大麦遗传多样性及连锁不平衡分析

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赖勇, 孟亚雄, 王晋, 范贵强, 司二静, 王鹏喜, 李葆春, 马小乐, 杨轲, 尚勋武, 王化俊. 大麦遗传多样性及连锁不平衡分析. 作物学报, 2013, 39(12): 2154-2161[LAI Yong, MENG Ya-Xiong, WANG Jin, FAN Gui-Qiang, SI Er-Jing, WANG Peng-Xi, LI Bao-Chun, MA Xiao-Le, YANG Ke, SHANG Xun-Wu, WANG Hua-Jun. Genetic Diversity and Linkage Disequilibrium Analysis in Barley. Acta Agronomica Sinica, 2013, 39(12): 2154-2161] 复制到剪切板

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大麦遗传多样性及连锁不平衡分析

赖勇^1,^2,^*, 孟亚雄^1,^2,^*, 王晋^1,², 范贵强^1,², 司二静^1,², 王鹏喜^1,², 李葆春^1,³, 马小乐², 杨轲^1,², 尚勋武², 王化俊^1,^2,^*

¹甘肃省作物遗传改良与种质创新重点实验室 / 甘肃省干旱生境作物学重点实验室, 甘肃兰州730070

²甘肃农业大学农学院, 甘肃兰州 730070

³甘肃农业大学生命科学技术学院, 甘肃兰州730070

^* 通讯作者(Corresponding author): 王化俊, E-mail:whuajun@yahoo.com

第一作者联系方式: E-mail:xlaiyong@163.com (赖勇); yxmeng1@163.com (孟亚雄) ** 同等贡献(Contributed equally to this work)

收稿日期:2013-07-26

基金:本研究由国家自然科学基金项目(31171558)和国家现代农业产业技术体系建设专项(CARS-05)资助。

摘要

为了合理评价引进种质资源, 为大麦基因发掘及育种组合配置提供依据, 选用分布于全基因组的64个SSR标记, 对221份大麦材料进行了基因型分析。共检测到192个等位变异, 变幅为2~7个; 基因频率变异范围为0.0090~ 0.9729, 平均0.3333; 全部位点的基因多样性变化范围在0.0528~0.7807, 平均0.4813; 多态性信息含量(PIC)变异范围在0.0514~0.7464, 平均0.4113。供试材料间遗传相似系数变幅为0.4844~0.9792, 平均0.7023。221份材料被划分成两大群7个亚群, 国内地方品种与1份北京品种为一大群, 国内育种品种与所有国外引进品种为另一大群。遗传结构分析与聚类结果基本一致, 两大类群间的遗传距离为0.3358, 且第二大群多样性比第一大群丰富。2016个SSR位点成对组合中, 不论共线性组合还是非共线性组合, 都存在一定程度的连锁不平衡(LD)。D统计概率(P<0.01)支持的LD成对位点830个, 占全部位点组合的41.2%,D平均值为0.4, 整体LD水平较高。栽培品种的LD水平高于地方品种, 且现代遗传改良的目标性状集中于2H、4H、6H和7H染色体。

关键词: 大麦; SSR; 遗传多样性; 连锁不平衡; 关联分析

Genetic Diversity and Linkage Disequilibrium Analysis in Barley

LAI Yong^1,^2,^**, MENG Ya-Xiong^1,^2,^**, WANG Jin^1,², FAN Gui-Qiang^1,², SI Er-Jing^1,², WANG Peng-Xi^1,², LI Bao-Chun^1,³, MA Xiao-Le², YANG Ke^1,², SHANG Xun-Wu², WANG Hua-Jun^1,^2,^*

¹Gansu Key Laboratory of Crop Improvement & Germplasm Enhancement / Gansu Provincial Key Laboratory of Aridland Crop Science, Lanzhou 730070, China

²College of Agronomy, Gansu Agricultural University, Lanzhou 730070, China

³College of Life Sciences and Technology of Gansu Agricultural University, Lanzhou 730070, China

Abstract

The objective of this study was to provide a suitable evaluation for introduced germplasm resources and useful information for associate analysis and parental combinations in barley (Hordeum valgare L.). A total of 192 alleles were detected by 64 SSR markers on chromosomes 1H to 7H in 221 barley accessions with 2-7 alleles per locus. The allelic frequency ranged from 0.0090 to 0.9729 with the mean of 0.3333. The gene diversity was from 0.0528 to 0.7807, averagely 0.4813. The polymorphism information content (PIC) value ranged from 0.0514 to 0.7464 with the mean of 0.4113. The genetic similarity of the 221 accessions ranged from 0.4844 to 0.9792 with the mean of 0.7023. All accessions were clustered into two major groups and seven subgroups. Most landraces or developed varieties fell into the same major group. Genetic structure analysis revealed two subpopulations of these accessions, with consistence to the clustering analysis. Genetic distance between the two subpopulations was 0.3358, and the second subpopulation had richer diversity than the first one. There was linkage disequilibrium (LD) among linked loci and unlinked loci pairs, and 830 out of 2016 loci pairs (41.2%) had significant LD (P< 0.01) with averageD-value of 0.4. The LD level of developed variety was higher than that of landraces. Target traits of developed varieties were mainly distributed on chromosomes 2H, 4H, 6H, and 7H.

Keyword: Barley; SSR; Genetic diversity; Linkage disequilibrium; Association analysis

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亲本遗传基础狭窄是制约育种的主要问题之一^{[ 1]}, 引进新的种质资源是解决这一问题的有效手段。分析引进种质资源的遗传多样性、发掘其中的有利基因, 对于种质创新和新品种选育具有重要意义。分子标记技术为种质资源的遗传多样性研究及有利基因发掘提供了便利。简单序列重复(simple sequence repeat, SSR)具有多态性高、数量丰富、重复性好、呈共显性、且广泛分布于基因组等优点^{[ 2, 3, 4, 5]}, 被广泛应用于大麦遗传多样性^{[ 6, 7, 8]}和基因发掘研究^{[ 9, 10, 11]}。通过遗传连锁分析发掘基因及鉴定基因功能需要花费大量的时间和精力构建作图群体, 而关联分析以自然群体为研究对象, 不用构建作图群体, 可以检测出大量的等位变异。基于连锁不平衡的关联分析可以将表型性状的多样性与基因或位点的多态性结合起来, 确定不同种质资源所携带的等位基因及其对目标性状的贡献^{[ 12, 13, 14]}。目前, 关联分析已广泛用于小麦^{[ 15]}、玉米^{[ 16]}、水稻^{[ 17]}等作物的基因发掘。在大麦上, 已对栽培品种、地方品种以及野生资源进行了关联分析^{[ 8, 18, 19]}, 发掘出许多有利等位基因。西藏地区为大麦起源中心之一, 拥有丰富的种质资源, 特别是一些野生材料具有丰富的遗传变异, 从中发掘有利基因对于大麦育种具有重要意义。但是野生材料未经驯化, 含有许多不利基因, 许多农艺性状表现较差, 在育种中难以利用。而该地区的许多地方品种来自一些野生材料长期的人工驯化, 遗传变异同样丰富, 农艺性状较野生材料更加优良, 更适合用于新品种的选育。因此本研究拟对本课题搜集的我国西藏、青海地区的地方品种、国内其他省份品种和一些国外品种进行遗传分析, 为今后发掘有利基因和标记辅助育种提供依据。

