Multilocus sequence data reveal extensive departures from equilibrium in domesticated tomato (Solanum lycopersicum L.)

Abstract

Limited genetic variation has been observed within tomato (Solanum lycopersicum L.), although no studies have extensively surveyed single nucleotide polymorphism (SNP) diversity among tomato landraces. We estimated intraspecific DNA sequence variation by analyzing 50 gene fragments (23.2 kb) per plant in a 31 plant diversity panel. The majority of loci (80%) were polymorphic with the minor allele at a frequency of 10% or less for most (141 of 155) SNPs. Mean diversity as estimated by y and p was approximately 1.5 SNPs per kb. Significant linkage disequilibrium was observed between 19% of locus pairs, and withinlocus population recombination estimates were negligible. We also sequenced 43 gene fragments from wild tomato Solanum arcanum Peralta as an outgroup. Various statistical tests rejected a neutral equilibrium model of molecular evolution at 10 of 50 loci. Rare, highly diverged alleles were observed, involving at least seven tomato lines and five loci. Some of these may represent introgressions that originated both from natural hybridization with Solanum pimpinellifolium L. and from crosses with S. pimpinellifolium and additional wild relatives for crop improvement. The former was reported from classical field studies carried out by CM Rick; the latter has been extensively documented in the crop, particularly for transfer of disease resistance alleles. Extensive introgression and frequent bottlenecks within S. lycopersicum will pose a challenge to reconstructing the genetic bases of domestication and selection using methods that rely on patterns of molecular polymorphism.

The heterogeneous levels of linkage disequilibrium in white spruce genes and comparative analysis with other conifers

“…Further studies are required, whether of empirical or simulation nature, to investigate the sensitivity of LD estimates to these factors. Within the same species, wild populations usually harbor lower LD compared with their domesticated counterparts, as shown in barley (Caldwell et al, 2006), soybean (Lam et al, 2010), rice (Zhu et al, 2007), tomato (Arunyawat et al, 2007;Labate et al, 2009) and common bean (Rossi et al, 2009), reflecting changes in effective population size (Mather et al, 2007). In cultivated maize, for which LD was estimated based on large sequence data sets, the mean r 2 was 0.24 over a distance of 100 nucleotides and remained above 0.20 within 2 kb (Yan et al, 2009).…”

Genetic Diversity in Tomato (Solanum lycopersicum) and Its Wild Relatives

“…If interspecific populations for genetic analyses and diversity studies answered to many questions, it has left a void in the understanding of genotypic variation within tomato breeding programs which focus on intra-specific populations (Van Deynze, Stoffel et al 2007). The recent discovery of SNP markers, first detected in EST (expressed sequenced tag) sequences (Van Deynze et al 2007; Jimenez-Gomez and Maloof 2009) then in non-coding sequences (Labate et al 2009) provided access to a higher level of polymorphism. Labate and colleagues estimated parameters of diversity among S. lycopersium accessions, first using the SNP detected in 50 loci that were resequenced in a diversity panel of 31 accessions.…”

“…Labate and colleagues estimated parameters of diversity among S. lycopersium accessions, first using the SNP detected in 50 loci that were resequenced in a diversity panel of 31 accessions. In a second investigation, multilocus estimates of polymorphism were obtained and led to rejection of the neutral equilibrium model of evolution within the studied collection (Labate, Robertson et al 2009). Public germplasm are potential allele mining sources for crop improvement as illustrated by previous authors who sampled among US seed banks 30 accessions from the five continents.…”

On the identification of human selected loci in grapevines

“…Therefore, to have a clear understanding of the impact of selection on genetic diversity around the selected genes, factors such as the local recombination rate, population size, population structure and breeding systems need to be considered. For instance, in Solanum lycopersicum, extensive introgression (from natural hybridization with S. pimpinellifolium, as well as from crosses with S. pimpinellifolium and additional wild relatives as an attempt to improve crops) and frequent bottlenecks need to be considered in order to be able to understand the genetic basis of domestication and selection in this species (Labate et al, 2009). When considering crops such as grapevines, making predictions becomes even harder.…”