Genetic structure analysis and selection of a core collection for carob tree germplasm conservation and management

Abstract

Carob (Ceratonia siliqua L.) is an important evergreen tree of the Mediterranean landscape. Its economic interest is increasing thanks also to the presence, in the seeds, of the locust bean gum (LBG), a galactomannan largely used by the food industry as a stabilizer and thickening agent. Its economic and ecological values make the understanding of carob genetic diversity of great interest both for breeding and conservation purposes. The world’s largest carob germplasm collection was genotyped using both eight carob-specific nuclear short sequence repeat (nSSR) and the sequencing of a chloroplast locus. The collection is composed of 215 accessions introduced from 12 countries of origin spanning from traditional to novel areas of cultivation. To assess the genetic diversity of the collection, several approaches were coupled: structure analysis, principal component analysis (PCA), and graphic clustering either from dissimilarity data and coancestry data. Structure analysis suggested the presence of two distinct genetic pools: one characterizing northeastern Spain and the second spread in other countries and southern Spain. The PCA and discriminant analysis of principal component (DAPC) complemented the structure results allowing a better understanding of the genetic differences between countries while the network-joining analysis provided additional insights on the similarity between individuals. Short sequence repeat (SSR) data coupled with phenotypic data (floral sex and status) were also used to define the first core collection of carobs. Multi-approach analysis of genetic diversity together with the definition of a core collection represent useful tools for the setup of genetic-guided intervention both for conservation and breeding purposes.