Discovery of single nucleotide polymorphisms in Lycopersicon esculentum by computer aided analysis of expressed sequence tags

Yang, Wencai; Bai, Xiaodong; Kabelka, Eileen A.; Eaton, Christina; Kamoun, Sophien; Knaap, Esther van der; Francis, David M.

doi:10.1023/b:molb.0000037992.03731.a5

Cited by 105 publications

(74 citation statements)

References 26 publications

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“…However, the sequences of PCR products obtained using 10 primers (see above) gave a lower density (1 SNP/520 bp), which is also understandable in view of the fact that only 7 out of 30 SNPs could be validated. The density of SNPs reported during the present study, however, falls within the range (1SNP/21bp to 1SNP/8500bp) of densities of SNPs reported in earlier studies on different tree and plant species (Bryan et al 1999;Schmid et al 2003;Blake et al 2004;Bundock & Henry 2004;Feltus et al 2004;Gupta & Rustgi 2004;Le Dantec et al 2004;Morales et al 2004;Russell et al 2004;Shen et al 2004;Yang et al 2004;Rostoks et al 2005), but is little above the density reported for bread wheat in an earlier study (1 SNP/540 bp; Somers et al 2003). We also noticed that in bread wheat the density of SNPs scored in EST databases (1SNP/144.9 bp; 1 SNP/540 bp) was higher than that reported in sequences of genes of economic importance (1SNP/1000bp to 1SNP/1700bp; Bryan et al 1999;Mochida et al 2003;Somers et al 2003;Zhang et al 2003;Blake et al 2004).…”

Section: Density Of Snpssupporting

confidence: 84%

EST-SNPs in bread wheat: discovery, validation, genotyping and haplotype structure

Rustgi¹,

Bandopadhyay²,

Balyan³

et al. 2009

CZECH J GENET PLANT

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Abstract:The present study involves discovery, validation and use of single-nucleotide polymorphisms (SNPs) in bread wheat utilizing 48 EST-contigs (individual contigs having 20-89 ESTs, derived from 2 to 11 different genotypes). In order to avoid a problem due to homoeologous relationships, the ESTs in each contig were classified into 175 sub-contigs (3.7 sub-contigs/EST-contig) using characteristic homoeologue sequence variants (HSVs), which had a density of 1 HSV every 136.7 bp. In silico analysis of sub-contigs led to the discovery of 230 candidate EST-SNPs with a density of 1SNP/273.9 bp. Locus specific primers (each primer pair flanking 1-18 SNPs) were designed utilizing one sub-contig each from 42 EST-contigs that contained SNPs, the remaining 6 contigs having no SNPs. To provide locus specificity to the PCR products, each primer was tagged with an HSV at its 3' end. Only 10 primer pairs, which gave each a characteristic solitary band, were utilized to validate EST-SNPs over 30 diverse bread wheat genotypes; 7 SNPs were validated through resequencing the PCR products. Allele specific primers were designed and utilized for genotyping of 50 diverse bread wheat accessions (including 30 bread wheat genotypes previously used for validation of SNPs), with an aim to test their utility in genotyping and map construction. The allele specific primers allowed the classification of 50 genotypes in two alternative allele groups for each SNP as expected, thus suggesting their utility for genotyping. Of the above 7 validated SNPs, 4 belonged to a solitary locus (PKS37); 7 haplotypes were available at this locus. Altogether, the results suggested that EST-SNPs constitute an important source of molecular markers for studies on wheat genomics.

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Section: Density Of Snpssupporting

confidence: 84%

EST-SNPs in bread wheat: discovery, validation, genotyping and haplotype structure

Rustgi¹,

Bandopadhyay²,

Balyan³

et al. 2009

CZECH J GENET PLANT

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“…A total of 300 markers including 149 markers from transcribed (exon) sequences (Yang et al, 2004(Yang et al, , 2005a and 151 markers from intron sequences (Van Deynze et al, 2007) were used to genotype the collection of cultivated tomato varieties. We used multiple genotyping platforms including agarose gel electrophoresis for SNP detection as cleaved amplified polymorphic sequences (CAPS) and the LUMINEX 200 (Luminex, Corp., Austin, TX, USA) for detection of SNPs using allele-specific primer extension (ASPE) (Lee et al, 2004).…”

Section: Genotypingmentioning

confidence: 99%

Population structure and genetic differentiation associated with breeding history and selection in tomato (Solanum lycopersicum L.)

et al. 2010

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Tomato (Solanum lycopersicum L.) has undergone intensive selection during and following domestication. We investigated population structure and genetic differentiation within a collection of 70 tomato lines representing contemporary (processing and fresh-market) varieties, vintage varieties and landraces. The model-based Bayesian clustering software, STRUCTURE, was used to detect subpopulations. Six independent analyses were conducted using all marker data (173 markers) and five subsets of markers based on marker type (single-nucleotide polymorphisms, simple sequence repeats and insertion/deletions) and location (exon and intron sequences) within genes. All of these analyses consistently separated four groups predefined by market niche and age into distinct subpopulations. Furthermore, we detected at least two subpopulations within the processing varieties. These subpopulations correspond to historical patterns of breeding conducted for specific production environments. We found no subpopulation within fresh-market varieties, vintage varieties and landraces when using all marker data. High levels of admixture were shown in several varieties representing a transition in the demarcation between processing and fresh-market breeding. The genetic clustering detected by using the STRUCTURE software was confirmed by two statistics, pairwise F st (y) and Nei's standard genetic distance. We also identified a total of 19 loci under positive selection between processing, freshmarket and vintage germplasm by using an F st -outlier method based on the deviation from the expected distribution of F st and heterozygosity. The markers and genome locations we identified are consistent with known patterns of selection and linkage to traits that differentiate the market classes. These results demonstrate how human selection through breeding has shaped genetic variation within cultivated tomato.

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“…Genetic diversity within cultivated tomato is understood to be low (Nesbitt and Tanksley, 2002) and has never been extensively surveyed in these large assemblages of accessions. Cost-effective molecular markers such as simple sequence repeats (SSRs) and single nucleotide polymorphisms (SNPs) are increasingly available for S. lycopersicum (He et al, 2003;Yang et al, 2004;Labate and Baldo, 2005;Ruiz et al, 2005;Van Deynze et al, 2007).…”

Section: Introductionmentioning

confidence: 99%

“…Saturating S. lycopersicum intraspecific genetic maps poses a challenge in the face of interspecific introgression because polymorphic markers may tend to cluster (Villand et al, 1998;Yang et al, 2004). In population genomics studies of domestication and selection (Nordborg et al, 2005;Ross-Ibarra et al, 2007), complex demographic processes (for example, bottlenecks, global exchange of germplasm and introgression from multiple wild species), must be incorporated.…”

Section: Introgressionmentioning

confidence: 99%

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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Discovery of single nucleotide polymorphisms in Lycopersicon esculentum by computer aided analysis of expressed sequence tags

Cited by 105 publications

References 26 publications

EST-SNPs in bread wheat: discovery, validation, genotyping and haplotype structure

EST-SNPs in bread wheat: discovery, validation, genotyping and haplotype structure

Population structure and genetic differentiation associated with breeding history and selection in tomato (Solanum lycopersicum L.)

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

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