Identification of cotton (Gossypium L.) chromosome substitution lines microsatellite markers

Cotton (Gossypium L.) is the most important natural fiber source for the textile industry and also an important oil crops world-wide. Several species of cotton are mainly grown as an important crop in more than 70 countries including China, USA, India and Uzbekistan. Although cotton plants are best known as the source of textile materials for clothing, the fiber, seed and plants have many other uses, including home insulation to save energy, protein-rich seed-derived feed for animals, cottonseed oil as a foodstuff for humans, and as a source of mulch and biomass.Cotton breeding studies rely primarily on crosses among closely related elite domesticated genotypes with high yield and superior fiber qualities, and on reselection from existing cultivars. Cotton breeding programs suffer from the narrow genetic base within the cultivated species. This encouraged the researchers to use of interspecific introgression lines. However there are several problems in interspecific introgression studies including complex antagonistic relationships among important traits; cytogenetic differences among the species due to different ploidy levels and chromosomal structural differences including translocations and inversions; linkage drag effects leading to poor agronomic qualities; reduced recombination; loss of alien genetic materials in early generations; sterility in the hybrids; complex genetic interactions such as Muller-Dobzhansky complexes and distorted segregation. However, the use of chromosome substitution lines in cotton breeding programs could solve several problems of interspecific introgression studies mentioned above.To data in cotton, a set of 17 disomic alien chromosome substitution lines, which consist of chromosome pair or chromosome arm pair of G. barbadense Pima 3-79 (CS-B) have been developed through hypoaneuploid-based backcrossing in a near-isogenic genetic background of Texas Marker-1 (TM-1) line. However, there are no reports on molecular markers developed for marker assisted selection (MAS) studies of hybrids between CS-B x CS-B and CS-B x any line or identification of CS-B lines.This study was conducted to identify genic microsatellite (EST-SSR), genomic microsatellite and CAPS-microsatellite markers to identify and determine each 17 CS-B of cotton substitution lines. Furthermore this study is also utilized 17 CS-B substitution line to identify chromosome locations of novel DNA markers.A total of 55 DNA samples obtained from 17 CS-B lines, TM-1 and Pima 3-79 were used in microsatellite and CAPS-microsatellite studies. Based on a total of 3 set genomic DNA samples and more than 225 loci the following results were obtained.In this study genic and genomic molecular markers were determined for the identification of each chromosome substitution lines (CS-B) with the exception of CS-B05Sh, CS-B12Sh, CS-B15Sh and CS-B25.In this study molecular markers were identified to differentiate TM-1 and its isogenic line whose chromosomes or chromosome arms were substituted with G. barbadense. This study clearly showed that all the CS-B lines were genetically identical with the exception of chromosomes or chromosome arms of G. barbadense Pima 3 -79.In this study results clearly showed that some CS-B lines contained physical contamination with other CS-B lines. Those CS-B lines containing physical contamination with other CS-B lines present in the research unit are required further studies using individual plant from the lines.In this study it was found that several CS-B lines have lost several alleles of loci or translocated within the genome of CS-B lines. Further studies are required to confirm translocation and the mode of chromosome translocation using new DNA markers.In this study it was found that chromosome substitution lines could be successfully used to locate DNA markers on chromosome or chromosome arm. A total of 16 MK loci were assigned to chromosome or chromosome arms in this study.In conclusion, results of this study revealed that those CS-B lines confirmed using molecular markers could be successfully used in cultivar development studies. In addition these CS-B lines could be used in genetic and gene interactions studies of fiber length, liber strength and fineness.