1 材料与方法

1.1 植物材料

以221份大麦品种(由甘肃省作物遗传改良与种质创新重点实验室和甘肃省干旱生境作物学重点实验室麦类种质创新课题组提供)构成自然群体, 包括74份西藏地方品种、16份青海地方品种、25份其他省份栽培品种、47份美国栽培品种、19份丹麦栽培品种、12份匈牙利栽培品种、15份德国栽培品种以及13份其他国外引进栽培品种(表1)。从每份材料取15粒饱满完整的种子置培养皿中, 于室内避光萌发。10 d后采黄化苗, -80℃保存备用。

表1 供试大麦品种的来源和类型 Table 1 Origin and type of barley accessions used in this study

1.2 SSR标记分析

采用CTAB法^{[ 20]}提取基因组DNA。选用64个分布于大麦1H~7H染色体的SSR标记(表2)进行多态性扫描。扩增程序为94℃预变性5 min; 94℃变性40 s, 64~55℃(touch-down PCR)退火40 s, 72℃下延伸50 s, 10个循环; 94℃变性40 s, 55℃退火40 s, 72℃延伸50 s, 30个循环; 72℃延伸5 min。扩增产物经8.0%非变性聚丙烯酰胺凝胶电泳分离, 银染显示。

表2 64个SSR标记的多样性参数 Table 2 Diversity parameters of 64 SSR markers used in this study

(续表2) 64个SSR标记的多样性参数 Table 2(continued) Diversity parameters of 64 SSR markers used in this study

1.3 数据统计分析

以二进制和基因型记录SSR分析结果, 同一位点上具有相同迁移率的条带记为1, 无带记为0; 以数字1、2、3等代表不同基因型。以Powermarker 3.25软件分析等位基因数、基因频率、基因多样性依据多态性信息量(polymorphism information content, PIC)。

PIC = 1-

式中, p_ij表示位点 i的第 j个等位变异出现的频率。以NTsys 2.10e软件计算遗传相似系数, 采用DARwin 5.0软件基于遗传距离的邻位相连(neighbor-joining, NJ)构建聚类图。参照Maccaferri等^{[ 21]}的方法处理频率小于0.01的稀有等位基因。以Structure 2.3.1软件分析群体遗传结构, 估计最佳群体组群数 K, 其取值范围为1~20, 将MCMC(Markov Chain Monte Carlo)开始时的不作数迭代(length of burn-in period)设为10 000次, 再将不作数迭代后的MCMC设为100 000次, 重复5次, 计算Q参数。若 K值持续增大, 参照Evanno等^{[ 22]}的方法计算Δ K确定 K值。以Popgene 32软件分析多样性指数。使用TASSEL 2.1软件计算共线、非共线SSR位点组合间的LD水平及支持概率, 绘制LD配对检测矩阵图。

2 结果与分析

2.1 SSR标记分析

以64个SSR标记从221份材料中共检出192个等位变异, 平均每个标记3.0个, 标记Bmac32检测到的等位变异最多, 为7个; MGB325等31个标记仅检测到2个等位变异。基因频率变异范围为0.0090~0.9729, 平均值为0.3333。GBM1274位点的B等位基因频率最高(0.9729), 同时稀有等位基因有4个。基因多样性变化范围为0.0528~0.7807, 平均0.4813, 其中GBM1274位点最低, Bmag173位点最高。PIC变异范围为0.0514~0.7464, 平均为0.4113, PIC最高的标记是Bmag173, 最小的是GBM1274 (表2)。

2.2 聚类分析

通过遗传相似系数(GS)分析, 发现美国品种M14与M15亲缘关系最近(GS=0.9792), 其次是ZDM6552与ZDM6553、M45与M47 (GS=0.9740); ZDM6114与青永4026 (墨西哥品种)的亲缘关系最远(GS=0.4844), 其次是ZDM6474与宝丹(GS=0.5000)。221份材料在聚类图中明显被分成两大类群、7个亚群(图1)。

第一大类群包括国内西藏和青海的地方品种及1份北京品种(08京358), 又可分为A、B两个亚类, 其中A亚类全部为西藏品种, 但还有26份西藏品种与16份青海品种被聚到B亚类中。08京358与国内西藏、青海地方品种划分到同一大类, 但是之间差异较大, 分隔较远。

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图1 221份大麦材料Neighbor-joining法聚类图红色: 中国西藏品种; 粉色: 中国青海品种; 浅褐色: 中国其他地区品种; 褐色: 美国品种; 绿色: 丹麦品种; 蓝色: 匈牙利品种: 黑色: 德国品种; 紫色: 其他国外品种。Fig. 1 Neighbor-joining tree of 221 barley accessionsRed: Accessions from Tibet, China; Pink: Accessions from Qinghai, China; Light brown: Accessions from other provinces of China; Brown: Accessions from America; Green: Accessions from Denmark; Blue: Accessions from Hungary; Black: Accessions from Germany; Purple: Accessions from other countries.

第二大类群主要为国外引进品种, 也包括部分国内除西藏和青海以外地区育成的品种, 又分成5个亚类。其中, C亚类主要为匈牙利和德国品种, 以及部

分美国(5份)、丹麦(3份)、波兰(2份)、瑞典(2份)、澳大利亚(2份)、阿富汗(1份)、叙利亚(1份)和加拿大(1份)品种, 2份中国西藏地方品种也在该亚群中; D亚类主要为美国品种和丹麦品种, 还包括1份匈牙利品种、3份中国甘肃品种和1份中国陕西品种; E亚类包括1份叙利亚品种、1份日本品种、1份墨西哥品种和4份国内育成品种; F亚类包括10份国内育成品种和1份日本品种; G亚类包括3份中国黑龙江品种和3份中国北京品种。

2.3 群体遗传结构分析

将221份材料分为2个亚群(图2, 当 K=2时Δ K最大), 第1亚群(POP1)有89份材料, 主要包括88份国内地方品种和1份北京品种; 第2亚群(POP2)有132份材料, 包括2份国内地方品种、其他省份育成栽培品种以及所有的国外引进品种。这与聚类分析结果一致, 说明这221份材料的群体结构较简单, 可以有效降低群体结构对关联分析的影响。记录各个材料的对应群体概率Q值, 为后期关联分析提供相应协变量数据。

POP1和POP2的遗传距离为0.3258, 群体内基因多样性指数分别为0.3626和0.4254, Shannon多样性指数分别为0.6221和0.7119 (表3), 说明POP2的资源多样性较POP1丰富, 可能与POP2的材料数量多、来源广泛有关。

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	图2 221份大麦材料的群体遗传结构Fig. 2 Population structure of 221 barley accessions

表3 亚群间多样性差异 Table 3 Diversity difference between two subpopulations

2.4 连锁不平衡分析

不同位点等位基因之间的连锁不平衡是关联分析的基础。通过64个SSR标记分析, 在2016个SSR位点成对组合中, 不论共线性组合还是非共线性组合, 都存在一定程度的LD。 D′统计概率( P<0.01)支持的LD成对位点830个, 占全部位点组合的41.2%, D′平均值为0.4, 整体LD水平较高。LD成对位点的 D′值范围主要集中在0.2~0.4和0.4~0.6间(表4), 较高水平的LD位点( D′ > 0.5)主要分布在2H、4H、6H和7H连锁群上。说明这4条染色体面临的选择压力要大于其他3条染色体。进一步分析共线性位点组合的LD状况, 发现2H、3H和6H连锁群上的LD成对位点分别有18、16和25个明显多于其他几个连锁群, 且较高水平的LD成对位点( D′>0.5)集中在2H、6H连锁群群上, 分别有8个和10个。

