ArticleBMC genomics2007
Diversity in conserved genes in tomato.
Article in BMC genomics, 2007. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 37 papers.
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Who cites it
37 citing papers in PubMed, 76 citations in OpenAlex.
- Plant mitochondrial introns as genetic markers - conservation and variation.Frontiers in plant science · 2023Article
- Use of modern tomato breeding germplasm for deciphering the genetic control of agronomical traits by Genome Wide Association study.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2017Article
- Article
- High density linkage mapping of genomic and transcriptomic SNPs for synteny analysis and anchoring the genome sequence of chickpea.Scientific reports · 2015Article
- Genes involved in floral meristem in tomato exhibit drastically reduced genetic diversity and signature of selection.BMC plant biology · 2014Article
- In silico identification and experimental validation of insertion-deletion polymorphisms in tomato genome.DNA research : an international journal for rapid publication of reports on genes and genomes · 2014Article
- SNP genotyping reveals genetic diversity between cultivated landraces and contemporary varieties of tomato.BMC genomics · 2013Article
- Whole genome resequencing in tomato reveals variation associated with introgression and breeding events.BMC genomics · 2013Article
- Phenotypic diversity and association mapping for fruit quality traits in cultivated tomato and related species.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2013Article
- Article
- Development of high-throughput SNP-based genotyping in Acacia auriculiformis x A. mangium hybrids using short-read transcriptome data.BMC genomics · 2012Article
- Genome wide SNP discovery in flax through next generation sequencing of reduced representation libraries.BMC genomics · 2012Article
- De novo assembly of the pepper transcriptome (Capsicum annuum): a benchmark for in silico discovery of SNPs, SSRs and candidate genes.BMC genomics · 2012Article
- Genome-wide association mapping in tomato (Solanum lycopersicum) is possible using genome admixture of Solanum lycopersicum var. cerasiforme.G3 (Bethesda, Md.) · 2012Article
- Development of a large SNP genotyping array and generation of high-density genetic maps in tomato.PloS one · 2012Article
- High-density SNP genotyping of tomato (Solanum lycopersicum L.) reveals patterns of genetic variation due to breeding.PloS one · 2012Article
- Article
- Increase in tomato locule number is controlled by two single-nucleotide polymorphisms located near WUSCHEL.Plant physiology · 2011Article
- Identification of SNP and SSR markers in eggplant using RAD tag sequencing.BMC genomics · 2011Article
- ngs_backbone: a pipeline for read cleaning, mapping and SNP calling using next generation sequence.BMC genomics · 2011Article
Corrections and comments
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Authors and funding
7 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundTomato has excellent genetic and genomic resources including a broad set of Expressed Sequence Tag (EST) data and high-density genetic maps. In addition, emerging physical maps and bacterial artificial clone sequence data serve as template to investigate genetic variation within the cultivated germplasm pool with the goal to manipulate agriculturally important traits. Unfortunately, the nearly exclusive focus of resource development on interspecific populations for genetic analyses and diversity studies has left a void in our understanding of genotypic variation within tomato breeding programs that focus on intra-specific populations. We describe the results of a study to identify nucleotide variation within tomato breeding germplasm and mapping parents for a set of conserved single-copy ESTs that are orthologous between tomato and Arabidopsis.
resultsUsing a pooled sequencing strategy, 967 tomato transcripts were screened for polymorphism in 12 tomato lines. Although intron position was conserved, intron lengths were 2-fold larger in tomato than in Arabidopsis. A total of 1,487 single nucleotide polymorphisms and 282 insertion/deletions were identified, of which 579 and 206 were polymorphic in breeding germplasm, respectively. Fresh market and processing germplasm were clearly divergent, as were Solanum lycopersicum var. cerasiformae and Solanum pimpinellifolium, tomato's closest relatives. The polymorphisms identified serve as marker resources for tomato. The COS is also applicable to other Solanaceae crops.
conclusionsThe results from this research enabled significant progress towards bridging the gap between genetic and genomic resources developed for populations derived from wide crosses and those applicable to intra-specific crosses for breeding in tomato.
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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.