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Kitagawa Y, Maloney SK, Pool KR, Webster D, Ohkura S, Blache D, Ding L. Behavioural and physiological responses to stressors in sheep with temperament classified by genotype or phenotype. Sci Rep 2024; 14:8147. [PMID: 38584170 PMCID: PMC10999442 DOI: 10.1038/s41598-024-58959-y] [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: 12/04/2023] [Accepted: 04/04/2024] [Indexed: 04/09/2024] Open
Abstract
The single nucleotide polymorphism (SNP) rs107856856, located in the tryptophan hydroxylase-2 gene, is associated with the behavioural phenotype for sheep temperament measured at weaning. Here, we tested the association between that SNP and physiological and behavioural responses to stressors in adult sheep. Two groups of adult sheep, one with genotype A/A (calm genotype) and the other with G/G (nervous genotype) in rs107856856, were selected from 160 sheep and were exposed, twice, to an open-field arena and an isolation box test (IBT). During each repeat, the behaviour and physiological responses (cortisol, prolactin, dehydroepiandrosterone [DHEA], brain derived neurotrophic factor [BDNF], characteristics of the response of body temperature, and oxidative stress) were measured. The behavioural and physiological responses of the sheep were compared between genotypes and also between groups classified on their phenotype as assessed by their initial isolation box score ("low responders" and "high responders"). The SNP rs107856856 had some effects on the behavioural phenotype (IBT score) but no effects on the physiological response to stress (cortisol, prolactin, DHEA, BDNF, oxidative stress or changes in body temperature) in the adult sheep, probably because the sheep were exposed, and therefore had adapted, to human contact during their life.
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Affiliation(s)
- Yuri Kitagawa
- Laboratory of Animal Production Science, Graduate School of Bioagricultural Sciences, Nagoya University, Togo-cho, Aichi, Japan
- School of Agriculture and Environment, M087, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Shane K Maloney
- School of Human Sciences, M309, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Kelsey R Pool
- School of Agriculture and Environment, M087, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Dane Webster
- School of Human Sciences, M309, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia
| | - Satoshi Ohkura
- Laboratory of Animal Production Science, Graduate School of Bioagricultural Sciences, Nagoya University, Togo-cho, Aichi, Japan
| | - Dominique Blache
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
- School of Agriculture and Environment, M087, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia.
| | - Luoyang Ding
- College of Animal Science and Technology, Yangzhou University, Yangzhou, 225009, China.
- School of Agriculture and Environment, M087, The University of Western Australia, 35 Stirling Highway, Perth, WA, 6009, Australia.
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Carrara ER, Lopes PS, Veroneze R, Pereira RJ, Zadra LEF, Peixoto MGCD. Assessment of runs of homozygosity, heterozygosity-rich regions and genomic inbreeding estimates in a subpopulation of Guzerá (Bos indicus) dual-purpose cattle. J Anim Breed Genet 2024; 141:207-219. [PMID: 38010317 DOI: 10.1111/jbg.12836] [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: 01/24/2023] [Revised: 11/14/2023] [Accepted: 11/15/2023] [Indexed: 11/29/2023]
Abstract
For decades, inbreeding in cattle has been evaluated using pedigree information. Nowadays, inbreeding coefficients can be obtained using genomic information such as runs of homozygosity (ROH). The aims of this study were to quantify ROH and heterozygosity-rich regions (HRR) in a subpopulation of Guzerá dual-purpose cattle, to examine ROH and HRR islands, and to compare inbreeding coefficients obtained by ROH with alternative genomic inbreeding coefficients. A subpopulation of 1733 Guzerá animals genotyped for 50k SNPs was used to obtain the ROH and HRR segments. Inbreeding coefficients by ROH (FROH ), by genomic relationship matrix based on VanRaden's method 1 using reference allele frequency in the population (FGRM ), by genomic relationship matrix based on VanRaden's method 1 using allele frequency fixed in 0.5 (FGRM_0.5 ), and by the proportion of homozygous loci (FHOM ) were calculated. A total of 15,660 ROH were identified, and the chromosome with the highest number of ROH was BTA6. A total of 4843 HRRs were identified, and the chromosome with the highest number of HRRs was BTA23. No ROH and HRR islands were identified according to established criteria, but the regions closest to the definition of an island were examined from 64 to 67 Mb of BTA6, from 36 to 37 Mb of BTA2 and from 0.50 to 1.25 Mb of BTA23. The genes identified in ROH islands have previously been associated with dairy and beef traits, while genes identified on HRR islands have previously been associated with reproductive traits and disease resistance. FROH was equal to 0.095 ± 0.084, and its Spearman correlation with FGRM was low (0.44) and moderate-high with FHOM (0.79) and with FGRM_0.5 (0.80). The inbreeding coefficients determined by ROH were higher than other cattle breeds' and higher than pedigree-based inbreeding in the Guzerá breed obtained in previous studies. It is recommended that future studies investigate the effects of inbreeding determined by ROH on the traits under selection in the subpopulation studied.
