玉米穗行数全基因组关联分析

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张焕欣, 翁建峰, 张晓聪, 刘昌林, 雍洪军, 郝转芳, 李新海. 玉米穗行数全基因组关联分析. 作物学报, 2014, 40(1): 1-6
ZHANG Huan-Xin, WENG Jian-Feng, ZHANG Xiao-Cong, LIU Chang-Lin, YONG Hong-Jun, HAO Zhuan-Fang, LI Xin-Hai. Genome-wide Association Analysis of Kernel Row Number in Maize. Acta Agron Sin, 2014, 40(1): 1-6 复制到剪切板

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作物学报编辑部

玉米穗行数全基因组关联分析

张焕欣, 翁建峰^*, 张晓聪, 刘昌林, 雍洪军, 郝转芳, 李新海^*

中国农业科学院作物科学研究所 / 作物分子育种国家工程实验室, 北京100081

^* 通讯作者(Corresponding authors): 翁建峰, E-mail:jfweng@126.com; 李新海, E-mail:lixinhai@caas.cn

第一作者联系方式: E-mail:zhanghuanxin150@163.com

收稿日期:2013-09-16

基金:本研究由国家自然科学基金项目(31201219)和国家重点基础研究发展计划(973计划)项目(2011CB100106)资助。

摘要

穗行数是玉米产量的重要组成性状, 其遗传解析对高产育种具有指导意义。本文以203份主要玉米自交系为材料, 2007年在新疆乌鲁木齐、吉林公主岭和海南三亚进行穗行数测定; 采用分布于玉米基因组的41 101个单核苷酸多态性(SNP)标记对穗行数进行关联分析。共鉴定出9个与穗行数显著关联(P< 0.0001)的SNP, 分别位于染色体框1.02、1.10、7.03、8.02、9.06和10.03。8个SNP位于已定位的数量性状座位(QTL)区间内。在显著SNP位点LD区域内发掘出4个候选基因, 分别编码含F-box结构域的生长素受体蛋白、玉米kn1蛋白、AP2结构域蛋白和富亮氨酸重复的跨膜蛋白激酶。采用全基因组关联分析策略发掘穗行数基因位点及候选基因, 将为克隆控制玉米产量性状基因奠定基础。

关键词: 玉米; 穗行数; 全基因组关联分析; 候选基因

Genome-wide Association Analysis of Kernel Row Number in Maize

ZHANG Huan-Xin, WENG Jian-Feng^*, ZHANG Xiao-Cong, LIU Chang-Lin, YONG Hong-Jun, HAO Zhuan-Fang, LI Xin-Hai^*

Institute of Crop Science, Chinese Academy of Agricultural Sciences / National Engineer Laboratory of Crop Molecular Breeding, Beijing 100081, China

Abstract

Kernel row number (KRN) is one of grain yield components in maize (Zea mays L.). Investigation of its genetic architecture will help develop high-yield varieties in maize. In this study, the KRN in a panel of 203 maize inbred lines was detected in Urumqi of Xinjiang, Gongzhuling of Jilin, and Sanya of Hainan in 2007, and used to perform the genome-wide analysis for KRN using MaizeSNP50 BeadChip. A total of nine SNPs were found to be significantly associated with KRN at a threshold ofP< 0.0001, which were on chromosome Bins 1.02, 1.10, 7.03, 8.02, 9.06, and 10.03, respectively. Eight of these SNPs were located in the QTL intervals reported previously. Meanwhile, four candidate genes were scanned, encoding auxin signaling F-box containing protein, kn1 protein, AP2 domain containing protein and leucine-rich repeat transmembrane protein kinase respectively. In summary, these identified genes and SNPs will offer essential information for cloning yield-related genes in maize.

Keyword: Maize; Kernel row number; Genome-wide association analysis; Candidate gene

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玉米穗行数(kernel row number, KRN)形成于小穗分化期, 由小穗成对分生组织数目决定^{[ 1]}。穗行数是决定玉米产量的主要构成因素, 属于数量性状, 广义遗传力较高^{[ 2]}, 其遗传解析对玉米高产育种具有指导意义。分子标记的发展使得QTL作图成为解析穗行数遗传结构的有效方法^{[ 3]}。目前, 关于穗行数定位研究报道较多, 影响穗行数的QTL在玉米10条染色体上均有分布。Ma等^{[ 4]}利用综3×87-1构建的294份重组自交系(recombinant inbred line, RIL)群体检测出13个穗行数QTL, 分别位于第1、第3、第4、第5、第8、第9和第10染色体。Lu等^{[ 5]}利用掖478×丹340的150个F_2:3家系共定位到13个控制穗行数的QTL, 位于染色体框7.03位点来自丹340的穗行数主效QTL qkrn7可解释平均表型变异17.86%。Guo等^{[ 6]}用郑58×昌7-2的231个F_2:3家系在两种播种密度下进行穗行数QTL定位, 分别检测到8个和7个穗行数QTL。谭巍巍等^{[ 7]}利用掖478×黄早四与齐319×黄早四构建的2套F_2:3家系在染色体框5.04、6.05-6.07、7.02和10.03鉴定出穗行数QTL。江培顺等^{[ 8]}采用元分析方法整合了35篇文献中定位的184个分布于玉米10条染色体上的穗行数QTL, 共发掘出除位于第6染色体外的22个Meta- QTL。

研究者利用不同的遗传群体和QTL作图方法挖掘出诸多穗行数QTL, 但是, 受标记密度的限制, 检测到的QTL置信区间较大、有效性较低, 而且当控制该性状的基因在两亲本之间相同时则不能被检测到, 难以提供育种群体中优良等位基因的信息。与传统双亲QTL作图相比, 全基因组关联分析(genome-wide association study, GWAS)具有高分辨率、高通量的优势, 有利于鉴定现有种质资源中的有利等位基因^{[ 9, 10]}。Huang等^{[ 11]}对950个水稻品种进行GWAS, 分别检测出32个和10个与开花期和产量性状显著关联的遗传位点。Weng等^{[ 12]}利用41 101个SNP对284个玉米自交系进行株高全基因组关联分析, 鉴定出105个遗传位点。借助关联分析与连锁作图, 将抗玉米丝黑穗病主效位点 qHS2.09精细定位至约1 Mb^{[ 13]}。Tian等^{[ 14]}、Buckler等^{[ 15]}和Brown 等^{[ 16]}以含5000个RIL的玉米巢式作图群体的全基因组分析, 鉴定出影响叶形、开花期和花序性状的遗传位点及候选基因。

迄今, 有关玉米穗行数的全基因组关联分析及相关候选基因发掘的研究报道较少。本文采用203份玉米自交系组成的关联作图群体进行全基因组分析, 挖掘玉米种质中蕴含的穗行数优异等位基因, 为克隆控制玉米产量性状基因奠定基础。

1 材料与方法

1.1 试验材料及基因型测定

203份玉米自交系, 由中国农业科学院作物科学研究所提供。2007年, 将其分别种植于新疆乌鲁木齐(XJ)、吉林公主岭(JL)和海南三亚(HN)。采用行长4.5 m, 行距0.6 m, 每行20株的完全随机区组试验设计, 2次重复。按照常规生产条件进行田间管理。收获后, 每个小区随机取10个果穗调查穗行数, 平均值用于统计分析。

采用改良CTAB法^{[ 17]}提取203份自交系幼叶基因组DNA, 用0.8%琼脂糖凝胶电泳和NanoDrop 2000分光光度计检测DNA质量, 合格的样品DNA用于SNP分型。本文采用Illumina公司开发的MaizeSNP50 BeadChip芯片, 该芯片包括56 110个SNP标记, 均匀覆盖玉米自交系B73全基因组。SNP基因型检测参照Illumina公司提供的操作指南, 采用Illumina BeadStation 500 G SNP分型系统完成。芯片基因型数据质量控制参考Weng等^{[ 12]}, 采用 41 101个高质量的SNP标记进行关联分析。

1.2 表型数据统计分析

采用SAS 9.1.3 (SAS Inc., Cary, NC)的PROC UNIVARIATE、PROC GLM和PROC CORR程序分别进行描述性统计量分析、方差分析和相关分析。按照Knapp等^{[ 18]}提出的公式 h² = σ_g²/( σ_g² + σ_gl²/ n + σ_e²/ nr)估算遗传力, 其中 σ_g²为遗传方差, σ_gl²为基因型与环境互作的方差, σ_e²为误差方差, n为地点数, r为重复数。

1.3 群体结构与亲缘关系分析

利用软件STRUCTURE V2.3^{[ 19]}检测该群体的遗传结构, 以5000个最小等位基因频率大于0.2且在染色体均匀分布的SNP标记进行估计, Weng等^{[ 12]}将该群体划分为旅大红骨、四平头、Lancaster、PB、BSSS和PA 6个亚群。通过软件SPAGeDi^{[ 20]}, 采用相同的5000个SNP估计自交系间的亲缘关系。

