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Devailly G, Fève K, Saci S, Sarry J, Valière S, Lluch J, Bouchez O, Ravon L, Billon Y, Gilbert H, Riquet J, Beaumont M, Demars J. Divergent selection for feed efficiency in pigs altered the duodenum transcriptomic response to feed intake and its DNA methylation profiles. Physiol Genomics 2024; 56:397-408. [PMID: 38497119 DOI: 10.1152/physiolgenomics.00123.2023] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 03/01/2024] [Accepted: 03/10/2024] [Indexed: 03/19/2024] Open
Abstract
Feed efficiency is a trait of interest in pigs as it contributes to lowering the ecological and economical costs of pig production. A divergent genetic selection experiment from a Large White pig population was performed for 10 generations, leading to pig lines with relatively low- (LRFI) and high- (HRFI) residual feed intake (RFI). Feeding behavior and metabolic differences have been previously reported between the two lines. We hypothesized that part of these differences could be related to differential sensing and absorption of nutrients in the proximal intestine. We investigated the duodenum transcriptome and DNA methylation profiles comparing overnight fasting with ad libitum feeding in LRFI and HRFI pigs (n = 24). We identified 1,106 differentially expressed genes between the two lines, notably affecting pathways of the transmembrane transport activity and related to mitosis or chromosome separation. The LRFI line showed a greater transcriptomic response to feed intake than the HRFI line. Feed intake affected genes from both anabolic and catabolic pathways in the pig duodenum, such as rRNA production and autophagy. Several nutrient transporter and tight junction genes were differentially expressed between lines and/or by short-term feed intake. We also identified 409 differentially methylated regions in the duodenum mucosa between the two lines, while this epigenetic mark was less affected by feeding. Our findings highlighted that the genetic selection for feed efficiency in pigs changed the transcriptome profiles of the duodenum, and notably its response to feed intake, suggesting key roles for this proximal gut segment in mechanisms underlying feed efficiency.NEW & NOTEWORTHY The duodenum is a key organ for the hunger/satiety loop and nutrient sensing. We investigated how the duodenum transcriptome and DNA methylation profiles are affected by feed intakes in pigs. We observed thousands of changes in gene expression levels between overnight-fasted and fed pigs in high-feed efficiency pig lines, but almost none in the related low-feed efficiency pig line.
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Affiliation(s)
| | - Katia Fève
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Safia Saci
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Julien Sarry
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Sophie Valière
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Jérôme Lluch
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Olivier Bouchez
- INRAE, US 1426, GeT-PlaGe, Genotoul, Castanet-Tolosan, France
| | - Laure Ravon
- Pig Phenotyping and Innovative Breeding Facility, GenESI, UE1372, INRAE, Surgères, France
| | - Yvon Billon
- Pig Phenotyping and Innovative Breeding Facility, GenESI, UE1372, INRAE, Surgères, France
| | - Hélène Gilbert
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Juliette Riquet
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Martin Beaumont
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
| | - Julie Demars
- GenPhySE, Université de Toulouse, INRAE, ENVT, Castanet Tolosan, France
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Freitas FAO, Brito LF, Fanalli SL, Gonçales JL, da Silva BPM, Durval MC, Ciconello FN, de Oliveira CS, Nascimento LE, Gervásio IC, Gomes JD, Moreira GCM, Silva-Vignato B, Coutinho LL, de Almeida VV, Cesar ASM. Identification of eQTLs using different sets of single nucleotide polymorphisms associated with carcass and body composition traits in pigs. BMC Genomics 2024; 25:14. [PMID: 38166730 PMCID: PMC10759680 DOI: 10.1186/s12864-023-09863-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2023] [Accepted: 11/30/2023] [Indexed: 01/05/2024] Open
Abstract
BACKGROUND Mapping expression quantitative trait loci (eQTLs) in skeletal muscle tissue in pigs is crucial for understanding the relationship between genetic variation and phenotypic expression of carcass traits in meat animals. Therefore, the primary objective of this study was to evaluate the impact of different sets of single nucleotide polymorphisms (SNP), including scenarios removing SNPs pruned for linkage disequilibrium (LD) and SNPs derived from SNP chip arrays and RNA-seq data from liver, brain, and skeletal muscle tissues, on the identification of eQTLs in the Longissimus lumborum tissue, associated with carcass and body composition traits in Large White pigs. The SNPs identified from muscle mRNA were combined with SNPs identified in the brain and liver tissue transcriptomes, as well as SNPs from the GGP Porcine 50 K SNP chip array. Cis- and trans-eQTLs were identified based on the skeletal muscle gene expression level, followed by functional genomic analyses and statistical associations