Discovery of intron polymorphisms in cultivated tomato using both tomato and Arabidopsis genomic information |
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Authors: | Yuanyuan Wang Jia Chen David M Francis Huolin Shen Tingting Wu Wencai Yang |
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Institution: | (1) Department of Vegetable Science, College of Agronomy and Biotechnology, China Agricultural University, Beijing, 100193, China;(2) Department of Horticulture and Crop Science, The Ohio State University/OARDC, 1680 Madison Ave, Wooster, OH 44691, USA; |
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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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