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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Publications at this Location » Publication #221820

Title: Developement of gene and EST-based markers and their chromosomal localization in cotton

item Saha, Sukumar
item Yu, John

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 12/10/2006
Publication Date: 1/12/2007
Citation: Buyyarapu, R., Kantety, R., Saha, S., Yu, J., Soliman, K., Sharma, G. 2007. Developement of gene and EST-based markers and their chromosomal localization in cotton [abstract]. In: Proceedings of Plant and Animal Genome XV Conference, January 13-17, 2007, San Diego, California. Paper No. P118.

Interpretive Summary:

Technical Abstract: Molecular markers are being used extensively in genetic studies and breeding programs of cotton. To screen the limited genetic diversity in cotton germplasm, we focused our efforts to develop candidate gene and expressed sequence tag (EST) based markers and in finding polymorphisms between genotypes at high resolution. We screened for polymorphism in twenty candidate genes by polyacrylamide gel electrophoresis (PAGE) and derived phylogenetic relationships among 32 genotypes that include 12 genotypes that make cotton microsatellite database (CMD) panel and 20 other Gossypium species. Polymorphism information content (PIC) for these markers ranged from 0.84 – 0.997. Cleaved Amplified Polymorphism (CAP) between G. hirsutum (TM-1) and G. barbadense (Pima 3-79) was detected for 12 of the 20 primer pairs using RsaI, MspI, HhaI, and HaeIII restriction enzymes. We localized five of these markers to chromosomes in the tetraploid genome using chromosome substitution lines of G. barbadense (CS-B) in G. hirsutum background. Similarly, 200 Mississippi Gossypium arboreum EST-SSR (MGAES) primer pairs were developed and screened for polymorphism between G. hirsutum and G. barbadense. 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. Candidate gene and EST based markers were genetically mapped using G. hirsutum (TM-1) X G. barbadense (Pima 3-79) recombinant inbred line (RIL) population and placed to different chromosomes using17 CS-B lines, 44 G. tomentosum and 41 G. barbadense aneuploid lines (USDA, Mississippi State, MS).