ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2010
Discovery of intron polymorphisms in cultivated tomato using both tomato and Arabidopsis genomic information.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2010. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 11 papers.
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11 citing papers in PubMed, 35 citations in OpenAlex.
- Plant mitochondrial introns as genetic markers - conservation and variation.Frontiers in plant science · 2023Article
- Chromosome-specific potential intron polymorphism markers for large-scale genotyping applications in pomegranate.Frontiers in plant science · 2022Article
- Novel intron length polymorphic (ILP) markers from starch biosynthesis genes reveal genetic relationships in Indian wheat varieties and related species.Molecular biology reports · 2020Article
- Exploring the basis of 2-propenyl and 3-butenyl glucosinolate synthesis by QTL mapping and RNA-sequencing in Brassica juncea.PloS one · 2019Article
- Miniature Inverted Repeat Transposable Element Insertions Provide a Source of Intron Length Polymorphism Markers in the Carrot (Frontiers in plant science · 2017Article
- Development of EST Intron-Targeting SNP Markers for Panax ginseng and Their Application to Cultivar Authentication.International journal of molecular sciences · 2016Article
- Genome-wide generation and use of informative intron-spanning and intron-length polymorphism markers for high-throughput genetic analysis in rice.Scientific reports · 2016Article
- Article
- 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
- Development and characterization of intron-flanking EST-PCR markers in rubber tree (Hevea brasiliensis Muell. Arg.).Molecular biotechnology · 2012Article
- Article
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Authors and funding
6 authors at 2 institutions in 2 countries.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A low level of genetic variation has limited the application of molecular markers for characterizing important traits in cultivated tomato. To detect polymorphisms in tomato conserved ortholog sets (COS), expressed sequence tags (ESTs) were searched against tomato and Arabidopsis genomic sequences to define the positions of introns. Introns were amplified from 12 different accessions of tomato by polymerase chain reaction and nucleotide sequences were determined by sequencing. Results indicated that there was a possibility of 71% to amplify introns from tomato genomic DNA through this approach. A total of 201 introns were sequenced from 86 COS unigenes. The intron positions and numbers were conserved between tomato and Arabidopsis, but average intron length was three times longer in tomato than in Arabidopsis. A total of 307 single nucleotide polymorphisms (SNPs) and 75 indels were detected in introns of 57 COS unigenes among 12 tomato lines. Within cultivated tomato germplasm 172 SNPs and 47 indels were detected in introns of 33 COS unigenes. In addition, 41 SNPs were identified in the exons of 27 COS unigenes. The frequency of SNPs was 2.4 times higher in introns than in exons in the 22 COS unigenes having both intronic and exonic polymorphisms. These results indicate that intronic regions may contain sufficient variation to develop sufficient marker resources for genome-wide analysis in cultivated tomato.
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