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Identification of Null Alleles and Deletions from SNP Genotypes for an Intercross Between Domestic and Wild Chickens
Uppsala University, Disciplinary Domain of Science and Technology, Biology, Department of Cell and Molecular Biology.
Swedish University of Agricultural Sciences, Uppsala, Sweden.ORCID iD: 0000-0002-2722-5264
2013 (English)In: G3: Genes, Genomes, Genetics, ISSN 2160-1836, E-ISSN 2160-1836, Vol. 3, no 8, 1253-1260 p.Article in journal (Refereed) Published
Abstract [en]

We analyzed genotypes from similar to 10K single-nucleotide polymorphisms (SNPs) in two families of an F-2 intercross between Red Junglefowl and White Leghorn chickens. Possible null alleles were found by patterns of incompatible and missing genotypes. We estimated that 2.6% of SNPs had null alleles compared with 2.3% with genotyping errors and that 40% of SNPs in which a parent and offspring were genotyped as different homozygotes had null alleles. Putative deletions were identified by null alleles at adjacent markers. We found two candidate deletions that were supported by fluorescence intensity data from a 60K SNP chip. One of the candidate deletions was from the Red Junglefowl, and one was present in both the Red Junglefowl and White Leghorn. Both candidate deletions spanned protein-coding regions and were close to a previously detected quantitative trait locus affecting body weight in this population. This study demonstrates that the similar to 50K SNP genotyping arrays now available for several agricultural species can be used to identify null alleles and deletions in data from large families. We suggest that our approach could be a useful complement to linkage analysis in experimental crosses.

Place, publisher, year, edition, pages
2013. Vol. 3, no 8, 1253-1260 p.
Keyword [en]
null allele, deletion, chicken
National Category
Natural Sciences
URN: urn:nbn:se:uu:diva-206988DOI: 10.1534/g3.113.006643ISI: 000322822300008OAI: oai:DiVA.org:uu-206988DiVA: diva2:646444
Available from: 2013-09-09 Created: 2013-09-09 Last updated: 2016-05-24Bibliographically approved

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Carlborg, Örjan
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Department of Cell and Molecular Biology
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