with carcass and body composition traits in Large White pigs. RESULTS The number of cis- and trans-eQTLs identified across different sets of SNPs (scenarios) ranged from 261 to 2,539 and from 29 to 13,721, respectively. Furthermore, 6,180 genes were modulated by eQTLs in at least one of the scenarios evaluated. The eQTLs identified were not significantly associated with carcass and body composition traits but were significantly enriched for many traits in the "Meat and Carcass" type QTL. The scenarios with the highest number of cis- (n = 304) and trans- (n = 5,993) modulated genes were the unpruned and LD-pruned SNP set scenarios identified from the muscle transcriptome. These genes include 84 transcription factor coding genes. CONCLUSIONS After LD pruning, the set of SNPs identified based on the transcriptome of the skeletal muscle tissue of pigs resulted in the highest number of genes modulated by eQTLs. Most eQTLs are of the trans type and are associated with genes influencing complex traits in pigs, such as transcription factors and enhancers. Furthermore, the incorporation of SNPs from other genomic regions to the set of SNPs identified in the porcine skeletal muscle transcriptome contributed to the identification of eQTLs that had not been identified based on the porcine skeletal muscle transcriptome alone.
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Affiliation(s)
- Felipe André Oliveira Freitas
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, 47907, USA
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635- 900, SP, Brazil
| | - Simara Larissa Fanalli
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635- 900, SP, Brazil
| | - Janaína Lustosa Gonçales
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil
| | | | - Mariah Castro Durval
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635- 900, SP, Brazil
| | - Fernanda Nery Ciconello
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil
| | | | | | - Izally Carvalho Gervásio
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil
| | - Julia Dezen Gomes
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil
| | | | - Bárbara Silva-Vignato
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635- 900, SP, Brazil
| | - Luiz Lehmann Coutinho
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil
| | - Vivian Vezzoni de Almeida
- College of Veterinary Medicine and Animal Science, Federal University of Goiás, Goiânia, 74001-970, GO, Brazil
| | - Aline Silva Mello Cesar
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, 13416-000, SP, Brazil.
- Faculty of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635- 900, SP, Brazil.
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Nosková A, Mehrotra A, Kadri NK, Lloret-Villas A, Neuenschwander S, Hofer A, Pausch H. Comparison of two multi-trait association testing methods and sequence-based fine mapping of six additive QTL in Swiss Large White pigs. BMC Genomics 2023; 24:192. [PMID: 37038103 PMCID: PMC10084639 DOI: 10.1186/s12864-023-09295-4] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/14/2022] [Accepted: 04/04/2023] [Indexed: 04/12/2023] Open
Abstract
BACKGROUND Genetic correlations between complex traits suggest that pleiotropic variants contribute to trait variation. Genome-wide association studies (GWAS) aim to uncover the genetic underpinnings of traits. Multivariate association testing and the meta-analysis of summary statistics from single-trait GWAS enable detecting variants associated with multiple phenotypes. In this study, we used array-derived genotypes and phenotypes for 24 reproduction, production, and conformation traits to explore differences between the two methods and used imputed sequence variant genotypes to fine-map six quantitative trait loci (QTL). RESULTS We considered genotypes at 44,733 SNPs for 5,753 pigs from the Swiss Large White breed that had deregressed breeding values for 24 traits. Single-trait association analyses revealed eleven QTL that affected 15 traits. Multi-trait association testing and the meta-analysis of the single-trait GWAS revealed between 3 and 6 QTL, respectively, in three groups of traits. The multi-trait methods revealed three loci that were not detected in the single-trait GWAS. Four QTL that were identified in the single-trait GWAS, remained undetected in the multi-trait analyses. To pinpoint candidate causal variants for the QTL, we imputed the array-derived genotypes to the sequence level using a sequenced reference panel consisting of 421 pigs. This approach provided genotypes at 16 million imputed sequence variants with a mean accuracy of imputation of 0.94. The fine-mapping of six QTL with imputed sequence variant genotypes revealed four previously proposed causal mutations among the top variants. CONCLUSIONS Our findings in a medium-size cohort of pigs suggest that multivariate association testing and the meta-analysis of summary statistics from single-trait GWAS provide very similar results. Although multi-trait association methods provide a useful overview of pleiotropic loci segregating in mapping populations, the investigation of single-trait association studies is still advised, as multi-trait methods may miss QTL that are uncovered in single-trait GWAS.
