Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea).
Isolation and characterization of novel microsatellite markers and their application for diversity assessment in cultivated groundnut (Arachis hypogaea).
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DOI：
10.1186/1471-2229-8-55
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发表时间：
2008-05-15
影响因子：
5.3
通讯作者：
Varshney, Rajeev K.
中科院分区：
文献类型：
--
作者：
Cuc, Luu M.;Mace, Emma S.;Crouch, Jonathan H.;Quang, Vu D.;Long, Tran D.;Varshney, Rajeev K.
栽培花生（arachhis hypogaea L.）是世界上第四大油料作物，主要生长在热带、亚热带和暖温带气候。由于栽培花生起源于单一和近期的多倍体事件，随后在育种努力中进行了连续的选择，因此栽培花生的遗传背景有限。在这些物种中，微卫星或简单序列重复（SSR）标记对育种应用非常有用。然而，栽培花生种质资源的多态性水平较低，因此需要大量的多态微卫星标记。利用TMV2基因型构建了微卫星富集文库。从总共3072个样本中对720个推测ssr阳性的克隆进行测序，得到490个ssr。完全型占71.2%，不完全型占13.1%，复合型占15.7%。其中，GT/CA重复基序最为常见（37.6%），其次是GA/CT重复基序（25.9%）。共设计了170个ssr引物对，并对两个基因型进行了初步优化。在32个栽培花生基因型中，有104对（61.2%）引物扩增出可得分的扩增子，46对（44.2%）引物多态性。多态性SSR标记检测到2 ~ 5个等位基因，平均每个位点2.44个。多态性信息含量（PIC）值在0.12 ~ 0.75之间变化，平均为0.46。以46个标记获得的112个等位基因为基础，构建了32个基因型的表型图。代表亚种的大部分基因型集中在一个聚类中，而属于亚种的基因型主要集中在两个聚类中。新开发的104个SSR标记扩展了栽培花生的SSR标记库。这些标记在栽培种质中具有较高的PIC值，可用于栽培花生及其近缘种的种质分析、连锁作图、多样性研究和系统发育关系研究。
Cultivated peanut or groundnut (Arachis hypogaea L.) is the fourth most important oilseed crop in the world, grown mainly in tropical, subtropical and warm temperate climates. Due to its origin through a single and recent polyploidization event, followed by successive selection during breeding efforts, cultivated groundnut has a limited genetic background. In such species, microsatellite or simple sequence repeat (SSR) markers are very informative and useful for breeding applications. The low level of polymorphism in cultivated germplasm, however, warrants a need of larger number of polymorphic microsatellite markers for cultivated groundnut. A microsatellite-enriched library was constructed from the genotype TMV2. Sequencing of 720 putative SSR-positive clones from a total of 3,072 provided 490 SSRs. 71.2% of these SSRs were perfect type, 13.1% were imperfect and 15.7% were compound. Among these SSRs, the GT/CA repeat motifs were the most common (37.6%) followed by GA/CT repeat motifs (25.9%). The primer pairs could be designed for a total of 170 SSRs and were optimized initially on two genotypes. 104 (61.2%) primer pairs yielded scorable amplicon and 46 (44.2%) primers showed polymorphism among 32 cultivated groundnut genotypes. The polymorphic SSR markers detected 2 to 5 alleles with an average of 2.44 per locus. The polymorphic information content (PIC) value for these markers varied from 0.12 to 0.75 with an average of 0.46. Based on 112 alleles obtained by 46 markers, a phenogram was constructed to understand the relationships among the 32 genotypes. Majority of the genotypes representing subspecies hypogaea were grouped together in one cluster, while the genotypes belonging to subspecies fastigiata were grouped mainly under two clusters. Newly developed set of 104 markers extends the repertoire of SSR markers for cultivated groundnut. These markers showed a good level of PIC value in cultivated germplasm and therefore would be very useful for germplasm analysis, linkage mapping, diversity studies and phylogenetic relationships in cultivated groundnut as well as related Arachis species.
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影响因子：
5.3
作者：
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通讯作者：
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2
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1.9
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