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Affiliation(s)
- E R Carrara
- Department of Animal Science, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | - P S Lopes
- Department of Animal Science, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | - R Veroneze
- Department of Animal Science, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | - R J Pereira
- Mato Grosso Animal Breeding Group, Institute of Agrarian and Technological Sciences, Federal University of Rondonópolis, Rondonópolis, Mato Grosso, Brazil
| | - L E F Zadra
- Brazilian Center for the Genetic Improvement of Guzerá, Belo Horizonte, Minas Gerais, Brazil
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3
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Munguía Vásquez MF, Gill CA, Riggs PK, Herring AD, Sanders JO, Riley DG. Genetic evaluation of crossbred Bos indicus cow temperament at parturition. J Anim Sci 2024; 102:skae022. [PMID: 38282422 PMCID: PMC10873775 DOI: 10.1093/jas/skae022] [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: 08/07/2023] [Accepted: 01/22/2024] [Indexed: 01/30/2024] Open
Abstract
Cow temperament at parturition may be mostly a measure of aggressiveness. The heritability of cow temperament at parturition in Bos taurus cows has been reported to be low. The objectives of this study were to estimate the heritability of cow temperament at parturition, conduct a genome-wide association analysis of cow temperament at the time of parturition, and estimate the correspondence of cow temperament at the time of parturition with cow productive performance and early-life temperament traits in Bos indicus crossbreds. Cow temperament was assessed from 1 to 5 indicating increasing levels of aggressiveness of cows (937 cows and 4,337 parturitions) from 2005 to 2022. Estimates of heritability and repeatability were 0.12 ± 0.024 and 0.24 ± 0.018. The estimates of proportion of phenotypic variance were 0.13 ± 0.019 and 0.02 ± 0.011 for permanent and maternal permanent environmental components, respectively. Estimates of heritability for maximum lifetime temperament score and proportions of temperament scores >1 were 0.18 ± 0.07 and 0.13 ± 0.072. Within cycles (generations), 2-yr-old cows had lower temperament score means than cows in most other age categories. There were low to moderate positive estimates of unadjusted correlation coefficients (r = 0.22 to 0.29; P < 0.05) of unadjusted temperament score with temperament measured on the same females when they were 8 mo old. There were low to moderate positive estimates of correlation coefficients (r = 0.09 to 0.37; P < 0.05) of unadjusted temperament score with calving rate, weaning rate, weaning weight per cow exposed, and weaning weight per 454 kg cow weight at weaning. Cows with the lowest temperament score had lower (P < 0.05) calving and weaning rate than cows in other temperament categories. Within 3 of 5 cycles, cows with the lowest temperament score (totally docile) had lower (P < 0.05) weaning weight per cow exposed than cows in other temperament categories. There were 2 SNP on BTA 4 associated with maximum lifetime temperament score (FDR < 0.05). The non-genetic influence of a cow's mother was documented in her own temperament measured at the time of calving; this may be a consequence of learned behavior. Less aggressiveness displayed by cows at the time of calving may be accompanied by lower reproductive and maternal performance.
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Affiliation(s)
- María F Munguía Vásquez
- Department of Animal Science, Texas A&M University, 2471 TAMU, College Station, TX 77843, USA, , +1 (979) 845-2667
| | - Clare A Gill
- Department of Animal Science, Texas A&M University, 2471 TAMU, College Station, TX 77843, USA, , +1 (979) 845-2667
| | - Penny K Riggs
- Department of Animal Science, Texas A&M University, 2471 TAMU, College Station, TX 77843, USA, , +1 (979) 845-2667
| | - Andy D Herring
- Department of Animal Science, Texas A&M University, 2471 TAMU, College Station, TX 77843, USA, , +1 (979) 845-2667
| | - James O Sanders
- Department of Animal Science, Texas A&M University, 2471 TAMU, College Station, TX 77843, USA
| | - David G Riley
- Department of Animal Science, Texas A&M University, 2471 TAMU, College Station, TX 77843, USA
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Behren LE, König S, May K. Genomic Selection for Dairy Cattle Behaviour Considering Novel Traits in a Changing Technical Production Environment. Genes (Basel) 2023; 14:1933. [PMID: 37895282 PMCID: PMC10606080 DOI: 10.3390/genes14101933] [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: 09/20/2023] [Revised: 10/05/2023] [Accepted: 10/06/2023] [Indexed: 10/29/2023] Open
Abstract
Cow behaviour is a major factor influencing dairy herd profitability and is an indicator of animal welfare and disease. Behaviour is a complex network of behavioural patterns in response to environmental and social stimuli and human handling. Advances in agricultural technology have led to changes in dairy cow husbandry systems worldwide. Increasing herd sizes, less time availability to take care of the animals and modern technology such as automatic milking systems (AMSs) imply limited human-cow interactions. On the other hand, cow behaviour responses to the technical environment (cow-AMS interactions) simultaneously improve production efficiency and welfare and contribute to simplified "cow handling" and reduced labour time. Automatic milking systems generate objective behaviour traits linked to workability, milkability and health, which can be implemented into genomic selection tools. However, there is insufficient understanding of the genetic mechanisms influencing cow learning and social behaviour, in turn affecting herd management, productivity and welfare. Moreover, physiological and molecular biomarkers such as heart rate, neurotransmitters and hormones might be useful indicators and predictors of cow behaviour. This review gives an overview of published behaviour studies in dairy cows in the context of genetics and genomics and discusses possibilities for breeding approaches to achieve desired behaviour in a technical production environment.
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Affiliation(s)
- Larissa Elisabeth Behren
- Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, 35390 Giessen, Germany
| | - Sven König
- Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, 35390 Giessen, Germany
| | - Katharina May
- Institute of Animal Breeding and Genetics, Justus-Liebig-University of Gießen, 35390 Giessen, Germany
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5
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Carrara ER, Peixoto MGCD, da Silva AA, Bruneli FAT, Ventura HT, Zadra LEF, Josahkian LA, Veroneze R, Lopes PS. Genomic prediction in Brazilian Guzerá cattle: application of a single-step approach to productive and reproductive traits. Trop Anim Health Prod 2023; 55:48. [PMID: 36705782 DOI: 10.1007/s11250-023-03484-9] [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: 09/13/2022] [Accepted: 01/23/2023] [Indexed: 01/28/2023]
Abstract
This study aimed to investigate the feasibility of genomic prediction for productive and reproductive traits in Guzerá cattle using single-step genomic best linear unbiased prediction (ssGBLUP). Evaluations included the 305-day cumulative yields (first lactation, in kg) of milk, lactose, protein, fat, and total solids; adjusted body weight (kg) at the ages of 450, 365, and 210 days; and age at first calving (in days), from a database containing 197,283 measurements from Guzerá males and females born between 1954 and 2018. The pedigree included 433,823 animals spanning up to 14 overlapping generations. A total of 1618 animals were genotyped. The analyses were performed using ssGBLUP and traditional BLUP methods. Predictive ability and bias were accessed using cross-validation: predictive ability was similar between the methods and ranged from 0.27 to 0.47 for the genomic-based model and from 0.30 to 0.45 for the pedigree-based model; the bias was also similar between the methods, ranging from 0.88 to 1.35 in the genomic-based model and from 0.96 to 1.41 in the pedigree-based model. The individual accuracies of breeding values were evidently increased in the genomic evaluation, with values ranging from 0.41 to 0.56 in the genomic-based model and from 0.26 to 0.54 in the pedigree-based model. Even based on a small number of genotyped animals and a small database for some traits, the results suggest that ssGBLUP is feasible and may be applied to national genetic evaluation of the breed to increase the accuracy of breeding values without greatly impacting predictive ability and bias.
