We describe the organization of a nascent international effort, the Functional Annotation of Animal Genomes (FAANG) project, whose aim is to produce comprehensive maps of functional elements in the genomes of domesticated animal species.Electronic supplementary materialThe online version of this article (doi:10.1186/s13059-015-0622-4) contains supplementary material, which is available to authorized users.

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Bim is a proapoptotic protein of the Bcl-2 family that shares only the short BH3 domain with other members. It has three isoforms, apparently produced by alternative splicing. The demonstration that Bim is essential for certain apoptotic responses and to prevent overproduction of hematopoietic cells suggests that it may be a tumor suppressor. We have, therefore, investigated the organization of the mouse Bim gene, delineating its promoter and splicing, and positioned the gene on both mouse and human chromosomes. Bim has six exons, but the third is a facultative intron that is spliced out in the mRNAs for the smaller isoforms (BimL and BimS), but not that encoding the largest isoform (BimEL). The 0.8-kb region 5' to exon 1, which contains a TATA-less promoter and binding sites for several transcription factors, can drive expression of a reporter gene. Mouse Bim localizes to the distal third of Chromosome (Chr) 2, near the F-G boundary, and its human counterpart to Chr 2q12 or q13. Deletions of these bands have been reported in ten tumors (eight hematopoietic), reinforcing the possibility that Bim is a tumor suppressor. These findings should help to clarify the regulation of Bim expression and to assess whether mutations involving Bim contribute to neoplastic and other diseases.

A quantitative trait locus (QTL) was identified by linkage analysis on bovine Chromosome 19 that affects the fatty acid, myristic acid (C14:0), in subcutaneous adipose tissue of pasture-fed beef cattle (99% level: experiment-wise significance). The QTL was also shown to have significant effects on ten fatty acids in the milk fat of pasture-fed dairy cattle. A positional candidate gene for this QTL was identified as fatty acid synthase (FASN), which is a multifunctional enzyme with a central role in the metabolism of lipids. Five single nucleotide polymorphisms (SNPs) were identified in the bovine FASN gene, and animals were genotyped for FASN SNPs in three different cattle resource populations. Linkage and association mapping results using these SNPs were consistent with FASN being the gene underlying the QTL. SNP substitution effects for C14:0 percentage were found to have an effect in the opposite direction in adipose fat to that in milk fat. It is concluded that SNPs in the bovine FASN gene are associated with variation in the fatty acid composition of adipose fat and milk fat.

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Single nucleotide polymorphisms (SNPs) in the calpain 1 (CAPN1) and calpastatin (CAST) genes were studied to determine their effects on meat tenderness in Bos taurus cattle. Strip loins (M. longissimus dorsi) were removed from cattle in four resource populations after slaughter (n = 1042), aged under controlled conditions until fixed times after rigor mortis, cooked and measured using a tenderometer. Animals were genotyped for the CAPN1 SNP c.947C>G (p.Ala316Gly; AF252504) and for the CAST SNP c.2959A>G (AF159246). Frequencies of CAPN1 C alleles ranged from 23% to 68%, and CAST A alleles from 84% to 99.5%. From all data combined, the CAPN1 CC genotype (compared with the GG genotype) was associated with a 20.1 +/- 1.7% reduced average shear force at intermediate stages of ageing (P < 0.001) and with a 9.5 +/- 1.3% reduction near ultimate tenderness (P < 0.001). The heterozygote was intermediate. For CAST, corresponding values for AA compared with AG genotypes were reductions of 8.6 +/- 2.0% and 5.1 +/- 1.6% respectively (both P < 0.001), but there were too few GG genotypes for comparison. There were small interactions between the CAPN1 and CAST genotypes. For the CAPN1 and CAST genotypes combined, the maximal genotype effect in average shear force was 25.7 +/- 5.5% (P < 0.001) at intermediate stages and 15.2 +/- 4.8% near ultimate tenderness (P < 0.01).

This study investigated the effects of a SNP in the myostatin gene (MSTN or growth differentiation factor 8, GDF8) on birth, growth, carcass, and beef quality traits in Australia (Aust.) and New Zealand (NZ). The SNP is a cytosine to adenine transversion in exon 1, causing an amino acid substitution of leucine for phenylalanine(94) (F94L). The experiment used crosses between the Jersey and Limousin breeds, with the design being a backcross using first-cross bulls of Jersey x Limousin or Limousin x Jersey breeding, mated to Jersey and Limousin cows. Progeny were genotyped for the myostatin SNP and phenotyped in Aust., with finishing on feedlot (366 calves, over 3 birth years) and in NZ with finishing on pasture (416 calves, over 2 birth years). The effect of the F94L allele (A allele) on birth and growth traits was not significant. The F94L allele in Limousin backcross calves was associated with an increase in meat weight (7.3 and 5.9% of the trait mean in Aust. and NZ, respectively, P < 0.001), and a reduction in fat depth (-13.9 and -18.7% of the trait means on live calves (600 d) and carcasses, respectively, Aust. only, P < 0.001), intramuscular fat content (-8.2% of the trait mean in Aust., P < 0.05; -7.1% in NZ, not significant), total carcass fat weight (-16.5 and -8.1% of the trait mean, Aust. and NZ; P < 0.001 and P < 0.05, respectively). Meat tenderness, pH, and cooking loss of the M. longissimus dorsi were not affected by the F94L variant. In the Jersey backcross calves, additive and dominance effects were confounded because the F94L allele was not segregating in the Jersey dams. The combined effects, however, were significant on LM area (4.4% in both Aust., P < 0.05, and NZ, P < 0.01), channel fat (-11.7%, NZ only, P < 0.01), rib fat depth (-11.2%, NZ only, P < 0.05), and carcass fat weight (-7.1%, NZ only, P < 0.05). The results provide strong evidence that this myostatin F94L variant provides an intermediate and more useful phenotype than the more severe double-muscling phenotype caused by knockout mutations in the myostatin gene.