NDLI: Discovery of intron polymorphisms in cultivated tomato using both tomato and Arabidopsis genomic information

Content Provider	Springer Nature Link
Author	Wang, Yuanyuan Chen, Jia Francis, David M. Shen, Huolin Wu, Tingting Yang, Wencai
Copyright Year	2010
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.
Starting Page	1199
Ending Page	1207
Page Count	9
File Format	PDF
ISSN	00405752
Journal	Theoretical and Applied Genetics
Volume Number	121
Issue Number	7
e-ISSN	14322242
Language	English
Publisher	Springer-Verlag
Publisher Date	2010-06-16
Publisher Place	Berlin/Heidelberg
Access Restriction	One Nation One Subscription (ONOS)
Subject Keyword	Biotechnology Biochemistry Plant Biochemistry Agriculture Plant Genetics & Genomics Plant Breeding/Biotechnology
Content Type	Text
Resource Type	Article
Subject	Genetics Medicine Biotechnology Agronomy and Crop Science

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