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Affiliation(s)
- Eula Regina Carrara
- Department of Animal Science, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil.
| | | | - Alessandra Alves da Silva
- Department of Agricultural Sciences, School of Agricultural and Veterinarian Sciences, São Paulo State University, Jaboticabal, São Paulo, Brazil
| | | | | | - Lenira El Faro Zadra
- Brazilian Center for the Genetic Improvement of Guzerá, Belo Horizonte, Minas Gerais, Brazil
| | | | - Renata Veroneze
- Department of Animal Science, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
| | - Paulo Sávio Lopes
- Department of Animal Science, Federal University of Viçosa, Viçosa, Minas Gerais, Brazil
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6
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Alvarenga AB, Oliveira HR, Miller SP, Silva FF, Brito LF. Genetic Modeling and Genomic Analyses of Yearling Temperament in American Angus Cattle and Its Relationship With Productive Efficiency and Resilience Traits. Front Genet 2022; 13:794625. [PMID: 35444687 PMCID: PMC9014094 DOI: 10.3389/fgene.2022.794625] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2021] [Accepted: 02/25/2022] [Indexed: 11/13/2022] Open
Abstract
Cattle temperament has been considered by farmers as a key breeding goal due to its relevance for cattlemen's safety, animal welfare, resilience, and longevity and its association with many economically important traits (e.g., production and meat quality). The definition of proper statistical models, accurate variance component estimates, and knowledge on the genetic background of the indicator trait evaluated are of great importance for accurately predicting the genetic merit of breeding animals. Therefore, 266,029 American Angus cattle with yearling temperament records (1-6 score) were used to evaluate statistical models and estimate variance components; investigate the association of sex and farm management with temperament; assess the weighted correlation of estimated breeding values for temperament and productive, reproductive efficiency and resilience traits; and perform a weighted single-step genome-wide association analysis using 69,559 animals genotyped for 54,609 single-nucleotide polymorphisms. Sex and extrinsic factors were significantly associated with temperament, including conception type, age of dam, birth season, and additional animal-human interactions. Similar results were observed among models including only the direct additive genetic effect and when adding other maternal effects. Estimated heritability of temperament was equal to 0.39 on the liability scale. Favorable genetic correlations were observed between temperament and other relevant traits, including growth, feed efficiency, meat quality, and reproductive traits. The highest approximated genetic correlations were observed between temperament and growth traits (weaning weight, 0.28; yearling weight, 0.28). Altogether, we identified 11 genomic regions, located across nine chromosomes including BTAX, explaining 3.33% of the total additive genetic variance. The candidate genes identified were enriched in pathways related to vision, which could be associated with reception of stimulus and/or cognitive abilities. This study encompasses large and diverse phenotypic, genomic, and pedigree datasets of US Angus cattle. Yearling temperament is a highly heritable and polygenic trait that can be improved through genetic selection. Direct selection for temperament is not expected to result in unfavorable responses on other relevant traits due to the favorable or low genetic correlations observed. In summary, this study contributes to a better understanding of the impact of maternal effects, extrinsic factors, and various genomic regions associated with yearling temperament in North American Angus cattle.
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Affiliation(s)
- Amanda B Alvarenga
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
| | - 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
| | - Stephen P Miller
- American Angus Association, Angus Genetics Inc., St Joseph, MO, United States
| | - Fabyano F Silva
- Department of Animal Sciences, Federal University of Vicosa, Viçosa, Brazil
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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7
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Duarte INH, Bessa AFDO, Rola LD, Genuíno MVH, Rocha IM, Marcondes CR, Regitano LCDA, Munari DP, Berry DP, Buzanskas ME. Cross-population selection signatures in Canchim composite beef cattle. PLoS One 2022; 17:e0264279. [PMID: 35363779 PMCID: PMC8975110 DOI: 10.1371/journal.pone.0264279] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/19/2021] [Accepted: 02/07/2022] [Indexed: 12/15/2022] Open
Abstract
Analyses of livestock genomes have been used to detect selection signatures, which are genomic regions associated with traits under selection leading to a change in allele frequency. The objective of the present study was to characterize selection signatures in Canchim composite beef cattle using cross-population analyses with the founder Nelore and Charolais breeds. High-density single nucleotide polymorphism genotypes were available on 395 Canchim representing the target population, along with genotypes from 809 Nelore and 897 Charolais animals representing the reference populations. Most of the selection signatures were co-located with genes whose functions agree with the expectations of the breeding programs; these genes have previously been reported to associate with meat quality, as well as reproductive traits. Identified genes were related to immunity, adaptation, morphology, as well as behavior, could give new perspectives for understanding the genetic architecture of Canchim. Some selection signatures identified genes that were recently introduced in Canchim, such as the loci related to the polled trait.
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Affiliation(s)
| | | | - Luciana Diniz Rola
- Departamento de Zootecnia, Universidade Federal da Paraíba, Areia, Paraíba, Brazil
| | | | - Iasmin Marques Rocha
- Departamento de Zootecnia, Universidade Federal da Paraíba, Areia, Paraíba, Brazil
| | | | | | - Danísio Prado Munari
- Departamento de Engenharia e Ciências Exatas, Universidade Estadual Paulista, Jaboticabal, São Paulo, Brazil
| | - Donagh Pearse Berry
- Teagasc, Animal & Grassland Research and Innovation Centre, Moorepark, Fermoy Co. Cork., Ireland
| | - Marcos Eli Buzanskas
- Departamento de Zootecnia, Universidade Federal da Paraíba, Areia, Paraíba, Brazil
- * E-mail:
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Rajawat D, Panigrahi M, Kumar H, Nayak SS, Parida S, Bhushan B, Gaur GK, Dutt T, Mishra BP. Identification of important genomic footprints using eight different selection signature statistics in domestic cattle breeds. Gene 2022; 816:146165. [PMID: 35026292 DOI: 10.1016/j.gene.2021.146165] [Citation(s) in RCA: 28] [Impact Index Per Article: 14.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/02/2021] [Revised: 12/13/2021] [Accepted: 12/20/2021] [Indexed: 12/25/2022]
Abstract
In the present study, the population genomic data of different cattle breeds were explored to decipher the genomic regions affected due to selective events and reflected in the productive, reproductive, thermo-tolerance, and health-related traits. To find out these genomic deviations due to selective sweeps, we used eight different statistical tools (Tajima's D, Fu & Li's D*, CLR, ROH, iHS, FST, FLK, and hapFLK) on seven indigenous and five exotic cattle breeds. We further performed composite analysis by comparing their covariance matrix. Several candidate genes were found to be related to milk production (ADARB, WDR70, and CA8), reproductive (PARN, FAM134B2, and ZBTB20), and health-related traits (SP110, CXCL2, CLXCL3, CXCL5, IRF8, and MYOM1). The outcome of this investigation provides a basis for detecting selective sweeps that explain the genetic variation of traits. They may possess functional importance for multiple cattle breeds in different subcontinents. However, further studies are required to improve the findings using high-density arrays or whole-genome sequencing with higher resolution and greater sample sizes.