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Affiliation(s)
- A Nosková
- ETH Zürich, Universitätstrasse 2, 8092, Zürich, Switzerland.
| | - A Mehrotra
- ETH Zürich, Universitätstrasse 2, 8092, Zürich, Switzerland
| | - N K Kadri
- ETH Zürich, Universitätstrasse 2, 8092, Zürich, Switzerland
| | | | | | - A Hofer
- SUISAG, Allmend 10, 6204, Sempach, Switzerland
| | - H Pausch
- ETH Zürich, Universitätstrasse 2, 8092, Zürich, Switzerland
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Sun J, Xiao J, Jiang Y, Wang Y, Cao M, Wei J, Yu T, Ding X, Yang G. Genome-Wide Association Study on Reproductive Traits Using Imputation-Based Whole-Genome Sequence Data in Yorkshire Pigs. Genes (Basel) 2023; 14:genes14040861. [PMID: 37107619 PMCID: PMC10137786 DOI: 10.3390/genes14040861] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2023] [Revised: 03/28/2023] [Accepted: 03/31/2023] [Indexed: 04/05/2023] Open
Abstract
Reproductive traits have a key impact on production efficiency in the pig industry. It is necessary to identify the genetic structure of potential genes that influence reproductive traits. In this study, a genome-wide association study (GWAS) based on chip and imputed data of five reproductive traits, namely, total number born (TNB), number born alive (NBA), litter birth weight (LBW), gestation length (GL), and number of weaned (NW), was performed in Yorkshire pigs. In total, 272 of 2844 pigs with reproductive records were genotyped using KPS Porcine Breeding SNP Chips, and then chip data were imputed to sequencing data using two online software programs: the Pig Haplotype Reference Panel (PHARP v2) and Swine Imputation Server (SWIM 1.0). After quality control, we performed GWAS based on chip data and the two different imputation databases by using fixed and random model circulating probability unification (FarmCPU) models. We discovered 71 genome-wide significant SNPs and 25 potential candidate genes (e.g., SMAD4, RPS6KA2, CAMK2A, NDST1, and ADCY5). Functional enrichment analysis revealed that these genes are mainly enriched in the calcium signaling pathway, ovarian steroidogenesis, and GnRH signaling pathways. In conclusion, our results help to clarify the genetic basis of porcine reproductive traits and provide molecular markers for genomic selection in pig breeding.
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Affiliation(s)
- Jingchun Sun
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Jinhong Xiao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Yifan Jiang
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Yaxin Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Minghao Cao
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Jialin Wei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Taiyong Yu
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
| | - Xiangdong Ding
- National Engineering Laboratory for Animal Breeding, Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture, College of Animal Science and Technology, China Agricultural University, Beijing 100193, China
| | - Gongshe Yang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Laboratory of Animal Fat Deposition & Muscle Development, College of Animal Science and Technology, Northwest A&F University, Xianyang 712100, China
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Analysis of merged transcriptomic and genomic datasets to identify genes and pathways underlying residual feed intake in growing pigs. Sci Rep 2022; 12:21946. [PMID: 36536008 PMCID: PMC9763391 DOI: 10.1038/s41598-022-26496-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 12/15/2022] [Indexed: 12/23/2022] Open
Abstract
Improvement of feed efficiency (FE) in pigs is an important milestone in order to reduce the economic and environmental impact of pig production. The goal of finding biomarkers for FE has persisted for decades. However, due to the complexity of the FE trait, these goals have still not been met. Here, we search for quantitative trait loci (QTL), candidate genes, and biological pathways associated with FE using both genotype and RNA-seq data. We obtained genotype and colon epithelium RNA-seq data for 375 and 96 pigs, respectively. In total, a genome-wide association study (GWAS) and differential expression (DE) analysis led to detection of three QTL on SSC9 and 17 DE-genes associated with FE. Possible intersection points between genes located in QTL and DE-genes were found on levels of transcription factor-target interaction. Moreover, cis-eQTL analysis revealed associations between genotype and expression levels of three DE-genes and three genes located in the GWAS QTLs, which may establish the connection between genotype and phenotype through DE. Finally, single nucleotide polymorphism calling using RNA-seq data for genes located in GWAS QTLs revealed 53 polymorphisms of which eleven were missense variants.
