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作物学报 ›› 2024, Vol. 50 ›› Issue (12): 2984-2997.doi: 10.3724/SP.J.1006.2024.44070

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

山西谷子种质资源株高全基因组关联分析

阳世杰1,2(), 王华智1,2, 潘怡敏1,2, 黄蕊2, 侯森2, 秦慧彬2, 穆志新2,*(), 王海岗2,*()   

  1. 1山西农业大学农学院, 山西太谷 030801
    2山西农业大学农业基因资源研究中心 / 农业农村部黄土高原作物基因资源与种质创制重点实验室, 山西太原 030031
  • 收稿日期:2024-04-26 接受日期:2024-08-15 出版日期:2024-12-12 网络出版日期:2024-08-29
  • 通讯作者: *穆志新, E-mail: muzx2008@sina.com; 王海岗, E-mail: wanghg@sxau.edu.cn
  • 作者简介:E-mail: dicmery@163.com
  • 基金资助:
    山西省科技重大专项计划“揭榜挂帅”项目(202101140601027);国家自然科学基金项目(32241041);山西农业大学生物育种工程项目(YZGC149)

Genome-wide association analysis for plant height in foxtail millet (Setaria italica L.) germplasm resources in Shanxi, China

YANG Shi-Jie1,2(), WANG Hua-Zhi1,2, PAN Yi-Min1,2, HUANG Rui2, HOU Sen2, QIN Hui-Bin2, MU Zhi-Xin2,*(), WANG Hai-Gang2,*()   

  1. 1College of Agronomy, Shanxi Agricultural University, Taigu 030801, Shanxi, China
    2Center for Agricultural Genetic Resources Research, Shanxi Agricultural University / Key Laboratory of Crop Gene Resources and Germplasm Enhancement on Loess Plateau, Ministry of Agriculture and Rural Affairs, Taiyuan 030031, Shanxi, China
  • Received:2024-04-26 Accepted:2024-08-15 Published:2024-12-12 Published online:2024-08-29
  • Contact: *E-mail: muzx2008@sina.com; E-mail: wanghg@sxau.edu.cn
  • Supported by:
    Major Special Science and Technology Plan ‘Unveiling and Commanding’ Projects in Shanxi Province(202101140601027);National Natural Science Foundation of China(32241041);Shanxi Agricultural University Biological Breeding Engineering(YZGC149)

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摘要：

适宜的株高能够有效增强谷子养分利用效率和抗倒伏能力。本研究以313份山西谷子地方品种微核心种质为关联群体, 在5个环境下调查谷子株高, 对其进行全基因组深度重测序, 数据质量控制后得到均匀分布于谷子9条染色体的3,160,066个SNP标记, 进行株高全基因组关联分析(GWAS)。共定位到8个与株高显著关联的QTL位点, 单个位点表型变异解释率为7.13%~12.08%。在8个稳定QTL位点上下游各25 kb的置信区间内共发现40个候选基因, 结合基因注释信息等筛选到6个候选基因, 主要参与激素合成、细胞分裂调控、信号转导和糖类物质代谢等途径, 并通过单倍型分析发现候选基因Millet_GLEAN_10031852的一个优异单倍型Hap2可以有效降低株高。

关键词: 谷子, 株高, 全基因组关联分析, 单倍型, 候选基因

Abstract:

A suitable plant height can effectively enhance the nutrient utilization efficiency and lodging resistance of millet. This study utilized 313 local millet varieties from Shanxi as an association group. Plant height was investigated in five different environments, followed by whole-genome deep resequencing. After quality control of the data, 3,160,066 SNP markers uniformly distributed across the nine chromosomes of millet were obtained for genome-wide association analysis (GWAS) of plant height. Eight QTL loci significantly associated with plant height were identified, with each locus explaining 7.13% to 12.08% of the phenotypic variation. Within the 25 kb upstream and downstream confidence intervals of these eight stable QTL loci, forty candidate genes were discovered. Integrating gene annotation information, six candidate genes were identified to be primarily involved in hormone synthesis, cell division regulation, signal transduction, and carbohydrate metabolism. Haplotype analysis revealed that the superior haplotype Hap2 of the candidate gene Millet_GLEAN_10031852 can effectively reduce plant height.

