Fine genetic mapping of the Mottled Rind Color (Morc) locus reveals a 4895-bp presence-absence variation contributing to the mottled or unmottled fruit rind color in cucumber

Abstract

Rind color and pattern is the crucial fruit trait that preferentially affects the commercial consumption of cucumber (Cucumis sativus L.). Knowing the genetic architecture of fruit rind color and pattern is essential for improving cucumber external qualities. However, the genetic basis of cucumber fruit rind patterns is still unclear, especially for the phenotypic variation of mottled or unmottled (uniform) fruit rind color. To explore the genetic architecture of mottled fruit rind color in cucumber, we constructed F2 segregating populations using two cucumber inbred lines WI7632 and XNS16–1 showing green mottled rind color and white uniform rind color, respectively. Inheritance analysis revealed that the mottled rind color in WI7632 is genetically controlled by a dominant locus Morc (Mottled rind color). Chlorophyll content determination and chloroplast observation show that the mottled fruit rind color in WI7632 might be due to the decrease of chlorophyll synthesis caused by abnormal chloroplast development at particular fruit rind areas. Fine genetic mapping delimited the Morc locus into a 29.5-kb physical region on chromosome 5, which included only one candidate gene CsaV3_5G028870 encoding a C2H2-type zinc finger transcription factor. Sequence alignment showed that CsaV3_5G028870 and its flanking region (4895-bp in size) were missed in unmottled XNS16–1. Transcriptome profiling revealed that Morc might regulate the biosynthesis balance of heme and chlorophyll. Furthermore, the pleiotropic effects and diverse functions of Morc locus on determining multiple cucumber fruit's external qualities were discussed.