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Identification of Differentially Expressed miRNAs in Porcine Adipose Tissues and Evaluation of Their Effects on Feed Efficiency. Genes (Basel) 2022; 13:genes13122406. [PMID: 36553673 PMCID: PMC9778086 DOI: 10.3390/genes13122406] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/13/2022] [Accepted: 12/16/2022] [Indexed: 12/23/2022] Open
Abstract
Feed efficiency (FE) is a very important trait affecting the economic benefits of pig breeding enterprises. Adipose tissue can modulate a variety of processes such as feed intake, energy metabolism and systemic physiological processes. However, the mechanism by which microRNAs (miRNAs) in adipose tissues regulate FE remains largely unknown. Therefore, this study aimed to screen potential miRNAs related to FE through miRNA sequencing. The miRNA profiles in porcine adipose tissues were obtained and 14 miRNAs were identified differentially expressed in adipose tissues of pigs with extreme differences in FE, of which 9 were down-regulated and 5 were up-regulated. GO and KEGG analyses indicated that these miRNAs were significantly related to lipid metabolism and these miRNAs modulated FE by regulating lipid metabolism. Subsequently, quantitative reverse transcription-polymerase chain reaction (qRT-PCR) of five randomly selected DEMs was used to verify the reliability of miRNA-seq data. Furthermore, 39 differentially expressed target genes of these DEMs were obtained, and DEMs-target mRNA interaction networks were constructed. In addition, the most significantly down-regulated miRNAs, ssc-miR-122-5p and ssc-miR-192, might be the key miRNAs for FE. Our results reveal the mechanism by which adipose miRNAs regulate feed efficiency in pigs. This study provides a theoretical basis for the further study of swine feed efficiency improvement.
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Genome-Wide Association Analysis and Genetic Parameters for Feed Efficiency and Related Traits in Yorkshire and Duroc Pigs. Animals (Basel) 2022; 12:ani12151902. [PMID: 35892552 PMCID: PMC9329986 DOI: 10.3390/ani12151902] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/24/2022] [Revised: 07/04/2022] [Accepted: 07/20/2022] [Indexed: 11/17/2022] Open
Abstract
Simple Summary Genetic improvements in feed efficiency (FE) and related traits could considerably reduce pig production costs and energy consumption. Thus, we performed a genetic parameter estimation and genome-wide association study of four FE and FE-related traits, namely, average daily feed intake, average daily gain, the feed conversion ratio, and residual feed intake, of two pig breeds, Yorkshire and Duroc. The results demonstrate the genetic relationships of FE and FE-related traits with two growth traits, age and backfat thickness at 100 kg. We also identified many single-nucleotide polymorphisms (SNPs) and novel candidate genes related to these traits. In addition, we found many pathways significantly associated with FE and FE-related traits, and they are generally involved in digestive and metabolic processes. The results of this study are expected to provide a valuable reference for the genomic selection of FE and FE-related traits in pigs. Abstract Feed efficiency (FE) traits are key factors that can influence the economic benefits of pig production. However, little is known about the genetic architecture of FE and FE-related traits. This study aimed to identify SNPs and candidate genes associated with FE and FE-related traits, namely, average daily feed intake (ADFI), average daily gain (ADG), the feed conversion ratio (FCR), and residual feed intake (RFI). The phenotypes of 5823 boars with genotyped data (50 K BeadChip) from 1365 boars from a nucleus farm were used to perform a genome-wide association study (GWAS) of two breeds, Duroc and Yorkshire. Moreover, we performed a genetic parameter estimation for four FE and FE-related traits. The heritabilities of the FE and FE-related traits ranged from 0.13 to 0.36, and there were significant genetic correlations (−0.69 to 0.52) of the FE and FE-related traits with two growth traits (age at 100 kg and backfat thickness at 100 kg). A total of 61 significant SNPs located on eight different chromosomes associated with the four FE and FE-related traits were identified. We further identified four regions associated with FE and FE-related traits that have not been previously reported, and they may be potential novel QTLs for FE. Considering their biological functions, we finally identified 35 candidate genes relevant for FE and FE-related traits, such as the widely reported MC4R and INSR genes. A gene enrichment analysis showed that FE and FE-related traits were highly enriched in the biosynthesis, digestion, and metabolism of biomolecules. This study deepens our understanding of the genetic mechanisms of FE in pigs and provides valuable information for using marker-assisted selection in pigs to improve FE.
