Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project

Andersson, Leif C.; Archibald, Alan; Bottema, Cynthia D.K.; Bräuning, Rüdiger; Burgess, Shane C.; Burt, David W.; Casas, Eduardo; Cheng, Hans H.; Clarke, Laura; Couldrey, Christine; Dalrymple, Brian P.; Elsik, Christine G.; Foissac, Sylvain; Giuffra, Elisabetta; Groenen, Martien A. M.; Hayes, Ben J.; Huang, Lu Sheng S.; Khatib, Hassan; Kijas, James W.; Kim, Heebal; Lunney, Joan K.; McCarthy, Fiona M.; McEwan, John C.; Moore, S. S.; Nanduri, Bindu; Notredame, Cédric; Palti, Yniv; Plastow, Graham; Reecy, James M.; Rohrer, G. A.; Sarropoulou, Elena; Schmidt, Carl J.; Silverstein, Jeffrey T.; Tellam, Ross L.; Tixier‐Boichard, Michèle; Tosser‐Klopp, Gwenola; Tuggle, Christopher K.; Vilkki, Johanna; White, Stephen N.; Zhao, Shuhong; Zhou, Huaijun

doi:10.1186/s13059-015-0622-4

Cited by 292 publications

(257 citation statements)

References 53 publications

(57 reference statements)

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“…In particular, about 14% of current porcine assembly is of low quality, according to (Warr et al, 2015). Ongoing annotation initiatives in livestock genomes such as FAANG (Andersson et al, 2015) and new assemblies should alleviate this problem.…”

Section: Discussionmentioning

confidence: 99%

The ‘heritability’ of domestication and its functional partitioning in the pig

et al. 2016

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We propose to estimate the proportion of variance explained by regression on genome-wide markers (or genomic heritability) when wild/domestic status is considered the phenotype of interest. This approach differs from the standard Fst in that it can accommodate genetic similarity between individuals in a general form. We apply this strategy to complete genome data from 47 wild and domestic pigs from Asia and Europe. When we partitioned the total genomic variance into components associated to subsets of single nucleotide polymorphisms (SNPs) defined in terms of their annotation, we found that potentially deleterious non-synonymous mutations (9566 SNPs) explained as much genetic variance as the whole set of 25 million SNPs. This suggests that domestication may have affected protein sequence to a larger extent than regulatory or other kinds of mutations. A pathway-guided analysis revealed ovarian steroidogenesis and leptin signaling as highly relevant in domestication. The genomic regression approach proposed in this study revealed molecular processes not apparent through typical differentiation statistics. We propose that at least some of these processes are likely new discoveries because domestication is a dynamic process of genetic selection, which may not be completely characterized by a static metric like Fst. Nevertheless, and despite some particularly influential mutation types or pathways, our analyses tend to rule out a simplistic genetic basis for the domestication process: neither a single pathway nor a unique set of SNPs can explain the process as a whole.

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Section: Discussionmentioning

confidence: 99%

The ‘heritability’ of domestication and its functional partitioning in the pig

et al. 2016

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“…A consortium called Functional Annotation of ANimal Genomes (FAANG [38]) is now planning to annotate livestock genomes for such histone marks as well as other markers of open chromatin in a similar fashion to that in humans (the ENCODE consortium).…”

Section: Discussionmentioning

confidence: 99%

Genetics of complex traits: prediction of phenotype, identification of causal polymorphisms and genetic architecture

Goddard

Kemper

MacLeod³

et al. 2016

Proc. R. Soc. B.

132

106

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Complex or quantitative traits are important in medicine, agriculture and evolution, yet, until recently, few of the polymorphisms that cause variation in these traits were known. Genome-wide association studies (GWAS), based on the ability to assay thousands of single nucleotide polymorphisms (SNPs), have revolutionized our understanding of the genetics of complex traits. We advocate the analysis of GWAS data by a statistical method that fits all SNP effects simultaneously, assuming that these effects are drawn from a prior distribution. We illustrate how this method can be used to predict future phenotypes, to map and identify the causal mutations, and to study the genetic architecture of complex traits. The genetic architecture of complex traits is even more complex than previously thought: in almost every trait studied there are thousands of polymorphisms that explain genetic variation. Methods of predicting future phenotypes, collectively known as genomic selection or genomic prediction, have been widely adopted in livestock and crop breeding, leading to increased rates of genetic improvement.

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“…Currently, important developments regarding the assembly and the annotation of genomes including cattle are on their way. These developments, more specifically the FAANG Consortium (Andersson et al, 2015), will contribute to identify candidate genes and regulatory elements more efficiently than at present.…”

Section: Challenges With High-density Genotypes For Gene Discoverymentioning

confidence: 99%

“…These studies enable the prediction of the function encoded in sequences. Andersson et al (2015) argue that filling the genotype-tophenotype gap requires functional genome annotation of species with substantial phenotype information. The FAANG initiative aims at improving the annotation of the genome of domesticated animal species by creating standardized protocols for sampling, storing, and analyzing the information among the participating research groups (Clarke et al, 2015).…”

Section: Annotation Of the Cattle Genomementioning

confidence: 99%

“…The FAANG consortium aims at identifying all functional elements in the genome of domesticated animal species (Andersson et al, 2015), and involves a collaboration between several research groups worldwide. In a first stage, many different tissues across domesticated animal species will be sampled, such as skeletal muscle, adipose and liver tissues, and in addition, samples of reproductive, immune and nervous systems will be collected.…”

Section: Annotation Of the Cattle Genomementioning

confidence: 99%

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Mapping and fine-mapping of genetic factors affecting bovine milk composition

Duchemin¹

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Coordinated international action to accelerate genome-to-phenome with FAANG, the Functional Annotation of Animal Genomes project

Cited by 292 publications

References 53 publications

The ‘heritability’ of domestication and its functional partitioning in the pig

The ‘heritability’ of domestication and its functional partitioning in the pig

Genetics of complex traits: prediction of phenotype, identification of causal polymorphisms and genetic architecture

Mapping and fine-mapping of genetic factors affecting bovine milk composition

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