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作物学报 ›› 2023, Vol. 49 ›› Issue (4): 1006-1015.doi: 10.3724/SP.J.1006.2023.24055

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基于BSA-seq技术对豌豆花色基因的精细定位

严昕1,**(), 项超2,**(), 刘荣1, 李冠1, 李孟伟1, 李正丽3, 宗绪晓1,*(), 杨涛1,*()   

  1. 1中国农业科学院作物科学研究所, 北京 100081
    2四川省农业科学院作物研究所, 四川成都 610066
    3贵州省农业科学院园艺研究所, 贵州贵阳 550006
  • 收稿日期:2022-03-10 接受日期:2022-07-21 出版日期:2023-04-12 网络出版日期:2022-08-22
  • 通讯作者: *杨涛, E-mail: yangtao02@caas.cn;宗绪晓, E-mail: zongxuxiao@caas.cn
  • 作者简介:严昕, E-mail: yanxin5290@163.com;
    项超, E-mail: xc2011cib@163.com
    **同等贡献
  • 基金资助:
    国家作物种质资源库-食用豆资源整合与共享项目(NCGRC-2021-07);普查收集食用豆资源鉴定评价与繁殖编目入库项目(19210867);财政部和农业农村部国家现代农业产业技术体系建设专项(CARS-08-G11)

Fine mapping of flower colour gene in pea (Pisum sativum L.) based on BSA-seq technique

YAN Xin1,**(), XIANG Chao2,**(), LIU Rong1, LI Guan1, LI Meng-Wei1, LI Zheng-Li3, ZONG Xu-Xiao1,*(), YANG Tao1,*()   

  1. 1Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
    2Institute of Crop Sciences, Sichuan Academy of Agricultural Sciences, Chengdu 610066, Sichuan, China
    3Institute of Horticulture, Guizhou Academy of Agricultural Sciences, Guiyang 550006, Guizhou, China
  • Received:2022-03-10 Accepted:2022-07-21 Published:2023-04-12 Published online:2022-08-22
  • Contact: *E-mail: yangtao02@caas.cn;E-mail: zongxuxiao@caas.cn
  • About author:**Contributed equally to this work
  • Supported by:
    National Infrastructure for Crop Germplasm Resources Project from the Ministry of Science and Technology of China(NCGRC-2021-07);Project of Identification, Evaluation, Replication, and Preservation of Food Legumes Collected by the Survey and Collection Action on Crop Germplasm Resources(19210867);China Agriculture Research System of MOF and MARA(CARS-08-G11)

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摘要：

BSA-seq技术在挖掘农艺性状相关的新基因中已被广泛应用, 随着豌豆首个参考基因组问世, 将BSA-seq技术结合豌豆基因组的基因定位策略势在必行。本研究利用紫花亲本G0004562、白花亲本G0002930以及F2群体, 通过BSA-seq技术对豌豆花色基因进行初步定位, 获得31.42 Mb定位区间, 再通过设计InDel分子标记分析进一步缩小定位区间, 最终将目标基因定位在包含19个基因的0.99 Mb区间内, 通过基因注释信息推测出Psat6g060480.1为豌豆花色候选基因。本研究结果验证了BSA-seq技术快速高效定位豌豆花色基因的可行性, 为利用该技术挖掘豌豆其他重要农艺性状相关基因奠定了基础。

关键词: 豌豆, BSA-seq, InDel, 基因定位

Abstract:

In recent years, BSA-seq technology has been widely used in the mining of new genes related to agronomic traits. With the development of the first reference genome of pea, it is imperative to combine BSA-seq method with genome-wide sequencing for gene mapping. In this study, we used purple flower parent G0004562, white flower parent G0002930, and F2 populations for preliminarily locate the target genes controlling flower color by BSA-seq technology, and a mapping region of 31.42 Mb was obtained. Then, the InDel molecular markers were designed to further narrow the mapping interval, and finally the target gene was located in the range of 0.99 Mb with 19 genes. Based on gene annotation, Psat6g060480.1 was considered as the candidate gene that controled the flower color. The results of this study verified the feasibility of gene mapping by BSA-seq technology in pea.

