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作物学报 ›› 2019, Vol. 45 ›› Issue (4): 568-577.doi: 10.3724/SP.J.1006.2019.83052

• 作物遗传育种·种质资源·分子遗传学 • 上一篇    下一篇

玉米Suwan种质改良过程中的关键基因组区段发掘

李秀诗,吴迅,吴文强,刘鹏飞,郭向阳,王安贵,祝云芳,陈泽辉()   

  1. 贵州省农业科学院旱粮研究所, 贵州贵阳 550006
  • 收稿日期:2018-06-26 接受日期:2018-12-24 出版日期:2019-04-12 网络出版日期:2019-01-04
  • 通讯作者: 陈泽辉
  • 基金资助:
    本研究由国家“七大作物育种”专项(2016YFD0101206-4)(2016YFD0101206);黔农科院自主创新科研专项字(2014)006(Special Character of Independent Innovation of Guizhou Academy of Agriculture [2014]006);国家自然科学基金项目(31760387);黔科合支撑([2016]2605, [2016]2549, [2017]2507, [2018]2296);黔科合基础资助([2017]1413)

Excavation of main candidate genome regions in Suwan germplasm improvement process of maize

LI Xiu-Shi,WU Xun,WU Wen-Qiang,LIU Peng-Fei,GUO Xiang-Yang,WANG An-Gui,ZHU Yun-Fang,CHEN Ze-Hui()   

  1. Upland Crops Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, Guizhou, China
  • Received:2018-06-26 Accepted:2018-12-24 Published:2019-04-12 Published online:2019-01-04
  • Contact: Ze-Hui CHEN
  • Supported by:
    This study was supported by the National Key Research and Development Program of China(2016YFD0101206);Innovation Program of QAAS(Special Character of Independent Innovation of Guizhou Academy of Agriculture [2014]006);National Natural Science Foundation of China(31760387);Science and Technology Support Project of Guizhou Province (Qiankehe support([2016]2605, [2016]2549, [2017]2507, [2018]2296);Science and Technology Project of Guizhou Province (Qiankehe Foundation)([2017]1413)

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摘要：

玉米Suwan种质抗性好、适应性强、籽粒品质优, 在现代育种尤其是南方玉米育种中具有不可替代的作用。明确Suwan种质优良特性在改良过程中的遗传机制对我国南方玉米生态区的玉米生产具有重要意义。本研究以Suwan 1 (Suwan 1C10)及其衍生群体(苏兰1号C0)不同改良世代为材料, 利用包含5.6万个SNP标记的MaizeSNP50芯片对供试群体进行基因型鉴定。遗传分析发现: Suwan 1群体不同改良世代间的基因组差异片段较少, 仅出现5个, 其中4个出现在第11轮改良世代(Suwan 1 C11), 1个出现在第15轮改良世代(Suwan 1 C15); 苏兰1号不同改良世代间的基因组差异片段相对较多, 共有18个, 其中8个在不同改良世代间稳定遗传; Suwan种质改良形成苏兰1号群体的过程中, 共获得43个Lancaster特异性遗传片段, 其中35个在苏兰1号不同改良世代间稳定遗传。全基因组关联分析共鉴定出16个与穗行数显著关联的QTN, 分别位于第2、第3、第5、第6、第7、第8、第9染色体上, 其中SYN25713和SYN36577位于苏兰1号群体的Lancaster特异性遗传片段内; 共检测到13个控制穗长相关的QTN, 分别位于第1、第2、第5、第7、第8、第9染色体上, 其中PZE-105143697位于苏兰1号群体的Lancaster特异性遗传片段内。该结果为后续全基因组关联研究和分子标记辅助选择等提供了重要的理论依据。

关键词: 玉米, 群体改良, 基因组特征, 全基因组关联分析, 遗传位点

Abstract:

Suwan germplasm with good resistance, strong adaptability and excellent grain quality has played an irreplaceable role in modern breeding, especially in the southern of China. It is important to clarify the genetic mechanism of Suwan germplasm. In this study, modified generations of Suwan 1 (Suwan 1 C10) and its derived population (Suwan-Lancaster 1 C0) were used to be genotyped by using MaizeSNP50 chips containing about 56,000 SNP markers. There was a smaller genome differences among different improved generations for Suwan 1 population, with only five different inherited fragments identified, among which four appeared only in the 11th improved generation (Suwan 1 C11), one appeared only in the 15th improved generation (Suwan 1 C15). For Suwan-Lancaster1 population, among 18 different genetic fragments eight were stably inherited in different improved generations. A total of 43 specific genetic segments of Lancaster germplasm were obtained, among them 35 were stably inherited in different improved generations. Genome-wide association studies (GWAS) showed that 16 QTNs significantly associated with kernel row number were located on chromosomes 2, 3, 5, 6, 7, 8, and 9, respectively, among them SYN25713 and SYN36577 were located in the Lancaster specific genetic fragment of the Suwan-Lancaster 1 population. A total of 13 QTNs related to ear length were located on chromosomes 1, 2, 5, 7, 8, and 9, respectively, among them PZE-105143697 was located in the Lancaster specific genetic fragment. These results provide an important theoretical basis for the subsequent genome-wide association study and molecular marker assisted selection.

