Tissue resources for the functional annotation of animal genomes

Authors: TIXIER-BOICHARD, MICHELE - Institut National De La Recherche Agronomique (INRA); FABRE, STEPHANIE - Institut National De La Recherche Agronomique (INRA); DHORNE-POLLET, SOPHIE - Institut National De La Recherche Agronomique (INRA); GOUBIL, ADELINE - Institut National De La Recherche Agronomique (INRA); ACLOQUE, HERVE - Institut National De La Recherche Agronomique (INRA); VINCENT-NAULLEAU, SILVIA - Université Paris-Saclay; ROSS, PABLO - University Of California, Davis; WANG, YING - University Of California, Davis; CHANTHAVIXAY, GANREA - University Of California, Davis; Cheng, Hans; CATHERINE, ERNST - Michigan State University; Leesburg, Vicki; GIUFFRA, ELISABETTA - Institut National De La Recherche Agronomique (INRA); ZHOU, HUAIJUN - University Of California, Davis

Submitted to: Frontiers in Genetics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 4/29/2021
Publication Date: 6/21/2021
Citation: Tixier-Boichard, M., Fabre, S., Dhorne-Pollet, S., Goubil, A., Acloque, H., Vincent-Naulleau, S., Ross, P., Wang, Y., Chanthavixay, G., Cheng, H.H., Catherine, E., Leesburg, V.L., Giuffra, E., Zhou, H. 2021. Tissue resources for the functional annotation of animal genomes. Frontiers in Genetics. 12:666265. https://doi.org/10.3389/fgene.2021.666265.
DOI: https://doi.org/10.3389/fgene.2021.666265

Interpretive Summary: With the advent of full genome sequences for many organisms including farm animals, biology is rapidly focusing on and utilizing genomics. While genome assemblies and the identification of coding genes greatly enhanced our ability to connect DNA sequence (genotype) to traits of interest (phenotype), it is becoming clear that genomes need to be more comprehensively annotated, especially with respect to regulatory elements. In this submission, as part of the international effort to functionally annotate animal genomes (FAANG), 73 different tissues and over 5,000 samples were collected from cattle, goat, pig, and chicken. Standards were established to define the type of tissue, how they were processed for specific protocols, and more. Once analyzed, this rich resource will help decipher farm animal animals, which will lead to superior genetic improvement and ultimately, healthier and more productive animals and animal products.

Technical Abstract: In order to generate an atlas of the functional elements driving genome expression in domestic animals, the FAANG strategy was to sample many tissues from a few animals of different species, sexes, ages, and production stages. This paper presents the collection of reference tissue samples for four species produced by two pilot projects, at INRAE and UC Davis (UCD). There were three mammals (cattle, goat, and pig) and one bird (chicken). It describes the metadata needed to characterize these reference sets (1) for animals with origin and selection history, physiological status and environmental conditions (2) for samples with collection site and tissue/cell processing (3) for quality control (4) for storage and further distribution. Three sets are identified: set 1 comprises tissues which collection can be standardized and for which representative aliquots can be easily distributed (liver, spleen, lung, heart, abdominal fat, skin, muscle); set 2 comprises tissues requiring special protocols because of their cellular heterogeneity (brain, digestive tract, secretory organs, gonads and gametes, reproductive tract, immune tissues, skin, cartilage); set 3 comprises specific cell preparations (immune cells, tracheal epithelial cells). Dedicated sampling protocols were established and uploaded on https://faang/data/protocol/samples. Specificities between mammals and chicken are described when relevant. A total of 73 different tissues or tissue sections were collected and 21 are common to the four species. Having a common set of tissues will facilitate the transfer of knowledge within and between species. Combining data on the same samples will facilitate data integration. Quality control was performed on a batch of tissues with RNA extraction and RNA quality control. A total of more than 5000 samples have been stored with unique identifiers and more than 4000 were uploaded onto the Biosamples database, provided that standard ontologies were available to describe the sample. Many tissues have already been used to implement FAANG assays, with published results. All samples are available without restriction for further assays. The requesting procedure is described. Members of FAANG are encouraged to apply a range of molecular assays to characterize the functional status of collected samples and share their results, in line with the FAIR data principles.