Key words: pea, BSA-seq, InDel, gene mapping

表1

F2群体中不同花色的植株数目"

杂交组合
Combination		 紫花株数
No. of purple flower plant		 白花株数
No. of white flower plant		 期望值
Expectation ratio		 卡方值
χ2		 检验值
χ2(0.05,1)
G0004562×G0002930 941 321 3:1 0.13 3.84

表2

不同样品测序比对结果"

样品编号
Sample ID		 全部reads数
Total_reads		 与参考基因组比对
Mapped (%)		 平均覆盖深度
Ave_depth		 基因组覆盖度
Cov_ratio_1× (%)		 碱基数质量值大于30
Q30 (%)
R125 584,524,436 99.78 21 83.02 92.96
R127 558,380,728 99.64 20 79.03 93.28
R135 882,730,682 99.73 30 86.34 92.70
R138 880,248,082 99.75 30 86.58 92.94

图1

关联值在染色体上的分布(SNP) A: ED关联分析结果。横坐标为染色体的分布, 每个点代表SNP位点的ED值。B: SNP-index关联分析结果。横坐标为染色体的分布, 每个点代表的ΔSNP-index值。"

图2

关联值在染色体上的分布(InDel) A: ED关联分析结果。横坐标为染色体的分布, 每个点代表InDel位点的ED值。B: SNP-index关联分析结果。横坐标为染色体的分布, 每个点代表的ΔInDel-index值。"

表3

不同关联分析方法获得的关联区域"

染色体位置
Chromosome ID		 关联区域始位置
Start		 关联区域终止位置
End		 关联区域大小
Size (Mb)		 关联区域内基因数量
Gene number
Chr6LG2 60,560,000 91,060,000 30.50 434
Chr6LG2 91,090,000 91,150,000 0.060 2
Chr6LG2 91,320,000 91,630,000 0.310 7
Chr6LG2 91,690,000 91,750,000 0.060 1
Chr6LG2 92,190,000 92,680,000 0.490 5
总共Total — — 31.42 449

表4

精细定位所用多态性分子标记"