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Guo Q, Huang L, Jiang Y, Wang Z, Bi Y, Chen G, Bai H, Chang G. Genome-Wide Association Study of Feed Efficiency Related Traits in Ducks. Animals (Basel) 2022; 12:ani12121532. [PMID: 35739869 PMCID: PMC9219419 DOI: 10.3390/ani12121532] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Revised: 06/07/2022] [Accepted: 06/12/2022] [Indexed: 01/21/2023] Open
Abstract
Simple Summary Good feed efficiency (FE) is an important trait to ensure the economic output of the livestock and poultry industries. Herein, a genome-wide association study was conducted to identify potential variants and genes associated with seven FE measures in ducks. Genomic DNA samples of 308 ducks were collected and sequenced. All animals were evaluated concerning body weight gain (BWG), feed intake (FI), residual feed intake (RFI), feed conversion ratio (FCR), and weight at 21 (BW21) and 42 days of age (BW42). Overall, 4 (FCR), 3 (FI), 36 (RFI), 6 (BWG), 8 (BW21), and 10 (BW42) single nucleotide polymorphisms (SNPs) were significantly associated with these FE traits, respectively. Moreover, candidate genes close to the identified variants were found to be mainly involved in key pathways and terms related to metabolism. In summary, these findings improve our understanding of poultry genetics and provide new foundations for breeding programs aimed at maximizing the economic potential of duck breeding and farming. Abstract Feed efficiency (FE) is the most important economic trait in the poultry and livestock industry. Thus, genetic improvement of FE may result in a considerable reduction of the cost and energy burdens. As genome-wide association studies (GWASs) can help identify candidate variants influencing FE, the present study aimed to analyze the phenotypic correlation and identify candidate variants of the seven FE traits in ducks. All traits were found to have significant positive correlations with varying degrees. In particular, residual feed intake presented correlation coefficients of 0.61, 0.54, and 0.13 with feed conversion ratio, and feed intake, respectively. Furthermore, data from seven FE-related GWAS revealed 4 (FCR), 3 (FI), 36 (RFI), 6 (BWG), 8 (BW21), and 10 (BW42) SNPs were significantly associated with body weight gain, feed intake, residual feed intake, feed conversion ratio, and weight at 21 and 42 days, respectively. Candidate SNPs of seven FE trait-related genes were involved in galactose metabolism, starch, propanoate metabolism, sucrose metabolism and etc. Taken together, these findings provide insight into the genetic mechanisms and genes involved in FE-related traits in ducks. However, further investigations are warranted to further validate these findings.
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Affiliation(s)
- Qixin Guo
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (L.H.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Lan Huang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (L.H.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Yong Jiang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (L.H.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Zhixiu Wang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (L.H.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Yulin Bi
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (L.H.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
| | - Guohong Chen
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (L.H.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
| | - Hao Bai
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence: (H.B.); (G.C.); Tel.:+86-187-9660-8824 (H.B.); + 86-178-5197-5060 (G.C.)
| | - Guobin Chang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (Q.G.); (L.H.); (Y.J.); (Z.W.); (Y.B.); (G.C.)
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Yangzhou University, Yangzhou 225009, China
- Correspondence: (H.B.); (G.C.); Tel.:+86-187-9660-8824 (H.B.); + 86-178-5197-5060 (G.C.)
