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ARS Home » Southeast Area » Mississippi State, Mississippi » Crop Science Research Laboratory » Genetics and Sustainable Agriculture Research » Research » Publications at this Location » Publication #200138

Title: Development of Gene-based Markers and their Chromosomal Localization in Cotton (Gossypium sp.)

item Saha, Sukumar
item Yu, John
item SHARMA, G

Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 1/13/2007
Publication Date: 1/13/2007
Citation: Buyyarapu, R., Kantety, R., Saha, S., Yu, J., Soliman, K., Sharma, G. 2007. Development of gene-based markers and their chromosomal localization in cotton (Gossypium sp.). Plant and Animal Genome Conference. p. 118.

Interpretive Summary:

Technical Abstract: Molecular markers are being used extensively in genetic studies and breeding programs of cotton. A majority of the marker systems were developed based on random genomic sequences, mainly due to the dearth of polymorphism detection systems that can distinguish fine differences in genetic regions between different genotypes. Therefore, an objective of our research program is to develop and map gene-based markers for cotton through the use of improved bioinformatics tools and polymorphism detection systems. Here, we report our initial attempts in marker development using candidate genes and expressed sequence tags (ESTs). Using twenty primer pairs for different candidate genes in cotton, we screened for polymorphism by polyacrylamide gel electrophoresis (PAGE) and derived phylogenetic relationships among 32 genotypes that include 12 genotypes that make cotton microsatellite database (CMD) panel and other diploid and tetraploid genotypes. Polymorphism information content (PIC) for these markers ranged from 0.84 - 0.997. We were able to localize five of these markers to chromosomes in the tetraploid genome using 17 chromosome substitution lines. A subset of the SSR-containing ESTs of G. arboreum EST database was used for designing 200 primer-pairs which were designated (MGAES) markers. One hundred and forty seven (74%) MGAES primer-pairs were successful in amplifying the two reference genotypes, TM-1 and Pima 3-79. A total of sixty five (44%) EST-SSR markers displayed fragment length polymorphism on polyacrylamide gels. The candidate gene and EST-SSR markers will be genetically mapped using the recombinant inbred line (RIL) population developed from the cross of TM-1 (G. hirsutum) and 3-79 (G. barbadense).