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作物学报 ›› 2021, Vol. 47 ›› Issue (10): 1891-1902.doi: 10.3724/SP.J.1006.2021.01078

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

小麦穗发芽性状的全基因组关联分析

谢磊1,2(), 任毅1,2, 张新忠1,3, 王继庆1,2, 张志辉1,2, 石书兵1,2, 耿洪伟1,2,*()   

  1. 1新疆农业大学农学院, 新疆乌鲁木齐 830052
    2新疆农业大学生物技术重点实验室, 新疆乌鲁木齐 830052
    3新疆农业科学院粮食作物研究所, 新疆乌鲁木齐 830091
  • 收稿日期:2020-10-04 接受日期:2021-01-13 出版日期:2021-10-12 网络出版日期:2021-02-24
  • 通讯作者: 耿洪伟
  • 作者简介:E-mail: 1784462634@qq.com
  • 基金资助:
    国家自然科学基金项目(31771786);新疆维吾尔自治区科技创新基地建设项目(PT1910)

Genome-wide association study of pre-harvest sprouting traits in wheat

XIE Lei1,2(), REN Yi1,2, ZHANG Xin-Zhong1,3, WANG Ji-Qing1,2, ZHANG Zhi-Hui1,2, SHI Shu-Bing1,2, GENG Hong-Wei1,2,*()   

  1. 1Agricultural College of Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
    2Key Laboratory of Biotechnology, Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
    3Institute of Grain Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830091, Xinjiang, China
  • Received:2020-10-04 Accepted:2021-01-13 Published:2021-10-12 Published online:2021-02-24
  • Contact: GENG Hong-Wei
  • Supported by:
    National Natural Science Foundation of China(31771786);Technical Innovation Bases Construction Project of Xinjiang Uygur Autonomous Region(PT1910)

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摘要：

为了解小麦穗发芽的遗传机制, 发掘与小麦穗发芽相关的候选基因, 采用整穗发芽法对来自全国的207份小麦品种(系)进行表型鉴定, 并结合小麦90K SNP基因芯片, 通过TASSLE软件的MLM (Q+K)模型对小麦的整穗发芽率进行全基因组关联分析(genome-wide association study, GWAS)。研究结果表明, 不同年份间小麦品种(系)的穗发芽表现出丰富的表型变异, 变异系数为0.34和0.25, 多态性信息含量(polymorphic information content, PIC)为0.01~0.38, 全基因组LD衰减距离为3 Mb。群体结构分析和主成分分析表明, 207份小麦品种(系)所构成的自然群体结构简单, 可分为3个亚群。GWAS检测结果显示, 在不同环境间共检测到34个与小麦穗发芽显著关联的SNP标记位点(P≤0.001), 分布在小麦3A、3B、4A、4B、5D、6A、6B、6D、7B和7D染色体上, 单个位点可解释5.55%~11.63%的表型变异, 16个标记位点在两个及以上环境下均被检测到, 其中6B染色体上的标记wsnp_Ex_c14101_22012676在E1、E2及平均环境下被共同检测到, 属稳定遗传的位点。通过对表型效应值大且稳定遗传的关联位点进行挖掘, 共筛选到13个与小麦穗发芽相关的候选基因。其中TraesCS3A01G589400LC、TraesCS6B01G138600/ TraeCS6B01G516 700LC/TraesCS6B01G548900LC、TraesCS6D01G103600及TraesCS7B01G200100等基因通过调控植物内源激素-脱落酸(abscisic acid, ABA)的灵敏性进而影响种子的休眠; TraesCS3B01G415900LC、TraesCS6A01G144700LC及TraesCS6B01G294800等基因编码的F-box蛋白在植物激素的信号转导、光信号转导以及花器官发育等生理过程中起重要作用; TraesCS6A01G108800、TraesCS6B01G138200/TraesCS6B01G293700基因编码Myb转录因子家族蛋白能调控种子中类黄酮的生物合成, 对籽粒颜色有重要影响, 这些候选基因是与小麦穗发芽相关的重要基因。

关键词: 小麦, 穗发芽, 全基因组关联分析, SNP, 候选基因

Abstract:

