1
|
Bucher EA, Mészáros G, Gebre KT, Emmerling R, Sölkner J. Genome-wide association study for milking speed in Fleckvieh cattle. J Dairy Sci 2024:S0022-0302(24)00960-3. [PMID: 38908711 DOI: 10.3168/jds.2024-24854] [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: 03/01/2024] [Accepted: 05/24/2024] [Indexed: 06/24/2024]
Abstract
Milking speed is an important trait influencing udder health of dairy cows as well as labor efficiency. Yet, it has received little attention in genomic association studies. The main objective of this study was to determine regions and genes on the genome with a potential effect on milking speed in Fleckvieh (dual purpose Simmental) cattle. Genome-wide association studies were conducted using de-regressed breeding values of bulls as phenotypes. Six SNP on 4 autosomes were significantly associated with milking speed for additive effects. Significant regions on BTA4 and BTA19 correspond with findings for other dairy cattle breeds. Based on the observation of Fleckvieh breed managers, variation of milking speed in batches of daughters of some bulls is much higher than in daughter groups of other bulls. This difference in within family variation may be caused by transmission of alternative alleles of bulls being heterozygous for a gene affecting milking speed. To check on this, we considered standard deviation of yield deviations in milking speed of half-sib daughters as a new trait and performed GWAS for dominance effects. One signal on BTA5 passed the genome wide Bonferroni threshold that corresponded to the significant signal from standard GWAS on de-regressed breeding values. The key conclusion of this study is that several strong genomic signals were found for milking speed in Fleckvieh cattle and that the strongest of them are supported by similar findings in Brown Swiss and Holstein Friesian cattle. Milking speed is a complex trait whose sub-processes have not yet been elucidated in detail. Hence, it remains a challenge to link the associated regions on the genome with causal genes and their functions.
Collapse
Affiliation(s)
- E A Bucher
- University of Natural Resources and Life Sciences of Vienna, Department of Sustainable Agricultural Systems, Gregor-Mendel-Strasse 33, 1180, Vienna, Austria
| | - G Mészáros
- University of Natural Resources and Life Sciences of Vienna, Department of Sustainable Agricultural Systems, Gregor-Mendel-Strasse 33, 1180, Vienna, Austria.
| | - K T Gebre
- University of Natural Resources and Life Sciences of Vienna, Department of Sustainable Agricultural Systems, Gregor-Mendel-Strasse 33, 1180, Vienna, Austria; Mekelle University, Department of Animal, Rangeland and Wildlife Sciences (ARWS), Enda-Eyesus campus, P.O Box 231, Mekelle, Ethiopia
| | - R Emmerling
- Institute of Animal Breeding, Bavarian State Research Center for Agriculture, 85586 Poing-Grub, Germany
| | - J Sölkner
- University of Natural Resources and Life Sciences of Vienna, Department of Sustainable Agricultural Systems, Gregor-Mendel-Strasse 33, 1180, Vienna, Austria
| |
Collapse
|
2
|
Graham JR, Montes ME, Pedrosa VB, Doucette J, Taghipoor M, Araujo AC, Gloria LS, Boerman JP, Brito LF. Genetic parameters for calf feeding traits derived from automated milk feeding machines and number of bovine respiratory disease treatments in North American Holstein calves. J Dairy Sci 2024; 107:2175-2193. [PMID: 37923202 DOI: 10.3168/jds.2023-23794] [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: 05/25/2023] [Accepted: 10/03/2023] [Indexed: 11/07/2023]
Abstract
Precision livestock farming technologies, such as automatic milk feeding machines, have increased the availability of on-farm data collected from dairy operations. We analyzed feeding records from automatic milk feeding machines to evaluate the genetic background of milk feeding traits and bovine respiratory disease (BRD) in North American Holstein calves. Data from 10,076 preweaning female Holstein calves were collected daily over a period of 6 yr (3 yr included per-visit data), and daily milk consumption (DMC), per-visit milk consumption (PVMC), daily sum of drinking duration (DSDD), drinking duration per-visit, daily number of rewarded visits (DNRV), and total number of visits per day were recorded over a 60-d preweaning period. Additional traits were derived from these variables, including total consumption and duration variance (TCV and TDV), feeding interval, drinking speed (DS), and preweaning stayability. A single BRD-related trait was evaluated, which was the number of times a calf was treated for BRD (NTT). The NTT was determined by counting the number of BRD incidences before 60 d of age. All traits were analyzed using single-step genomic BLUP mixed-model equations and fitting either repeatability or random regression models in the BLUPF90+ suite of programs. A total of 10,076 calves with phenotypic records and genotypic information for 57,019 SNP after the quality control were included in the analyses. Feeding traits had low heritability estimates based on repeatability models (0.006 ± 0.0009 to 0.08 ± 0.004). However, total variance traits using an animal model had greater heritabilities of 0.21 ± 0.023 and 0.23 ± 0.024, for TCV and TDV, respectively. The heritability estimates increased with the repeatability model when using only the first 32 d preweaning (e.g., PVMC = 0.040 ± 0.003, DMC = 0.090 ± 0.009, DSDD = 0.100 ± 0.005, DS = 0.150 ± 0.007, DNRV = 0.020 ± 0.002). When fitting random regression models (RRM) using the full dataset (60-d period), greater heritability estimates were obtained (e.g., PVMC = 0.070 [range: 0.020, 0.110], DMC = 0.460 [range: 0.050, 0.680], DSDD = 0.180 [range: 0.010, 0.340], DS = 0.19 [range: 0.070, 0.430], DNRV = 0.120 [range: 0.030, 0.450]) for the majority of the traits, suggesting that RRM capture more genetic variability than the repeatability model with better fit being found for RRM. Moderate negative genetic correlations of -0.59 between DMC and NTT were observed, suggesting that automatic milk feeding machines records have the potential to be used for genetically improving disease resilience in Holstein calves. The results from this study provide key insights of the genetic background of early in-life traits in dairy cattle, which can be used for selecting animals with improved health outcomes and performance.
Collapse
Affiliation(s)
- Jason R Graham
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Maria E Montes
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Victor B Pedrosa
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Jarrod Doucette
- Agriculture Information Technology (AgIT), Purdue University, West Lafayette, IN 47907
| | - Masoomeh Taghipoor
- Université Paris-Saclay, INRAE, AgroParisTech, UMR Modélisation Systémique Appliquée aux Ruminants, 91120, Palaiseau, France
| | - André C Araujo
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Leonardo S Gloria
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | | | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907.
| |
Collapse
|
3
|
Lee J, Mun H, Koo Y, Park S, Kim J, Yu S, Shin J, Lee J, Son J, Park C, Lee S, Song H, Kim S, Dang C, Park J. Enhancing Genomic Prediction Accuracy for Body Conformation Traits in Korean Holstein Cattle. Animals (Basel) 2024; 14:1052. [PMID: 38612291 PMCID: PMC11011013 DOI: 10.3390/ani14071052] [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: 12/31/2023] [Revised: 03/18/2024] [Accepted: 03/28/2024] [Indexed: 04/14/2024] Open
Abstract
The Holstein breed is the mainstay of dairy production in Korea. In this study, we evaluated the genomic prediction accuracy for body conformation traits in Korean Holstein cattle, using a range of π levels (0.75, 0.90, 0.99, and 0.995) in Bayesian methods (BayesB and BayesC). Focusing on 24 traits, we analyzed the impact of different π levels on prediction accuracy. We observed a general increase in accuracy at higher levels for specific traits, with variations depending on the Bayesian method applied. Notably, the highest accuracy was achieved for rear teat angle when using deregressed estimated breeding values including parent average as a response variable. We further demonstrated that incorporating parent average into deregressed estimated breeding values enhances genomic prediction accuracy, showcasing the effectiveness of the model in integrating both offspring and parental genetic information. Additionally, we identified 18 significant window regions through genome-wide association studies, which are crucial for future fine mapping and discovery of causal mutations. These findings provide valuable insights into the efficiency of genomic selection for body conformation traits in Korean Holstein cattle and highlight the potential for advancements in the prediction accuracy using larger datasets and more sophisticated genomic models.
