李秀诗, 吴迅, 吴文强, 刘鹏飞, 郭向阳, 王安贵, 祝云芳, 陈泽辉^,*贵州省农业科学院旱粮研究所, 贵州贵阳 550006

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^,*Upland Crops Institute, Guizhou Academy of Agricultural Sciences, Guiyang 550006, Guizhou, China

通讯作者: *陈泽辉, E-mail: chenzh907@sina.com

收稿日期:2018-06-26接受日期:2018-12-24网络出版日期:2019-01-04

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

Received:2018-06-26Accepted:2018-12-24Online:2019-01-04

Fund supported:

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

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.
Keywords：maize;population improvement;genome characteristics;genome-wide association study;genetic loci


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本文引用格式
李秀诗, 吴迅, 吴文强, 刘鹏飞, 郭向阳, 王安贵, 祝云芳, 陈泽辉. 玉米Suwan种质改良过程中的关键基因组区段发掘[J]. 作物学报, 2019, 45(4): 568-577. doi:10.3724/SP.J.1006.2019.83052
LI Xiu-Shi, WU Xun, WU Wen-Qiang, LIU Peng-Fei, GUO Xiang-Yang, WANG An-Gui, ZHU Yun-Fang, CHEN Ze-Hui. Excavation of main candidate genome regions in Suwan germplasm improvement process of maize[J]. Acta Crops Sinica, 2019, 45(4): 568-577. doi:10.3724/SP.J.1006.2019.83052


近年来, 随着高通量基因型鉴定技术的不断发展, 研究者从分子水平上解析了温带玉米种质的遗传基础。如兰进好等^[9]利用黄早四和Mo17构建的F_2:3群体, 基于SSR和ALFP标记鉴定出一批控制穗行数、行粒数、百粒重等性状的QTL; Wu等^[10]利用包含56,110个SNP标记的基因芯片对367份重要自交系的遗传多样性、群体结构、亲缘关系等进行分析, 并结合全基因组关联分析策略共定位到158个与株型相关性状的SNP位点; Yang等^[11]利用B73、SICAU1212及其F₂群体, 结合SSR标记基因型进行连锁分析, 共定位到33个QTL与12个农艺性状相关。但是针对Suwan种质的遗传研究较少, 主要集中在表型数据或少数标记的配合力分析、杂种优势分析和群体结构分析等, 所揭示的信息量较为有限。如杨文鹏等^[12]利用88个SSR标记对贵州2000年来审定的玉米品种70份亲本材料分析发现, 泰国苏湾热带种质被分为一个亚群, 揭示出贵州以地方亚热带种质和泰国苏湾热带种质为主要杂种优势群的玉米育种模式; 闫飞燕等^[13]和番兴明等^[14]对热带、亚热带玉米种质群体及自交系的配合力效应和杂种优势分析表明, Suwan 1群体及其衍生自交系具有较高的一般配合力, Suwan 1×Ried是表现较好的杂优模式之一; Zhang等^[15]利用MaizeSNP50芯片对西南地区362份玉米自交系的群体结构和遗传多样性进行全基因组关联分析发现, 位于第2染色体130 Mb的一个区域遗传多样性较为丰富, 第7染色体30~120 Mb是S37在西南区玉米育种的一个保守区域; 陈泽辉等^[16]利用属Reid自交系和属Tuxpeno自交系构建人工合成群体墨瑞1号, 用属Suwan自交系、Mo17和78599构建人工合成群体苏兰1号, 并利用半同胞相互轮回选择法进行改良, 通过田间鉴定发现Reid-Tuxpeno×Lancaster-Suwan 可作为我国南方玉米杂种优势利用的重要模式之一。然而, 关于Suwan种质改良的遗传基础以及在改良过程中是否存在一些重要遗传区段等研究则属于空白。因此, 本研究利用包含5.6万个标记的MaizeSNP50芯片对Suwan及其衍生群体(苏兰1号)不同改良世代进行基因型鉴定, 基于高密度的基因型鉴定结果分析Suwan及其衍生群体不同改良世代之间的基因组演化特征; 结合全基因组关联分析策略, 初步揭示Suwan种质改良过程中的关键遗传区段并明确其效应, 为玉米Suwan种质改良利用和后续分子标记辅助育种提供参考。