To understand the genetic mechanism of wheat pre-harvest sprouting (PHS) in wheat breeding, it is significant to explore marker loci and candidate genes associated with PHS resistance using intact spikes. In this study, a total of 207 wheat varieties (lines) from China and 16,686 SNP markers were analyzed in wheat whole genome. The mixed liner model (Q + K) was used to analyze PHS phenotypic data in three environments. Genome-wide association study showed that there were abundant phenotypic variations in different environments and wheat varieties (lines). The coefficient of variation was 0.34 and 0.25, the polymorphic information content of value (PIC) was from 0.01 to 0.38, and the attenuation distance of whole genome LD was 3 Mb. The population structure and principal component analysis revealed that 207 wheat varieties (lines) could be divided into three subgroups. GWAS results indicated that 34 SNP markers were detected, which were significantly associated with pre-harvest sprouting at P < 0.001. They were located on chromosomes 3A, 3B, 4A, 4B, 5D, 6A, 6B, 6D, 7B, and 7D, and each explained 5.55%-11.63% of phenotypic variation. There were 16 markers loci detected in more than two environments, and the marker Np_Ex_c14101_22,012,676 on 6B chromosome detected in E1, E2, and average environment. Meanwhile, 13 candidate genes were screened out by mining association loci with large phenotypic effect value and stable inheritance. TraesCS3A01G589400LC, TraesCS6B01G138600/TraesCS6B01G516700LC/TraesCS6B01G548900LC, TraesCS6D01G103600, and TraesCS7B01G200100 could affect seed dormancy by regulating the sensitivity of endogenous ABA in plants. The F-box proteins were encoded by TraesCS3B01G415900LC, TraesCS6A01G144700LC, and TraesCS6B01G294800, which played major roles in plant hormone signal transduction, light signal transduction, and flower organ development. TraesCS6A01G108800, TraesCS6B01G138200/ TraesCS6B01G293700 encoded Myb transcription factor family. These candidate genes are important genes related to wheat sprouting.

Key words: wheat, pre-harvest sprouting, genome-wide association analysis, SNP, candidate gene

图1

部分供试材料的整穗发芽图 A: 京冬8号; B: 淮麦20号; C: 郑麦2号。"

图2

207份材料在2个环境下的整穗发芽率变异 SR: 整穗发芽率。"

表1

207份自然群体小麦穗发芽方差分析"

变异来源
Source of variance		 自由度
DF		 平方和
SS		 均方
MS		 F值
F-value		 P值
P-value		 遗传力
h2
基因型Genotype (G) 206 95,102,272.00 312,836.40 540.38 0.00001 0.60
环境Environment (E) 1 756,525,632.00 378,262,816.00 653,396.18 0.00001
基因型×环境G×E 443 94,041,216.00 212,282.65 366.68 0.00001
误差Error 747 432,451.71 578.91
总变异Total 1397 946,109,312.00

表2

标记的分布及多态性"

染色体
Chromosome		 标记数目
No. of markers		 染色体长度
Chromosome length (Mb)		 标记密度
Density of marker		 多态信息量 PIC
平均值Mean 变异范围Range
1A 1263 592.38 0.47 0.27 0.01-0.38
2A 1145 780.46 0.68 0.24 0.01-0.38
3A 891 749.46 0.84 0.25 0.01-0.38
4A 708 741.73 1.05 0.25 0.01-0.38
5A 960 709.43 0.74 0.28 0.01-0.38
6A 1006 617.40 0.61 0.27 0.03-0.38
7A 1172 736.44 0.63 0.25 0.01-0.38
1B 1292 688.60 0.53 0.27 0.01-0.38
2B 1291 799.62 0.62 0.26 0.01-0.38
3B 1087 829.32 0.76 0.27 0.01-0.38
4B 571 672.56 1.18 0.26 0.01-0.38
5B 1156 712.82 0.62 0.28 0.01-0.38
6B 1085 720.82 0.66 0.25 0.01-0.38
7B 861 750.49 0.87 0.26 0.02-0.38
1D 568 495.14 0.87 0.13 0.01-0.38
2D 482 650.94 1.35 0.25 0.02-0.38
3D 232 613.92 2.65 0.24 0.01-0.38
4D 99 508.58 5.14 0.25 0.08-0.38
5D 240 563.41 2.35 0.26 0.02-0.38
6D 319 472.61 1.48 0.25 0.03-0.38
7D 260 637.17 2.45 0.23 0.01-0.38
A染色体组 Total genome A 7145 4927.30 0.72 0.26 0.01-0.38
B染色体组 Total genome B 7343 5174.23 0.75 0.27 0.01-0.38
D染色体组 Total genome D 2198 3941.77 2.33 0.23 0.01-0.38
总计Total 16686 14043.30 1.27 0.25 0.01-0.38

图3

207份小麦品种(系)群体结构分析"

图4

不同环境中穗发芽的曼哈顿图和Q-Q图 E1: 2017-2018年, 玛纳斯; E2: 2018-2019年, 玛纳斯; E3: 平均环境。"

表3

小麦穗发芽显著关联位点信息"