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Oliveira HC, Derks MFL, Lopes MS, Madsen O, Harlizius B, van Son M, Grindflek EH, Gòdia M, Gjuvsland AB, Otto PI, Groenen MAM, Guimaraes SEF. Fine Mapping of a Major Backfat QTL Reveals a Causal Regulatory Variant Affecting the CCND2 Gene. Front Genet 2022; 13:871516. [PMID: 35692822 PMCID: PMC9180923 DOI: 10.3389/fgene.2022.871516] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2022] [Accepted: 04/29/2022] [Indexed: 12/13/2022] Open
Abstract
Backfat is an important trait in pork production, and it has been included in the breeding objectives of genetic companies for decades. Although adipose tissue is a good energy storage, excessive fat results in reduced efficiency and economical losses. A large QTL for backfat thickness on chromosome 5 is still segregating in different commercial pig breeds. We fine mapped this QTL region using a genome-wide association analysis (GWAS) with 133,358 genotyped animals from five commercial populations (Landrace, Pietrain, Large White, Synthetic, and Duroc) imputed to the porcine 660K SNP chip. The lead SNP was located at 5:66103958 (G/A) within the third intron of the CCND2 gene, with the G allele associated with more backfat, while the A allele is associated with less backfat. We further phased the QTL region to discover a core haplotype of five SNPs associated with low backfat across three breeds. Linkage disequilibrium analysis using whole-genome sequence data revealed three candidate causal variants within intronic regions and downstream of the CCND2 gene, including the lead SNP. We evaluated the association of the lead SNP with the expression of the genes in the QTL region (including CCND2) in a large cohort of 100 crossbred samples, sequenced in four different tissues (lung, spleen, liver, muscle). Results show that the A allele increases the expression of CCND2 in an additive way in three out of four tissues. Our findings indicate that the causal variant for this QTL region is a regulatory variant within the third intron of the CCND2 gene affecting the expression of CCND2.
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Wolc A, Dekkers JCM. Application of Bayesian genomic prediction methods to genome-wide association analyses. Genet Sel Evol 2022; 54:31. [PMID: 35562659 PMCID: PMC9103490 DOI: 10.1186/s12711-022-00724-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/27/2022] [Indexed: 11/19/2022] Open
Abstract
Background Bayesian genomic prediction methods were developed to simultaneously fit all genotyped markers to a set of available phenotypes for prediction of breeding values for quantitative traits, allowing for differences in the genetic architecture (distribution of marker effects) of traits. These methods also provide a flexible and reliable framework for genome-wide association (GWA) studies. The objective here was to review developments in Bayesian hierarchical and variable selection models for GWA analyses. Results By fitting all genotyped markers simultaneously, Bayesian GWA methods implicitly account for population structure and the multiple-testing problem of classical single-marker GWA. Implemented using Markov chain Monte Carlo methods, Bayesian GWA methods allow for control of error rates using probabilities obtained from posterior distributions. Power of GWA studies using Bayesian methods can be enhanced by using informative priors based on previous association studies, gene expression analyses, or functional annotation information. Applied to multiple traits, Bayesian GWA analyses can give insight into pleiotropic effects by multi-trait, structural equation, or graphical models. Bayesian methods can also be used to combine genomic, transcriptomic, proteomic, and other -omics data to infer causal genotype to phenotype relationships and to suggest external interventions that can improve performance. Conclusions Bayesian hierarchical and variable selection methods provide a unified and powerful framework for genomic prediction, GWA, integration of prior information, and integration of information from other -omics platforms to identify causal mutations for complex quantitative traits.
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Affiliation(s)
- Anna Wolc
- Department of Animal Science, Iowa State University, 806 Stange Road, 239 Kildee Hall, Ames, IA, 50010, USA.,Hy-Line International, 2583 240th Street, Dallas Center, IA, 50063, USA
| | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, 806 Stange Road, 239 Kildee Hall, Ames, IA, 50010, USA.
