|Van Deynze, Allen|
Submitted to: Plant and Animal Genome Conference Proceedings
Publication Type: Abstract Only
Publication Acceptance Date: 12/10/2007
Publication Date: 1/12/2008
Citation: Van Deynze, A., Lund, J., Yu, J., Kohel, R.J., Yang, S.S., Stelly, D.M. 2008. The utility of a 384 illumina bead array in cotton [abstract]. In: Proceedings of Plant and Animal Genome XVI Conference, January 12-16, 2008, San Diego, California. Paper No. W252. Interpretive Summary:
Technical Abstract: Development of high-throughput (HT) marker platforms for cotton would make it possible to take greater advantage of pre-existing and new resources for germplasm introgression and genome analysis of the cultivated cottons G. hirsutum (Gh) and G. barbadense (Gb). Among new resources are  191 recombinant inbred lines (RILs) developed from the Gh*Gb interspecific cross between genetics standards TM-1*3-79,  quasi-isogenic Gh chromosome substitutions from Gb (CS-B lines) and, soon, G. tomentosum (Gt) and G. mustelinum (Gm), and  wide-cross whole-genome radiation hybrids for physical mapping. Chromosome-specific RILs are also forthcoming. In addition, population-based methods are being used for genome-wide introgression of novel alleles from G. longicalyx (Gl), G. armourianum (Ga), Gm and Gt into Gh using combinations of backcrossing, selfing, and intermating. HT comparisons across derived populations will make possible extensive analyses of alien chromosome retention as it relates to phenotypic performance and efficiency of breeding schemes to transfer traits from exotic germplasm. Toward empowering public cotton research with HT capabilities, we have recently identified 1158 SNPs from 282 loci and 315 indels from 92 loci segregating in Gh and Gb. Furthermore we have genotyped these loci across a standard panel of 24 lines, 16 of which are Gh breeding lines and 8 mapping parents of populations from various cottons including Gh, Gb, G. arboreum, G. raimondii, G. mustelinum, G. tomentosum. A 384 Illumina bead array was developed to implement these markers in breeding programs. The loci were selected for their polymorphism between a core mapping population, TM-1 and 3-79 and in G. hirsutum breeding germplasm. This array was used to genotype some of the populations described above, for which results will be presented.