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Affiliation(s)
- Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - G K Gaur
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - B P Mishra
- Division of Animal Biotechnology, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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Baesjou JP, Wellenreuther M. Genomic Signatures of Domestication Selection in the Australasian Snapper ( Chrysophrys auratus). Genes (Basel) 2021; 12:1737. [PMID: 34828341 PMCID: PMC8623400 DOI: 10.3390/genes12111737] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/14/2021] [Revised: 10/15/2021] [Accepted: 10/26/2021] [Indexed: 01/10/2023] Open
Abstract
Domestication of teleost fish is a recent development, and in most cases started less than 50 years ago. Shedding light on the genomic changes in key economic traits during the domestication process can provide crucial insights into the evolutionary processes involved and help inform selective breeding programmes. Here we report on the recent domestication of a native marine teleost species in New Zealand, the Australasian snapper (Chrysophrys auratus). Specifically, we use genome-wide data from a three-generation pedigree of this species to uncover genetic signatures of domestication selection for growth. Genotyping-By-Sequencing (GBS) was used to generate genome-wide SNP data from a three-generation pedigree to calculate generation-wide averages of FST between every generation pair. The level of differentiation between generations was further investigated using ADMIXTURE analysis and Principal Component Analysis (PCA). After that, genome scans using Bayescan, LFMM and XP-EHH were applied to identify SNP variants under putative selection following selection for growth. Finally, genes near candidate SNP variants were annotated to gain functional insights. Analysis showed that between generations FST values slightly increased as generational time increased. The extent of these changes was small, and both ADMIXTURE analysis and PCA were unable to form clear clusters. Genome scans revealed a number of SNP outliers, indicative of selection, of which a small number overlapped across analyses methods and populations. Genes of interest within proximity of putative selective SNPs were related to biological functions, and revealed an association with growth, immunity, neural development and behaviour, and tumour repression. Even though few genes overlapped between outlier SNP methods, gene functionalities showed greater overlap between methods. While the genetic changes observed were small in most cases, a number of outlier SNPs could be identified, of which some were found by more than one method. Multiple outlier SNPs appeared to be predominately linked to gene functionalities that modulate growth and survival. Ultimately, the results help to shed light on the genomic changes occurring during the early stages of domestication selection in teleost fish species such as snapper, and will provide useful candidates for the ongoing selective breeding in the future of this and related species.
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Affiliation(s)
- Jean-Paul Baesjou
- The New Zealand Institute for Plant and Food Research Ltd., 1025 Auckland, New Zealand;
| | - Maren Wellenreuther
- The New Zealand Institute for Plant and Food Research Ltd., 7010 Nelson, New Zealand
- School of Biological Sciences, University of Auckland, 1010 Auckland, New Zealand
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Colditz IG. Adrenergic Tone as an Intermediary in the Temperament Syndrome Associated With Flight Speed in Beef Cattle. FRONTIERS IN ANIMAL SCIENCE 2021. [DOI: 10.3389/fanim.2021.652306] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023] Open
Abstract
The temperament of farm animals can influence their resilience to everyday variations within the managed production environment and has been under strong direct and indirect selection during the course of domestication. A prominent objective measure used for assessing temperament in beef cattle is the behavioral flight response to release from confinement in a crush or chute. This behavioral measure, termed flight speed (also known as escape velocity) is associated with physiological processes including body temperature, feeding behavior, growth rate, carcass composition, immune function, and health outcomes. This review examines the functional links between this suite of traits and adrenergic activity of the sympathetic nervous system and the adrenomedullary hormonal system. It is suggested that flight speed is the behavioral aspect of an underlying “flightiness” temperament syndrome, and that elevated adrenergic tone in animals with a high level of flightiness (i.e., flighty animals) tunes physiological activities toward a sustained “fight or flight” defense profile that reduces productivity and the capacity to flourish within the production environment. Nonetheless, despite a common influence of adrenergic tone on this suite of traits, variation in each trait is also influenced by other regulatory pathways and by the capacity of tissues to respond to a range of modulators in addition to adrenergic stimuli. It is suggested that tuning by adrenergic tone is an example of homeorhetic regulation that can help account for the persistent expression of behavioral and somatic traits associated with the flight speed temperament syndrome across the life of the animal. At a population level, temperament may modulate ecological fit within and across generations in the face of environmental variability and change. Associations of flight speed with the psychological affective state of the animal, and implications for welfare are also considered. The review will help advance understanding of the developmental biology and physiological regulation of temperament syndromes.
