Identification and characterization of candidate genes controlling fruit shape and size in pepper

Pepper (Capsicum annum L.), a member of the Solanaceae family, is an economically important crop, being used worldwide as a vegetable, spice and food additive. Pepper fruits show a remarkable range of morphological variation, particularly in terms of shape and size. These traits are important factors determining yield, quality and consumer acceptability for many crops. In tomato, the major QTL affecting fruit shape and size have been identified, and for some of them, including ovate, sun, fasciated (fas) and fw3.2, the underlying genes have been cloned (OVATE, SUN, FAS and KLUH, respectively). In pepper, among the several fruit shape and size QTL identified so far, only the OVATE gene has been cloned. In this study, using comparative analysis, the putative ORFs of SUN, FAS and KLUH genes have been identified in pepper (namely CaSUN, CaFAS, and CaKLUH). CaFAS and CaSUN, consisting of 540 bp and 1248 bp, were predicted to encode proteins of 179 and 415 amino acid residues, respectively. The deduced amino acid sequences of CaFAS and CaSUN showed the YABBY and IQ67 domains, respectively. In addition, CaKLUH ORF consisting of 1551 bp was also isolated and cloned. Amino acid sequence alignments revealed that CaKLUH shares high sequence identity with cytochrome P450 78A4-like of Solanum lycopersicum (XP_004236064; 100%). In order to assess the structure of CaKLUH gene, we also cloned the genomic sequence. Alignment between the genomic and cDNA sequences revealed that the CaKLUH gene spanned 2.4 Kb in length and was organized into 2 exons and 1 intron. The expression patterns of the three putative genes were determined by Real-Time PCR in different organs and development stages of four pepper cultivars characterized by different fruit shapes and sizes. For functional analysis, development of TRV based VIGS vectors is in progress.