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David I, Ricard A, Huynh-Tran VH, Dekkers JCM, Gilbert H. Quality of breeding value predictions from longitudinal analyses, with application to residual feed intake in pigs. Genet Sel Evol 2022; 54:32. [PMID: 35562648 PMCID: PMC9103455 DOI: 10.1186/s12711-022-00722-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2021] [Accepted: 04/20/2022] [Indexed: 11/10/2022] Open
Abstract
Background An important goal in animal breeding is to improve longitudinal traits. The objective of this study was to explore for longitudinal residual feed intake (RFI) data, which estimated breeding value (EBV), or combination of EBV, to use in a breeding program. Linear combinations of EBV (summarized breeding values, SBV) or phenotypes (summarized phenotypes) derived from the eigenvectors of the genetic covariance matrix over time were considered, and the linear regression method (LR method) was used to facilitate the evaluation of their prediction accuracy. Results Weekly feed intake, average daily gain, metabolic body weight, and backfat thickness measured on 2435 growing French Large White pigs over a 10-week period were analysed using a random regression model. In this population, the 544 dams of the phenotyped animals were genotyped. These dams did not have own phenotypes. The quality of the predictions of SBV and breeding values from summarized phenotypes of these females was evaluated. On average, predictions of SBV at the time of selection were unbiased, slightly over-dispersed and less accurate than those obtained with additional phenotypic information. The use of genomic information did not improve the quality of predictions. The use of summarized instead of longitudinal phenotypes resulted in predictions of breeding values of similar quality. Conclusions For practical selection on longitudinal data, the results obtained with this specific design suggest that the use of summarized phenotypes could facilitate routine genetic evaluation of longitudinal traits. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00722-w.
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Affiliation(s)
- Ingrid David
- GenPhySE, INRAE, Université de Toulouse, INPT, 31326, Castanet Tolosan, France.
| | - Anne Ricard
- Université Paris Saclay, INRAE, AgroParisTech, GABI, 78352, Jouy-en-Josas, France.,Département Recherche et Innovation, Institut Français du Cheval et de l'Equitation, 61310, Exmes, France
| | - Van-Hung Huynh-Tran
- GenPhySE, INRAE, Université de Toulouse, INPT, 31326, Castanet Tolosan, France
| | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, Ames, IA, 50011, USA
| | - Hélène Gilbert
- GenPhySE, INRAE, Université de Toulouse, INPT, 31326, Castanet Tolosan, France
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Miao Y, Fu C, Liao M, Fang F. Differences in Liver microRNA profiling in pigs with low and high
feed efficiency. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2022; 64:312-329. [PMID: 35530409 PMCID: PMC9039951 DOI: 10.5187/jast.2022.e4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 10/26/2021] [Revised: 12/20/2021] [Accepted: 01/09/2022] [Indexed: 11/21/2022]
Abstract
Feed cost is the main factor affecting the economic benefits of pig industry.
Improving the feed efficiency (FE) can reduce the feed cost and improve the
economic benefits of pig breeding enterprises. Liver is a complex metabolic
organ which affects the distribution of nutrients and regulates the efficiency
of energy conversion from nutrients to muscle or fat, thereby affecting feed
efficiency. MicroRNAs (miRNAs) are small non-coding RNAs that can regulate feed
efficiency through the modulation of gene expression at the post-transcriptional
level. In this study, we analyzed miRNA profiling of liver tissues in High-FE
and Low-FE pigs for the purpose of identifying key miRNAs related to feed
efficiency. A total 212~221 annotated porcine miRNAs and 136~281 novel
miRNAs were identified in the pig liver. Among them, 188 annotated miRNAs were
co-expressed in High-FE and Low-FE pigs. The 14 miRNAs were significantly
differentially expressed (DE) in the livers of high-FE pigs and low-FE pigs, of
which 5 were downregulated and 9 were upregulated. Kyoto Encyclopedia of Genes
and Genomes analysis of liver DE miRNAs in high-FE pigs and low-FE pigs
indicated that the target genes of DE miRNAs were significantly enriched in
insulin signaling pathway, Gonadotropin-releasing hormone signaling pathway, and
mammalian target of rapamycin signaling pathway. To verify the reliability of
sequencing results, 5 DE miRNAs were randomly selected for quantitative reverse
transcription-polymerase chain reaction (qRT-PCR). The qRT-PCR results of miRNAs
were confirmed to be consistent with sequencing data. DE miRNA data indicated
that liver-specific miRNAs synergistically acted with mRNAs to improve feed
efficiency. The liver miRNAs expression analysis revealed the metabolic pathways
by which the liver miRNAs regulate pig feed efficiency.
