Clustering, haplotype diversity and locations of MIC-3: a unique root-specific defense-related gene family in Upland cotton (Gossypium hirsutum L.)

• Published in: Theoretical and applied genetics Vol. 120; no. 3; pp. 587 - 606
• Main Authors: Buriev, Zabardast T, Saha, Sukumar, Abdurakhmonov, Ibrokhim Y, Jenkins, Johnie N, Abdukarimov, Abdusattor, Scheffler, Brian E, Stelly, David M
• Format: Journal Article
• Language: English
• Published: Berlin/Heidelberg Berlin/Heidelberg : Springer-Verlag 01.02.2010; Springer-Verlag; Springer; Springer Nature B.V
• Subjects: Agriculture; Base Sequence; Biochemistry; Biological and medical sciences; Biomedical and Life Sciences; Biotechnology; chromosome mapping; Chromosomes, Plant - genetics; Classical genetics, quantitative genetics, hybrids; Cluster Analysis; cotton; DNA, Intergenic - genetics; Ecosystem; Electrophoresis, Agar Gel; Fundamental and applied biological sciences. Psychology; genes; Genes, Plant - genetics; Genetic aspects; Genetic Variation; Genetics of eukaryotes. Biological and molecular evolution; Gossypium; Gossypium - genetics; Gossypium - immunology; Gossypium hirsutum; Haplotypes; Haplotypes - genetics; Identification and classification; Life Sciences; MIC-3 genes; molecular cloning; multigene family; Multigene Family - genetics; Nematoda; nucleotide sequences; Organ Specificity - genetics; Original Paper; pest resistance; Phylogeny; Plant Biochemistry; Plant Breeding/Biotechnology; Plant Genetics and Genomics; Plant immunology; Plant Roots - genetics; Pteridophyta, spermatophyta; Reproducibility of Results; root-knot nematodes; roots; Vegetals; Gossypium Species; Cotton Genome; Cotton Genotype; Cotton Root; Tetraploid Cotton; Malvaceae; Root; Dicotyledones; Angiospermae; Diversity; Genetics; Multigene family; Spermatophyta; Agriculture; Organism defense; Gossypium hirsutum; Haplotype
• ISSN: 0040-5752; 1432-2242
• DOI: 10.1007/s00122-009-1178-z

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. Here, we cloned and sequenced MIC-3 genes from selected diploid and tetraploid cotton species to reveal sequence 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 among consensus sequences across genotypes within an individual clade in the phylogram to overcome the problem of duplicated loci in the tetraploid cotton. 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 intergenic regions using At-genome-specific MIC-3 primer pairs. The clustered distribution may have been favored by selection for responsiveness to evolving disease and/or pest pressures, because large variants of the MIC-3 gene family may have been recovered from small physical areas by recombination. This could give a buffer against selection pressure from a broad range of pest and pathogens in the future. To our knowledge, these are the first results on the evolution of clustering and genome-specific haplotype members of a unique cotton gene family associated with resistant response against a major pathogen.