根据聚类和群体遗传结构分析结果, 将221份材料分成地方品种和栽培品种两大类群, 分别进行连锁不平衡分析。从地方品种检测出183个LD成对位点( P<0.01), D′平均值为0.5; 栽培品种中检测出LD成对位点332个, D′平均值为0.4。说明地方品种的LD水平要低于育成栽培品种, 且受到的选择压力小于栽培种。从图4可以看出, 地方品种较高水平的LD位点( D′> 0.5)在7个连锁群上均存在, 而栽培品种主要分布在2H、4H、6H和7H连锁群上。说明在现代育种过程中, 许多目标性状所对应的基因多集中于这4条染色体。

表4 不同 D'值范围LD成对位点数 Table 4 Number of LD pairs in different D' value ranges

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	图3 共线LD成对位点的大麦染色体上的分布Fig. 3 Distribution of LD between linked SSR loci on different chromosomes of barley

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图4 大麦7个连锁群SSR位点的连锁不平衡分布箭头指示连锁群区域, 对角线上方为成对位点间 D′值, 下方为成对位点间LD的支持概率。 A: 地方品种; B: 栽培品种, 椭圆圈显示较高水平的LD位点分布。Fig. 4 Distribution of LD among SSR loci on 7 linkage groups of barleyDouble-headed arrows show the region of linkage groups. D′ value of the corresponding marker pair and its P-value are shown in the upper and lower triangles, respectively. A: landrace; B: developed variety. The oval circles show distribution of LD loci in high levels.

3 讨论

丰富的种质资源是取得育种突破性进展的基础, 利用分子标记可以对不同种质进行合理的评价, 对后期育种工作中的组合配置具有指导意义。有研究表明, 我国大麦遗传基础明显比国外品种狭窄, 但是野生资源遗传变异丰富^{[ 23, 24, 25, 26]}, 因此需要引进不同国家和地区的材料改良大麦品种。本研究选用115份来自国内不同地区的地方品种和栽培品种, 以及96份来源于12个国家的品种, SSR标记分析表明, 平均基因多样性为0.3333, 平均遗传相似系数为0.7023, 整体遗传多样性不够丰富, 主要是因为这些材料大部分为栽培品种, 经过人工选择后, 保留的遗传变异较少。聚类分析将供试材料分成两大类, 地方品种为一类, 栽培品种为一类, 说明地方品种与栽培品种的遗传差异较大。本研究发现栽培品种遗传变异较地方品种丰富, 可能与地方品种样本量较小有关。某些标记在地方品种中检测出较丰富的等位基因, 例如标记Bmac32, 在地方品种中检出7个等位基因, 而在栽培品种中只有3个; 因此, 如果增加地方品种的样本量, 可能会提高整体的遗传多样性。Maroof等^{[ 27]}利用4对SSR引物检测104份栽培大麦和103份来自以色列不同生态区的二棱野生大麦, 其中2个标记分别检测到28个和37个等位变异; Struss等^{[ 28]}用15对SSR引物研究由野生大麦、地方品种和选育品种组成的163份大麦品种的遗传多样性, 共检测到130个等位基因, 单个标记检测到的最多等位变异数为15。说明从丰富遗传基础角度考虑, 仍然需要引进一些野生资源, 从中挖掘更多的有利基因为育种服务。

Hansen等^{[ 29]}利用AFLP标记对野生甜菜生长习性首次进行植物全基因组关联分析, Thornsberry等^{[ 30]}首次运用基于候选基因检测方法对玉米中 Dwarf8基因的9个多态性位点与玉米开花时间相关联的研究, 此后陆续有很多利用关联分析方法的报道。对大麦的研究表明, LD衰减距离在10~20 cM^{[ 31, 32]}, 说明大麦的LD水平较高, 有利于进行全基因组关联分析, 发掘种质资源中的有利基因。Katherine等^{[ 19]}报道, 栽培大麦的LD水平最高, 地方品种次之, 野生资源LD水平最低。本研究利用覆盖全基因组的64个SSR标记, 检测出供试材料的LD水平较高, 在2016个SSR位点成对组合中, 不论同一连锁群的共线性组合还是不同连锁群间的非共线性组合, 都存在一定程度的LD, D′统计概率( P<0.01)支持的LD成对位点占41.2%, D′平均值为0.4, 可能的原因是221份材料中栽培品种较多, 并且没有野生资源。人工选择会增加LD水平^{[ 11]}。对于一组自然群体, 如果经过某些目标性状的集中选择, 该性状对应的染色体LD水平会相应提高。目前, GrainGenes2.0网站(http://wheat.pw.usda.gov/GG2/index.shtml)公布了大量的大麦各性状相关QTL, 其中株高、穗型、产量等农艺性状的相关QTL多集中于2H、3H、4H、5H和6H染色体, 而一些抗性及品质性状的相关QTL多集中于1H、2H、5H和7H染色体。本研究中较高水平的LD成对位点( D′ > 0.5)主要分布在2H、4H、6H和7H连锁群上, 以及与其组合的位点。说明这4条染色体面临的选择压力大于其他3条染色体, 这些材料多经历了较多农艺性状的选择。进一步分析共线性位点组合的LD状况, 发现2H、3H和6H连锁群上的LD成对位点分别有18、16和25个明显多于其他几个连锁群(1H有11个、4H有12个、5H有7个、7H有13个), 且较高水平的LD成对位点( D′> 0.5)集中在2H、6H连锁群上, 分别有8个和10个。

4 结论

用64个多态性SSR标记将221份大麦品种分成地方品种与栽培品种两大类, 其遗传距离为0.3258, 栽培品种的多样性较地方品种丰富。国内育成品种与国外品种有较近的亲缘关系, 群体遗传结构相对简单。共线性或非共线行位点组合均有一定程度的LD, 并且整体LD水平较高, 有利于关联分析和发掘有利基因。栽培品种的LD水平高于地方品种, 尤其在2H、4H、6H和7H染色体上。

The authors have declared that no competing interests exist.

作者已声明无竞争性利益关系。The authors have declared that no competing interests exist.

参考文献

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1997

0.0

Science. 1997, 277(5329):1063-1066

Seed Banks and Molecular Maps: Unlocking Genetic Potential from the Wild

Steven D. Tanksley, Susan R. McCouch

The authors are in the Department of Plant Breeding, 252 Emerson Hall, Cornell University, Ithaca, NY 14853, USA.

... 亲本遗传基础狭窄是制约育种的主要问题之一^[1], 引进新的种质资源是解决这一问题的有效手段 ...

1992

4.007

0.0

... 简单序列重复(simple sequence repeat, SSR)具有多态性高、数量丰富、重复性好、呈共显性、且广泛分布于基因组等优点^[2,3,4,5], 被广泛应用于大麦遗传多样性^[6,7,8]和基因发掘研究^[9,10,11] ...

1994

9.737

0.0

PNAS. 1994, 91(12):5466-5470

Extraordinarily polymorphic microsatellite DNA in barley: species diversity, chromosomal locations, and population dynamics

M A Saghai Maroof, R M Biyashev, G P Yang, Q Zhang, and R W Allard

Department of Crop and Soil Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg 24061.