1 材料与方法

1.1 试验材料

以玉米种质群体Suwan 1 (Suwan 1 C₁₀)、苏兰1号的不同改良世代为材料。其中, Suwan 1群体的第11轮(C₁₁)是贵州省农业科学院旱粮研究所1992年从泰国的苏湾农场引进; 而Suwan 1群体的不同改良世代[第10轮(C₁₀)、第12轮(C₁₂)、第13轮(C₁₃)、第15轮(C₁₅)]则是课题组2014年从苏湾农场引进; 苏兰1号(SL1C₀)是由苏湾种质与Lancaster种质的优良自交系的人工合成群体, 并通过3次半同胞相互轮回选择法获得SL1C₁、SL1C₂、SL1C₃三轮改良世代^[16]。供试材料系谱来源和类群见表1。

Table 1
表1
表1供试材料系谱和类群
Table 1Pedigree and groups of accessions used in this paper

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

Suwan-Lancaster 1简写为“SL1”。Suwan-Lancaster 1 is abbreviated as "SL1".

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1.2 试验方法

1.2.1 田间鉴定 2017年春, 将Suwan 1及4个改良世代、苏兰1号及其3轮改良世代分别在贵州贵阳(26.33°N, 106.64°E)、贵州大方(26.98°N, 105.66°E)和云南罗平(24.78°N, 104°E) 3个不同环境下进行田间鉴定。采用完全随机区组设计, 3次重复, 2行区, 行长5 m, 行距0.7 m, 每行定苗22株。按照常规生产条件进行田间管理。参照石云素等编写的《玉米种质资源描述规范和数据标准》调查表型^[17], 即收获后, 从每个小区随机取10个果穗调查穗长、穗行数, 取平均值用于统计分析。

1.2.2 基因型鉴定 2016年冬, 在海南省三亚市九所镇贵州南繁基地从Suwan 1及其衍生群体各改良世代中取样。即在玉米大喇叭口时期, 首先依据植株高度将每个群体分为高、中、低3种类型, 从每种类型中取30株幼嫩叶片等量混合和提取DNA, 并采用Illumina公司开发的MaizeSNP50芯片对所取样本进行基因型鉴定, 该芯片包括56,110个SNP标记。参照Illumina 公司提供的操作指南检测基因型。其中DNA提取和基因型鉴定工作均委托北京康普森生物科技有限公司完成。

1.3 表型数据统计分析

采用Microsoft Excel 2007和SAS 9.2软件^[18]的PROC UNIVARIATE和PROC GLM程序对田间统计数据进行描述性统计和方差分析等。

1.4 候选遗传区段鉴定

基于不同世代的基因型鉴定结果, 通过全基因组比较, 利用GGT32软件鉴定出在各改良世代间稳定遗传和差异的候选区域。

1.5 全基因组关联分析

根据最小等位基因频率MAF > 0.05且样本缺失率 < 20%的标准^[19], 筛选出43,980个高质量的SNP标记, 利用TASSEL软件的混合线性模型^[20]对表型和基因型进行全基因组关联分析。以P < 0.0001为阈值, 鉴定出控制目标性状的关键QTN。在此基础上, 利用生物信息分析手段, 借助公共数据库的定位结果, 初步揭示出目标区段的遗传效应。

2 结果与分析

2.1 穗长和穗行数分析

随着改良轮次的增加, 苏兰1号群体的穗长增加, 从改良前的17.67 cm增长到改良后的18.27 cm, 明显高于Suwan 1群体(17.22 cm); 穗行数性状变化较小, 但各世代间存在着明显差异。供试群体在贵阳、大方和罗平3个点的穗长性状的平均值分别为17.56、18.65和17.06 cm, 变异系数分别为6.21%、3.91%和4.92%; 穗行数性状的平均值分别为15.07、14.93和14.45行, 变异系数分别为4.45%、2.82%和4.50% (表2), 说明Suwan 1及其衍生群体各改良世代间穗长和穗行数差异明显。

Table 2
表2
表29个供试群体穗长和穗行数
Table 2Ear length and ear row number of nine tested groups

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

Suwan-Lancaster 1简写为“SL1”。Suwan-Lancaster 1 is abbreviated as “SL1”.