Key words: maize, population improvement, genome characteristics, genome-wide association study, genetic loci

表1

供试材料系谱和类群"

序号
No.		 材料
Accession		 系谱
Pedigree		 类群
Group
1 Suwan 1 (Suwan 1 C10) Suwan 1 C9 Suwan
2 Suwan 1 C11 Suwan 1 C10 Suwan
3 Suwan 1 C12 Suwan 1 C11 Suwan
4 Suwan 1 C13 Suwan 1 C12 Suwan
5 Suwan 1 C15 Suwan 1 C14 Suwan
6 苏兰1号C0 SL1C0 Suwan, Lancaster及78599选系
Synthetic populations of Suwan, Lancaster and 78599 selected lines		 Suwan-Lancaster
7 苏兰1号C1 SL1C1 苏兰1号C0 SL1C0 Suwan-Lancaster
8 苏兰1号C2 SL1C2 苏兰1号C1 SL1C1 Suwan-Lancaster
9 苏兰1号C3 SL1C3 苏兰1号C2 SL1C2 Suwan-Lancaster

表2

9个供试群体穗长和穗行数"

材料
Accession		 穗长 Ear length 穗行数 Kernel row number
贵阳
Guiyang		 大方
Dafang		 罗平
Luoping		 平均值
Mean		 贵阳
Guiyang		 大方
Dafang		 罗平
Luoping		 平均值
Mean
苏兰1号C0 SL1C0 17.67 18.77 17.40 17.94 15.47 14.53 14.67 14.89
苏兰1号C1 SL1C1 18.13 19.33 17.17 18.21 15.33 14.73 14.27 14.78
苏兰1号C2 SL1C2 17.87 18.97 18.20 18.34 14.27 14.27 14.47 14.33
苏兰1号C3 SL1C3 18.27 19.57 17.73 18.52 15.00 15.53 15.20 15.24
Suwan 1 (Suwan 1 C10) 17.47 18.33 16.43 17.41 15.00 14.93 14.00 14.64
Suwan 1 C11 17.67 18.23 17.03 17.64 15.40 14.93 14.13 14.82
Suwan 1 C12 16.87 17.97 16.33 17.06 15.13 15.87 14.60 15.20
Suwan 1 C13 16.53 18.17 16.20 16.97 15.40 14.93 14.20 14.84
Suwan 1 C15 17.60 18.53 17.03 17.72 14.60 14.60 14.53 14.58
平均值Mean 17.56 18.65 17.06 17.76 15.07 14.93 14.45 14.81
标准差Standard deviation 1.09 0.73 0.84 1.11 0.67 0.57 0.65 0.68
变异系数Coefficient of variation (%) 6.21 3.91 4.92 6.25 4.45 3.82 4.50 4.59

图1

Suwan 1群体不同改良世代间的基因组特征 特异性SNP标记在染色体上的物理位置见附表1。"

表1

1 附Suwan 1群体不同改良世代的特异性标记"

SNP 染色体
Chr.		 物理位置
Position		 SNP 染色体
Chr.		 物理位置
Position
SYN450 1 35968064 PZE-106016986 6 32497838
PZE-103104159 3 164159285 PZE-106016987 6 32498979
PZE-106016953 6 32495316 PZE-106017115 6 32905813
PZE-106016962 6 32495710 PZE-106017122 6 32908494
PZE-106016971 6 32496071 PZE-106099248 6 152896893
PZA00540.3 6 32496071 PZE-108113902 8 163858777

图2

苏兰1号群体不同改良世代间的基因组特征 特异性SNP标记在染色体上的物理位置见附表2。"

表2

2 苏兰1号群体不同改良世代的特异性标记"

SNP 染色体
Chr.		 物理位置
Position		 SNP 染色体
Chr.		 物理位置
Position
PZE-101205609 1 253344590 PZE-102156731 2 203902578
PZE-101205965 1 253895960 SYN15645 3 182660027
SYN6838 1 297376850 PZE-105016506 4 7204051
PZE-103008521 2 4666469 PZE-106033525 5 76988770
PZE-102060229 2 38551101 SYN25006 6 8192709
PZE-102060230 2 39031517 PZE-107126153 7 163083361
PZE-102061400 2 39748797 PZE-109019803 7 20222259
SYN26925 2 200353907 PZE-109051268 9 85880947
SYN26929 2 200359094 PZE-109051619 9 86414796
SYN10568 2 200723525 PZE-109052137 9 86974491
SYN35589 2 201246108