This study was undertaken to assess the extent of genetic variation in barley simple sequence repeats (SSRs) and to studythe evolutionary dynamics of SSR alleles. SSR polymorphisms were resolved by the polymerase chain reaction with four pairsof primers. In total, 71 variants were observed in a sample of 207 accessions of wild and cultivated barley. Analyses of wheat-barleyaddition lines and barley doubled haploids identified these variants (alleles) with four loci, each located on a differentchromosome. The numbers of alleles detected at a locus corresponded to the number of nucleotide repeats in the microsatellitesequences. The numbers of alleles at two loci were 28 and 37; to our knowledge these are the largest numbers of alleles forsingle Mendelian loci reported in plants. Three alleles were resolved by each of the other two loci. Allelic diversity wasgreater in wild than in cultivated barley and surveys of two generations (F8 and F53) of Composite Cross II, an experimentalpopulation of cultivated barley, showed that few of the alleles present in the 28 parents survived into generation F53, whereassome infrequent alleles reached high frequencies. Such changes in frequency indicate that the chromosomal segments markedby the SSR alleles are under the influence of natural selection. The SSR variants allow specific DNA sequences to be followedthrough generations. Thus, the great resolving power of SSR assays may provide clues regarding the precise targets of naturaland man-directed selection.

1990

3.019

0.0

. 1990, 7(4):524â530-null

1994

3.297

0.0

2002

1.653

0.0

2007

1.554

0.0

Genet Resour Crop Ev. 2007, 54(4):749 - 758 DOI:10.1007/s10722-006-9159-4

Genetic diversity changes and relationships in spring barley (Hordeum vulgare L.) germplasm of Nordic and Baltic areas as shown by SSR markers

A. Kolodinska Brantestam(1) R. von Bothmer(1) C. Dayteg(3) I. Rashal(2) S. Tuvesson(3) J. Weibull(4)

1.Department of Crop Science, Swedish University of Agricultural Sciences, P.O. Box 44, SE-230 53 Alnarp, Sweden
2.Laboratory of Plant Genetics, Institute of Biology, University of Latvia, LV-2169 Salaspils, Latvia
3.SW Laboratory, Sval?f Weibull AB, SE-268 81 Sval?v, Sweden
4.Swedish Biodiversity Centre, P.O. Box 54, SE-230 53 Alnarp, Sweden

To examine changes in the level of and pattern in variability in 197 Nordic and Baltic spring barley cultivars over time we used 21 mapped barley simple sequence repeats (SSRs). A total number of 191 alleles were found from 22 SSR loci. The number of alleles per locus ranged from 2 to 23, with average of 8.63 107 alleles were rare (frequency<0.05) among the cultivars and only one allele was frequently observed (frequency >0.95). The gene diversity between loci in Nordic and Baltic material varied between 0.033 and 0.891. Average gene diversity was 0.623. The SSR data separated two-rowed and six-rowed cultivars. According to analysis of molecular variance (AMOVA) differentiation in two-rowed vs six-rowed accounted for 23.6% of the total variation. Overall no significant decrease of average gene diversity over time could be found. However, differences were observed when spring barleys from northern (north of ∼58°) and southern (south of ∼58°) parts of the Nordic and Baltic area were compared. For the southern ecogeographical region significant decrease of genetic diversity was observed in the middle of the 20th century, whereas no significant changes in the northern part were found. We found larger differentiation between modern and old cultivars in the South compared to the ones in North parts of the region. The magnitude of changes in genetic diversity differed also with the country of origin. Danish cultivars had a significant decrease in diversity in the middle of century, whereas changes in Finland, Norway and Sweden were not significant.

2011

1.554

0.0

Euphytica. 2011, 178(1):31 - 43 DOI:10.1007/s10681-010-0260-6

Molecular diversity and association mapping of quantitative traits in Tibetan wild and worldwide originated barley (Hordeum vulgare L.) germplasm

Dongfa Sun(1) Wenbin Ren(1) Genlou Sun(12) Junhua Peng(3)

1.College of Plant Science and Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei China
2.Biology Department, Saint Mary’s University, Halifax, NS B3H 3C3, Canada
3.Wuhan Botanical Garden/Institute, Chinese Academy of Sciences, Wuhan, 430074 Hubei China

Molecular diversity of 40 accessions of Tibetan wild barley (TB), 10 Syrian (SY), 72 North American (NA), 36 European (EU), 9 South American (SA) and 8 Australian (AU) varieties were characterized using multiple microsatellite loci. The 42 SSR primers amplified 278 alleles across the 175 barley accessions tested in the present study. The average gene diversity for the whole sample was 0.3387 whereas the mean value for the each population was as follows: TB = 0.3286, SY = 0.2474, EU = 0.299, AU = 0.2867, NA = 0.3138, SA = 0.2536. Clustering analysis based on Nei’s original genetic distance showed that the EU and NA barley populations were grouped together. The TB population was well separated from the other 5 barley populations. Associations between microsatellite markers and 14 quantitative traits were also investigated. Significant associations were found for 18 microsatellite marker loci. The number of marker loci associated with each trait ranged from one (stem diameter, filled grains per plant, grain weight per plant, length of main spike and awn length) to seven (plant height). The percentage of the total variation explained by each marker ranged from 4.59% (HVM2 associated with plant height) to 17.48% (Bmac90 associated with density of main spike). This study provides candidate markers for further QTL mapping of these traits and for marker-assisted selection.

... 在大麦上, 已对栽培品种、地方品种以及野生资源进行了关联分析^[8,18,19], 发掘出许多有利等位基因 ...

2001

3.297

0.0

Theor Appl Genet. 2001, 103(1):161 - 170 DOI:10.1007/s001220000503

New QTLs identified for plant water status, water-soluble carbohydrate and osmotic adjustment in a barley population grown in a growth-chamber under two water regimes

B. Teulat(1) C. Borries(1) D. This(1)

1.UFR de Génétique et d’Amélioration des Plantes, AgroM-INRA, 2 place P. Viala 34060 Montpellier cedex, France Fax: +33-467045415 FR

Quantitative trait locus (QTL) analysis was carried out with 167 recombinant inbred lines (RILs) of barley derived from a cross between Tadmor and Er/Apm to identify the genomic regions controlling traits related to plant water status and osmotic adjustment (OA). The experiment was conducted in a growth chamber using a random incomplete block design (nine blocks). Relative water content (RWC) and leaf osmotic potential (ψ_π) were measured at 100% and 14% of the field capacity on 105 RILs in each block. In addition, the water-soluble carbohydrate concentration (WSC) was measured in the four first-blocks. The leaf osmotic potential at full turgor (ψ_π100), the water-soluble carbohydrate concentration at full turgor (WSC100), and also OA, the accumulation of water-soluble carbohydrates (dWSC100), the contribution of a change in water content to OA (CWC) and of the net solute accumulation to OA (SA) have also been calculated. In a previous paper (Teulat et al. 1998), 12 QTLs were identified for RWC, ψ_π, ψ_π100 and OA with adjusted means (block effects and pot-within-block effects fixed) with an incomplete genetic map. In the present paper, a more-saturated and improved map is described. A new QTL analysis as been performed with adjusted means. The new QTLs identified for previous evaluated traits, as well as the QTLs for the new traits, are presented. Eight additional regions (22 QTLs) were identified which increased to 13 the total number of chromosomal regions (32 QTLs) controlling traits related to plant water status and/or osmotic adjustment in this barley genetic background. The results emphasise the value of the experimental design employed for the evaluation of traits difficult to assess in genetic studies. The putative target regions for drought-tolerance improvement are discussed combining arguments on the consistency of QTLs and, when possible, the physiological value of QTLs (trait relevance, syntenic relationships and clustering of QTLs).

