Plant disease resistance gene (R gene); defense response gene encode some conserved motifs. In the present work, a PCR strategy was used to clone resistance gene analogs (RGAs); defense gene analogs (DGAs) from Sea-island cotton variety Hai7124 using oligonucleotide primers based on the nucleotide-binding site (NBS); serine/threonine kinase (STK) in the R-gene; pathogenesis-related proteins of class 2 (PR2) of defense response gene. 79 NBS sequences, 21 STK sequences; 11 DGAs were cloned from disease-resistance cotton. Phylogenic analysis of 79 NBS-RGAs; NBS-RGAs nucleotide sequences of cotton already deposited in GenBank identified one new sub-cluster. The deduced amino acid sequences of NBS-RGAs; STK-RGAs were divided into two distinct groups respectively: Toll/Interleukin-1 receptor (TIR) group; non-TIR group, A group; B group. The expression of RGAs; DGAs having consecutive open reading frame (ORF) was also investigated; it was found that 6 NBS-RGAs; 1 STK-RGA were induced,; 1 DGA was up-regulated by infection of Verticillium dahliae strain VD8. 4 TIR-NBS-RGAs; 4 non-TIR-NBS-RGAs were arbitrarily used as probes for Southern-blotting. There existed 2–10 blotted bands. In addition, since three non-TIR-NBS-RGAs have the same hybridization pattern, we conjecture that these three RGAs form a cluster distribution in the genome.