图3

Suwan 1与苏兰1号不同改良世代间的基因组特征 特异性SNP标记在染色体上的物理位置见附表3。"

表3

3 Suwan 1与苏兰1号不同改良世代间的特异性标记"

SNP 染色体
Chr.		 物理位置
Position		 SNP 染色体
Chr.		 物理位置
Position
SYN11491 1 3683507 PZE-104127854 4 212788677
PZE-101054452 1 38617583 PZE-104127855 4 212788991
PZE-101178005 1 222370910 PZE-104152999 4 243521349
PZE-101192090 1 237838603 SYN28825 5 7319620
PZE-101192133 1 237900682 PZE-105051178 5 43960922
PZE-101192647 1 238680213 PZE-105051179 5 43961044
PZE-101195574 1 242361972 PZE-105051200 5 43966297
PZE-101195592 1 242398910 PZE-105099516 5 146942464
PZE-101196147 1 243255282 PZE-105101687 5 152095801
PZE-101196704 1 244083020 PZE-105102557 5 154315332
PZE-101196940 1 244512792 PZE-105144984 5 197943057
PZE-101197050 1 244678601 PZB02424.1 5 199531408
SYN12881 1 245242156 SYN30468 5 199531778
PZE-101197856 1 245308899 PZA00540.3 6 32496071
SYN15061 1 261370341 PZE-106016971 6 32496071
PZE-102060229 2 38551101 PZE-106017115 6 32905813
PZE-102060230 2 39031517 PZE-106017122 6 32908494
SYN26925 2 200353907 SYN25006 7 8192709
SYN26929 2 200359094 PZE-107018281 7 15776884
SYN35589 2 201246108 PZE-107126153 7 163083361
PZE-103025362 3 17738644 SYN34213 8 5090046
PZE-103056619 3 68433447 PZE-108010963 8 11645850
PZE-103068285 3 108233400 PUT-163a-78089347-4225 8 169951365
PZE-103076844 3 123683053 PUT-163a-78089347-4224 8 169951478
PZE-103083872 3 135004208 PZE-109008703 9 9247324
SYN34685 4 202660380 SYN36362 9 9247324
PZE-104126691 4 210495187 PZE-109051619 9 86414796
PZE-104127248 4 211708774 PZE-109101971 9 141650742
PZE-104127853 4 212785374 PZE-110080467 10 134211006

表3

穗行数显著关联的SNP位点"

SNP 染色体
Chr.		 物理位置
Position		 P值
P-value (×10-4)		 最小等位基因频率
Minimum allele frequency
PZE-102049428 2 27586143 0.83 0.22
SYN29936 3 214728752 0.79 0.53
SYN25713 4 218657640 0.50 0.39
PZE-104012465 4 10671690 0.95 0.39
PZE-105068275 5 70167652 0.38 0.50
SYN35408 5 64502995 0.64 0.53
ZM013904-0312 5 64757602 0.64 0.53
PZE-105060180 5 58448124 0.80 0.44
PZE-106105143 6 155807238 0.29 0.42
PUT-163a-60355888-2779 6 30864359 0.32 0.61
PUT-163a-60355888-2773 6 30864423 0.32 0.61
SYN36577 7 9216854 0.53 0.67
SYN36527 8 166695438 0.72 0.17
SYN36532 8 166695690 0.72 0.83
PZE-108065598 8 115805296 0.89 0.33
PZE-109004718 9 5289730 0.54 0.31

图4

穗行数相关QTNA和B分别代表曼哈顿图和QQ图。A and B represent Manhattan plot and QQ plot, respectively."

表4

穗长显著关联的SNP位点"

SNP 染色体
Chr.		 物理位置
Position		 P值
P-value (×10-4)		 最小等位基因频率
Minimum allele frequency
SYN28790 1 198085193 3.55 0.56
PZE-102089207 2 89322082 3.55 0.83
PZE-102089216 2 89350485 7.42 0.17
PZE-102094273 2 103594813 7.42 0.28
PZE-103146876 3 199472604 5.85 0.64
PZE-105143697 5 196993540 6.06 0.22
SYN2938 5 212502760 2.47 0.44
PZE-105181391 5 215066204 8.77 0.22
SYN19052 7 125475003 6.64 0.78
SYN10053 8 1816317 7.98 0.39
PZA-000908002 8 99959553 2.84 0.44
PZE-108076469 8 130589109 3.55 0.83
PZE-109008801 9 9401106 7.42 0.44

图5

穗长相关QTNA和B分别代表曼哈顿图和QQ图。A and B represent Manhattan plot and QQ plot, respectively."

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