Identification of DNA marker for root-knot nematode resistance gene and characterization of disease resistance gene candidates in cotton

Abstract

Cotton is the leading textile fiber and the second most important oilseed in the world. Disease is one of the most significant limiting biotic constraints in cotton production. Therefore, breeding for resistance to different diseases has been a major target in cotton breeding. To enhance the efficiency of the breeding process, it is necessary to develop molecular tools for marker-assisted selection and germplasm analysis. This research focused on investigation of the underlying genetics of root-knot nematode resistance (RNR) in Auburn 623 - one of the most desirable sources for RNR in Upland cottons, identification of DNA markers for the RNR genes and characterization of disease resistance gene candidates in cotton. Genetic analysis indicates that the Auburn 623 RNR is likely to be controlled by two linked and additive genes. Six RAPD fragments that differentiate RNR lines from root-knot nematode susceptible lines were identified. Of these six markers, R12 is the most promising DNA marker for RNR. It is not only present in all resistant lines and absent in all susceptible lines tested, but also present as a single-copy in the cotton genomes. To characterize the genes conferring resistance to different pathogens, including fungi, bacteria, viruses and nematodes, in cotton, resistance gene candidates were cloned by PCR using a pair of degenerate primers designed from the conserved sequences of disease resistance genes cloned from a variety of plant taxa. From a 96-clone sample, 23 were identified to share high similarities (>85%) at the nucleotide sequence level to disease resistance genes cloned from different plant species. These clones were categorized into three groups based on the similarity of their sequences. RFLP mapping techniques were used to map these resistance gene candidates against an existing genetic map. Sixteen of them were mapped, nine being mapped to a single linkage group (U4), whereas the remaining 7 clones being located to six linkage groups (A1, A3, 6, 20b, 23 and U3), respectively. These results have provided valuable resources and tools for detailed characterization of genes conferring resistance to different pathogens and final cloning of the genes for RNR in cotton.