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Title of Journal: Chin Sci Bull

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Abbravation: Chinese Science Bulletin

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SP Science China Press

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DOI

10.1007/bf00939308

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ISSN

1861-9541

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Mining characterization and exploitation of EST

Authors: YuanDa Lü CaiPing Cai Lei Wang ShaoYan Lin Liang Zhao LiangLiang Tian JunHong Lü TianZhen Zhang WangZhen Guo
Publish Date: 2010/06/13
Volume: 55, Issue: 18, Pages: 1889-1893
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Abstract

Simple sequence repeats SSRs have been widely applied as molecular markers in genetic studies However the number of expressed sequence tags ESTs and SSR markers from Gossypium barbadense is fewer than those from other cotton species In this study ESTSSR distribution from G barbadense was characterized and new G barbadensederived ESTSSR markers were determined on the basis of the ESTs obtained by randomly sequencing 2 cDNA libraries associated with fiber development in G barbadense By mining 9697 nonredundant ESTs a total of 638 SSR loci derived from 595 ESTs were observed In G barbadense the frequency of ESTs containing SSRs was 613 with an average of 1 SSR in every 104 kb of EST sequence Furthermore trinucleotide was found to be the most abundant repeat type among 2–6nucleotide repeat types It accounted for 266 of the total followed by the hexanucleotide 260 and pentanucleotide repeats 259 Among all the repeat motifs AAGn accounted for the highest proportion ESTSSR primer pairs were developed using the Primer3 program and the redundant primers were removed using the virtual PCR approach As a result 380 nonredundant ESTSSR primer pairs were developed and used to detect polymorphisms between the mapping parents G hirsutum ‘TM1’ and G barbadense ‘Hai7124’ for constructing linkage groups in cultivated allotetraploid cotton Out of these 98 258 primer pairs detected polymorphisms Finally 95 polymorphic loci from 82 primer pairs were integrated into the backbone genetic map of these 42 were mapped into the A subgenome and 53 into the D subgenome The present work provided the foundation for constructing saturated genetic maps and conducting comparative genomic studies on different cotton species

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