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Genetic mapping of new cotton fiber loci usingEST-derived microsatellites in and recombinant inbred lines cotton populationAbstract:there is an immediate need for a high density genetic map of cotton embeddedwith fiber genes to facilitate marker assisted selection (MAS) for improvedfiber traits. With the goal in mind, genetic mapping with a new set of amicrosatellite markers was performed on 183 recombinant inbred lines developedfrom the progeny of the interspecific cross Gossypium  hirsutum L. cv.

TM1* Gossypium barbadense L.Pima  3-79. Microsatellite developedusing 1557 ESTs containing SSRs and 5794 EST containing CSRs obtained from thecultivated diploid species Gossypium arboreum L. ,  AKA8401.

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From a total of 1232 EST derived SSRand CSR primer pairs, 1019 successfully amplified PCR products from a surveypanel of six Gossypium species; 202 were polymorphic between the G. hirsutum L.and G. barbadense L. parents of the interspecific mapping population.

Amongthese polymorphic markers, only 86 showed significant sequence homology toannotated genes with known functions. The chromosomal locations of 36microsatellites were associated with 14 chromosomes or 13 chromosomes arms ofthe cotton genome by hypoaneuploid deficiency analysis, enabling us to assigngenetic linkage groups to specific chromosomes. The resulting genetic mapconsists of 193 loci, including 121 new fiber loci not previously mapped. Thesefiber loci were mapped to 19 chromosomes and 11 LG spanning 1277 cM, providingapproximately trait loci analysis suggested that chromosomes 2, 3, 15, and 18may harbor genes for trait related to fiber quality. These new PCR basesmicrosatellite markers derived from cotton fiber ESTs will facilitate thedevelopment of a high resolution integrated genetic map of cotton forstructural and functional study of fiber genes and MAS of genes that enhancefiber quality.

Results:Grownin more than 80, countries cotton is a major cropp and important renewableresource, privoiding the world’s leading natural fiber for the manufacture oftextiles.    Cotton belongs to the genusGossypium, which consists of at least 45 diploid and five allo-tetraploidspecies. Gossypium barbadense are modern allotetraploid cottons, which togetherrepresent the most extensively cultivated species worldwide. While Gh is themost widely cultivated species—prized for its higher yield and widerenvironmental adaptation, Gb boasts vastly superior fiber quality. Theallotetraplloid species are thought to have formed about 1.1-1.9 million yearsago after polypoidization event that brought together the genomes of diploidsclosely related to Gossypium herbaceum L. or Gossypium arboretum and Gossypiumraimondii and were domesticated through extensive human selection.

A genomediploid cottons produce spinnable fibers and have been cultivated. While D-genomespecies produce very short and appressed fibers. However, many quantitativetrait loci for fiber traits have been associated with D-subgenome inallotetraploid cottons indicating that the D genome contributes to fibermorphogenesis and the determination of fiber properties.Themain goals of cotton breeding programs wordwide are the genetic enhancement ofyield and, more recently, fiber quality. Improvement for fiber properties isrequired to keep pace with the rapid changes taking place in the technology ofthe manufacturing procedure. Key fiber quality traits, such as fiber elongation,length, fitness and bundle strength are controlled by QTLs, which complicateconventional breeding for fiber improvement.

Molecular markers offer efficienttools for dissecting QTLs affecting traits with complex genetic inheritance,and facilitate marker-assisted selection and map based cloning.Improvingcotton fiber quality while maintaining fiber yield is a challenging task forconventional breeding, because of the negative association between thesetwo  traits and the genetic complexity offiber QTLs. The genetic enhancement of fiber traits can be facilitated by usingmolecular approaches, such as the construction of a high density genetic mapbased on functionally embedded fiber genes and by subsequent molecular taggingof fiber QTLs for MAS. As a step

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