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作物学报 ›› 2020, Vol. 46 ›› Issue (12): 1839-1849.doi: 10.3724/SP.J.1006.2020.04075

• 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技术挖掘大豆中黄622的多小叶基因

张之昊1,2(), 王俊1, 刘章雄2,*(), 邱丽娟1,2,*()   

  1. 1长江大学农学院, 湖北荆州 434025
    2中国农业科学院作物科学研究所, 北京 100081
  • 收稿日期:2020-03-24 接受日期:2020-08-19 出版日期:2020-12-12 网络出版日期:2020-09-02
  • 通讯作者: 刘章雄,邱丽娟
  • 基金资助:
    国家自然科学基金项目(31630056)

Mapping of an incomplete dominant gene controlling multifoliolate leaf by BSA-Seq in soybean (Glycine max L.)

ZHANG Zhi-Hao1,2(), WANG Jun1, LIU Zhang-Xiong2,*(), QIU Li-Juan1,2,*()   

  1. 1School of Agriculture, Yangtze University, Jingzhou 434025, Hubei, China
    2Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2020-03-24 Accepted:2020-08-19 Published:2020-12-12 Published online:2020-09-02
  • Contact: LIU Zhang-Xiong,QIU Li-Juan
  • Supported by:
    National Natural Science Foundation of China(31630056)

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摘要：

栽培大豆(Glycine max)叶片一般为三出复叶, 也有个别品种或植株突变体产生4~7个小叶, 为多小叶。复叶的形成使植物对外界环境的适应能力增强, 对大豆多小叶相关基因的挖掘和研究有助于改善大豆农艺性状和产量表现。本研究从大豆栽培品种中品661的突变体库中鉴定出一个多小叶突变体——中黄622, 每个复叶有4~9个小叶。利用该突变体与中品661配制组合, 分别于北京和海南调查F2和F2:3植株叶片表型, 结果表明, 多小叶性状受1对不完全显性基因控制。采用BSA-seq方法进行定位, 利用F2正常三出复叶和多小叶个体分别构建混池, 测序结果与参考基因组平均比对效率为98.83%, 平均覆盖深度为32.75×, 基因组覆盖度为99.22%。ED方法关联分析发现, 在11号染色体定位到2个区域, 总长度为5.29 Mb, 共包含1103个基因。根据SNP-index方法关联分析, 当置信度为0.99时, 在11号染色体鉴定出3个区域, 总长度为3.42 Mb, 共包含701个基因。2种关联分析方法同时定位的基因有690个, 亲本之间存在SNP的基因有6个。本研究结果为大豆多小叶基因图位克隆奠定了基础。

关键词: 大豆, 突变体, 混池测序

Abstract:

The leaves of cultivated soybean (Glycine max L.) are comprising of three leaflets in general, but there are also individual varieties or mutants which have a high frequency of compound leaves with 4-7 leaflets, named multifoliolate leaves. Compound leaf formation enhances the plant's ability to adapt to the external environment. Study of related genes to multifoliolate leaves might contribute to the improvement yield level of and soybean agronomic traits. In this study, a multifoliolate leaf mutant Zhonghuang 622 was identified from the mutant library of soybean cultivar Zhongpin 661, which had 4-9 leaflets in each compound leaf. The compound leaf phenotypes of F2 and F2:3 population from a cross between Zhongpin 661 and Zhonghuang 622 were investigated in Beijing and Hainan, respectively. Analysis of phenotypic data from F2 and F2:3 population revealed that the multifoliolate leaf trait was controlled by an incomplete dominant gene. BSA-Seq method was used for gene mapping. The two bulks of normal trifoliate and multifoliolate individuals in F2 population were constructed and sequenced for an average depth of 32.75×, which covered 99.22% genome compared to the reference genome. Through correlation analysis of mixed pool sequencing results by ED method, two regions were located on chromosome 11, with a total length of 5.29 Mb and a total length of 1103 genes. Three regions were identified on chromosome 11 at confidence of 0.99, with a total length of 3.42 Mb and a total of 701 genes by the association analysis of SNP-index method. There were 690 genes located simultaneously and six SNP genes between parents by the two association analysis methods. These results lay the foundation for map-based cloning of the genes related to compound leaf development.

Key words: soybean, mutant, BSA-Seq

图1

BSA-Seq数据分析流程"

表1

F2群体中不同基因型和表型的单株数目"

表型
Phenotype		 基因型Genotype 期望比
Expectation ratio		 χ2 P0.05, 0.01
lf alf a lf alf b lf blf b
I 54 2 0 — — —
II 0 99 0 — — —
III 0 4 80 — — —
总数Total 54 105 80 1︰2︰1 9.18 5.99, 9.27

图2

利用2种关联方法鉴定多小叶基因候选区间 A: ED关联分析结果, 横坐标为染色体位置, 纵坐标代表拟合后的欧式距离(ED)值的5次方, 黑色的线为拟合后的ED的5次方作关联值, 红色的虚线代表显著性关联阈值。B: SNP-index关联分析结果, 横坐标为染色体位置, 黑色的线为拟合后的ΔSNP-index值, 红色的线代表置信度为0.99的阈值线, 蓝色的线代表置信度为0.95的阈值线, 绿色的线代表置信度为0.90的阈值线。2种关联分析结果均表明, 与多小叶相关的关联区域位于11号染色体末端。"

