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作物学报 ›› 2024, Vol. 50 ›› Issue (5): 1091-1103.doi: 10.3724/SP.J.1006.2024.34142

• 作物遗传育种·种质资源·分子遗传学 •    下一篇

大豆根茎过渡区弯曲突变体Mrstz的鉴定与基因定位

苗龙1**(), 舒阔1**(), 李娟1, 黄茹1, 王业杏1, Soltani Muhammad YOUSOF1, 许竞好1, 吴传磊1, 李佳佳1, 王晓波1,*(), 邱丽娟2,*()   

  1. 1安徽农业大学农学院, 安徽合肥 230036
    2中国农业科学院作物科学研究所 / 农业农村部作物基因资源与遗传改良重大科学工程 / 农业农村部作物基因资源与种质创制重点实验室, 北京 100081
  • 收稿日期:2023-07-20 接受日期:2024-01-12 出版日期:2024-05-12 网络出版日期:2024-02-08
  • 通讯作者: 王晓波, E-mail: wxbphd@163.com; 邱丽娟, E-mail: qiulijuan@caas.cn
  • 作者简介:苗龙, E-mail: lmiao5@163.com;
    舒阔, E-mail: 1125974604@qq.com第一联系人：

    **同等贡献

  • 基金资助:
    国家重点研发计划项目(2021YFD1201605);安徽省自然科学基金项目(2308085MC88);安徽省自然科学基金项目(2108085QC114);安徽农业大学自然科学基金项目(k2031005)

Identification and gene mapping of soybean mutant Mrstz in root-stem transition zone

MIAO Long1**(), SHU Kuo1**(), LI Juan1, HUANG Ru1, WANG Ye-Xing1, Soltani Muhammad YOUSOF1, XU Jing-Hao1, WU Chuan-Lei1, LI Jia-Jia1, WANG Xiao-Bo1,*(), QIU Li-Juan2,*()   

  1. 1College of Agriculture, Anhui Agricultural University, Hefei 230036, Anhui, China
    2Institute of Crop Sciences, Chinese Academy of Agricultural Sciences / the National Key Facility for Crop Gene Resources and Genetic Improvement (NFCRI), the Ministry of Agriculture and Rural Affairs / Key Laboratory of Crop Gene Resource and Germplasm Enhancement, the Ministry of Agriculture and Rural Affairs, Beijing 100081, China
  • Received:2023-07-20 Accepted:2024-01-12 Published:2024-05-12 Published online:2024-02-08
  • Contact: E-mail: wxbphd@163.com; E-mail: qiulijuan@caas.cn
  • About author:First author contact:

    **Contributed equally to this work

  • Supported by:
    National Key Research and Development Program of China(2021YFD1201605);Natural Science Foundation of Anhui Province(2308085MC88);Natural Science Foundation of Anhui Province(2108085QC114);Natural Science Foundation Project of Anhui Agricultural University(k2031005)

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摘要：

植物根茎过渡区(root-stem transition zone, RSTZ)将根和茎相互连接, 其发育形态决定了大豆的地上部株型和抗倒伏潜力。本研究通过EMS诱变获得一个RSTZ弯曲或旋转的大豆突变体Mrstz, 其形态特征能够稳定遗传, 是探究大豆茎秆发育规律的特异材料。将该突变体和栽培大豆中黄13杂交构建重组自交系群体, 对群体中直立和弯曲型后代的RSTZ进行解剖结构比较, 发现弯曲型株系比直立型株系的维管形成层较宽、次生木质部细胞层数较多、细胞形状不规则, 表明维管组织分化可能是导致RSTZ形态发生差异的重要因素之一。进一步对化学组分测定发现, 木质素和粗纤维含量越高越不易弯曲。选取RIL群体中弯曲型和直立型2种极端株系进行BSA-Seq, 采用SNP-index和InDel-index关联分析方法鉴定到调控RSTZ形态的关联区域Chr19: 43030943~45849854, 该区间共含有319个基因。结合生物信息学分析、基因注释信息和表达丰度分析筛选到7个候选基因, 分别为Glyma.19G170200、Glyma.19G201500、Glyma.19G187800、Glyma.19G178200、Glyma.19G197000、Glyma.19G179100、Glyma.19G196900。其中, Glyma.19G187800、Glyma.19G178200和Glyma.19G196900在大豆驯化中潜在影响RSTZ形态建成。本研究为解析大豆RSTZ组织形成及其遗传基础提供了材料基础, 并为挖掘调控大豆茎秆发育基因提供新的见解。