2006

3.297

0.0

Theor Appl Genet. 2006, 112(7):1221 - 1231 DOI:10.1007/s00122-006-0223-4

AB-QTL analysis in spring barley: II. Detection of favourable exotic alleles for agronomic traits introgressed from wild barley (H. vulgare ssp.spontaneum)

M. von Korff(12) H. Wang(13) J. Léon(1) K. Pillen(1)

1.Institute of Crop Science and Resource Conservation, Chair of Crop Science and Plant Breeding, University of Bonn, Katzenburgweg 5, 53115 Bonn, Germany
2.Department of Biochemistry and Biology, University of Potsdam, Karl-Liebknecht-Str. 24-25, Haus 26, 14476 Golm, Germany
3.Gansu Agricultural University, Yinmencun 1, 730070 Anningqu, Lanzhou China

The objective of the present study was to identify favourable exotic Quantitative Trait Locus (QTL) alleles for the improvement of agronomic traits in the BC₂DH population S42 derived from a cross between the spring barley cultivar Scarlett and the wild barley accession ISR42-8 (Hordeum vulgare ssp.spontaneum). QTLs were detected as a marker main effect and/or a marker × environment interaction effect (M × E) in a three-factorial ANOVA. Using field data of up to eight environments and genotype data of 98 SSR loci, we detected 86 QTLs for nine agronomic traits. At 60 QTLs the marker main effect, at five QTLs theM × E interaction effect, and at 21 QTLs both the effects were significant. The majority of theM × E interaction effects were due to changes in magnitude and are, therefore, still valuable for marker assisted selection across environments. The exotic alleles improved performance in 31 (36.0%) of 86 QTLs detected for agronomic traits. The exotic alleles had favourable effects on all analysed quantitative traits. These favourable exotic alleles were detected, in particular on the short arm of chromosome 2H and the long arm of chromosome 4H. The exotic allele on 4HL, for example, improved yield by 7.1%. Furthermore, the presence of the exotic allele on 2HS increased the yield component traits ears per m² and thousand grain weight by 16.4% and 3.2%, respectively. The present study, hence, demonstrated that wild barley does harbour valuable alleles, which can enrich the genetic basis of cultivated barley and improve quantitative agronomic traits.

2012

3.297

0.0

Theor Appl Genet. 2012, 124(2):373-384

High resolution mapping of Dense spike-ar (dsp.ar) to the genetic centromere of barley chromosome 7H

Fahimeh Shahinnia⁽¹⁾⁽²⁾, Arnis Druka⁽³⁾, Jerome Franckowiak⁽⁴⁾, Michele Morgante⁽⁵⁾, Robbie Waugh⁽³⁾, Nils Stein⁽¹⁾

1.Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Gatersleben, Germany
2.National Institute of Genetic Engineering and Biotechnology (NIGEB), 14965/161, Tehran, Iran
3.The James Hutton Institute, Invergowrie, Dundee, Scotland, DD2 5DA, UK
4.Agric-Science Queensland, Department of Employment, Economic Development and Innovation, Hermitage Research Station, 604 Yangan Road, Warwick, QLD, 4370, Australia
5.Dipartimento di Scienze Agrarie ed Ambientali, Università di Udine, 33100, Udine, Italy

Spike density in barley is under the control of several major genes, as documented previously by genetic analysis of a number of morphological mutants. One such class of mutants affects the rachis internode length leading to dense or compact spikes and the underlying genes were designateddense spike (dsp). We previously delimited two introgressed genomic segments on chromosome 3H (21 SNP loci, 35.5 cM) and 7H (17 SNP loci, 20.34 cM) in BW265, a BC₇F₃ nearly isogenic line (NIL) ofcv. Bowman as potentially containing the dense spike mutant locusdsp.ar, by genotyping 1,536 single nucleotide polymorphism (SNP) markers in both BW265 and its recurrent parent. Here, the gene was allocated by high-resolution bi-parental mapping to a 0.37 cM interval between markers SC57808(Hv_SPL14)–CAPSK06413 residing on the short and long arm at the genetic centromere of chromosome 7H, respectively. This region putatively contains more than 800 genes as deduced by comparison with the collinear regions of barley, rice, sorghum andBrachypodium, Classical map-based isolation of the genedsp.ar thus will be complicated due to the infavorable relationship of genetic to physical distances at the target locus.

... 人工选择会增加LD水平^[11] ...

2003

25.962

0.0

... 基于连锁不平衡的关联分析可以将表型性状的多样性与基因或位点的多态性结合起来, 确定不同种质资源所携带的等位基因及其对目标性状的贡献^[12,13,14] ...

2004

38.075

0.0

2005

4.15

0.0

Plant Mol Biol. 2005, 57(4):461 - 485 DOI:10.1007/s11103-005-0257-z

Linkage disequilibrium and association studies in higher plants: Present status and future prospects

Pushpendra K. Gupta(1) Sachin Rustgi(1) Pawan L. Kulwal(1)

1.Molecular Biology Laboratory, Department of Genetics & Plant Breeding, Ch. Charan Singh University, Meerut, 250 004 (UP) India

During the last two decades, DNA-based molecular markers have been extensively utilized for a variety of studies in both plant and animal systems. One of the major uses of these markers is the construction of genome-wide molecular maps and the genetic analysis of simple and complex traits. However, these studies are generally based on linkage analysis in mapping populations, thus placing serious limitations in using molecular markers for genetic analysis in a variety of plant systems. Therefore, alternative approaches have been suggested, and one of these approaches makes use of linkage disequilibrium (LD)-based association analysis. Although this approach of association analysis has already been used for studies on genetics of complex traits (including different diseases) in humans, its use in plants has just started. In the present review, we first define and distinguish between LD and association mapping, and then briefly describe various measures of LD and the two methods of its depiction. We then give a list of different factors that affect LD without discussing them, and also discuss the current issues of LD research in plants. Later, we also describe the various uses of LD in plant genomics research and summarize the present status of LD research in different plant genomes. In the end, we discuss briefly the future prospects of LD research in plants, and give a list of softwares that are useful in LD research, which is available as electronic supplementary material (ESM)

2005

2.852

0.0

Mol Breeding. 2005, 15(3):271 - 290 DOI:10.1007/s11032-004-7012-z

Population structure and long-range linkage disequilibrium in a durum wheat elite collection

Marco Maccaferri(1) Maria Corinna Sanguineti(1) Enrico Noli(1) Roberto Tuberosa(1)

1.Department of Agroenvironmental Science and Technology University of Bologna Viale Fanin n. 44 40127 Bologna Italy