1.4 穗行数全基因组关联分析

运用软件TASSEL V3.0^{[ 21]}中的混合线性模型(mixed-linear model, MLM)程序, 在考虑研究材料群体结构与亲缘关系情况下, 进行SNP标记与穗行数的关联分析。在 P< 0.0001水平上, 判定SNP标记与穗行数关联的显著性。

1.5 穗行数定位结果比较分析

收集1994—2013年定位的穗行数QTL信息; 借助玉米基因组数据库MaizeGDB确定其物理位置。若GWAS检测到的SNP在物理位置上与前人QTL定位结果重叠, 则认为二者具有一致性。

1.6 穗行数候选基因挖掘

基于GWAS结果, 利用与穗行数显著相关SNP的60 bp源序列, 比对B73的参考序列RefGen_v2 (MGSC) (http://blast.maizegdb.org/home.php?A=LAST_UI)。依据Weng等^{[ 12]}研究结果, 本文关联群体平均LD衰减距离为27.7 kb, 在30.0 kb窗口范围内扫描穗行数候选基因。

2 结果与分析

2.1 穗行数分析

新疆、吉林和海南3个环境中的穗行数均值分别为13.29、13.86和13.61, 变异系数分别为13.87%、13.84%和14.67%, 说明不同自交系间穗行数的差异较大。穗行数遗传力为81.07%, 与Lu等^{[ 5]}的结果相近。Pearson 相关分析表明, 3个环境中的穗行数数据显著相关(表1)。

表1 203份自交系穗行数统计分析 Table 1 Statistics on kernel row number evaluated on 203 inbred lines in three environments

2.2 穗行数全基因组关联分析

采用TASSEL V3.0软件MLM模型程序, 对203份玉米自交系进行穗行数的全基因组关联分析。 3个环境下共检测到9个与穗行数显著关联( P< 0.0001)的SNP, 分别位于玉米染色体框1.02、1.10、7.03、8.02、9.06和10.03, 其中, 染色体框1.10和7.03分别检测出2个和3个显著性SNP, 最高可解释15.00%的表型变异率(表2)。位于第1染色体框1.10的PZE101220014在新疆和吉林2个环境均被检测到(表2和图1), 而在海南环境中检测到的SNP PZE-101219999与其相差约6 kb。通过TASSEL V3.0软件, 获得3个环境下穗行数全基因组关联分析的QQ图(图2), 关联群体的群体结构得到了较好控制。

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	图1 穗行数全基因组关联分析XJ、JL和HN分别代表新疆、吉林和海南。黑色水平线代表全基因组关联分析的显著阈值。Fig. 1 Genome-wide association study of kernel row number with mixed linear modelXJ, JL, and HN indicate experiments at Xinjiang, Jilin and Hainan, respectively. Black horizontal line indicates the genome-wide significance threshold.

表2 与穗行数显著关联的SNP位点( P< 0.0001) Table 2 SNPs identified to be associated with kernel row number ( P< 0.0001)

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	图2 3个环境下全基因组关联分析的QQ图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。Fig. 2 Quantile-quantile plot for kernel row number in three environmentsThe horizontal axis shows -lg transformed expected P-values, and the vertical axis shows -lg transformed observed P-values.

2.3 候选基因分析

对9个与穗行数显著关联( P< 0.0001)的SNP标记位点进行扫描分析, 获得4个候选基因(表2)。 GRMZM2G398848编码产物是一个含F-box结构域的生长素受体蛋白(auxin signaling F-box containing protein)。 GRMZM2G017087 ( knotted1, kn1)是玉米同源异型盒基因家族成员, 最早发现于玉米顶端分生组织中^{[ 23]}, 参与生物发育调控过程。 GRMZM2G 069146编码一个含AP2结构域的蛋白(AP2 domain containing protein)。 GRMZM2G151567的编码产物是富亮氨酸重复的跨膜蛋白激酶(leucine-rich repeat transmembrane protein kinase)。

3 讨论

3.1 穗行数定位结果比较分析

GWAS是一种以连锁不平衡为基础, 利用分布于全基因组的SNP, 借助统计学工具分析某一群体内目标性状遗传变异的方法。目前, GWAS已应用于鉴定植物病害、开花期、籽粒性状、株高等QTL^{[ 9, 10, 11, 12, 15, 24, 25, 26]}, 但玉米穗行数的GWAS研究较少。本文采用203份玉米自交系组成的关联作图群体进行全基因组分析, 在3个环境中共检测出9个与穗行数显著关联( P< 0.0001)的SNP。Massman等^{[ 27]}认为距离小于5 cM的显著SNP可以归为一个QTL, 本文在染色体框1.10检测到的PZE-101219999和PZE-101220014物理距离相距约6.5 kb, 换算后遗传距离小于5 cM, 因此, PZE-101219999和PZE- 101220014应位于同一个QTL。该QTL在3个环境中被重复检测到。连锁不平衡是不同基因座位上等位基因的非随机组合关系^{[ 28]}。关联分析中, 常用 r²度量位点之间连锁不平衡的程度, 当 r²≥ 0.8时认为两位点不独立, 即处于连锁不平衡状态^{[ 27]}。利用HAPLOVIEW V4.0^{[ 29]}, SYN17065与PZE-107084987的 r²为0.14, PZE-107084987与PZE-107085390的 r²为0.33, 因此位于染色体框7.03的这3个与穗行数显著关联的标记是独立位点。

连锁定位和关联分析都可以检测数量性状位点, 两种方法定位到的QTL在位置上大部分具有一致性^{[ 14, 16, 30]}。本文检测到的9个SNP中, 有8个位于已定位的QTL区段内(表2)。PZE-101030429位于第1染色体框1.02, 与Guo等^{[ 6]}的研究结果一致。Ma等^{[ 4]}利用综3×87-1构建的294份重组自交系在染色体框1.10的bnlg1597-umc2149处定位到穗行数QTL, 本研究检测到的SNP PZE-101219999和PZE-101220014也位于该区间两标记的物理位置内。位于第8染色体框8.02的PZE-108018598与Liu等^{[ 22]}的研究结果吻合。染色体框7.03共有3个标记与穗行数显著关联, SYN17065、PZE-107084987与PZE-107085390均位于Lu等^{[ 5]}定位的bnlg339- umc1865区间。PZE-110033446位于第10染色体框10.03位置, 与Lu、谭巍巍等^{[ 5, 7]}结果一致。但是本研究发现并非所有GWAS检测到的显著位点(如PZE-109090136)都与已定位的QTL重叠, 原因可能是前人采用的双亲QTL作图法受亲本种质背景和检测微效QTL功效较低的影响。这表明采用全基因组关联分析策略是一种解析穗行数遗传结构的有效方法。

3.2 候选基因分析

Aranzana等^{[ 31]}对95个拟南芥品种进行GWAS, 发现几个开花期和病原基因均被检测到。Huang等^{[ 32]}利用3 600 000个SNP标记对517个水稻品种开展全基因组分析, 发现6个SNP位点分别与已知基因 qSW5、 GS3、 ALK、 Waxy、 OsC1和 Rc临近。本文对检测出的9个与穗行数显著关联( P< 0.0001)的SNP位点进行扫描分析, 得到4个候选基因。 GRMZM2G398848编码一个含F-box结构域的生长素受体蛋白。F-box蛋白TIR1是生长素的受体, 通过介导一系列生长素反应来参与植物生长发育的调控^{[ 33]}。PZE-101219999位于 GRMZM2G017087( kn1)内部, PZE-101220014位于 kn1上游约6 kb处。 kn1可能维持分生组织细胞的自我更新和控制分枝原基分生组织属性的建成, 玉米突变体 kn1的雄穗分枝数和小穗数均减少, 雌穗小穗对数降低且多数小花不育^{[ 1, 34]}。 GRMZM2G069146编码一个含AP2结构域的蛋白。 IDS1是AP2基因家族成员, 参与调控玉米小穗分生组织的有限性, ids1突变体的每个小穗产生额外的小花^{[ 35]}; IDS1的横向同源基因 SID1与小花分生组织启动及小穗调控有关^{[ 36]}; 水稻基因 SNB与 OsIDS1分别是 ids1和 sid1的直系同源基因, 在控制花序结构与花序分生组织建成等方面具有重要作用^{[ 37]}。 GRMZM2G151567编码一个富亮氨酸重复的蛋白激酶, td1同样编码一个富亮氨酸重复的蛋白激酶, 玉米突变体 td1的雄穗小穗密度、雄蕊数目增加, 雌穗的籽粒行数增加^{[ 38]}; fea2编码一个富亮氨酸的受体样蛋白, 可能通过控制花序分生组织的大小来调控玉米穗行数^{[ 39, 40]}。上述基因信息可能为克隆玉米产量性状相关候选基因提供一定基础。

4 结论

利用41 101个SNP标记对203份玉米自交系进行穗行数全基因组关联分析, 发现9个与穗行数显著关联( P< 0.0001)的SNP。在显著SNP位点LD区域内发掘出4个候选基因, 分别为 GRMZM2G398848、 GRMZM2G017087、 GRMZM2G069146和 GRMZM2G 151567。

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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1997

0.0

0.1123

... 玉米穗行数(kernel row number, KRN)形成于小穗分化期, 由小穗成对分生组织数目决定^[1] ...