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Alvarenga AB, Oliveira HR, Chen SY, Miller SP, Marchant-Forde JN, Grigoletto L, Brito LF. A Systematic Review of Genomic Regions and Candidate Genes Underlying Behavioral Traits in Farmed Mammals and Their Link with Human Disorders. Animals (Basel) 2021; 11:ani11030715. [PMID: 33800722 PMCID: PMC7999279 DOI: 10.3390/ani11030715] [Citation(s) in RCA: 10] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Revised: 02/21/2021] [Accepted: 02/27/2021] [Indexed: 12/25/2022] Open
Abstract
Simple Summary This study is a comprehensive review of genomic regions associated with animal behavior in farmed mammals (beef and dairy cattle, pigs, and sheep) which contributes to a better understanding of the biological mechanisms influencing the target indicator trait and to gene expression studies by suggesting genes likely controlling the trait, and it will be useful in optimizing genomic predictions of breeding values incorporating biological information. Behavioral mechanisms are complex traits, genetically controlled by multiple genes spread across the whole genome. The majority of the genes identified in cattle, pigs, and sheep in association with a plethora of behavioral measurements (e.g., temperament, terrain use, milking speed, tail biting, and sucking reflex) are likely controlling stimuli reception (e.g., olfactory), internal recognition of stimuli (e.g., neuroactive ligand–receptor interaction), and body response to a stimulus (e.g., blood pressure, fatty acidy metabolism, hormone signaling, and inflammatory pathways). Six genes were commonly identified between cattle and pigs. About half of the genes for behavior identified in farmed mammals were also identified in humans for behavioral, mental, and neuronal disorders. Our findings indicate that the majority of the genes identified are likely controlling animal behavioral outcomes because their biological functions as well as potentially differing allele frequencies between two breed groups (subjectively) clustered based on their temperament characteristics. Abstract The main objectives of this study were to perform a systematic review of genomic regions associated with various behavioral traits in the main farmed mammals and identify key candidate genes and potential causal mutations by contrasting the frequency of polymorphisms in cattle breeds with divergent behavioral traits (based on a subjective clustering approach). A total of 687 (cattle), 1391 (pigs), and 148 (sheep) genomic regions associated with 37 (cattle), 55 (pigs), and 22 (sheep) behavioral traits were identified in the literature. In total, 383, 317, and 15 genes overlap with genomic regions identified for cattle, pigs, and sheep, respectively. Six common genes (e.g., NR3C2, PITPNM3, RERG, SPNS3, U6, and ZFAT) were found for cattle and pigs. A combined gene-set of 634 human genes was produced through identified homologous genes. A total of 313 out of 634 genes have previously been associated with behavioral, mental, and neurologic disorders (e.g., anxiety and schizophrenia) in humans. Additionally, a total of 491 candidate genes had at least one statistically significant polymorphism (p-value < 0.05). Out of those, 110 genes were defined as having polymorphic regions differing in greater than 50% of exon regions. Therefore, conserved genomic regions controlling behavior were found across farmed mammal species and humans.
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Affiliation(s)
- Amanda B. Alvarenga
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.); (S.-Y.C.); (L.G.)
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.); (S.-Y.C.); (L.G.)
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Shi-Yi Chen
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.); (S.-Y.C.); (L.G.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu 625014, China
| | | | - Jeremy N. Marchant-Forde
- Livestock Behavior Research Unit, United States Department of Agriculture—Agricultural Research Service (USDA–ARS), West Lafayette, IN 47907, USA;
| | - Lais Grigoletto
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.); (S.-Y.C.); (L.G.)
- Department of Veterinary Medicine, College of Animal Science and Food Engineering, University of Sao Paulo, Pirassununga 05508, São Paulo, Brazil
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.); (S.-Y.C.); (L.G.)
- Correspondence:
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A genome-wide association study for prolificacy in three Polish sheep breeds. J Appl Genet 2021; 62:323-326. [PMID: 33608865 PMCID: PMC8032615 DOI: 10.1007/s13353-021-00615-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Revised: 11/02/2020] [Accepted: 02/05/2021] [Indexed: 11/29/2022]
Abstract
Reproductive traits (especially litter size) are usually characterized by low heritability, and thus, phenotypic selection is often ineffective and slow. In order to improve fertility characteristics such as ovulation rate and litter size, it seems more effective to select breeding animals based on their genotype. The aim of the study was to use genome-wide association study (GWAS) in three sheep breeds to identify the genetic variants affecting the litter size in sheep. The study allowed us to identify one genome-wide significant SNP (rs402032081—located in ephrin type-A receptor 6, EPHA6) showing an association with litter size in Polish Mountain Sheep. We suggest that the EPHA6 gene can be a candidate gene for prolificacy trait in selected breeds of sheep; however, it needs further functional data for validation.
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Li W, Zheng M, Zhao G, Wang J, Liu J, Wang S, Feng F, Liu D, Zhu D, Li Q, Guo L, Guo Y, Liu R, Wen J. Identification of QTL regions and candidate genes for growth and feed efficiency in broilers. Genet Sel Evol 2021; 53:13. [PMID: 33549052 PMCID: PMC7866652 DOI: 10.1186/s12711-021-00608-3] [Citation(s) in RCA: 11] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/11/2019] [Accepted: 01/26/2021] [Indexed: 11/23/2022] Open
Abstract
BACKGROUND Feed accounts for about 70% of the total cost of poultry meat production. Residual feed intake (RFI) has become the preferred measure of feed efficiency because it is phenotypically independent of growth rate and body weight. In this study, our aim was to estimate genetic parameters and identify quantitative trait loci (QTL) for feed efficiency in 3314 purebred broilers using a genome-wide association study. Broilers were genotyped using a custom 55 K single nucleotide polymorphism (SNP) array. RESULTS Estimates of genomic heritability for seven growth and feed efficiency traits, including body weight at 28 days of age (BW28), BW42, average daily feed intake (ADFI), RFI, and RFI adjusted for weight of abdominal fat (RFIa), ranged from 0.12 to 0.26. Eleven genome-wide significant SNPs and 15 suggestively significant SNPs were detected, of which 19 clustered around two genomic regions. A region on chromosome 16 (2.34-2.66 Mb) was associated with both BW28 and BW42, and the most significant SNP in this region, AX_101003762, accounted for 7.6% of the genetic variance of BW28. The other region, on chromosome 1 (91.27-92.43 Mb) was associated with RFI and ADFI, and contains the NSUN3 and EPHA6 as candidate genes. The most significant SNP in this region, AX_172588157, accounted for 4.4% of the genetic variance of RFI. In addition, a genomic region containing the gene AGK on chromosome 1 was found to be associated with RFIa. The NSUN3 and AGK genes were found to be differentially expressed in breast muscle, thigh muscle, and abdominal fat between male broilers with high and low RFI. CONCLUSIONS We identified QTL regions for BW28 and BW42 (spanning 0.32 Mb) and RFI (spanning 1.16 Mb). The NSUN3, EPHA6, and AGK were identified as the most likely candidate genes for these QTL. These genes are involved in mitochondrial function and behavioral regulation. These results contribute to the identification of candidate genes and variants for growth and feed efficiency in poultry.
