Identification and characterization of ClAPRR2, a key candidate gene controlling watermelon stripe color

The stripe color of watermelon is a vital commercial trait and is the focus of attention of consumers and researchers. However, the genetic determinants of watermelon stripe color are incompletely understood. Based on the results of preliminary localization studies, we constructed a large-capacity F₂ generation population (710 plants) using light-green striped ZXG1555 and green-striped Cream of Saskatchewan (COS) watermelon strains as parental lines for fine mapping. Genes controlling stripe color were located in an 85.284 kb region on chromosome 9, which contained five candidate genes. Combined with parental phenotypes, chlorophyll contents of rinds and stripes were assayed. Gene sequence alignment and transcriptional level analysis of parental lines predicted Cla97C09G175170 (encoding a two-component response regulator-like protein, APRR2) as the best candidate gene for stripe color trait. Two SNPs in the ClAPRR2 coding region caused amino acid substitutions, but were not located in the conserved domain, while a 12 bp insertion caused premature translation termination and a 35 amino acid deletion in the conserved domain and may have affected ClAPRR2 function in ZXG1555. Subcellular localization analysis showed that ClAPRR2 was expressed in the ZXG1555 cell membrane but was located in the nucleus and cell membrane of COS. Nucleotide polymorphisms and deletions were also detected in the promoter region between parental lines and caused cis-acting element variations. Luciferase activity suggested that promoter variations may not be the main factor in the regulation of ClAPRR2 expression.