... kn1可能维持分生组织细胞的自我更新和控制分枝原基分生组织属性的建成, 玉米突变体kn1的雄穗分枝数和小穗数均减少, 雌穗小穗对数降低且多数小花不育^[1,34] ...

1977

2.041

0.0

. 1977, 88:257-265

Estimation and inheritance of stability parameters of grain yield in maize

Dhillon B S , Singh J

One hundred and ninety hybrids involving 20 broad-based yellow maize populations were evaluated together with their parents for stability in expression of their grain yield potential by means of linear regression on to an environmental index. Both linear and non-linear components were observed to be significant; the linear component, in general, being the more important. Two high yielding parents, namely variety A 3D and composite Jawahar, had general adaptability, while synthetic A 22 was suited to poor environment and variety SO 4D to good environment. Seventeen hybrids had above average yield and the majority of these exhibited general adaptability.

Combining ability analysis revealed that GCA (general combining ability) was more important than SCA (specific combining ability) in the expression of mean yield. Inheritance of linear regression was controlled predominantly by GCA whereas both GCA and SCA were equally important in the expression of non-linear fluctuations. Variety Cuba was the most desirable parent, as it transmitted to its progeny high grain yield potential and low linear response. The other good combiners for grain yield were variety SC 4D and Prolific composite but these transmitted above average linear response.

Lack of association between grain yield and linear regression of both parents and GCA effects indicated their independent mode of inheritance. It suggested, therefore, that high yield can be combined with general adaptability or responsiveness to either good or poor environment.

... 穗行数是决定玉米产量的主要构成因素, 属于数量性状, 广义遗传力较高^[2], 其遗传解析对玉米高产育种具有指导意义 ...

2006

2.852

0.0

Mol Breeding. 2006, 17(3):227 - 239 DOI:10.1007/s11032-005-5679-4

Mapping QTL for Grain Yield and Plant Traits in a Tropical Maize Population

Milena de Luna Alves Lima(2) Cláudio Lopes de Souza(1) Dyeme Antonio Vieira Bento(1) Anete Pereira de Souza(2) Luciana Aparecida Carlini-Garcia(1)

1.Universidade de S?o Paulo Departamento de Genética, Escola Superior de Agricultura “Luiz de Queiroz” Caixa Postal 83 13.400-970 Piracicaba SP Brazil Caixa Postal 83 13.400-970 Piracicaba SP Brazil
2.Universidade Estadual de Campinas Centro de Biologia Molecular e Engenharia Genética Caixa Postal 6010 13.083-970 Campinas SP Brazil Caixa Postal 6010 13.083-970 Campinas SP Brazil

The vast majority of reported QTL mapping for maize (Zea mays L.) traits are from temperate germplasm and, also, QTL by environment interaction (QTL × E) has not been thoroughly evaluated and analyzed in most of these papers. The maize growing areas in tropical regions are more prone to environmental variability than in temperate areas, and, therefore, genotype by environment interaction is of great concern for maize breeders. The objectives of this study were to map QTL and to test their interaction with environments for several traits in a tropical maize population. Two-hundred and fifty-six F_2:3 families evaluated in five environments, a genetic map with 139 microsatellites markers, and the multiple-environment joint analysis (mCIM) were used to map QTL and to test QTL × E interaction. Sixteen, eight, six, six, nine, and two QTL were mapped for grain yield, ears per plant, plant lodging, plant height, ear height, and number of leaves, respectively. Most of these QTL interacted significantly with environments, most of them displayed overdominance for all traits, and genetic correlated traits had a low number of QTL mapped in the same genomic regions. Few of the QTL mapped had already been reported in both temperate and tropical germplasm. The low number of stable QTL across environments imposes additional challenges to design marker-assisted selection in tropical areas, unless the breeding programs could be directed towards specific target areas.

... 分子标记的发展使得QTL作图成为解析穗行数遗传结构的有效方法^[3] ...

2007

2.852

0.0

Mol Breeding. 2007, 20(1):41 - 51 DOI:10.1007/s11032-006-9071-9

Epistatic interaction is an important genetic basis of grain yield and its components in maize

X. Q. Ma(1) J. H. Tang(1) W. T. Teng(1) J. B. Yan(1) Y. J. Meng(1) J. S. Li(1)

1.National Maize Improvement Center of China, China Agricultural University, Yuanmingyuan West Road, Haidian, Beijing, 100094 China

A population of 294 recombinant inbred lines (RIL) derived from Yuyu22, an elite maize hybrid extending broadly in China, has been constructed to investigate the genetic basis of grain yield, and associated yield components in maize. The main-effect quantitative trait loci (QTL), digenic epistatic interactions, and their interactions with the environment for grain yield and its three components were identified by using the mixed linear model approach. Thirty-two main-effect QTL and forty-four pairs of digenic epistatic interactions were detected for the four measured traits in four environments. Our results suggest that both additive effects and epistasis (additive × additive) effects are important genetic bases of grain yield and its components in the RIL population. Only 30.4% of main-effect QTL for ear length were involved in epistatic interactions. This implies that many loci in epistatic interactions may not have significant effects for traits alone but may affect trait expression by epistatic interaction with the other loci.

... Ma等^[4]利用综3×87-1构建的294份重组自交系(recombinant inbred line, RIL)群体检测出13个穗行数QTL, 分别位于第1、第3、第4、第5、第8、第9和第10染色体 ...

... Ma等^[4]利用综3×87-1构建的294份重组自交系在染色体框1 ...

2010

2.852

0.0

. 2010, 28:143-152

Mapping of quantitative trait loci for kernel row number in maize across seven environments

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

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.

... Lu等^[5]利用掖478×丹340的150个F_2:3家系共定位到13个控制穗行数的QTL, 位于染色体框7 ...

... 07%, 与Lu等^[5]的结果相近 ...

... 03共有3个标记与穗行数显著关联, SYN17065、PZE-107084987与PZE-107085390均位于Lu等^[5]定位的bnlg339- umc1865区间 ...

... 03位置, 与Lu、谭巍巍等^[5,7]结果一致 ...

2011

1.554

0.0

Euphytica. 2011, 182(3):409 - 422 DOI:10.1007/s10681-011-0517-8

Identification of genetic factors affecting plant density response through QTL mapping of yield component traits in maize (Zea mays L.)

Jinjie Guo⁽¹⁾,Zongliang Chen⁽¹⁾,Zhipeng Liu⁽¹⁾,Baobao Wang⁽¹⁾,Weibin Song⁽¹⁾,Wei Li⁽¹⁾,Jing Chen⁽¹⁾,Jingrui Dai⁽¹⁾,Jinsheng Lai

⁽¹⁾

1.State Key Laboratory of Agrobiotechnology and National Maize Improvement Center, China Agricultural University, 2 Yuan-ming-yuan West Road, Beijing, 100193, China

Abstract

It is generally believed that grain yield per unit area of modern maize hybrids is related to their adaptability to high plant population density. In this study, the effects of two different plant densities (52,500 and 90,000 plants/hm²) on 12 traits associated with yield were evaluated using a set of 231 F_2:3 families derived from two elite inbred lines, Zheng58 and Chang7-2. Evaluation of the phenotypes expressed under the two plant density conditions showed that high plant density condition could decrease the value of 10 measured yield component traits, while the final grain yield per hectare and the rate of kernel production were increased. Twenty-seven quantitative trait loci (QTLs) for 10 traits were detected in both high and low plant density conditions; among them, some QTLs were shown to locate in five clusters. Thirty QTLs were only detected under high plant density. These results suggest that some of the yield component traits perhaps were controlled by a common set of genes, and that kernel number per row, ear length, row number per ear, cob diameter, cob weight, and ear diameter may be influenced by additional genetic mechanisms when grown under high plant density. The QTLs identified in this study provide useful information for marker-assisted selection of varieties targeting increased plant density.

... Guo等^[6]用郑58×昌7-2的231个F_2:3家系在两种播种密度下进行穗行数QTL定位, 分别检测到8个和7个穗行数QTL ...

... 02, 与Guo等^[6]的研究结果一致 ...

