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Iannuccelli N, Sarry J, Billon Y, Aymard P, Helies V, Cabau C, Donnadieu C, Demars J. Rabbit targeted genomic sequences after heterologous hybridization using human exome. BMC Res Notes 2022; 15:282. [PMID: 35986355 PMCID: PMC9389681 DOI: 10.1186/s13104-022-06162-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2022] [Accepted: 07/27/2022] [Indexed: 11/16/2022] Open
Abstract
Causal mutations for major genes that underlie a broad range of morphological traits are often located within exons of genes that then affect protein functions. Non-model organism genetic studies are not easy to perform due to the lack of genome-wide molecular tools such as SNP genotyping array. Genotyping-By-Sequencing (GBS) methods offer an alternative. Consequently, we used this approach that is focused on the exome to target and identify major genes in rabbit populations. Data description We used a heterologous enrichment method before sequencing, allowing us to capture the rabbit exome using the marketed human panel since mammal protein coding genes are well conserved across the phylogenic tree of species. This targeted strategy was performed on 52 French rabbits from 5 different French strains (Californian, New-Zealand, Castor, Chinchilla and Laghmere). We generated 3.4 billion sequencing reads and approximately 29–140 million of reads per DNA sample. The expected exome coverage per sample ranged between 118 and 566X. The present dataset could be useful for the scientific community working on rabbit species in order to (i) improve the annotation of the rabbit reference genome Oryctolagus cuniculus (OryCun2.0), (ii) enrich the characterization of polymorphisms segregating in rabbits and (iii) evaluate the genetic biodiversity in different rabbit strains. Raw sequences were deposited in the European Nucleotide Archive (ENA) at the European Molecular Biology Laboratory- European Bioinformatics Institute (EMBL-EBI) data portal under bioproject accession number PRJEB37917.
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Demars J, Labrune Y, Iannuccelli N, Deshayes A, Leroux S, Gilbert H, Aymard P, Benitez F, Riquet J. A genome-wide epistatic network underlies the molecular architecture of continuous color variation of body extremities. Genomics 2022; 114:110361. [PMID: 35378242 DOI: 10.1016/j.ygeno.2022.110361] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/17/2021] [Revised: 03/22/2022] [Accepted: 03/29/2022] [Indexed: 01/14/2023]
Abstract
Deciphering the molecular architecture of coat coloration for a better understanding of the biological mechanisms underlying pigmentation still remains a challenge. We took advantage of a rabbit French experimental population in which both a pattern and a gradient of coloration from white to brown segregated within the himalayan phenotype. The whole experimental design was genotyped using the high density Affymetrix® AxiomOrcun™ SNP Array and phenotyped into 6 different groups ordered from the lighter to the darker. Genome-wide association analyses pinpointed an oligogenic determinism, under recessive and additive inheritance, involving genes already known in melanogenesis (ASIP, KIT, MC1R, TYR), and likely processed pseudogenes linked to ribosomal function, RPS20 and RPS14. We also identified (i) gene-gene interactions through ASIP:MC1R affecting light cream/beige phenotypes while KIT:RPS responsible of dark chocolate/brown colors and (ii) a genome-wide epistatic network involving several others coloration genes such as POT1 or HPS5. Finally, we determined the recessive inheritance of the English spotting phenotype likely involving a copy number variation affecting at least the end of the coding sequence of the KIT gene. Our analyses of coloration as a continuous trait allowed us to go beyond much of the established knowledge through the detection of additional genes and gene-gene interactions that may contribute to the molecular architecture of the coloration phenotype.
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Affiliation(s)
- Julie Demars
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326 Castanet-Tolosan, France.
| | - Yann Labrune
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326 Castanet-Tolosan, France.
| | - Nathalie Iannuccelli
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326 Castanet-Tolosan, France.
| | - Alice Deshayes
- UMR967, CEA, INSERM, Institut de Radiobiologie Cellulaire et Moléculaire, Télomères et réparation du chromosome, F- 92265 Fontenay-aux-Roses, France.
| | - Sophie Leroux
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326 Castanet-Tolosan, France.
| | - Hélène Gilbert
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326 Castanet-Tolosan, France.
| | - Patrick Aymard
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326 Castanet-Tolosan, France.
| | - Florence Benitez
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326 Castanet-Tolosan, France.
| | - Juliette Riquet
- GenPhySE, Université de Toulouse, INRAE, ENVT, Toulouse INP, F-31326 Castanet-Tolosan, France.
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Adaptation of Livestock to New Diets Using Feed Components without Competition with Human Edible Protein Sources-A Review of the Possibilities and Recommendations. Animals (Basel) 2021; 11:ani11082293. [PMID: 34438751 PMCID: PMC8388495 DOI: 10.3390/ani11082293] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/15/2021] [Revised: 07/12/2021] [Accepted: 07/14/2021] [Indexed: 01/30/2023] Open
Abstract
Simple Summary Livestock feed contains components that can also be consumed by humans, which may become less available for livestock. Proteins are such components that may become less available for livestock feed. This review focuses on using alternative protein sources in feed. We may expect protein efficiency problems and we discuss how these could be solved using a combination of alternative protein sources and animal breeding. We make recommendations for the use and optimization of novel protein sources. Abstract Livestock feed encompasses both human edible and human inedible components. Human edible feed components may become less available for livestock. Especially for proteins, this calls for action. This review focuses on using alternative protein sources in feed and protein efficiency, the expected problems, and how these problems could be solved. Breeding for higher protein efficiency leading to less use of the protein sources may be one strategy. Replacing (part of) the human edible feed components with human inedible components may be another strategy, which could be combined with breeding for livestock that can efficiently digest novel protein feed sources. The potential use of novel protein sources is discussed. We discuss the present knowledge on novel protein sources, including the consequences for animal performance and production costs, and make recommendations for the use and optimization of novel protein sources (1) to improve our knowledge on the inclusion of human inedible protein into the diet of livestock, (2) because cooperation between animal breeders and nutritionists is needed to share knowledge and combine expertise, and (3) to investigate the effect of animal-specific digestibility of protein sources for selective breeding for each protein source and for precision feeding. Nutrigenetics and nutrigenomics will be important tools.
