Abstract
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.
Highlights
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)
Cotton fiber genes were mapped with expressed sequence tags (ESTs)-derived simple sequence repeat (SSR) loci using recombinant inbred line (RIL) population derived from an interspecific cross between G. hirsutum × G. barbadense
Using the abundant sequence information available for G. arboreum fiber ESTs in GenBank, we designed over 700 nonredundant primer pairs based on the identification of the SSR regions, and tested 200 primer pairs using the two major cultivated tetraploid species G. hirsutum (TM-1) and G. barbadense (3–79), the parents for RIL population used in this study
Summary
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].
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