ArticleBMC plant biology2012
Evidence of cryptic introgression in tomato (Solanum lycopersicum L.) based on wild tomato species alleles.
Article in BMC plant biology, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
What it found
Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.
The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.
The trial behind it
Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.
Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.
Who cites it
12 citing papers in PubMed.
- Genome-Wide Identification, Expression, and Response toInternational journal of molecular sciences · 2023Article
- Alternative Modes of Introgression-Mediated Selection Shaped Crop Adaptation to Novel Climates.Genome biology and evolution · 2022Article
- The tomato pan-genome uncovers new genes and a rare allele regulating fruit flavor.Nature genetics · 2019Article
- Genome-wide identification of quantitative trait loci for important plant and flower traits in petunia using a high-density linkage map and an interspecific recombinant inbred population derived fromHorticulture research · 2019Article
- Mediterranean Long Shelf-Life Landraces: An Untapped Genetic Resource for Tomato Improvement.Frontiers in plant science · 2019Article
- 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
- Tomato Fruits Show Wide Phenomic Diversity but Fruit Developmental Genes Show Low Genomic Diversity.PloS one · 2016Article
- Comparative genomics and phylogenetic discordance of cultivated tomato and close wild relatives.PeerJ · 2015Article
- Multiple QTL for horticultural traits and quantitative resistance to Phytophthora infestans linked on Solanum habrochaites chromosome 11.G3 (Bethesda, Md.) · 2014Article
- Analysis of wild-species introgressions in tomato inbreds uncovers ancestral origins.BMC plant biology · 2014Article
- Linkage relationships among multiple QTL for horticultural traits and late blight (P. infestans) resistance on chromosome 5 introgressed from wild tomato Solanum habrochaites.G3 (Bethesda, Md.) · 2013Article
- Tomato breeding in the genomics era: insights from a SNP array.BMC genomics · 2013Article
Corrections and comments
PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.
Authors and funding
2 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
backgroundMany highly beneficial traits (e.g. disease or abiotic stress resistance) have been transferred into crops through crosses with their wild relatives. The 13 recognized species of tomato (Solanum section Lycopersicon) are closely related to each other and wild species genes have been extensively used for improvement of the crop, Solanum lycopersicum L. In addition, the lack of geographical barriers has permitted natural hybridization between S. lycopersicum and its closest wild relative Solanum pimpinellifolium in Ecuador, Peru and northern Chile. In order to better understand patterns of S. lycopersicum diversity, we sequenced 47 markers ranging in length from 130 to 1200 bp (total of 24 kb) in genotypes of S. lycopersicum and wild tomato species S. pimpinellifolium, Solanum arcanum, Solanum peruvianum, Solanum pennellii and Solanum habrochaites. Between six and twelve genotypes were comparatively analyzed per marker. Several of the markers had previously been hypothesized as carrying wild species alleles within S. lycopersicum, i.e., cryptic introgressions.
resultsEach marker was mapped with high confidence (e<1 x 10-30) to a single genomic location using BLASTN against tomato whole genome shotgun chromosomes (SL2.40) database. Neighbor-joining trees showed high mean bootstrap support (86.8 ± 2.34%) for distinguishing red-fruited from green-fruited taxa for 38 of the markers. Hybridization and parsimony splits networks, genomic map positions of markers relative to documented introgressions, and historical origins of accessions were used to interpret evolutionary patterns at nine markers with putatively introgressed alleles.
conclusionOf the 47 genetic markers surveyed in this study, four were involved in linkage drag on chromosome 9 during introgression breeding, while alleles at five markers apparently originated from natural hybridization with S. pimpinellifolium and were associated with primitive genotypes of S. lycopersicum. The positive identification of introgressed genes within crop species such as S. lycopersicum will help inform conservation and utilization of crop germplasm diversity, for example, facilitating the purging of undesirable linkage drag or the exploitation of novel, favorable alleles.
Indexed as
Identifiers
What OpenQuestion holds
Registered trials
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.