Simple sequence repeat marker development from bacterial artificial chromosome end sequences and expressed sequence tags of flax (Linum usitatissimum L.).
Simple sequence repeat marker development from bacterial artificial chromosome end sequences and expressed sequence tags of flax (Linum usitatissimum L.).
复制标题
DOI：
10.1007/s00122-012-1860-4
复制
发表时间：
2012-08
影响因子：
5.4
通讯作者：
Ragupathy, Raja
中科院分区：
文献类型：
--
作者：
Cloutier, Sylvie;Miranda, Evelyn;Ward, Kerry;Radovanovic, Natasa;Reimer, Elsa;Walichnowski, Andrzej;Datla, Raju;Rowland, Gordon;Duguid, Scott;Ragupathy, Raja
亚麻是北美洲一种重要的油料作物，在欧洲主要作为纤维作物种植。作为一种自花授粉的二倍体，其预估的基因组大小约为370Mb，很适合在基因组学方面快速取得进展。在过去几年中，为这种作物开发了重要的遗传资源。在此，我们描述了对1506个假定的简单重复序列（SSR）的评估和比较分析，其中1164个来自细菌人工染色体末端序列（BES），342个来自表达序列标签（EST）。这些SSR在一组16个亚麻品种上进行了评估，其中673对（58%）BES引物和145对（42%）EST引物分别具有多态性。本研究报道了818对新的多态性SSR引物，亚麻可用的SSR数量比以往所有报道的508对的总和增加了一倍多。在核苷酸基序中，无论类别如何，三核苷酸都是最丰富的，但二核苷酸是多态性最高的。SSR长度也与多态性呈正相关。两种二核苷酸（AT/TA和AG/GA）以及两种三核苷酸（AAT/ATA/TAA和GAA/AGA/AAG）基序及其重复序列，与许多其他作物所报道的不同，占所有SSR的一半以上，并且比其他标记（42.7%）具有更高的多态性（63.4%）。这种改进的资源有望在遗传、数量性状位点（QTL）和关联图谱分析以及将物理/遗传图谱与亚麻全基因组鸟枪法参考序列锚定方面发挥作用。
本文的网络版（doi:10.1007/s00122 - 012 - 1860 - 4）包含补充材料，授权用户可获取。
Flax is an important oilseed crop in North America and is mostly grown as a fibre crop in Europe. As a self-pollinated diploid with a small estimated genome size of ~370 Mb, flax is well suited for fast progress in genomics. In the last few years, important genetic resources have been developed for this crop. Here, we describe the assessment and comparative analyses of 1,506 putative simple sequence repeats (SSRs) of which, 1,164 were derived from BAC-end sequences (BESs) and 342 from expressed sequence tags (ESTs). The SSRs were assessed on a panel of 16 flax accessions with 673 (58 %) and 145 (42 %) primer pairs being polymorphic in the BESs and ESTs, respectively. With 818 novel polymorphic SSR primer pairs reported in this study, the repertoire of available SSRs in flax has more than doubled from the combined total of 508 of all previous reports. Among nucleotide motifs, trinucleotides were the most abundant irrespective of the class, but dinucleotides were the most polymorphic. SSR length was also positively correlated with polymorphism. Two dinucleotide (AT/TA and AG/GA) and two trinucleotide (AAT/ATA/TAA and GAA/AGA/AAG) motifs and their iterations, different from those reported in many other crops, accounted for more than half of all the SSRs and were also more polymorphic (63.4 %) than the rest of the markers (42.7 %). This improved resource promises to be useful in genetic, quantitative trait loci (QTL) and association mapping as well as for anchoring the physical/genetic map with the whole genome shotgun reference sequence of flax. The online version of this article (doi:10.1007/s00122-012-1860-4) contains supplementary material, which is available to authorized users.
登录
查看更多内容
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
影响因子：
3.1
作者：
Han, ZG;Guo, WZ;Zhang, TZ
通讯作者：
Zhang, TZ
影响因子：
5.4
作者：
Choudhary, Shalu;Sethy, Niroj Kumar;Bhatia, Sabhyata
通讯作者：
Bhatia, Sabhyata
影响因子：
5.2
作者：
Cordeiro, GM;Casu, R;Henry, RJ
通讯作者：
Henry, RJ
RCPdb： 含重复蛋白质的进化分类和密码子使用数据库
影响因子：
7
作者：
Faux, Noel G.;Huttley, Gavin A.;Whisstock, James C.
通讯作者：
Whisstock, James C.