Use of chromosome walking in discovery of single-nucleotide polymorphism in noncoding regions of a candidate actin gene in Pinus radiata

• Authors: W. Li , H. Li , H. Wu , X.-Y. Chen
• Languages of publication: EN

Abstracts

EN

Untranslated regions (UTRs) of eukaryotic mRNAs play crucial roles in post-transcriptional regulation of gene expression via the modulation of nucleocytoplasmic mRNA transport, translation efficiency, subcellular localization, and message stability. Single-nucleotide polymorphisms (SNPs) in UTRs of a candidate gene may also change the post-transcriptional regulation of a gene or function by nucleotide mutation. For species that have not been entirely sequenced genomically, new methods need to be devised to discover SNPs in noncoding regions of candidate genes. In this study, based on the expressed sequence tag (EST) of Pinus radiata (Monterey pine), we obtained all the sequences of UTRs of the actin gene by using a chromosome walking method. We also detected all the SNPs in and around the coding region of the actin gene. In this way, the full genomic sequence (2154 bp) of the actin gene was identified, including the 5'UTR, introns, the coding sequence, and the 3'UTR. PCR amplification and DNA fragment sequencing from 200 unrelated P. radiata trees revealed a total of 21 SNPs in the actin gene, of which 3 were located in the 5'UTR, 3 in the introns, 10 in the coding sequence, and 5 in the 3'UTR. We show that chromosome walking can be used for obtaining the sequence of UTRs, and then, based on this sequence, to discover SNPs in the noncoding regions of candidate genes from this species without an entire genomic sequence.

Keywords

EN

ACTIN EST; CHROMOSOME; NONCODING REGION; PINUS RADIATA

Discipline

• GENETICS: GENETICS

• Publisher: Institute of Plant Genetics, Polish Academy of Sciences
• Journal: Journal of Applied Genetics
• Year: 2010
• Volume: 51
• Issue: 3
• Pages: 275-281

Contributors

author

W. Li

author

H. Li

author

H. Wu

author

X.-Y. Chen

• Document Type: ARTICLE
• Publication order reference: X-Y. Chen, College of Forestry, South China Agriculture University, Guangzhou 510642, China