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作物学报

作物学报 ›› 2018, Vol. 44 ›› Issue (05): 672-685.doi: 10.3724/SP.J.1006.2018.00672

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

玉米种子萌发相关性状的全基因组关联分析

田润苗1,*(), 张雪海1,*, 汤继华1, 白光红2, 付志远1,*()   

  1. 1河南农业大学农学院, 河南郑州 450002
    2新疆农业大学, 新疆乌鲁木齐830052
  • 收稿日期:2017-11-02 接受日期:2018-03-15 出版日期:2018-05-20 网络出版日期:2018-03-16
  • 通讯作者: 田润苗,张雪海,付志远
  • 作者简介:

    第一作者联系方式: E-mail: tianrunmiao@foxmail.com ** 同等贡献(Contributed equally to this work)

  • 基金资助:
    本研究由国家自然科学基金地区科学基金项目(31760389)资助

Genome-wide Association Studies of Seed Germination Related Traits in Maize

Run-Miao TIAN1,**(), Xue-Hai ZHANG1,**, Ji-Hua TANG1, Guang-Hong BAI2, Zhi-Yuan FU1,*()   

  1. 1 College of Agronomy, Henan Agricultural University, Zhengzhou 450002, Henan, China
    2 Xinjiang Agricultural University, Urumqi 830052, Xinjiang, China
  • Received:2017-11-02 Accepted:2018-03-15 Published:2018-05-20 Published online:2018-03-16
  • Contact: Run-Miao TIAN,Xue-Hai ZHANG,Zhi-Yuan FU
  • Supported by:
    This study was supported by the Regional Science Foundation of National Natural Science Foundation of China (31760389).

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摘要：

种子萌发是出苗的前提, 对玉米产量影响重大。为了解玉米种子萌发相关性状的遗传机制, 本研究对476份玉米自交系种子萌发相关的6个性状进行调查, 结合125万个(1.25M) SNP标记, 利用3种统计模型(Q, K, Q+K)进行全基因关联分析(GWAS)。结果表明K模型能够较好地评价吸胀前重量、吸胀前体积、吸胀后重量、吸胀后体积和吸胀体积5个性状; Q+K模型能更好地评价吸胀重量性状。基于这6个性状的最优模型的GWAS结果, 共检测到15个种子萌发相关性状的显著SNP, 15个SNP对应6个QTL, 集中分布在玉米第3、第6、第7和第10染色体上, QTL内单个SNP能解释的表型变异为5.09%~7.85%。其中5个QTL可在多个生物学重复中被检测到。以最显著SNP所在基因或附近基因作为QTL的候选基因, 共筛选到6个最可能的候选基因。GRMZM2G148411是吸胀后重量、吸胀重量和吸胀体积3个性状共同鉴定到的QTL候选基因, 根据基因的功能注释, 该基因编码一个包含TLD-domain的钙离子结合蛋白, 可能是一种调控种子休眠与萌发的信号分子。本研究鉴定的QTL为解析玉米种子萌发的遗传机制和相应功能标记的开发奠定了基础。

关键词: 玉米, 种子萌发, 全基因组关联分析, 候选基因

Abstract:

Germination is important for seed emergence, which has significant impact on maize yield. To reveal the genetic mechanism of maize seed germination, we investigated six traits related to seed germination using 467 diverse inbred lines. The genome-wide association studies (GWAS) between the six traits and 1.25M SNPs were implemented in three different models (Q model, K model, and Q+K model). The K model was much better than the other two models for weight before imbibition, volume before imbibition, weight after imbibition, volume after imbibition and volume of imbibition. While weight of imbibition trait could be well evaluated by Q+K model. In total, 15 SNPs were significantly associated with the six traits by the optimal model. These SNPs correspond to six QTLs, including five QTLs co-located in different biological replications. The six QTLs were located on chromosomes 3, 6, 7, and 10. The single SNP could explain 5.09%-7.85% variation of phenotype. Genes within or nearby most significant SNP were selected as candidates, and six candidate genes were identified for seed germination related traits in the six loci. Among these genes, GRMZM2G148411 encoding a TLD-domain calcium ion binding protein according to the annotations associated with weight after imbibition, volume after imbibition and volume of imbibition might be a signal molecule regulating seed germination and dormancy. The QTLs identified in this study are useful for developing functional markers and elucidating the genetic basis of seed germination.

