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作物学报

作物学报 ›› 2023, Vol. 49 ›› Issue (11): 2935-2948.doi: 10.3724/SP.J.1006.2023.24276

• 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方法挖掘大豆再生相关候选基因

赵宇晶1(), 张滨烁1, 苏安玉2, 于振海1, 李佳欢1, 林洋1, 张艳婷1, 武小霞1,*(), 赵莹1,*()   

  1. 1东北农业大学农学院, 黑龙江哈尔滨 150030
    2东北农业大学资环学院, 黑龙江哈尔滨 150030
  • 收稿日期:2022-12-12 接受日期:2023-04-17 出版日期:2023-11-12 网络出版日期:2023-05-12
  • 通讯作者: 武小霞, E-mail: xxwu2012@126.com; 赵莹, E-mail: tianshi198937@126.com
  • 作者简介:赵宇晶, E-mail: yujingzhao99@163.com第一联系人：

    **同等贡献

  • 基金资助:
    国家自然科学基金项目(31971899);国家自然科学基金项目(32272093);国家重点研发计划项目(2021YFD120160204);国家重点研发计划项目(2021YFD12011040202);黑龙江省自然科学基金项目(TD2022C003);黑龙江省自然科学基金项目(JJ2022YX0475)

Mining candidate genes related to soybean regeneration based on BSA-seq method

ZHAO Yu-Jing1(), ZHANG Bin-Shuo1, SU An-Yu2, YU Zhen-Hai1, LI Jia-Huan1, LIN Yang1, ZHANG Yan-Ting1, WU Xiao-Xia1,*(), ZHAO Ying1,*()   

  1. 1College of Agronomy, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
    2College of Resources and Environment, Northeast Agricultural University, Harbin 150030, Heilongjiang, China
  • Received:2022-12-12 Accepted:2023-04-17 Published:2023-11-12 Published online:2023-05-12
  • About author:First author contact:

    **Contributed equally to this study

  • Supported by:
    National Natural Science Foundation of China(31971899);National Natural Science Foundation of China(32272093);National Key Research and Development Program of China(2021YFD120160204);National Key Research and Development Program of China(2021YFD12011040202);Heilongjiang Natural Science Foundation(TD2022C003);Heilongjiang Natural Science Foundation(JJ2022YX0475)

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摘要：

转基因生物育种技术可以定向改良大豆品种, 为大豆定向育种提供一种新思路。为寻找与大豆再生相关的基因, 探索大豆再生规律、提高遗传转化效率, 本研究利用再生能力强材料东农50、再生能力弱材料Keburi及其子代RIL群体的200份材料进行大豆器官发生试验, 比较不同基因型之间再生能力的差异, 筛选出极端材料各20份, 后通过BSA-seq (bulked segregant analysis sequencing)技术对大豆再生候选基因进行初步定位, 共获得88.04 G的clean data, 平均测序深度为20.03×, 定位到2 Mb区间, 利用GO等数据库对区间内基因进行富集分析, 差异表达基因主要富集在纤维素微纤维组织、植物型细胞壁组织或生物发生等20个条目中, 其中被显著富集的植物型细胞壁组织或生物发生条目中共有6个基因, 对6个基因进行组织表达量分析, 在丛生芽伸长期间表达水平较高, 说明其在大豆再生过程中发挥作用, 可能为影响大豆再生的关键基因。本研究为大豆再生机制研究提供了重要的候选基因信息与必要的材料基础。

关键词: 大豆, 再生, 器官发生, BSA-seq

Abstract:

Transgenic breeding technology can improve soybean directionally, and provide a new idea for improving soybean yield. In order to search for the genes related to soybean regeneration, explore the rules of soybean regeneration, and improve the efficiency of genetic transformation, we conducted soybean organogenesis experiment with 200 materials including DN50 (a material with strong regeneration ability), Keburi (a material with weak regeneration ability), and RILs of its offspring with strong regeneration ability. Compared the differences in regeneration ability between different genotypes, 20 extreme materials each were screened. Preliminary localization of soybean regeneration candidate genes by BSA-seq (bulked segregant analysis sequencing) technology, 88.04 G clean data were obtained in the 2 Mb interval with an average sequencing depth of 20.03 ×. The differentially expressed genes were mainly enriched in 20 items such as cellulose microfiber tissue, plant type cell wall tissue, or biogenesis, among which there were 6 genes in plant type cell wall tissue or biogenesis item significantly enriched. The tissue expression analysis of 6 genes showed that the relative expression level was high during cluster bud elongation, which indicating that it played a role in the process of soybean regeneration and might be the key gene affecting soybean regeneration. This study provides the basic materials for breeding new regenerated soybean varieties, and confirms the feasibility of BSA-seq technology in mining regenerated genes.

