A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L.) genome.
A SSR-based composite genetic linkage map for the cultivated peanut (Arachis hypogaea L.) genome.
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DOI：
10.1186/1471-2229-10-17
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发表时间：
2010-01-27
影响因子：
5.3
通讯作者：
Guo B
中科院分区：
文献类型：
--
作者：
Hong Y;Chen X;Liang X;Liu H;Zhou G;Li S;Wen S;Holbrook CC;Guo B
花生遗传连锁图谱的构建已经并且继续是促进数量性状基因座（QTL）分析和基因标记用于育种中的标记辅助选择的重要研究目标。尽管已经开发了一些地图，但它们是使用二倍体或种间四倍体群体构建的。最新发表的花生种内遗传图谱是利用栽培花生杂交构建的，其中只有135个SSR标记稀疏分布在22个连锁群中。为便于QTL定位和分子标记辅助选择，必须构建具有足够标记的连锁图谱。利用花生基因组序列、表达序列标签（EST）和GenBank中的“数据挖掘”技术构建花生遗传连锁图谱。以西班牙高产玉米品种粤优13为母本，通过3个杂交组合构建了3个重组自交系（RILs）群体。用设计的1044对引物对4个亲本进行了筛选，其中901对引物产生了清晰的PCR产物。在901对引物中，分别有146、124和64对引物（标记）在这些群体中表现出多态性，并用于这些RIL群体的基因分型。从三个群体中的每一个构建了个体连锁图，并使用JoinMap创建了基于93个共同位点的复合图。该复合连锁图谱由22个复合连锁群（LG）和175个SSR标记组成（包括已发表的AA基因组图谱上的47个SSR标记），代表了AA的20条染色体。hypogaea。合成图总长度为885.4cM，平均标记密度为5.8cM。标记在3个群体中的偏分离率分别为23.0%、13.5%和7.8%。这些畸变位点倾向于聚集在LG 1、LG 3、LG 4和LG 5上。由于多态性较低，仅定位了15个EST-SSR标记。通过比较发现，这些图谱之间以及与AA基因组之间存在潜在的同线性、共线顺序和共线连锁群的保守性，但并不完全保守。利用175个SSR标记构建了3个作图群体的22个复合连锁群的复合连锁图谱。这个复合遗传连锁图谱是第一个“真正的”四倍体花生图谱。该图谱还包括已发表的AA基因组图谱中使用的47个SSR标记，可用于比较作图研究。本研究中描述的引物是基于PCR的标记，易于在花生遗传作图中共享。所有1044对引物都作为附加文件提供，三个RIL群体将根据要求向公众提供数量性状位点（QTL）分析和连锁图谱改进。
The construction of genetic linkage maps for cultivated peanut (Arachis hypogaea L.) has and continues to be an important research goal to facilitate quantitative trait locus (QTL) analysis and gene tagging for use in a marker-assisted selection in breeding. Even though a few maps have been developed, they were constructed using diploid or interspecific tetraploid populations. The most recently published intra-specific map was constructed from the cross of cultivated peanuts, in which only 135 simple sequence repeat (SSR) markers were sparsely populated in 22 linkage groups. The more detailed linkage map with sufficient markers is necessary to be feasible for QTL identification and marker-assisted selection. The objective of this study was to construct a genetic linkage map of cultivated peanut using simple sequence repeat (SSR) markers derived primarily from peanut genomic sequences, expressed sequence tags (ESTs), and by "data mining" sequences released in GenBank. Three recombinant inbred lines (RILs) populations were constructed from three crosses with one common female parental line Yueyou 13, a high yielding Spanish market type. The four parents were screened with 1044 primer pairs designed to amplify SSRs and 901 primer pairs produced clear PCR products. Of the 901 primer pairs, 146, 124 and 64 primer pairs (markers) were polymorphic in these populations, respectively, and used in genotyping these RIL populations. Individual linkage maps were constructed from each of the three populations and a composite map based on 93 common loci were created using JoinMap. The composite linkage maps consist of 22 composite linkage groups (LG) with 175 SSR markers (including 47 SSRs on the published AA genome maps), representing the 20 chromosomes of A. hypogaea. The total composite map length is 885.4 cM, with an average marker density of 5.8 cM. Segregation distortion in the 3 populations was 23.0%, 13.5% and 7.8% of the markers, respectively. These distorted loci tended to cluster on LG1, LG3, LG4 and LG5. There were only 15 EST-SSR markers mapped due to low polymorphism. By comparison, there were potential synteny, collinear order of some markers and conservation of collinear linkage groups among the maps and with the AA genome but not fully conservative. A composite linkage map was constructed from three individual mapping populations with 175 SSR markers in 22 composite linkage groups. This composite genetic linkage map is among the first "true" tetraploid peanut maps produced. This map also consists of 47 SSRs that have been used in the published AA genome maps, and could be used in comparative mapping studies. The primers described in this study are PCR-based markers, which are easy to share for genetic mapping in peanuts. All 1044 primer pairs are provided as additional files and the three RIL populations will be made available to public upon request for quantitative trait loci (QTL) analysis and linkage map improvement.
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影响因子：
5.3
作者：
Foncéka D;Hodo-Abalo T;Rivallan R;Faye I;Sall MN;Ndoye O;Fávero AP;Bertioli DJ;Glaszmann JC;Courtois B;Rami JF
通讯作者：
Rami JF
影响因子：
5.4
作者：
HALWARD, T;STALKER, HT;KOCHERT, G
通讯作者：
KOCHERT, G
影响因子：
5.4
作者：
DEVEY, ME;FIDDLER, TA;NEALE, DB
通讯作者：
NEALE, DB
影响因子：
5.3
作者：
Leal-Bertioli SC;José AC;Alves-Freitas DM;Moretzsohn MC;Guimarães PM;Nielen S;Vidigal BS;Pereira RW;Pike J;Fávero AP;Parniske M;Varshney RK;Bertioli DJ
通讯作者：
Bertioli DJ
DOI：
10.1155/2009/715605
发表时间：
2009
期刊：
International journal of plant genomics
影响因子：
--
作者：
Guo B;Chen X;Hong Y;Liang X;Dang P;Brenneman T;Holbrook C;Culbreath A
通讯作者：
Culbreath A