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作物学报

作物学报 ›› 2022, Vol. 48 ›› Issue (2): 304-319.doi: 10.3724/SP.J.1006.2022.13002

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

基于全基因组关联分析解析玉米籽粒大小的遗传结构

渠建洲1,2(), 冯文豪1, 张兴华1,2, 徐淑兔1,2,*(), 薛吉全1,2,*()   

  1. 1西北农林科技大学农学院/农业农村部西北旱区玉米生物与遗传改良重点实验室, 陕西杨凌 712100
    2陕西省玉米工程技术研究中心, 陕西杨凌 712100
  • 收稿日期:2021-01-06 接受日期:2021-04-26 出版日期:2022-02-12 网络出版日期:2021-06-03
  • 通讯作者: 徐淑兔,薛吉全
  • 作者简介:E-mail: qujz0220@163.com
  • 基金资助:
    本研究由国家重点研发计划项目(2018YFD0100203);国家现代农业产业技术体系建设专项(玉米)资助(CARS-02-64)

Dissecting the genetic architecture of maize kernel size based on genome-wide association study

QU Jian-Zhou1,2(), FENG Wen-Hao1, ZHANG Xing-Hua1,2, XU Shu-Tu1,2,*(), XUE Ji-Quan1,2,*()   

  1. 1Key Laboratory of Biology and Genetic Improvement of Maize in Arid Area of Northwest Region, Ministry of Agriculture and Rural Affairs / College of Agronomy, Northwest A&F University, Yangling 712100, Shaanxi, China;
    2Maize Engineering Technology Research Centre of Shaanxi Province, Yangling 712100, Shaanxi, China
  • Received:2021-01-06 Accepted:2021-04-26 Published:2022-02-12 Published online:2021-06-03
  • Contact: XU Shu-Tu,XUE Ji-Quan
  • Supported by:
    This study was supported by the National Key Research and Development Program of China(2018YFD0100203);the Agricultural Research System (Maize).(CARS-02-64)

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摘要：

玉米籽粒大小是产量重要构成因子之一, 也是受多基因调控的复杂数量性状, 挖掘玉米籽粒大小相关性状的关键调控基因, 将有助于提高玉米的产量。本研究以212份优良玉米自交系为材料, 于2018年和2019年分别对粒长、粒宽和粒厚进行测定, 并结合均匀分布于玉米基因组的73,006个单核苷酸多态性(single nucleotide polymorphism, SNP)标记进行全基因组关联分析。基于FarmCPU算法, 在玉米的10条染色体上检测到47个与籽粒大小相关性状关联的SNP。结合B73玉米自交系籽粒发育的动态时空转录数据, 在显著SNP标记的连锁不平衡区域内, 共检测到58个与籽粒大小相关的候选基因, 其编码的蛋白与多种蛋白存在互作关系, 参与并调控多个与籽粒发育密切相关的生物学过程。本研究为解析玉米籽粒发育的分子调控机制, 改良籽粒大小和提高作物产量提供了新的参考。

关键词: 玉米, 籽粒大小, 全基因组关联分析, 基因表达

Abstract:

Kernel size related traits are one of the important compounds of yield, and they are also complex quantitative traits regulated by multiple genes. Mining the key regulatory genes of maize kernel size related traits will help to improve the yield. In this study, 212 excellent maize inbred lines were selected as materials. The kernel length, kernel width, and kernel thickness were measured in 2018 and 2019, respectively, and we performed genome-wide association study (GWAS) based on 73,006 single nucleotide polymorphic (SNP) markers uniformly distributed in maize genome. Based on the FarmCPU algorithm, 47 SNP markers associated with kernel size related traits were detected on 10 chromosomes in maize. Combined with the public dynamic spatio-temporal transcriptional data of kernel development of B73 maize inbred line, 58 candidate genes related to kernel size were detected in the linkage disequilibrium (LD) region marked by significant SNP. The proteins encoded by candidate genes interacted with multiple proteins and participated in and regulated many biological processes closely related to kernel development. These results provide a new reference for understanding the molecular regulation mechanism of maize kernel development, improving kernel size and increasing crop yield.

