Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh].
Development of genic-SSR markers by deep transcriptome sequencing in pigeonpea [Cajanus cajan (L.) Millspaugh].
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DOI：
10.1186/1471-2229-11-17
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发表时间：
2011-01-20
影响因子：
5.3
通讯作者：
Singh NK
中科院分区：
文献类型：
--
作者：
Dutta S;Kumawat G;Singh BP;Gupta DK;Singh S;Dogra V;Gaikwad K;Sharma TR;Raje RS;Bandhopadhya TK;Datta S;Singh MN;Bashasab F;Kulwal P;Wanjari KB;K Varshney R;Cook DR;Singh NK
木豆[Cajanus cajan (L.) Millspaugh]是半干旱热带和亚热带地区最重要的食用豆类之一，其基因组资源有限，特别是基于表达序列（基因）的标记。我们利用深度转录组测序报道了一套经过验证的基因简单序列重复（SSR）标记，并阐述了其在遗传多样性分析和作图中的应用。
在本研究中，从分别取自两个木豆品种（Asha和UPAS 120）的叶、根、茎和未成熟种子的混合cDNA文库的169.6万个454 GS - FLX序列读数中组装出43324个转录组鸟枪法组装单基因重叠群。共鉴定出3771个基因 - SSR位点（不包括同聚物和复合重复序列）；其中为标记开发设计了2877对PCR引物。二核苷酸是最常见的重复基序，频率为60.41%，其次是三核苷酸（34.52%）、六核苷酸（2.62%）、四核苷酸（1.67%）和五核苷酸（0.76%）重复基序。合成了引物并对其中772个重复长度≥18bp的位点进行了测试。其中，550个标记在8个不同的木豆品种中被验证能稳定扩增；71个在琼脂糖凝胶电泳中被发现具有多态性。利用20个高度多态性的基因 - SSR标记对22个木豆品种和8个野生种进行了遗传多样性分析。这些位点的等位基因数量在4 - 10个之间，多态性信息含量值在0.46到0.72之间。邻接聚类图显示木豆栽培品种和野生种的不同群体有明显的分离。对两个亲本系进行深度转录组测序有助于通过计算机鉴定多态性基因 - SSR位点，以促进种内参考遗传图谱的快速构建，其中一部分在参考作图群体中被验证具有预期的等位基因分离。
我们利用深度转录组测序在木豆中开发了550个经过验证的基因 - SSR标记。从中选取20个高度多态性的标记用于评估木豆属物种间的遗传关系。开发的一套全面的基因 - SSR标记是木豆多样性分析和遗传作图的重要基因组资源。
Pigeonpea [Cajanus cajan (L.) Millspaugh], one of the most important food legumes of semi-arid tropical and subtropical regions, has limited genomic resources, particularly expressed sequence based (genic) markers. We report a comprehensive set of validated genic simple sequence repeat (SSR) markers using deep transcriptome sequencing, and its application in genetic diversity analysis and mapping. In this study, 43,324 transcriptome shotgun assembly unigene contigs were assembled from 1.696 million 454 GS-FLX sequence reads of separate pooled cDNA libraries prepared from leaf, root, stem and immature seed of two pigeonpea varieties, Asha and UPAS 120. A total of 3,771 genic-SSR loci, excluding homopolymeric and compound repeats, were identified; of which 2,877 PCR primer pairs were designed for marker development. Dinucleotide was the most common repeat motif with a frequency of 60.41%, followed by tri- (34.52%), hexa- (2.62%), tetra- (1.67%) and pentanucleotide (0.76%) repeat motifs. Primers were synthesized and tested for 772 of these loci with repeat lengths of ≥18 bp. Of these, 550 markers were validated for consistent amplification in eight diverse pigeonpea varieties; 71 were found to be polymorphic on agarose gel electrophoresis. Genetic diversity analysis was done on 22 pigeonpea varieties and eight wild species using 20 highly polymorphic genic-SSR markers. The number of alleles at these loci ranged from 4-10 and the polymorphism information content values ranged from 0.46 to 0.72. Neighbor-joining dendrogram showed distinct separation of the different groups of pigeonpea cultivars and wild species. Deep transcriptome sequencing of the two parental lines helped in silico identification of polymorphic genic-SSR loci to facilitate the rapid development of an intra-species reference genetic map, a subset of which was validated for expected allelic segregation in the reference mapping population. We developed 550 validated genic-SSR markers in pigeonpea using deep transcriptome sequencing. From these, 20 highly polymorphic markers were used to evaluate the genetic relationship among species of the genus Cajanus. A comprehensive set of genic-SSR markers was developed as an important genomic resource for diversity analysis and genetic mapping in pigeonpea.
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影响因子：
4.4
作者：
Luro, Francois L.;Costantino, Gilles;Terol, Javier;Argout, Xavier;Allario, Thierry;Wincker, Patrick;Talon, Manuel;Ollitrault, Patrick;Morillon, Raphael
通讯作者：
Morillon, Raphael
影响因子：
5.4
作者：
Fraser, LG;Harvey, CF;De Silva, HN
通讯作者：
De Silva, HN
影响因子：
5.4
作者：
RATNAPARKHE, MB;GUPTA, VS;RANJEKAR, PK
通讯作者：
RANJEKAR, PK
DOI：
10.1046/j.1471-8278.2001.00109.x
发表时间：
2001-12-01
期刊：
MOLECULAR ECOLOGY NOTES
影响因子：
--
作者：
Burns, MJ;Edwards, KJ;Baggott, CD
通讯作者：
Baggott, CD
影响因子：
3.1
作者：
Han, ZG;Guo, WZ;Zhang, TZ
通讯作者：
Zhang, TZ