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2.2 基因组特征

在Suwan 1群体的不同改良世代中, 共鉴定出9个稳定遗传片段和5个差异遗传片段(图1)。说明Suwan 1群体在改良过程中, 保持着群体内丰富的遗传变异, 其不同改良世代间基因发生交换重组的频率较低, 仅出现5个差异遗传片段, 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), 其原因是Suwan 1 C₁₁的引入时间较早, 与其他改良世代批次不同, 受到环境驯化和选择发生基因漂移, 而且这9个稳定遗传片段可能在保持Suwan群体优势抗性、适应性等热带种质特征方面发挥作用。而其中的5个差异遗传区段可能是Suwan种质改良过程中的重组热点区域, 可为后续的种质改良提供依据。

图1

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图1Suwan 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。
Fig. 1Genomic characteristics of Suwan 1 in different improved generations

The physical location of the specific SNP markers on chromosome is shown in the Supplementary table 1.


Table 1
表1
表11 附Suwan 1群体不同改良世代的特异性标记
Table 11 Supplementary table 1 Specific markers for different improvement generations of Suwan 1 population

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

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在苏兰1号C₀群体不同改良世代中, 共鉴定出26个稳定遗传片段和18个差异遗传片段(图2), 分别位于第1、第2、第3、第4、第5、第6、第7、第9染色体上。其中, 第2、第5、第6染色体上的8个差异遗传片段在其改良世代间稳定出现, 以第2染色体上的多态性最高。说明苏兰1号群体在改良过程中, 不同改良世代间保持着群体内丰富的遗传变异, 少数基因发生交换重组, 获得18个差异遗传片段, 而且这些差异遗传区段可能与苏兰1号群体改良世代间秃尖长、行粒数等产量性状特征方面发挥作用, 可为后续利用分子标记辅助育种提供重要依据。

图2

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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。
Fig. 2Genomic characteristics of Suwan-Lancaster1 in different improved generations

The physical location of the specific SNP markers on chromosome is shown in Supplementary table 2.


Table 2
表2
表22 苏兰1号群体不同改良世代的特异性标记
Table 22 Supplementary table 2 Specific markers for different improvement generations of Suwan-Lancaster 1 population

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

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基因组信息比对发现, Suwan种质改良形成苏兰1号群体的过程中, 共有53个区段来自Suwan群体和43个区段来自Lancaster种质(图3), 其中有35个Lancaster来源区段在苏兰1号C₀群体不同改良世代间稳定出现, 分别位于第1、第3、第4、第5染色体, 说明这些区域发生交换重组的频率较高, 多态性较丰富。

图3

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图3Suwan 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。
Fig. 3Genomic characteristics between Suwan 1 and Suwan-Lancaster 1 in different improved generations

The physical location of the specific SNP markers on chromosome is shown in Supplementary table 3.


Table 3
表3
表33 Suwan 1与苏兰1号不同改良世代间的特异性标记
Table 33 Supplementary table 3 Specific markers between Suwan 1 and Suwan-Lancaster 1 in different improved generations

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

新窗口打开|下载CSV

2.3 全基因组关联分析

共发掘出16个与穗行数显著关联(P<0.0001)的QTN (表3和图4), 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分别位于苏兰1号群体的第4染色体Lancaster特异性遗传区段212.79~243.52 Mb和第7染色体8.19~15.78 Mb范围内(附表3)。

Table 3
表3
表3穗行数显著关联的SNP位点
Table 3Association of SNP loci with kernel rows per ear

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

新窗口打开|下载CSV

图4

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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.

