W208 Development of a Whole Genome Marker Map Based on the Cotton D-genome Sequence of Gossypium raimondii

Date: Sunday, January 15, 2012
Time: 4:10 PM
Room: Pacific Salon 3
Zining Wang , Plant Genome Mapping Lab - University of Georgia, Athens, GA
Dong Zhang , Plant Genome Mapping Lab - University of Georgia, Athens, GA
Xiyin Wang , Plant Genome Mapping Lab - University of Georgia, Athens, GA
Andrew Paterson , Plant Genome Mapping Lab - University of Georgia, Athens, GA
Whole genome marker maps (WGMM) are very useful tools for gene cloning, genome evolution studies and comparative genetic studies. WGMMs have been constructed for some genomes, such as rice and sorghum, using the whole genome sequence and SNP information. Recently, the cotton D-genome of Gossypium raimondii was sequenced and assembled. Even though only 1,005 cotton SNPs are available publicly, about 19,976 SSR and RFLP markers have been discovered, and a subset of these used, by the cotton research community. In this study, we constructed a whole genome marker map using all SSR, RFLP and SNP markers available. About 20,000 markers were assigned to 80,000 loci on the D-genome. A subset of 962 genetically mapped markers were used as anchoring markers to align the genome sequence and genetic maps, including locations along cotton consensus, At and Dt chromosomes. The genetic distance of the non-anchoring markers were interpolated by using the two nearest anchoring markers.  The average map density of 11 kb per marker is far higher than any individual genetic map for cotton. Annotated genes and QTLs were also assigned to their corresponding locations on the genome. It is anticipated that there will be substantial enrichment for whole genome SNPs, as several SNP discovery efforts mature. This map will be of high value for identifying markers to map closely-related germplasm (where DNA polymorphism is rare so many markers must be screened), as well as to facilitate fine mapping and identification of candidate genes. A whole genome marker map mitigates many obstacles associated with use of different genetic maps, unifying these resources. With the markers, annotated genes and trait locations on the chromosomes, this map will increase the efficiency of cotton gene cloning. The high quality D-genome marker map will be also a very useful tool for genome evolution and comparative studies.