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作物学报 ›› 2021, Vol. 47 ›› Issue (8): 1460-1471.doi: 10.3724/SP.J.1006.2021.04195

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

基于BSA-Seq和RNA-Seq方法鉴定大豆抗豆卷叶螟候选基因

曾维英(), 赖振光(), 孙祖东*(), 杨守臻, 陈怀珠, 唐向民   

  1. 广西农业科学院经济作物研究所/农业农村部西南玉米大豆间套作区农业科学观测实验站, 广西南宁 530007
  • 收稿日期:2020-08-25 接受日期:2021-01-13 出版日期:2021-08-12 网络出版日期:2021-02-18
  • 通讯作者: 孙祖东
  • 作者简介:曾维英, E-mail: zengweiying_1981@163.com|赖振光, E-mail: 519229671@qq.com
  • 基金资助:
    广西自然科学基金项目(2017GXNSFDA198037);广西农业科学院科技发展基金项目(桂农科2020YM116, 2015YT58)

Identification of the candidate genes of soybean resistance to bean pyralid (Lamprosema indicata Fabricius) by BSA-Seq and RNA-Seq

ZENG Wei-Ying(), LAI Zhen-Guang(), SUN Zu-Dong*(), YANG Shou-Zhen, CHEN Huai-Zhu, TANG Xiang-Min   

  1. Institute of Economic Crops, Guangxi Academy of Agricultural Sciences/Southwest Experimental Station of Maize-Soybean Intercrop, Ministry of Agriculture and Rural Affairs, Nanning 530007, Guangxi, China
  • Received:2020-08-25 Accepted:2021-01-13 Published:2021-08-12 Published online:2021-02-18
  • Contact: SUN Zu-Dong
  • Supported by:
    Natural Science Foundation of Guangxi Province, China(2017GXNSFDA198037);Science and Technology Development Fund of Guangxi Academy of Agricultural Sciences (Guinongke 2020YM116, 2015YT58)

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摘要：

豆卷叶螟(Lamprosema indicata Fabricius)是重要的大豆食叶性害虫, 挖掘大豆抗豆卷叶螟相关基因对大豆抗虫品种选育和遗传改良至关重要。本研究用大豆高抗豆卷叶螟材料赶泰-2-2和高感豆卷叶螟材料皖82-178进行杂交构建F2代分离群体, 从303个F2代单株中挑选出高抗豆卷叶螟和高感豆卷叶螟的单株各30株, 分别构建2个极端性状的DNA混合池用于全基因组重测序以分析控制豆卷叶螟相关的候选基因。结果表明, 4个样本中共有11,963,077个单核苷酸多态性(SNPs)标记, 根据SNP-index方法关联分析, 共有329个基因位于99%置信区间外, 这些基因主要集中在7号染色体5,601,065~5,865,237 bp区间(总长为0.26 Mb)、16号染色体2,975,110~6,336,096 bp区间(总长为3.36 Mb)、18号染色体44,366,115~54,297,600 bp区间(总长为9.93 Mb)等区域内。将BSA-Seq结果与转录组测序结果进行联合分析发现, 有12个基因相关联; 最后, 结合生物信息学分析、候选基因的表达模式和基因的同源注释, 锁定CNGC4、WRKY16转录因子、AAP7、丝氨酸/苏氨酸蛋白激酶、ZPR1B等12个基因为控制豆卷叶螟性状相关的候选基因。本研究结果不仅为解析大豆抗豆卷叶螟的分子机理奠定重要的基础, 也将为大豆抗虫基因的克隆奠定坚实的理论基础。

关键词: 大豆, 豆卷叶螟, BSA-Seq, RNA-Seq, 候选基因

Abstract:

Bean pyralid is an important leaf-feeding insect in soybean. Identification of insect-tolerant genes from soybean has great significant to the crop insect-tolerant breeding and genetic improvement. In this study, an F2 population with 303 individuals was constructed using insect-resistant line Gantai-2-2 and insect-sensitive line Wan 82-178. 30 F2 insect-resistant individuals and 30 insect-sensitive individuals were selected respectively to construct two DNA pools which were used for the whole-genome re-sequencing. The results showed that there were a total of 11,963,077 single nucleotide polymorphism (SNPs) markers identified in two parental lines and two mixed pools. According to the association analysis of SNP-index method, a total of 329 genes were located outside the 99% confidence interval. These genes were mainly concentrated in the regions of 5,601,065-5,865,237 bp with a total of 0.26 Mb on chromosome 7, 2,975,110-6,336,096 bp with a total of 3.36 Mb on chromosome 16, and 44,366,115-54,297,600 bp with a total of 9.93 Mb on chromosome 18. Correlation analysis of BSA-Seq and transcriptome sequencing showed that 12 genes were correlated. Then, 12 candidate genes, including CNGC4, WRKY transcription factor 16, AAP7, serine/threonine protein kinase and ZPR1B were identified by bioinformatics analysis, differential expression analysis, and homologous annotation. This study laid an important foundation for the analysis of the molecular mechanism of soybean resistance to bean pyralid and the cloning of anti-insect genes.