Key words: maize, kernel size, genome-wide association study, gene expression

表1

不同年份玉米籽粒大小相关性状的基本统计分析"

性状
Trait		 年份
Year		 平均值
Average
(mm)		 标准差
SD		 变异范围
Range
(mm)		 变异系数
CV		 峰度
Kurt.		 偏度
Skew.		 遗传力
H2
(%)		 相关系数
Correlation coefficient
粒长KL
(mm)		 粒宽KW
(mm)		 粒厚KT
(mm)
粒长
KL (mm)		 2018 10.89 1.04 8.52-13.47 0.10 -0.50 0.19 55.12 1.00 0.09 -0.22**
2019 8.96 0.73 6.39-11.87 0.10 0.77 0.04 1.00 0.31** 0.04
BLUP 9.95 0.42 8.74-11.19 0.05 0.10 0.18 1.00 0.22** 0.03
粒宽
KW (mm)		 2018 7.86 0.87 6.22-9.95 0.09 -0.14 0.33 80.76 0.09 1.00 0.24**
2019 7.45 0.66 6.13-9.32 0.09 -0.13 0.35 0.31** 1.00 0.43**
BLUP 7.62 0.44 6.69-8.99 0.06 -0.09 0.30 0.22** 1.00 0.36**
粒厚
KT (mm)		 2018 4.61 0.45 3.60-5.80 0.09 -0.16 0.40 55.52 -0.22** 0.24** 1.00
2019 4.59 0.47 3.41-5.80 0.10 -0.34 0.37 0.04 0.43** 1.00
BLUP 4.60 0.19 4.10-5.14 0.04 -0.22 0.25 0.03 0.36** 1.00

图1

群体连锁不平衡(LD)和群遗传结构分析 A: 横轴表示同一染色体上单核苷酸位点(SNP)之间的物理距离, 纵轴表示连锁不平衡参数r2值, 颜色条表示不同的关联群体。B: K = 1~20范围内的交叉验证误差值曲线图。"

图2

粒长、粒宽和粒厚显著相关的SNP分布统计 红色、蓝色和黄色背景分别代表粒长、粒宽和粒厚; 竖线表示籽粒大小性状关联到的位点在染色体上的位置; 比例尺表示关联位点的显著水平; 直方图的高度表示位点的频率。"

表2

不同年份粒长、粒宽和粒厚显著相关的SNP"

