%0 Journal Article
%T Development of New Candidate Gene and EST-Based Molecular Markers for Gossypium Species
%A Ramesh Buyyarapu
%A Ramesh V. Kantety
%A John Z. Yu
%A Sukumar Saha
%A Govind C. Sharma
%J International Journal of Plant Genomics
%D 2011
%I Hindawi Publishing Corporation
%R 10.1155/2011/894598
%X New source of molecular markers accelerate 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 EST sequences that were used for polymorphism detection followed by genetic and physical mapping. Nineteen gene-based markers were surveyed for polymorphism detection in 26 Gossypium species. Cluster analysis generated a phylogenetic tree with four major sub-clusters for 23 species while three species branched out individually. CAP method enhanced the rate of polymorphism of candidate gene-based markers between G. hirsutum and G. barbadense. Two hundred A-genome based SSR markers were designed after datamining of G. arboreum EST sequences (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 RIL population and formed 14 linkage groups. Chromosomal localization of both candidate gene-based and MGAES markers was assisted by euploid and 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. 1. Introduction Molecular markers provide valuable information in assessing the genetic variability, generating linkage maps, enabling better understanding of the genome organization, and deciphering quantitative trait loci (QTLs). Initial effort to map the cotton genome using an F2 population utilized 705 restriction fragment length polymorphism (RFLP) probes that were polymorphic between G. hirsutum and G. barbadense and generated 41 linkage groups spanning 4675£¿cM [1]. Genetic variation at molecular level in cotton has been characterized using isozyme/allozyme markers [2], RFLPs [1, 3, 4], AFLPs [5, 6], and microsatellites [7, 8] in G. hirsutum and its related species. A comprehensive comparative genetic map with 2584£¿loci at ~1.72£¿cM intervals for tetraploid (AtDt) cotton and with 662 loci at ~1.96£¿cM intervals for diploid (D) genome was constructed using RFLPs, genomic SSRs, and sequence tagged sites (STS) as probes [9]. Advances in technology have facilitated sequencing of complete transcriptomes and genomes that are accessible through public domain databases. Increasing number of expressed sequence tags (ESTs) for cotton facilitated the identification of simple sequence repeat (SSR) regions from the ESTs through data mining
%U http://www.hindawi.com/journals/ijpg/2011/894598/