Usefulness of WRKY gene-derived markers for assessing genetic population structure: An example with Florida coconut cultivars

Abstract

We previously analyzed genetic diversity and population structure of eight cultivars within Florida coconut ( Cocos nucifera L.) germplasm using 15 microsatellite (simple sequence repeat, SSR) markers. Here we report on the analysis of the same genotypes using 13 markers derived from WRKY sequences containing single nucleotide polymorphisms (SNP) and one microsatellite. WRKY transcription factors are unique to plants and are involved in numerous vital processes including disease resistance. Our objective was to determine the value of this type of gene to assess the genetic diversity of this species. Overall, the WRKY results are similar to those with microsatellite markers. Despite the lower number of alleles identified with the WRKY-derived markers (37 versus 67 total alleles identified with the SSR markers), individuals of cultivars ‘Red Malayan Dwarf’, ‘Fiji Dwarf’ (‘Niu Leka’) and ‘Red Spicata’ were clearly clustered, as in the previous analysis. However, individuals of ‘Green Malayan Dwarf’ and ‘Yellow Malayan Dwarf’ cultivars were resolved with other varieties, perhaps due to selective forces operating on these functional genes. Most samples of the ‘Atlantic Tall’ and ‘Panama Tall’ cultivars clustered together as in the previous microsatellite study. We discuss the utility of WRKY-derived markers for assessing the genetic diversity of coconut, and their possible value in the study of other species.