关键词: 大豆, 根茎过渡区, 突变体, BSA-seq, 候选基因

Abstract:

Root-stem transition zone (RSTZ) connects roots and stems, and its morphology modifies the structure of aerial part and lodging resistance potential in soybean. In this study, a soybean mutant Mrstz, appearing with curved or rotated RSTZ, was obtained by EMS mutagenesis. Its morphological characteristics were stably inherited and could provide specific sources for exploring the development patterns of soybean stems. Therefore, this mutant was crossed with Zhonghuang 13 to construct a recombinant inbred line population. By comparing the anatomical structure of vertical RSTZ and curved RSTZ, the wider vascular cambium, more secondary xylem cell layers and irregular cell shape were identified in curved lines, indicating that vascular cambium differentiation may be one of the important factors leading to the difference of RSTZ morphology. Subsequently, the chemical compositions of lines with vertical RSTZ or curved RSTZ were determined, respectively. It was found that the higher lignin and crude fiber content in the RSTZ, the more difficult to bend. The RSTZ with curved or vertical lines were further selected for BSA-seq. SNP-index and InDel-index methods were employed to mine a significant association region, Chr. 19: 43,030,943-45,849,854 containing 319 genes, which may regulate RSTZ morphology. Combined bioinformatics analysis, gene annotation information and expression abundance analysis, seven candidate genes (Glyma.19G170200, Glyma.19G201500, Glyma.19G187800, Glyma.19G178200, Glyma.19G197000, Glyma.19G179100, Glyma.19G196900) were screened. Among them, Glyma.19G187800, Glyma.19G178200, and Glyma.19G196900 potentially affected RSTZ morphogenesis in soybean domestication. This study not only provides germplasm resources for the understanding of soybean RSTZ tissue formation and its genetic basis, but also provides new insights for further exploration of genes regulating soybean stalk development.

Key words: soybean, root and stem transition zone, mutant, BSA-seq, candidate genes

图1

根茎过渡区直立型与弯曲型植株及其解剖结构比较 A: VC、V6、R5、R8时期根茎过渡区直立型与弯曲型大豆植株; B: R5时期直立型与弯曲型株系下胚轴解剖结构。Vc: 维管形成层; Sx: 次生木质部; Sp: 次生韧皮部。A图标尺表示2 cm, B图标尺表示50 μm。VC: 子叶期; V6: 六叶期; R5: 始粒期; R8: 完熟期。"

图2

弯曲型与直立型根茎过渡区的化学组分分布及比较 A、B、C分别为弯曲型与直立型根茎过渡区中粗纤维、纤维素、木质素化学组分分布图; D、E、F柱状图代表平均值±标准差(*: P < 0.05, **: P < 0.01, t检验)。"

表1

样品测序数据的质量评估"

样本类型
Sample type		 纯化后读数
Clean reads		 纯化后碱基数
Clean base		 GC
(%)		 Q30
(%)		 比对上的序列
Mapped reads (%)
中黄13 Zhonghuang 13 37,644,247 11,293,274,100 36.24 94.85 98.40
根茎过渡区弯曲突变体MRstz 43,314,597 12,994,379,100 35.16 94.54 98.32
RSTZ直立型株系Vertical RSTZ lines 126,937,624 38,081,287,200 35.10 94.94 97.99
RSTZ弯曲型株系Curved RSTZ lines 130,489,056 39,146,716,800 35.88 94.56 98.14

