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Detection of sequence polymorphisms in red junglefowl and White Leghorn ESTs
KTH, Superseded Departments, Biotechnology.ORCID iD: 0000-0002-1495-8338
KTH, Superseded Departments, Biotechnology.
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2004 (English)In: Animal Genetics, ISSN 0268-9146, E-ISSN 1365-2052, Vol. 35, no 5, 391-396 p.Article in journal (Refereed) Published
Abstract [en]

Over 16 000 high quality expressed sequence tags (ESTs) from red junglefowl (RJ) and White Leghorn (WL) brain and testis cDNA libraries were generated. Here, we have used this resource for detection of single nucleotide polymorphisms (SNPs), and also completed full-length sequencing of 46 pairs of clones, representing the same gene from both the RJ and WL libraries. From the main set of ESTs, which were assembled using Phrap, 746 putative SNPs were identified, of which 76% were transitions and 24% were transversions. A subset of SNPs was evaluated by sequence analysis of five RJ and five WL birds. Nine of 12 SNPs were verified in this limited sample, suggesting that a majority of the putative polymorphisms documented in this study represent real SNPs. During full-length sequencing of the 46 RJ/WL clones 100 SNPs were identified, which translated to a frequency of 1.90 SNPs/1000 bp. The number of transitions and transversions were 77% and 23%, respectively, and the proportion of non-synonymous vs. synonymous SNPs was 20% and 80%, respectively. Four large insertions/deletions were identified between the RJ and WL full-length sequences, and they appear to represent different splice variants.

Place, publisher, year, edition, pages
2004. Vol. 35, no 5, 391-396 p.
Keyword [en]
chicken, expressed sequence tag, Gallus gallus, polymorphism, single nucleotide polymorphism, embryo cdna library, production traits, chicken genome, intercross, behavior, growth, fowl, qtls, tags, tool
National Category
Production Engineering, Human Work Science and Ergonomics
URN: urn:nbn:se:kth:diva-23733DOI: 10.1111/j.1365-2052.2004.01184.xISI: 000223952600005ScopusID: 2-s2.0-5044238538OAI: diva2:342432
QC 20100525 QC 20110922Available from: 2010-08-10 Created: 2010-08-10 Last updated: 2011-09-22Bibliographically approved

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Savolainen, PeterAmini, BahramLundeberg, Joakim
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