1
|
George L, Alex R, Gowane G, Vohra V, Joshi P, Kumar R, Verma A. Weighted single step GWAS reveals genomic regions associated with economic traits in Murrah buffaloes. Anim Biotechnol 2024; 35:2319622. [PMID: 38437001 DOI: 10.1080/10495398.2024.2319622] [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] [Indexed: 03/05/2024]
Abstract
The objective of the present study was to identify genomic regions influencing economic traits in Murrah buffaloes using weighted single step Genome Wide Association Analysis (WssGWAS). Data on 2000 animals, out of which 120 were genotyped using a double digest Restriction site Associated DNA (ddRAD) sequencing approach. The phenotypic data were collected from NDRI, India, on growth traits, viz., body weight at 6M (month), 12M, 18M and 24M, production traits like 305D (day) milk yield, lactation length (LL) and dry period (DP) and reproduction traits like age at first calving (AFC), calving interval (CI) and first service period (FSP). The biallelic genotypic data consisted of 49353 markers post-quality check. The heritability estimates were moderate to high, low to moderate, low for growth, production, reproduction traits, respectively. Important genomic regions explaining more than 0.5% of the total additive genetic variance explained by 30 adjacent SNPs were selected for further analysis of candidate genes. In this study, 105 genomic regions were associated with growth, 35 genomic regions with production and 42 window regions with reproduction traits. Different candidate genes were identified in these genomic regions, of which important are OSBPL8, NAP1L1 for growth, CNTNAP2 for production and ILDR2, TADA1 and POGK for reproduction traits.
Collapse
Affiliation(s)
- Linda George
- National Dairy Research Institute, Karnal, India
| | - Rani Alex
- National Dairy Research Institute, Karnal, India
| | - Gopal Gowane
- National Dairy Research Institute, Karnal, India
| | - Vikas Vohra
- National Dairy Research Institute, Karnal, India
| | - Pooja Joshi
- National Dairy Research Institute, Karnal, India
| | - Ravi Kumar
- National Dairy Research Institute, Karnal, India
| | | |
Collapse
|
2
|
Sainz RD, Baldi F, Temp LB, Ribeiro LB. Estimation of genetic parameters for maintenance energy requirements and residual feed intake in Nellore cattle. J Anim Breed Genet 2024. [PMID: 38712720 DOI: 10.1111/jbg.12870] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/16/2023] [Revised: 04/14/2024] [Accepted: 04/16/2024] [Indexed: 05/08/2024]
Abstract
We estimated heritabilities and genetic and phenotypic correlation estimates for maintenance energy requirements (NEmR), residual feed intake (RFI), growth, carcass and reproductive indicator traits, using data from 41 feed efficiency trials in Brazil, comprising 4381 males and females. Continuous traits were analysed using a linear animal model and threshold traits were analysed using a threshold animal model. The heritability estimates were low for RFI (0.190) and NEmR (0.193); other heritabilities were mainly moderate (growth and carcass traits) or high (sexual precocity traits). The genetic correlation of RFI with NEmR was high (0.701). The genetic correlations of NEmR were low with carcass and reproductive traits, and moderate with growth traits. Thus, selection to improve weaning weight and female sexual precocity indicator traits would not affect maintenance energy requirement. Genetic selection to reduce maintenance energy requirements is feasible and would also reduce DMI and RFI. Selection to improve RFI can be used to identify animals with lower maintenance energy requirements. Long-term selection to reduce RFI and NEmR would have favourable effects on yearling weight, carcass muscle indicator traits and female sexual precocity. Genetic (co)variance component estimates for NEmR, in conjunction with economic values of selection criteria, may be used to develop novel approaches for genetic selection to improve efficiency of beef production.
Collapse
Affiliation(s)
- Roberto D Sainz
- Department of Animal Science, University of California, Davis, California, USA
| | - Fernando Baldi
- Animal Science Department, State University of São Paulo, Jaboticabal, Brazil
| | - Larissa Bordin Temp
- Animal Science Department, State University of São Paulo, Jaboticabal, Brazil
| | | |
Collapse
|
3
|
Mota LFM, Arikawa LM, Santos SWB, Fernandes Júnior GA, Alves AAC, Rosa GJM, Mercadante MEZ, Cyrillo JNSG, Carvalheiro R, Albuquerque LG. Benchmarking machine learning and parametric methods for genomic prediction of feed efficiency-related traits in Nellore cattle. Sci Rep 2024; 14:6404. [PMID: 38493207 PMCID: PMC10944497 DOI: 10.1038/s41598-024-57234-4] [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: 07/03/2023] [Accepted: 03/15/2024] [Indexed: 03/18/2024] Open
Abstract
Genomic selection (GS) offers a promising opportunity for selecting more efficient animals to use consumed energy for maintenance and growth functions, impacting profitability and environmental sustainability. Here, we compared the prediction accuracy of multi-layer neural network (MLNN) and support vector regression (SVR) against single-trait (STGBLUP), multi-trait genomic best linear unbiased prediction (MTGBLUP), and Bayesian regression (BayesA, BayesB, BayesC, BRR, and BLasso) for feed efficiency (FE) traits. FE-related traits were measured in 1156 Nellore cattle from an experimental breeding program genotyped for ~ 300 K markers after quality control. Prediction accuracy (Acc) was evaluated using a forward validation splitting the dataset based on birth year, considering the phenotypes adjusted for the fixed effects and covariates as pseudo-phenotypes. The MLNN and SVR approaches were trained by randomly splitting the training population into fivefold to select the best hyperparameters. The results show that the machine learning methods (MLNN and SVR) and MTGBLUP outperformed STGBLUP and the Bayesian regression approaches, increasing the Acc by approximately 8.9%, 14.6%, and 13.7% using MLNN, SVR, and MTGBLUP, respectively. Acc for SVR and MTGBLUP were slightly different, ranging from 0.62 to 0.69 and 0.62 to 0.68, respectively, with empirically unbiased for both models (0.97 and 1.09). Our results indicated that SVR and MTGBLUBP approaches were more accurate in predicting FE-related traits than Bayesian regression and STGBLUP and seemed competitive for GS of complex phenotypes with various degrees of inheritance.
Collapse
Affiliation(s)
- Lucio F M Mota
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil.
| | - Leonardo M Arikawa
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Samuel W B Santos
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Gerardo A Fernandes Júnior
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Anderson A C Alves
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
| | - Guilherme J M Rosa
- Department of Animal and Dairy Sciences, University of Wisconsin, Madison, WI, 53706, USA
| | - Maria E Z Mercadante
- Institute of Animal Science, Beef Cattle Research Center, Sertãozinho, SP, 14174-000, Brazil
- National Council for Science and Technological Development, Brasilia, DF, 71605-001, Brazil
| | - Joslaine N S G Cyrillo
- Institute of Animal Science, Beef Cattle Research Center, Sertãozinho, SP, 14174-000, Brazil
| | - Roberto Carvalheiro
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil
- National Council for Science and Technological Development, Brasilia, DF, 71605-001, Brazil
| | - Lucia G Albuquerque
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal, SP, 14884-900, Brazil.
- National Council for Science and Technological Development, Brasilia, DF, 71605-001, Brazil.
| |
Collapse
|
4
|
Taiwo G, Morenikeji OB, Idowu M, Sidney T, Adekunle A, Cervantes AP, Peters S, Ogunade IM. Characterization of rumen microbiome and immune genes expression of crossbred beef steers with divergent residual feed intake phenotypes. BMC Genomics 2024; 25:245. [PMID: 38443809 PMCID: PMC10913640 DOI: 10.1186/s12864-024-10150-3] [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: 04/08/2023] [Accepted: 02/21/2024] [Indexed: 03/07/2024] Open
Abstract
We investigated whole blood and hepatic mRNA expressions of immune genes and rumen microbiome of crossbred beef steers with divergent residual feed intake phenotype to identify relevant biological processes underpinning feed efficiency in beef cattle. Low-RFI beef steers (n = 20; RFI = - 1.83 kg/d) and high-RFI beef steers (n = 20; RFI = + 2.12 kg/d) were identified from a group of 108 growing crossbred beef steers (average BW = 282 ± 30.4 kg) fed a high-forage total mixed ration after a 70-d performance testing period. At the end of the 70-d testing period, liver biopsies and blood samples were collected for total RNA extraction and cDNA synthesis. Rumen fluid samples were also collected for analysis of the rumen microbial community. The mRNA expression of 84 genes related to innate and adaptive immunity was analyzed using pathway-focused PCR-based arrays. Differentially expressed genes were determined using P-value ≤ 0.05 and fold change (FC) ≥ 1.5 (in whole blood) or ≥ 2.0 (in the liver). Gene ontology analysis of the differentially expressed genes revealed that pathways related to pattern recognition receptor activity, positive regulation of phagocytosis, positive regulation of vitamin metabolic process, vascular endothelial growth factor production, positive regulation of epithelial tube formation and T-helper cell differentiation were significantly enriched (FDR < 0.05) in low-RFI steers. In the rumen, the relative abundance of PeH15, Arthrobacter, Moryella, Weissella, and Muribaculaceae was enriched in low-RFI steers, while Methanobrevibacter, Bacteroidales_BS11_gut_group, Bacteroides and Clostridium_sensu_stricto_1 were reduced. In conclusion, our study found that low-RFI beef steers exhibit increased mRNA expression of genes related to immune cell functions in whole blood and liver tissues, specifically those involved in pathogen recognition and phagocytosis regulation. Additionally, these low-RFI steers showed differences in the relative abundance of some microbial taxa which may partially account for their improved feed efficiency compared to high-RFI steers.
Collapse
Affiliation(s)
- Godstime Taiwo
- Division of Animal and Nutritional Science, West Virginia University, 26505, Morgantown, WV, USA
| | - Olanrewaju B Morenikeji
- Division of Biological and Health Sciences, University of Pittsburgh at Bradford, 300 Campus Drive, 16701, Bradford, PA, USA.
| | - Modoluwamu Idowu
- Division of Animal and Nutritional Science, West Virginia University, 26505, Morgantown, WV, USA
| | - Taylor Sidney
- Division of Animal and Nutritional Science, West Virginia University, 26505, Morgantown, WV, USA
| | - Ajiboye Adekunle
- Division of Animal and Nutritional Science, West Virginia University, 26505, Morgantown, WV, USA
| | | | - Sunday Peters
- Department of Animal Science, Berry College, Mount Berry, GA, USA
| | - Ibukun M Ogunade
- Division of Animal and Nutritional Science, West Virginia University, 26505, Morgantown, WV, USA.
| |
Collapse
|
5
|
A V, Kumar A, Mahala S, Chandra Janga S, Chauhan A, Mehrotra A, Kumar De A, Ranjan Sahu A, Firdous Ahmad S, Vempadapu V, Dutt T. Revelation of genetic diversity and genomic footprints of adaptation in Indian pig breeds. Gene 2024; 893:147950. [PMID: 37918549 DOI: 10.1016/j.gene.2023.147950] [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: 08/04/2023] [Revised: 10/16/2023] [Accepted: 10/30/2023] [Indexed: 11/04/2023]
Abstract
In the present study, the genetic diversity measures among four Indian domestic breeds of pig namely Agonda Goan, Ghurrah, Ghungroo, and Nicobari, of different agro-climatic regions of country were explored and compared with European commercial breeds, European wild boar and Chinese domestic breeds. The double digest restriction site-associated DNA sequencing (ddRADseq) data of Indian pigs (102) and Landrace (10 animals) were generated and whole genome sequencing data of exotic pigs (60 animals) from public data repository were used in the study. The principal component analysis (PCA), admixture analysis and phylogenetic analysis revealed that Indian breeds were closer in ancestry to Chinese breeds than European breeds. European breeds exhibited highest genetic diversity measures among all the considered breeds. Among Indian breeds, Agonda Goan and Ghurrah were found to be more genetically diverse than Nicobari and Ghungroo. The selection signature regions in Indian pigs were explored using iHS and XP-EHH, and during iHS analysis, it was observed that genes related to growth, reproduction, health, meat quality, sensory perception and behavior were found to be under selection pressure in Indian pig breeds. Strong selection signatures were recorded in 24.25-25.25 Mb region of SSC18, 123.25-124 Mb region of SSC15 and 118.75-119.5 Mb region of SSC2 in most of the Indian breeds upon pairwise comparison with European commercial breeds using XP-EHH. These regions were harboring some important genes such as EPHA4 for thermotolerance, TAS2R16, FEZF1, CADPS2 and PTPRZ1 for adaptability to scavenging system of rearing, TRIM36 and PGGT1B for disease resistance and CCDC112, PIAS1, FEM1B and ITGA11 for reproduction.
Collapse
Affiliation(s)
- Vani A
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Amit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India.
| | - Sudarshan Mahala
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Sarath Chandra Janga
- Luddy School of Informatics, Computing, and Engineering, Indiana University, IUPUI, Indianapolis, IN, USA
| | - Anuj Chauhan
- Livestock Production and Management, Indian Veterinary Research Institute, Bareilly, UP, India
| | | | - Arun Kumar De
- Central Island Agricultural Research Institute, Port Blair, Andaman and Nicobar Islands, India
| | - Amiya Ranjan Sahu
- Central Coastal Agricultural Research Institute, Old Goa, Goa, India
| | - Sheikh Firdous Ahmad
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Varshini Vempadapu
- Division of Animal Genetics, Indian Veterinary Research Institute, Bareilly, UP, India
| | - Triveni Dutt
- Livestock Production and Management, Indian Veterinary Research Institute, Bareilly, UP, India
| |
Collapse
|
6
|
Shi L, Hu M, Lai W, Yi W, Liu Z, Sun H, Li F, Yan S. Detection of genomic variations and selection signatures in Wagyu using whole-genome sequencing data. Anim Genet 2023; 54:808-812. [PMID: 37792466 DOI: 10.1111/age.13364] [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: 04/28/2023] [Revised: 07/28/2023] [Accepted: 09/21/2023] [Indexed: 10/05/2023]
Abstract
Wagyu is recognized for producing marbled beef with high nutritional value and flavor. Reportedly, Wagyu has been widely used to improve the meat quality of local breeds around the world. However, studies on the genetic mechanism of meat quality in Wagyu at the whole-genome level are rarely reported. Here, whole-genome sequencing data of 11 Wagyu and 115 other individuals were used to explore the genomic variations and genes under selection pressure in Wagyu. A total of 31 349 non-synonymous variants and 53 102 synonymous variants were identified in Wagyu. The population structure analysis showed that Wagyu had the closest genetic relationship with Mishima-Ushi cattle and was apparently separated from other cattle breeds. Then, composite likelihood ratio (CLR), integrated haplotype score, fixation index and cross-population composite likelihood ratio (XP-CLR) tests were performed to identify the candidate genes under positive selection in Wagyu. In total, 770 regions containing 312 genes were identified by at least three methods. Among them, 97 regions containing 27 genes were detected by all four methods. We specifically illustrate a list of interesting genes, including LRP2BP, GAA, CACNG6, CXADR, GPCPD1, KLF2, KLF13, SOX5, MYBPC1, SLC25A10, ATP8A1 and MYH15, which are associated with lipid metabolism, fat deposition, muscle development, bone development, feed intake and growth traits in Wagyu. This is the first study to explore the genomic variations and selection signatures of Wagyu at the whole-genome level. These results will provide significant help to beef cattle improvement and breeding.
