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作物学报 ›› 2020, Vol. 46 ›› Issue (6): 819-831.doi: 10.3724/SP.J.1006.2020.93063

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

玉米叶向值的全基因组关联分析

彭勃1,赵晓雷1,王奕1,袁文娅1,李春辉2,李永祥2,张登峰2,石云素2,宋燕春2,王天宇2,*(),黎裕2,*()   

  1. 1天津市农作物研究所 / 天津市农作物遗传育种重点实验室, 天津300384
    2中国农业科学院作物科学研究所, 北京100081
  • 收稿日期:2019-12-03 接受日期:2020-01-15 出版日期:2020-06-12 网络出版日期:2020-02-17
  • 通讯作者: 王天宇,黎裕
  • 作者简介:彭勃, E-mail: snbopeng@163.com
  • 基金资助:
    国家自然科学基金项目(31601308);青年科研人员创新研究与实验项目(2018004);天津市自然科学基金项目(19JCZDJC34500);天津市农业科学院院长基金项目(17007)

Genome-wide association studies of leaf orientation value in maize

PENG Bo1,ZHAO Xiao-Lei1,WANG Yi1,YUAN Wen-Ya1,LI Chun-Hui2,LI Yong-Xiang2,ZHANG Deng-Feng2,SHI Yun-Su2,SONG Yan-Chun2,WANG Tian-Yu2,*(),LI Yu2,*()   

  1. 1Tianjin Crop Research Institute / Tianjin Key Laboratory of Crop Genetics and Breeding, Tianjin 300384, China
    2Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China
  • Received:2019-12-03 Accepted:2020-01-15 Published:2020-06-12 Published online:2020-02-17
  • Contact: Tian-Yu WANG,Yu LI
  • Supported by:
    National Natural Science Foundation of China(31601308);Innovative Research and Experiment Project for Young Researchers(2018004);Tianjin Natural Science Foundation(19JCZDJC34500);President’s Fund of Tianjin Academy of Agricultural Sciences(17007)

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摘要：

叶向值是反映叶片“直”和“立”两个特性的综合指标。叶向值高的品种, 叶片直而不弯, 叶夹角小, 有利于群体通风透光, 在群体密度较高时比平展型更容易获得高产。阐明叶向值的遗传基础, 对玉米理想株型分子设计育种具有重要的意义。本研究以285份多样性玉米自交系为材料, 利用Illumina的maizeSNP50芯片基因分型结合连续2年的叶向值表型鉴定, 通过全基因组关联分析方法挖掘玉米叶向值显著关联的SNP位点。方差分析表明, 不同自交系的叶向值差异达到极显著水平(P<0.01)。在最优模型选择时, 发现Q+K模型最适合本研究的叶向值关联分析。在2个年份下, 共检测到15个与叶向值显著关联的位点(P<4.05E-5), 包括27个SNP, 解释5.54%~8.73%的表型变异, 并挖掘了15个候选基因。其中1.07 bin上的位点2是本研究发现的重要位点, 其候选基因可能是编码细胞周期蛋白依赖性蛋白激酶的Zm00001d032050, 有待进一步图位克隆工作验证。

关键词: 玉米, 叶向值, 叶夹角, 单核苷酸多态性, 关联分析

Abstract:

Leaf orientation value is a comprehensive index reflecting the two characteristics of “straight” and “vertical” of leaves. The varieties with high leaf orientation value have straight and not curved leaves, and small angle, which are conducive to the wind ventilation and light transmission for maize population. When the planting density is high, it is easier to obtain high yield than the expanded plant-type. It is of great significance for molecular design breeding of ideal plant type to clarify the genetic basis of leaf orientation value. In this study, 285 diverse lines genotyped by the MaizeSNP50 chip were evaluated for leaf orientation in 2017 and 2018. The genome-wide association analysis (GWAS) were used to identified the SNPs, which were significant association with leaf orientation values. The analysis of variance showed that the significant variations were observed for leaf orientation value of different inbred lines (P < 0.01). In the selection of the optimal model, it was found that the Q + K model was the most suitable for the leaf orientation association analysis in this study. A total of 15 loci (P < 4.05E-5) were detected by GWAS, including 27 SNPs, explaining 5.54%-8.73% of phenotypic variation, and 15 candidate genes were mined in two years. Among them, site 2 in 1.07 bin was an important site found in this study, and its candidate gene might be Zm00001d032050 encoding cyclin dependent protein kinase, which needed to be further confirmed by map-based cloning.

Key words: maize, leaf orientation value, leaf angle, single nucleotide polymorphism, association analysis

表1

不同年份叶向值的基本统计量分析及相关分析"

年份
Year		 均值
Mean		 变异范围
Range		 标准差
SD		 偏度
Skewness		 峰度
Kurtosis		 相关系数Correlation coefficient
2017 2018
2017 59.45 12.99-86.28 13.77 -0.58 0.13
2018 63.86 17.05-90.00 13.11 -0.79 0.59 0.75**
BLUP 61.58 23.46-82.65 11.14 -0.63 0.30 0.95** 0.90**

图1

不同年份玉米叶向值的频率分布图 A: 2017年; B: 2018年; C: 2年联合的BLUP值。"

表2

不同年份叶向值的方差分析"

变异来源
Variation source		 方差分量
Variance		 遗传力
H2 (%)
基因型 Genotype 141.46** 87.86
年份Year 8.97**
基因型×年份 Genotype×year 21.41**
重复Replication 14.63
残差Residual 35.32

图2

285份自交系全基因组LD衰减图"

图3

不同年份玉米叶向值3种GWAS模型的QQ图 A: 2017年; B: 2018年; C: 2年联合的BLUP值。绿色点: Q模型; 蓝色点: K模型; 紫色点: Q+K模型。"