A collection of 134 durum wheat accessions, mainly including cultivars (cvs.) representative of the major gene pools, was assembled and characterized with 70 SSRs for genetic diversity and level of long-range linkage disequilibrium (LD). Results of both a distance-based and a model-based (Bayesian) cluster analysis evidenced the presence of a structured diversity. In the model-based analysis, six to eight main distinct subpopulations were identified based on the molecular data. Only a relatively small portion (20%) of the molecular variation was accounted for by the geographical origin of the accessions. Major differences were detected between the North American and the Mediterranean cvs., while a considerable overlap characterized the cvs. from CIMMYT-ICARDA and Italy. The North American cvs. showed the highest within group mean genetic similarity (GS_m = 0.68). French cvs. revealed sizeable similarities with both the North American as well as the Italian and CIMMYT-ICARDA pools. Considering the germplasm as a whole, high levels of LD were found both at locus pairs with an intrachromosomal distance<50 cm as="" well="" as="" at="" those="" with="" distances="" more="" than="" 50 cm="" and="" independent="" (86,="" 52="" and="" 54%="" of="" ssr="" pairs="" at="">p < 0.01, respectively).="" after="" re-evaluating="" ld="" within="" each="" of="" the="" three="" main="" subgroups="" identified="" through="" the="" analysis="" of="" the="" germplasm="" structure,="" the="" ld="" level="" remained="" high="" for="" tightly="" to="" moderately="" linked="" locus="" pairs=""><20 cm apart),="" but="" was="" greatly="" reduced="" in="" the="" loosely="" linked="" (more="" than="" 50 cm="" apart)="" and="" independent="" locus="" pairs.="" the="" implications="" of="" these="" findings="" as="" to="" the="" possibility="" of="" using="" association="" mapping="" for="" gene/qtl="" discovery="" in="" durum="" wheat="" are="">

... 目前, 关联分析已广泛用于小麦^[15]、玉米^[16]、水稻^[17]等作物的基因发掘 ...

2005

6.16

0.0

. 2005, 44(6):1054-1064

Maize association population: a high-resolution platform for quantitative trait locus dissection

Sherry A. Flint-Garcia^1,2,Anne-Céline Thuillet³,Jianming Yu⁴,Gael Pressoir⁴,Susan M. Romero⁴,Sharon E. Mitchell⁴,John Doebley³,Stephen Kresovich⁴,Major M. Goodman⁵,Edward S. Buckler^4,6,*

¹ US Department of Agriculture – Agricultural Research Service, Plant Genetics Research Unit, Columbia, MO 65211, USA
² Division of Plant Sciences, University of Missouri, Columbia, MO 65211, USA,
³ Department of Genetics, University of Wisconsin, Madison, WI 65211, USA,
⁴ Institute for Genomic Diversity, Cornell University, Ithaca, NY 14853, USA,
⁵ Department of Crop Science, North Carolina State University, Raleigh, NC 27695, USA, and
⁶ US Department of Agriculture – Agricultural Research Service, US Plant, Soil and Nutrition Research Unit, Ithaca, NY 14853, USA
^* (fax +1 607 255 6249; e-mailesb33@cornell.edu).

Crop improvement and the dissection of complex genetic traits require germplasm diversity. Although this necessary phenotypic variability exists in diverse maize, most research is conducted using a small subset of inbred lines. An association population of 302 lines is now available – a valuable research tool that captures a large proportion of the alleles in cultivated maize. Provided that appropriate statistical models correcting for population structure are included, this tool can be used in association analyses to provide high-resolution evaluation of multiple alleles. This study describes the population structure of the 302 lines, and investigates the relationship between population structure and various measures of phenotypic and breeding value. On average, our estimates of population structure account for 9.3% of phenotypic variation, roughly equivalent to a major quantitative trait locus (QTL), with a high of 35%. Inclusion of population structure in association models is critical to meaningful analyses. This new association population has the potential to identify QTL with small effects, which will aid in dissecting complex traits and in planning future projects to exploit the rich diversity present in maize.

... 目前, 关联分析已广泛用于小麦^[15]、玉米^[16]、水稻^[17]等作物的基因发掘 ...

2010

35.532

0.0

. 2010, 42(11):961-967

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

Matt Estep^1,4 ,Lingling Suo^2,3 ,Bin Han^1,2 ,Xuewen Wang⁵ ,Chanchan Wang^1,2 ,Edward S Buckler^5,7 ,Qi Feng¹ ,Jingchu Hu¹ ,Lin Wang⁹ ,Liang Feng¹ ,Jennifer Hawkins^1,12 ,Taoying Zhou¹ ,Changlei Han¹ ,Katrien M Devos⁵ ,Qiang Zhao^1,2 ,Mats Bentsen^1,2,3 ,Jane Grimwood^2,3 ,Shweta Deshpande³ ,Odd Helge Otterå^1,2,3 ,Yunli Guo¹ ,Justin N Vaughn¹ ,Xiaomei Wu^5,12 ,Danlin Fan¹ ,Qijun Weng¹ ,Ryan Percifield^1,12 ,Margarita Mauro-Herrera⁸ ,Shifeng Cheng¹ ,Uffe Hellsten³ ,Xiaohua Peng^1,2 ,Qingchun Chen^1,2 ,Gerald A Tuskan⁷ ,Chu-Yu Ye⁷ ,Ning Li^1,2 ,Yan Zhao¹ ,Olivier Panaud¹¹ ,Meng Li^5,6 ,Manoj Sharma¹⁰ ,Rita Sharma¹⁰ ,Ping Huang^1,2 ,Qi-Fa Zhang⁸ ,Liuwei Deng¹ ,Wenjun Li¹ ,Jiayang Li⁹ ,Xuehui Huang^1,2 ,Shengkai Pan¹ ,Therese Mitros⁶ ,Peng Zeng¹ ,Yanjie Cai^1,2 ,Jeremy Schmutz^2,3 ,Erika Lindquist³ ,Yinxin Zhang^1,2 ,Kunyan Liu¹ ,Yufeng Jing¹ ,Pamela C Ronald¹⁰ ,Dongliang Zhan¹ ,Xinghua Wei³ ,Jimmy Triplett^4,12 ,Elizabeth A Kellogg⁴ ,Jerry Jenkins^2,3 ,Renyi Wang^1,2 ,Thomas P Brutnell^9,12 ,Helge Drange^1,2,4 ,Hao Wang¹ ,Xinhua Yang¹ ,Yingrui Li¹ ,Daniel Rokhsar³ ,Xiaohan Yang⁷ ,Xun Xu^1,2,3 ,Ahong Wang¹ ,Canyang Li¹ ,Zhiwu Zhang⁵ ,Haitao Xiang^1,2 ,Tao Sang⁴ ,Gengyun Zhang^1,2 ,Qiuxiang Shi^1,2 ,Min Xie¹ ,Yiqi Lu¹ ,Ye Tao¹ ,Henan Li^1,2 ,Jun Wang^1,4 ,Andrew N Doust⁸ ,Chuanrang Zhu¹ ,Kerrie Barry³ ,Zhihai Zhao⁵ ,Xin Liu¹ ,Hua Li^1,2 ,Chengzhang Liu^1,2 ,Jeffrey L Bennetzen¹ ,Qian Qian³ ,Zhen Yue¹ ,Zhiwu Quan^1,2 ,Tingting Lu¹ ,Tao Huang¹ ,Wei Li¹ ,Qiuju Xia^1,2 ,Junyi Wang¹ ,Wenliang Wang¹ ,Rui Cao¹ ,Lu Wang¹ ,Chao Bian¹ ,Tao Guo^1,2 ,Jian Wang^1,2 ,Ana C Pontaroli^1,12 ,Pinghua Li⁹ ,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.
¹⁰ The Joint Bioenergy Institute, Emeryville, and the Department of Plant Pathology and Genome Center at the University of California, Davis, California, USA.
¹¹ Université de Perpignan, Perpignan, France.
¹² Present addresses: Department of Biochemistry, West Virginia University, Morgantown, West Virginia, USA (R.P.); Department of Biology, West Virginia University, Morgantown, West Virginia, USA (J.H.); EEA Balcarce, Instituto Nacional de Tecnología Agropecuaria—CONICET, Balcarce, Argentina (A.C.P.); Department of Biology, Jacksonville State University, Jacksonville, Alabama, USA (J.T.); Center for Plant Environmental Sensing, Hangzhou Normal University, Hangzhou, China (X.W.); and Danforth Plant Science Center, St. Louis, Missouri, USA (T.B.).

