Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes.
Nucleotide diversity maps reveal variation in diversity among wheat genomes and chromosomes.
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DOI：
10.1186/1471-2164-11-702
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发表时间：
2010-12-14
期刊：
影响因子：
4.4
通讯作者：
Dvorak J
中科院分区：
文献类型：
--
作者：
Akhunov ED;Akhunova AR;Anderson OD;Anderson JA;Blake N;Clegg MT;Coleman-Derr D;Conley EJ;Crossman CC;Deal KR;Dubcovsky J;Gill BS;Gu YQ;Hadam J;Heo H;Huo N;Lazo GR;Luo MC;Ma YQ;Matthews DE;McGuire PE;Morrell PL;Qualset CO;Renfro J;Tabanao D;Talbert LE;Tian C;Toleno DM;Warburton ML;You FM;Zhang W;Dvorak J
对多倍体物种中核苷酸多样性的全基因组评估必须最大限度地减少多样性估计中同源序列的包含，并可靠地将个体单倍型分配到各自的基因组中。同样的要求使多倍体物种中单核苷酸多态性 (SNP) 标记的开发和部署变得复杂。我们在此报告了一种满足这些要求的策略，并将其应用于来自土耳其小麦驯化假定地点的栽培六倍体小麦（Triticum aestivum，基因组 AABBDD）和野生四倍体小麦（Triticum turgidum ssp. dicoccoides，基因组 AABB）的基因测序。数据用于评估小麦基因组之间和内部的多样性分布，并开发一组多倍体小麦的 SNP 标记。在 2114 个小麦基因中估计了核苷酸多样性，A 和 B 基因组之间的核苷酸多样性相似，但 D 基因组中的核苷酸多样性有所减少。在基因组内，某些染色体的多样性减少了。低多样性总是伴随着过多的稀有等位基因。在1791个小麦基因中总共发现了5471个SNP。在小麦推定二倍体祖先 T. urartu、Aegilops speltoides 和 Ae 的 488、463 和 641 个基因中总共发现了 1,271、1,218 和 2,203 个 SNP。分别是节节。构建了包含基因组特异性引物、SNP 和其他信息的公共数据库。估计一个或多个小麦基因组中总共 987 个具有核苷酸多样性的基因被放置在 Ae 上。节节小麦遗传图谱，并将该图谱叠加在小麦缺失箱图谱上。评估了地图之间的一致性。在年轻的多倍体中，以普通小麦为例，祖先物种是遗传多样性的主要来源。由于自花授粉和多倍体减数分裂期间排除同源染色体配对的遗传机制导致的低有效重组可能导致大染色体区域多样性的丧失。这些因素在普通小麦中的净效应是基因组和染色体之间多样性的巨大变化，这影响了 SNP 标记的开发及其实际应用。较老的多倍体物种（例如野生二粒小麦）中新突变的积累导致多样性增加及其在整个基因组中的分布更加均匀。
A genome-wide assessment of nucleotide diversity in a polyploid species must minimize the inclusion of homoeologous sequences into diversity estimates and reliably allocate individual haplotypes into their respective genomes. The same requirements complicate the development and deployment of single nucleotide polymorphism (SNP) markers in polyploid species. We report here a strategy that satisfies these requirements and deploy it in the sequencing of genes in cultivated hexaploid wheat (Triticum aestivum, genomes AABBDD) and wild tetraploid wheat (Triticum turgidum ssp. dicoccoides, genomes AABB) from the putative site of wheat domestication in Turkey. Data are used to assess the distribution of diversity among and within wheat genomes and to develop a panel of SNP markers for polyploid wheat. Nucleotide diversity was estimated in 2114 wheat genes and was similar between the A and B genomes and reduced in the D genome. Within a genome, diversity was diminished on some chromosomes. Low diversity was always accompanied by an excess of rare alleles. A total of 5,471 SNPs was discovered in 1791 wheat genes. Totals of 1,271, 1,218, and 2,203 SNPs were discovered in 488, 463, and 641 genes of wheat putative diploid ancestors, T. urartu, Aegilops speltoides, and Ae. tauschii, respectively. A public database containing genome-specific primers, SNPs, and other information was constructed. A total of 987 genes with nucleotide diversity estimated in one or more of the wheat genomes was placed on an Ae. tauschii genetic map, and the map was superimposed on wheat deletion-bin maps. The agreement between the maps was assessed. In a young polyploid, exemplified by T. aestivum, ancestral species are the primary source of genetic diversity. Low effective recombination due to self-pollination and a genetic mechanism precluding homoeologous chromosome pairing during polyploid meiosis can lead to the loss of diversity from large chromosomal regions. The net effect of these factors in T. aestivum is large variation in diversity among genomes and chromosomes, which impacts the development of SNP markers and their practical utility. Accumulation of new mutations in older polyploid species, such as wild emmer, results in increased diversity and its more uniform distribution across the genome.
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影响因子：
2.9
作者：
Ching A;Caldwell KS;Jung M;Dolan M;Smith OS;Tingey S;Morgante M;Rafalski AJ
通讯作者：
Rafalski AJ
影响因子：
3
作者：
Beisvag V;Jünge FK;Bergum H;Jølsum L;Lydersen S;Günther CC;Ramampiaro H;Langaas M;Sandvik AK;Laegreid A
通讯作者：
Laegreid A
影响因子：
3.3
作者：
Dvorak, J;Yang, ZL;Luo, MC
通讯作者：
Luo, MC
影响因子：
3.1
作者：
DVORAK, J;MCGUIRE, PE;CASSIDY, B
通讯作者：
CASSIDY, B
影响因子：
3.3
作者：
Dvorak, J.;Deal, K. R.;Luo, M. -C.
通讯作者：
Luo, M. -C.