ARS | Publication request: WRKY AND RESISTANCE GENE HOMOLOGUE SEQUENCES AS GENETIC MARKERS IN COCONUT (COCOS NUCIFERA) USING SSCP

Submitted to: Plant and Animal Genome Conference
Publication Type: Abstract
Publication Acceptance Date: January 5, 2006
Publication Date: N/A

Technical Abstract: Candidate genes, such as those involved in the stress response of plants to their environment, can be useful for the differentiation of cultivars. We designed degenerate primers for WRKY and resistance gene homologue (RGH) sequences that were tested in several coconut genotypes (two genotypes for the WRKY primers and four for the RGH primers). Several amplification products were obtained. PCR fragments were cloned and sequenced. Sequences were assembled in clusters to evaluate the possible number of loci obtained with each primer pair. Twenty-one potential loci were identified with the WRKY primers based on sequence clustering. Four clusters plus four distinct sequences were found among the RGH amplification products. Clusters were examined for the presence of single nucleotide polymorphisms (SNPs). We designed primers flanking the SNPs identified for each locus/cluster. Both primers flanking the SNPs were fluorescently labeled. Single strand conformational polymorphism analysis (SSCP) was used to determine the level of polymorphism among fifty genotypes. We report the successful utilization of these markers in the differentiation of some coconut cultivars.