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Sánchez JP, Legarra A, Velasco-Galilea M, Piles M, Sánchez A, Rafel O, González-Rodríguez O, Ballester M. Genome-wide association study for feed efficiency in collective cage-raised rabbits under full and restricted feeding. Anim Genet 2020; 51:799-810. [PMID: 32697387 PMCID: PMC7540659 DOI: 10.1111/age.12988] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2019] [Revised: 06/16/2020] [Accepted: 06/26/2020] [Indexed: 01/30/2023]
Abstract
Feed efficiency (FE) is one of the most economically and environmentally relevant traits in the animal production sector. The objective of this study was to gain knowledge about the genetic control of FE in rabbits. To this end, GWASs were conducted for individual growth under two feeding regimes (full feeding and restricted) and FE traits collected from cage groups, using 114 604 autosome SNPs segregating in 438 rabbits. Two different models were implemented: (1) an animal model with a linear regression on each SNP allele for growth trait; and (2) a two‐trait animal model, jointly fitting the performance trait and each SNP allele content, for FE traits. This last modeling strategy is a new tool applied to GWAS and allows information to be considered from non‐genotyped individuals whose contribution is relevant in the group average traits. A total of 189 SNPs in 17 chromosomal regions were declared to be significantly associated with any of the five analyzed traits at a chromosome‐wide level. In 12 of these regions, 20 candidate genes were proposed to explain the variation of the analyzed traits, including genes such as FTO, NDUFAF6 and CEBPA previously associated with growth and FE traits in monogastric species. Candidate genes associated with behavioral patterns were also identified. Overall, our results can be considered as the foundation for future functional research to unravel the actual causal mutations regulating growth and FE in rabbits.
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Affiliation(s)
- J P Sánchez
- Animal Breeding and Genetic Program, Institute of Agriculture and Food Research and Technology, Caldes de Montbui, 08140, Spain
| | - A Legarra
- GenPhySE, National Institute for Agronomic Research, Castanet-Tolosan, 31326, France
| | - M Velasco-Galilea
- Animal Breeding and Genetic Program, Institute of Agriculture and Food Research and Technology, Caldes de Montbui, 08140, Spain
| | - M Piles
- Animal Breeding and Genetic Program, Institute of Agriculture and Food Research and Technology, Caldes de Montbui, 08140, Spain
| | - A Sánchez
- Centre for Research in Agricultural Genomics, Campus Universitat Autònoma de Barcelona, Cerdanyola, 08193, Spain
| | - O Rafel
- Animal Breeding and Genetic Program, Institute of Agriculture and Food Research and Technology, Caldes de Montbui, 08140, Spain
| | - O González-Rodríguez
- Animal Breeding and Genetic Program, Institute of Agriculture and Food Research and Technology, Caldes de Montbui, 08140, Spain
| | - M Ballester
- Animal Breeding and Genetic Program, Institute of Agriculture and Food Research and Technology, Caldes de Montbui, 08140, Spain
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Fang S, Chen X, Zhou L, Wang C, Chen Q, Lin R, Xiao T, Gan Q. Faecal microbiota and functional capacity associated with weaning weight in meat rabbits. Microb Biotechnol 2019; 12:1441-1452. [PMID: 31571427 PMCID: PMC6801154 DOI: 10.1111/1751-7915.13485] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/08/2019] [Revised: 05/15/2019] [Accepted: 08/15/2019] [Indexed: 12/18/2022] Open
Abstract
Weaning weight is an important economic trait in the meat rabbit industry. Evidence has linked the gut microbiota to health and production performance in rabbits. However, the effect of gut microbiota on meat rabbit weaning weight remains unclear. In this study, we performed 16S rRNA gene sequencing analysis of 135 faecal samples from commercial Ira rabbits. We detected 50 OTUs significantly associated with weaning weight. OTUs that showed positive associations with weaning weight were mostly members of the family Ruminococcaceae which are important in degrading dietary fibres and producing butyrate. On the contrary, OTUs annotated to genera Blautia, Lachnoclostridium and Butyricicoccus correlated with fat deposition were negatively associated with weaning weight. Predicted functional capacity analysis revealed that 91 KOs and 26 KEGG pathways exhibited potential correlations with weaning weight. We found that gut microbiota involved in the metabolism of amino acids, butanoate, energy and monosaccharides affected weaning weight. Additionally, cross-validation analysis indicated that 16.16% of the variation in weaning weight was explained by the gut microbiome. Our findings provide important information to improve weaning weight of meat rabbits by modulating their gut microbiome.
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Affiliation(s)
- Shaoming Fang
- College of Animal ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Xuan Chen
- College of Life ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Liwen Zhou
- College of Animal ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Chongchong Wang
- College of Animal ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Qiaohui Chen
- College of Animal ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Ruiyi Lin
- College of Animal ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - Tianfang Xiao
- College of Animal ScienceFujian Agriculture and Forestry UniversityFuzhouChina
| | - QianFu Gan
- College of Animal ScienceFujian Agriculture and Forestry UniversityFuzhouChina
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