表2

利用不同方法在11号染色体获得关联区域"

关联分析方法
Association analysis method		 染色体
Chromosome		 关联区域
起始位置
Start of associated regions		 关联区域
终止位置
End of associated regions		 关联区域
大小
Associated region size (Mb)		 关联区域内的
基因数量
Gene number in the associated regions
欧氏距离
Euclidean distance (ED)		 Chr. 11 0 4,150,000 4.15 896
Chr. 11 5,570,000 6,710,000 1.14 207
总计Total — — 5.29 1103
SNP-index Chr. 11 0 250,000 0.25 44
Chr. 11 1,510,000 3,480,000 1.97 439
Chr. 11 5,570,000 6,770,000 1.20 218
总计Total — — 3.42 701
2种方法交集
Intersection of two methods		 Chr. 11 0 250,000 0.25 44
Chr. 11 1,510,000 3,480,000 1.97 439
Chr. 11 5,570,000 6,710,000 1.14 207
总计Total — — 3.36 690

图3

样品间SNP及关联信号在染色体上的分布 从外到里依次为: 第1圈: 染色体坐标; 第2圈: 基因分布; 第3圈: SNP密度分布; 第4圈: ED值分布; 第5圈: ΔSNP-index值分布。"

表3

引物序列和信息"

引物名称
Primer ID		 上游引物序列
Forward primer (5°-3°)		 下游引物序列
Reverse primer (5°-3°)		 产物大小
Product size (bp)		 检测位点数目
Number of detection sites
SNP 1 GCCGTAGCACTTCACTCATTCA ATGTTCTATAAGCCGTTTTTTGGAAG 5633 5
SNP 2 TCTACTCGCAAAAGGCACAG CATTTATATGTTCGTCAATATTTAG 7016 1
SNP 3 GGAATGCCAATGGGCTTTAATT GATCTTGCTTACCAATTTCTCG 1247 3

表4

对区间内部分SNP位点进行鉴定"

染色体
Chr.		 SNP位点
SNP loci		 参考碱基
Reference base		 突变碱基
Altered base		 混池read值Bulk read value in mixed pool SNP质量评价
SNP quality evaluation		 鉴定结果
Appraisal results
中品661
Zhongpin 661		 中黄622
Zhonghuang 622		 正常叶混池
Normal leaf mixing pool		 多小叶混池
Multi-leaflet mixing pool
Chr.11 1738094 C T 14,7 8,0 32,0 42,0 低 Low 假False
Chr.11 1738120 C T 14,5 8,0 33,0 39,0 低Low 假False
Chr.11 1738157 G A 10,0 9,1 32,5 38,4 低Low 假False
Chr.11 1738175 A T 9,0 9,1 34,9 39,6 低Low 假False
Chr.11 1738511 A T 20,0 9,1 37,4 39,10 低Low 假False
Chr.11 1947868 A T 12,0 0,7 27,0 0,48 高High 真True
Chr.11 1964348 C T 9,0 5,1 42,5 41,7 低Low 假False
Chr.11 1964460 T C 8,0 9,5 37,28 44,28 低Low 假False
Chr.11 1964710 T A 9,0 6,2 36,8 38,8 低Low 假False

表5

2种方法共定位区间内亲本之间SNP类型"

SNP位点
SNP loci		 碱基类型 Base type 突变类型
Mutation type		 基因ID
Gene ID		 基因功能注释
Annotated function
中品661 Zhongpin 661 中黄622 Zhonghuang 622
1947868 A T 非同义SNV
Nonsynonymous SNV		 Glyma.11G027100 同源盒蛋白knotted-1-like-7
Homeobox protein knotted-1-like-7
2489820 G A 同义SNV
Synonymous SNV		 Glyma.11G034100 亮氨酸-tRNA连接酶/亮氨酰-tRNA合成酶
Leucine-tRNA ligase/Leucyl-tRNA synthetase
2954231 G A 非同义SNV
Nonsynonymous SNV		 Glyma.11G040200 无意义转录物1的调节因子(UPF1, RENT1)
Regulator of nonsense transcripts 1 (UPF1, RENT1)
3156378 G A 非同义SNV
Nonsynonymous SNV		 Glyma.11G043100 At-hook motif核定位蛋白21相关
At-hook motif nuclear localized protein 21- related
3334413 C A 基因上游
Upstream		 Glyma.11G045200 核基质构成蛋白1蛋白相关
Nuclear matrix constituent protein 1-like protein-related
6288434 C T 内含子
Intron		 Glyma.11G083800 酰基激活酶1, 过氧化物酶体相关
Acyl-activating enzyme 1, peroxisomal-related

图4

6个候选基因的表达图谱 方块内颜色显示候选基因表达水平: 蓝色最低, 白色居中, 红色最高。"

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