 Marker3332493/33871753 6.71×10-4

Fig. 3

Relative expression profiling of candidate genes for 100-seed weight trait during seed development period in soybean Underline gene: the candidate gene for 100-seed weight of soybean. DAF: days after flowering."

Table 3

Summary of candidate genes for 100-seed weight trait in soybean"

QTL 基因
qSW2-1 Glyma.02G073200 Chr02:6399972..6405250 α-1,4-岩藻糖基转移酶 Alpha-1,4-fucosyltransferase
qSW2-1 Glyma.02G075000 Chr02:6535991..6539362 蔗糖转运蛋白(SUT1) Sugar transport protein (SUT1)
qSW4-1 Glyma.04G082300 Chr04:6945685..6946469 维生素E生物合成(生育酚环化酶)Vitamin E biosynthesis (tocopherols)
qSW4-1 Glyma.04G082500 Chr04:6948445..6954177 维生素E生物合成(生育酚环化酶)Vitamin E biosynthesis (tocopherols)
qSW7-2 Glyma.07G200700 Chr07:36897410..36898244 HSP20家族蛋白 HSP20 family protein
qSW9-2 Glyma.09G249500 Chr09:47056885..47062577 羧肽酶C Carboxypeptidase C
qSW14-1 Glyma.14G101900 Chr14:10079123..10080100 ncRNA
qSW14-2 Glyma.14G170900 Chr14:42298358..42306613 β-D-木糖苷酶7相关 β-D-xylosidase 7-related
qSW16-1 Glyma.16G176000 Chr16:33732712..33735090 葡萄糖基/葡萄糖醛基转移酶Glucosyl/glucuronosyl transferases

Fig. 4

Haplotype analysis of candidate genes for 100-seed weight trait in soybean"

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