Collapse
Affiliation(s)
- Lulu Shi
- College of Animal Science, Jilin University, Changchun, China
| | - Mingyue Hu
- College of Animal Science, Jilin University, Changchun, China
| | - Weining Lai
- College of Animal Science, Jilin University, Changchun, China
| | - Wenfeng Yi
- College of Animal Science, Jilin University, Changchun, China
| | - Zhengxi Liu
- College of Animal Science, Jilin University, Changchun, China
| | - Hao Sun
- College of Animal Science, Jilin University, Changchun, China
| | - Feng Li
- Shandong Binzhou Animal Science and Veterinary Medicine Academy, Binzhou, China
| | - Shouqing Yan
- College of Animal Science, Jilin University, Changchun, China
| |
Collapse
|
7
|
Lukic B, Curik I, Drzaic I, Galić V, Shihabi M, Vostry L, Cubric-Curik V. Genomic signatures of selection, local adaptation and production type characterisation of East Adriatic sheep breeds. J Anim Sci Biotechnol 2023; 14:142. [PMID: 37932811 PMCID: PMC10626677 DOI: 10.1186/s40104-023-00936-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/15/2023] [Accepted: 09/04/2023] [Indexed: 11/08/2023] Open
Abstract
BACKGROUND The importance of sheep breeding in the Mediterranean part of the eastern Adriatic has a long tradition since its arrival during the Neolithic migrations. Sheep production system is extensive and generally carried out in traditional systems without intensive systematic breeding programmes for high uniform trait production (carcass, wool and milk yield). Therefore, eight indigenous Croatian sheep breeds from eastern Adriatic treated here as metapopulation (EAS), are generally considered as multipurpose breeds (milk, meat and wool), not specialised for a particular type of production, but known for their robustness and resistance to certain environmental conditions. Our objective was to identify genomic regions and genes that exhibit patterns of positive selection signatures, decipher their biological and productive functionality, and provide a "genomic" characterization of EAS adaptation and determine its production type. RESULTS We identified positive selection signatures in EAS using several methods based on reduced local variation, linkage disequilibrium and site frequency spectrum (eROHi, iHS, nSL and CLR). Our analyses identified numerous genomic regions and genes (e.g., desmosomal cadherin and desmoglein gene families) associated with environmental adaptation and economically important traits. Most candidate genes were related to meat/production and health/immune response traits, while some of the candidate genes discovered were important for domestication and evolutionary processes (e.g., HOXa gene family and FSIP2). These results were also confirmed by GO and QTL enrichment analysis. CONCLUSIONS Our results contribute to a better understanding of the unique adaptive genetic architecture of EAS and define its productive type, ultimately providing a new opportunity for future breeding programmes. At the same time, the numerous genes identified will improve our understanding of ruminant (sheep) robustness and resistance in the harsh and specific Mediterranean environment.
Collapse
Affiliation(s)
- Boris Lukic
- Faculty of Agrobiotechnical Sciences Osijek, J.J, Strossmayer University of Osijek, Vladimira Preloga 1, 31000, Osijek, Croatia.
| | - Ino Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000, Zagreb, Croatia.
| | - Ivana Drzaic
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000, Zagreb, Croatia
| | - Vlatko Galić
- Department of Maize Breeding and Genetics, Agricultural Institute Osijek, Južno predgrađe 17, 31000, Osijek, Croatia
| | - Mario Shihabi
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000, Zagreb, Croatia
| | - Luboš Vostry
- Czech University of Life Sciences Prague, Kamýcká 129, 165 00, Praque, Czech Republic
| | - Vlatka Cubric-Curik
- Department of Animal Science, Faculty of Agriculture, University of Zagreb, Svetošimunska Cesta 25, 10000, Zagreb, Croatia
| |
Collapse
|
8
|
Jourshari MG, Shadparvar AA, Ghavi Hossein-Zadeh N, Rafeie F, Banabazi MH, Johansson AM. Genome-wide association study on abdomen depth, head width, hip width, and withers height in native cattle of Guilan (Bos indicus). PLoS One 2023; 18:e0289612. [PMID: 37595009 PMCID: PMC10437930 DOI: 10.1371/journal.pone.0289612] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2023] [Accepted: 07/22/2023] [Indexed: 08/20/2023] Open
Abstract
Native breeds in any country are a national capital, and their preservation is of great importance. Native Cattle of Guilan (NCG) is one of the few pure native breeds in Iran and the West Asia region. During the last decade, NCG population has decreased by more than 40%. This study aimed to identify significant single nucleotide polymorphisms (SNPs) and candidate genes associated with meat production traits in NCG using a genome-wide association study (GWAS). The blood and hair samples were collected from 72 NCG individuals and genotyped using the Illumina Bovine SNP50 chip. The results of the genomic scan showed that several SNPs were associated with abdominal depth, head width, hip width, and withers height in NCG. Several candidate genes were identified, including multiple epidermal growth factor-like domains 11 (MEGF11), Methionine Sulfoxide Reductase A (MSRA), chondroitin sulfate synthase 3 (CHSY3), Cyclin-Dependent Kinase 7 (CDK7), and Parkin (PRKN) genes, which are involved in muscle growth, meat tenderness, differentiation of fat cells, fat metabolism, and adipogenesis. These genes can contribute to meat quantity and quality in NCG. This study provided valuable insights into the genetics of NCG and the identification of effective genes associated with meat production traits. The results of this study could be used for the preservation and sustainable use of this breed of native cattle, as an important genetic resource in Iran.
Collapse
Affiliation(s)
| | - Abdol Ahad Shadparvar
- Department of Animal Science, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | | | - Farjad Rafeie
- Department of Agricultural Biotechnology, Faculty of Agricultural Sciences, University of Guilan, Rasht, Iran
| | - Mohammad Hossein Banabazi
- Department of Biotechnology, Animal Science Research Institute of IRAN (ASRI), Agricultural Research, Education & Extension Organization (AREEO), Karaj, Iran
- Department of Animal Breeding and Genetics (HGEN), Centre for Veterinary Medicine and Animal Science (VHC), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| | - Anna Maria Johansson
- Department of Animal Breeding and Genetics (HGEN), Centre for Veterinary Medicine and Animal Science (VHC), Swedish University of Agricultural Sciences (SLU), Uppsala, Sweden
| |
Collapse
|
9
|
Santana ML, Bignardi AB, Pereira RJ, Oliveira Junior GA, Freitas AP, Carvalheiro R, Eler JP, Ferraz JBS, Cyrillo JNSG, Mercadante MEZ. Genotype by Prenatal Environment Interaction for Postnatal Growth of Nelore Beef Cattle Raised under Tropical Grazing Conditions. Animals (Basel) 2023; 13:2321. [PMID: 37508098 PMCID: PMC10376603 DOI: 10.3390/ani13142321] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/14/2023] [Revised: 07/03/2023] [Accepted: 07/09/2023] [Indexed: 07/30/2023] Open
Abstract
The prenatal environment is recognized as crucial for the postnatal performance in cattle. In tropical regions, pregnant beef cows commonly experience nutritional restriction during the second half of the gestation period. Thus, the present study was designed to analyze the genotype by prenatal environment interaction (G × Epn) and to identify genomic regions associated with the level and response in growth and reproduction-related traits of beef cattle to changes in the prenatal environment. A reaction norm model was applied to data from two Nelore herds using the solutions of contemporary groups for birth weight as a descriptor variable of the gestational environment quality. A better gestational environment favored weights until weaning, scrotal circumference at yearling, and days to first calving of the offspring. The G × Epn was strong enough to result in heterogeneity of variance components and genetic parameters in addition to reranking of estimated breeding values and SNPs effects. Several genomic regions associated with the level of performance and specific responses of the animals to variations in the gestational environment were revealed, which harbor QTLs and can be exploited for selection purposes. Therefore, genetic evaluation models considering G × Epn and special management and nutrition care for pregnant cows are recommended.
Collapse
Affiliation(s)
- Mário L Santana
- Grupo de Melhoramento Animal de Mato Grosso (GMAT), Instituto de Ciências Agrárias e Tecnológicas, Universidade Federal de Rondonópolis (UFR), Rondonópolis 78735-901, Brazil
| | - Annaiza B Bignardi
- Grupo de Melhoramento Animal de Mato Grosso (GMAT), Instituto de Ciências Agrárias e Tecnológicas, Universidade Federal de Rondonópolis (UFR), Rondonópolis 78735-901, Brazil
| | - Rodrigo J Pereira
- Grupo de Melhoramento Animal de Mato Grosso (GMAT), Instituto de Ciências Agrárias e Tecnológicas, Universidade Federal de Rondonópolis (UFR), Rondonópolis 78735-901, Brazil
| | - Gerson A Oliveira Junior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Anielly P Freitas
- Centro de Pesquisa em Bovinos de Corte, Instituto de Zootecnia (IZ), Sertãozinho 14160-900, Brazil
| | - Roberto Carvalheiro
- Faculdade de Ciências Agrárias e Veterinárias, Universidade Estadual Paulista (UNESP), Jaboticabal 14884-900, Brazil
| | - Joanir P Eler
- Grupo de Melhoramento Animal e Biotecnologia (GMAB), Departamento de Medicina Veterinária, FZEA, Universidade de São Paulo (USP), Pirassununga 13635-900, Brazil
| | - José B S Ferraz
- Grupo de Melhoramento Animal e Biotecnologia (GMAB), Departamento de Medicina Veterinária, FZEA, Universidade de São Paulo (USP), Pirassununga 13635-900, Brazil
| | - Joslaine N S G Cyrillo
- Centro de Pesquisa em Bovinos de Corte, Instituto de Zootecnia (IZ), Sertãozinho 14160-900, Brazil
| | - Maria E Z Mercadante
- Centro de Pesquisa em Bovinos de Corte, Instituto de Zootecnia (IZ), Sertãozinho 14160-900, Brazil
| |
Collapse
|
10
|
Brunes LC, de Faria CU, Magnabosco CU, Lobo RB, Peripolli E, Aguilar I, Baldi F. Genomic prediction ability and genetic parameters for residual feed intake calculated using different approaches and their associations with growth, reproductive, and carcass traits in Nellore cattle. J Appl Genet 2023; 64:159-167. [PMID: 36376720 DOI: 10.1007/s13353-022-00734-8] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2022] [Revised: 09/03/2022] [Accepted: 10/26/2022] [Indexed: 11/16/2022]
Abstract
This study aimed to estimate prediction ability and genetic parameters for residual feed intake (RFI) calculated using a regression equation for each test (RFItest) and for the whole population (RFIpop) in Nellore beef cattle. It also aimed to evaluate the correlations between RFIpop and RFItest with growth, reproductive, and carcass traits. Genotypic and phenotypic records from 8354 animals were used. An analysis of variance (ANOVA) was performed to verify the adequacy of the regression equations applied to estimate the RFItest and RFIpop. The (co)variance components were obtained using the single-step genomic best linear unbiased prediction under single and two-trait animal model analyses. The genetic and phenotypic correlations between RFItest and RFIpop with dry matter intake, frame, growth, reproduction, and carcass-related traits were evaluated. The prediction ability and bias were estimated to compare the RFItest and RFIpop genomic breeding values (GEBV). The RFIpop ANOVA showed a higher significance level (p < 0.0001) than did the RFItest for the fixed effects. The RFIpop displayed higher additive genetic variance estimated than the RFItest, although the RFIpop and RFItest displayed similar heritabilities. Overall, the RFItest showed higher residual correlations with growth, reproductive, and carcass traits, while the RFIpop displayed higher genetic correlations with such traits. The GEBV for the RFItest was slightly biased than GEBV RFIpop. The approach to calculate the RFI influenced the decomposition and estimation of variance components and genomic prediction for RFI. The application of RFIpop would be more appropriate for genetic evaluation purpose to adjust or correct for non-genetic effects and to decrease the prediction bias for RFI.
Collapse
Affiliation(s)
| | | | | | | | - Elisa Peripolli
- Departament of Animal Science, College of Agricultural and Veterinary Sciences, Sao Paulo State University (UNESP), Jaboticabal, 14884-900, Brazil
| | - Ignacio Aguilar
- Instituto Nacional de Investigación Agropecuaria (INIA), 11500, Montevideo, Uruguay
| | - Fernando Baldi
- Departament of Animal Science, College of Agricultural and Veterinary Sciences, Sao Paulo State University (UNESP), Jaboticabal, 14884-900, Brazil
| |
Collapse
|
11
|
Neumann GB, Korkuć P, Arends D, Wolf MJ, May K, König S, Brockmann GA. Genomic diversity and relationship analyses of endangered German Black Pied cattle (DSN) to 68 other taurine breeds based on whole-genome sequencing. Front Genet 2023; 13:993959. [PMID: 36712857 PMCID: PMC9875303 DOI: 10.3389/fgene.2022.993959] [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: 07/14/2022] [Accepted: 11/28/2022] [Indexed: 01/05/2023] Open
Abstract
German Black Pied cattle (Deutsches Schwarzbuntes Niederungsrind, DSN) are an endangered dual-purpose cattle breed originating from the North Sea region. The population comprises about 2,500 cattle and is considered one of the ancestral populations of the modern Holstein breed. The current study aimed at defining the breeds closest related to DSN cattle, characterizing their genomic diversity and inbreeding. In addition, the detection of selection signatures between DSN and Holstein was a goal. Relationship analyses using fixation index (FST), phylogenetic, and admixture analyses were performed between DSN and 68 other breeds from the 1000 Bull Genomes Project. Nucleotide diversity, observed heterozygosity, and expected heterozygosity were calculated as metrics for genomic diversity. Inbreeding was measured as excess of homozygosity (FHom) and genomic inbreeding (FRoH) through runs of homozygosity (RoHs). Region-wide FST and cross-population-extended haplotype homozygosity (XP-EHH) between DSN and Holstein were used to detect selection signatures between the two breeds, and RoH islands were used to detect selection signatures within DSN and Holstein. DSN showed a close genetic relationship with breeds from the Netherlands, Belgium, Northern Germany, and Scandinavia, such as Dutch Friesian Red, Dutch Improved Red, Belgian Red White Campine, Red White Dual Purpose, Modern Angler, Modern Danish Red, and Holstein. The nucleotide diversity in DSN (0.151%) was higher than in Holstein (0.147%) and other breeds, e.g., Norwegian Red (0.149%), Red White Dual Purpose (0.149%), Swedish Red (0.149%), Hereford (0.145%), Angus (0.143%), and Jersey (0.136%). The FHom and FRoH values in DSN were among the lowest. Regions with high FST between DSN and Holstein, significant XP-EHH regions, and RoH islands detected in both breeds harbor candidate genes that were previously reported for milk, meat, fertility, production, and health traits, including one QTL detected in DSN for endoparasite infection resistance. The selection signatures between DSN and Holstein provide evidence of regions responsible for the dual-purpose properties of DSN and the milk type of Holstein. Despite the small population size, DSN has a high level of diversity and low inbreeding. FST supports its relatedness to breeds from the same geographic origin and provides information on potential gene pools that could be used to maintain diversity in DSN.