Collapse
Affiliation(s)
- Jungjae Lee
- Department of Animal Science and Technology, College of Biotechnology and Natural Resources, Chung-Ang University, Anseong 17546, Republic of Korea;
| | - Hyosik Mun
- Korea Animal Improvement Association, Seoul 06668, Republic of Korea; (H.M.); (Y.K.); (S.P.); (J.K.); (S.Y.); (J.S.); (C.P.); (S.K.)
| | - Yangmo Koo
- Korea Animal Improvement Association, Seoul 06668, Republic of Korea; (H.M.); (Y.K.); (S.P.); (J.K.); (S.Y.); (J.S.); (C.P.); (S.K.)
| | - Sangchul Park
- Korea Animal Improvement Association, Seoul 06668, Republic of Korea; (H.M.); (Y.K.); (S.P.); (J.K.); (S.Y.); (J.S.); (C.P.); (S.K.)
| | - Junsoo Kim
- Korea Animal Improvement Association, Seoul 06668, Republic of Korea; (H.M.); (Y.K.); (S.P.); (J.K.); (S.Y.); (J.S.); (C.P.); (S.K.)
| | - Seongpil Yu
- Korea Animal Improvement Association, Seoul 06668, Republic of Korea; (H.M.); (Y.K.); (S.P.); (J.K.); (S.Y.); (J.S.); (C.P.); (S.K.)
| | - Jiseob Shin
- Dairy Cattle Improvement Center of NH-Agree Business Group, National Agricultural Cooperative Federation, Goyang 10292, Republic of Korea; (J.S.); (S.L.); (H.S.)
| | - Jaegu Lee
- Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Republic of Korea;
| | - Jihyun Son
- Korea Animal Improvement Association, Seoul 06668, Republic of Korea; (H.M.); (Y.K.); (S.P.); (J.K.); (S.Y.); (J.S.); (C.P.); (S.K.)
| | - Chanhyuk Park
- Korea Animal Improvement Association, Seoul 06668, Republic of Korea; (H.M.); (Y.K.); (S.P.); (J.K.); (S.Y.); (J.S.); (C.P.); (S.K.)
| | - Seokhyun Lee
- Dairy Cattle Improvement Center of NH-Agree Business Group, National Agricultural Cooperative Federation, Goyang 10292, Republic of Korea; (J.S.); (S.L.); (H.S.)
| | - Hyungjun Song
- Dairy Cattle Improvement Center of NH-Agree Business Group, National Agricultural Cooperative Federation, Goyang 10292, Republic of Korea; (J.S.); (S.L.); (H.S.)
| | - Sungjin Kim
- Korea Animal Improvement Association, Seoul 06668, Republic of Korea; (H.M.); (Y.K.); (S.P.); (J.K.); (S.Y.); (J.S.); (C.P.); (S.K.)
| | - Changgwon Dang
- Animal Breeding and Genetics Division, National Institute of Animal Science, Rural Development Administration, Cheonan 31000, Republic of Korea;
| | - Jun Park
- Department of Animal Biotechnology, Jeonbuk National University, Jeonju 54896, Republic of Korea
| |
Collapse
|
4
|
Saravanan KA, Rajawat D, Kumar H, Nayak SS, Bhushan B, Dutt T, Panigrahi M. Signatures of selection in riverine buffalo populations revealed by genome-wide SNP data. Anim Biotechnol 2023; 34:3343-3354. [PMID: 36384399 DOI: 10.1080/10495398.2022.2145292] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The detection of selection signatures assists in understanding domestication, evolution, and the identification of genomic regions related to adaptation and production traits in buffaloes. The emergence of high-throughput technologies like Next Generation Sequencing and SNP genotyping had expanded our ability to detect these signatures of selection. In this study, we sought to identify signatures of selection in five buffalo populations (Brazilian Murrah, Bulgarian Murrah, Indian Murrah, Nili-Ravi, and Kundi) using Axiom Buffalo 90 K Genotyping Array data. Using seven different methodologies (Tajima's D, CLR, ROH, iHS, FST, FLK and hapFLK), we identified selection signatures in 374 genomic regions, spanning a total of 381 genes and 350 quantitative trait loci (QTLs). Among these, several candidate genes were associated with QTLs for milk production, reproduction, growth and carcass traits. The genes and QTLs reported in this study provide insight into selection signals shaping the genome of buffalo breeds. Our findings can aid in further genomic association studies, genomic prediction, and the implementation of breeding programmes in Indian buffaloes.
Collapse
Affiliation(s)
- K A Saravanan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| |
Collapse
|
5
|
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.