标记名称
SNP ID		 年份
Year		 性状
Trait		 基因型
Genotype		 最小等位基因频率
MAF		 染色体
Chr.		 位置
Position		 P值
P-value		 表型贡献率
R2 (%)
Affx-291392839 2018 KL C/T 0.45 2 205,144,469 1.29E-05 0.36
Affx-291410933 2018 KL A/C 0.23 2 191,587,706 1.35E-05 4.52
Affx-291385262 2018 KL C/T 0.40 4 188,701,278 8.25E-06 6.96
Affx-158858862 2018 KL A/G 0.47 7 132,422,651 5.35E-07 20.90
Affx-88989857 2019 KL C/A 0.43 5 172,855,146 1.02E-05 11.64
Affx-291391022 2019 KL T/C 0.41 9 207,693,32 8.33E-06 14.53
Affx-291390553 BLUP KL C/T 0.46 1 14,651,295 6.14E-06 1.24
Affx-291430755 BLUP KL T/G 0.26 1 52,391,689 5.62E-07 13.31
Affx-291442609 BLUP KL G/A 0.37 2 134,763,888 2.39E-06 8.31
Affx-291378135 BLUP KL C/T 0.10 3 210,753,912 2.08E-07 5.97
Affx-291412195 BLUP KL C/T 0.30 3 128,909,025 4.11E-07 16.92
Affx-291417243 BLUP KL G/T 0.20 5 132,317,996 6.14E-10 13.73
Affx-291423518 BLUP KL A/G 0.36 5 10,908,609 2.63E-09 22.90
Affx-159157467 BLUP KL G/A 0.38 9 20,345,047 4.14E-06 12.08
Affx-291421141 2018 KW T/C 0.21 1 244,696,518 6.28E-11 18.69
Affx-291429284 2018 KW C/A 0.45 1 95,971,671 4.07E-08 18.38
Affx-291434526 2018 KW C/T 0.21 3 212,098,697 1.14E-05 0.62
Affx-291383862 2018 KW T/C 0.42 4 229,953,723 3.18E-06 14.42
Affx-291396984 2018 KW T/C 0.44 4 118,709,183 3.67E-06 2.38
Affx-291430867 2018 KW G/A 0.33 4 74,628,134 1.30E-05 11.78
Affx-291433635 2018 KW G/A 0.33 4 186,554,980 7.87E-06 19.65
Affx-291390831 2019 KW A/G 0.23 2 7,631,038 1.63E-07 6.09
Affx-291416165 2019 KW G/A 0.27 2 41,515,971 4.32E-07 1.50
Affx-291388322 2019 KW A/G 0.36 6 94,087,816 5.57E-08 5.08
Affx-291396454 2019 KW G/A 0.07 6 21,380,243 9.41E-07 15.80
Affx-291421141 BLUP KW T/C 0.23 1 244,696,518 4.18E-09 18.51
Affx-291391782 BLUP KW G/A 0.49 2 214,513,500 6.90E-12 18.84
Affx-291386982 BLUP KW G/A 0.38 3 140,660,245 7.62E-10 4.90
Affx-291443225 BLUP KW C/T 0.47 5 1,250,179 5.12E-07 1.73
Affx-291416220 BLUP KW G/A 0.41 6 98,426,114 1.09E-05 1.67
Affx-291424033 2018 KT G/A 0.32 1 279,751,443 1.88E-06 7.04
Affx-291437625 2018 KT C/T 0.23 1 246,781,098 1.58E-06 8.62
Affx-291442339 2018 KT T/G 0.10 1 198,355,431 2.82E-06 13.41
Affx-291423488 2018 KT G/A 0.39 3 117,603,753 5.43E-08 14.05
Affx-123595299 2018 KT T/C 0.46 4 33,851,115 6.28E-08 3.06
Affx-291407692 2018 KT C/T 0.47 4 68,756,350 2.42E-10 7.53
Affx-291421461 2018 KT T/G 0.24 5 190,291,719 7.78E-07 12.80
Affx-291440347 2018 KT T/C 0.27 5 46,983,911 2.69E-07 3.51
Affx-291431852 2018 KT C/T 0.09 8 33,721,488 1.07E-12 11.05
Affx-291393756 2018 KT T/C 0.17 10 144,450,832 2.09E-06 4.11
Affx-291392059 2019 KT A/T 0.47 1 204,796,933 1.16E-05 19.87
Affx-291380154 2019 KT T/C 0.13 2 196,175,692 1.10E-05 19.15
Affx-291409744 BLUP KT A/G 0.37 1 181,908,322 1.49E-06 3.75
Affx-291424033 BLUP KT G/A 0.31 1 279,751,443 1.17E-09 10.20
Affx-291384679 BLUP KT C/A 0.32 3 56,819,365 7.59E-06 8.77
Affx-291424461 BLUP KT T/C 0.39 4 43,693,955 1.31E-06 1.38
Affx-291442826 BLUP KT G/A 0.29 4 38,973,447 2.77E-06 15.91
Affx-291427217 BLUP KT T/C 0.46 5 59,748,660 3.61E-06 6.66
Affx-291432324 BLUP KT A/G 0.08 8 18,220,008 1.22E-07 14.41

表3

玉米粒长、粒宽和粒厚的候选基因及功能注释"

