Submitted to: Molecular Genetics and Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/1/2005
Publication Date: 7/1/2005
Citation: Park, Y.H., Alabady, M.S., Ulloa, M., Sickler, B., Wilkins, T.A., Yu, J., Stelly, D.M., Kohel, R.J., El-Shihy, O.M., Cantrell, R.G. 2005. Genetic mapping of new cotton fiber loci using EST-derived microsatellites in an interspecific recombinant inbred line cotton population. Mol. Genet.Genom. 274:428-441.
Interpretive Summary: Cotton is one of the world’s most important fiber crops and efforts continue to improve the fiber qualities. While traditional breeding techniques are time consuming and laborious molecular genetic techniques may accelerate the process of improving commercial cotton. Toward this goal, a genetic map was developed with a new set of molecular markers (e.g., EST-derived microsatellites, or simple (SSR) and complex (CSR) sequence repeat markers) that can identify specific fragments of DNA. Microsatellites were developed from 1,232 ESTs (expressed genes) in cotton fibers. Assignment of these markers to specific chromosomes is essential so the genes can be followed during the breeding process. The genetic map identifies that 121 new genes, some of which control fiber qualities are located across 19 chromosomes spanning approximately 25% of the cotton genome. Analysis of marker-fiber trait associations revealed that chromosome 2, 3, 15 and 18 may harbor fiber quality-related genes. These data are useful to scientists involved in cotton breeding because most of these microsatellite markers provide information about fiber and other functional genes. These markers, in addition to assisting selection of fiber quality related genes, may be useful in the analysis of the genome of cotton.
Technical Abstract: There is an immediate need for a high-density genetic map of cotton anchored with fiber genes to facilitate marker-assisted selection (MAS) to improve important fiber traits. Toward this goal, genetic mapping with a new set of microsatellites, or simple (SSR) and complex (CSR) sequence repeat markers, was performed on 183 recombinant inbred lines (RIL) from the interspecific cross Gossypium hirsutum L. cv. TM1 x G. barbadense L. Pima 3-79. Microsatellites were developed using 1,557 EST-containing SSRs (>10bp) and 5,794 EST-containing CSRs (>12bp) sequences obtained from ~14,000 assembled fiber EST consensus sequences generated from the cultivated diploid species Gossypium arboreum L. cv AKA8401. From a total of 1,232 EST-derived SSR (MUSS) and CSR (MUCS) primer-pairs, 1,019 (83%) of the DNA markers successfully amplified PCR products from a survey panel of six Gossypium species, of which 202 (19.8%) were polymorphic between the G. hirsutum L. and G. barbadense L. parents of an interspecific mapping population. Among these polymorphic markers, only 86 (42.6%) showed significant sequence homology to annotated genes with known function. The chromosomal locations of 36 microsatellites were associated with 14 chromosomes and/or 13 chromosome arms of the cotton genome by hypoaneuploid deficiency analysis to assign genetic linkage groups to specific chromosomes. The resulting genetic map consists of 193 loci, including 121 new fiber loci not previously mapped. These fiber loci were mapped to 19 chromosomes and 11 linkage groups spanning 1,277 centiMorgans (cM), providing approximately 25 % genome coverage. Preliminary QTL analysis suggested that chromosomes 2, 3, 15 and 18 may harbor fiber quality-related gene-traits. These new PCR-based microsatellite DNA markers derived from cotton fiber ESTs will enhance development of a high resolution integrated cotton genetic map for structural and functional study of fiber genes and marker-assisted selection (MAS) of fiber quality-related genes.