ARS | Publication request: AFLP-RGA Markers in Comparison with RGA and AFLP in Cultivated Tetraploid Cotton

Submitted to: Crop Science
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: March 1, 2007
Publication Date: May 1, 2007
Citation: Zhang, J., Yuan, Y., Niu, C., Hinchliffe, D.J., Lu, Y., Yu, S., Percy, R.G., Ulloa, M., Cantrell, R.G. 2007. AFLP-RGA markers in comparison with RGA and AFLP in cultivated tetraploid cotton. Crop Science 47:180-187.

Interpretive Summary: The development of molecular markers and molecular mapping of cotton and will provide a means of identifying and locating genes for cotton improvement. The use of markers can subsequently greatly increase the speed and efficiency of cotton improvement efforts. However, to date, insufficient markers have been developed to adequately map cotton. This research has developed a new method for creating markers to use in cotton, and thus has increased the potential number of markers available to researchers. The methodology also has created a means to locate potential resistance genes to diseases of cotton. While the immediate impact of this accomplishment will be to the researcher, the potential of identifying resistance genes to disease impacts industry and the consumer.

Technical Abstract: Disease resistance (R) genes have been isolated in many plant species and R genes with domains of nucleotide binding sites (NBS) and leucine rich repeats (LRR) represent the largest R gene family. The objective of this investigation was to test a resistance gene analog (RGA) anchored marker system, called amplified fragment length polymorphism (AFLP)-RGA in cotton (Gossypium spp.). The AFLP-RGA analysis uses one degenerate RGA primer designed from various NBS and LRR domains of R genes in combination with one selective AFLP primer in a PCR reaction. Out of a total of 446 AFLP-RGA bands amplified by 22 AFLP-RGA primer combinations, 76 (17.0%) and 37 (8.3%) were polymorphic within four upland cotton (Gossypium hirsutum L.) genotypes and four Pima cotton (G. barbadense L.) genotypes, respectively. The number of polymorphic AFLP-RGA bands (256) between G. hirsutum and G. barbadense was much higher (57.4%). This level of polymorphism mirrors that of AFLP. The genetic similarity between the eight genotypes based on AFLP-RGA or AFLP lead to similar results in genotype grouping at the species and intraspecies level. AFLP-RGA offers a great flexibility for numerous primer combinations in a genome-wide search for RGAs. Genome-wide AFLP-RGA analysis provides a useful resource for candidate gene mapping of R genes for disease resistance in cotton.