位置
Position		 引物名称
Primer name		 正向引物
Forward sequence (5-3°)		 反向引物
Reverse sequence (5-3°)
62,185,053 WDBH141-1 TGATTCCAAGGGCCAATGACA GCACGAAGCTAGCTAGTGAATAA
62,390,612 WDBH144-1 TTGTTCCACCACTGCAACCT TGGATTTACCCGCAGTTGGT
62,698,646 WDBH147-1 TGAAACGCCCCTTATTGAAGT TCTTCGAGTTCGGCTTTGCT
位置
Position		 引物名称
Primer name		 正向引物
Forward sequence (5-3°)		 反向引物
Reverse sequence (5-3°)
64,421,149 WDBH172-1 ACCCAAAGCCACCAAAGAGAA TGACACAACTGTTTGACACCA
64,707,966 WDBH008-3 ATGAGGTGCCCCTATGTGAG TAATTGGTGGTGGTGAGATGGG
65,304,246 WDBH028-1 AGTCACGGCAATGGATGGAA ACATGTGCAAGCGACCTTCA
65,627,591 WDBH179-2 GGTGGGATGTATCTGCTGACC TCTGGTAGGAACACAAGTGGTTA
66,874,335 WDBH183-1 AACTGTGAGGAATGTCTATCCCA AGGTTTGCTCCCATTTGTCAC
66,960,275 WDBH013-2 GTTCGGTCTAGTGTGCTCGT TGCCAGCTGTACCATAGCAAA
67,036,795 WDBH194-1 ACTGTGTACACCCTTGCACT TCCATATTCTAGCCAACACCACC
67,579,583 WDBH187-1 CGGTCCAACTGAGATGGCAA TGGCTAGGGCTATAGGTATGAAGT
67,645,017 WDBH209-1 TGGGAGTTTGAAGTTGAGGGG TCCCTAAAATGAGGGAACTCAAA
67,998,027 WDBH084-1 GTGCAGGCTTGAGGGTTTTG TGTGTTCCCCAGTGTGTATCTC
68,240,556 WDBH200-1 TGTGGTGAGGAAATCGACGAA CCGAAACATGAGCGCGTAAC
68,307,829 WDBH113-1 TTTTCCTGTCCTGGCGTGAC AGGGTTGGGCGGTAATTCAA
68,309,277 WDBH090-1 GCTTCTTTGGCAGCGTTTGT TACACAATCCCGAGTCATGGT
68,551,555 WDBH029-1 TAGGGTTGCATGGGTTGCTT CACAAGTTGCTGCACACATTTC
68,566,772 WDBH220-1 CCATAGACTAAAGTTGAGACGAGC GATTGTGCCCCTGGAAGTGA
68,673,374 WDBH133-1 TCCCACAAGCCATGTCCAAA CGTGCACGAGAACGAAGGTT
69,494,713 WDBH129-1 CAGAACATGGCCAGGATCAATG TGCAGAGGCGTGTCTTTCAA
69,965,980 WDBH051-1 GAGATGCAGTGAAATCGCCG CAATTGGGGTGATGCACTCG
70,060,557 WDBH104-1 TCACCTCCATCATTTAAGCGGA ACATCGCGCGTCTCAATCTA
70,411,248 WDBH053-1 CCGATCCGCAGGTTGGAAAA GTGTGCAGACGAACCGATTT
72,140,477 WDBH059-1 AGTCCAATGGTCTGATAGCGT TTGTGCGAACCTCTTTCTGC
73,347,184 WDBH063-1 GAAAAACGCGAGCAGAGAGC TCCGAGTGGTCCGAGTATGT
75,496,657 WDBH032-1 ACGGAGGTCAGAGGCTACAA CGGCATAGGTTGACACATACG
75,976,029 WDBH080-1 TGGCCAATTCCCAAGCTCAA TTTGGGCTAGATGCGGAGAC
84,516,982 WDBH109-1 ACACGTTGATGAAAATGGGCG ATTTTGGTCTCCGACAGCGT
84,765,375 WDBH037-1 TTGCCCCTAGACGGTAGTGA TTTCCTGAGCCCACACATGG
86,084,668 WDBH011-2 CGGGTACCACGGGAATATACG GTTCGGCGGCGAATATGTTT
92,203,258 WDBH044-1 GCCACCTATTCGTCCATCGT AAGGGGACAAAGCACCCTTC

图3

精细定位豌豆花色基因的目标区域"

附表1

InDel标记检测到的交换单株统计结果"