标记
Marker		 染色体
Chr.		 位置
Position (Mb)		 MLM 环境
Environment		 已报道的QTL/标记/基因Known QTL/marker/gene
P值
P-value		 贡献率
R2 (%)
Kukri_c8465_54 3A 684.04-685.36 2.35E-04-9.14E-04 5.55-8.75 E2/E3 TaVp-1[32]
Kukri_c9259_421 4A 673.07 5.95E-04 6.34 E2 IWB23723[23]
RAC875_rep_c107892_142 6A 77.78 2.56E-05-9.28E-05 8.04-9.25 E1/E3
Kukri_c5744_92 6A 483.90 2.78E-05-7.41E-04 8.34-9.25 E1/E3
RAC875_c43536_193 6A 490.50 3.03E-04 6.94 E1
IAAV8536 3B 422.52 6.78E-05 9.81 E1 TaDFR[33]
Tdurum_contig60051_838 4B 644.68 7.10E-04 9.42 E2 Xwmc349[34]
CAP11_c2542_147 6B 24.92 7.71E-05-3.83E-04 6.71-8.29 E1/E3 TaCYP707A1[35]
Kukri_c33668_877 6B 119.53 4.55E-04-5.32E-04 6.05-6.16 E2/E3 AX-108844376[24]
GENE-3171_203 6B 135.11-138.65 2.15E-05-5.50E-04 6.09-9.71 E1/E3
BS00069412_51 6B 143.20 9.03E-04 5.64 E1
Excalibur_c18382_760 6B 151.13 9.24E-04 5.60 E3
wsnp_Ku_c2614_4970880 6B 226.87 8.44E-04 5.59 E3
Tdurum_contig13698_141 6B 475.73 7.54E-04 5.70 E3
RFL_Contig6050_941 6B 481.47-481.86 3.10E-06-1.63E-04 8.83-11.63 E1/E3
wsnp_Ex_c3640_6644345 6B 485.54 2.36E-05-1.08E-04 8.21-11.04 E1/E3 IWB2831[24]
wsnp_Ex_c14101_22012676 6B 492.02 2.26E-06-6.77E-04 5.86-11.61 E1/E2/E3
wsnp_Ex_c6143_10747643 6B 516.08-519.15 1.30E-05-1.65E-04 8.30-10.65 E1/E3
Kukri_c16568_287 6B 522.49 4.81E-05-1.69E-04 7.21-8.45 E1/E3
Excalibur_c7785_123 6B 526.48-528.92 1.19E-056.21E-04 5.94-10.02 E1/E3
Excalibur_c11245_880 6B 530.57 2.79E-04-5.34E-04 6.06-6.83 E1/E3
wsnp_Ex_c3990_7223090 6B 577.48 1.67E-05-6.19E-05 8.45-9.95 E1/E3 Qphs.ahau-6B[36]
RAC875_c57261_265 6B 609.38 6.10E-04-6.34E-04 5.99-6.02 E1
标记
Marker		 染色体
Chr.		 位置
Position (Mb)		 MLM 环境
Environment		 已报道的QTL/标记/基因Known QTL/marker/gene
P值
P-value		 贡献率
R2 (%)
RAC875_rep_c117796_352 6B 632.97 5.23E-04-5.35E-04 6.19-6.21 E3
wsnp_CV776265A_Ta_2_1 6B 651.01-652.00 1.21E-04-7.21E-04 5.78-7.51 E1/E3
BS00023032_51 6B 664.38 8.28E-04 5.90 E3
IAE36519 6B 701.98-704.04 7.44E-04-9.92E-04 5.87-6.09 E2
wsnp_Ku_c18780_28136150 7B 223.61 8.12E-05 10.12 E2
Excalibur_c25719_238 7B 363.24 3.92E-05-3.24E-04 6.64-8.89 E2/E3
RAC875_c4834_694 7B 613.38 7.14E-04 5.87 E2 Dorm-1[37]
BobWhite_c8092_726 5D 246.30 4.94E-04 6.22 E3
wsnp_Ex_c1249_2399894 6D 67.39-68.10 8.81E-04-9.23E-04 5.72-5.78 E1
D_wsnpbe403818_Contig1_1 6D 389.70 6.71E-04 5.79 E3
D_contig10382_335 7D 23.50-55.42 7.24E-04-9.41E-04 5.70-6.15 E2 MST101[37]

表4

候选基因信息"

位点
Marker		 染色体
Chr.		 物理位置
Position (Mb)		 基因
Gene		 基因注释或编码蛋白
Gene annotation or coding protein
Kukri_c8465_54 3A 684.76 TraesCS3A01G589400LC Zinc finger MYM-type-like protein
IAAV8536 3B 421.53 TraesCS3B01G415900LC F-box protein
RAC875_rep_c107892_142 6A 77.61 TraesCS6A01G144700LC F-box family protein
6A 77.54 TraesCS6A01G108800 Myb-like transcription factor family protein
GENE-3171_203 6B 135.71 TraesCS6B01G138200 Myb family transcription factor-like
6B 135.94 TraesCS6B01G138600 RING/U-box superfamily protein
RFL_Contig6050_941 6B 481.79 TraesCS6B01G511400LC Anaerobic nitric oxide reductase transcription regulator NorR
wsnp_Ex_c14101_22012676 6B 491.55 TraesCS6B01G516700LC Zinc finger (C3HC4-type RING finger) family protein
Excalibur_c7785_123 6B 528.92 TraesCS6B01G294800 F-box protein
6B 527.93 TraesCS6B01G293700 Myb family transcription factor-like
6B 526.49 TraesCS6B01G548900LC Zinc finger MYM-type-like protein
Excalibur_c25719_238 7B 363.00 TraesCS7B01G200100 Zinc finger C-x8-C-x5-C-x3-H type family protein
wsnp_Ex_c1249_2399894 6D 67.39 TraesCS6D01G103600 Zinc finger BED domain-containing protein DAYSLEEPER
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