Collapse
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
| |
Collapse
|
6
|
Pedrosa VB, Boerman JP, Gloria LS, Chen SY, Montes ME, Doucette JS, Brito LF. Genomic-based genetic parameters for milkability traits derived from automatic milking systems in North American Holstein cattle. J Dairy Sci 2023; 106:2613-2629. [PMID: 36797177 DOI: 10.3168/jds.2022-22515] [Citation(s) in RCA: 11] [Impact Index Per Article: 11.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2022] [Accepted: 10/12/2022] [Indexed: 02/16/2023]
Abstract
The number of dairy farms adopting automatic milking systems (AMS) has considerably increased around the world aiming to reduce labor costs, improve cow welfare, increase overall performance, and generate a large amount of daily data, including production, behavior, health, and milk quality records. In this context, this study aimed to (1) estimate genomic-based variance components for milkability traits derived from AMS in North American Holstein cattle based on random regression models; and (2) derive and estimate genetic parameters for novel behavioral indicators based on AMS-derived data. A total of 1,752,713 daily records collected using 36 milking robot stations and 70,958 test-day records from 4,118 genotyped Holstein cows were used in this study. A total of 57,600 SNP remained after quality control. The daily-measured traits evaluated were milk yield (MY, kg), somatic cell score (SCS, score unit), milk electrical conductivity (EC, mS), milking efficiency (ME, kg/min), average milk flow rate (FR, kg/min), maximum milk flow rate (FRM, kg/min), milking time (MT, min), milking failures (MFAIL), and milking refusals (MREF). Variance components and genetic parameters for MY, SCS, ME, FR, FRM, MT, and EC were estimated using the AIREMLF90 software under a random regression model fitting a third-order Legendre orthogonal polynomial. A threshold Bayesian model using the THRGIBBS1F90 software was used for genetically evaluating MFAIL and MREF. The daily heritability estimates across days in milk (DIM) ranged from 0.07 to 0.28 for MY, 0.02 to 0.08 for SCS, 0.38 to 0.49 for EC, 0.45 to 0.56 for ME, 0.43 to 0.52 for FR, 0.47 to 0.58 for FRM, and 0.22 to 0.28 for MT. The estimates of heritability (± SD) for MFAIL and MREF were 0.02 ± 0.01 and 0.09 ± 0.01, respectively. Slight differences in the genetic correlations were observed across DIM for each trait. Strong and positive genetic correlations were observed among ME, FR, and FRM, with estimates ranging from 0.94 to 0.99. Also, moderate to high and negative genetic correlations (ranging from -0.48 to -0.86) were observed between MT and other traits such as SCS, ME, FR, and FRM. The genetic correlation (± SD) between MFAIL and MREF was 0.25 ± 0.02, indicating that both traits are influenced by different sets of genes. High and negative genetic correlations were observed between MFAIL and FR (-0.58 ± 0.02) and MFAIL and FRM (-0.56 ± 0.02), indicating that cows with more MFAIL are those with lower FR. The use of random regression models is a useful alternative for genetically evaluating AMS-derived traits measured throughout the lactation. All the milkability traits evaluated in this study are heritable and have demonstrated selective potential, suggesting that their use in dairy cattle breeding programs can improve dairy production efficiency in AMS.
Collapse
Affiliation(s)
- Victor B Pedrosa
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907; Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil
| | | | - Leonardo S Gloria
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Shi-Yi Chen
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907; Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, Sichuan, 611130, China
| | - Maria E Montes
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Jarrod S Doucette
- Agriculture Information Technology (AgIT), Purdue University, West Lafayette, IN 47907
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907.
| |
Collapse
|
7
|
Al Kalaldeh M, Swaminathan M, Podtar V, Jadhav S, Dhanikachalam V, Joshi A, Gibson JP. Detection of genomic regions that differentiate Bos indicus from Bos taurus ancestral breeds for milk yield in Indian crossbred cows. Front Genet 2023; 13:1082802. [PMID: 36699459 PMCID: PMC9868639 DOI: 10.3389/fgene.2022.1082802] [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: 10/28/2022] [Accepted: 12/20/2022] [Indexed: 01/11/2023] Open
Abstract
Introduction: In India, crossbred cows incorporate the high production of B. taurus dairy breeds and the environmental adaptation of local B. indicus cattle. Adaptation to different environments and selection in milk production have shaped the genetic differences between B. indicus and B. taurus cattle. The aim of this paper was to detect, for milk yield of crossbred cows, quantitative trait loci (QTL) that differentiate B. indicus from B. taurus ancestry, as well as QTL that are segregating within the ancestral breeds. Methods: A total of 123,042 test-day milk records for 4,968 crossbred cows, genotyped with real and imputed 770 K SNP, were used. Breed origins were assigned to haplotypes of crossbred cows, and from that, were assigned to SNP alleles. Results: At a false discovery rate (FDR) of 30%, a large number of genomic regions showed significant effects of B. indicus versus B. taurus origin on milk yield, with positive effects coming from both ancestors. No significant regions were detected for Holstein Friesian (HF) versus Jersey effects on milk yield. Additionally, no regions for SNP alleles segregating within indigenous, within HF, and within Jersey were detected. The most significant effects, at FDR 5%, were found in a region on BTA5 (43.98-49.44 Mbp) that differentiates B. indicus from B. taurus, with an estimated difference between homozygotes of approximately 10% of average yield, in favour of B. indicus origin. Discussion: Our results indicate that evolutionary differences between B. indicus and B. taurus cattle for milk yield, as expressed in crossbred cows, occur at many causative loci across the genome. Although subject to the usual first estimation bias, some of the loci appear to have large effects that might make them useful for genomic selection in crossbreds, if confirmed in subsequent studies.