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.

... 目前, 关联分析已广泛用于小麦^[15]、玉米^[16]、水稻^[17]等作物的基因发掘 ...

2006

2.852

0.0

Mol Breeding. 2006, 17(1):41 - 58 DOI:10.1007/s11032-005-1119-8

Linkage Disequilibrium Mapping of Morphological, Resistance, and Other Agronomically Relevant Traits in Modern Spring Barley Cultivars

A. T. W. Kraakman(1) F. Martínez(1) B. Mussiraliev(1) F. A. van Eeuwijk(1) R. E. Niks(1)

1.Laboratory of Plant Breeding, Wageningen University and Research Center, P.O. Box 386, 6700 Wageningen, AJ The Netherlands

A set of 148 modern spring barley cultivars was explored for the extent of linkage disequilibrium (LD) between genes governing traits and nearby marker alleles. Associations of agronomically relevant traits (days to heading, plant height), resistance traits (leaf rust, barley yellow dwarf virus (BYD)), and morphological traits (rachilla hair length, lodicule size) with AFLP markers and SSR markers were found. Known major genes and QTLs were confirmed, but also new putative QTLs were found. The LD mapping clearly indicated the common occurrence ofRph3, a gene for hypersensitivity resistance againstPuccinia hordei, and also confirmed the QTLRphq2 for prolonging latency period ofP. hordei in seedlings. We also found strong indication for a hitherto not reported gene for resistance or tolerance to BYD on chromosome 2, linked to SSR marker HVM054. Our conclusion is that LD mapping is a valuable additional tool in the search for applicable marker associations with major genes and QTLs.

... 在大麦上, 已对栽培品种、地方品种以及野生资源进行了关联分析^[8,18,19], 发掘出许多有利等位基因 ...

2006

0.0

... 在大麦上, 已对栽培品种、地方品种以及野生资源进行了关联分析^[8,18,19], 发掘出许多有利等位基因 ...

... Katherine等^[19]报道, 栽培大麦的LD水平最高, 地方品种次之, 野生资源LD水平最低 ...

1993

2.453

0.0

Plant Mol Biol Rep. 1993, 11(2):122-127

A rapid method for extraction of cotton (Gossypium spp.) genomic DNA suitable for RFLP or PCR analysis

Andrew H. Paterson⁽¹⁾, Curt L. Brubaker⁽²⁾, Jonathan F. Wendel⁽¹⁾

1.Department of Soil and Crop Sciences, Texas A & M University, 77843-2474, College Station, TX, USA
2.Department of Botany, Iowa State University, 50011, Ames, IA, USA

Extraction of high-quality genomic DNA fromGossypium (cotton) species is difficult due to high levels of polysaccharide, oxidizable quinones, and other interfering substances. We describe a procedure that consistently permits isolation of cotton genomic DNA of satisfactory size and quality for RFLP and PCR analysis, as well as for most routine cloning applications. Several antioxidants, phenol-binding reagents, and phenol oxidase inhibitors are used throughout the procedure, and most polysaccharides are eliminated early in the procedure by isolation of nuclei.

... 2 SSR标记分析采用CTAB法^[20]提取基因组DNA ...

2005

2.852

0.0

Mol Breeding. 2005, 15(3):271 - 290 DOI:10.1007/s11032-004-7012-z

Population structure and long-range linkage disequilibrium in a durum wheat elite collection

Marco Maccaferri(1) Maria Corinna Sanguineti(1) Enrico Noli(1) Roberto Tuberosa(1)

1.Department of Agroenvironmental Science and Technology University of Bologna Viale Fanin n. 44 40127 Bologna Italy

... 参照Maccaferri等^[21]的方法处理频率小于0 ...

2005

5.522

0.0

. 2005, 14(8):2611-2620

Detecting the number of clusters of individuals using the softwarestructure

G. EVANNO,S. REGNAUT,J. GOUDET^*

Department of Ecology and Evolution, Biology building, University of Lausanne, CH 1015 Lausanne, Switzerland
^* Jérôme Goudet, Fax: + 41 21 692 42 65; E-mail:Jerome.goudet@unil.ch

The identification of genetically homogeneous groups of individuals is a long standing issue in population genetics. A recent Bayesian algorithm implemented in the softwarestructure allows the identification of such groups. However, the ability of this algorithm to detect the true number of clusters (K) in a sample of individuals when patterns of dispersal among populations are not homogeneous has not been tested. The goal of this study is to carry out such tests, using various dispersal scenarios from data generated with an individual-based model. We found that in most cases the estimated ‘log probability of data’ does not provide a correct estimation of the number of clusters,K. However, using an ad hoc statistic ΔK based on the rate of change in the log probability of data between successiveK values, we found thatstructure accurately detects the uppermost hierarchical level of structure for the scenarios we tested. As might be expected, the results are sensitive to the type of genetic marker used (AFLP vs. microsatellite), the number of loci scored, the number of populations sampled, and the number of individuals typed in each sample.

... 若K值持续增大, 参照Evanno等^[22]的方法计算ΔK确定K值 ...

2002

2.534

0.7555

J Integr Plant Biol. 2002, (11):1327 - 1332

Genetic Diversity of Hordeum bogdanii Wilensky Native to Xinjiang,China,Based on STS-PCR Markers

应用STS-PCR标记研究新疆布顿大麦的遗传多样性

GUOHong^[1];WEIYu-Ming^[2];CHENFang^[3];ZHENGYou-Liang^[2]

郭红^[1];魏育明^[2];陈放^[3];郑有良^[2]

利用22个来源于小麦(Triticum aestivum L.)和栽培大麦(Hordeum vulgare L.)的STS-PCR标记,研究了32份新疆布顿大麦(Hordeum bogdanii Wilensky)的遗传多样性.在这22个STS-PCR标记中,仅有3个标记的扩增产物经HinfⅠ、HhaⅠ、HaeⅢ和RsaⅠ 4种限制性内切酶消化后没有产生多态性DNA片段,而19个标记(占86.4%)和46种标记/酶组合(占52.3%)能够揭示材料间的多态性.在32份布顿大麦材料的88种STS-PCR标记/酶组合中,总共得到315条DNA片段,平均每个标记/酶组合能得到3.6条DNA片段.在这315条DNA片段中,共有123条片段(占39.0%)具有多态性,每一个多态性标记/酶组合能获得1～6条多态性DNA片段.STS-PCR标记揭示的32份布顿大麦的遗传距离变化范围为0.078～0.352,平均为0.198.根据STS-PCR标记的遗传距离矩阵,采用不完全加权算术平均数法(UPGMA)构建了32份布顿大麦群体间的遗传关系树状图,结果表明STS-PCR标记能将32份材料完全区分开来.同时,来源于同一地方的不同居群没有明显地聚类在一起,表明新疆布顿大麦的遗传多样性与其地理分布相关不紧密.

