DArTseq molecular markers associated with the piping leaf margin phenotype in pineapple (Ananas comosus L.)

This study sought to understand the genetic basis of the piping leaf margin phenotype in pineapple. To achieve this aim, a genome-wide association study (GWAS) using mixed linear regression and logistic regression analysis was conducted on three pineapple diversity panels including seedling populations segregating for spiny, spiny-tip and piping leaf margins. This study identified single nucleotide polymorphism (SNP) markers associated with the piping and spiny-tip leaf margin phenotypes. A broad quantitative trait locus (QTL) positioned on chromosome 23 between positions 240,475 and 2,369,197 bp was the most highly associated with piping leaf margin in all analyses. Major candidate genes proposed are a Zinc finger protein 2, a Zinc finger protein 3, a WUSCHEL-related homeobox 2, a WUSCHEL-related homeobox 1 and a Zinc finger protein CONSTANS-like. Some other genes of a lower association, linked or nearby genes of interest, are also considered potentially involved to varying degrees. All candidate genes are known to be involved in aspects of stem cell maintenance, cell proliferation, epidermal cell differentiation, organogenesis, leaf polarity, cell wall modification or hormone signalling. It is possible each plays a role in either differentiation or morphological aspects of the spiny-tip and piping leaf margin phenotypes. It is expected the relative role of each associated gene might vary with genetic background.