Key words: maize, seed germination, genome-wide association study, candidate gene

图1

种子萌发性状的频次分布图各性状详细名称见表1。"

表1

种子萌发性状表型统计分析"

性状
Trait		 平均值±标准差
Mean± SD		 变幅
Range		 变异系数
CV (%)		 峰度
Skewness		 偏度
Kurtosis
W1 (g) 4.92±0.92 1.63-7.40 18.77 0.22 0.07
V1 (mL) 4.43±0.77 2.57-6.47 17.35 0.42 -0.03
W2 (g) 6.52±1.19 2.02-9.86 18.29 0.25 0.23
V2 (mL) 5.87±1.06 1.93-9.20 18.06 0.43 0.33
W3 (g) 1.61±0.35 0.38-2.72 21.77 0.55 0.54
V3 (mL) 1.44±0.41 0.35-2.76 28.41 0.25 -0.13

表2

种子萌发性状方差分析"

性状
Trait		 变异来源
Variation source		 自由度
df		 均方
MS		 F值
F-value
W1 材料Variety 475 2.56 52.99**
重复Repeat 2 0.11 2.27
误差Error 940 0.05
V1 材料Variety 475 1.77 14.50**
重复Repeat 2 0.96 7.85**
误差Error 941 0.12
W2 材料Variety 475 4.24 32.12**
重复Repeat 2 4.31 32.68**
误差Error 940 0.13
V2 材料Variety 475 3.35 19.35**
重复Repeat 2 0.33 1.93
误差Error 93 0.17
W3 材料Variety 475 0.36 8.28**
重复Repeat 2 4.02 92.23**
误差Error 934 0.04
V3 材料Variety 475 0.50 2.62**
重复Repeat 2 1.32 6.96**
误差Error 932 0.19

表3

种子萌发性状皮尔逊关联分析"

性状 Trait W1 V1 W2 V2 W3
V1 0.955**
W2 0.976** 0.956**
V2 0.935** 0.942** 0.966**
W3 0.675** 0.725** 0.821** 0.811**
V3 0.606** 0.543** 0.682** 0.793** 0.724**

图2

种子萌发性状3种模型比较的QQ图各性状详细名称见表1。横轴表示经过负的常数对数转换的期望P值, 纵轴表示经过负的常数对数转换观察到的P值。"

图3

种子萌发性状全基因组关联分析曼哈顿图各性状详细名称见表1。黑色虚线代表全基因组关联分析的显著阈值。"

图4

种子萌发性状全基因组关联分析曼哈顿图(单个重复) 各性状详细名称见表1。R1: 第1重复; R2: 第2重复, R3: 第3重复。黑色虚线代表全基因组关联分析的显著阈值。"

表4

种子萌发候选基因及功能注释"

表5

种子萌发性状显著关联位点"

