Abstract
BackgroundThe natural phenotypic variability present in the germplasm of cultivated plants can be linked to molecular polymorphisms using association genetics. However it is necessary to consider the genetic structure of the germplasm used to avoid false association. The knowledge of genetic structure of plant populations can help in inferring plant evolutionary history. In this context, we genotyped 360 wild, feral and cultivated accessions with 20 simple sequence repeat markers and investigated the extent and structure of the genetic variation. The study focused on the red fruited tomato clade involved in the domestication of tomato and confirmed the admixture status of cherry tomatoes (Solanum lycopersicum var. cerasiforme). We used a nested sample strategy to set-up core collection maximizing the genetic diversity with a minimum of individuals.ResultsMolecular diversity was considerably lower in S. lycopersicum i.e. the domesticated form. Model-based analysis showed that the 144 S. lycopersicum var. cerasiforme accessions were structured into two groups: one close to the domesticated group and one resulting from the admixture of the S. lycopersicum and S. pimpinellifolium genomes. SSR genotyping also indicates that domesticated and wild tomatoes have evolved as a species complex with intensive level of hybridization. We compiled genotypic and phenotypic data to identify sub-samples of 8, 24, 32 and 64 cherry tomato accessions that captured most of the genetic and morphological diversity present in the entire S. lycopersicum var. cerasiforme collection.ConclusionThe extent and structure of allelic variation is discussed in relation to historical events like domestication and modern selection. The potential use of the admixed group of S. lycopersicum var. cerasiforme for association genetics studies is also discussed. Nested core collections sampled to represent tomato diversity will be useful in diversity studies. Molecular and phenotypic variability of these core collections is defined. These collections are available for the scientific community and can be used as standardized panels for coordinating efforts on identifying novel interesting genes and on examining the domestication process in more detail.
Highlights
The natural phenotypic variability present in the germplasm of cultivated plants can be linked to molecular polymorphisms using association genetics
This study highlighted the unknown genetic structure of our wild and cultivated germplasm, enhancing the understanding of the history of the tomato complex. It clarified the position of S. l. cerasiforme in the evolution of the cultivated tomato
Part of this sub-species is genetically close to the cultivated S. lycopersicum group and the other part is in admixture between cultivated and wild related groups
Summary
The natural phenotypic variability present in the germplasm of cultivated plants can be linked to molecular polymorphisms using association genetics. The knowledge of genetic structure of plant populations can help in inferring plant evolutionary history In this context, we genotyped 360 wild, feral and cultivated accessions with 20 simple sequence repeat markers and investigated the extent and structure of the genetic variation. Over the last few years, there has been renewed interest in the study of naturally occurring variation in crop genetic collections. Motivations for such studies are (i) to use natural allelic diversity for the evaluation of gene function, (ii) to find new genes or new alleles involved in specific aspects of plant physiology or development and (iii) to try to understand the molecular basis of adaptation to local environments [5]. In contrast to the situation in multigenerational pedigrees, LD in natural populations is not broken artificially and we need to overcome this restriction
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