Submitted to: Theoretical and Applied Genetics
Publication Type: Peer reviewed journal
Publication Acceptance Date: 9/30/2009
Publication Date: 1/1/2010
Citation: Buriev, Z.T., Saha, S., Abdurakhmonov, I.Y., Jenkins, J.N., Abdukarimov, A., Scheffler, B.E., Stelly, D.M. 2010. Clustering, haplotype diversity and locations of MIC-3: a unique root-specific defense-related gene family in upland cotton (Gossypium hirsutum L.). Theoretical and Applied Genetics. 120:587-606. Interpretive Summary: MIC-3 is a recently identified gene family shown to exhibit increased root-specific expression following nematode infection of cotton plants that are resistant to root-knot nematode (RKN). We cloned and sequenced the members of this gene family to:  determine sequence variation and identify SNPs in MIC-3 family members of the selected diploid and tetraploid species in cotton;  identify haplotypes associated with these MIC-3 family members and  discover the chromosomal location(s) of the MIC-3 family members. SNP markers were identified from MIC-3 genomic sequences of four tetraploid species (Gossypium hirsutum L., G. barbadense L., G. tomentosum L., G. mustelinum L.) and three diploid species (G. herbacium L., G. raimondii L. and G. longicalyx L.). Five different SNP markers, associated with five different MIC-3 family members, were delimited to the short arm of chromosome-4 by deletion analysis. We discovered: 1) SNP markers and haplotypes associated with the MIC-3 gene memebers; 2) the first molecular evidence for the clustering of genes associated with a major pest (RKN) resistance response in cotton; and 3) the chromosomal locations of the MIC-3 gene members. MIC-3-derived candidate gene markers should be very useful in future molecular mapping and functional gene analysis and marker assisted selection.
Technical Abstract: MIC-3-related genes of cotton (Gossypium spp.) were identified and shown to have root-specific expression, associated with pathogen defense-related function and specifically increased expression in root-knot nematode (RKN) resistant plants after nematode infection. Here we cloned and sequenced MIC-3 genes from selected diploid and tetraploid cotton species to reveal structural differences at the molecular level and identify chromosomal locations of MIC-3 genes in Gossypium species. Detailed sequence analysis and phylogenetic clustering of MIC-3 genes indicated the presence of multiple MIC-3 gene members in Gossypium species. Haplotypes of a MIC-3 gene family member were discovered by comparative analysis of consensus sequences across genotypes within the phylogenetic clades. Deficiency tests of the SNPs delimited six At-genome members of the MIC-3 family clustered to chromosome arm 4sh, and one Dt-genome member to chromosome 19. Clustering was confirmed by long-PCR amplification of the intergenetic regions using At-genome-specific MIC-3 primer pairs. The clustered features may have been favored by selection for responsiveness to evolving disease and/or pest pressures. To our knowledge, these are the first results on the evolution of clustering and genome specific (GSP) haplotype members of a unique cotton gene family associated with resistant response against a major pathogen.