CLONING, CHARACTERIZATION, AND EVOLUTION OF THE NBS-LRR-ENCODING RESISTANCE GENE ANALOGUE FAMILY IN POLYPLOID COTTON (GOSSYPIUM HIRSUTUM L.)

Authors: HE, L - TEXAS A&M UNIVERSITY; DU, C - MONTCLAIR STATE UNIVERSIT; COVALEDA, L - TEXAS A&M UNIVERSITY; Robinson, Arin; Yu, John; Kohel, Russell; ZHANG, H - TEXAS A&M UNIVERSITY

Submitted to: Molecular Plant-Microbe Interactions
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 6/17/2004
Publication Date: 11/1/2004
Citation: He, L.M., Du, C.G., Covaleda, L., Robinson, A.F., Yu, J., Kohel, R.J., Zhang, H.B. 2004. Cloning, characterization, and evolution of the NBS-LRR-encoding resistance gene analogue family in polyploid cotton (Gossypium hirsutum L.). Molecular Plant-Microbe Interactions. 17(11):1234-1241.

Interpretive Summary: There are thousands of kinds of microscopic fungi, bacteria, viruses, and worms called nematodes, that grow on or in the roots, leaves, stems, and fruit of cotton and other crops, causing plant diseases that debilitate the plants and markedly decrease yields. Scientists studying the DNA of crop plants have found that all plants seem to have a number of genes that make them resistant to these microorganisms. More than 100 such genes have been identified and they have been given the name R genes, or resistance genes. Many more or less similar R genes seem to be shared by a wide range of plants. They are not exactly the same, however, and the specific combination present in a particular plant is very important in determining its relative level of resistance to specific disease causing microorganisms. In this study, 62 of the most common type of R genes from cotton plants were studied in order to find out where they are located on the cotton plant's 52 chromosomes. The results showed that they tend to be clustered on just a few of the 52 chromosomes, and based on the places where they occur it is possible to make some educated guesses about how they evolved and the extent to which groups of them tend to be inherited together. This information will be very useful in the future in understanding plant disease in cotton and in the identification of DNA markers that plant breeders at seed companies can use to simultaneously cut costs and speed up development of new disease-resistant varieties of cotton and other crops for farmers to grow.

Technical Abstract: The NBS-LRR-encoding gene family has attracted research interests of many scientists because approximately 3/4 of the plant disease resistance (R) genes cloned to date are from this gene family. We cloned the NBS-LRR-encoding genes from polyploid cotton by a PCR-based approach using degenerate primers designed based on the conserved NBS motifs of several cloned plant R genes representing the TIR-NBS-LRR and nonTIR-NBS-LRR classes and conferring resistance to bacteria, viruses, fungi and nematodes. A sample of 150 clones was selected from the NBS-LRR gene sequence library and sequenced. Sixty-two resistance gene analogues (RGAs) were identified, suggesting that approximately 40% of the NBS-LRR-encoding genes likely contribute to plant defenses. Sequence analysis revealed that RGAs are abundant and highly diverged in the cotton genome, and they could be categorized into 12 distinct subfamilies based on the similarities of their nucleotide sequences. It was found that the abundances among different subfamilies vary by many fold and they are likely to be at different stages of RGA family evolution. A selected group of RGAs were mapped to an existing cotton genetic map to estimate their distribution on the two subgenomes, A and D, of cotton. The result showed that the cotton RGAs seem to reside on a limited number of the cotton chromosomes, with those from a single subfamily tending to cluster. The distribution of RGAs between the two subgenomes is uneven, with the A subgenome being more abundant in RGAs than the D subgenome. The data provide new insights into the evolution of the NBS-LRR-encoding RGA family in polyploid plants.