Functional Markers for Cellulose Synthase and Their Comparison to SSRs in Cotton

Abstract

Cellulose synthase genes are very important in cotton, where they are involved in both fiber development and plant architecture. In order to make use of these genes in cotton genetics and breeding, we developed functional markers using in silico single nucleotide polymorphism (SNP) identification and Primer-BLAST designing gene-specific markers. A total of 10 SNP markers and 82 gene-specific markers were developed. Of these, 39 markers showed polymorphism between cotton species, generating 74 polymorphic loci. These markers can identify genotypes from different species. However, unlike simple sequence repeats (SSRs), they cannot distinguish 3-79 and DP340, and some genotypes differently clustered under functional marker examination than under SSR examination. Genetic similarity coefficients, measured by functional markers and SSRs, are highly correlated, indicating that these functional markers are very effective. Results also show that the development of gene-specific markers is an effective way of developing functional markers in cotton.