InDel标记
InDel markers		 F2交换单株F2 exchange individual plant
003 013 014 034 038 044 049 057 079 082 089 094 099 115 122 123 131 148 186 198 206 216 240 242 250 254 279 285 300 302 320
WDBH141-1 + + - + - + - - + + + + + - + + - - - - + - - + - - - - - + -
WDBH144-1 + + - + - + - - + + + + - + + - - - - + - - + - - - - - + -
WDBH147-1 + + - + - + - - + + + + + - + + - - - - + - - + - - - - - + -
WDBH172-1 + - - + - - - - - - - + - - + + - - - - + - - - - - - - - - -
WDBH008-3 + - - + - - - - - - - + - - + + - - - - + - - - - - - - - - -
WDBH028-1 + - - + - - - - - - - + - - + + - - - - + - - - - - - - - - -
WDBH179-2 + - - - - - - - - - - + - - - + - - - - + - - - - - - - - - -
WDBH183-1 + - - - - - - - - - - + - - - + - - - - + - - - - - - - - - -
WDBH013-2 + - - - - - - - - - - + - - - + - - - - + - - - - - - - - - -
WDBH194-1 + - - - - - - - - - - - - - - - - - - - + - - - - - - - - - -
WDBH187-1 + - - - - - - - - - - - - - - - - - - - + - - - - - - - - - -
WDBH209-1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
WDBH084-1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
WDBH200-1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
WDBH113-1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
WDBH090-1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
WDBH029-1 - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -
WDBH220-1 - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - -
WDBH133-1 - - - - - - - - - - - - - - - - + - - - - - - - - - - - - - -
WDBH129-1 - - + - - - - + - - - - - - - - + + - - - - + - + - - - - - -
WDBH051-1 - - + - - - - + - - - - - - - - + + - - - - + - + - - - - - -
WDBH104-1 - - + - - - - + - - - - - - - - + + - + - - + - + - - - + - -
WDBH053-1 - - + - - - - + - - - - - - - - + + - + - - + - + - - - + - -
WDBH059-1 - - + - - - + + - - - - - + - - + + - + - - + - + - - + + - -
WDBH063-1 - - + - - - + + - - - - - + - - + + - + - - + - + - - + + - -
WDBH032-1 - - + - + - + + - - - - - + - - + + - + - + + - + - + + + - -
WDBH080-1 - - + - + - + + - - - - - + - - + + - + - + + - + - + + + - -
WDBH109-1 - - + - + - + + - - - - - + - - + + + + - + + - + - + + + - -
WDBH037-1 - - + - + - + + - - - - - + - - + + + + - + + - + - + + + - +
WDBH011-2 - - + - + - + + - - - - - + - - + + + + - + + - + + + + + - +
WDBH044-1 - - + - + - + + - - - - - + - - + + + + - + + - + + + + + - +

表5

定位区间内的基因及功能预测"

基因ID
Gene ID		 起始位置
Start		 终止位置
End		 基因功能注释
Gene function annotation
Psat6g060000.1 67,641,138 67,657,547 —
Psat6g060040.1 67,824,817 67,825,137 —
Psat6g060080.1 67,833,124 67,835,423 41 kD的叶绿体茎环结合蛋白 Chloroplast stem-loop binding protein of 41 kD
Psat6g060120.1 67,836,103 67,837,783 RAN GTP酶激活蛋白1 RAN GTPase-activating protein 1
Psat6g060160.1 67,921,631 67,923,302 —
Psat6g060200.1 67,934,766 67,936,280 —
Psat6g060240.1 68,020,488 68,022,587 不活跃Patatin类蛋9 Probable inactive patatin-like protein 9
Psat6g060280.1 68,235,164 68,237,023 保卫细胞S型阴离子通道SLAC1 Guard cell S-type anion channel SLAC1
Psat6g060320.1 68,259,311 68,271,214 类Rac GTP结合蛋白RAC9 (前体)
Rac-like GTP-binding protein RAC9 (precursor)
Psat6g060360.1 68,302,270 68,302,889 —
Psat6g060400.1 68,305,575 68,309,198 五肽重复含蛋白 Pentatricopeptide repeat-containing protein
Psat6g060440.1 68,328,642 68,331,221 —
Psat6g060480.1 68,330,158 68,340,923 碱性螺旋-环-螺旋蛋白A Basic helix-loop-helix protein A
Psat6g060560.1 68,369,085 68,372,125 F-box蛋白 F-box protein
Psat6g060600.1 68,422,110 68,426,447 Sm类蛋白 LSM4 Sm-like protein LSM4
Psat6g060640.1 68,458,147 68,461,838 核糖体循环因子, 叶绿体(前体)
Ribosome-recycling factor, chloroplastic (precursor)
Psat6g060680.1 68,511,345 68,517,001 TIME FOR COFFEE蛋白 Protein TIME FOR COFFEE
Psat6g060720.1 68,549,094 68,551,796 Mut11蛋白 Protein Mut11
Psat6g060760.1 68,554,342 68,554,618 —
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