Collapse
Affiliation(s)
- Guilherme B. Neumann
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Paula Korkuć
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany
| | - Danny Arends
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany,Department of Applied Sciences, Northumbria University, Newcastle Upon Tyne, United Kingdom
| | - Manuel J. Wolf
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Katharina May
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-Universität, Giessen, Germany
| | - Gudrun A. Brockmann
- Animal Breeding Biology and Molecular Genetics, Albrecht Daniel Thaer-Institute for Agricultural and Horticultural Sciences, Humboldt-Universität zu Berlin, Berlin, Germany,*Correspondence: Gudrun A. Brockmann,
| |
Collapse
|
12
|
Dressler EA, Shaffer W, Bruno K, Krehbiel CR, Calvo-Lorenzo M, Richards CJ, Place SE, DeSilva U, Kuehn LA, Weaber RL, Bormann JM, Rolf MM. Heritability and variance component estimation for feed and water intake behaviors of feedlot cattle. J Anim Sci 2023; 101:skad386. [PMID: 37967310 DOI: 10.1093/jas/skad386] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2023] [Accepted: 11/14/2023] [Indexed: 11/17/2023] Open
Abstract
Feed and water intake are two important aspects of cattle production that greatly impact the profitability, efficiency, and sustainability of producers. Feed and, to a lesser degree, water intake have been studied previously; however, there is little research on their associated animal behaviors and there is a lack of standardized phenotypes for these behaviors. Feed and water intakes obtained with an Insentec system (Hokofarm Group, The Netherlands) from 830 crossbred steers were used to compute five intake behaviors for both feed and water: daily sessions (DS), intake rate (IR), session size (SS), time per session (TS), and session interval (SI). Variance components and heritabilities were estimated for each trait. Heritabilities for feed intake behaviors were 0.50 ± 0.12, 0.63 ± 0.12, 0.40 ± 0.13, 0.35 ± 0.12, and 0.60 ± 0.12 for DS, IR, SS, TS, and SI, respectively. Heritabilities for water intake behaviors were 0.56 ± 0.11, 0.88 ± 0.07, 0.70 ± 0.11, 0.54 ± 0.12, and 0.80 ± 0.10 for NS, IR, SS, TS, and SI, respectively. Daily dry matter intake (DDMI) and daily water intake (DWI) had heritabilities of 0.57 ± 0.11 and 0.44 ± 0.11. Phenotypic correlations varied between pairs of traits (-0.83 to 0.82). Genetic correlations between DDMI and feed intake behaviors were moderate to high, while genetic correlations between DWI and water intake behaviors were low to moderate. Several significant single nucleotide polymorphisms (SNP) were identified for the feed and water intake behaviors. Genes and previously reported quantitative trait loci near significant SNPs were evaluated. The results indicated that feed and water intake behaviors are influenced by genetic factors and are heritable, providing one additional route to evaluate or manipulate feed and water intake.
Collapse
Affiliation(s)
- Elizabeth A Dressler
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, KS 66506, USA
| | - William Shaffer
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, KS 66506, USA
| | - Kelsey Bruno
- Department of Animal Science, Oklahoma State University, Stillwater, OK 74078, USA
| | - Clint R Krehbiel
- Department of Animal Science, Oklahoma State University, Stillwater, OK 74078, USA
- Department of Animal Science, University of Nebraska-Lincoln, Lincoln, NE 68583, USA
| | - Michelle Calvo-Lorenzo
- Department of Animal Science, Oklahoma State University, Stillwater, OK 74078, USA
- Farm Animal Business, Elanco Animal Health, Greenfield, IN 46140, USA
| | - Chris J Richards
- Department of Animal Science, Oklahoma State University, Stillwater, OK 74078, USA
| | - Sara E Place
- Department of Animal Science, Oklahoma State University, Stillwater, OK 74078, USA
- Department of Animal Sciences, Colorado State University, Fort Collins, CO 80523, USA
| | - Udaya DeSilva
- Department of Animal Science, Oklahoma State University, Stillwater, OK 74078, USA
| | - Larry A Kuehn
- USDA, ARS, Roman L. Hruska U.S. Meat Animal Research Center, Clay Center, NE 68933, USA
| | - Robert L Weaber
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, KS 66506, USA
| | - Jennifer M Bormann
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, KS 66506, USA
| | - Megan M Rolf
- Department of Animal Sciences and Industry, Kansas State University, Manhattan, KS 66506, USA
| |
Collapse
|
13
|
Ribeiro G, Baldi F, Cesar ASM, Alexandre PA, Peripolli E, Ferraz JBS, Fukumasu H. Detection of potential functional variants based on systems-biology: the case of feed efficiency in beef cattle. BMC Genomics 2022; 23:774. [PMID: 36434498 PMCID: PMC9700932 DOI: 10.1186/s12864-022-08958-y] [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: 08/25/2021] [Accepted: 10/20/2022] [Indexed: 11/26/2022] Open
Abstract
BACKGROUND Potential functional variants (PFVs) can be defined as genetic variants responsible for a given phenotype. Ultimately, these are the best DNA markers for animal breeding and selection, especially for polygenic and complex phenotypes. Herein, we described the identification of PFVs for complex phenotypes (in this case, Feed Efficiency in beef cattle) using a systems-biology driven approach based on RNA-seq data from physiologically relevant organs. RESULTS The systems-biology coupled with deep molecular phenotyping by RNA-seq of liver, muscle, hypothalamus, pituitary, and adrenal glands of animals with high and low feed efficiency (FE) measured by residual feed intake (RFI) identified 2,000,936 uniquely variants. Among them, 9986 variants were significantly associated with FE and only 78 had a high impact on protein expression and were considered as PFVs. A set of 169 significant uniquely variants were expressed in all five organs, however, only 27 variants had a moderate impact and none of them a had high impact on protein expression. These results provide evidence of tissue-specific effects of high-impact PFVs. The PFVs were enriched (FDR < 0.05) for processing and presentation of MHC Class I and II mediated antigens, which are an important part of the adaptive immune response. The experimental validation of these PFVs was demonstrated by the increased prediction accuracy for RFI using the weighted G matrix (ssGBLUP+wG; Acc = 0.10 and b = 0.48) obtained in the ssGWAS in comparison to the unweighted G matrix (ssGBLUP; Acc = 0.29 and b = 1.10). CONCLUSION Here we identified PFVs for FE in beef cattle using a strategy based on systems-biology and deep molecular phenotyping. This approach has great potential to be used in genetic prediction programs, especially for polygenic phenotypes.
Collapse
Affiliation(s)
- Gabriela Ribeiro
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil
| | - Fernando Baldi
- grid.410543.70000 0001 2188 478XDepartment of Animal Science, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil
| | - Aline S. M. Cesar
- grid.11899.380000 0004 1937 0722Escola Superior de Agricultura “Luiz de Queiroz”, University of Sao Paulo, Piracicaba, São Paulo, Brazil
| | - Pâmela A. Alexandre
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil ,CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD 4067 Australia
| | - Elisa Peripolli
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil ,grid.410543.70000 0001 2188 478XDepartment of Animal Science, São Paulo State University (UNESP), Jaboticabal, São Paulo, Brazil
| | - José B. S. Ferraz
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil
| | - Heidge Fukumasu
- grid.11899.380000 0004 1937 0722Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Sao Paulo, 13635-900 Brazil
| |
Collapse
|
14
|
Heritability and genetic correlations between marbling in longissimus dorsi muscle and conventional economic traits in Nellore beef cattle. Trop Anim Health Prod 2022; 54:274. [PMID: 36068366 DOI: 10.1007/s11250-022-03293-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2022] [Accepted: 08/31/2022] [Indexed: 10/14/2022]
Abstract
In Nellore beef cattle, studies addressing genetic correlations between ultrasound marbling content and other economically important traits are still incipient. Therefore, this work aimed to estimate heritability and genetic correlations between ultrasound marbling content in the longissimus dorsi muscle (MARB) and growth, reproductive, feed efficiency, and carcass-related traits in a Nellore beef cattle population from Brazil. Phenotypic records of 614,395 Nellore animals were used and included adjusted weight at 210 (W210) and 450 (W450) days of age, adult cow weight (AW), early heifer pregnancy (EH), stayability (STAY), adjusted scrotal circumference at 365 days of age (SC365), ribeye area (REA), subcutaneous backfat thickness (BF), rump fat thickness (RF), and marbling (MARB). The genetic parameters for all traits but EH and STAY were estimated considering a linear animal model, whereas for those two nonlinear traits, a threshold animal model was used. The direct and correlated response to selection for MARB versus the other traits, and the relative efficiency of selection, were also calculated. The heritability estimate for MARB was 0.31 and for the other conventional evaluated traits was low to moderate, with values ranging from 0.14 to 0.41. The genetic correlations between MARB and growth, reproductive, feed efficiency, and carcass-related trait were very low, with values close to zero, with similar correlated responses. The MARB displayed adequate genetic variability to respond to selection and crossbreeding programs looking forward to higher meat quality and differential market standards for the Nellore beef. The selection for growth, reproductive, feed efficiency, and carcass-related traits would not affect MARB in Nellore beef cattle and vice versa. Therefore, this trait should be included as a selection criterion in the Nellore breeding program.
Collapse
|
15
|
Mota LFM, Santos SWB, Júnior GAF, Bresolin T, Mercadante MEZ, Silva JAV, Cyrillo JNSG, Monteiro FM, Carvalheiro R, Albuquerque LG. Meta-analysis across Nellore cattle populations identifies common metabolic mechanisms that regulate feed efficiency-related traits. BMC Genomics 2022; 23:424. [PMID: 35672696 PMCID: PMC9172108 DOI: 10.1186/s12864-022-08671-w] [Citation(s) in RCA: 5] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/01/2021] [Accepted: 05/03/2022] [Indexed: 11/28/2022] Open
Abstract
Background Feed efficiency (FE) related traits play a key role in the economy and sustainability of beef cattle production systems. The accurate knowledge of the physiologic background for FE-related traits can help the development of more efficient selection strategies for them. Hence, multi-trait weighted GWAS (MTwGWAS) and meta-analyze were used to find genomic regions associated with average daily gain (ADG), dry matter intake (DMI), feed conversion ratio (FCR), feed efficiency (FE), and residual feed intake (RFI). The FE-related traits and genomic information belong to two breeding programs that perform the FE test at different ages: post-weaning (1,024 animals IZ population) and post-yearling (918 animals for the QLT population). Results The meta-analyze MTwGWAS identified 14 genomic regions (-log10(p -value) > 5) regions mapped on BTA 1, 2, 3, 4, 7, 8, 11, 14, 15, 18, 21, and 29. These regions explained a large proportion of the total genetic variance for FE-related traits across-population ranging from 20% (FCR) to 36% (DMI) in the IZ population and from 22% (RFI) to 28% (ADG) in the QLT population. Relevant candidate genes within these regions (LIPE, LPL, IGF1R, IGF1, IGFBP5, IGF2, INS, INSR, LEPR, LEPROT, POMC, NPY, AGRP, TGFB1, GHSR, JAK1, LYN, MOS, PLAG1, CHCD7, LCAT, and PLA2G15) highlighted that the physiological mechanisms related to neuropeptides and the metabolic signals controlling the body's energy balance are responsible for leading to greater feed efficiency. Integrated meta-analysis results and functional pathway enrichment analysis highlighted the major effect of biological functions linked to energy, lipid metabolism, and hormone signaling that mediates the effects of peptide signals in the hypothalamus and whole-body energy homeostasis affecting the genetic control of FE-related traits in Nellore cattle. Conclusions Genes and pathways associated with common signals for feed efficiency-related traits provide better knowledge about regions with biological relevance in physiological mechanisms associated with differences in energy metabolism and hypothalamus signaling. These pleiotropic regions would support the selection for feed efficiency-related traits, incorporating and pondering causal variations assigning prior weights in genomic selection approaches. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08671-w.
Collapse
Affiliation(s)
- Lucio F M Mota
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SP, São Paulo, 14884-900, Brazil.
| | - Samuel W B Santos
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SP, São Paulo, 14884-900, Brazil
| | - Gerardo A Fernandes Júnior
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SP, São Paulo, 14884-900, Brazil
| | - Tiago Bresolin
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SP, São Paulo, 14884-900, Brazil
| | - Maria E Z Mercadante
- Institute of Animal Science, Beef Cattle Research Center, Sertãozinho - SP, São Paulo, 14174-000, Brazil.,National Council for Science and Technological Development, Brasilia - DF, 71605-001, Brazil
| | - Josineudson A V Silva
- National Council for Science and Technological Development, Brasilia - DF, 71605-001, Brazil.,School of Veterinary Medicine and Animal Science, São Paulo State University (UNESP), Botucatu - SP, 18618-681, Brazil
| | - Joslaine N S G Cyrillo
- Institute of Animal Science, Beef Cattle Research Center, Sertãozinho - SP, São Paulo, 14174-000, Brazil
| | - Fábio M Monteiro
- Institute of Animal Science, Beef Cattle Research Center, Sertãozinho - SP, São Paulo, 14174-000, Brazil
| | - Roberto Carvalheiro
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SP, São Paulo, 14884-900, Brazil.,National Council for Science and Technological Development, Brasilia - DF, 71605-001, Brazil
| | - Lucia G Albuquerque
- School of Agricultural and Veterinarian Sciences, São Paulo State University (UNESP), Jaboticabal - SP, São Paulo, 14884-900, Brazil. .,National Council for Science and Technological Development, Brasilia - DF, 71605-001, Brazil.
| |
Collapse
|
16
|
Waters DL, Clark SA, Moghaddar N, van der Werf JH. Genomic analysis of the slope of the reaction norm for body weight in Australian sheep. Genet Sel Evol 2022; 54:40. [PMID: 35659541 PMCID: PMC9164502 DOI: 10.1186/s12711-022-00734-6] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2022] [Accepted: 05/20/2022] [Indexed: 11/23/2022] Open
Abstract
Background Selection of livestock based on their robustness or sensitivity to environmental variation could help improve the efficiency of production systems, particularly in the light of climate change. Genetic variation in robustness arises from genotype-by-environment (G × E) interactions, with genotypes performing differently when animals are raised in contrasted environments. Understanding the nature of this genetic variation is essential to implement strategies to improve robustness. In this study, our aim was to explore the genetics of robustness in Australian sheep to different growth environments using linear reaction norm models (RNM), with post-weaning weight records of 22,513 lambs and 60 k single nucleotide polymorphisms (SNPs). The use of scale-corrected genomic estimated breeding values (GEBV) for the slope to account for scale-type G × E interactions was also investigated. Results Additive genetic variance was observed for the slope of the RNM, with genetic correlations between low- and high-growth environments indicating substantial re-ranking of genotypes (0.44–0.49). The genetic variance increased from low- to high-growth environments. The heritability of post-weaning body weight ranged from 0.28 to 0.39. The genetic correlation between intercept and slope of the reaction norm for post-weaning body weight was low to moderate when based on the estimated (co)variance components but was much higher when based on back-solved SNP effects. An initial analysis suggested that a region on chromosome 11 affected both the intercept and the slope, but when the GEBV for the slope were conditioned on the GEBV for the intercept to remove the effect of scale-type G × E interactions on SNP effects for robustness, a single genomic region on chromosome 7 was found to be associated with robustness. This region included genes previously associated with growth traits and disease susceptibility in livestock. Conclusions This study shows a significant genetic variation in the slope of RNM that could be used for selecting for increased robustness of sheep. Both scale-type and rank-type G × E interactions contributed to variation in the slope. The correction for scale effects of GEBV for the slope should be considered when analysing robustness using RNM. Overall, robustness appears to be a highly polygenic trait. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00734-6.
