Abstract
BackgroundOpportunity and challenges of the agriculture scenario of the next decades will face increasing demand for secure food through approaches able to minimize the input to cultivations. Large panels of tomato varieties represent a valuable resource of traits of interest under sustainable cultivation systems and for genome-wide association studies (GWAS). For mapping loci controlling the variation of agronomic, fruit quality, and root architecture traits, we used a heterogeneous set of 244 traditional and improved tomato accessions grown under organic field trials. Here we report comprehensive phenotyping and GWAS using over 37,300 SNPs obtained through double digest restriction-site associated DNA (dd-RADseq).ResultsA wide range of phenotypic diversity was observed in the studied collection, with highly significant differences encountered for most traits. A variable level of heritability was observed with values up to 69% for morphological traits while, among agronomic ones, fruit weight showed values above 80%. Genotype by environment analysis highlighted the strongest genotypic effect for aboveground traits compared to root architecture, suggesting that the hypogeal part of tomato plants has been a minor objective for breeding activities. GWAS was performed by a compressed mixed linear model leading to 59 significantly associated loci, allowing the identification of novel genes related to flower and fruit characteristics. Most genomic associations fell into the region surrounding SUN, OVATE, and MYB gene families. Six flower and fruit traits were associated with a single member of the SUN family (SLSUN31) on chromosome 11, in a region involved in the increase of fruit weight, locules number, and fruit fasciation. Furthermore, additional candidate genes for soluble solids content, fruit colour and shape were found near previously reported chromosomal regions, indicating the presence of synergic and multiple linked genes underlying the variation of these traits.ConclusionsResults of this study give new hints on the genetic basis of traits in underexplored germplasm grown under organic conditions, providing a framework for the development of markers linked to candidate genes of interest to be used in genomics-assisted breeding in tomato, in particular under low-input and organic cultivation conditions.
Highlights
Opportunity and challenges of the agriculture scenario of the decades will face increasing demand for secure food through approaches able to minimize the input to cultivations
Results of this study give new hints on the genetic basis of traits in underexplored germplasm grown under organic conditions, providing a framework for the development of markers linked to candidate genes of interest to be used in genomics-assisted breeding in tomato, in particular under low-input and organic cultivation conditions
Its exploration is fundamental for adding value to local genotypes rediscovering those traits lost in modern varieties that have been mostly developed for their yielding capacity and attitudes to processing [9]
Summary
Opportunity and challenges of the agriculture scenario of the decades will face increasing demand for secure food through approaches able to minimize the input to cultivations. Since the beginning of the twentieth century, intense breeding activities have been principally focused on the development of morphologically diverse and high-yielding varieties [5] These efforts have been mostly addressed for high input conditions while few attempts have been carried out for low input and/or organic farming. A large reservoir of traits is present in the existing array of traditional varieties adapted to natural and/or marginal environments in which they have been differentially selected by local farmers across years This germplasm is considered highly valuable in terms of characters related to agro-ecological adaptation as well as consumer preferences [7]. Its exploration is fundamental for adding value to local genotypes rediscovering those traits lost in modern varieties that have been mostly developed for their yielding capacity and attitudes to processing [9]
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