ARS | Publication request: Addition of Four-hundred Fifty-five Microsatellite Marker Loci to the High Density Gossypium hirsutum TM-1 x G. barbadense 3-79 Genetic Map

Submitted to: Journal of Cotton Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: July 11, 2012
Publication Date: December 5, 2012
Citation: Fang, D.D., Yu, J. 2012. Addition of Four-hundred Fifty-five Microsatellite Marker Loci to the High Density Gossypium hirsutum TM-1 x G. barbadense 3-79 Genetic Map. Journal of Cotton Science. 16, 229-248.

Interpretive Summary: A high density genetic map is very important to the studies such as understanding genome structure of cultivated cotton, dissecting economically important traits, using molecular markers to assist breeding, and cloning a gene of interest through map-based cloning strategy. Four hundred fifty five new microsatellite (a kind of DNA marker type), also known as simple sequence repeat (SSR) marker loci were added to the previously published 2072-loci genetic map that was constructed using 186 recombinant inbred lines from an interspecific cross between Upland cotton Gossypium hirsutum TM-1 and Pima cotton G. barbadense 3-79. The new high density map contained 2527 loci and covered 3430 cM with an average interval between two loci of 1.36 cM. An addition of 455 new marker loci (a net increase 21.96%) resulted in only 50 cM or 1.78% net increase of total genetic distance, but reduced the number of large gaps (>10 cM) from 21 to 13. About 400 pairs of duplicate SSR loci were present in this map. Most duplicate loci were mapped between chromosomes that are suggested as homeologous (partially homologous in origin, sequences and structure). Duplicate loci within a chromosome were observed in at least ten chromosomes. Telomeric regions (tips of a chromosome) are hot spots for intra-chromosomal loci duplication. This high density map is a saturated genetic map of tetraploid cotton genome whose total genetic distance is estimated around 3500 cM. This map will facilitate more in-depth study on tetraploid cotton genome structure, whole-genome physical alignment, sequencing, and mapping of genes for cotton improvement.

Technical Abstract: A high density genetic linkage map plays important roles in understanding genome structure of tetraploid cotton, dissecting economically important traits, identifying molecular markers associated with a trait, and cloning a gene of interest through map-based cloning strategy. Four hundred fifty five new microsatellite, also known as simple sequence repeat (SSR) marker loci were added to the previously published 2072-loci genetic map that was constructed using 186 recombinant inbred lines from an interspecific cross between Gossypium hirsutum TM-1 and G. barbadense 3-79. The new high density map contained 2527 loci (2280 SSRs and 247 SNPs) and covered 3430 cM with an average marker interval of 1.36 cM. An addition of 455 new marker loci (a net increase 21.96%) resulted in only 50 cM or 1.78% net increase of total genetic distance, but reduced the number of large gaps (>10 cM) from 21 to 13. About 400 pairs of duplicate SSR loci were present in this map. Most duplicate loci were mapped between homeologous chromosomes. Duplicate loci within a chromosome were observed in at least ten chromosomes. It is intriguing to note that the telomeric regions are hot spots for intra-chromosomal loci duplication. This high density map is a saturated genetic map of tetraploid cotton genome whose total genetic distance is estimated around 3500 cM. This map will facilitate more in-depth study on tetraploid cotton genome structure, whole-genome physical alignment, sequencing, and mapping of genes for cotton improvement.