Genetics. Published Articles Ahead of Print: April 3, 2007, Copyright © 2007
doi:10.1534/genetics.107.070375


A more recent version of this article appeared on May 1, 2007.

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A microsatellite-based, gene-rich linkage map reveals genome structure, function, and evolution in Gossypium

Wangzhen Guo 1, Caiping Cai 1, Changbiao Wang 1, Zhiguo Han 1, Xianliang Song 1, Kai Wang 1, Xiaowei Niu 1, Cheng Wang 1, Keyu Lu 1, Ben Shi 1 and Tianzhen Zhang 1*

1 Cotton Research Institute

* To whom correspondence should be addressed. E-mail: cotton{at}njau.edu.cn.

Submitted on January 10, 2007
Revised on February 14, 2007
Accepted on 27 February 2007


Abstract

The mapping of functional genes plays an important role in studies of genome structure, function, and evolution, as well as allowing gene cloning and marker-assisted selection to improve agriculturally-important traits. Simple sequence repeats (SSRs) developed from expressed sequence tags (ESTs), EST-SSR (eSSR), can be employed as putative functional marker loci to easily tag corresponding functional genes. In this paper, 2,218 eSSRs, 1,554 from G. raimondii-derived and 754 from G. hirsutum-derived ESTs, were developed and used to screen polymorphisms in order to enhance our backbone genetic map in allotetraploid cotton. Out of 1,554 G. raimondii-derived eSSRs, 744 eSSRs were able to successfully amplify polymorphisms between our two mapping parents, TM-1 and Hai7124, presenting a polymorphic rate of 47.9%. However, an only 23.9% (159/754) polymorphic rate was produced from G. hirsutum-derived eSSRs. No relationship was observed between the level of polymorphism, motif type, and tissue origin, but the polymorphism appeared to be correlated with repeat type. After integrating these new eSSRs, our enhanced genetic map consists of 1,790 loci in 26 linkage groups and covers 3425.8 cM with an average inter-marker distance of 1.91 cM. This microsatellite-based, gene-rich linkage map contains 71.96% functional marker loci, of which 87.11% are eSSR loci. There were 132 duplicated loci bridging 13 homeologous At/Dt chromosome pairs. Two reciprocal translocations after polyploidization between A2 and A3, and between A4 and A5 chromosomes were further confirmed. A functional analysis of 975 ESTs producing 1,122 eSSR loci tagged in the map revealed that 60% had clear BLASTX hits (<1e-10) to the Uniprot database and that 475 were mainly associated with genes belonging to the three major gene ontology categories of biological-process, cellular-component, and molecular-function; many of the ESTs were associated with two or more category functions. The results presented here will provide new insights for future investigations of functional and evolutionary genomics, especially those associated with cotton fiber improvement.

Key Words: cotton, functional marker, genetic mapping




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