性状
Trait		 重复
Repeat		 候选位点
Locus		 SNP 染色体
Chr.		 物理位置
Position		 P值
P-value		 贡献率
R2 (%)
W1 1 Chr4: 2865435-2865435? Chr4.S_2925435 4 2925435 7.76×10-7 8.33
Chr7: 4798028-4858028 Chr7.S_4828028 7 4828028 1.48×10-6 5.58
2 Chr10: 139810517-139870517 Chr10.S_139840517 10 139840517 1.87×10-6 9.60
W1 Chr7: 4798028-4858028 Chr7.S_4828028 7 4828028 4.34×10-7 6.10
Chr7.S_4828028 7 4828028 7.66×10-7 5.84
W2 1 Chr10: 6343038-6403038 Chr10.S_6373105 10 6373105 1.81×10-6 5.16
Chr10: 117510861-117630861 Chr10.S_117570861 10 117570861 1.16×10-6 5.21
Chr4: 2865435-2865435 Chr4.S_2925435 4 2925435 3.83×10-7 8.73
Chr7: 4798028-4858028 Chr7.S_4828028 7 4828028 1.57×10-6 5.54
2 Chr10: 6343038-6403038 Chr10.S_6373105 10 6373105 1.86×10-6 5.14
Chr3: 209027864-209147864 Chr3.S_209087864 3 209087864 1.58×10-6 9.50
Chr10: 6343038-6403038 Chr10.S_6373038 10 6373038 1.75×10-6 5.25
Chr10.S_6373105 10 6373105 1.50×10-6 5.27
Chr9: 144257637-144377637 Chr9.S_144308026 9 144308026 1.77×10-6 5.08
Chr9.S_144308098 9 144308098 2.01×10-6 5.05
Chr9.S_144309854 9 144309854 1.77×10-6 5.08
Chr9.S_144309860 9 144309860 3.69×10-7 5.77
W2 Chr9.S_144317637 9 144317637 2.21×10-7 6.56
Chr10: 6343038-6403038 Chr10.S_6373038 10 6373038 1.86×10-6 5.17
Chr10.S_6373105 10 6373105 1.16×10-6 5.34
W3 1 Chr1: 206063394-206183394 Chr1.S_206123394 1 206123394 1.55×10-6 5.31
3 Chr10: 6343038-6403038 Chr10.S_6373038 10 6373038 1.01×10-7 5.92
Chr10.S_6373105 10 6373105 1.75×10-8 6.60
Chr2: 152687771-152807771 Chr2.S_205719834 2 205719834 6.26×10-7 7.05
Chr2.S_205770041 2 205770041 5.71×10-7 5.02
Chr2.S_205771072 2 205771072 5.71×10-7 5.02
Chr2.S_205771170 2 205771170 5.71×10-7 5.02
Chr2.S_205771560 2 205771560 5.71×10-7 5.02
Chr2.S_205771697 2 205771697 5.71×10-7 5.02
Chr2.S_205772111 2 205772111 5.71×10-7 5.02
Chr2.S_205773201 2 205773201 5.71×10-7 5.02
Chr2.S_205774142 2 205774142 5.71×10-7 5.02
Chr5:152687771-152807771 Chr5.S_152747771 5 152747771 4.70×10-7 8.78
Chr6: 95574386-95634386 Chr6.S_98573207 6 98573207 4.22×10-7 5.78
Chr9: 26957278-27077278 Chr9.S_27017278 9 27017278 1.47×10-6 5.13
W3 Chr10: 6343038-6403038 Chr10.S_6373038 10 6373038 3.22×10-9 8.06
Chr10.S_6373105 10 6373105 5.75×10-9 7.73
V1 1 Chr4: 2865435- 2865435? Chr4.S_2925435 4 2925435 8.89×10-7 8.44
Chr6: 6778454-6838454 Chr6.S_6808454 6 6808454 1.38×10-6 8.07
2 Chr10: 139780517-139900517 Chr10.S_139840517 10 139840517 3.47×10-7 10.56
Chr9: 144257637- 144377637 Chr9.S_144309860 9 144309860 1.60×10-6 5.12
3 Chr6: 95574386-95634386 Chr6.S_95604386 6 95604386 8.22×10-7 5.32
Chr6.S_95604517 6 95604517 1.42×10-6 5.08
Chr6.S_95604625 6 95604625 1.42×10-6 5.08
性状
Trait		 重复
Repeat		 候选位点
Locus		 SNP 染色体
Chr.		 物理位置
Position		 P值
P-value		 贡献率
R2 (%)
Chr6.S_95604950 6 95604950 1.11×10-6 5.20
Chr6.S_95605307 6 95605307 1.21×10-6 5.14
Chr6.S_95605330 6 95605330 1.10×10-6 5.22
Chr6.S_95605331 6 95605331 1.95×10-6 5.04
Chr6.S_95605458 6 95605458 1.21×10-6 5.14
Chr6.S_95605541 6 95605541 1.21×10-6 5.14
Chr8: 14037401-14157401 Chr8.S_14097401 8 14097401 1.93×10-6 5.71
V1 Chr6: 6778454-6838454 Chr6.S_6808454 6 6808454 2.01×10-6 7.85
Chr6: 95574386-95634386 Chr6.S_95604386 6 95604386 8.76×10-7 5.28
Chr6.S_95604517 6 95604517 1.31×10-6 5.10
Chr6.S_95604625 6 95604625 1.31×10-6 5.10
Chr6.S_95604950 6 95604950 1.08×10-6 5.19
Chr6.S_95605307 6 95605307 1.14×10-6 5.16
Chr6.S_95605330 6 95605330 1.03×10-6 5.23
Chr6.S_95605331 6 95605331 1.67×10-6 5.09
Chr6.S_95605458 6 95605458 1.14×10-6 5.16
Chr6.S_95605541 6 95605541 1.14×10-6 5.16
V2 1 Chr10: 6343038-6403038 Chr10.S_6373038 10 6373038 5.73×10-7 5.73
Chr4: 2865435-2865435 Chr4.S_2925435 4 2925435 1.49×10-6 7.54
Chr4: 185676597-185796597 Chr4.S_185736597 4 185736597 5.59×10-7 7.89
2 Chr10: 6147016-6267016 Chr10.S_6207016 10 6207016 1.14×10-6 8.84
V3 1 Chr2: 182455178-182575178 Chr2.S_182515178 2 182515178 9.03×10-7 5.98
Chr7: 145940024-146000024 Chr7.S_145970024 7 145970024 4.26×10-7 5.75
2 Chr1: 262661257-262781257 Chr1.S_262721257 1 262721257 1.59×10-6 5.55
Chr5: 213497149-213617149 Chr5.S_213557149 5 213557149 8.90×10-7 5.68
3 Chr7: 95428593-95548593 Chr7.S_95488593 7 95488593 1.05×10-6 7.48
Chr7.S_95488613 7 95488613 1.43×10-6 6.80
V3 Chr10: 6343038-6403038 Chr10.S_6373038 10 6373038 1.60×10-6 5.21
Chr3: 197628474-197688474 Chr3.S_197658474 3 197658474 1.72×10-6 5.93
Chr7: 145940024-146000024 Chr7.S_145970024 7 145970024 1.70×10-6 5.13
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