Abstract：

The genetic diversity among 32 accessions of Hordeum bogdanii Wilensky native to Xinjiang, China, was evaluated by 22 STS-PCR primer sets derived from RFLP clones of the wheat (Triticum aestivum L.) or barley (Hordeum vulgare L.) mapping. Out of the 22 STS-PCR markers, only three markers gave products which did not generate polymorphic bands upon digestion with HinfⅠ, HhaⅠ, HaeⅢ and RsaⅠ, while 19 out of 22 markers (86.4%) and 46 out of 88 marker/enzyme combinations (52.3%) revealed polymorphisms. Among the 32 H. bogdanii accessions, a total of 315 bands were observed in 88 STS-PCR marker/enzyme combinations, with 3.6 bands each. One hundred and twenty-three out of 315 bands (39.0%) were polymorphic, among which 1 to 6 polymorphic bands were generated by each polymorphic marker/enzyme combination. The STS-PCR-based genetic diversity index (GD) among 32 H. bogdanii accessions ranged between 0.078 to 0.352, with a mean of 0.198. Based on the GD matrix, a dendrogram showing the genetic relationships between accessions was constructed using the unweighted pair-group method with arithmetic average (UPGMA). Results showed that all 32 accessions could be distinguished by STS-PCR markers. The accessions originated from the same region were distributed within different groups or subgroups. This study indicates that the genetic diversity of H. bogdanii is not closely correlated with the geographical distribution.

... 有研究表明, 我国大麦遗传基础明显比国外品种狭窄, 但是野生资源遗传变异丰富^{[23,24,25,26]}, 因此需要引进不同国家和地区的材料改良大麦品种 ...

2004

0.0

1.8267

Acta Agron Sin. 2004, 30(3):258 - 265

Genetic Variation Analysis by RAPD of Some Barley Cultivars in China

中国江、浙地区栽培大麦遗传资源的RAPD研究

SHI Yong-Tai;ZHU Mu-Yuan

施永泰;朱睦元

College of Life Sciences, Zhejiang University, Hangzhou 310012, Zhejiang; 2 Ningbo Academy of Agricultural Science, Ningbo 315040, Zhejiang

Genetic variation is essential for genetic improvement and plant breeding. 200 arbitrary primers (10-mers) were used for the PCR amplification of random genetic DNA fragments in this study to estimate the genetic variation of 67 barley cultivars in China by RAPD, most of which were derived from the

采用随机扩增多态性（RAPD）标记，探讨了我国部分栽培大麦品种的遗传背景。结果表明：200个随机引物中，有30个引物扩增出的产物具有多态性，30个引物共扩增出223条谱带，其中130条谱带具有多态性，每个引物可扩增出2~9条多态性谱带，平均4.19条。67个大麦品种平均表型多样性值0.369，裸麦的表型多样性高于皮麦的表型多样性

... 有研究表明, 我国大麦遗传基础明显比国外品种狭窄, 但是野生资源遗传变异丰富^{[23,24,25,26]}, 因此需要引进不同国家和地区的材料改良大麦品种 ...

2008

0.0

0.8529

J Trit Crops. 2008, (2):214 - 219

Genetic Diversity Assessment of Barley Germplasm Resources Using SSR Markers

大麦品种资源遗传多样性的SSR标记评价

ZHANGChi-hong;ZHANGJing

张赤红;张京

为了有效利用大麦种质资源,利用49对SSR引物,对中国240份和国外60份大麦品种资源进行了遗传多样性研究.结果表明,大麦7条染色体中第五和第六条染色体遗传多样性较高,第三、四、七条染色体遗传多样性比较低.300份材料中,遗传多样性最丰富的是非洲、亚洲和中东的大麦资源;中国西藏、四川、云南及育成品种的遗传多样性较为丰富.基于SSR数据,对300份大麦材料进行了聚类分析,结果聚为三组,来自土库曼斯坦(TKM)的一份材料划分为一组, 43份国外材料划分为一组,其他材料为一组,同一栽培地区的品种基本聚在同一组中.

... 有研究表明, 我国大麦遗传基础明显比国外品种狭窄, 但是野生资源遗传变异丰富^{[23,24,25,26]}, 因此需要引进不同国家和地区的材料改良大麦品种 ...

2011

0.0

... 有研究表明, 我国大麦遗传基础明显比国外品种狭窄, 但是野生资源遗传变异丰富^{[23,24,25,26]}, 因此需要引进不同国家和地区的材料改良大麦品种 ...

1994

9.737

0.0

PNAS. 1994, 91(12):5466-5470

Extraordinarily polymorphic microsatellite DNA in barley: species diversity, chromosomal locations, and population dynamics

M A Saghai Maroof, R M Biyashev, G P Yang, Q Zhang, and R W Allard

Department of Crop and Soil Environmental Sciences, Virginia Polytechnic Institute and State University, Blacksburg 24061.

... Maroof等^[27]利用4对SSR引物检测104份栽培大麦和103份来自以色列不同生态区的二棱野生大麦, 其中2个标记分别检测到28个和37个等位变异 ...

1998

3.297

0.0

Theor Appl Genet. 1998, 97(1-2):308-315

The use of microsatellite markers for detection of genetic diversity in barley populations

D. Struss^(A1), J. Plieske^(A1)

A1.Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstrasse 3, 06466 Gatersleben, Germany, DE

A barley lambda-phage library was screened with (GA)n and (GT)n probes for developing microsatellite markers. The number of repeats ranged from 2 to 58 for GA and from 2 to 24 for GT. Fifteen selected microsatellite markers were highly polymorphic for barley. These microsatellite markers were used to estimate the genetic diversity among 163 barley genotypes chosen from the collection of the IPK Genebank, Germany. A total of 130 alleles were detected by 15 barley microsatellite markers. The number of alleles per microsatellite marker varied from 5 to 15. On average 8.6 alleles per locus were observed. Except for GMS004 all other barley microsatellite markers showed on average a high value of gene diversity ranging from 0.64 to 0.88. The mean value of gene diversity in the wild forms and landraces was 0.74, and even among the cultivars the gene diversity ranged from 0.30 to 0.86 with a mean of 0.72. No significant differences in polymorphism were detected by the GA and GT microsatellite markers. The estimated genetic distances revealed by the microsatellite markers were, on average , 0.75 for the wild forms, 0.72 for landraces and 0.70 among cultivars. The microsatellite markers were able to distinguish between different barley genotypes. The high degree of polymorphisms of microsatellite markers allows a rapid and efficient identification of barley genotypes.

... Struss等^[28]用15对SSR引物研究由野生大麦、地方品种和选育品种组成的163份大麦品种的遗传多样性, 共检测到130个等位基因, 单个标记检测到的最多等位变异数为15 ...

2001

1.712

0.0

... Hansen等^[29]利用AFLP标记对野生甜菜生长习性首次进行植物全基因组关联分析, Thornsberry等^[30]首次运用基于候选基因检测方法对玉米中Dwarf8基因的9个多态性位点与玉米开花时间相关联的研究, 此后陆续有很多利用关联分析方法的报道 ...

2001

35.532

0.0

. , :null-null

2003

0.0

... 对大麦的研究表明, LD衰减距离在10~20 cM^[31,32], 说明大麦的LD水平较高, 有利于进行全基因组关联分析, 发掘种质资源中的有利基因 ...

2004

4.007

0.0

... 对大麦的研究表明, LD衰减距离在10~20 cM^[31,32], 说明大麦的LD水平较高, 有利于进行全基因组关联分析, 发掘种质资源中的有利基因 ...