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Originally published as Genetics Published Articles Ahead of Print on October 22, 2006.
Genetics, Vol. 174, 2119-2127, December 2006, Copyright © 2006
doi:10.1534/genetics.106.063057
Unexpected High Polymorphism at the FABP4 Gene Unveils a Complex History for Pig Populations
Ana Ojeda*,
Julio Rozas
,
Josep M. Folch* and
Miguel Pérez-Enciso*,
,1
* Departament de Ciència Animal i dels Aliments, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain, Departament de Genètica, Universitat de Barcelona, 08071 Barcelona, Spain and Institut Català de Recerca i Estudis Avançats, 08010 Barcelona, Spain
1 Corresponding author: Departament de Ciència Animal i dels Aliments, Facultat de Veterinária, Universitat Autònoma de Barcelona, 08193 Bellaterra, Spain.
E-mail: miguel.perez{at}uab.es
Fatty acid bing protein 4 (FABP4) plays a key role in fat regulation in mammals and is a strong positional candidate gene for the FAT1 quantitative trait locus located on porcine chromosome 4. DNA resequencing of the FABP4 gene region in 23 pigs from 10 breeds and wild boar revealed 134 variants in 6.4 kb, representing a silent nucleotide diversity of 
S = 0.01, much higher than reported so far in animal domestic species. Moreover, this diversity was highly structured. Also strikingly, the FABP4 phylogenetic tree did not show any geographical or breed origin clustering, with distant breeds sharing similar haplotypes and some of the most heterozygous samples pertaining to highly inbred animals like Iberian Guadyerbas (inbreeding coefficient 
0.3) or British Tamworth. In contrast, the cytochrome b (mtDNA) phylogenetic tree was coherent with geographical origin. The estimated age of the most recent common ancestor for the most divergent Iberian or Tamworth haplotypes was much older than domestication. An additional panel of 100 pigs from 8 different breeds and wild boar from Spain, Tunisia, Sardinia, and Japan was genotyped for seven selected single nucleotide polymorphisms and shows that high variability at the porcine FABP4 is the rule rather than the exception. Pig populations, even highly inbred, can maintain high levels of variability for surprisingly long periods of time.
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Genetics 2006 174: NP.
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