Collapse
Affiliation(s)
- Dominic L Waters
- School of Environmental & Rural Science, University of New England, Armidale, NSW, 2351, Australia.
| | - Sam A Clark
- School of Environmental & Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - Nasir Moghaddar
- School of Environmental & Rural Science, University of New England, Armidale, NSW, 2351, Australia
| | - Julius H van der Werf
- School of Environmental & Rural Science, University of New England, Armidale, NSW, 2351, Australia
| |
Collapse
|
17
|
Maiorano AM, Cardoso DF, Carvalheiro R, Júnior GAF, de Albuquerque LG, de Oliveira HN. Signatures of selection in Nelore cattle revealed by whole-genome sequencing data. Genomics 2022; 114:110304. [DOI: 10.1016/j.ygeno.2022.110304] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Revised: 01/07/2022] [Accepted: 02/01/2022] [Indexed: 11/04/2022]
|
18
|
Mancin E, Tuliozi B, Pegolo S, Sartori C, Mantovani R. Genome Wide Association Study of Beef Traits in Local Alpine Breed Reveals the Diversity of the Pathways Involved and the Role of Time Stratification. Front Genet 2022; 12:746665. [PMID: 35058966 PMCID: PMC8764395 DOI: 10.3389/fgene.2021.746665] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/24/2021] [Accepted: 12/02/2021] [Indexed: 12/12/2022] Open
Abstract
Knowledge of the genetic architecture of key growth and beef traits in livestock species has greatly improved worldwide thanks to genome-wide association studies (GWAS), which allow to link target phenotypes to Single Nucleotide Polymorphisms (SNPs) across the genome. Local dual-purpose breeds have rarely been the focus of such studies; recently, however, their value as a possible alternative to intensively farmed breeds has become clear, especially for their greater adaptability to environmental change and potential for survival in less productive areas. We performed single-step GWAS and post-GWAS analysis for body weight (BW), average daily gain (ADG), carcass fleshiness (CF) and dressing percentage (DP) in 1,690 individuals of local alpine cattle breed, Rendena. This breed is typical of alpine pastures, with a marked dual-purpose attitude and good genetic diversity. Moreover, we considered two of the target phenotypes (BW and ADG) at different times in the individuals' life, a potentially important aspect in the study of the traits' genetic architecture. We identified 8 significant and 47 suggestively associated SNPs, located in 14 autosomal chromosomes (BTA). Among the strongest signals, 3 significant and 16 suggestive SNPs were associated with ADG and were located on BTA10 (50-60 Mb), while the hotspot associated with CF and DP was on BTA18 (55-62 MB). Among the significant SNPs some were mapped within genes, such as SLC12A1, CGNL1, PRTG (ADG), LOC513941 (CF), NLRP2 (CF and DP), CDC155 (DP). Pathway analysis showed great diversity in the biological pathways linked to the different traits; several were associated with neurogenesis and synaptic transmission, but actin-related and transmembrane transport pathways were also represented. Time-stratification highlighted how the genetic architectures of the same traits were markedly different between different ages. The results from our GWAS of beef traits in Rendena led to the detection of a variety of genes both well-known and novel. We argue that our results show that expanding genomic research to local breeds can reveal hitherto undetected genetic architectures in livestock worldwide. This could greatly help efforts to map genomic complexity of the traits of interest and to make appropriate breeding decisions.
Collapse
|
19
|
Vanvanhossou SFU, Yin T, Scheper C, Fries R, Dossa LH, König S. Unraveling Admixture, Inbreeding, and Recent Selection Signatures in West African Indigenous Cattle Populations in Benin. Front Genet 2021; 12:657282. [PMID: 34956303 PMCID: PMC8694269 DOI: 10.3389/fgene.2021.657282] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/22/2021] [Accepted: 10/07/2021] [Indexed: 11/13/2022] Open
Abstract
The Dwarf Lagune and the Savannah Somba cattle in Benin are typical representatives of the endangered West African indigenous Shorthorn taurine. The Lagune was previously exported to African and European countries and bred as Dahomey cattle, whereas the Somba contributed to the formation of two indigenous hybrids known as Borgou and Pabli cattle. These breeds are affected by demographic, economic, and environmental pressures in local production systems. Considering current and historical genomic data, we applied a formal test of admixture, estimated admixture proportions, and computed genomic inbreeding coefficients to characterize the five breeds. Subsequently, we unraveled the most recent selection signatures using the cross-population extended haplotype homozygosity approach, based on the current and historical genotypes. Results from principal component analyses and high proportion of Lagune ancestry confirm the Lagune origin of the European Dahomey cattle. Moreover, the Dahomey cattle displayed neither indicine nor European taurine (EUT) background, but they shared on average 40% of autozygosity from common ancestors, dated approximately eight generations ago. The Lagune cattle presented inbreeding coefficients larger than 0.13; however, the Somba and the hybrids (Borgou and Pabli) were less inbred (≤0.08). We detected evidence of admixture in the Somba and Lagune cattle, but they exhibited a similar African taurine (AFT) ancestral proportion (≥96%) to historical populations, respectively. A moderate and stable AFT ancestral proportion (62%) was also inferred for less admixed hybrid cattle including the Pabli. In contrast, the current Borgou samples displayed a lower AFT ancestral proportion (47%) than historical samples (63%). Irrespective of the admixture proportions, the hybrid populations displayed more selection signatures related to economic traits (reproduction, growth, and milk) than the taurine. In contrast, the taurine, especially the Somba, presented several regions known to be associated with adaptive traits (immunity and feed efficiency). The identified subregion of bovine leukocyte antigen (BoLA) class IIb (including DSB and BOLA-DYA) in Somba cattle is interestingly uncommon in other African breeds, suggesting further investigations to understand its association with specific adaptation to endemic diseases in Benin. Overall, our study provides deeper insights into recent evolutionary processes in the Beninese indigenous cattle and their aptitude for conservation and genetic improvement.
Collapse
Affiliation(s)
| | - Tong Yin
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany
| | - Carsten Scheper
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany
| | - Ruedi Fries
- Chair of Animal Breeding, Technische Universität München, Freising-Weihenstephan, Germany
| | - Luc Hippolyte Dossa
- School of Science and Technics of Animal Production, Faculty of Agricultural Sciences, University of Abomey-Calavi, Abomey-Calavi, Benin
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany
| |
Collapse
|
20
|
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.
Collapse
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
| |
Collapse
|
21
|
Manca E, Cesarani A, Falchi L, Atzori AS, Gaspa G, Rossoni A, Macciotta NPP, Dimauro C. Genome-wide association study for residual concentrate intake using different approaches in Italian Brown Swiss. ITALIAN JOURNAL OF ANIMAL SCIENCE 2021. [DOI: 10.1080/1828051x.2021.1963864] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Affiliation(s)
- E. Manca
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - A. Cesarani
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - L. Falchi
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - A. S. Atzori
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
| | - G. Gaspa
- Dipartimento di Scienze Agrarie, Forestali e Alimentari, University of Torino, Grugliasco, Italy
| | - A. Rossoni
- Associazione Nazionale degli Allevatori di Razza Bruna (ANARB), Verona, Italy
| | | | - C. Dimauro
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
| |
Collapse
|
22
|
Niu Q, Zhang T, Xu L, Wang T, Wang Z, Zhu B, Zhang L, Gao H, Song J, Li J, Xu L. Integration of selection signatures and multi-trait GWAS reveals polygenic genetic architecture of carcass traits in beef cattle. Genomics 2021; 113:3325-3336. [PMID: 34314829 DOI: 10.1016/j.ygeno.2021.07.025] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2021] [Revised: 05/05/2021] [Accepted: 07/22/2021] [Indexed: 11/18/2022]
Abstract
Carcass merits are widely considered as economically important traits affecting beef production in the beef cattle industry. However, the genetic basis of carcass traits remains to be well understood. Here, we applied multiple methods, including the Composite of Likelihood Ratio (CLR) and Genome-wide Association Study (GWAS), to explore the selection signatures and candidate variants affecting carcass traits. We identified 11,600 selected regions overlapping with 2214 candidate genes, and most of those were enriched in binding and gene regulation. Notably, we identified 66 and 110 potential variants significantly associated with carcass traits using single-trait and multi-traits analyses, respectively. By integrating selection signatures with single and multi-traits associations, we identified 12 and 27 putative genes, respectively. Several highly conserved missense variants were identified in OR5M13D, NCAPG, and TEX2. Our study supported polygenic genetic architecture of carcass traits and provided novel insights into the genetic basis of complex traits in beef cattle.
Collapse
Affiliation(s)
- Qunhao Niu
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tianliu Zhang
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ling Xu
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Tianzhen Wang
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Zezhao Wang
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Bo Zhu
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lupei Zhang
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Huijiang Gao
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Jiuzhou Song
- Department of Animal and Avian Science, University of Maryland, College Park, USA
| | - Junya Li
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| | - Lingyang Xu
- Key Laboratory of Animal Genetics Breeding and Reproduction, Ministry of Agriculture and Rural Affairs, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
| |
Collapse
|
23
|
Genome-Wide Association Study Provides Insights into Important Genes for Reproductive Traits in Nelore Cattle. Animals (Basel) 2021; 11:ani11051386. [PMID: 34068162 PMCID: PMC8152989 DOI: 10.3390/ani11051386] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Revised: 05/05/2021] [Accepted: 05/07/2021] [Indexed: 12/03/2022] Open
Abstract
Simple Summary In this study, we investigated the association between single nucleotide polymorphisms (SNPs) and reproductive traits in order to identify candidate genes and biological pathways associated with these traits in Nelore beef cattle. The genome-wide association analysis revealed genomic regions that could explain part of the genetic variance of the studied traits. The results revealed genes with important functions for reproductive traits, such as fertility and precocity. Some genes were associated with more than one trait, being important for reproductive efficiency. The identification of candidate genes that were associated with the studied traits as well as genes enriched in the functional terms and pathways may be useful for exploring the genetic architecture underlying reproductive traits and may be used in Nelore breeding programs. Abstract The identification of genomic regions associated with reproductive traits as well as their biological processes allows a better understanding of the phenotypic variability of these traits. This information could be applied to animal breeding programs to accelerate genetic gain. The aim of this study was to evaluate the association between single nucleotide polymorphisms (SNP) with a scrotal circumference at 365 days of age (SC365) and at 450 days of age (SC450), gestation length (GL) as a calf trait, age at first calving (AFC), accumulated productivity (ACP), heifer early calving until 30 months (HC30), and stayability (STAY) traits, in order to identify candidate genes and biological pathways associated with reproductive traits in Nelore cattle. The data set consisted of pedigree, phenotypes, and genotypes of Nelore cattle from the “Associação Nacional de Criadores e Pesquisadores” (ANCP). The association analyses were performed using the Weighted Single-Step Genome-Wide Association method; the regions, consisting of 10 consecutive SNP, which explained more than 0.5% of additive genetic variance, were considered as a significant association. A total of 3, 6, 7, 5, 10, 25, and 12 windows were associated with SC355, SC450, GL, AFC, ACP, HC30, and STAY, respectively. The results revealed genes with important functions for reproductive traits, such as fertility and precocity. Some genes were associated with more than one trait, among them CAMK1D, TASP1, ACOXL, RAB11FIP5, and SFXN5. Moreover, the genes were enriched in functional terms, like negative regulation of fat cell differentiation, fatty acid alpha-oxidation, and sphingolipids signaling pathway. The identification of the genes associated with the traits, as well as genes enriched in the terms and pathway mentioned above, should contribute to future biological validation studies and may be used as candidate genes in Nelore breeding programs.
Collapse
|
24
|
Freitas PHF, Wang Y, Yan P, Oliveira HR, Schenkel FS, Zhang Y, Xu Q, Brito LF. Genetic Diversity and Signatures of Selection for Thermal Stress in Cattle and Other Two Bos Species Adapted to Divergent Climatic Conditions. Front Genet 2021; 12:604823. [PMID: 33613634 PMCID: PMC7887320 DOI: 10.3389/fgene.2021.604823] [Citation(s) in RCA: 28] [Impact Index Per Article: 9.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2020] [Accepted: 01/15/2021] [Indexed: 12/21/2022] Open
Abstract
Understanding the biological mechanisms of climatic adaptation is of paramount importance for the optimization of breeding programs and conservation of genetic resources. The aim of this study was to investigate genetic diversity and unravel genomic regions potentially under selection for heat and/or cold tolerance in thirty-two worldwide cattle breeds, with a focus on Chinese local cattle breeds adapted to divergent climatic conditions, Datong yak (Bos grunniens; YAK), and Bali (Bos javanicus) based on dense SNP data. In general, moderate genetic diversity levels were observed in most cattle populations. The proportion of polymorphic SNP ranged from 0.197 (YAK) to 0.992 (Mongolian cattle). Observed and expected heterozygosity ranged from 0.023 (YAK) to 0.366 (Sanhe cattle; SH), and from 0.021 (YAK) to 0.358 (SH), respectively. The overall average inbreeding (±SD) was: 0.118 ± 0.028, 0.228 ± 0.059, 0.194 ± 0.041, and 0.021 ± 0.004 based on the observed versus expected number of homozygous genotypes, excess of homozygosity, correlation between uniting gametes, and runs of homozygosity (ROH), respectively. Signatures of selection based on multiple scenarios and methods (F ST, HapFLK, and ROH) revealed important genomic regions and candidate genes. The candidate genes identified are related to various biological processes and pathways such as heat-shock proteins, oxygen transport, anatomical traits, mitochondrial DNA maintenance, metabolic activity, feed intake, carcass conformation, fertility, and reproduction. This highlights the large number of biological processes involved in thermal tolerance and thus, the polygenic nature of climatic resilience. A comprehensive description of genetic diversity measures in Chinese cattle and YAK was carried out and compared to 24 worldwide cattle breeds to avoid potential biases. Numerous genomic regions under positive selection were detected using three signature of selection methods and candidate genes potentially under positive selection were identified. Enriched function analyses pinpointed important biological pathways, molecular function and cellular components, which contribute to a better understanding of the biological mechanisms underlying thermal tolerance in cattle. Based on the large number of genomic regions identified, thermal tolerance has a complex polygenic inheritance nature, which was expected considering the various mechanisms involved in thermal stress response.
Collapse
Affiliation(s)
- Pedro H. F. Freitas
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - Yachun Wang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Ping Yan
- Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou, China
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Flavio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, Canada
| | - Yi Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA – National Engineering Laboratory for Animal Breeding – College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Qing Xu
- College of Life Sciences and Bioengineering, School of Science, Beijing Jiaotong University, Beijing, China
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| |
Collapse
|
25
|
Brunes LC, Baldi F, Lopes FB, Lobo RB, Espigolan R, Costa MFO, Magnabosco CU. Selection criteria for feed efficiency-related traits and their association with growth, reproductive and carcass traits in Nelore cattle. ANIMAL PRODUCTION SCIENCE 2021. [DOI: 10.1071/an20487] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
Context
Livestock feed costs have a higher impact on the profitability of beef production systems and are directly related to feed efficiency. However, these traits are hard and have high costs to measure, reducing the availability of phenotypic records and reliability of genetic evaluations. Thus, the use of genomic information can increase the robustness of genetic studies that address them.