2011

0.0

1.8267

Acta Agron Sin. 2011, 37(2):235 - 248 DOI:10.3724/SP.J.1006.2011.00235

QTL Mapping of Ear Traits of Maize under Different Water Regimes

在干旱和正常水分条件下玉米穗部性状QTL分析

TAN Wei-Wei^1,2,WANG Yang²,LI Yong-Xiang²,LIU Cheng³,LIU Zhi-Zhai^2,4,PENG Bo²,WANG Di²,ZHANG Yan²,SUN Bao-Cheng³,SHI Yun-Su²,SONG Yan-Chun²,YANG De-Guang^1,*,WANG Tian-Yu², and LI Yu2,*

谭巍巍^1,2,李永祥^2,**,王阳²,刘成³,刘志斋^2,4,彭勃²,王迪²,张岩²,孙宝成³,石云素²,宋燕春²,杨德光^1,*,王天宇²,黎裕^2,*

1 College of Agronomy, Northeast Agricultural University, Harbin 150030, China; 2 Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing 100081, China; 3Institute of Food Crops, Xinjiang Academy of Agricultural Sciences, Urumqi 830000, China; 4 Southwest University, Chongqing 400716, China

Ear traits are closely associated with maize yield. Therefore, genetic dissection of ear traits can provide clues to maize high-yield breeding and is especially important in breeding for drought tolerance. In this study, seven ear related traits including ear length (EL), ear diameter (ED), row number (KRN), kernel number per row (KRE), grain yield per ear (GW), cob diameter (AD) and weight per ear (EW), were investigated using two sets of F_2:3 populations, which were derived from crosses of Ye478×Huangzaosi (Y/H) and Qi319×Huangzaosi (Q/H), respectively. The two populations were evaluated under different water conditions in Xinjiang in 2007 and 2008. The results showed that those ear traits under drought were phenotypically lower than those under normal water regime and ear length, ear diameter, weight per ear had positive correlation with GW. A total of 75 QTL were identified under different water regimes using mixed linear model with two methods of single-experiment analysis and water regime joint analysis, including 20 QTL detected under normal water regime and 55 QTL detected under drought stress. The QTL detected in Y/H were located on chromosome 1, 2, 5, 6, 7, and 10, and the QTL detected in Q/H were distributed on chromosome 2, 3, 4, 5, 6, 7, 9, and 10. However, only four and nineteen QTL was identified in the two populations under drought stress respectively, significantly lower than that detected under normal water regime. Meanwhile, in the joint analysis, only three QTL had significant interaction with environments and six QTL had epistatic interaction, showing that the genetic feature of ear traits was complex. In Y/H, two congruent QTL,qKRE1-5-1 andqKRE1-7-1, were detected under different water levels, with the phenotypic contribution from 6.15% to 19.48%, while in Q/H, three congruent QTL,qKRE2-5-1,qGW2-10-1, andqKRE2-3-1, were detected under different water levels, with the phenotypic contribution from 7.14% to 16.65%. These results implied that these QTL were little influenced by environment and could stably expressed, which can be used in marker-assisted selection.

穗部性状与产量密切相关，因此对其进行遗传剖析可为玉米高产育种提供理论基础，尤其是对干旱胁迫下的稳产有重要意义。本研究以玉米骨干亲本黄早四分别与自交系掖478和齐319进行杂交，构建了两套F_2:3群体(分别记为Y/H和Q/H)。在正常水分灌溉和干旱胁迫下对穗长、穗粗、轴粗、穗行数、行粒数、穗粒重和穗重等7个穗部性状进行了表型鉴定，采用基于混合线性模型的单环境分析和相同处理水平的联合分析方法进行了QTL分析。结果表明，在干旱胁迫下，2个群体的亲本及F_2:3家系的各性状值均低于正常水分条件，且穗粒重与穗长、穗重、穗粗呈正相关。在干旱胁迫下和正常水分条件下，通过两种检测方法共定位到75个玉米穗部性状QTL，其中Y/H群体共定位了20个QTL，分布在第1、第2、6、第5、第7、第10染色体上；Q/H群体共定位了55个QTL，分布在第2、第3、第4、第5、第6、第7、第9、第10染色体上；但是在干旱条件下两群体分别只检测到4个和19个QTL，明显低于正常水分条件下检测到的QTL数目。通过联合分析只检测到3个QTL与环境发生显著互作和6对QTL存在上位性互作效应，说明玉米穗部性状的遗传基础较为复杂。同时还发现，Y/H群体在正常灌溉与干旱条件下检测到2个一致性的QTL，分别是qKRE1-5-1和qKRE1-7-1，对表型变异解释的变化范围是6.15%~19.48%；Q/H群体检测到3个一致性QTL，分别是qKRE2-5-1、qGW2-10-1和qKRE2-3-1，对表型变异解释的变化范围是7.14%~16.65%，说明这些QTL受环境影响较小，能够稳定遗传，可以作为分子标记辅助选择的候选区间应用于玉米穗部性状抗旱性改良。

... 谭巍巍等^[7]利用掖478×黄早四与齐319×黄早四构建的2套F_2:3家系在染色体框5 ...

... 03位置, 与Lu、谭巍巍等^[5,7]结果一致 ...

2013

0.0

1.8267

Acta Agron Sin. 2013, 39(6):969 - 978 DOI:10.3724/SP.J.1006.2013.00969

Analysis of Meta-QTL and Candidate Genes Related to Yield Components in Maize

玉米产量相关性状Meta-QTL及候选基因分析

IANG Pei-Shun^1,2,**,ZHANG Huan-Xin^2,**,LÜ Xiang-Ling¹,HAO Zhuan-Fang²,LI Bo¹,LI Ming-Shun²,WANG Hong-Wei¹,CI Xiao-Ke²,ZHANG Shi-Huang²,LI Xin-Hai²,SHI Zhen-Sheng^1,*,WENG Jian-Feng^2,*

江培顺^1,2,**,张焕欣^2,**,吕香玲¹,郝转芳²,李博¹,李明顺²,王宏伟¹,慈晓科²,张世煌²,李新海²,史振声^1,*,翁建峰^2,*

1 Special Maize Institute, Shenyang Agricultural University, Shenyang 110161, China; 2 Institute of Crop Sciences, Chinese Academy of Agricultural Sciences / National Engineer Laboratory of Crop Molecular Breeding, Beijing 100081, China

In this study, 584 QTLs related to grain yield components (row number, kernel number per row and kernel weight) in maize were integrated from the published papers between 1994 and 2012 using the reference map of IBM2 2008 Neighbors high density maize genetic map. By Meta-analysis method, 73 Meta-QTLs for grain yield components were estimated, including 22QTLs for row number, 7 QTLs for kernel number per row and 44 QTLs for kernel weight. With the B73 genome sequences, 10 maize genes and 12 rice homologous candidate genes related to yield components were comparatively and electronically mapped in consensus map, andthese genes are located in maize chromosome Bins 1.04, 1.06, 1.07, 2.04, 2.06, 3.04, 4.05, 4.07, 4.09, 5.03, 5.04, 5.05, 7.02, 8.03, 9.03, 10.06 and 10.07. Theanalysis of Meta-QTL and candidate genes related to grain yield components will provide useful information for marker-assisted selection breeding and gene cloning in maize.

借助IBM2 2008 Neighbors高密度玉米遗传图谱整合了1994—2012年文献发表的玉米产量性状(穗行数、行粒数、粒重)584个QTL。采用元分析方法，确定了22个穗行数、7个行粒数和44个粒重Meta-QTL。根据B73基因组序列进行产量相关基因的重定位，在Meta-QTL区段内分别获得10个玉米产量基因和12个与水稻7个产量基因同源的候选基因，分别位于玉米染色体Bins 1.04、1.06、1.07、2.04、2.06、3.04、4.05、4.07、4.09、5.03、5.04、5.05、7.02、8.03、9.03、10.06和10.07。玉米产量性状Meta-QTL及相关候选基因分析可以为分子标记辅助育种和基因克隆提供有用的信息。

... 江培顺等^[8]采用元分析方法整合了35篇文献中定位的184个分布于玉米10条染色体上的穗行数QTL, 共发掘出除位于第6染色体外的22个Meta- QTL ...

2006

7.711

0.0

Curr Opin Biotech. 2006, 17(2):155 - 160 DOI:10.1016/j.copbio.2006.02.003

Genetic association mapping and genome organization of maize

Association mapping, a high-resolution method for mapping quantitative trait loci based on linkage disequilibrium, holds great promise for the dissection of complex genetic traits. The recent assembly and characterization of maize association mapping panels, development of improved statistical methods, and successful association of candidate genes have begun to realize the power of candidate-gene association mapping. Although the complexity of the maize genome poses several significant challenges to the application of association mapping, the ongoing genome sequencing project will ultimately allow for a thorough genome-wide examination of nucleotide polymorphism-trait association.

... 与传统双亲QTL作图相比, 全基因组关联分析(genome-wide association study, GWAS)具有高分辨率、高通量的优势, 有利于鉴定现有种质资源中的有利等位基因^[9,10] ...

... 目前, GWAS已应用于鉴定植物病害、开花期、籽粒性状、株高等QTL^{[9,10,11,12,15,24,25,26]}, 但玉米穗行数的GWAS研究较少 ...

2008

0.0

. 2008, 1:5-20

Status and prospects of association mapping in plants

Zhu C S , Gore M , Buckler E S , Yu J M

There is tremendous interest in using association mapping to identify genes responsible for quantitative variation of complex traits with agricultural and evolutionary importance. Recent advances in genomic technology, impetus to exploit natural diversity, and development of robust statistical analysis methods make association mapping appealing and affordable to plant research programs. Association mapping identifies quantitative trait loci (QTLs) by examining the marker-trait associations that can be attributed to the strength of linkage disequilibrium between markers and functional polymorphisms across a set of diverse germplasm. General understanding of association mapping has increased significantly since its debut in plants. We have seen a more concerted effort in assembling various association-mapping populations and initiating experiments through either candidate-gene or genome-wide approaches in different plant species. In this review, we describe the current status of association mapping in plants and outline opportunities and challenges in complex trait dissection and genomics-assisted crop improvement.