图4

不同环境下玉米叶向值GWAS (Q+K模型)的曼哈顿图 A: 2017年; B: 2018年; C: 2年联合的BLUP值。绿色点: 位点2峰值SNP上下游各50个SNP在不同年份的曼哈顿图。"

表3

不同年份玉米叶向值全基因组关联分析检测的显著的SNP位点及其候选基因"

位点a
Locusa		 Bin 年份
Year		 SNP 基因型
Genotype		 物理位置b
Physical position		 P值
P-value		 贡献率
R2 (%)		 峰值SNP
物理位置b
Lead SNP physical position		 QTL区间b QTL region b 候选基因
Candidate gene		 基因功能注释
Gene annotation
-LD +LD
1 1.02 BLUP PUT-163a-149085801-877 [A/G] 28,638,770 9.25E-06 7.95 28,638,770 28,306,770 28,638,770 Zm00001d028265 细胞分裂素响应因子
Cytokinin response regulator
1 1.02 2017 PUT-163a-149085801-877 [A/G] 28,638,770 3.21E-06 8.73
2 1.07 BLUP PZE-101164453 [T/C] 210,517,983 3.22E-05 6.94 211,113,165 210,781,165 211,445,165 Zm00001d032050 细胞周期蛋白依赖性蛋白激酶
Regulation of cyclin-dependent protein serine/threonine kinase activity
2 1.07 BLUP PZE-101164815 [A/G] 210,772,541 1.16E-06 8.15
2 1.07 2017 PZE-101164815 [A/G] 210,772,541 9.67E-07 8.49
2 1.07 2018 PZE-101164815 [A/G] 210,772,541 2.71E-05 6.24
2 1.07 2017 SYN25384 [A/G] 211,113,165 3.97E-05 6.99
2 1.07 BLUP SYN25375 [T/C] 211,116,324 1.90E-05 7.32
2 1.07 2017 SYN25375 [T/C] 211,116,324 3.78E-05 6.93
3 1.07 BLUP PZE-101165699 [A/G] 211,785,378 2.04E-05 7.55 211,785,378 211,453,378 212,117,378 Zm00001d032078 细胞分裂周期相关蛋白激酶
Cell division cycle 2-related protein kinase 7
3 1.07 2017 PZE-101165699 [A/G] 211,785,378 3.02E-05 7.30
4 1.07 BLUP PZE-101166565 [A/G] 212,687,705 1.20E-06 7.65 212,687,705 212,355,705 213,019,705 Zm00001d032100 果胶酶/果胶酶抑制剂
Pectinesterase/pectinesterase inhibitor 13
4 1.07 2017 PZE-101166565 [A/G] 212,687,705 5.31E-06 6.93
4 1.07 2018 PZE-101166565 [A/G] 212,687,705 9.69E-06 6.67
5 1.08 BLUP PZE-101196520 [A/G] 248,302,322 1.38E-05 7.78 248,302,322 247,970,322 248,634,322 Zm00001d033047 含SPX结构域蛋白
SPX domain-containing protein 3
6 1.08 2017 PZE-101199858 [T/C] 252,942,320 2.99E-05 6.73 252,942,320 252,610,320 253,274,320 Zm00001d033180 油菜素内酯缺乏性矮秆基因 Brassinosteroid-deficient dwarf1,brd1
6 1.08 2017 PZE-101199859 [A/G] 252,942,792 2.99E-05 6.73
7 2.01 BLUP SYN9223 [A/G] 3,825,340 3.71E-05 7.11 3,825,340 3,526,340 4,124,340 Zm00001d001968 细胞周期相关蛋白
Cyclin-related
8 2.04 BLUP PZE-102062747 [A/C] 43,019,177 1.98E-05 7.91 43,019,177 42,720,177 43,318,177 Zm00001d003401 类似14-3-3蛋白
14-3-3-like protein GF14-6
9 2.04 BLUP SYN29642 [T/C] 50,700,996 3.50E-05 6.15 50,700,996 50,401,996 50,999,996 Zm00001d003626 NAC-转录因子
NAC-transcription factor 76
10 2.07 2017 PZE-102150850 [T/G] 203,858,592 3.50E-05 6.82 203,858,592 203,559,592 204,157,592 Zm00001d006293 NLP转录因子
NLP-transcription factor 17
11 2.07 BLUP PZE-102152182 [A/G] 205,338,006 3.24E-05 5.54 205,338,006 205,039,006 205,637,006 Zm00001d006348 生长调节因子
Growth-regulating factor 9
12 5.06 BLUP PZE-105142621 [A/G] 201,997,615 9.76E-06 7.70 201,997,615 201,615,615 202,379,615 Zm00001d017618 ABI3-VP1-转录因子
ABI3-VP1-transcription factor 16
12 5.06 2017 PZE-105142621 [A/G] 201,997,615 1.72E-05 7.52
13 7.02 BLUP PZE-107043106 [A/G] 87,913,892 3.32E-05 8.24 87,913,892 87,468,892 88,358,892 Zm00001d020041 参与细胞壁果胶代谢蛋白
Cell wall pectin metabolic process
14 10.03 2017 PZE-110020884 [T/C] 28,391,702 2.32E-05 7.65 28,391,702 27,697,702 29,085,702 Zm00001d023927 锌指CCCH结构域蛋白
Zinc finger CCCH domain-containing protein 30
15 10.04 BLUP PZE-110053328 [A/G] 100,750,723 4.02E-05 6.73 100,750,723 100,056,723 101,444,723 Zm00001d025033 TCP转录因子
TCP-transcription factor 40

图5

本研究检测的与叶向值显著关联的位点在染色体上的分布及与前人研究结果的比较 染色体上粗体的bin代表本研究检测的与叶向值显著关联的位点。"

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