Unexpected High Polymorphism at the FABP4 Gene Unveils a Complex History for Pig Populations

Abstract

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 p S ¼ 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.

The FABP4 gene polymorphism is associated with meat tenderness in three Chinese native sheep breeds

“…There are many papers concerned with FABP4 as a candidate gene for fat traits of meat quality in pigs, and FABP4 shows high nucleotide variability (Nechtelberger et al, 2001;Mercadé et al, 2006;Ojeda et al, 2006). A mutation of the sheep FABP4 gene, which is located in intron 1 at nt 209 was associated with meat quality traits in our study.…”

Artificial selection of the melanocortin receptor 1 gene in Chinese domestic pigs during domestication

“…In addition to the p value, Watterson's estimator (y w ) was calculated from the observed number of polymorphic sites in samples, and this also suggested that the level of diversity in the MC1R-coding region was low in Chinese domestic pigs (y w ¼ 0.00049), comprising 14% of the diversity found in Chinese wild boars (y w ¼ 0.00356). Together, our findings show low levels of MC1R-coding region diversity in Chinese domestic pigs, which is in contrast to previous observations of higher levels of genetic diversity in domesticated pigs (Wu et al, 2007;Ojeda et al, 2006Ojeda et al, , 2008a. Our findings are consistent, however, with the logical theory of domestication events in that genetic diversity is generally thought to become lower after domestication.…”

“…Lower genetic diversity could be caused by population dynamics or artificial selection, which evidently happens in several crops (for example, sorghum, rice and maize) (Wang et al, 1999;Hamblin et al, 2006;Olsen et al, 2006). By contrast, previous studies reported unexpectedly high sequence variation in domesticated pigs even when considering the influences of target genes on economically important traits and the presence of strong artificial selection (Ojeda et al, 2006(Ojeda et al, , 2008a. More recently, Ramírez et al (2009) conducted a joint analysis of mitochondrial microsatellite and Y-chromosome polymorphisms, and showed that levels of genetic variation are similar in pigs and wild boars.…”

“…However, in Chinese domestic pigs, the p value was significantly smaller in the flanking 'MC1R whole' denotes the 1552 bp region, including the 5 0 untranslated region (5 0 UTR), the coding region and 3 0 UTR. The glucose phosphate isomerase pseudogene (GPIP) and melanocortin receptor 1 (MC1R) data are from this study, and the other data are from previous reports: FABP4 (Ojeda et al, 2006), mitochondrial DNA (Wu et al, 2007), FABP5 (Ojeda et al, 2008a) and IGF2 (Ojeda et al, 2008b).…”

Partial short-read sequencing of a highly inbred Iberian pig and genomics inference thereof

“…We did a grid search using this procedure for different values of N IB , N DU , m and t; assuming a true y ¼ 0.0013 for the autosomes and y ¼ 0.0005 for the X chromosome, and r, scaled recombination rate, 0.001. These values are taken from the literature (Ojeda et al, 2006;Amaral et al, 2009). The whole procedure was implemented in a Perl script with calls to MaCS and R.…”