... 目前, GWAS已应用于鉴定植物病害、开花期、籽粒性状、株高等QTL^{[9,10,11,12,15,24,25,26]}, 但玉米穗行数的GWAS研究较少 ...

2012

35.532

0.0

. 2012, 44:32-39

Genome-wide association study of flowering time and grain yield traits in a worldwide collection of rice germplasm

Huang X H , Zhao Y , Wei X H , Li C Y , Wang A H , Zhao Q , Li W J , Guo Y L , Deng L W , Zhu C R , Fan D L , Lu Y Q , Weng Q J , Liu K Y , Zhou T Y , Jing Y F , Si L Z , Dong G J , Huang T , Lu T T , Feng Q , Qian Q , Li J Y , Han B

A high-density haplotype map recently enabled a genome-wide association study (GWAS) in a population ofindica subspecies of Chinese rice landraces. Here we extend this methodology to a larger and more diverse sample of 950 worldwide rice varieties, including theOryza sativa indica andOryza sativa japonica subspecies, to perform an additional GWAS. We identified a total of 32 new loci associated with flowering time and with ten grain-related traits, indicating that the larger sample increased the power to detect trait-associated variants using GWAS. To characterize various alleles and complex genetic variation, we developed an analytical framework for haplotype-basedde novo assembly of the low-coverage sequencing data in rice. We identified candidate genes for 18 associated loci through detailed annotation. This study shows that the integrated approach of sequence-based GWAS and functional genome annotation has the potential to match complex traits to their causal polymorphisms in rice.

... Huang等^[11]对950个水稻品种进行GWAS, 分别检测出32个和10个与开花期和产量性状显著关联的遗传位点 ...

... 目前, GWAS已应用于鉴定植物病害、开花期、籽粒性状、株高等QTL^{[9,10,11,12,15,24,25,26]}, 但玉米穗行数的GWAS研究较少 ...

2011

4.092

0.0

. 2011, 6:e29229-null

Genome-wide association study identifies candidate genes that affect plant height in Chinese elite maize (Zea mays L. ) inbred lines

Weng J F , Xie C X , Hao Z F , Wang J J , Liu C L , Li M S , Zhang D G , Bai L , Zhang S H , Li X H

Background
The harvest index for many crops can be improved through introduction of dwarf stature to increase lodging resistance, combined with early maturity. The inbred line Shen5003 has been widely used in maize breeding in China as a key donor line for the dwarf trait. Also, one major quantitative trait locus (QTL) controlling plant height has been identified in bin 5.05–5.06, across several maize bi-parental populations. With the progress of publicly available maize genome sequence, the objective of this work was to identify the candidate genes that affect plant height among Chinese maize inbred lines with genome wide association studies (GWAS).
Methods and Findings
A total of 284 maize inbred lines were genotyped using over 55,000 evenly spaced SNPs, from which a set of 41,101 SNPs were filtered with stringent quality control for further data analysis. With the population structure controlled in a mixed linear model (MLM) implemented with the software TASSEL, we carried out a genome-wide association study (GWAS) for plant height. A total of 204 SNPs (P≤0.0001) and 105 genomic loci harboring coding regions were identified. Four loci containing genes associated with gibberellin (GA), auxin, and epigenetic pathways may be involved in natural variation that led to a dwarf phenotype in elite maize inbred lines. Among them, a favorable allele for dwarfing on chromosome 5 (SNP PZE-105115518) was also identified in six Shen5003 derivatives.
Conclusions
The fact that a large number of previously identified dwarf genes are missing from our study highlights the discovery of the consistently significant association of the gene harboring the SNP PZE-105115518 with plant height (P = 8.91e-10) and its confirmation in the Shen5003 introgression lines. Results from this study suggest that, in the maize breeding schema in China, specific alleles were selected, that have played important roles in maize production.

... Weng等^[12]利用41 101个SNP对284个玉米自交系进行株高全基因组关联分析, 鉴定出105个遗传位点 ...

... 芯片基因型数据质量控制参考Weng等^[12], 采用 41 101个高质量的SNP标记进行关联分析 ...

... 2且在染色体均匀分布的SNP标记进行估计, Weng等^[12]将该群体划分为旅大红骨、四平头、Lancaster、PB、BSSS和PA 6个亚群 ...

... 依据Weng等^[12]研究结果, 本文关联群体平均LD衰减距离为27 ...

... 目前, GWAS已应用于鉴定植物病害、开花期、籽粒性状、株高等QTL^{[9,10,11,12,15,24,25,26]}, 但玉米穗行数的GWAS研究较少 ...

2012

2.799

0.0

... 09精细定位至约1 Mb^[13] ...

2011

35.532

0.0

. 2011, 43:159-162

Genome-wide association study of leaf architecture in the maize nested association mapping population

Tian F , Bradbury P J , Brown P J , Hung H , Sun Q , Flint-Garcia S , Rocheford T R , McMullen M D , Holland J B , Buckler E S

US maize yield has increased eight-fold in the past 80 years, with half of the gain attributed to selection by breeders. During this time, changes in maize leaf angle and size have altered plant architecture, allowing more efficient light capture as planting density has increased. Through a genome-wide association study (GWAS) of the maize nested association mapping panel, we determined the genetic basis of important leaf architecture traits and identified some of the key genes. Overall, we demonstrate that the genetic architecture of the leaf traits is dominated by small effects, with little epistasis, environmental interaction or pleiotropy. In particular, GWAS results show that variations at theliguleless genes have contributed to more upright leaves. These results demonstrate that the use of GWAS with specially designed mapping populations is effective in uncovering the basis of key agronomic traits.

... Tian等^[14]、Buckler等^[15]和Brown 等^[16]以含5000个RIL的玉米巢式作图群体的全基因组分析, 鉴定出影响叶形、开花期和花序性状的遗传位点及候选基因 ...

... 连锁定位和关联分析都可以检测数量性状位点, 两种方法定位到的QTL在位置上大部分具有一致性^[14,16,30] ...

2009

0.0

. 2009, 325:714-718

The genetic architecture of maize flowering time

Buckler E S , Holland J B , Bradbury P J , Acharya C B , Brown P J , Browne C , Ersoz E , Flint-Garcia S , Garcia A , Glaubitz J C , Goodman M M , Harjes C , Guill K , Kroon D E , Larsson S , Lepak N K , Li H H , Mitchell S E , Pressoir G , Peiffer J A , Rosas M O , Rocheford T R , Romay M C , Romero S , Salvo S , Villeda H S , Sun Q , Tian F , Upadyayula N , Ware D , Yates H , Yu J M , Zhang Z W , Kresovich S , McMullen M D

Flowering time is a complex trait that controls adaptation of plants to their local environment in the outcrossing speciesZea mays (maize). We dissected variation for flowering time with a set of 5000 recombinant inbred lines (maize Nested Association Mapping population, NAM). Nearly a million plants were assayed in eight environments but showed no evidence for any single large-effect quantitative trait loci (QTLs). Instead, we identified evidence for numerous small-effect QTLs shared among families; however, allelic effects differ across founder lines. We identified no individual QTLs at which allelic effects are determined by geographic origin or large effects for epistasis or environmental interactions. Thus, a simple additive model accurately predicts flowering time for maize, in contrast to the genetic architecture observed in the selfing plant species rice andArabidopsis.

... Tian等^[14]、Buckler等^[15]和Brown 等^[16]以含5000个RIL的玉米巢式作图群体的全基因组分析, 鉴定出影响叶形、开花期和花序性状的遗传位点及候选基因 ...

... 目前, GWAS已应用于鉴定植物病害、开花期、籽粒性状、株高等QTL^{[9,10,11,12,15,24,25,26]}, 但玉米穗行数的GWAS研究较少 ...

2011

8.694

0.0

. 2011, 7:e1002383-null

Distinct genetic architectures for male and female inflorescence traits of maize

Brown P J , Upadyayula N , Mahone G S , Tian F , Bradbury P J , Myles S , Holland J B , Flint-Garcia S , McMullen M D , Buckler E S , Rocheford T R

We compared the genetic architecture of thirteen maize morphological traits in a large population of recombinant inbred lines. Four traits from the male inflorescence (tassel) and three traits from the female inflorescence (ear) were measured and studied using linkage and genome-wide association analyses and compared to three flowering and three leaf traits previously studied in the same population. Inflorescence loci have larger effects than flowering and leaf loci, and ear effects are larger than tassel effects. Ear trait models also have lower predictive ability than tassel, flowering, or leaf trait models. Pleiotropic loci were identified that control elongation of ear and tassel, consistent with their common developmental origin. For these pleiotropic loci, the ear effects are larger than tassel effects even though the same causal polymorphisms are likely involved. This implies that the observed differences in genetic architecture are not due to distinct features of the underlying polymorphisms. Our results support the hypothesis that genetic architecture is a function of trait stability over evolutionary time, since the traits that changed most during the relatively recent domestication of maize have the largest effects.