Fig. 4Kernel rows per ear related QTN



穗长关联分析结果显示,共发掘出13个与穗长显著关联(P < 0.001)的SNP位点(表4和图5),分别位于第1、第2、第5、第7、第8、第9染色体上,其中PZE-105143697 (196993540)位于苏兰1号群体的第5染色体Lancaster特异性遗传区段157.32~ 197.94 Mb范围内(附表3)。

Table 4
表4
表4穗长显著关联的SNP位点
Table 4Association of SNP loci with ear length

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

新窗口打开|下载CSV

图5

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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.

Fig. 5Ear length related QTN

3 讨论

3.1 Suwan种质改良过程中的一些重要区段

群体改良是一种打破有利基因与不利基因连锁, 使有利基因频率得到提高, 从而改良玉米育种材料的过程^[1,21]。如雍红军等^[22]以辽旅综、中综3号、BSCB1等10个玉米群体改良杂交种吉单261的育种利用发现, 供试群体具有改良杂交种性状的利用价值, 能提高杂交种产量和穗行数的潜力; 贵州省农业科学院将Lancaster种质导入Suwan种质形成苏兰1号群体, 与墨瑞1号群体进行半同胞相互轮回选择改良后, 形成新一轮改良群体组配群体杂交组合, 通过田间鉴定表明, 墨瑞1号C₁×苏兰1号C₁比墨瑞1号C₀×苏兰1号C₀的产量提高7.84%, 群体间的平均杂种优势也从改良前的9.86%提高到改良后的16.29%^[16]。李芦江等^[23]研究5轮控制双亲混合选择对2个玉米人工合成窄基群体P3C₀和P4C₀的改良效果发现, 控制双亲混合选择对群体单株产量和主要构成性状及其一般配合力(GCA)改良效果明显, 多数性状及其GCA均大于C₀, 但是当选择响应到达最大以后, 持续改良会使群体的选择增益下降, 甚至出现负增益。说明群体在改良过程中, 其农艺性状会随着改良轮次的增加呈现出不同的改良效应。

本研究结果表明, 群体在改良过程中, 保持着群体内丰富的遗传变异, 不同改良世代间有少数基因发生交换重组, 其中在Suwan 1群体的改良世代中仅获得5个差异遗传片段, 苏兰1号C₀群体改良世代中共获得18个差异遗传区段, 有8个在其不同改良世代间稳定出现。另外, Suwan种质改良形成苏兰1号群体的过程中, 共获得53个来自Suwan群体的稳定遗传区段和43个来自Lancaster的差异遗传区段, 而且有35个差异遗传片段在苏兰1号C₀群体及其改良世代间稳定出现。说明这些Suwan来源的稳定遗传区段可能在保持Suwan种质优势性状方面发挥作用, 所以在育种选择中被保留下来, 而Lancaster来源的差异遗传区段则可能在改良Suwan种质生育期长、株高等性状缺点方面起作用。这些研究结果从分子水平上解释了苏兰1号群体在育种和生产中应用与Suwan种质存在差异的原因, 也为后续Suwan 1及其衍生群体(苏兰1号)的改良利用提供了一定的理论支撑。

