Submitted to: Meeting Abstract
Publication Type: Abstract Only
Publication Acceptance Date: 9/10/2006
Publication Date: 9/20/2006
Citation: Buriev, Z., Saha, S., Abdurakhmonov, I.Y., Jenkins, J.N., Abdukarimov, A., Scheffler, B.E., Stelly, D.M., Wubben, M. 2006. A strategy for developing snp markers for the mic-3 root-specific gene family associated with nematode resistance in gossypium spp. [abstract]. Proceedings International Cotton Genome Initiative Conference. Available: http:\\cgi.tamu.edu\pds\icgi06-abs-final.
Technical Abstract: Candidate gene association mapping using SNPs has become a powerful tool to find genes that are associated with complex traits and diseases. SNP discovery in candidate genes of interest is key among the early steps in association mapping. Disomic polyploids such as cotton usually contain two divergent “paralogous” copies of each gene, one per subgenome, which complicates the SNP discovery process due to the presence of duplicate loci. Efficient discovery of any SNP markers needs to distinguish differences between subgenomes as well as allelic variants at a locus. MIC-3 is a recently identified gene shown to exhibit increased root-specific expression following nematode infection of plants that are resistant to root-knot nematode (RKN). We cloned and sequenced PCR-amplicons (derived from MIC-3-specific degenerate primers) from individual plant DNAs to  identify sequence variation;  discover SNPs in MIC-3 family members of selected diploid and tetraploid species in cotton and  discover the chromosomal location(s) of the MIC-3 family members. Phylogenetic trees were constructed based on the analysis of consensus sequences using the most parsimonious algorithm of the PAUP software. SNP markers were discovered from the comparative analysis of the consensus sequences of the tetraploid lines within individual Phylogram clades. Parsimony analysis revealed the presence of several putative haplotype members of MIC-3 gene. BLASTn results suggested that MIC-3 is a novel gene present only in cotton. Five different SNP markers associated with five different MIC-3 family members were delimited to chromosome arm 04sh by hypoaneuploid cytogenetic deficiency tests. Intergenic regions of these clustered genes were localized to the same chromosome arm, further confirming their clustering and physical location within the cotton genome. Chromosomal localization via deletion analysis would be possible only if the associated SNP marker could detect variation at a single locus. In addition, the phylogenetic tree suggested significant homology of the clustered MIC-3 members with the diploid ancestral A-genome. Recombination among the clustered genes associated with disease and pest resistance may confer evolutionary robustness to the organism by creating new variants that might offer opportunities for response to selection pressures from evolving pests and pathogens.