Exploring a Tomato Landraces Collection for Fruit-Related Traits by the Aid of a High-Throughput Genomic Platform

Abstract

During its evolution and domestication Solanum lycopersicum has undergone various genetic ‘bottlenecks’ and extreme inbreeding of limited genotypes. In Europe the tomato found a secondary centre for diversification, which resulted in a wide array of fruit shape variation given rise to a range of landraces that have been cultivated for centuries. Landraces represent a reservoir of genetic diversity especially for traits such as abiotic stress resistance and high fruit quality. Information about the variation present among tomato landrace populations is still limited. A collection of 123 genotypes from different geographical areas was established with the aim of capturing a wide diversity. Eighteen morphological traits were evaluated, mainly related to the fruit. About 45% of morphological variation was attributed to fruit shape, as estimated by the principal component analysis, and the dendrogram of relatedness divided the population in subgroups mainly on the basis of fruit weight and locule number. Genotyping was carried out using the tomato array platform SolCAP able to interrogate 7,720 SNPs. In the whole collection 87.1% markers were polymorphic but they decreased to 44–54% when considering groups of genotypes with different origin. The neighbour-joining tree analysis clustered the 123 genotypes into two main branches. The STRUCTURE analysis with K = 3 also divided the population on the basis of fruit size. A genomic-wide association strategy revealed 36 novel markers associated to the variation of 15 traits. The markers were mapped on the tomato chromosomes together with 98 candidate genes for the traits analyzed. Six regions were evidenced in which candidate genes co-localized with 19 associated SNPs. In addition, 17 associated SNPs were localized in genomic regions lacking candidate genes. The identification of these markers demonstrated that novel variability was captured in our germoplasm collection. They might also provide a viable indirect selection tool in future practical breeding programs.

Exploiting the great potential of Sequence Capture data by a new tool, SUPER-CAP

“…Taking into account the Ho alternative variants only, an average of 95% concordance was found. Another validation was carried out by comparing SNPs detected on a tomato population genotyped using a SolCAP arrays, 30 , 32 which included 7,720 SNPs. Only 170 of the 7,720 SNPs fall in the targeted region considered in the present study, since the targeted regions represent ∼1% (378/34,725) of the tomato genes.…”

“…The variants selected or prioritized in this way would be highly preferred marker sets to be subjected to association studies using suitably larger populations, for which panels with considerable genotype and phenotype information has already been collected 30 , 32 …”

“…A panel of 44 genetically diverse Solanum lycopersicum genotypes was selected from a wide collection of tomato landraces 30 available at the University of Naples, department of Agricultural Sciences. Plants were grown in a greenhouse under controlled conditions at the aforementioned Department; detailed information, including source and geographic origin for each genotype, is presented in Supplementary Table S1.…”

“…In particular, data from a previous genotyping experiment which detected variants for 7,720 SNPs through the SolCAP array, 30 , 32 as well as data concerning the resequencing of 360 tomato genomes, 42 were considered. Of the 44 genotypes used in this study, 37 were common to those used in the SolCAP experiment and 9 in the 360 genome project.…”

Association mapping reveals the genetic architecture of tomato response to water deficit: focus on major fruit quality traits

“…In tomato ( Solanum lycopersicum L.), QTLs were mapped for fruit quality traits measured under optimal watering conditions using linkage (Causse et al , 2001; Saliba-Colombani et al , 2001; Tieman et al , 2006; Zanor et al , 2009 b ; Capel et al , 2015) and association mapping (Xu et al , 2013; Ruggieri et al , 2014; Sauvage et al , 2014; Sacco et al , 2015). The studies of QTLs by water regime interactions focused on introgression lines between the cultivated tomato and its wild relatives (mainly S. habrochaites and S. pennellii ), leading to low mapping resolution (Semel et al , 2007; Gur et al , 2011; Arms et al , 2015).…”