标记名称
SNP ID		 基因
Gene		 性状
Trait		 染色体
Chr.		 位置
Position		 功能注释
Annotation		 模块
Module
Affx-291430755 GRMZM2G033570 KL 1 52,391,689 ETHYLENE-INSENSITIVE3-like 1 protein M1
Affx-291410933 GRMZM2G014313 KL 2 191,587,706 Protein pob M2
Affx-291410933 GRMZM2G007885 KL 2 191,587,706 Myosin heavy chain-related protein M3
Affx-291410933 GRMZM2G150319 KL 2 191,587,706 O-fucosyltransferase family protein M4
Affx-291392839 GRMZM5G821439 KL 2 205,144,469 Chitin-inducible gibberellin-responsive protein 1 M5
Affx-291392839 GRMZM2G046011 KL 2 205,144,469 60S ribosomal protein L38 M6
Affx-291392839 GRMZM2G163233 KL 2 205,144,469 Male sterile 32 M7
Affx-291412195 GRMZM2G122443 KL 3 128,909,025 OS-9-like protein M8
Affx-291412195 GRMZM2G122481 KL 3 128,909,025 Cytochrome c oxidase subunit 5C M9
Affx-291412195 GRMZM2G138077 KL 3 128,909,025 Uncharacterized protein —
Affx-291378135 AC230013.2_FG007 KL 3 210,753,912 60S ribosomal protein L18a —
Affx-291378135 GRMZM2G150631 KL 3 210,753,912 Transducin/WD40 repeat-like superfamily protein M10
Affx-88989857 GRMZM2G119517 KL 5 172,855,146 ACT domain-containing protein ACR3 M11
Affx-291423518 GRMZM2G145854 KL 5 10,908,609 NADH-ubiquinone oxidoreductase subunit M12
Affx-291423518 GRMZM2G569855 KL 5 10,908,609 Threonine dehydratase 1 biosynthetic M13
Affx-291423518 GRMZM2G109383 KL 5 10,908,609 Phosphoglucomutase 2 M14
Affx-291391022 GRMZM5G829544 KL 9 20,769,332 Fatty acyl-ACP thioesterase 2 M15
Affx-291391022 GRMZM2G147399 KL 9 20,769,332 Early nodulin 93 M16
Affx-291391022 GRMZM2G131421 KL 9 20,769,332 Early nodulin 93 M17
Affx-291391022 GRMZM2G404897 KL 9 20,769,332 Zinc finger protein M18
Affx-159157467 GRMZM2G173693 KL 9 20,345,047 Pre-mRNA-splicing factor 38B-like M19
Affx-291416165 GRMZM2G325131 KW 2 41,515,971 Anthranilate synthase homolog 1 M20
Affx-291391782 GRMZM2G049347 KW 2 214,513,500 Synaptotagmin-5 M21
Affx-291434526 GRMZM2G152686 KW 3 212,098,697 Pyruvate kinase M22
Affx-291434526 GRMZM2G070360 KW 3 212,098,697 V-type proton ATPase subunit E-like M23
Affx-291430867 GRMZM2G117755 KW 4 74,628,134 Hypersensitive-induced response protein 2 M24
Affx-291383862 GRMZM2G162992 KW 4 229,953,723 KH domain-containing protein M25
Affx-291443225 GRMZM2G034326 KW 5 1,250,179 DNA-directed RNA polymerases II, IV, and V subunit 8B M26
Affx-291443225 GRMZM2G069916 KW 5 1,250,179 LUC7 related protein M27
Affx-291443225 GRMZM2G138676 KW 5 1,250,179 Shaggy-related protein kinase kappa M28
Affx-291396454 GRMZM2G060856 KW 6 21,380,243 Membrane protein M29
Affx-291442339 GRMZM2G318475 KT 1 198,355,431 Eukaryotic translation initiation factor 6 M30
Affx-291442339 GRMZM2G017110 KT 1 198,355,431 Glutamate decarboxylase M31
Affx-291437625 GRMZM2G012119 KT 1 246,781,098 Post-illumination chlorophyll fluorescence increase M32
Affx-291437625 GRMZM2G013600 KT 1 246,781,098 DNA-directed RNA polymerases I, II, and III polypeptide M33
Affx-291437625 GRMZM2G146819 KT 1 246,781,098 Uncharacterized protein M34
Affx-291437625 GRMZM2G146818 KT 1 246,781,098 40S ribosomal protein —
Affx-291437625 GRMZM2G146589 KT 1 246,781,098 Lysine-tRNA ligase M35
Affx-291437625 GRMZM2G146486 KT 1 246,781,098 P-loop containing nucleoside triphosphate hydrolase Superfamily protein M36
Affx-291437625 GRMZM2G034417 KT 1 246,781,098 Inositol-phosphate phosphatase M37
Affx-291424033 GRMZM2G047456 KT 1 279,751,443 Peroxidase 35 M38
Affx-291424033 GRMZM2G307252 KT 1 279,751,443 SecY protein transport family protein M39
Affx-291392059 GRMZM2G357804 KT 1 204,796,933 UDP-N-acetylglucosamine-peptide N-acetylglucosaminyltransferase SPINDLY M40
Affx-291392059 GRMZM2G057608 KT 1 204,796,933 40S ribosomal protein S25-1 M41
Affx-291392059 GRMZM2G167548 KT 1 204,796,933 Multiple myeloma tumor-associated protein 2 M42
Affx-291392059 GRMZM2G167836 KT 1 204,796,933 Vesicle-associated membrane protein 727 M43
Affx-291380154 GRMZM2G073942 KT 2 196,175,692 Uncharacterized protein —
Affx-291423488 GRMZM2G138268 KT 3 117,603,753 Auxin-responsive protein IAA 10 M44
Affx-123595299 GRMZM2G139550 KT 4 33,851,115 Aldolase superfamily protein M45
Affx-123595299 GRMZM5G870572 KT 4 33,851,115 BSD domain containing protein M46
Affx-291442826 GRMZM2G064807 KT 4 38,973,447 Pentatricopeptide repeat-containing protein M47
Affx-291442826 GRMZM2G158153 KT 4 38,973,447 KH domain-containing protein M48
Affx-291421461 GRMZM2G004847 KT 5 190,291,719 Pectin lyase-like superfamily protein M49
Affx-291427217 GRMZM2G102447 KT 5 59,748,660 WAS/WASL-interacting protein family member 1-like M50
Affx-291431852 GRMZM2G180990 KT 8 33,721,488 Ligatin M51
Affx-291432324 GRMZM2G107696 KT 8 18,220,008 Ubiquitin carboxyl-terminal hydrolase M52
Affx-291432324 GRMZM2G107639 KT 8 18,220,008 Transaminase M53
Affx-291393756 GRMZM2G086030 KT 10 144,450,832 Tetratricopeptide repeat (TPR)-like superfamily protein M54