Key words: foxtail millet, plant height, genome-wide association analysis, haplotypes, candidate genes

表1

株高表型数据统计分析"

环境
Environment		 均值±标准差
Mean ± SD		 变异系数
CV (%)		 变异范围
Range		 偏度
Skewness		 峰度
Kurtosis		 遗传力
H2
18JZ 118.71±19.06 16.06 44.20-167.20 -0.63 0.24 0.96
19JZ 109.57±16.33 14.90 55.80-156.80 -0.38 -0.09
20JZ 118.33±20.82 17.59 70.00-154.00 -0.50 -0.03
20DT 120.39±15.57 12.93 40.80-163.60 -0.57 0.06
20YC 124.84±14.63 11.71 66.30-164.40 -0.62 0.84

图1

不同环境株高频率分布直方图 缩写同表1。"

图2

313份SNP变异信息的基因型特征 a: K值折线图; b: 主成分分析图; c: 连锁不平衡衰减LD图; d: 系统发育树与群体结构图。"

图3

7个亚群不同环境下株高性状显著性分析 缩写同表1。BLUE: 最佳线性无偏估计值。不同小写字母代表在0.05概率水平差异显著。"

图4

谷子株高GWAS分析结果 缩写同表1。BLUE: 最佳线性无偏估计值。"

表2

与株高相关的稳定QTL标记及候选基因"