图3

SNP-index和InDel-index关联值在染色体上的分布 RSTZ两种类型的delta-SNP-index (A)和delta-InDel-index (B)拟合图; 横坐标表示染色体的位置, 黑色曲线表示相应的关联值, 最上侧的红线代表置信度为99%的阈值线, 红色箭头指示定位的候选区域。"

表2

BSA-seq关联分析获得大豆根茎过渡区形态的候选区域"

关联分析方法
Association analysis methods		 染色体
Chr.		 起点
Start
(bp)		 终点
End
(bp)		 区间大小
Region size (Mb)		 基因数
Number of genes		 已报道倒伏性状相关候选位点
Candidate loci for inversion reported
Delta-SNP-index 19 43,030,943 46,037,125 3.01 346 Lodging 1-1, Lodging 4-2, Lodging 4-3, Lodging 8-4, Lodging 9-5[32]
Delta-InDel-index 19 42,975,089 45,849,854 2.87 323 Lodging 1-1, Lodging 4-2, Lodging 4-3, Lodging 8-4, Lodging 9-5[32]
Delta-SNP-index and delta-InDel-index 19 43,030,943 45,849,854 2.82 319 Lodging 1-1, Lodging 4-2, Lodging 4-3, Lodging 8-4, Lodging 9-5[32]

图4

候选区域内基因GO注释分类 横坐标为GO各分类内容, 纵坐标左边和右边分别表示基因数目所占百分比和基因数目。"

图5

一致性关联区间内所有基因在不同大豆组织中的表达水平聚类热图"

图6

根茎过渡区弯曲型和直立型株系中候选基因表达水平比较 GmCYP2用作内参, 候选基因在不同株系中的相对表达量进行t检验(*: P < 0.05; **: P < 0.01; ***: P < 0.001)。"

表3

大豆根茎过渡区形态候选基因的遗传多样性分析"

基因
Gene		 单倍型
Haplotype		 频率* Frequency* 核苷酸多态性 π 遗传
分化指数 FST
野生品种
Wild		 当地品种
Landrace		 育成品种
Cultivar		 野生大豆
Wild soybean		 栽培大豆
Cultivated soybean
Glyma.19G170200 Hap0-Hap6 0.095, 0.05, 0.139, 0.275, 0.160, 0.142, 0.139 0.616, 0.352, 0.032, 0, 0, 0, 0 0.719, 0.262, 0.020, 0, 0, 0, 0 0.00364 0.00198 0.22
Glyma.19G201500 Hap0-Hap6 0.305, 0.006, 0.013, 0.242, 0.082, 0.198, 0.154 0.524, 0.408, 0.052, 0, 0.013, 0, 0.002 0.612, 0.323, 0.055, 0, 0.001, 0, 0 0.00257 0.00171 0.16
Glyma.19G187800 Hap0-Hap3 0.212, 0.361, 0.206, 0.222 0.737, 0.126, 0.137, 0 0.862, 0.099, 0.039, 0 0.00373 0.00173 0.26
Glyma.19G178200 Hap0-Hap9 0.075, 0.024, 0.008, 0.012, 0.811, 0.004, 0.028, 0.004, 0.035, 0 0.258, 0.066, 0.171, 0.136, 0.002, 0.116, 0.116, 0.073, 0.021, 0.041 0.338, 0.316, 0.123, 0.082, 0.003, 0.075, 0.008, 0.026, 0.019, 0.012 0.00170 0.00107 0.32
Glyma.19G197000 Hap0-Hap2 0.695, 0.194, 0.111 0.83, 0.168, 0.002 0.727, 0.273, 0 0.00322 0.00258 0.16
Glyma.19G179100 Hap0-Hap2 0.46, 0.003, 0.537 0.965, 0.035, 0 0.937, 0.062, 0 0.00223 0.00069 0.17
Glyma.19G196900 Hap0-Hap4 0.05, 0.528, 0.142, 0.184, 0.096 0.437, 0.385, 0.174, 0.003, 0.002 0.512, 0.212, 0.275, 0, 0 0.00195 0.00123 0.28
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