Aims
The aim of the present study was to estimate genetic parameters for feed efficiency, growth, reproductive and carcass traits in Nelore cattle and the correlated response among them, using genomic information.
Methods
Residual feed intake (RFI), dry-matter intake, feed conversion ratio, feed efficiency (FE), residual average daily gain (RG), residual feed intake and average daily gain (RIG), birthweight, weight at 120, 240, 365 and 450 days of age, scrotal circumference at 365 and 450 days of age, rib-eye area, backfat thickness and rump fat thickness were evaluated. The genetic parameters were estimated using the single-step genomic best linear unbiased prediction approach.
Key results
The FE-related traits showed low to moderate heritability ranging from 0.07 to 0.23. Feed efficiency-related traits showed low genetic correlations with reproductive (–0.24 to 0.27), carcass (–0.17 to 0.27) and growth (–0.19 to 0.24) traits, except for growth with dry-matter intake (0.32–0.56) and weight at 365 days of age with FE (–0.40).
Conclusions
The selection to improve growth, reproductive and carcass traits would not change RFI, RG and RIG. The choice of the most adequate selection criterion depends on the production system, that is, RFI might be used for low-input beef cattle systems, and RIG would be used for more intensive and without-any-dietary-restrictions beef cattle systems.
Implications
The estimates of heritability and genetic correlations suggest that genetic selection for feed efficiency using RFI, RG and RIG in Nellore cattle leads to higher genetic gain than does that using FE and feed conversion ratio without affecting other profitability traits.
Collapse
|
26
|
Brunes LC, Baldi F, Lopes FB, Narciso MG, Lobo RB, Espigolan R, Costa MFO, Magnabosco CU. Genomic prediction ability for feed efficiency traits using different models and pseudo-phenotypes under several validation strategies in Nelore cattle. Animal 2020; 15:100085. [PMID: 33573965 DOI: 10.1016/j.animal.2020.100085] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/27/2020] [Revised: 09/09/2020] [Accepted: 09/15/2020] [Indexed: 10/22/2022] Open
Abstract
There is a growing interest to improve feed efficiency (FE) traits in cattle. The genomic selection was proposed to improve these traits since they are difficult and expensive to measure. Up to date, there are scarce studies about the implementation of genomic selection for FE traits in indicine cattle under different scenarios of pseudo-phenotypes, models, and validation strategies on a commercial large scale. Thus, the aim was to evaluate the feasibility of genomic selection implementation for FE traits in Nelore cattle applying different models and pseudo-phenotypes under validation strategies. Phenotypic and genotypic information from 4 329 and 3 467 animals were used, respectively, which were tested for residual feed intake, DM intake, feed efficiency, feed conversion ratio, residual BW gain, and residual intake and BW gain. Six prediction methods were used: single-step genomic best linear unbiased prediction, Bayes A, Bayes B, Bayes Cπ, Bayesian least absolute shrinkage and selection operator (BLASSO), and Bayes R. Phenotypes adjusted for fixed effects (Y*), estimated breeding value (EBV), and EBV deregressed (DEBV) were used as pseudo-phenotypes. The validation approaches used were: (1) random: the data was randomly divided into ten subsets and the validation was done in each subset at a time; (2) age: the partition into training and testing sets was based on year of birth and testing animals were born after 2016; and (3) EBV accuracy: the data was split into two groups, being animals with accuracy above 0.45 the training set; and below 0.45 the validation set. In the analyses that used the Y* as pseudo-phenotype, prediction ability (PA) was obtained by dividing the correlation between pseudo-phenotype and genomic EBV (GEBV) by the square root of the heritability of the trait. When EBV and DEBV were used as the pseudo-phenotype, the simple correlation of this quantity with the GEBV was considered as PA. The prediction methods show similar results for PA and bias. The random cross-validation presented higher PA (0.17) than EBV accuracy (0.14) and age (0.13). The PA was higher for Y* than for EBV and DEBV (30.0 and 34.3%, respectively). Random validation presented the highest PA, being indicated for use in populations composed mainly of young animals and traits with few generations of data recording. For high heritability traits, the validation can be done by age, enabling the prediction of the next-generation genetic merit. These results would support breeders to identify genomic approaches that are more viable for genomic prediction for FE-related traits.
Collapse
Affiliation(s)
- L C Brunes
- Animal Science Department, Goiás Federal University, 74690-900 Goiânia, GO, Brazil; Embrapa Rice and Beans, GO-462, km 12, 75375-000 Santo Antônio de Goiás, GO, Brazil.
| | - F Baldi
- Animal Science Department, São Paulo State University - Júlio de Mesquita Filho (UNESP), Prof. Paulo Donato Castelane, 14884-900 Jaboticabal, SP, Brazil
| | - F B Lopes
- Cobb-Vantress, Inc., 72761 Siloam Springs, AR, USA
| | - M G Narciso
- Embrapa Rice and Beans, GO-462, km 12, 75375-000 Santo Antônio de Goiás, GO, Brazil
| | - R B Lobo
- National Association of Breeders and Researchers, 14020-230 Ribeirão Preto, Brazil
| | - R Espigolan
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, 13635-900 Pirassununga, SP, Brazil
| | - M F O Costa
- Embrapa Rice and Beans, GO-462, km 12, 75375-000 Santo Antônio de Goiás, GO, Brazil
| | - C U Magnabosco
- Embrapa Cerrados, BR-020, 18 Sobradinho, 70770-901 Brasilia, DF, Brazil
| |
Collapse
|
27
|
Brito LF, Oliveira HR, Houlahan K, Fonseca PA, Lam S, Butty AM, Seymour DJ, Vargas G, Chud TC, Silva FF, Baes CF, Cánovas A, Miglior F, Schenkel FS. Genetic mechanisms underlying feed utilization and implementation of genomic selection for improved feed efficiency in dairy cattle. CANADIAN JOURNAL OF ANIMAL SCIENCE 2020. [DOI: 10.1139/cjas-2019-0193] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/11/2022]
Abstract
The economic importance of genetically improving feed efficiency has been recognized by cattle producers worldwide. It has the potential to considerably reduce costs, minimize environmental impact, optimize land and resource use efficiency, and improve the overall cattle industry’s profitability. Feed efficiency is a genetically complex trait that can be described as units of product output (e.g., milk yield) per unit of feed input. The main objective of this review paper is to present an overview of the main genetic and physiological mechanisms underlying feed utilization in ruminants and the process towards implementation of genomic selection for feed efficiency in dairy cattle. In summary, feed efficiency can be improved via numerous metabolic pathways and biological mechanisms through genetic selection. Various studies have indicated that feed efficiency is heritable, and genomic selection can be successfully implemented in dairy cattle with a large enough training population. In this context, some organizations have worked collaboratively to do research and develop training populations for successful implementation of joint international genomic evaluations. The integration of “-omics” technologies, further investments in high-throughput phenotyping, and identification of novel indicator traits will also be paramount in maximizing the rates of genetic progress for feed efficiency in dairy cattle worldwide.
Collapse
Affiliation(s)
- Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Kerry Houlahan
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Pablo A.S. Fonseca
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Stephanie Lam
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Adrien M. Butty
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Dave J. Seymour
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
- Centre for Nutrition Modelling, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Giovana Vargas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Tatiane C.S. Chud
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Fabyano F. Silva
- Department of Animal Sciences, Federal University of Viçosa, Viçosa, Minas Gerais 36570-000, Brazil
| | - Christine F. Baes
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
- Vetsuisse Faculty, Institute of Genetics, University of Bern, Bern 3001, Switzerland
| | - Angela Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Filippo Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Flavio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| |
Collapse
|
28
|
Vanvanhossou SFU, Scheper C, Dossa LH, Yin T, Brügemann K, König S. A multi-breed GWAS for morphometric traits in four Beninese indigenous cattle breeds reveals loci associated with conformation, carcass and adaptive traits. BMC Genomics 2020; 21:783. [PMID: 33176675 PMCID: PMC7656759 DOI: 10.1186/s12864-020-07170-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/04/2020] [Accepted: 10/20/2020] [Indexed: 12/19/2022] Open
Abstract
BACKGROUND Specific adaptive features including disease resistance and growth abilities in harsh environments are attributed to indigenous cattle breeds of Benin, but these breeds are endangered due to crossbreeding. So far, there is a lack of systematic trait recording, being the basis for breed characterizations, and for structured breeding program designs aiming on conservation. Bridging this gap, own phenotyping for morphological traits considered measurements for height at withers (HAW), sacrum height (SH), heart girth (HG), hip width (HW), body length (BL) and ear length (EL), including 449 cattle from the four indigenous Benin breeds Lagune, Somba, Borgou and Pabli. In order to utilize recent genomic tools for breed characterizations and genetic evaluations, phenotypes for novel traits were merged with high-density SNP marker data. Multi-breed genetic parameter estimations and genome-wide association studies (GWAS) for the six morphometric traits were carried out. Continuatively, we aimed on inferring genomic regions and functional loci potentially associated with conformation, carcass and adaptive traits. RESULTS SNP-based heritability estimates for the morphometric traits ranged between 0.46 ± 0.14 (HG) and 0.74 ± 0.13 (HW). Phenotypic and genetic correlations ranged from 0.25 ± 0.05 (HW-BL) to 0.89 ± 0.01 (HAW-SH), and from 0.14 ± 0.10 (HW-BL) to 0.85 ± 0.02 (HAW-SH), respectively. Three genome-wide and 25 chromosome-wide significant SNP positioned on different chromosomes were detected, located in very close chromosomal distance (±25 kb) to 15 genes (or located within the genes). The genes PIK3R6 and PIK3R1 showed direct functional associations with height and body size. We inferred the potential candidate genes VEPH1, CNTNAP5, GYPC for conformation, growth and carcass traits including body weight and body fat deposition. According to their functional annotations, detected potential candidate genes were associated with stress or immune response (genes PTAFR, PBRM1, ADAMTS12) and with feed efficiency (genes MEGF11 SLC16A4, CCDC117). CONCLUSIONS Accurate measurements contributed to large SNP heritabilities for some morphological traits, even for a small mixed-breed sample size. Multi-breed GWAS detected different loci associated with conformation or carcass traits. The identified potential candidate genes for immune response or feed efficiency indicators reflect the evolutionary development and adaptability features of the breeds.
Collapse
Affiliation(s)
| | - Carsten Scheper
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany
| | - Luc Hippolyte Dossa
- School of Science and Technics of Animal Production, Faculty of Agricultural Sciences, University of Abomey-Calavi, Cotonou, Benin
| | - Tong Yin
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany
| | - Kerstin Brügemann
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University Gießen, Gießen, Germany.
| |
Collapse
|
29
|
Taussat S, Boussaha M, Ramayo-Caldas Y, Martin P, Venot E, Cantalapiedra-Hijar G, Hozé C, Fritz S, Renand G. Gene networks for three feed efficiency criteria reveal shared and specific biological processes. Genet Sel Evol 2020; 52:67. [PMID: 33167870 PMCID: PMC7653997 DOI: 10.1186/s12711-020-00585-z] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2020] [Accepted: 10/27/2020] [Indexed: 12/26/2022] Open
Abstract
Background French beef producers suffer from the decrease in profitability of their farms mainly because of the continuous increase in feed costs. Selection for feed efficiency in beef cattle represents a relevant solution to face this problem. However, feed efficiency is a complex trait that can be assessed by three major criteria: residual feed intake (RFI), residual gain (RG) and feed efficiency ratio (FE), which involve different genetic determinisms. An analysis that combines phenotype and whole-genome sequence data provides a unique framework for genomic studies. The aim of our study was to identify the gene networks and the biological processes that are responsible for the genetic determinism that is shared between these three feed efficiency criteria. Results A population of 1477 French Charolais young bulls was phenotyped for feed intake (FI), average daily gain (ADG) and final weight (FW) to estimate RFI, RG and FE. A subset of 789 young bulls was genotyped on the BovineSNP50 single nucleotide polymorphism (SNP) array and imputed at the sequence level using RUN6 of the 1000 Bull Genomes Project. We conducted a genome-wide association study (GWAS) to estimate the individual effect of 8.5 million SNPs and applied an association weight matrix (AWM) approach to analyse the results, one for each feed efficiency criterion. The results highlighted co-association networks including 626 genes for RFI, 426 for RG and 564 for FE. Enrichment assessment revealed the biological processes that show the strongest association with RFI, RG and FE, i.e. digestive tract (salivary, gastric and mucin secretion) and metabolic processes (cellular and cardiovascular). Energetic functions were more associated with RFI and FE and cardio-vascular and cellular processes with RG. Several hormones such as apelin, glucagon, insulin, aldosterone, the gonadotrophin releasing hormone and the thyroid hormone were also identified, and these should be tested in future studies as candidate biomarkers for feed efficiency. Conclusions The combination of network and pathway analyses at the sequence level led to the identification of both common and specific mechanisms that are involved in RFI, RG and FE, and to a better understanding of the genetic determinism underlying these three criteria. The effects of the genes involved in each of the identified processes need to be tested in genomic evaluations to confirm the potential gain in reliability of using functional variants to select animals for feed efficiency.
Collapse
Affiliation(s)
- Sébastien Taussat
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France. .,Allice, 75012, Paris, France.
| | - Mekki Boussaha
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | | | - Pauline Martin
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | - Eric Venot
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| | | | - Chris Hozé
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.,Allice, 75012, Paris, France
| | - Sébastien Fritz
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France.,Allice, 75012, Paris, France
| | - Gilles Renand
- Université Paris-Saclay, INRAE, AgroParisTech, GABI, 78350, Jouy-en-Josas, France
| |
Collapse
|
30
|
Lam S, Zeidan J, Miglior F, Suárez-Vega A, Gómez-Redondo I, Fonseca PAS, Guan LL, Waters S, Cánovas A. Development and comparison of RNA-sequencing pipelines for more accurate SNP identification: practical example of functional SNP detection associated with feed efficiency in Nellore beef cattle. BMC Genomics 2020; 21:703. [PMID: 33032519 PMCID: PMC7545862 DOI: 10.1186/s12864-020-07107-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2020] [Accepted: 09/28/2020] [Indexed: 12/14/2022] Open
Abstract
Background Optimization of an RNA-Sequencing (RNA-Seq) pipeline is critical to maximize power and accuracy to identify genetic variants, including SNPs, which may serve as genetic markers to select for feed efficiency, leading to economic benefits for beef production. This study used RNA-Seq data (GEO Accession ID: PRJEB7696 and PRJEB15314) from muscle and liver tissue, respectively, from 12 Nellore beef steers selected from 585 steers with residual feed intake measures (RFI; n = 6 low-RFI, n = 6 high-RFI). Three RNA-Seq pipelines were compared including multi-sample calling from i) non-merged samples; ii) merged samples by RFI group, iii) merged samples by RFI and tissue group. The RNA-Seq reads were aligned against the UMD3.1 bovine reference genome (release 94) assembly using STAR aligner. Variants were called using BCFtools and variant effect prediction (VeP) and functional annotation (ToppGene) analyses were performed. Results On average, total reads detected for Approach i) non-merged samples for liver and muscle, were 18,362,086.3 and 35,645,898.7, respectively. For Approach ii), merging samples by RFI group, total reads detected for each merged group was 162,030,705, and for Approach iii), merging samples by RFI group and tissues, was 324,061,410, revealing the highest read depth for Approach iii). Additionally, Approach iii) merging samples by RFI group and tissues, revealed the highest read depth per variant coverage (572.59 ± 3993.11) and encompassed the majority of localized positional genes detected by each approach. This suggests Approach iii) had optimized detection power, read depth, and accuracy of SNP calling, therefore increasing confidence of variant detection and reducing false positive detection. Approach iii) was then used to detect unique SNPs fixed within low- (12,145) and high-RFI (14,663) groups. Functional annotation of SNPs revealed positional candidate genes, for each RFI group (2886 for low-RFI, 3075 for high-RFI), which were significantly (P < 0.05) associated with immune and metabolic pathways. Conclusion The most optimized RNA-Seq pipeline allowed for more accurate identification of SNPs, associated positional candidate genes, and significantly associated metabolic pathways in muscle and liver tissues, providing insight on the underlying genetic architecture of feed efficiency in beef cattle.