QTL标记
QTL marker		 染色体
Chr.		 QTL 区间
QTL region (bp)		 QTN标记
QTN marker		 P值
P-value		 性状环境
Trait environment		 表型解释率
Phenotypic variation explained (%)		 候选基因
Candidate gene		 基因功能注释
Gene annotation
qPM3_1 3 18,916,296-18,966,346 PMG_18941296 7.45E-06 18JZ/19JZ/20JZ/20DT/BLUE 9.69 Millet_GLEAN_10028058 Myb DNA结构域
Myb-like DNA-binding domain
PMG_18941340 5.59E-07 18JZ/19JZ/20JZ/20DT/BLUE 9.69
PMG_18941346 5.59E-07 18JZ/19JZ/20JZ/20DT/BLUE 9.69
qPM5_2 5 1,178,009-1,236,158 PMG_1203009 9.72E-07 20YC/BLUE 10.78 Millet_GLEAN_10034090 细胞分裂素反应因子4
Cytokinin response factor 4
PMG_1207247 8.24E-06 20YC/BLUE 9.71 Millet_GLEAN_10034089 s位点凝集素蛋白激酶家族蛋白
s-locus lectin protein kinase family protein
PMG_1208529 7.19E-08 20YC/BLUE 9.63 Millet_GLEAN_10034086 s位点凝集素蛋白激酶家族蛋白
s-locus lectin protein kinase family protein
PMG_1210670 7.22E-07 20YC/BLUE 8.42 Millet_GLEAN_10034085 富亮氨酸重复蛋白激酶家族蛋白
Leucine-rich repeat protein kinase family protein
PMG_1210687 7.22E-07 20YC/BLUE 8.40 Millet_GLEAN_10034088 s位点凝集素蛋白激酶家族蛋白
s-locus lectin protein kinase family protein
PMG_1210696 7.19E-08 20DT/20YC/BLUE 8.43
PMG_1210700 7.19E-08 20DT/20YC/BLUE 8.43
PMG_1211104 7.22E-07 20YC/BLUE 9.63
PMG_1211147 7.22E-07 20YC/BLUE 9.12
PMG_1211158 7.22E-07 20YC/BLUE 9.12
qPM6_2 6 29,775,230-29,825,230 PMG_29800230 6.82E-06 20JZ/20DT/BLUE 8.39 Millet_GLEAN_10001507 受体样蛋白41
Receptor like protein 41
Millet_GLEAN_10001508 转移酶家族
Transferase family
Millet_GLEAN_10001510 转移酶家族
Transferase family
Millet_GLEAN_10001511 QWRF家族
QWRF family
qPM7_1 7 13,431,973-13,481,973 PMG_13456973 6.18E-09 18JZ/19JZ/20JZ/20DT/BLUE 9.69 Millet_GLEAN_10031850 LEA富含羟基脯氨酸糖蛋白家族
LEA hydroxyproline-rich glycoprotein family
Millet_GLEAN_10031851 肽酶M20/M25/M40家族蛋白
Peptidase M20/M25/M40 family protein
Millet_GLEAN_10031852 肽酶M20/M25/M40家族蛋白
Peptidase M20/M25/M40 family protein
Millet_GLEAN_10031853 肽酶M20/M25/M40家族蛋白
Peptidase M20/M25/M40 family protein
Millet_GLEAN_10031849 NDR1/HIN1-蛋白2
NDR1/HIN1-like protein 2
Millet_GLEAN_10031855 Dcp1 脱酶家族
Dcp1-like decapping family
qPM7_2 7 29,921,803-29,971,803 PMG_29946803 6.82E-06 19JZ/20JZ/BLUE 8.17 Millet_GLEAN_10037443 抗病蛋白
Disease resistance protein
Millet_GLEAN_10037449 蛋白酪氨酸激酶
Protein tyrosine kinase
Millet_GLEAN_10037450 含有LRR和NB-ARC结构域的抗病蛋白
LRR and NB-ARC domains-containing disease resistance protein
Millet_GLEAN_10037452 含NB-ARC结构域的抗病蛋白
NB-ARC domain-containing disease resistance protein
Millet_GLEAN_10037453 溴域末端外转录调控
Bromodomain extra-terminal - transcription regulation
qPM8_1 8 32,285,639-32,335,639 PMG_32310639 7.45E-06 18JZ/19JZ/20JZ/20DT/BLUE 9.68 Millet_GLEAN_10007111 BURP 域
BURP domain
Millet_GLEAN_10007109 多铜氧化酶家族
The multicopper oxidase family
Millet_GLEAN_10007108 蛋白激酶结构域
Protein kinase domain
Millet_GLEAN_10007107 BURP结构域蛋白
BURP domain-containing protein
Millet_GLEAN_10007105 胞苷转移酶
Cytidylyltransferase-like
qPM9_1 9 906,306-956,306 PMG_931306 6.40E-10 18JZ/20YC/BLUE 12.08 Millet_GLEAN_10004992 Prolycopene异构酶
Prolycopene isomerase
Millet_GLEAN_10004994 FAD/NAD(P)结合氧化还原酶家族蛋白
FAD/NAD(P)-binding oxidoreductase family protein
Millet_GLEAN_10004995 蛋白激酶超家族
The protein kinase superfamily
Millet_GLEAN_10004996 SPFH域/ Band 7家族
SPFH domain / Band 7 family
Millet_GLEAN_10004999 磷脂酶D
Phospholipase D delta
Millet_GLEAN_10004993 肽酶C13家族
Peptidase C13 family
qPM9_2 9 1,033,570-1,109,794 PMG_1058570 8.46E-06 19JZ/20JZ/BLUE 7.17 Millet_GLEAN_10005900 肽酶抑制剂I9
Peptidase inhibitor I9
PMG_1073463 10.65 Millet_GLEAN_10005901 铵转运蛋白家族
Ammonium Transporter Family
PMG_1076745 7.57 Millet_GLEAN_10005902 丝氨酸苏氨酸蛋白激酶
Serine threonine-protein kinase
PMG_1076759 7.57 Millet_GLEAN_10005904 argonaute家族
the argonaute family
PMG_1077324 7.94 Millet_GLEAN_10005905 丝氨酸苏氨酸蛋白激酶
Serine threonine-protein kinase
PMG_1077758 7.13 Millet_GLEAN_10005908 转录因子GHD7
Transcription factor GHD7
PMG_1083194 10.60 Millet_GLEAN_10005911 烟酸转磷酸核糖基酶
Nicotinate phosphoribosyl transferase
PMG_1084794 8.43 Millet_GLEAN_10005912 植物纤维素合成酶
Plant cellulose synthase subfamily

图5

Millet_GLEAN_10031852基因结构、单倍型分析、多重检验显著性差异图 缩写同表1。BLUE: 最佳线性无偏估计值。*、**、***和****分别表示在0.05、0.01、0.001和0.0001概率水平差异显著; ns: 无显著性差异。"

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