Characterization of EST-derived microsatellites in the wheat genome and development of eSSR markers

被引：178

作者：

Peng J.H. ^{[1
]}

Lapitan N.L.V. ^{[1
]}

机构：

[1] Department of Soil and Crop Sciences, Colorado State University, Fort Collins

来源：

Functional & Integrative Genomics | 2005年 / 5卷 / 2期

基金：

美国国家科学基金会;

关键词：

Chromosome bin maps; EST-derived simple sequence repeats (eSSR); Expressed sequence tags (EST); Molecular markers; Triticeae;

D O I：

10.1007/s10142-004-0128-8

中图分类号：

学科分类号：

摘要：

EST-derived microsatellites or simple sequence repeats (eSSR) occur in expressed sequence tags (EST). Here we report characteristics of eSSRs in the wheat genome, construction of consensus chromosome bin maps of SSR-containing ESTs (SSRESTs), and development of eSSR markers for the 21 wheat chromosomes. A Perl script known as MISA was used to identify eSSRs in wheat ESTs available in the database http://wheat.pw.usda.gov/cgi-bin/ace/search/wEST). Among 492,832 ESTs from the database, 36,520 (7.41%) contained 43,598 eSSRs. This is equivalent to 1 eSSR per 5.46 kb EST sequence. About 60% of the eSSRs were trinucleotides, 19.7% were mononucleotide, 16.7% were dinucleotides, and the remaining ∼3% consisted of tetra-, penta-, and hexanucleotides. Among the identified eSSRs, (CCG/CGG)n is the most frequent (20.5%) followed by (A/T)n at 13.6%, (AAC/GTT)n at 11.7%, and (AG/CT)n at 8.7%. Among ESTs previously mapped to wheat chromosome bins, a total of 1,010 eSSR loci were derived from 341 SSRESTs. Consensus chromosome bin maps showing the chromosome locations of SSRESTs, SSR sequence motif, and cDNA library were constructed. A χ2 test indicated that the distribution pattern of eSSR loci was generally similar to that of the original mapped ESTs in the wheat genome. Forty-eight SSRESTs were converted into PCR-based eSSR markers, and 266 eSSR loci were mapped to specific chromosome arms using wheat cytogenetic stocks. The average polymorphism information content (0.45±0.16) of eSSR markers was lower than that reported for genomic SSRs (0.54±0.19), but higher than RFLPs (0.30±0.27). The eSSR markers were transferable among related Triticeae species, Triticum aestivum, T. durum, T. dicoccoides, Hordeum spontaneum, H. vulgare, and Secale cereale. The results confirm the presence of SSRs in expressed genes of wheat and demonstrate another application of ESTs in genomics research. eSSRs will be useful for gene tagging, gene cloning, and comparative genomics studies of cereal crops. © Springer-Verlag 2005.

引用

页码：80 / 96

页数：16

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