Diversity and linkage disequilibrium analysis within a selected set of cultivated tomatoes

Berloo, R. van; Zhu, Aiguo; Ursem, Remco; Verbakel, Henk; Gort, Gerrit; Eeuwijk, F.A. van

doi:10.1007/s00122-008-0755-x

Cited by 54 publications

(69 citation statements)

References 35 publications

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“…cerasiforme is not recognized in the recent taxonomic revision of genus Lycopersicon into Solanum L. section Lycopersicon (Peralta et al, 2008) and may represent an admixture of S. lycopersicum and S. pimpinellifolium L. (Nesbitt and Tanksley, 2002). Cherry tomato cultivars were shown to be genetically distinct from beef and round tomato cultivars using amplified fragment length polymorphism markers (van Berloo et al, 2008). Only one accession in our panel was classified as cherry.…”

Section: Introductionmentioning

confidence: 85%

“…The majority of pairs of loci were in linkage equilibrium. Similarly, interlocus LD was rare in a study of European greenhouse tomato cultivars (van Berloo et al, 2008). In a study of Italian tomato landraces 0.04 of SSR loci pairs were in LD, mostly due to interchromosomal LD (Mazzucato et al, 2008).…”

Section: Neutrality Testsmentioning

confidence: 96%

“…LD estimates are valuable for understanding whether association mapping will be efficient within (Simko et al, 2006), soybean (Hyten et al, 2007), rice (Mather et al, 2007), maize (Yu et al, 2008), sorghum (Casa et al, 2008), sugarcane (Saccharum spp. ; Raboin et al, 2008), sunflower (H. annuus;Fusari et al, 2008), tomato (Mazzucato et al, 2008;van Berloo et al, 2008) and wheat (Triticum spp. ; Somers et al, 2007).…”

Section: Neutrality Testsmentioning

confidence: 99%

“…Some LD is required for association mapping to identify candidate functional polymorphisms (Rafalski, 2002). Commercial tomato cultivars showed strong intrachromosomal LD extending up to 15-20 cM (van Berloo et al, 2008). S. lycopersicum commercial cultivars and landraces are potentially useful for broad genome scans although the low frequency of most polymorphisms presents a disadvantage.…”

Section: Neutrality Testsmentioning

confidence: 99%

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

Labate¹,

Robertson²,

Baldo³

2009

Heredity

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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.

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Section: Introductionmentioning

confidence: 85%

Section: Neutrality Testsmentioning

confidence: 96%

Section: Neutrality Testsmentioning

confidence: 99%

Section: Neutrality Testsmentioning

confidence: 99%

See 2 more Smart Citations

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

Labate¹,

Robertson²,

Baldo³

2009

Heredity

View full text Add to dashboard Cite

show abstract

“…The same data set, has been studied by Ursem et al (2008), van Berloo et al (2008a, where more details about the data and their preparation can be found.…”

Section: Data Descriptionmentioning

confidence: 99%

Penalized regression techniques for modeling relationships between metabolites and tomato taste attributes

et al. 2011

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The search for models which link tomato taste attributes to their metabolic profiling, is a main challenge within the breeding programs that aim to enhance tomato flavor. In this paper, we compared such models calculated by the traditional statistical approach, stepwise regression, with models obtained by the new generation of regression techniques, known as penalized regression or regularization methods. In addition, for penalized regression, different scenarios and various model selection criteria were discussed to conclude that classical crossvalidation, selects models with many superfluous variables whereas model selection criteria such as Bayesian information criterion, seem to be more suitable, when the goal is to find parsimonious models, to explain tomato taste attributes based on metabolic information. An exhaustive comparison of the discussed methodology was done for six sensory traits, showing that the most important covariates were identified by the stepwise regression as well as by some of the penalized regression methods, despite the general disagreement on the size of the regression coefficients between them. In particular, for stepwise regression the coefficients are inflated due to their high variance which is not the case with penalized regression, showing that this new methodology, can be an alternative to obtain more accurate models.

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Steroidal alkaloid biosynthesis is coordinately regulated and differs among tomatoes in the red‐fruited clade

2022

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The tomato (Solanum spp.) clade of Solanaceae features a unique assortment of cholesterol-derived steroidal alkaloids. However, little quantitative data exists reporting the profile and concentration of these alkaloids across diverse fruit germplasm. To address the lack of knowledge regarding the chemical diversity, concentration, and genetic architecture controlling tomato steroidal alkaloids, we quantitatively profiled and genotyped two tomato populations representing diversity in the red-fruited clade. We grew 107 genetically diverse fresh market, processing, landrace, and wild tomato in multiple environments. Nine steroidal alkaloid groups were quantified using ultrahigh performance liquid chromatography tandem mass spectrometry. The diversity panel and a biparental population segregating for high alpha-tomatine were genotyped to identify and validate quantitative trait loci (QTL) associated with steroidal alkaloids. Landraces and wild material exhibited higher alkaloid concentrations and more chemical diversity. Average total content of steroidal alkaloids, often dominated by lycoperoside F/G/esculeoside A, ranged from 1.9 to 23.3 mg 100 g −1 fresh wt. across accessions. Landrace and wild cherry accessions distinctly clustered based on elevated concentrations of early or late-pathway steroidal alkaloids. Significant correlations were observed among alkaloids from the early and late parts of the biosynthetic pathway in a species-dependent manner. A QTL controlling multiple, early steroidal alkaloid pathway intermediates on chromosome 3 was identified by genome-wide association studies (GWAS) and validated in a backcross population. Overall, tomato steroidal alkaloids are diverse in the red-fruited clade and their biosynthesis is regulated in a coordinated manner.

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Diversity and linkage disequilibrium analysis within a selected set of cultivated tomatoes

Cited by 54 publications

References 35 publications

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

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

Penalized regression techniques for modeling relationships between metabolites and tomato taste attributes

Steroidal alkaloid biosynthesis is coordinately regulated and differs among tomatoes in the red‐fruited clade

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