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Affiliation(s)
- Wei Li
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Maiqing Zheng
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Guiping Zhao
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Jie Wang
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Jie Liu
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Shunli Wang
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Furong Feng
- Foshan Gaoming Xinguang Agricultural and Animal Industrials Corporation, Foshan, 528515 China
| | - Dawei Liu
- Foshan Gaoming Xinguang Agricultural and Animal Industrials Corporation, Foshan, 528515 China
| | - Dan Zhu
- Foshan Gaoming Xinguang Agricultural and Animal Industrials Corporation, Foshan, 528515 China
| | - Qinghe Li
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Liping Guo
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Yuming Guo
- College of Animal Science and Technology, China Agricultural University, Beijing, 100193 China
| | - Ranran Liu
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
| | - Jie Wen
- State Key Laboratory of Animal Nutrition; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences, Beijing, 100193 China
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Paiva JT, Peixoto MGCD, Bruneli FAT, Alvarenga AB, Oliveira HR, Silva AA, Silva DA, Veroneze R, Silva FF, Lopes PS. Genetic parameters, genome-wide association and gene networks for milk and reproductive traits in Guzerá cattle. Livest Sci 2020. [DOI: 10.1016/j.livsci.2020.104273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Peripolli E, Reimer C, Ha NT, Geibel J, Machado MA, Panetto JCDC, do Egito AA, Baldi F, Simianer H, da Silva MVGB. Genome-wide detection of signatures of selection in indicine and Brazilian locally adapted taurine cattle breeds using whole-genome re-sequencing data. BMC Genomics 2020; 21:624. [PMID: 32917133 PMCID: PMC7488563 DOI: 10.1186/s12864-020-07035-6] [Citation(s) in RCA: 13] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2020] [Accepted: 08/27/2020] [Indexed: 12/30/2022] Open
Abstract
BACKGROUND The cattle introduced by European conquerors during the Brazilian colonization period were exposed to a process of natural selection in different types of biomes throughout the country, leading to the development of locally adapted cattle breeds. In this study, whole-genome re-sequencing data from indicine and Brazilian locally adapted taurine cattle breeds were used to detect genomic regions under selective pressure. Within-population and cross-population statistics were combined separately in a single score using the de-correlated composite of multiple signals (DCMS) method. Putative sweep regions were revealed by assessing the top 1% of the empirical distribution generated by the DCMS statistics. RESULTS A total of 33,328,447 biallelic SNPs with an average read depth of 12.4X passed the hard filtering process and were used to access putative sweep regions. Admixture has occurred in some locally adapted taurine populations due to the introgression of exotic breeds. The genomic inbreeding coefficient based on runs of homozygosity (ROH) concurred with the populations' historical background. Signatures of selection retrieved from the DCMS statistics provided a comprehensive set of putative candidate genes and revealed QTLs disclosing cattle production traits and adaptation to the challenging environments. Additionally, several candidate regions overlapped with previous regions under selection described in the literature for other cattle breeds. CONCLUSION The current study reported putative sweep regions that can provide important insights to better understand the selective forces shaping the genome of the indicine and Brazilian locally adapted taurine cattle breeds. Such regions likely harbor traces of natural selection pressures by which these populations have been exposed and may elucidate footprints for adaptation to the challenging climatic conditions.
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Affiliation(s)
- Elisa Peripolli
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, 14884-900, Brazil
| | - Christian Reimer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
- Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
| | - Ngoc-Thuy Ha
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
- Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
| | - Johannes Geibel
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
- Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
| | - Marco Antonio Machado
- National Council for Scientific and Technological Development (CNPq), Lago Sul, 71605-001, Brazil
- Embrapa Dairy Cattle, Juiz de Fora, 36038-330, Brazil
| | | | | | - Fernando Baldi
- São Paulo State University (Unesp), School of Agricultural and Veterinarian Sciences, Jaboticabal, 14884-900, Brazil
| | - Henner Simianer
- Animal Breeding and Genetics Group, Department of Animal Sciences, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
- Center for Integrated Breeding Research, University of Goettingen, Albrecht-Thaer-Weg 3, 37075, Goettingen, Germany
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Paredes-Sánchez FA, Sifuentes-Rincón AM, Casas E, Arellano-Vera W, Parra-Bracamonte GM, Riley DG, Welsh TH, Randel RD. Novel genes involved in the genetic architecture of temperament in Brahman cattle. PLoS One 2020; 15:e0237825. [PMID: 32822435 PMCID: PMC7446865 DOI: 10.1371/journal.pone.0237825] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2020] [Accepted: 08/03/2020] [Indexed: 12/13/2022] Open
Abstract
Cattle temperament is a complex and economically relevant trait. The objective of this study was to identify genomic regions and genes associated with cattle temperament. From a Brahman cattle population of 1,370 animals evaluated for temperament traits (Exit velocity-EV, Pen Score-PS, Temperament Score-TS), two groups of temperament-contrasting animals were identified based on their EV-average values ±1/2 standard deviation (SD). To be considered in the calm group, the EV of females ranged between 0.16–1.82 m/s (n = 50) and the EV of males ranged between 0.4–1.56 m/s (n = 48). Females were classified as temperamental if their EV ranged between 3.13–7.66 m/s (n = 46) and males were classified as temperamental if their EV ranged between 3.05–10.83 m/s (n = 45). Selected animals were genotyped using a total of 139,376 SNPs (GGP-HD-150K), evaluated for their association with EV. The Genome-Wide Association analysis (GWAS) identified fourteen SNPs: rs135340276, rs134895560, rs110190635, rs42949831, rs135982573, rs109393235, rs109531929, rs135087545, rs41839733, rs42486577, rs136661522, rs110882543, rs110864071, rs109722627, (P<8.1E-05), nine of them were located on intergenic regions, harboring seventeen genes, of which only ACER3, VRK2, FANCL and SLCO3A1 were considered candidate associated with bovine temperament due to their reported biological functions. Five SNPs were located at introns of the NRXN3, EXOC4, CACNG4 and SLC9A4 genes. The indicated candidate genes are implicated in a wide range of behavioural phenotypes and complex cognitive functions. The association of the fourteen SNPs on bovine temperament traits (EV, PS and TS) was evaluated; all these SNPs were significant for EV; only some were associated with PS and TS. Fourteen SNPs were associated with EV which allowed the identification of twenty-one candidate genes for Brahman temperament. From a functional point of view, the five intronic SNPs identified in this study, are candidates to address control of bovine temperament, further investigation will probe their role in expression of this trait.