... Tian等^[14]、Buckler等^[15]和Brown 等^[16]以含5000个RIL的玉米巢式作图群体的全基因组分析, 鉴定出影响叶形、开花期和花序性状的遗传位点及候选基因 ...

... 连锁定位和关联分析都可以检测数量性状位点, 两种方法定位到的QTL在位置上大部分具有一致性^[14,16,30] ...

1980

0.0

... 采用改良CTAB法^[17]提取203份自交系幼叶基因组DNA, 用0 ...

1985

1.641

0.0

... 按照Knapp等^[18]提出的公式h² = σ_g²/(σ_g² + σ_gl²/n + σ_e²/nr)估算遗传力, 其中σ_g²为遗传方差, σ_gl²为基因型与环境互作的方差, σ_e²为误差方差, n为地点数, r为重复数 ...

2000

4.007

0.0

... 3^[19]检测该群体的遗传结构, 以5000个最小等位基因频率大于0 ...

2002

2.384

0.0

. 2002, 2(4):618-620

spag

Olivier J. Hardy^*,Xavier Vekemans

Laboratoire de Génétique et Ecologie végétales, Université Libre de Bruxelles, 1850 chaussée de Wavre, B-1160 Bruxelles, Belgium
^* Olivier Hardy. Fax: + 32 2650 91 70; E-mail:ohardy@ulb.ac.be

spag ed i version 1.0 is a software primarily designed to characterize the spatial genetic structure of mapped individuals or populations using genotype data of codominant markers. It computes various statistics describing genetic relatedness or differentiation between individuals or populations by pairwise comparisons and tests their significance by appropriate numerical resampling.spag ed i is useful for: (i) detecting isolation by distance within or among populations and estimating gene dispersal parameters; (ii) assessing genetic relatedness between individuals and its actual variance, a parameter of interest for marker based inferences of quantitative inheritance; (iii) assessing genetic differentiation among populations, including the case of haploids or autopolyploids.

... 通过软件SPAGeDi^[20], 采用相同的5000个SNP估计自交系间的亲缘关系 ...

2007

5.468

0.0

... 0^[21]中的混合线性模型(mixed-linear model, MLM)程序, 在考虑研究材料群体结构与亲缘关系情况下, 进行SNP标记与穗行数的关联分析 ...

2007

0.0

1.4522

Sci Agric Sin. 2007, 40(11):2409 - 2417

Relationship and QTL Mapping of Ear Traits under N-Stress Condition in Maize

氮胁迫和正常条件下玉米穗部性状的QTL分析

刘宗华,汤继华,卫晓轶,王春丽,田国伟,胡彦民,陈伟程

河南农业大学郑州国家玉米改良分中心

Ear traits are most important factors in yield components.In this investigation，six ear traits including ear length(EL), ear diameter(ED),ear row number(ERN),row kernel number (RKN),grain yield per ear(GY) and 100 kernel weight(KW), had been analyzed using a population with 203 F2：3 families derived from an elite maize（Zea mays L.） cultivar Nongda 108（Huang C×Xu 178）， field trials were conducted under nitrogen input (N+) and stress( N-) conditions in Zhengzhou and Xinzheng in 2004, the linkage map including 189 SSR markers covering the 10 chromosomes of maize and the Composite Interval Mapping(CIM) method were used to localize the quantitative trait Loci of ear traits. The results showed that N- stress had more influence to the parent Huang C than to Xu 178. Correlation analysis indicated that EL, ED,ERN and RKN were mainly significant/highly significant positive correlation with GY. Through 1000 times permutation test to have proper LOD threshold values for ear traits, total of 53 QTLs were identified under N+ and N- conditions in two locations. The 28 QTLs detected in Zhengzhou mainly clustered in chromosome 2,8 and 9(occupied by 57.14%),while the 25 QTLs identified in Xinzheng mainly clustered in chromosome 1,2,6,7 and 8 (occupied by 60%). Among the 53 QTLs, 13（24.53%）QTLs appeared to be additive, 20（37.74%）partial dominance , 6（11.32%）dominance and 14（26.42%） over- dominance , the phenotype variation explained by a single QTL varied from 7% to 23%. Only 3 QTLs(qED2a,qKW8a,qKW10a)were both detected under the two nitrogen levels in Zhengzhou，and 1 QTL(qEL1a) both detected in Xinzheng，While only 2 QTLs(qRKN8b,qGY1a) detected at both sites. However，the rest QTLs located in different chromosome or different position on the same chromosome. The QTLs of all traits identified only under low nitrogen stress condition might be relation with nitrogen high use efficiency in maize.

【目的】分析氮胁迫和正常条件下玉米穗部性状的QTL。【方法】以优良玉米杂交种“农大108”的一套203个F2：3 家系为材料，构建了包含189个SSR标记的遗传连锁图谱，在施氮（N+）和不施氮（N-）条件下，通过一年两点的田间试验，利用复合区间作图法对玉米穗长、穗粗、穗行数、行粒数、穗粒重和百粒重等6个穗部性状进行了QTL分析。【结果】亲本许178对N胁迫的敏感程度远小于黄C；F2:3群体的穗长、穗粗、穗行数和行粒数与单株产量大多呈显著或极显著正相关。在郑州和新郑两地，2种氮处理水平下定位了玉米穗部性状的53个QTL，其中郑州点检测到28个QTL，主要集中在第2、8和9染色体上（占57.14%）；新郑点检测到25个QTL，主要分布在第1、2、6、7和8 染色体上（占60%）；在所检测到的53个QTL中，表现加性、部分显性、显性和超显性效应的QTL依次为13（24.5%）、20（37.7%）、6（11.3%）和14（26.4%）个，单个QTL解释表型变异介于7.1%～23.3%之间。N+条件下6个性状在两个地间检测到的QTL数量明显高于N－条件下检测到的QTL数量，同时在郑州点2种氮处理水平下检测到3个相同的QTL（qED2a, qKW8a, qKW10a），新郑点检测到1个相同的QTL(qEL1a)，推断在缺氮条件下检测到的各性状特异表达的QTL可能与玉米的氮高效利用有关。【结论】在两地、2种供氮水平下所定位的53个穗部性状QTL，主要集中在第1、2、8和9染色体上，部分显性和超显性效应的QTL占60%以上。

... 02的PZE-108018598与Liu等^[22]的研究结果吻合 ...

1992

0.0

0.1123

... GRMZM2G017087 (knotted1, kn1)是玉米同源异型盒基因家族成员, 最早发现于玉米顶端分生组织中^[23], 参与生物发育调控过程 ...

2011

35.532

0.0

. 2011, 43(2):163-168

Genome-wide association study of quantitative resistance to southern leaf blight in the maize nested association mapping population

Edward S Buckler^2,3 ,Michael D McMullen⁶ ,Randall J Wisser⁴ ,Peter J Bradbury^2,3 ,Peter J Balint-Kurti^5,7 ,Araby R Belcher⁵ ,Doreen Ware³ ,John C Zwonitzer⁵ ,Stephen Kresovich³ ,Kristen L Kump¹ ,James B Holland^1,7 ,Marco A Oropeza-Rosas¹

¹ Department of Crop Science, North Carolina State University, Raleigh, North Carolina, USA.
² US Department of Agriculture–Agricultural Research Service (USDA-ARS) and Department of Plant Breeding and Genetics, Cornell University, Ithaca, New York, USA.
³ Institute for Genomic Diversity, Cornell University, Ithaca, New York, USA.
⁴ Department of Plant and Soil Sciences, University of Delaware, Newark, Delaware, USA.
⁵ Department of Plant Pathology, North Carolina State University, Raleigh, North Carolina, USA.
⁶ USDA-ARS and Division of Plant Sciences, University of Missouri, Columbia, Missouri, USA.
⁷ USDA-ARS, Raleigh, North Carolina, USA.

Nested association mapping (NAM) offers power to resolve complex, quantitative traits to their causal loci. The maize NAM population, consisting of 5,000 recombinant inbred lines (RILs) from 25 families representing the global diversity of maize, was evaluated for resistance to southern leaf blight (SLB) disease. Joint-linkage analysis identified 32 quantitative trait loci (QTLs) with predominantly small, additive effects on SLB resistance. Genome-wide association tests of maize HapMap SNPs were conducted by imputing founder SNP genotypes onto the NAM RILs. SNPs both within and outside of QTL intervals were associated with variation for SLB resistance. Many of these SNPs were within or near sequences homologous to genes previously shown to be involved in plant disease resistance. Limited linkage disequilibrium was observed around some SNPs associated with SLB resistance, indicating that the maize NAM population enables high-resolution mapping of some genome regions.

... 目前, GWAS已应用于鉴定植物病害、开花期、籽粒性状、株高等QTL^{[9,10,11,12,15,24,25,26]}, 但玉米穗行数的GWAS研究较少 ...

