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 [1] determine sequence
variation and identify SNPs in MIC-3 family members of selected diploid and tetraploid
species in cotton; [2] identify haplotypes
associated with these MIC-3 family
members and [3] 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, G. barbadense, G. tomentosum, G. mustelinum) and three diploid species (G. herbacium, G. raimondii
and G. longicalyx). Phylogenetic trees
were constructed based on the most parsimonious algorithm of the PAUP software.
Comparative analysis of tetraploid sequences
within individual clade of the Phylogram
suggested several putative haplotype variants. 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 similarly located on the same chromosome arm. Multiple
sequence alignments of consensus sequences of MIC-3 family members showed high level of homology with the GenBank EST sequences, isolated from the Fusarium wilt and
RKN infected cotton roots. Results
suggested that some members of MIC-3
gene family were associated with the response to RKN and Fusarium oxysporum f. sp. vasinfectum infection. It has been reported previously that RKN
increases the incidence and severity of cotton to Fusarium wilt. The findings
document a strategy for developing SNP markers for candidate genes in cotton, demonstrate
the clustered organization of various MIC-3
family members, and provide molecular evidence on the association of a
candidate gene with both Fusarium
wilt and RKN diseases in cotton.