3.2 Suwan群体改良过程中候选区段的效应

本研究共发掘出16个与穗行数显著关联的QTN位点, 分别位于第2、第3、第5、第6、第7、第8、第9染色体上, 其中有2个位点(SYN25713和SYN36577)位于苏兰1号群体的Lancaster来源的遗传区段内; 发掘出13个与穗长显著相关联的QTN位点, 分别位于第1、第2、第5、第7、第8、第9染色体上, 有1个位点(PZE-105143697)位于Lancaster来源的特异性遗传区段内, 研究这些位点对理解玉米Suwan种质遗传机制有重要作用。与前人研究结果的比较发现, Lu等^[24]利用B73/丹340的F₂群体进行QTL定位, 在第4染色体上检测到qERN4a (umc1294-bnlg1265)和qERN4c (umc2188-umc1101), 与本文第4染色体上发掘出的2个穗行数QTN (PZE-104012465和SYN25713)位于同一位置, 这一结果与Yan等^[25]的定位结果相一致。王辉等^[26]利用郑58/HD568构建重组自交系群体进行QTL定位, 检测到qEL3 (198.52~201.32 Mb)和qERN4 (211.08~ 219.99 Mb)与本文在第3染色体发掘出的穗长SNP标记PZE-103146876 (199472604)和第4染色体发掘出的穗行数SNP标记 SYN25713 (218657640)位于同一染色体区段的位点; Zhou等^[27]利用掖478/ SL17-1构建群体进行QTL定位, 在第7染色体上定位到多效性qEL7.02 (umc1393-bnlg657)与本文在第7染色体发掘出的穗长SNP标记SYN19052 (125475003)所在标记区间一致。说明在这些区段内含有控制相关性状的基因位点且可靠性较高, 该区域在玉米产量相关性状改良过程中起到一定作用, 可以作为今后精细定位的候选区域。

4 结论

在Suwan种质改良形成苏兰1号群体的过程中, 共发现53个Suwan来源的稳定遗传区段和43个Lancaster来源的差异遗传区段, 这些区段内存在控制穗行数和穗长的QTN, 对于保持各自优势性状具有重要意义。该研究结果将为Suwan种质改良过程中的优势基因聚合提供很好的借鉴。

The authors have declared that no competing interests exist.

作者已声明无竞争性利益关系。

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Summary: Association analyses that exploit the natural diversity of a genome to map at very high resolutions are becoming increasingly important. In most studies, however, researchers must contend with the confounding effects of both population and family structure. TASSEL (Trait Analysis by aSSociation, Evolution and Linkage) implements general linear model and mixed linear model approaches for controlling population and family structure. For result interpretation, the program allows for linkage disequilibrium statistics to be calculated and visualized graphically. Database browsing and data importation is facilitated by integrated middleware. Other features include analyzing insertions/deletions, calculating diversity statistics, integration of phenotypic and genotypic data, imputing missing data and calculating principal components. Availability: The TASSEL executable, user manual, example data sets and tutorial document are freely available at http://www.maizegenetics.net/tassel. The source code for TASSEL can be found at http://sourceforge.net/projects/tassel. Contact: pjb39@cornell.edu

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Chen Z H. Population and Quantitative Genetics. Guiyang: Guizhou Science and Technology Publishing House, 2009. pp 28-53(in Chinese).
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雍洪军, 张芳军, 张德贵, 张晓聪, 李明顺, 潘光堂, 张世煌, 李新海, 荣廷昭 . 10个玉米群体改良杂交种吉单261的育种利用分析
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Yong H J, Zhang F J, Zhang D G, Zhang X C, Li M S, Pan G T, Zhang S H, Li X H, Rong Y Z . Analysis on breeding potential of ten populations to improve a Chinese maize hybrid ‘Jidan 261’
J Nucl Agric Sci, 2014,28:765-771 (in Chinese with English abstract).
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[22] 李芦江, 陈文生, 杨克诚, 潘光堂, 荣廷昭 . 控制双亲混合选择对2个玉米窄基群体主要性状的改良效果
中国农业科学, 2010,43:4775-4786.
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Li L J, Chen W S, Yang K C, Pan G T, Rong T Z . Effects of biparental mass selection on two narrow-base maize populations
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[23] Lu M, Xie C X, Li X H, Hao Z F, Li M S, Weng J F, Zhang D G, Bai L, Zhang S H . Mapping of quantitative trait loci for kernel row number in maize across seven environments
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DOI:10.1007/s11032-010-9468-3URL [本文引用: 1]
Genetic factors controlling quantitative inheritance of grain yield and its components have been intensively investigated during recent decades using diverse populations in maize (Zea mays L.). Notwithstanding this, quantitative trait loci (QTL) for kernel row number (KRN) with large and consistent effect have not been identified. In this study, a linkage map of 150 simple sequence repeat (SSR) loci was constructed by using a population of 500 F2 individuals derived from a cross between elite inbreds Ye478 and Dan340. The linkage map spanned a total of 1478 cM with an average interval of 10.0 cM. A total of 397 F2:3 lines were evaluated across seven diverse environments for mapping QTL for KRN. Some QTL for grain yield and its components had previously been confirmed with this population across environments. A total of 13 QTL for KRN were identified, with each QTL explaining from 3.0 to 17.9% of phenotypic variance. The gene action for KRN was mainly additive to partial dominance. A large-effect QTL (qkrn7) with partial dominance effect accounting for 17.9% of the phenotypic variation for KRN was identified on chromosome 7 near marker umc1865 with consistent gene effect across seven diverse environments. This study has laid a foundation for map-based cloning of this major QTL and for developing molecular markers for marker-assisted selection of high KRN.