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Affiliation(s)
| | | | - Eduardo Casas
- USDA, ARS, National Animal Disease Center, Ames, IA, United States of America
| | | | | | - David G. Riley
- Texas A&M University, College Station, TX, United States of America
| | - Thomas H. Welsh
- Texas A&M University, College Station, TX, United States of America
| | - Ronald D. Randel
- Texas A&M AgriLife Research, Overton, TX, United States of America
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Chen Q, Qu K, Ma Z, Zhan J, Zhang F, Shen J, Ning Q, Jia P, Zhang J, Chen N, Chen H, Huang B, Lei C. Genome-Wide Association Study Identifies Genomic Loci Associated With Neurotransmitter Concentration in Cattle. Front Genet 2020; 11:139. [PMID: 32292413 PMCID: PMC7119242 DOI: 10.3389/fgene.2020.00139] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/13/2019] [Accepted: 02/06/2020] [Indexed: 11/30/2022] Open
Abstract
Abnormal neurotransmitter concentration is one of the factors that affect the health status, behavioral personality, and welfare level of animals, but the genetic basis of the abnormality is still largely unknown. The objective of this study is to identify putative genomic loci associated with neurotransmitter concentration in cattle. We measured serotonin (5HT), dopamine (DA), cortisol, glutamate (Glu), and ACTH concentrations in blood serum using double-antibody sandwich ELISA in 30 Brahman cattle and 127 Yunling cattle. Interestingly, we found that ACTH concentration was positively correlated with body weight, cannon circumference, and hip width (P < 0.05). Genome-wide association study (GWAS) was performed with mixed linear models using autosomal SNPs derived from the whole-genome sequence. We identified five, five, two, three, and five suggestive loci associated with 5HT, DA, cortisol, Glu, and ACTH concentration, respectively. These 20 associated loci implicated 18 candidate genes. For Glu concentration, the most significant association locus was assigned to MCHR1, a G-coupled receptor that could modulate glutamate release. For dopamine concentration, a very strong association locus was located in the intron of SLC18A2, which is a critical mediator of dopamine dynamics. However, for ACTH concentration, a very strong association locus was assigned to HTR1F, a G protein-coupled receptor that can influence the release of ACTH. Other candidate genes of interest identified for neurotransmitter concentration were PRMT6, GADD45A, PCCA, ANGPT1, ACCS, LOC100336971, TNR, GSDMA, CNTN3, CARMIL1, CDKAL1, RBFOX1, PCDH15, and LGALS12. Our findings will provide targets for the genetic improvement of neurotransmitter-related traits in domestic cattle and basic materials for studying the mechanism of neurotransmitter synthesis, release, and transport in human and animals.
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Affiliation(s)
- Qiuming Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Kaixing Qu
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Zhijie Ma
- Academy of Animal Science and Veterinary Medicine, Qinghai University, Xining, China
| | - Jingxi Zhan
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Fengwei Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jiafei Shen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qingqing Ning
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Peng Jia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Chen Q, Zhang F, Qu K, Hanif Q, Shen J, Jia P, Ning Q, Zhan J, Zhang J, Chen N, Chen H, Huang B, Lei C. Genome-wide association study identifies genomic loci associated with flight reaction in cattle. J Anim Breed Genet 2019; 137:477-485. [PMID: 31828846 DOI: 10.1111/jbg.12461] [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: 08/27/2019] [Revised: 11/19/2019] [Accepted: 11/21/2019] [Indexed: 11/29/2022]
Abstract
Lower flight reaction is closely related to higher production in cattle, but the genetic basis of lower flight reaction is not clearly understood. Here, we sampled a total of 45 Brahman cattles and 166 Yunling cattles with flight distance (FD), and 73 Brahman cattles and 288 Yunling cattles with crush score (CS) and flight speed (FS), whereas there were 45 Brahman cattles and 161 Yunling cattles with all three traits. The FD, CS and FS in Brahman cattle were significantly lower than those in Yunling cattle. The flight reaction traits had negative correlation with conformational traits (e.g., body weight, withers height and body length). Based on SNPs derived from a subset of 162 whole genomes (25 Brahman genomes and 100 Yunling genomes with FD, 30 Brahman and 131 Yunling genomes with CS and FS), genome-wide association study with mixed linear model was performed to test potential associations between flight reaction traits and genomic variants. We identified five, two and two genomic loci suggestively associated with FD, CS and FS, respectively. Five out of five candidate genes for FD (LOC789753, LRP6, CTIF, SLC9A9 and ZEB1) were reported to be related to Alzheimer's disease representing cognitive impairment in human, which was consistent with the finding that cognitive-behavioural intervention decreased the FD of cows to human. In CS, a very strong association locus was assigned to CDH8, a cadherin involved in synaptic adhesion, axon outgrowth and guidance, whose deletion was associated with autism spectrum disorder. In FS, a very strong association locus was assigned to GABRG2, a gamma-aminobutyric acid (a major inhibitory neurotransmitter in brain) receptor, whose polymorphisms were associated with suicidal behaviour in schizophrenia patients. Our findings will provide targets for molecular-marker selection and genetic manipulation of cattle improvement to meeting the growing demand for lower flight reaction to human.
