Development of chromosome-specific markers with high polymorphism for allotetraploid cotton based on genome-wide characterization of simple sequence repeats in diploid cottons (Gossypium arboreum L. and Gossypium raimondii Ulbrich).
Development of chromosome-specific markers with high polymorphism for allotetraploid cotton based on genome-wide characterization of simple sequence repeats in diploid cottons (Gossypium arboreum L. and Gossypium raimondii Ulbrich).
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基于二倍体棉花（Gossypium arboreum L.和Gossypium raimondii Ulbrich）简单序列重复的全基因组表征，开发异源四倍体棉花的高多态性染色体特异性标记
DOI：
10.1186/s12864-015-1265-2
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发表时间：
2015-02-06
期刊：
影响因子：
4.4
通讯作者：
Song G
中科院分区：
文献类型：
--
作者：
Lu C;Zou C;Zhang Y;Yu D;Cheng H;Jiang P;Yang W;Wang Q;Feng X;Prosper MA;Guo X;Song G
四倍体棉花含有两套同源染色体，即At-和Dt-亚基因组。因此，在棉花连锁遗传图谱构建过程中，许多标记被定位到多个位置，这对锚定连锁群和将经济重要基因定位到特定染色体提出了挑战。染色体特异性标记可以解决这个问题。最近，两个二倍体物种的基因组进行了测序，其祖先是推定的贡献者的AT和DT亚基因组的四倍体棉花。鉴于四倍体和二倍体棉花基因组之间的高水平同线性，这些序列为开发染色体特异性标记提供了有力的工具。在这项研究中，在两个二倍体基因组中的每个染色体上的简单序列重复（SSR）的特点。结果在亚洲棉13条染色体上分别检测到200，744和142，409个SSR标记。和棉属（Gossypium raimondii Ulbrich）。通过比较每条染色体与其他25条染色体的SSR侧翼序列，获得染色体特异性SSR。平均每个染色体有7,996个。为了验证它们的染色体特异性，利用这些SSR标记通过构建连锁群来区分四倍体棉花中的两条同源染色体。染色体特异性SSR与已报道的染色体标记聚在一起，没有标记定位到同源染色体上，证明染色体特异性SSR具有独特性，可以区分四倍体棉花的同源染色体。由于较长的二核苷酸AT-丰富的重复序列是最多态性在以前的报告中，每个染色体上的SSR排序的基序类型和重复长度，以方便选择。所有染色体特异性SSR的引物序列也公开。ConclusionChromosome-specific SSR是染色体鉴定的有效工具，通过锚定连锁群，以特定的染色体在遗传作图，特别是在质量性状基因或数量性状基因座的映射只有几个标记。这些SSR标记将有助于棉花的遗传和基因组研究，包括高密度遗传图谱的构建、定位基因的克隆、指纹图谱的构建、遗传多样性的分析以及棉花种间的比较进化分析。
BackgroundTetraploid cotton contains two sets of homologous chromosomes, the At- and Dt-subgenomes. Consequently, many markers in cotton were mapped to multiple positions during linkage genetic map construction, posing a challenge to anchoring linkage groups and mapping economically-important genes to particular chromosomes. Chromosome-specific markers could solve this problem. Recently, the genomes of two diploid species were sequenced whose progenitors were putative contributors of the At- and Dt-subgenomes to tetraploid cotton. These sequences provide a powerful tool for developing chromosome-specific markers given the high level of synteny among tetraploid and diploid cotton genomes. In this study, simple sequence repeats (SSRs) on each chromosome in the two diploid genomes were characterized. Chromosome-specific SSRs were developed by comparative analysis and proved to distinguish chromosomes.ResultsA total of 200,744 and 142,409 SSRs were detected on the 13 chromosomes ofGossypium arboreumL. andGossypium raimondiiUlbrich, respectively. Chromosome-specific SSRs were obtained by comparing SSR flanking sequences from each chromosome with those from the other 25 chromosomes. The average was 7,996 per chromosome. To confirm their chromosome specificity, these SSRs were used to distinguish two homologous chromosomes in tetraploid cotton through linkage group construction. The chromosome-specific SSRs and previously-reported chromosome markers were grouped together, and no marker mapped to another homologous chromosome, proving that the chromosome-specific SSRs were unique and could distinguish homologous chromosomes in tetraploid cotton. Because longer dinucleotide AT-rich repeats were the most polymorphic in previous reports, the SSRs on each chromosome were sorted by motif type and repeat length for convenient selection. The primer sequences of all chromosome-specific SSRs were also made publicly available.ConclusionChromosome-specific SSRs are efficient tools for chromosome identification by anchoring linkage groups to particular chromosomes during genetic mapping and are especially useful in mapping of qualitative-trait genes or quantitative trait loci with just a few markers. The SSRs reported here will facilitate a number of genetic and genomic studies in cotton, including construction of high-density genetic maps, positional gene cloning, fingerprinting, and genetic diversity and comparative evolutionary analyses amongGossypiumspecies.
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影响因子：
5.8
作者：
Kofler, Robert;Schloetterer, Christian;Lelley, Tamas
通讯作者：
Lelley, Tamas
影响因子：
4.4
作者：
Cavagnaro PF;Senalik DA;Yang L;Simon PW;Harkins TT;Kodira CD;Huang S;Weng Y
通讯作者：
Weng Y
DOI：
10.1073/pnas.95.18.10774
发表时间：
1998-09-01
影响因子：
11.1
作者：
Kruglyak, S;Durrett, RT;Aquadro, CF
通讯作者：
Aquadro, CF
影响因子：
5.4
作者：
Han, ZG;Wang, CB;Zhang, TZ
通讯作者：
Zhang, TZ
影响因子：
3.1
作者：
Lacape, JM;Nguyen, TB;Hau, B
通讯作者：
Hau, B