图3

玉米粒长相关候选基因的动态表达模式 比例尺表示标准化的基因表达水平。"

图4

玉米粒宽相关候选基因的动态表达模式 比例尺表示标准化的基因表达水平。"

图5

玉米粒厚相关候选基因的动态表达模式 比例尺表示标准化的基因表达水平。"

图6

54个高表达的候选基因编码蛋白互作网络 节点表示蛋白, 连线表示蛋白之间的互作关系。红色表示候选基因, 其他颜色表示候选基因编码蛋白的互作网络。"

图7

候选基因编码蛋白互作网络的功能富集分析 圆圈大小表示基因富集数目, 标准化的Q值表示富集的显著程度。A代表M6、M8、M24、M26、M29、M33、M39、M41、M47和M51中蛋白显著富集的生物学过程; B代表M11、M18、M31、M36、M49和M53中蛋白显著富集的生物学过程。"

附图1

群体遗传结构分析 基于k = 15的群体结构, 不同颜色片段的长度表示该个体基因组中某个亲本所占的比例。"

附图2

全基因组关联分析曼哈顿图 A~C: 2018年的粒长、粒宽和粒厚; D~F: 2019年的粒长、粒宽和粒厚; G~I: 2年的粒长、粒宽和粒厚的BLUP值。黑色水平线代表全基因组关联分析的显著阈值。"

附图3

全基因组关联分析QQ图 A~C: 2018年的粒长、粒宽和粒厚; D~F: 2019年的粒长、粒宽和粒厚; G~I: 2年的粒长、粒宽和粒厚的BLUP值。横轴表示标准化的期望P值, 纵轴表示标准化的观察到的P值。"

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