Collapse
Affiliation(s)
- S Lam
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario, N1G2W1, Canada
| | - J Zeidan
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario, N1G2W1, Canada
| | - F Miglior
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario, N1G2W1, Canada
| | - A Suárez-Vega
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario, N1G2W1, Canada
| | - I Gómez-Redondo
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario, N1G2W1, Canada.,Spanish National Institute for Agriculture and Food Research and Technology, Carretera de La Coruña, 28040, Madrid, Spain
| | - P A S Fonseca
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario, N1G2W1, Canada
| | - L L Guan
- Department of Agriculture, Food & Nutritional Science, University of Alberta, Edmonton, Alberta, T6H 2P5, Canada
| | - S Waters
- Teagasc, Animal & Grassland Research and Innovation Centre, Grange, Dunsany, Co. Meath, C15 PW93, Ireland
| | - A Cánovas
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, 50 Stone Road E, Guelph, Ontario, N1G2W1, Canada.
| |
Collapse
|
31
|
Uemoto Y, Takeda M, Ogino A, Kurogi K, Ogawa S, Satoh M, Terada F. Genetic and genomic analyses for predicted methane-related traits in Japanese Black steers. Anim Sci J 2020; 91:e13383. [PMID: 32410280 PMCID: PMC7379199 DOI: 10.1111/asj.13383] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2020] [Revised: 04/01/2020] [Accepted: 04/10/2020] [Indexed: 12/26/2022]
Abstract
The objectives of this study were to estimate genetic parameters and to perform a genome‐wide association study (GWAS) for predicted methane‐related traits in Japanese Black steers. The methane production and yield traits were predicted using on‐farm measurable traits, such as dry matter intake and average daily gain. A total of 4,578 Japanese Black steers, which were progenies of 362 sires genotyped with imputed 551,995 single nucleotide polymorphisms (SNPs), had phenotypes of predicted methane‐related traits during the total fattening period (52 weeks). For the estimation of genetic parameters, the estimated heritabilities were moderate (ranged from 0.57 to 0.60). In addition, the estimated genetic correlations of methane production traits with most of carcass traits and feed‐efficiency traits were unfavorable, but those of methane yield traits were favorable or low. For the GWAS, no genome‐wide significant SNP was detected, but a total of four quantitative trait locus (QTL) regions that explained more than 5.0% of genetic variance were localized on the genome, and some candidate genes associated with growth and feed‐efficiency traits were located on the regions. Our results suggest that the predicted methane‐related traits are heritable and some QTL regions for the traits are localized on the genome in Japanese Black steers.
Collapse
Affiliation(s)
- Yoshinobu Uemoto
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | | | - Atushi Ogino
- Maebashi Institute of Animal Science, Livestock Improvement Association of Japan, Inc., Maebashi, Japan
| | - Kazuhito Kurogi
- Cattle Breeding Department, Livestock Improvement Association of Japan, Inc., Tokyo, Japan
| | - Shinichro Ogawa
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Masahiro Satoh
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Fuminori Terada
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| |
Collapse
|
32
|
Ghoreishifar SM, Eriksson S, Johansson AM, Khansefid M, Moghaddaszadeh-Ahrabi S, Parna N, Davoudi P, Javanmard A. Signatures of selection reveal candidate genes involved in economic traits and cold acclimation in five Swedish cattle breeds. Genet Sel Evol 2020; 52:52. [PMID: 32887549 PMCID: PMC7487911 DOI: 10.1186/s12711-020-00571-5] [Citation(s) in RCA: 39] [Impact Index Per Article: 9.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/23/2020] [Accepted: 08/21/2020] [Indexed: 02/01/2023] Open
Abstract
Background Thousands of years of natural and artificial selection have resulted in indigenous cattle breeds that are well-adapted to the environmental challenges of their local habitat and thereby are considered as valuable genetic resources. Understanding the genetic background of such adaptation processes can help us design effective breeding objectives to preserve local breeds and improve commercial cattle. To identify regions under putative selection, GGP HD 150 K single nucleotide polymorphism (SNP) arrays were used to genotype 106 individuals representing five Swedish breeds i.e. native to different regions and covering areas with a subarctic cold climate in the north and mountainous west, to those with a continental climate in the more densely populated south regions. Results Five statistics were incorporated within a framework, known as de-correlated composite of multiple signals (DCMS) to detect signatures of selection. The obtained p-values were adjusted for multiple testing (FDR < 5%), and significant genomic regions were identified. Annotation of genes in these regions revealed various verified and novel candidate genes that are associated with a diverse range of traits, including e.g. high altitude adaptation and response to hypoxia (DCAF8, PPP1R12A, SLC16A3, UCP2, UCP3, TIGAR), cold acclimation (AQP3, AQP7, HSPB8), body size and stature (PLAG1, KCNA6, NDUFA9, AKAP3, C5H12orf4, RAD51AP1, FGF6, TIGAR, CCND2, CSMD3), resistance to disease and bacterial infection (CHI3L2, GBP6, PPFIBP1, REP15, CYP4F2, TIGD2, PYURF, SLC10A2, FCHSD2, ARHGEF17, RELT, PRDM2, KDM5B), reproduction (PPP1R12A, ZFP36L2, CSPP1), milk yield and components (NPC1L1, NUDCD3, ACSS1, FCHSD2), growth and feed efficiency (TMEM68, TGS1, LYN, XKR4, FOXA2, GBP2, GBP5, FGD6), and polled phenotype (URB1, EVA1C). Conclusions We identified genomic regions that may provide background knowledge to understand the mechanisms that are involved in economic traits and adaptation to cold climate in cattle. Incorporating p-values of different statistics in a single DCMS framework may help select and prioritize candidate genes for further analyses.
Collapse
Affiliation(s)
- Seyed Mohammad Ghoreishifar
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Susanne Eriksson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden.
| | - Anna M Johansson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, SE-75007, Uppsala, Sweden
| | - Majid Khansefid
- AgriBio Centre for AgriBioscience, Agriculture Victoria, Bundoora, VIC, 3083, Australia
| | - Sima Moghaddaszadeh-Ahrabi
- Department of Animal Science, Faculty of Agriculture and Natural Resources, Islamic Azad University, Tabriz Branch, Tabriz, Iran
| | - Nahid Parna
- Department of Animal Science, University College of Agriculture and Natural Resources, University of Tehran, Karaj, 31587-11167, Iran
| | - Pourya Davoudi
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS, B2N5E3, Canada
| | - Arash Javanmard
- Department of Animal Science, Faculty of Agriculture, University of Tabriz, Tabriz, Iran
| |
Collapse
|
33
|
Brunes LC, Baldi F, Lopes FB, Lôbo RB, Espigolan R, Costa MFO, Stafuzza NB, Magnabosco CU. Weighted single-step genome-wide association study and pathway analyses for feed efficiency traits in Nellore cattle. J Anim Breed Genet 2020; 138:23-44. [PMID: 32654373 DOI: 10.1111/jbg.12496] [Citation(s) in RCA: 21] [Impact Index Per Article: 5.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Revised: 06/11/2020] [Accepted: 06/13/2020] [Indexed: 02/06/2023]
Abstract
The aim was to conduct a weighted single-step genome-wide association study to detect genomic regions and putative candidate genes related to residual feed intake, dry matter intake, feed efficiency (FE), feed conversion ratio, residual body weight gain, residual intake and weight gain in Nellore cattle. Several protein-coding genes were identified within the genomic regions that explain more than 0.5% of the additive genetic variance for these traits. These genes were associated with insulin, leptin, glucose, protein and lipid metabolisms; energy balance; heat and oxidative stress; bile secretion; satiety; feed behaviour; salivation; digestion; and nutrient absorption. Enrichment analysis revealed functional pathways (p-value < .05) such as neuropeptide signalling (GO:0007218), negative regulation of canonical Wingless/Int-1 (Wnt) signalling (GO:0090090), bitter taste receptor activity (GO:0033038), neuropeptide hormone activity (GO:0005184), bile secretion (bta04976), taste transduction (bta0742) and glucagon signalling pathway (bta04922). The identification of these genes, pathways and their respective functions should contribute to a better understanding of the genetic and physiological mechanisms regulating Nellore FE-related traits.
Collapse
Affiliation(s)
- Ludmilla C Brunes
- Department of Animal Science, Federal University of Goiás (UFG), Goiânia, Brazil.,Embrapa Rice and Beans, Santo Antônio de Goiás, Brazil
| | - Fernando Baldi
- Department of Animal Science, São Paulo State University (UNESP), Jaboticabal, Brazil
| | | | - Raysildo B Lôbo
- National Association of Breeders and Researchers (ANCP), Ribeirão Preto, Brazil
| | - Rafael Espigolan
- Department of Veterinary Medicine, Faculty of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga, Brazil
| | | | - Nedenia B Stafuzza
- Beef Cattle Research Center, Animal Science Institute, Sertãozinho, Brazil
| | | |
Collapse
|
34
|
Salek Ardestani S, Aminafshar M, Zandi Baghche Maryam MB, Banabazi MH, Sargolzaei M, Miar Y. Signatures of selection analysis using whole-genome sequence data reveals novel candidate genes for pony and light horse types. Genome 2020; 63:387-396. [PMID: 32407640 DOI: 10.1139/gen-2020-0001] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/23/2022]
Abstract
Natural selection and domestication have shaped modern horse populations, resulting in a vast range of phenotypically diverse breeds. Horse breeds are classified into three types (pony, light, and draft) generally based on their body type. Understanding the genetic basis of horse type variation and selective pressures related to the evolutionary trend can be particularly important for current selection strategies. Whole-genome sequences were generated for 14 pony and 32 light horses to investigate the genetic signatures of selection of the horse type in pony and light horses. In the overlapping extremes of the fixation index and nucleotide diversity results, we found novel genomic signatures of selective sweeps near key genes previously implicated in body measurements including C4ORF33, CRB1, CPN1, FAM13A, and FGF12 that may influence variation in pony and light horse types. This study contributes to a better understanding of the genetic background of differences between pony and light horse types.
Collapse
Affiliation(s)
- Siavash Salek Ardestani
- Department of Animal Science, Science and Research Branch, Islamic Azad University, Tehran 1477893855, Iran
| | - Mehdi Aminafshar
- Department of Animal Science, Science and Research Branch, Islamic Azad University, Tehran 1477893855, Iran
| | | | - Mohammad Hossein Banabazi
- Department of Biotechnology, Animal Science Research Institute of Iran, Agricultural Research, Education & Extension Organization, Karaj 3146618361, Iran
| | - Mehdi Sargolzaei
- Department of Pathobiology, University of Guelph, Guelph, ON NIG 2W1, Canada.,Select Sires Inc., Plain City, OH 43064, USA
| | - Younes Miar
- Department of Animal Science and Aquaculture, Dalhousie University, Truro, NS B2N 5E3, Canada
| |
Collapse
|
35
|
Hlongwane NL, Hadebe K, Soma P, Dzomba EF, Muchadeyi FC. Genome Wide Assessment of Genetic Variation and Population Distinctiveness of the Pig Family in South Africa. Front Genet 2020; 11:344. [PMID: 32457791 PMCID: PMC7221027 DOI: 10.3389/fgene.2020.00344] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/07/2018] [Accepted: 03/23/2020] [Indexed: 12/12/2022] Open
Abstract
Genetic diversity is of great importance and a prerequisite for genetic improvement and conservation programs in pigs and other livestock populations. The present study provides a genome wide analysis of the genetic variability and population structure of pig populations from different production systems in South Africa relative to global populations. A total of 234 pigs sampled in South Africa and consisting of village (n = 91), commercial (n = 60), indigenous (n = 40), Asian (n = 5) and wild (n = 38) populations were genotyped using Porcine SNP60K BeadChip. In addition, 389 genotypes representing village and commercial pigs from America, Europe, and Asia were accessed from a previous study and used to compare population clustering and relationships of South African pigs with global populations. Moderate heterozygosity levels, ranging from 0.204 for Warthogs to 0.371 for village pigs sampled from Capricorn municipality in Eastern Cape province of South Africa were observed. Principal Component Analysis of the South African pigs resulted in four distinct clusters of (i) Duroc; (ii) Vietnamese; (iii) Bush pig and Warthog and (iv) a cluster with the rest of the commercial (SA Large White and Landrace), village, Wild Boar and indigenous breeds of Koelbroek and Windsnyer. The clustering demonstrated alignment with genetic similarities, geographic location and production systems. The PCA with the global populations also resulted in four clusters that where populated with (i) all the village populations, wild boars, SA indigenous and the large white and landraces; (ii) Durocs (iii) Chinese and Vietnamese pigs and (iv) Warthog and Bush pig. K = 10 (The number of population units) was the most probable ADMIXTURE based clustering, which grouped animals according to their populations with the exception of the village pigs that showed presence of admixture. AMOVA reported 19.92%-98.62% of the genetic variation to be within populations. Sub structuring was observed between South African commercial populations as well as between Indigenous and commercial breeds. Population pairwise F ST analysis showed genetic differentiation (P ≤ 0.05) between the village, commercial and wild populations. A per marker per population pairwise F ST analysis revealed SNPs associated with QTLs for traits such as meat quality, cytoskeletal and muscle development, glucose metabolism processes and growth factors between both domestic populations as well as between wild and domestic breeds. Overall, the study provided a baseline understanding of porcine diversity and an important foundation for porcine genomics of South African populations.