Key words: soybean, regeneration, organogenesis, BSA-seq

图1

器官发生试验流程图 A: 萌发; B、C: 诱导丛生芽; D: 丛生芽伸长; E、F: 生根培养。"

图2

DN50和Keburi各个时期生长情况 A、D: 丛生芽诱导; B、E: 丛生芽伸长; C、F: 生根情况。标尺为1 cm。"

图3

显微镜下DN50和Keburi丛生芽生长情况 红色三角形标注点处均为丛生芽。"

图4

父母本再生指标对比 RP: 再生潜力; RA: 再生能力; RE: 再生效率; RR: 再生率。P值由假设方差相等的双尾t检验, **P < 0.01, *P < 0.05。"

图5

极端材料各个时期生长情况 a: 强再生材料; b: 弱再生材料。A、D: 丛生芽诱导; B、E: 丛生芽伸长; C、F: 生根情况。标尺为1 cm。"

图6

显微镜下极端材料丛生芽生长情况 A: 再生好材料; B: 再生差材料。红色三角形标注点处均为丛生芽。"

图7

子代材料数据统计 A: 再生潜力统计; B: 再生能力统计; C: 再生效率统计; D: 再生率统计。"

表1

主成分特征值及贡献率"

性状
Trait		 主成分Comprehensive index
F1 F2
再生潜力Regeneration potential -0.07 0.99
再生能力Regeneration ability 0.57 -0.10
再生效率Regeneration efficiency 0.58 0.08
再生率Regeneration rate 0.58 0.03
特征值Eigen values 2.81 1.02
贡献率Contributive ratio (%) 70.15 25.42
累计贡献率Cumulative contributive ratio (%) 70.15 95.57

表2

极端材料的主成分值、隶属函数值、D值"

株系
Strain line		 主成分
Comprehensive index		 隶属函数
Membership function		 D值
D-value		 综合评价
Comprehensive valuation
F1 F2 F1* F2*
Z14 9.05 -0.34 1.00 0.36 6.55 强再生Strong regenerative ability
Z6 7.22 2.47 0.82 0.95 5.95 强再生Strong regenerative ability
Z1 6.22 -0.6 0.72 0.30 4.41 强再生Strong regenerative ability
Z142 5.51 -0.58 0.65 0.31 3.88 强再生Strong regenerative ability
Z20 5.02 -0.14 0.60 0.40 3.65 强再生Strong regenerative ability
Z77 4.10 2.32 0.51 0.92 3.63 强再生Strong regenerative ability
Z168 4.33 0.76 0.53 0.59 3.38 强再生Strong regenerative ability
Z2 5.22 -1.75 0.62 0.06 3.36 强再生Strong regenerative ability
Z35 5.07 -1.53 0.61 0.11 3.32 强再生Strong regenerative ability
Z98 4.38 0.08 0.54 0.45 3.24 强再生Strong regenerative ability
Z16 4.04 -0.94 0.50 0.23 2.72 强再生Strong regenerative ability
Z3 3.69 -0.01 0.47 0.43 2.70 强再生Strong regenerative ability
Z155 3.56 0.11 0.46 0.45 2.64 强再生Strong regenerative ability
Z53 3.25 0.49 0.42 0.53 2.52 强再生Strong regenerative ability
Z30 3.12 0.71 0.41 0.58 2.48 强再生Strong regenerative ability
Z184 2.36 1.84 0.34 0.82 2.22 强再生Strong regenerative ability
Z176 2.93 0.10 0.39 0.45 2.18 强再生Strong regenerative ability
Z4 3.12 -0.80 0.41 0.26 2.08 强再生Strong regenerative ability
Z52 2.49 0.26 0.35 0.49 1.90 强再生Strong regenerative ability
Z149 2.37 0.53 0.34 0.54 1.88 强再生Strong regenerative ability
Z39 -0.71 -1.88 0.03 0.03 -1.03 弱再生Weak regenerative ability
Z153 -0.71 -1.88 0.03 0.03 -1.03 弱再生Weak regenerative ability
Z180 -0.71 -1.88 0.03 0.03 -1.03 弱再生Weak regenerative ability
Z152 -0.73 -1.63 0.03 0.08 -0.97 弱再生Weak regenerative ability
Z95 -0.74 -1.47 0.03 0.12 -0.94 弱再生Weak regenerative ability
Z161 -0.74 -1.47 0.03 0.12 -0.94 弱再生Weak regenerative ability
Z165 -0.74 -1.47 0.03 0.12 -0.94 弱再生Weak regenerative ability
Z193 -0.74 -1.47 0.03 0.12 -0.94 弱再生Weak regenerative ability
Z44 -0.76 -1.22 0.03 0.17 -0.88 弱再生Weak regenerative ability
Z84 -0.76 -1.22 0.03 0.17 -0.88 弱再生Weak regenerative ability
Z147 -0.76 -1.22 0.03 0.17 -0.88 弱再生Weak regenerative ability
Z197 -0.77 -1.14 0.03 0.19 -0.87 弱再生Weak regenerative ability
Z25 -0.77 -1.05 0.03 0.21 -0.85 弱再生Weak regenerative ability
Z62 -0.77 -1.05 0.03 0.21 -0.85 弱再生Weak regenerative ability
Z96 -0.77 -1.05 0.03 0.21 -0.85 弱再生Weak regenerative ability
Z108 -0.77 -1.05 0.03 0.21 -0.85 弱再生Weak regenerative ability
Z111 -0.77 -1.05 0.03 0.21 -0.85 弱再生Weak regenerative ability
Z120 -0.77 -1.05 0.03 0.21 -0.85 弱再生Weak regenerative ability
Z127 -0.77 -1.05 0.03 0.21 -0.85 弱再生Weak regenerative ability
Z129 -0.77 -1.05 0.03 0.21 -0.85 弱再生Weak regenerative ability

