Genetics and comparative molecular mapping of biochemical and morphological fruit characters in Capsicum
Authors: Paran Ilan , Jahn Molly 
Published: December 2021

Original objectives: The overall goal of our work was to gain information regarding the genetic and molecular control of pathways leading to the production of secondary metabolites determining major fruit quality traits in pepper and to develop tools based on this information to assist in crop improvement. The specific objectives were to: (1) Generate a molecular map of pepper based on simple sequence repeat (SSR) markers. (2) Map QTL for capsaicinoid (pungency) content (3) Determine possible association between capsaicinoid and carotenoid content and structural genes for capsaicinoid and carotenoid biosynthesis. (4) Map QTL for quantitative traits controlling additional fruit traits. (5) Map fruit-specific ESTs and determine possible association with fruit QTL (6) Map the C locus that determines the presence and absence of capsaicinoid in pepper fruit and identify candidate genes for C.locus. Background: Pungency, color, fruit shape and fruit size are among the most important fruit quality characteristics of pepper. Despite the importance of the pepper crop both in the USA and Israel, the genetic basis of these traits was poorly understood prior to the studies conducted in the present proposal. In addition, molecular tools for use in pepper improvement were lacking. Major conclusions and achievements: Our studies enabled the development of a saturated genetic map of pepper that includes numerous SSR markers. This map has been integrated with a number of other independent maps resulting in the publication of a single resource map consisting of more than 2000 markers. Unlike previous maps based primarily on tomato-originated RFLP markers, the new maps are based on PCR markers that originate in Capsicum providing a comprehensive and versatile resource for marker-assisted selection in pepper. We determined the genetic and molecular bases of qualitative and quantitative variation of pungency, a character unique to pepper fruit. We mapped and subsequently cloned the Pun1 gene that serves as a master regulatoar for capsaicinoid accumulation and showed that it is an acyltransferase. By sequencing the Pun1 gene in pungent and non-pungent cultivars we identified a deletion that abolishes the expression of the gene in the latter cultivars. We also identified QTL that control capsaicinoid content and therefore pungency level. These genes will allow pepper breeders to manipulate the level of pungency for specific agricultural and industrial purposes. In addition to pungency we identified genes and QTL that control other key developmental processes of fruit development such as color, texture and fruit shape. The A gene controlling anthocyanin accumulation in the immature fruit was found as the ortholog of the petunia transcription factor Anthocyanin2. The S gene required for the soft flesh and deciduous fruit nature typical of wild peppers was identified as the ortholog of tomato polygalacturonase. We identified two major QTL controlling fruit shape, fs3.1 and fs10.1, that differentiate elongated and blocky and round fruit shapes, respectively. Scientific and agricultural implications: Our studies allowed significant advances in our understanding of important processes of pepper fruit development including the isolation and characterization of several well known genes. These results also provided the basis for the development of molecular tools that can be implemented for pepper improvement. A total of eleven refereed publications have resulted from this work, and several more are in preparation.