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作物学报 ›› 2022, Vol. 48 ›› Issue (3): 635-643.doi: 10.3724/SP.J.1006.2022.14008

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

利用PyBSASeq算法挖掘大豆百粒重相关位点与候选基因

王娟1(), 张彦威2, 焦铸锦1, 刘盼盼1, 常玮1,*()   

  1. 1南阳师范学院生命科学与农业工程学院, 河南南阳 473061
    2山东省农业科学院作物研究所, 山东济南 250100
  • 收稿日期:2021-01-18 接受日期:2021-04-26 出版日期:2022-03-12 网络出版日期:2021-06-04
  • 通讯作者: 常玮
  • 作者简介:E-mail: 252576027@qq.com
  • 基金资助:
    河南省科技攻关项目(192102110125);南阳师范学院青年基金项目(QN2016003)

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 Published:2022-03-12 Published online:2021-06-04
  • Contact: CHANG Wei
  • Supported by:
    Science and Technology Project of Henan Province(192102110125);Youth Foundation Project of Nanyang Normal University(QN2016003)

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摘要：

基于量化染色体区间上与目标性状相关多态性位点的富集程度这一原理开发的PyBSASeq算法, 被证实更适合进行基于BSA-seq技术的复杂数量性状遗传解析。本研究采用该算法, 以‘滑皮豆’和‘齐黄26’为亲本杂交所衍生的包含149个RILs为材料, 挖掘与大豆百粒重相关位点, 共获得11个与目标性状紧密关联的候选区域, 分别位于1号、2号、4号、7号、9号、14号和16号染色体, 其中qSW4-1、qSW9-1、qSW9-2和qSW7-1与已报道大豆百粒重QTL位置一致。候选区域共包含218个编码基因, 根据基因表达特性和单倍型分析结果, 最终获得2个与目标性状相关的候选基因Glyma.02G075000和Glyma.04G082500, 分别参与蔗糖的运输和维生素E的生物合成。研究结果将有助于大豆百粒重遗传机制的阐释, 并为基于BSA-Seq技术的数量性状研究提供参考。

关键词: 大豆, 百粒重, PyBSASeq, SLAF-Seq

Abstract:

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

图1

RIL群体及亲本百粒重分布直方图"

表1

大豆百粒重相关sSNP汇总表"

染色体
Chromosome		 QTL数量
Numbers of QTLs		 SNP总数
Total number of SNP		 QTL/SNP
(%)		 P值范围
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

图2

基于PyBSASeq算法定位的大豆百粒重相关QTL位点"

表2

大豆百粒重相关QTL位点汇总"

QTL 染色体
Chromosome		 置信区间
Confidence interval (bp)		 N_s/N_t 阈值
Threshold		 标记/位置
Marker/position		 P值
P-value
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

图3

种子发育不同时期大豆百粒重相关候选基因特异性表达结果 带有下画线的基因: 大豆百粒重候选基因。DAF: 开花后天数。"

表3

大豆百粒重相关候选基因汇总表"

QTL 基因
Gene		 位置
Position		 功能注释
Annotation
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

图4

候选基因单倍型分析 *, P < 0.05; **, P < 0.01"

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