附表1

4个样本测序比对结果"

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
Cleans bases		 GC含量
Clean_GC_Rate%		 Clean Q30% 平均
测序深度
Average depth		 基因组
覆盖率
genome coverage (1X)		 基因组
覆盖率
genome coverage (5X)
DN50 150971394 22796680494 148291154 22248395146 35.0791 89.6463 20.25 95.57 93.65
Keburi 145486518 21968464218 143073908 21437801507 35.8134 88.8524 19.87 95.76 93.87
高池Highly pool 151202346 22831554246 147403650 22105336093 35.173 89.5264 19.79 96.75 95.01
低池Lowly pool 151325210 22850106710 148367314 22245451907 35.4202 90.2708 20.22 96.73 94.96

图8

ED关联值在染色体上的分布 横坐标为染色体名称, 彩色的点代表每个SNP位点的ED值, 黑色的线为拟合后的ED值, 红色的虚线代表显著性关联阈值, ED值越高, 代表该点关联效果越好。"

表3

关联分析基因区域内信息统计"

染色体号
Chromosome ID		 起始位置
Start position		 终止位置
End position		 区间距离
Size (Mb)		 基因数目
Number of genes
Chr. 18 54560000 55560000 1 185
Chr. 18 55910000 56910000 1 194
总计Total — — 2 379

图9

候选区域内基因GO注释聚类图"

附表2

候选基因注释"

基因号
Gene ID		 NCBI登录号
RefSeq ID		 物理位置Physical position
(bp)		 拟南芥同源基因Arabidopsis homologous gene CDS
长度
CDS length (bp)		 氨基酸
长度
ORF (aa)		 分子量
大小
Molecular weight
(kD)		 pI 亚细胞定位预测Subcellular localization prediction 基因注释
Gene function prediction
Glyma.18G260900 XM_003552487.5 Gm18：54674591-54677015 AT3G29030 798 266 29.1 9.51 细胞壁
Cell wall		 Pollen allergen (Pollen_allerg_1)
Glyma.18G265400 XM_041012184.1 Gm18： 55017312-55018922 AT5G39280 687 229 25.26 8.66 细胞壁
Cell wall		 EXPANSIN-A21-RELATED
Glyma.18G271900 XM_014770962.3 Gm18： 55493601-55497764 AT5G60920 1263 421 47.06 9.64 细胞膜
Cell membrane		 COBRA-LIKE EXTRACELLULAR GLYCOSYL-PHOSPHATIDYL INOSITOL-ANCHORED FAMILY PROTEIN-RELATED
Glyma.18G272000 XM_003552552.4 Gm18： 55503155-55508039 AT5G60920 1347 449 49.87 8.9 细胞膜
Cell membrane		 COBRA-like protein (COBRA)
Glyma.18G272100 NM_001255848.2 Gm18： 55506268-55509726 AT5G15630 1296 432 48.44 9 细胞膜
Cell membrane		 COBRA-LIKE PROTEIN 4
Glyma.18G272200 XM_003552554.5 Gm18： 55515800-55518328 AT3G02230 1062 354 40.12 5.61 高尔基体
Golgi apparatus		 UDP-ARABINOPYRANOSE MUTASE 1-RELATED

图10

候选基因在不同时期不同材料中的表达量 I-0为SIM-0; I-14为SIM-14; E-3为SEM-3; E-5为SEM-5; E-7为SEM-7; E-14为SEM-14。*和**分别在0.05和0.01概率水平差异显著。"

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