2011

9.737

0.0

PNAS. 2011, 108(17):6893-6898

Genome-wide nested association mapping of quantitative resistance to northern leaf blight in maize

Jesse A. Poland^a^,¹, Peter J. Bradbury^a^,^b, Edward S. Buckler^a^,^b, and Rebecca J. Nelson^a^,^c^,²

^aDepartment of Plant Breeding and Genetics, Cornell University, Ithaca, NY 14853;^bUS Department of Agriculture, Agricultural Research Service, Ithaca, NY 14853; and^cDepartment of Plant Pathology and Plant-Microbe Biology, Cornell University, Ithaca, NY 14853

Quantitative resistance to plant pathogens, controlled by multiple loci of small effect, is important for food production,food security, and food safety but is poorly understood. To gain insights into the genetic architecture of quantitative resistancein maize, we evaluated a 5,000-inbred-line nested association mapping population for resistance to northern leaf blight, amaize disease of global economic importance. Twenty-nine quantitative trait loci were identified, and most had multiple alleles.The large variation in resistance phenotypes could be attributed to the accumulation of numerous loci of small additive effects.Genome-wide nested association mapping, using 1.6 million SNPs, identified multiple candidate genes related to plant defense,including receptor-like kinase genes similar to those involved in basal defense. These results are consistent with the hypothesisthat quantitative disease resistance in plants is conditioned by a range of mechanisms and could have considerable mechanisticoverlap with basal resistance.

... 目前, GWAS已应用于鉴定植物病害、开花期、籽粒性状、株高等QTL^{[9,10,11,12,15,24,25,26]}, 但玉米穗行数的GWAS研究较少 ...

2010

9.737

0.0

PNAS. 2010, 107(49):21199-21204

Association mapping of local climate-sensitive quantitative trait loci inArabidopsis thaliana

Yan Li^a, Yu Huang^b, Joy Bergelson^a, Magnus Nordborg^b^,^c, and Justin O. Borevitz^a^,¹

^aDepartment of Ecology and Evolution, University of Chicago, Chicago, IL 60637;^bMolecular and Computational Biology, University of Southern California, Los Angeles, CA 90089; and^cThe Gregor Mendel Institute, 1030 Vienna, Austria

Flowering time (FT) is the developmental transition coupling an internal genetic program with external local and seasonalclimate cues. The genetic loci sensitive to predictable environmental signals underlie local adaptation. We dissected naturalvariation in FT across a new global diversity set of 473 unique accessions, with >12,000 plants across two seasonal plantingsin each of two simulated local climates, Spain and Sweden. Genome-wide association mapping was carried out with 213,497 SNPs.A total of 12 FT candidate quantitative trait loci (QTL) were fine-mapped in two independent studies, including 4 locatedwithin ±10 kb of previously cloned FT alleles and 8 novel loci. All QTL show sensitivity to planting season and/or simulatedlocation in a multi-QTL mixed model. Alleles at four QTL were significantly correlated with latitude of origin, implying pastselection for faster flowering in southern locations. Finally, maximum seed yield was observed at an optimal FT unique toeach season and location, with four FT QTL directly controlling yield. Our results suggest that these major, environmentallysensitive FT QTL play an important role in spatial and temporal adaptation.

... 目前, GWAS已应用于鉴定植物病害、开花期、籽粒性状、株高等QTL^{[9,10,11,12,15,24,25,26]}, 但玉米穗行数的GWAS研究较少 ...

2011

2.852

0.0

Mol Breeding. 2011, 27(4):439 - 454 DOI:10.1007/s11032-010-9442-0

Genome-wide association mapping of Fusarium head blight resistance in contemporary barley breeding germplasm

J. Massman(1) B. Cooper(5) R. Horsley(3) S. Neate(4) R. Dill-Macky(2) S. Chao(6) Y. Dong(2) P. Schwarz(3) G. J. Muehlbauer(1) K. P. Smith(1)

1.Department of Agronomy and Plant Genetics, University of Minnesota, 1991 Upper Buford Circle, Ste 411, Saint Paul, MN 55108, USA
2.Department of Plant Pathology, University of Minnesota, Saint Paul, MN 55108, USA
3.Department of Plant Sciences, North Dakota State University, Fargo, ND 58105, USA
4.Department of Plant Pathology, North Dakota State University, Fargo, ND 58105, USA
5.Busch Agricultural Resources LLC, Ft. Collins, CO, USA
6.USDA-ARS, Fargo, ND 58105, USA

Utilization of quantitative trait loci (QTL) identified in bi-parental mapping populations has had limited success for improving complex quantitative traits with low to moderate heritability. Association mapping in contemporary breeding germplasm may lead to more effective marker strategies for crop improvement. To test this approach, we conducted association mapping of two complex traits with moderate heritability; Fusarium head blight (FHB) severity and the grain concentration of mycotoxin associated with disease, deoxynivalenol (DON). To map FHB resistance in barley, 768 breeding lines were evaluated in 2006 and 2007 in four locations. All lines were genotyped with 1,536 SNP markers and QTL were mapped using a mixed model that accounts for relatedness among lines. Average linkage disequilibrium within the breeding germplasm extended beyond 4 cM. Four QTL were identified for FHB severity and eight QTL were identified for the DON concentration in two independent sets of breeding lines. The QTL effects were small, explaining 1–3% of the phenotypic variation, as might be expected for complex polygenic traits. We show that using breeding germplasm to map QTL can complement bi-parental mapping studies by providing independent validation, mapping QTL with more precision, resolving questions of linkage and pleiotropy, and identifying genetic markers that can be applied immediately in crop improvement.

... 本文采用203份玉米自交系组成的关联作图群体进行全基因组分析, 在3个环境中共检测出9个与穗行数显著关联(P [27]认为距离小于5 cM的显著SNP可以归为一个QTL, 本文在染色体框1 ...

... 8时认为两位点不独立, 即处于连锁不平衡状态^[27] ...

2003

25.962

0.0

... 连锁不平衡是不同基因座位上等位基因的非随机组合关系^[28] ...

2005

5.468

0.0

... 0^[29], SYN17065与PZE-107084987的r²为0 ...

2007

0.0

1.8267

Acta Agron Sin. 2007, 33(4):523 - 530

Reviews of Association Analysis for Quantitative Traits in Plants

植物数量性状关联分析研究进展

YANG Xiao-Hong¹,YAN Jian-Bing¹,ZHENG Yan-Ping¹,YU Jian-Ming²,LI Jian-Sheng^1*

杨小红¹;严建兵¹;郑艳萍¹;余建明²;李建生^1,*

1National Maize Improvement Center of China, Key Lab of Crop Genomics & Genetic Improvement of Ministry of Agriculture, China Agricultural University, Beijing, 100094, China; 23004 Throckmorton Plant Science Center, Kansas State University, Manhattan, KS, 66506-5501, USA

Recently, association analysis has been widely employed to investigate quantitative traits in plant genetics and breeding. Association analysis is an approach to identify the relationship of molecular markers or candidate genes with traits in a given population based on linkage disequilibrium (LD). Here, we introduced the definition and measurements of LD and reviewed the advances of association analysis for the investigation of quantitative traits in plants. The effects of mating systems, such as recombination, genetic drift, and population structure to the patterns of LD were discussed. Finally, we also discussed the potential application of association analysis for dissecting quantitative traits and plant molecular breeding.

关联分析是新近开始在植物数量性状研究和植物育种中应用的一种分析方法。它以连锁不平衡为基础鉴定某一群体内性状与遗传标记或候选基因间的关系。本文在介绍连锁不平衡的定义和度量方法的基础上，综述了连锁不平衡和关联分析在植物方面的研究进展，并讨论了交配体系、重组、遗传漂变等对连锁不平衡程度的影响，以及连锁不平衡程度、群体结构对关联分析的影响，最后讨论了关联分析在植物数量性状和分子育种研究中可能的应用。

... 连锁定位和关联分析都可以检测数量性状位点, 两种方法定位到的QTL在位置上大部分具有一致性^[14,16,30] ...

2005

8.694

0.0

... 2 候选基因分析Aranzana等^[31]对95个拟南芥品种进行GWAS, 发现几个开花期和病原基因均被检测到 ...