Key words: soybean, bean pyralid, BSA-Seq, RNA-Seq, candidate genes

表1

原始测序数据统计表"

样本
Sample		 原始序列数
Raw reads		 原始碱基数
Raw bases		 过滤后序列数
Clean reads		 过滤后碱基数
Clean bases		 有效率
Clean_data/
raw_data (%)		 GC含量
Clean_GC_rate (%)		 Q20含量
Q20
(%)		 Q30含量Q30
(%)
皖82-178 Wan 82-178 438,210,500 65,731,575,000 432,474,442 64,871,166,300 98.69 35.57 96.50 92.13
赶泰-2-2 Gantai-2-2 441,716,184 66,257,427,600 433,990,902 65,098,635,300 98.25 35.60 96.34 91.79
高感子代池
Highly susceptible pool		 206,898,280 31,034,742,000 202,406,834 30,361,025,100 97.83 35.54 96.44 92.01
高抗子代池
Highly resistant pool		 210,122,884 31,518,432,600 206,805,618 31,020,842,700 98.42 35.46 96.29 91.70

表2

质控后测序数据与参考基因组比对结果统计分析"

样本
Sample		 过滤后序
列数
Clean reads		 比对上数据
Mapping reads		 比对率
Mapping rate (%)		 优质比对率
Properly paired ratio (%)		 平均测序深度
Mean depth		 1×覆盖度Coverage ≥ 1× (%) 5×覆盖度
Coverage ≥ 5× (%)		 10×覆盖度
Coverage ≥ 10× (%)		 20×覆盖度
Coverage ≥ 20× (%)
皖82-178 Wan 82-178 43,4152,986 433,232,376 99.79 99.73 65.78 96.67 96.12 95.67 94.62
赶泰-2-2 Gantai-2-2 435,703,158 434,715,984 99.77 99.72 65.98 96.68 96.13 95.68 94.60
高感子代池
Highly susceptible pool		 203,202,650 202,820,220 99.81 99.76 30.78 95.75 94.55 93.29 83.88
高抗子代池
Highly resistant pool		 207,33,600 207,143,542 99.76 99.71 31.44 95.76 94.56 93.32 84.44

表3

多态性位点注释统计表"

变异位点信息
Variation sites information		 皖82-178
Wan 82-178		 赶泰-2-2
Gantai-2-2		 高感子代池
Highly susceptible pool		 高抗子代池
Highly resistant pool
内含子Intron 324,202 324,333 230,606 231,332
基因区间Intergenic region 2,589,457 2,588,540 1,851,943 1,867,897
可变剪切位点Splicing 612 620 449 444
基因上游Upstream 192,755 192,753 133,797 136,203
基因下游Downstream 162,024 161,574 113,186 114,671
基因上游/基因下游Upstream/downstream 12,038 12,088 8296 8733
5°非翻译区UTR5° 23,658 23,746 68,071 16,818
3°非翻译区UTR3° 29,843 29,595 20,949 21,579
终止子提前Stop gain 1652 1649 1177 1225
终止子丢失Stop loss 270 276 197 204
同义突变Synonymous 48,462 48,433 35,671 35,492
非同义突变Non-synonymous 67,206 67,040 49,333 49,653
SNP总数SNP numbers 3,487,363 3,485,674 2,483,855 2,506,185
纯合突变SNP Hom SNP number 3,480,115 3,478,433 2,477,251 2,499,464
杂合突变SNP Hete SNP number 7248 7241 6604 6721
纯合突变SNP比率Hom SNP rate (%) 99.79 99.79 99.73 99.73
杂合突变SNP比率Het SNP rate (%) 0.21 0.21 0.27 0.27
转换Ts 2,264,913 2,264,110 1,606,918 1,617,797
颠换Tv 1,218,400 1,217,609 872,951 884,443
转换/颠换Ts/Tv 1.86 1.86 1.84 1.83

图1

所有染色体Delta SNP-index图 横坐标为染色体编号, 纵坐标为Delta SNP-index值。不同颜色的点表示不同染色体上筛选后的SNP, 红色曲线表示滑窗后的Delta SNP-index值, 蓝色直线表示99%置信区间值。"

图2

候选基因GO富集分析情况"

图3

前20条富集通路注释情况"

表4

候选基因信息表"

序号
No.		 基因ID
Gene ID		 基因注释
Gene annotation		 染色体
Chr.		 比较组
Comparison group		 上调或下调a
Up or down a
1 XM_003526153.4 环核苷酸门控离子通道4
Cyclic nucleotide-gated ion channel 4 (CNGC4)		 Chr. 6 HR0/HR48
HS0/HS48		 Up
2 XM_003533631.4 纤维素合成酶A催化亚基4 (CesA4)
Cellulose synthase A catalytic subunit 4 [UDP-forming]		 Chr. 9 HR0/HR48
HS0/HS48		 Down
3 NM_001250658.2 WRKY16转录因子
WRKY transcription factor 16		 Chr. 12 HR0/HR48 Up
4 NM_001255802.1 赤霉素2-β加双氧酶8
Gibberellin 2-beta-dioxygenase 8-like		 Chr. 11 HR0/HR48 Up
5 XM_003519602.4 氨基酸透性酶7 (AAP7)
Probable amino acid permease 7		 Chr. 2 HR0/HR48 Up
6 XM_026126143.1 Mdis1相互受体激酶2
MDIS1-interacting receptor like kinase 2		 Chr. 16 HR0/HR48 Up
7 XM_006601656.3 丝氨酸/苏氨酸蛋白激酶
Serine/threonine protein kinase-like protein		 Chr. 18 HR0/HR48
 Up
8 NM_001248669.2 ZPR1B
Protein LITTLE ZIPPER 2-like		 Chr. 18 HS0/HS48 Up
9 XM_026126905.1 类枯草杆菌蛋白酶
Subtilisin-like protease Glyma18g48580		 Chr. 18 HS0/HR0
 Down
10 XM_026125778.1 抗病蛋白RGA3
Putative disease resistance protein RGA3		 Chr. 15 HS0/HR0
 Down
11 XM_026126161.1 无特征LOC100809946
Uncharacterized LOC100809946		 Chr. 16 HS0/HR0 Up
12 XM_026127992.1 硫氰酸酶结构域蛋白酶10
Rhodanese-like domain-containing protein 10		 Chr. 3 HS48/HR48
HS0/HR0		 Down
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