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United States Department of Agriculture

Agricultural Research Service

Research Project: COTTON GENOMICS AND GENETIC ANALYSIS Title: Development of new candidate gene and EST-based molecular markers for Gossypium species

Authors
item Buyyarapu, Ramesh -
item Kantety, Ramesh -
item Yu, John
item Saha, Sukumar
item Sharma, Govind -

Submitted to: International Journal of Plant Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: November 9, 2011
Publication Date: December 1, 2011
Citation: Buyyarapu, R., Kantety, R.V., Yu, J., Saha, S., Sharma, G.C. 2011. Development of new candidate gene and EST-based molecular markers for Gossypium species. International Journal of Plant Genomics. 2011:Article 894598.

Interpretive Summary: New molecular markers were developed for cotton fiber improvement and genetic map integration. Nineteen DNA markers were developed from functional genes of Upland cotton and 200 DNA markers were derived from an expressed sequence tag (EST) library of an Asiatic cotton. Some of these markers were converted via the cleaved amplified fragment polymorphism (CAP) technique. The CAP markers detected a high genetic diversity (58%) among the cotton accessions and they were physically located to seven chromosomes via a technique called deletion analysis. Sixty-five EST-derived markers that showed a DNA polymorphism between TM-1 and 3-79, the parents of 186 recombinant inbred lines (RILs) were mapped to 14 linkage groups that were physically assigned to 11 chromosomes. These new molecular markers were highly informative as were developed from the candidate genes and the fiber transcript collection. They provide useful resources for cotton genetic improvement with a potential to be integrated into existing cotton genome maps.

Technical Abstract: New source of molecular markers accelerates the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum expressed sequence tag (EST) sequences, and validated them through amplification, genetic and physical mapping. Nineteen gene-based markers were successfully amplified across five tetraploid and 21 diploid Gossypium species. Cluster analysis of fragment data generated a phylogenetic tree with four major sub-clusters for 23 species while three species branched out individually. A higher level of polymorphism (~58%) was observed through the use of cleaved amplified fragment polymorphism (CAP) techniques between G. hirstutum and G. barbadense. Euploid G. barbadense chromosome substitution (CS-B) lines were employed to locate the 11 CAPs markers of which five CAPs markers were localized to seven different chromosomes in the cotton genome. Two hundred A-genome based simple sequence repeat (SSR) markers were designed after data mining of G. arboreum ESTs (Mississippi Gossypium arboreum EST-SSR – MGAES). Over 70% of MGAES markers successfully produced amplicons while 65 of them demonstrated polymorphism between the parents of G. hirsutum and G. barbadense recombinant inbred line (RIL) population. When used to determine linkage relationships among them, MGAES markers formed 14 linkage groups that were assigned to 11 chromosomes and 11 chromosome arms in cotton genome through the use of euploid/hypoaneuploid CS-B analysis. Gene-based and MGAES markers were highly informative as they were designed from candidate genes and fiber transcriptome with a potential to be integrated into the existing cotton genetic and physical maps.

Last Modified: 10/31/2014
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