2010

35.532

0.0

. 2010, 42(11):961-967

Genome-wide association studies of 14 agronomic traits in rice landraces

Kunyan Liu¹ ,Yufeng Jing¹ ,Chuanrang Zhu¹ ,Xinghua Wei³ ,Bin Han^1,2 ,Marco A Oropeza-Rosas¹ ,Edward S Buckler^2,3,5,7 ,Qi Feng¹ ,Randall J Wisser⁴ ,Qian Qian³ ,Araby R Belcher⁵ ,Doreen Ware³ ,Stephen Kresovich³ ,Yan Zhao¹ ,Meng Li^5,6 ,Ahong Wang¹ ,Canyang Li¹ ,Zhiwu Zhang⁵ ,Tao Huang¹ ,Tingting Lu¹ ,Wei Li¹ ,Peter J Bradbury^2,3 ,Peter J Balint-Kurti^5,7 ,Tao Sang⁴ ,Taoying Zhou¹ ,John C Zwonitzer⁵ ,Qi-Fa Zhang⁸ ,Liuwei Deng¹ ,Wenjun Li¹ ,James B Holland^1,7 ,Qiang Zhao^1,2 ,Jiayang Li⁹ ,Lu Wang¹ ,Xuehui Huang^1,2 ,Michael D McMullen⁶ ,Yiqi Lu¹ ,Yunli Guo¹ ,Kristen L Kump¹ ,Qijun Weng¹ ,Danlin Fan¹ ,Zhang Lin¹

¹ National Center for Gene Research, Institute of Plant Physiology and Ecology, Shanghai Institutes for Biological Sciences, Chinese Academy of Sciences, Shanghai, China.
² CAS Key Laboratory of Genome Sciences and Information, Beijing Institute of Genomics, Chinese Academy of Sciences, Beijing, China.
³ State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China.
⁴ Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA.
⁵ Institute for Genomic Diversity, Cornell University, Ithaca, New York, USA.
⁶ National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, China.
⁷ US Department of Agriculture–Agricultural Research Service, Ithaca, New York, USA.
⁸ National Key Laboratory of Crop Genetic Improvement, National Center for Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China.
⁹ National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.

Uncovering the genetic basis of agronomic traits in crop landraces that have adapted to various agro-climatic conditions is important to world food security. Here we have identified ~3.6 million SNPs by sequencing 517 rice landraces and constructed a high-density haplotype map of the rice genome using a novel data-imputation method. We performed genome-wide association studies (GWAS) for 14 agronomic traits in the population ofOryza sativa indica subspecies. The loci identified through GWAS explained ~36% of the phenotypic variance, on average. The peak signals at six loci were tied closely to previously identified genes. This study provides a fundamental resource for rice genetics research and breeding, and demonstrates that an approach integrating second-generation genome sequencing and GWAS can be used as a powerful complementary strategy to classical biparental cross-mapping for dissecting complex traits in rice.

... Huang等^[32]利用3 600 000个SNP标记对517个水稻品种开展全基因组分析, 发现6个SNP位点分别与已知基因qSW5、GS3、ALK、Waxy、OsC1和Rc临近 ...

2005

36.28

0.0

. 2005, 435(7041):446-451

The Arabidopsis F-box protein TIR1 is an auxin receptor

Nature is the international weekly journal of science: a magazine style journal that publishes full-length research papers in all disciplines of science, as well as News and Views, reviews, news, features, commentaries, web focuses and more, covering all branches of science and how science impacts upon all aspects of society and life.

... F-box蛋白TIR1是生长素的受体, 通过介导一系列生长素反应来参与植物生长发育的调控^[33] ...

2000

0.0

0.1123

1998

11.659

0.0

... IDS1是AP2基因家族成员, 参与调控玉米小穗分生组织的有限性, ids1突变体的每个小穗产生额外的小花^[35] ...

2008

0.0

0.1123

... IDS1的横向同源基因SID1与小花分生组织启动及小穗调控有关^[36] ...

2012

6.16

0.0

. 2012, 69(3):445-461

Two AP2 family genes,SUPERNUMERARY BRACT (SNB) andOsINDETERMINATE SPIKELET 1 (OsIDS1), synergistically control inflorescence architecture and floral meristem establishment in rice

Dong-Yeon Lee,Gynheung An^*

Department of Plant Molecular Systems Biotechnology, Crop Biotech Institute, Kyung Hee University, Yongin 446-701, Korea
^* (fax +82 31 204 3178; e-mailgenean@khu.ac.kr).

Meristem identity is crucial in determining the inflorescence architecture of grass species. We previously reported thatSUPERNUMERARY BRACT (SNB) regulates the transition of spikelet meristems into floral meristems in rice (Oryza sativa). Here we demonstrated thatSNB andOryza sativa INDETERMINATE SPIKELET 1 (OsIDS1) together play important roles in inflorescence architecture and the establishment of floral meristems. Insnb osids1 double mutants, the numbers of branches and spikelets within a panicle are significantly decreased, and the transition to a floral meristem is further delayed compared with thesnb single mutant. Expression analyses showed thatSNB andOsIDS1 are required for spatio-temporal expression of B- and E-function floral organ identity genes in the lodicules. In addition, the AP2 family genes are important for determining the degree of ramification in branch meristems, regulating the spatio-temporal expression of spikelet meristem genes, such asFRIZZY PANICLE (FZP). Furthermore, overexpression ofmicroRNA172 (miR172) causes reductions inSNB andOsIDS1 transcript levels, and phenotypes of the transgenic plants are more severe than forsnb osids1. This indicates that additional gene(s) participate in the development of branch and floral meristems. Preferential expression of maturemiR172s in the area around the spikelet meristems implies that depletion of the AP2 family genes in those meristems viamiR172 is an important step in controlling inflorescence branching and the formation of floral organs.

... 水稻基因SNB与OsIDS1分别是ids1和sid1的直系同源基因, 在控制花序结构与花序分生组织建成等方面具有重要作用^[37] ...

2005

0.0

0.1123

... GRMZM2G151567编码一个富亮氨酸重复的蛋白激酶, td1同样编码一个富亮氨酸重复的蛋白激酶, 玉米突变体td1的雄穗小穗密度、雄蕊数目增加, 雌穗的籽粒行数增加^[38] ...

2001

11.659

0.0

... fea2编码一个富亮氨酸的受体样蛋白, 可能通过控制花序分生组织的大小来调控玉米穗行数^[39,40] ...

2013

35.532

0.0

. 2013, 45(3):334-337

Quantitative variation in maize kernel row number is controlled by the FASCIATED EAR2 locus

Kunyan Liu¹ ,Yufeng Jing¹ ,Chuanrang Zhu¹ ,Xinghua Wei³ ,Bin Han^1,2 ,Marco A Oropeza-Rosas¹ ,Namiko Satoh Nagasawa^1,2 ,Edward S Buckler^2,3,5,7 ,Qi Feng¹ ,Randall J Wisser⁴ ,Qian Qian³ ,Araby R Belcher⁵ ,Doreen Ware³ ,Stephen Kresovich³ ,Yan Zhao¹ ,Meng Li^5,6 ,Ahong Wang¹ ,Canyang Li¹ ,Zhiwu Zhang⁵ ,Tao Huang¹ ,Tingting Lu¹ ,Wei Li¹ ,Peter J Bradbury^2,3 ,Peter J Balint-Kurti^5,7 ,Tao Sang⁴ ,Taoying Zhou¹ ,John C Zwonitzer⁵ ,Qi-Fa Zhang⁸ ,Liuwei Deng¹ ,Wenjun Li¹ ,James B Holland^1,7 ,David Jackson¹ ,Qiang Zhao^1,2 ,Jiayang Li⁹ ,Lu Wang¹ ,Xuehui Huang^1,2 ,Michael D McMullen⁶ ,Yiqi Lu¹ ,Yunli Guo¹ ,Kristen L Kump¹ ,Peter Bommert¹ ,Qijun Weng¹ ,Danlin Fan¹ ,Zhang Lin¹

¹ Cold Spring Harbor Laboratory, Cold Spring Harbor, New York, USA.
² Present address: Laboratory of Plant Genetics and Breeding, Akita Prefectural University, Akita, Japan.
³ State Key Laboratory of Rice Biology, China National Rice Research Institute, Chinese Academy of Agricultural Sciences, Hangzhou, China.
⁴ Department of Plant Biology, Michigan State University, East Lansing, Michigan, USA.
⁵ Institute for Genomic Diversity, Cornell University, Ithaca, New York, USA.
⁶ National Center for Soybean Improvement, State Key Laboratory of Crop Genetics and Germplasm Enhancement, College of Agriculture, Nanjing Agricultural University, Nanjing, China.
⁷ US Department of Agriculture–Agricultural Research Service, Ithaca, New York, USA.
⁸ National Key Laboratory of Crop Genetic Improvement, National Center for Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, China.
⁹ National Center for Plant Gene Research, Institute of Genetics and Developmental Biology, Chinese Academy of Sciences, Beijing, China.

Domestication of cereal crops, such as maize, wheat and rice, had a profound influence on agriculture and the establishment of human civilizations. One major improvement was an increase in seed number per inflorescence, which enhanced yield and simplified harvesting and storage^1,2. The ancestor of maize, teosinte, makes 2 rows of kernels, and modern varieties make ~8–20 rows³. Kernel rows are initiated by the inflorescence shoot meristem, and shoot meristem size is controlled by a feedback loop involving the CLAVATA signaling proteins and the WUSCHEL transcription factor^4,5. We present a hypothesis that variation in inflorescence meristem size affects kernel row number (KRN), with the potential to increase yield. We also show that variation in the CLAVATA receptor–like protein FASCIATED EAR2 leads to increased inflorescence meristem size and KRN. These findings indicate that modulation of fundamental stem cell proliferation control pathways has the potential to enhance crop yields.

... fea2编码一个富亮氨酸的受体样蛋白, 可能通过控制花序分生组织的大小来调控玉米穗行数^[39,40] ...