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ARS Home » Plains Area » College Station, Texas » Southern Plains Agricultural Research Center » Crop Germplasm Research » Research » Publications at this Location » Publication #220908

Title: Separation of homologous BAC contigs in the tetraploid Upland cotton

item Kohel, Russell
item Cho, Jaemin
item YU, JING
item Yu, John

Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 12/10/2007
Publication Date: 1/12/2008
Citation: Xu, Z., Kohel, R.J., Song, G., Cho, J., Yu, J., Dong, J., Tomkins, J., Yu, J. 2008. Separation of homologous BAC contigs in the tetraploid Upland cotton [abstract]. In: Proceedings of Plant and Animal Genome XVI Conference, January 12-16, 2008, San Diego, California. Paper No. P212.

Interpretive Summary:

Technical Abstract: Upland cotton has an allotetraploid genome. Separation of homologous BAC contigs to their sub-genomes and further to individual chromosomes is a great challenge for genome-wide integrated genetic and physical mapping. As a pilot experiment to test the feasibility of separating the contigs in sub-genome At from the contigs in subgenome Dt, 166 and 128 markers with whole fragment sequences that were genetically mapped to chromosomes 12 and 26 were collected to design Overgo primers to develop an integrated genetic and physical map for one pair of homoeologous chromosomes 12 and 26 in Upland cotton. Both chromosome-specific and locus-specific markers were used for the contig separation. New SSR markers were developed from both BAC-end sequences and BAC sub-clone sequences for mixed contigs. The results show that about 70% of the contigs were anchored to chromosomes 12 and 26 unambiguously, and 30% of the contigs needed more markers to locate them in the chromosomes. Homologous contigs identified by markers are being sequenced to verify the contigs and homologous rate between the two chromosomes. Our preliminary data show that the strategy and procedure used for the contig separation is capable to separate the contigs to their chromosomes at genome-wide level.