Collapse
Affiliation(s)
- Nompilo Lucia Hlongwane
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Pietermartizburg, South Africa
| | - Khanyisile Hadebe
- Biotechnology Platform, Agricultural Research Council, Onderstepoort, South Africa
| | - Pranisha Soma
- Animal Production Institute, Agricultural Research Council, Irene, South Africa
| | - Edgar Farai Dzomba
- Discipline of Genetics, School of Life Sciences, University of KwaZulu-Natal, Pietermartizburg, South Africa
| | | |
Collapse
|
36
|
de Lima AO, Koltes JE, Diniz WJS, de Oliveira PSN, Cesar ASM, Tizioto PC, Afonso J, de Souza MM, Petrini J, Rocha MIP, Cardoso TF, Neto AZ, Coutinho LL, Mourão GB, Regitano LCA. Potential Biomarkers for Feed Efficiency-Related Traits in Nelore Cattle Identified by Co-expression Network and Integrative Genomics Analyses. Front Genet 2020; 11:189. [PMID: 32194642 PMCID: PMC7064723 DOI: 10.3389/fgene.2020.00189] [Citation(s) in RCA: 20] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/21/2019] [Accepted: 02/17/2020] [Indexed: 12/14/2022] Open
Abstract
Feed efficiency helps to reduce environmental impacts from livestock production, improving beef cattle profitability. We identified potential biomarkers (hub genes) for feed efficiency, by applying co-expression analysis in Longissimus thoracis RNA-Seq data from 180 Nelore steers. Six co-expression modules were associated with six feed efficiency-related traits (p-value ≤ 0.05). Within these modules, 391 hub genes were enriched for pathways as protein synthesis, muscle growth, and immune response. Trait-associated transcription factors (TFs) ELF1, ELK3, ETS1, FLI1, and TCF4, were identified with binding sites in at least one hub gene. Gene expression of CCDC80, FBLN5, SERPINF1, and OGN was associated with multiple feed efficiency-related traits (FDR ≤ 0.05) and were previously related to glucose homeostasis, oxidative stress, fat mass, and osteoblastogenesis, respectively. Potential regulatory elements were identified, integrating the hub genes with previous studies from our research group, such as the putative cis-regulatory elements (eQTLs) inferred as affecting the PCDH18 and SPARCL1 hub genes related to immune system and adipogenesis, respectively. Therefore, our analyses contribute to a better understanding of the biological mechanisms underlying feed efficiency in bovine and the hub genes disclosed can be used as biomarkers for feed efficiency-related traits in Nelore cattle.
Collapse
Affiliation(s)
- Andressa O de Lima
- Center for Biological and Health Sciences, Federal University of São Carlos, São Carlos, Brazil
| | - James E Koltes
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Wellison J S Diniz
- Center for Biological and Health Sciences, Federal University of São Carlos, São Carlos, Brazil
| | | | - Aline S M Cesar
- Department of Agroindustry, Food and Nutrition, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | | | - Juliana Afonso
- Center for Biological and Health Sciences, Federal University of São Carlos, São Carlos, Brazil
| | - Marcela M de Souza
- Department of Animal Science, Iowa State University, Ames, IA, United States
| | - Juliana Petrini
- Exact Sciences Institute, Federal University of Alfenas, Alfenas, Brazil
| | - Marina I P Rocha
- Center for Biological and Health Sciences, Federal University of São Carlos, São Carlos, Brazil
| | - Tainã F Cardoso
- Embrapa Pecuária Sudeste, Empresa Brazileira de Pesquisa Agropecuária, São Carlos, Brazil
| | - Adhemar Zerlotini Neto
- Embrapa Informática Agropecuária, Empresa Brazileira de Pesquisa Agropecuária, Campinas, Brazil
| | - Luiz L Coutinho
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Gerson B Mourão
- Department of Animal Science, Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, Brazil
| | - Luciana C A Regitano
- Embrapa Pecuária Sudeste, Empresa Brazileira de Pesquisa Agropecuária, São Carlos, Brazil
| |
Collapse
|
37
|
Banerjee P, Carmelo VAO, Kadarmideen HN. Genome-Wide Epistatic Interaction Networks Affecting Feed Efficiency in Duroc and Landrace Pigs. Front Genet 2020; 11:121. [PMID: 32184802 PMCID: PMC7058701 DOI: 10.3389/fgene.2020.00121] [Citation(s) in RCA: 18] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2019] [Accepted: 01/31/2020] [Indexed: 12/12/2022] Open
Abstract
Interactions among genomic loci have often been overlooked in genome-wide association studies, revealing the combinatorial effects of variants on phenotype or disease manifestation. Unexplained genetic variance, interactions among causal genes of small effects, and biological pathways could be identified using a network biology approach. The main objective of this study was to determine the genome-wide epistatic variants affecting feed efficiency traits [feed conversion ratio (FCR) and residual feed intake (RFI)] based on weighted interaction SNP hub (WISH-R) method. Herein, we detected highly interconnected epistatic SNP modules, pathways, and potential biomarkers for the FCR and RFI in Duroc and Landrace purebreds considering the whole population, and separately for low and high feed efficient groups. Highly interacting SNP modules in Duroc (1,247 SNPs) and Landrace (1,215 SNPs) across the population and for low feed efficient (Duroc-80 SNPs, Landrace-146 SNPs) and high feed efficient group (Duroc-198 SNPs, Landrace-232 SNPs) for FCR and RFI were identified. Gene and pathway analyses identified ABL1, MAP3K4, MAP3K5, SEMA6A, KITLG, and KAT2B from chromosomes 1, 2, 5, and 13 underlying ErbB, Ras, Rap1, thyroid hormone, axon guidance pathways in Duroc. GABBR2, GNA12, and PRKCG genes from chromosomes 1, 3, and 6 pointed towards thyroid hormone, cGMP-PKG and cAMP pathways in Landrace. From Duroc low feed efficient group, the TPK1 gene was found involved with thiamine metabolism, whereas PARD6G, DLG2, CRB1 were involved with the hippo signaling pathway in high feed efficient group. PLOD1 and SETD7 genes were involved with lysine degradation in low feed efficient group in Landrace, while high feed efficient group pointed to genes underpinning valine, leucine, isoleucine degradation, and fatty acid elongation. Some SNPs and genes identified are known for their association with feed efficiency, others are novel and potentially provide new avenues for further research. Further validation of epistatic SNPs and genes identified here in a larger cohort would help to establish a framework for modelling epistatic variance in future methods of genomic prediction, increasing the accuracy of estimated genetic merit for FE and helping the pig breeding industry.
Collapse
Affiliation(s)
- Priyanka Banerjee
- Quantitative Genomics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Victor Adriano Okstoft Carmelo
- Quantitative Genomics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Haja N Kadarmideen
- Quantitative Genomics, Bioinformatics and Computational Biology Group, Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| |
Collapse
|
38
|
Barbato M, Hailer F, Upadhyay M, Del Corvo M, Colli L, Negrini R, Kim ES, Crooijmans RPMA, Sonstegard T, Ajmone-Marsan P. Adaptive introgression from indicine cattle into white cattle breeds from Central Italy. Sci Rep 2020; 10:1279. [PMID: 31992729 PMCID: PMC6987186 DOI: 10.1038/s41598-020-57880-4] [Citation(s) in RCA: 24] [Impact Index Per Article: 6.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/10/2019] [Accepted: 12/26/2019] [Indexed: 11/19/2022] Open
Abstract
Cattle domestication occurred at least twice independently and gave rise to the modern taurine and indicine cattle breeds. European cattle diversity is generally dominated by taurine cattle, although elevated levels of indicine ancestry have been recorded in several breeds from southern Europe. Here we use genome-wide high-density SNP genotyping data to investigate the taurine and indicine ancestry in southern European cattle, based on a dataset comprising 508 individuals from 23 cattle breeds of taurine, indicine and mixed ancestry, including three breeds from Central Italy known to exhibit the highest levels of indicine introgression among southern European breeds. Based on local genomic ancestry analyses, we reconstruct taurine and indicine ancestry genome-wide and along chromosomes. We scrutinise local genomic introgression signals and identify genomic regions that have introgressed from indicine into taurine cattle under positive selection, harbouring genes with functions related to body size and feed efficiency. These findings suggest that indicine-derived traits helped enhance Central Italian cattle through adaptive introgression. The identified genes could provide genomic targets for selection for improved cattle performance. Our findings elucidate the key role of adaptive introgression in shaping the phenotypic features of modern cattle, aided by cultural and livestock exchange among historic human societies.
Collapse
Affiliation(s)
- Mario Barbato
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy.
| | - Frank Hailer
- School of Biosciences, Cardiff University, Cardiff, Wales, UK
| | - Maulik Upadhyay
- Animal Breeding and Genomics, Wageningen University & Research, Wageningen, The Netherlands.,Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Marcello Del Corvo
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Licia Colli
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | - Riccardo Negrini
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy
| | | | | | | | - Paolo Ajmone-Marsan
- Università Cattolica del Sacro Cuore, Department of Animal Science Food and Nutrition - DIANA, Nutrigenomics and Proteomics Research Centre - PRONUTRIGEN, and Biodiversity and Ancient DNA Research Centre, Università Cattolica del Sacro Cuore, Piacenza, Italy.
| |
Collapse
|
39
|
|
40
|
de las Heras-Saldana S, Clark SA, Duijvesteijn N, Gondro C, van der Werf JHJ, Chen Y. Combining information from genome-wide association and multi-tissue gene expression studies to elucidate factors underlying genetic variation for residual feed intake in Australian Angus cattle. BMC Genomics 2019; 20:939. [PMID: 31810463 PMCID: PMC6898931 DOI: 10.1186/s12864-019-6270-4] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 11/07/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Genome-wide association studies (GWAS) are extensively used to identify single nucleotide polymorphisms (SNP) underlying the genetic variation of complex traits. However, much uncertainly often still exists about the causal variants and genes at quantitative trait loci (QTL). The aim of this study was to identify QTL associated with residual feed intake (RFI) and genes in these regions whose expression is also associated with this trait. Angus cattle (2190 steers) with RFI records were genotyped and imputed to high density arrays (770 K) and used for a GWAS approach to identify QTL associated with RFI. RNA sequences from 126 Angus divergently selected for RFI were analyzed to identify the genes whose expression was significantly associated this trait with special attention to those genes residing in the QTL regions. RESULTS The heritability for RFI estimated for this Angus population was 0.3. In a GWAS, we identified 78 SNPs associated with RFI on six QTL (on BTA1, BTA6, BTA14, BTA17, BTA20 and BTA26). The most significant SNP was found on chromosome BTA20 (rs42662073) and explained 4% of the genetic variance. The minor allele frequencies of significant SNPs ranged from 0.05 to 0.49. All regions, except on BTA17, showed a significant dominance effect. In 1 Mb windows surrounding the six significant QTL, we found 149 genes from which OAS2, STC2, SHOX, XKR4, and SGMS1 were the closest to the most significant QTL on BTA17, BTA20, BTA1, BTA14, and BTA26, respectively. In a 2 Mb windows around the six significant QTL, we identified 15 genes whose expression was significantly associated with RFI: BTA20) NEURL1B and CPEB4; BTA17) RITA1, CCDC42B, OAS2, RPL6, and ERP29; BTA26) A1CF, SGMS1, PAPSS2, and PTEN; BTA1) MFSD1 and RARRES1; BTA14) ATP6V1H and MRPL15. CONCLUSIONS Our results showed six QTL regions associated with RFI in a beef Angus population where five of these QTL contained genes that have expression associated with this trait. Therefore, here we show that integrating information from gene expression and GWAS studies can help to better understand the genetic mechanisms that determine variation in complex traits.
Collapse
Affiliation(s)
| | - Samuel A. Clark
- School of Environmental and Rural Science, University of New England, Armidale, NSW Australia
| | - Naomi Duijvesteijn
- School of Environmental and Rural Science, University of New England, Armidale, NSW Australia
| | - Cedric Gondro
- School of Environmental and Rural Science, University of New England, Armidale, NSW Australia
- Department of Animal Science, Michigan State University, East Lansing, MI USA
| | | | - Yizhou Chen
- Department of Primary Industries, Elizabeth Macarthur Agricultural Institute, Menangle, NSW Australia
| |
Collapse
|
41
|
Takeda M, Uemoto Y, Inoue K, Ogino A, Nozaki T, Kurogi K, Yasumori T, Satoh M. Genome-wide association study and genomic evaluation of feed efficiency traits in Japanese Black cattle using single-step genomic best linear unbiased prediction method. Anim Sci J 2019; 91:e13316. [PMID: 31769129 DOI: 10.1111/asj.13316] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2019] [Revised: 09/30/2019] [Accepted: 10/23/2019] [Indexed: 01/18/2023]
Abstract
The objectives of this study were to better understand the genetic architecture and the possibility of genomic evaluation for feed efficiency traits by (i) performing genome-wide association studies (GWAS), and (ii) assessing the accuracy of genomic evaluation for feed efficiency traits, using single-step genomic best linear unbiased prediction (ssGBLUP)-based methods. The analyses were performed in residual feed intake (RFI), residual body weight gain (RG), and residual intake and body weight gain (RIG) during three different fattening periods. The phenotypes from 4,578 Japanese Black steers, which were progenies of 362 progeny-tested bulls and the genotypes from the bulls were used in this study. The results of GWAS showed that a total of 16, 8, and 12 gene ontology terms were related to RFI, RG, and RIG, respectively, and the candidate genes identified in RFI and RG were involved in olfactory transduction and the phosphatidylinositol signaling system, respectively. The realized reliabilities of genomic estimated breeding values were low to moderate in the feed efficiency traits. In conclusion, ssGBLUP-based method can lead to understand some biological functions related to feed efficiency traits, even with small population with genotypes, however, an alternative strategy will be needed to enhance the reliability of genomic evaluation.
Collapse
Affiliation(s)
- Masayuki Takeda
- National Livestock Breeding Center, Fukushima, Japan.,Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - Yoshinobu Uemoto
- Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| | - Keiichi Inoue
- National Livestock Breeding Center, Fukushima, Japan
| | - Atushi Ogino
- Maebashi Institute of Animal Science, Livestock Improvement Association of Japan, Inc, Gunma, Japan
| | - Takayoshi Nozaki
- Cattle Breeding Department, Livestock Improvement Association of Japan, Inc, Tokyo, Japan
| | - Kazuhito Kurogi
- Maebashi Institute of Animal Science, Livestock Improvement Association of Japan, Inc, Gunma, Japan
| | - Takanori Yasumori
- Cattle Breeding Department, Livestock Improvement Association of Japan, Inc, Tokyo, Japan
| | - Masahiro Satoh
- Graduate School of Agricultural Science, Tohoku University, Miyagi, Japan
| |
Collapse
|
42
|
de Araujo Neto FR, Santos DJDA, Fernandes Júnior GA, Aspilcueta-Borquis RR, Nascimento AVD, de Oliveira Seno L, Tonhati H, de Oliveira HN. Genome-wide association studies for growth traits in buffaloes using the single step genomic BLUP. J Appl Genet 2019; 61:113-115. [PMID: 31673966 DOI: 10.1007/s13353-019-00528-5] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/21/2019] [Revised: 09/11/2019] [Accepted: 10/16/2019] [Indexed: 01/12/2023]
Abstract
Growth traits are important for the profitability of buffalo breeding systems, since in general, these animals are raised both for meat and milk. In this study, the single-step genomic BLUP method was employed to prospect the genomic regions' associated with weight at standard ages of 100, 210, 365, and 550 days in a buffalo population, aiming to identify genes with stronger expression for those characteristics. We found 6, 1, 2, and 5 SNPs significantly associated (p value < 10-5) with weight at 100, 210, 365, and 550 days of age, respectively, where those SNPs respectively explained 0.164, 0.040, 0.044, and 0.213% of the additive variance of each trait. SNP AX-85099682 (BBU24) was significant for weight at 100, 210, and 365 days, indicating the existence of a possible QTL affecting the initial growth rate of buffaloes. All told, eight genes (CBLB, TRNAG-UCC, GADD45B, LOC112583811, MGAT4C, KCNMA1, SLC5A2, and TGFB1I1) were identified as candidates for the growth traits of buffaloes. However, molecular and gene expression studies are necessary to validate these genes for subsequent use in programs for genetic improvement of the species.
