Clustering, haplotype diversity and locations of MIC-3: a unique root-specific defense-related gene family in Upland cotton (Gossypium hirsutum L.).
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 A(t)-genome members of the MIC-3 family clustered to chromosome arm 4sh, and one D(t)-genome member to chromosome 19. Clustering was confirmed by long-PCR amplification of the intergenic regions using A(t)-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.
Buriev
Zabardast T
ZT
Center of Genomic Technologies, Institute of Genetics and Plant Experimental Biology, Academy of Sciences of Uzbekistan, Yuqori Yuz, Qibray Region, 111226 Tashkent, Uzbekistan. zabar75@yahoo.com
Saha
Sukumar
S
Abdurakhmonov
Ibrokhim Y
IY
Jenkins
Johnie N
JN
Abdukarimov
Abdusattor
A
Scheffler
Brian E
BE
Stelly
David M
DM
D001483:Base Sequence; D032461:Chromosomes, Plant / Q000235:genetics; D016000:Cluster Analysis; D021901:DNA, Intergenic / Q000235:genetics; D017753:Ecosystem; D004587:Electrophoresis, Agar Gel; D017343:Genes, Plant / Q000235:genetics; D014644:Genetic Variation; D003368:Gossypium / Q000235:genetics* / Q000276:immunology*; D006239:Haplotypes / Q000235:genetics*; D005810:Multigene Family / Q000235:genetics*; D009928:Organ Specificity / Q000235:genetics; D010802:Phylogeny; D018517:Plant Roots / Q000235:genetics*; D015203:Reproducibility of Results
D021901:DNA, Intergenic