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Affiliation(s)
- Yuanxin Miao
- College of Bioengineering,Jingchu
University of Technology, Jingmen 448000, Hubei, China
- Key Laboratory of Agricultural Animal
Genetics, Breeding and Reproduction of Ministry of Education, Huazhong
Agricultural University, Wuhan 430070, China
| | - Chuanke Fu
- Key Laboratory of Agricultural Animal
Genetics, Breeding and Reproduction of Ministry of Education, Huazhong
Agricultural University, Wuhan 430070, China
| | - Mingxing Liao
- Key Laboratory of Agricultural Animal
Genetics, Breeding and Reproduction of Ministry of Education, Huazhong
Agricultural University, Wuhan 430070, China
| | - Fang Fang
- Key Laboratory of Agricultural Animal
Genetics, Breeding and Reproduction of Ministry of Education, Huazhong
Agricultural University, Wuhan 430070, China
- National Center for International Research
on Animal Genetics, Breeding and Reproduction (NCIRAGBR), Huazhong
Agricultural University, Wuhan 430070, China
- Corresponding author: Fang Fang, Key Laboratory of
Agricultural Animal Genetics, Breeding and Reproduction of Ministry of
Education, Huazhong Agricultural University, Wuhan 430070, China. Tel:
+86-278-728-2091, E-mail:
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Zhang X, Luan P, Cao D, Hu G. A High-Density Genetic Linkage Map and Fine Mapping of QTL For Feed Conversion Efficiency in Common Carp ( Cyprinus carpio). Front Genet 2021; 12:778487. [PMID: 34868267 PMCID: PMC8633483 DOI: 10.3389/fgene.2021.778487] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/17/2021] [Accepted: 10/22/2021] [Indexed: 12/02/2022] Open
Abstract
Feed conversion efficiency (FCE) is an economically crucial trait in fish, however, little progress has been made in genetics and genomics for this trait because phenotypes of the trait are difficult to measure. In this study, we constructed a high-density and high-resolution genetic linkage map with 28,416 SNP markers for common carp (Cyprinus carpio) based on high throughput genotyping with the carp 250K single nucleotide polymorphism (SNP) array in a full-sib F1 family of mirror carp (Cyprinus carpio) consisting of 141 progenies. The linkage map contained 11,983 distinct loci and spanned 3,590.09 cM with an average locus interval of 0.33 cM. A total of 17 QTL for the FCE trait were detected on four LGs (LG9, LG20, LG28, and LG32), explaining 8.9-15.9% of the phenotypic variations. One major cluster containing eight QTL (qFCE1-28, qFCE2-28, qFCE3-28, qFCE4-28, qFCE5-28, qFCE6-28, qFCE7-28, and qFCE8-28) was detected on LG28. Two clusters consisting of four QTL (qFCE1-32, qFCE2-32, qFCE3-32, and qFCE4-32) and three QTL (qFCE1-20, qFCE2-20, and qFCE3-20) were detected on LG32 and LG20, respectively. Nine candidate genes (ACACA, SCAF4, SLC2A5, TNMD, PCDH1, FOXO, AGO1, FFAR3, and ARID1A) underlying the feed efficiency trait were also identified, the biological functions of which may be involved in lipid metabolism, carbohydrate metabolism, energy deposition, fat accumulation, digestion, growth regulation, and cell proliferation and differentiation according to GO (Gene Ontology). As an important tool, high-density and high-resolution genetic linkage maps play a crucial role in the QTL fine mapping of economically important traits. Our novel findings provided new insights that elucidate the genetic basis and molecular mechanism of feed efficiency and the subsequent marker-assisted selection breeding in common carp.
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Affiliation(s)
- Xiaofeng Zhang
- National and Local United Engineering Laboratory for Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
| | | | | | - Guo Hu
- National and Local United Engineering Laboratory for Freshwater Fish Breeding, Heilongjiang River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Harbin, China
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