Collapse
Affiliation(s)
| | | | | | | | | | | | - Humberto Tonhati
- Universidade Estadual Paulista Júlio de Mesquita Filho, Câmpus de Jaboticabal, São Paulo, Brazil
| | | |
Collapse
|
43
|
Li Y, Lee YM, Kim YS, Park SP, Kim JJ. Identifying Loci Under Positive Selection in Yellow Korean Cattle (Hanwoo). Evol Bioinform Online 2019; 15:1176934319859001. [PMID: 35210744 PMCID: PMC8862131 DOI: 10.1177/1176934319859001] [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: 05/05/2019] [Accepted: 05/23/2019] [Indexed: 11/21/2022] Open
Abstract
Jeju Black cattle is one of the aboriginal Korean cattle breeds that has been isolated in Jeju island for a long time, while Yellow Hanwoo cattle has been extensively selected for beef production traits for the last several decades. Aiming to investigate broader patterns of selection, we genotyped 352 Yellow Hanwoo and 169 Jeju Black cattle using a customized 150 K bovine chip. Our composite selection signals’ analysis to identify selection signatures (cross-population extended haplotype homozygosity [XP-EHH], ΔSAF, and FST) identified recent and strong signature of selection near many loci with mutations affecting the traits under strong selection as outlier in Yellow Hanwoo, including SCP2 (P = 8.41 × 10−10) that may be involved in the meat quality. We found nine candidate regions with significant clusters of selection signals, and further bioinformatics analyses of the genes located within these regions revealed mainly genes involved in G-protein coupled receptor signaling pathway (GO:0007186) or olfactory transduction (bta04740), which may be due to adaptation to natural environments in Jeju island. Based on the stronger correlation of Ne10/Ne100 ratio between Yellow Hanwoo (0.61) and Jeju Black (0.66) cattle, our results suggest that the difference of chromosomal regions of selection signature between the 2 cattle breeds was due to a consequence of selection processes to adapt to environmental differences between Jeju island and the main inland, Korean peninsula.
Collapse
Affiliation(s)
- Yi Li
- School of Statistics, Shanxi University of Finance and Economics, Taiyuan, China
| | - Yun-Mi Lee
- Department of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
| | - You-Sam Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
| | - Se-Pil Park
- Faculty of Biotechnology, Jeju National University, Jeju, Republic of Korea
| | - Jong-Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan, Republic of Korea
| |
Collapse
|
44
|
Fonseca LD, Eler JP, Pereira MA, Rosa AF, Alexandre PA, Moncau CT, Salvato F, Rosa-Fernandes L, Palmisano G, Ferraz JBS, Fukumasu H. Liver proteomics unravel the metabolic pathways related to Feed Efficiency in beef cattle. Sci Rep 2019; 9:5364. [PMID: 30926873 PMCID: PMC6441086 DOI: 10.1038/s41598-019-41813-x] [Citation(s) in RCA: 31] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2018] [Accepted: 03/19/2019] [Indexed: 12/11/2022] Open
Abstract
Improving nutrient utilization efficiency is essential for livestock, given the current scenario of increasing demand for animal protein and sustainable resource use. In this context, understanding the biology of feed efficiency (FE) in beef cattle allows the development of markers for identification and selection of best animals for animal production. Thus, 98 young Nellore bulls were evaluated for FE and at the end of the experiment liver samples from six High Feed Efficient (HFE) and six Low Feed Efficient (LFE) animals were collected for protein extraction, digestion and analysis by HPLC-MS/MS. Data were analyzed for differential abundant proteins (DAPs), protein networks, and functional enrichment. Serum endotoxin was also quantified. We found 42 DAPs and 3 protein networks significantly related to FE. The main pathways associated with FE were: microbial metabolism; biosynthesis of fatty acids, amino acids and vitamins; glycolysis/gluconeogenesis; xenobiotic metabolism and; antigen processing and presentation. Serum endotoxins were significantly higher in LFE animals supporting the results. Therefore, the findings presented here confirmed the altered hepatic metabolism and pronounced hepatic inflammation in LFE animals supporting that the increased bacterial load is at least in part responsible for the hepatic lesions and inflammation in LFE animals.
Collapse
Affiliation(s)
- Leydiana D Fonseca
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Joanir P Eler
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Mikaele A Pereira
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Alessandra F Rosa
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Pâmela A Alexandre
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Cristina T Moncau
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Fernanda Salvato
- Institute of Biology, State University of Campinas, Campinas, 13083-862, Brazil
| | - Livia Rosa-Fernandes
- Department of Parasitology, Biomedical Sciences Institute, University of São Paulo, São Paulo, 05508-900, Brazil
| | - Giuseppe Palmisano
- Department of Parasitology, Biomedical Sciences Institute, University of São Paulo, São Paulo, 05508-900, Brazil
| | - José B S Ferraz
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil
| | - Heidge Fukumasu
- Department of Veterinary Medicine, School of Animal Science and Food Engineering, University of São Paulo, Pirassununga, 13635-900, Brazil.
| |
Collapse
|
45
|
Connor EE, Zhou Y, Liu GE. The essence of appetite: does olfactory receptor variation play a role? J Anim Sci 2018. [PMID: 29534194 DOI: 10.1093/jas/sky068] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/06/2023] Open
Abstract
Olfactory receptors are G-protein-coupled chemoreceptors expressed on millions of olfactory sensory neurons within the nasal cavity. These receptors detect environmental odorants and signal the brain regarding the location of feed, potential mates, and the presence of possible threats (e.g., predators or chemical toxins). Olfactory receptors also are present in organs outside of the nasal cavity where they bind to molecules such as nutrients and metabolites from the animal's internal environment to elicit physiological responses, including changes in gut motility, ventilation rate, and cellular migration. Recent evidence supports an additional role of olfactory receptors in the regulation of appetite in humans and rodents. In particular, genetic variation among individuals in specific odorant receptor genes has been linked to differences in their feeding behaviors, food choices, and the regulation of energy balance. This review provides a general overview of the olfactory receptors of vertebrates and their genetic variability and provides supporting evidence for a physiological role of olfactory receptors in appetite regulation of livestock. Basic research on olfactory receptors of livestock and their ligands should facilitate the development of novel odorant receptor agonists and identification of specific olfactory receptor variants that may be developed to enhance animal production efficiency.
Collapse
Affiliation(s)
- Erin E Connor
- USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD
| | - Yang Zhou
- USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD
| | - George E Liu
- USDA, Agricultural Research Service, Animal Genomics and Improvement Laboratory, Beltsville, MD
| |
Collapse
|
46
|
Genetic correlations and heritability estimates for dry matter intake, weight gain and feed efficiency of Nellore cattle in feedlot. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.06.013] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022]
|
47
|
Cardoso DF, de Albuquerque LG, Reimer C, Qanbari S, Erbe M, do Nascimento AV, Venturini GC, Scalez DCB, Baldi F, de Camargo GMF, Mercadante MEZ, do Santos Gonçalves Cyrillo JN, Simianer H, Tonhati H. Genome-wide scan reveals population stratification and footprints of recent selection in Nelore cattle. Genet Sel Evol 2018; 50:22. [PMID: 29720080 PMCID: PMC5930444 DOI: 10.1186/s12711-018-0381-2] [Citation(s) in RCA: 20] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/30/2017] [Accepted: 02/20/2018] [Indexed: 12/11/2022] Open
Abstract
Background This study aimed at (1) assessing the genomic stratification of experimental lines of Nelore cattle that have experienced different selection regimes for growth traits, and (2) identifying genomic regions that have undergone recent selection. We used a sample of 763 animals genotyped with the Illumina BovineHD BeadChip, among which 674 animals originated from two lines that are maintained under directional selection for increased yearling body weight and 89 animals from a control line that is maintained under stabilizing selection. Results Multidimensional analysis of the genomic dissimilarity matrix and admixture analysis revealed a substantial level of population stratification between the directional selection lines and the stabilizing selection control line. Two of the three tests used to detect selection signatures (FST, XP-EHH and iHS) revealed six candidate regions with indications of selection, which strongly indicates truly positive signals. The set of identified candidate genes included several genes with roles that are functionally related to growth metabolism, such as COL14A1, CPT1C, CRH, TBC1D1, and XKR4. Conclusions The current study identified genetic stratification that resulted from almost four decades of divergent selection in an experimental Nelore population, and highlighted autosomal genomic regions that present patterns of recent selection. Our findings provide a basis for a better understanding of the metabolic mechanism that underlies the growth traits, which are modified by selection for yearling body weight. Electronic supplementary material The online version of this article (10.1186/s12711-018-0381-2) contains supplementary material, which is available to authorized users.
Collapse
Affiliation(s)
- Diercles F Cardoso
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil.
| | - Lucia Galvão de Albuquerque
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil.,National Counsel of Technological and Scientific Development (CNPq), Brasília, DF, Brazil
| | - Christian Reimer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany
| | - Saber Qanbari
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany
| | - Malena Erbe
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany.,Institute for Animal Breeding, Bavarian State Research Center for Agriculture, Grub, Germany
| | - André V do Nascimento
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil
| | - Guilherme C Venturini
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil
| | - Daiane C Becker Scalez
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil
| | - Fernando Baldi
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil.,National Counsel of Technological and Scientific Development (CNPq), Brasília, DF, Brazil
| | - Gregório M Ferreira de Camargo
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil
| | - Maria E Zerlotti Mercadante
- National Counsel of Technological and Scientific Development (CNPq), Brasília, DF, Brazil.,APTA Beef Cattle Center, Institute of Animal Science, Sertãozinho, SP, Brazil
| | | | - Henner Simianer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Goettingen, Germany
| | - Humberto Tonhati
- Department of Animal Science, Faculty of Agrarian and Veterinary Sciences, Sao Paulo State University, Jaboticabal, SP, Brazil.,National Counsel of Technological and Scientific Development (CNPq), Brasília, DF, Brazil
| |
Collapse
|
48
|
Miao J, Wang X, Bao J, Jin S, Chang T, Xia J, Yang L, Zhu B, Xu L, Zhang L, Gao X, Chen Y, Li J, Gao H. Multimarker and rare variants genomewide association studies for bone weight in Simmental cattle. J Anim Breed Genet 2018; 135:159-169. [DOI: 10.1111/jbg.12326] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/18/2017] [Accepted: 03/27/2018] [Indexed: 12/30/2022]
Affiliation(s)
- J. Miao
- Laboratory of Molecular Biology and Bovine Breeding; Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
- College of Animal Sciences; Fujian Agriculture and Forestry University; Fujian China
| | - X. Wang
- Laboratory of Molecular Biology and Bovine Breeding; Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| | - J. Bao
- Veterinary Bureau of Wulagai Precinct in Xilin Gol League; Wulagai China
| | - S. Jin
- Veterinary Bureau of Wulagai Precinct in Xilin Gol League; Wulagai China
| | - T. Chang
- Laboratory of Molecular Biology and Bovine Breeding; Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| | - J. Xia
- Laboratory of Molecular Biology and Bovine Breeding; Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| | - L. Yang
- Laboratory of Molecular Biology and Bovine Breeding; Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province; Sichuan Agricultural University; Sichuan China
| | - B. Zhu
- Laboratory of Molecular Biology and Bovine Breeding; Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| | - L. Xu
- Laboratory of Molecular Biology and Bovine Breeding; Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| | - L. Zhang
- Laboratory of Molecular Biology and Bovine Breeding; Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| | - X. Gao
- Laboratory of Molecular Biology and Bovine Breeding; Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| | - Y. Chen
- Laboratory of Molecular Biology and Bovine Breeding; Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| | - J. Li
- Laboratory of Molecular Biology and Bovine Breeding; Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| | - H. Gao
- Laboratory of Molecular Biology and Bovine Breeding; Institute of Animal Sciences; Chinese Academy of Agricultural Sciences; Beijing China
| |
Collapse
|
49
|
Association study between copy number variation and beef fatty acid profile of Nellore cattle. J Appl Genet 2018. [DOI: 10.1007/s13353-018-0436-7] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/20/2022]
|
50
|
Lu Y, Vandehaar MJ, Spurlock DM, Weigel KA, Armentano LE, Connor EE, Coffey M, Veerkamp RF, de Haas Y, Staples CR, Wang Z, Hanigan MD, Tempelman RJ. Genome-wide association analyses based on a multiple-trait approach for modeling feed efficiency. J Dairy Sci 2018; 101:3140-3154. [PMID: 29395135 DOI: 10.3168/jds.2017-13364] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2017] [Accepted: 11/27/2017] [Indexed: 11/19/2022]
Abstract
Genome-wide association (GWA) of feed efficiency (FE) could help target important genomic regions influencing FE. Data provided by an international dairy FE research consortium consisted of phenotypic records on dry matter intakes (DMI), milk energy (MILKE), and metabolic body weight (MBW) on 6,937 cows from 16 stations in 4 counties. Of these cows, 4,916 had genotypes on 57,347 single nucleotide polymorphism (SNP) markers. We compared a GWA analysis based on the more classical residual feed intake (RFI) model with one based on a previously proposed multiple trait (MT) approach for modeling FE using an alternative measure (DMI|MILKE,MBW). Both models were based on a single-step genomic BLUP procedure that allowed the use of phenotypes from both genotyped and nongenotyped cows. Estimated effects for single SNP markers were small and not statistically important but virtually identical for either FE measure (RFI vs. DMI|MILKE,MBW). However, upon further refining this analysis to develop joint tests within nonoverlapping 1-Mb windows, significant associations were detected between either measure of FE with a window on each of Bos taurus autosomes BTA12 and BTA26. There was, as expected, no overlap between detected genomic regions for DMI|MILKE,MBW and genomic regions influencing the energy sink traits (i.e., MILKE and MBW) because of orthogonal relationships clearly defined between the various traits. Conversely, GWA inferences on DMI can be demonstrated to be partly driven by genetic associations between DMI with these same energy sink traits, thereby having clear implications when comparing GWA studies on DMI to GWA studies on FE-like measures such as RFI.
Collapse
Affiliation(s)
- Y Lu
- Department of Animal Science, Michigan State University, East Lansing 48824
| | - M J Vandehaar
- Department of Animal Science, Michigan State University, East Lansing 48824
| | - D M Spurlock
- Department of Animal Science, Iowa State University, Ames 50011
| | - K A Weigel
- Department of Dairy Science, University of Wisconsin, Madison 53706
| | - L E Armentano
- Department of Dairy Science, University of Wisconsin, Madison 53706
| | - E E Connor
- Animal Genomics and Improvement Laboratory, Agricultural Research Service, USDA, Beltsville, MD 20705
| | - M Coffey
- Animal and Veterinary Sciences Group, Scotland's Rural College (SRUC), Roslin Institute Building, Easter Bush, Midlothian, EH25 9RG, United Kingdom
| | - R F Veerkamp
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, 6700 AH Wageningen, the Netherlands
| | - Y de Haas
- Animal Breeding and Genomics Centre, Wageningen UR Livestock Research, 6700 AH Wageningen, the Netherlands
| | - C R Staples
- Department of Animal Sciences, University of Florida, Gainesville 32611
| | - Z Wang
- Department of Agricultural, Food and Nutritional Science, University of Alberta, Edmonton, AB, T6G 2P5 Canada
| | - M D Hanigan
- Department of Dairy Science, Virginia Tech, Blacksburg 24061
| | - R J Tempelman
- Department of Animal Science, Michigan State University, East Lansing 48824.
| |
Collapse
|