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Affiliation(s)
- Qiuming Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Fengwei Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Kaixing Qu
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Quratulain Hanif
- National Institute for Biotechnology and Genetic Engineering, Pakistan Institute of Engineering and Applied Sciences, Faisalabad, Pakistan
| | - Jiafei Shen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Peng Jia
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Qingqing Ning
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Jingxi Zhan
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Jicai Zhang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Ningbo Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Hong Chen
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Bizhi Huang
- Yunnan Academy of Grassland and Animal Science, Kunming, China
| | - Chuzhao Lei
- Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, College of Animal Science and Technology, Northwest A&F University, Yangling, China
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Di Gerlando R, Sardina MT, Tolone M, Sutera AM, Mastrangelo S, Portolano B. Genome-wide detection of copy-number variations in local cattle breeds. ANIMAL PRODUCTION SCIENCE 2019. [DOI: 10.1071/an17603] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/26/2022]
Abstract
The aim of the present study was to identify copy-number variations (CNVs) in Cinisara (CIN) and Modicana (MOD) cattle breeds on the basis of signal intensity (logR ratio) and B allele frequency of each marker, using Illumina’s BovineSNP50K Genotyping BeadChip. The CNVs were detected with the PennCNV and SVS 8.7.0 software and were aggregated into CNV regions (CNVRs). PennCNV identified 487 CNVs in CIN that aggregated into 86 CNVRs, and 424 CNVs in MOD that aggregated into 81 CNVRs. SVS identified a total of 207 CNVs in CIN that aggregated into 39 CNVRs, and 181 CNVs in MOD that aggregated into 41 CNVRs. The CNVRs identified with the two softwares contained 29 common CNVRs in CIN and 17 common CNVRs in MOD. Only a small number of CNVRs identified in the present study have been identified elsewhere, probably because of the limitations of the array used. In total, 178 and 208 genes were found within the CNVRs of CIN and MOD respectively. Gene Ontology and KEGG pathway analyses showed that several of these genes are involved in milk production, reproduction and behaviour, the immune response, and resistance/susceptibility to infectious diseases. Our results have provided significant information for the construction of more-complete CNV maps of the bovine genome and offer an important resource for the investigation of genomic changes and traits of interest in the CIN and MOD cattle breeds. Our results will also be valuable for future studies and constitute a preliminary report of the CNV distribution resources in local cattle genomes.
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Peripolli E, Metzger J, de Lemos MVA, Stafuzza NB, Kluska S, Olivieri BF, Feitosa FLB, Berton MP, Lopes FB, Munari DP, Lôbo RB, Magnabosco CDU, Di Croce F, Osterstock J, Denise S, Pereira ASC, Baldi F. Autozygosity islands and ROH patterns in Nellore lineages: evidence of selection for functionally important traits. BMC Genomics 2018; 19:680. [PMID: 30223795 PMCID: PMC6142381 DOI: 10.1186/s12864-018-5060-8] [Citation(s) in RCA: 28] [Impact Index Per Article: 4.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 09/07/2018] [Indexed: 12/20/2022] Open
Abstract
Background The aim of this study was to assess genome-wide autozygosity in a Nellore cattle population and to characterize ROH patterns and autozygosity islands that may have occurred due to selection within its lineages. It attempts also to compare estimates of inbreeding calculated from ROH (FROH), genomic relationship matrix (FGRM), and pedigree-based coefficient (FPED). Results The average number of ROH per animal was 55.15 ± 13.01 with an average size of 3.24 Mb. The Nellore genome is composed mostly by a high number of shorter segments accounting for 78% of all ROH, although the proportion of the genome covered by them was relatively small. The genome autozygosity proportion indicates moderate to high inbreeding levels for classical standards, with an average value of 7.15% (178.70 Mb). The average of FPED and FROH, and their correlations (− 0.05 to 0.26) were low. Estimates of correlation between FGRM-FPED was zero, while the correlation (− 0.01 to − 0.07) between FGRM-FROH decreased as a function of ROH length, except for FROH > 8Mb (− 0.03). Overall, inbreeding coefficients were not high for the genotyped animals. Autozygosity islands were evident across the genome (n = 62) and their genomic location did not largely differ within lineages. Enriched terms (p < 0.01) associated with defense response to bacteria (GO:0042742), immune complex reaction (GO:0045647), pregnancy-associated glycoproteins genes (GO:0030163), and organism growth (GO:0040014) were described within the autozygotic islands. Conclusions Low FPED-FROH correlation estimates indicate that FPED is not the most suitable method for capturing ancient inbreeding when the pedigree does not extend back many generations and FROH should be used instead. Enriched terms (p < 0.01) suggest a strong selection for immune response. Non-overlapping islands within the lineages greatly explain the mechanism underlying selection for functionally important traits in Nellore cattle. Electronic supplementary material The online version of this article (10.1186/s12864-018-5060-8) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Elisa Peripolli
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil.
| | - Julia Metzger
- Institute for Animal Breeding and Genetics, University of Veterinary Medicine Hannover, 30559, Hannover, Germany
| | - Marcos Vinícius Antunes de Lemos
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Nedenia Bonvino Stafuzza
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Sabrina Kluska
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Bianca Ferreira Olivieri
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Fabieli Louise Braga Feitosa
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Mariana Piatto Berton
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Fernando Brito Lopes
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Danísio Prado Munari
- Departamento de Ciências Exatas, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
| | - Raysildo Barbosa Lôbo
- Associação Nacional de Criadores e Pesquisadores (ANCP), Ribeirão Preto, 14020-230, Brazil
| | | | | | | | | | | | - Fernando Baldi
- Departamento de Zootecnia, Faculdade de Ciências Agrárias e Veterinárias, UNESP Univ Estadual Paulista Júlio de Mesquita Filho, Jaboticabal, 14884-900, Brazil
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Chillemi G, Bongiorni S, Gioiosa S, Flati T, Castrignanò T, Milanesi M, Ajmone Marsan P, Valentini A. Missense mutations of NCPAG gene affect calving ease in Piedmontese cattle: preliminary evidences. ITALIAN JOURNAL OF ANIMAL SCIENCE 2017. [DOI: 10.1080/1828051x.2017.1370362] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Affiliation(s)
- Giovanni Chillemi
- SuperComputing Applications and Innovation Department, CINECA, SCAI, Roma, Italy
| | - Silvia Bongiorni
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, Viterbo, Italy
| | - Silvia Gioiosa
- SuperComputing Applications and Innovation Department, CINECA, SCAI, Roma, Italy
- Istituto di Biomembrane e Bioenergetica, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Tiziano Flati
- SuperComputing Applications and Innovation Department, CINECA, SCAI, Roma, Italy
- Istituto di Biomembrane e Bioenergetica, Consiglio Nazionale delle Ricerche, Bari, Italy
| | - Tiziana Castrignanò
- SuperComputing Applications and Innovation Department, CINECA, SCAI, Roma, Italy
| | - Marco Milanesi
- Istituto di Zootecnica, Università Cattolica del Sacro Cuore, Piacenza (PC), Italy
| | - Paolo Ajmone Marsan
- Istituto di Zootecnica, Università Cattolica del Sacro Cuore, Piacenza (PC), Italy
| | - Alessio Valentini
- Dipartimento per la Innovazione nei Sistemi Biologici, Agroalimentari e Forestali, Università della Tuscia, Viterbo, Italy
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