[24] Yan J B, Tang H, Huang Y Q, Zheng Y L, Li J S . Quantitative trait loci mapping and epistatic analysis for grain yield and yield components using molecular markers with an elite maize hybrid
Euphytica, 2006,149:121-131.
DOI:10.1007/s10681-005-9060-9URL [本文引用: 1]
The aim of this investigation was to map quantitative trait loci (QTL) associated with grain yield and yield components in maize and to analyze the role of epistasis in controlling these traits. An F 2:3 population from an elite hybrid (Zong387-1) was used to evaluate grain yield and yield components in two locations (Wuhan and Xiangfan, China) using a randomized complete-block design. The mapping population included 266 F 2:3 family lines. A genetic linkage map containing 150 simple sequence repeats and 24 restriction fragment length polymorphism markers was constructed, spanning a total of 2531.6 cM with an average interval of 14.5 cM. A logarithm-of-odds threshold of 2.8 was used as the criterion to confirm the presence of one QTL after 1000 permutations. Twenty-nine QTL were detected for four yield traits, with 11 of them detected simultaneously in both locations. Single QTL contribution to phenotypic variations ranged from 3.7% to 16.8%. Additive, partial dominance, dominance, and overdominance effects were all identified for investigated traits. A greater proportion of overdominance effects was always observed for traits that exhibited higher levels of heterosis. At the P 0.005 level with 1000 random permutations, 175 and 315 significant digenic interactions were detected in two locations for four yield traits using all possible locus pairs of molecular markers. Twenty-four significant digenic interactions were simultaneously detected for four yield traits at both locations. All three possible digenic interaction types were observed for investigated traits. Each of the interactions accounted for only a small proportion of the phenotypic variation, with an average of 4.0% for single interaction. Most interactions (74.9%) occurred among marker loci, in which significant effects were not detected by single-locus analysis. Some QTL (52.2%) detected by single-locus analysis were involved in epistatic interactions. These results demonstrate that digenic interactions at the two-locus level might play an important role in the genetic basis of maize heterosis.

[25] 王辉, 梁前进, 胡小娇, 李坤, 黄长玲, 王琪, 何文昭, 王红武, 刘志芳 . 不同密度下玉米穗部性状的QTL分析
作物学报, 2016,42:1592-1600.
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Wang H, Liang Q J, Hu X J, Li K, Huang C L, Wang Q, He W Z, Wang H W, Liu Z F . QTL mapping for ear architectural traits under three plant densities in maize
Acta Agron Sin, 2016,42:1592-1600 (in Chinese with English abstract).
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[26] Zhou G, Zhu Q, Yang G, Huang J, Cheng S, Yue B, Zhang Z . qEL7.2 is a pleiotropic QTL for kernel number per row, ear length and ear weight in maize( Zea mays L.). Euphytica, 2015,203:429-436.
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