Collapse
Affiliation(s)
- Mohammad Al Kalaldeh
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia,*Correspondence: Mohammad Al Kalaldeh, ; John P. Gibson,
| | - Marimuthu Swaminathan
- BAIF Development Research Foundation and Central Research Station, Pune, Maharashtra, India
| | - Vinod Podtar
- BAIF Development Research Foundation and Central Research Station, Pune, Maharashtra, India
| | - Santoshkumar Jadhav
- BAIF Development Research Foundation and Central Research Station, Pune, Maharashtra, India
| | - Velu Dhanikachalam
- BAIF Development Research Foundation and Central Research Station, Pune, Maharashtra, India
| | - Akshay Joshi
- BAIF Development Research Foundation and Central Research Station, Pune, Maharashtra, India
| | - John P. Gibson
- Centre for Genetic Analysis and Applications, School of Environmental and Rural Science, University of New England, Armidale, NSW, Australia,*Correspondence: Mohammad Al Kalaldeh, ; John P. Gibson,
| |
Collapse
|
8
|
Machado PC, Brito LF, Martins R, Pinto LFB, Silva MR, Pedrosa VB. Genome-Wide Association Analysis Reveals Novel Loci Related with Visual Score Traits in Nellore Cattle Raised in Pasture-Based Systems. Animals (Basel) 2022; 12:ani12243526. [PMID: 36552446 PMCID: PMC9774243 DOI: 10.3390/ani12243526] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/03/2022] [Revised: 12/06/2022] [Accepted: 12/10/2022] [Indexed: 12/15/2022] Open
Abstract
Body conformation traits assessed based on visual scores are widely used in Zebu cattle breeding programs. The aim of this study was to identify genomic regions and biological pathways associated with body conformation (CONF), finishing precocity (PREC), and muscling (MUSC) in Nellore cattle. The measurements based on visual scores were collected in 20,807 animals raised in pasture-based systems in Brazil. In addition, 2775 animals were genotyped using a 35 K SNP chip, which contained 31,737 single nucleotide polymorphisms after quality control. Single-step GWAS was performed using the BLUPF90 software while candidate genes were identified based on the Ensembl Genes 69. PANTHER and REVIGO platforms were used to identify key biological pathways and STRING to create gene networks. Novel candidate genes were revealed associated with CONF, including ALDH9A1, RXRG, RAB2A, and CYP7A1, involved in lipid metabolism. The genes associated with PREC were ELOVL5, PID1, DNER, TRIP12, and PLCB4, which are related to the synthesis of long-chain fatty acids, lipid metabolism, and muscle differentiation. For MUSC, the most important genes associated with muscle development were SEMA6A, TIAM2, UNC5A, and UIMC1. The polymorphisms identified in this study can be incorporated in commercial genotyping panels to improve the accuracy of genomic evaluations for visual scores in beef cattle.
Collapse
Affiliation(s)
- Pamela C. Machado
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa 84030-900, PR, Brazil
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
| | - Rafaela Martins
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa 84030-900, PR, Brazil
| | - Luis Fernando B. Pinto
- Department of Animal Science, Federal University of Bahia, Av. Adhemar de Barros 500, Ondina, Salvador 40170-110, BA, Brazil
| | - Marcio R. Silva
- Melhore Animal and Katayama Agropecuaria Lda, Guararapes 16700-000, SP, Brazil
| | - Victor B. Pedrosa
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa 84030-900, PR, Brazil
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA
- Correspondence:
| |
Collapse
|
9
|
Behavioural Traits in Bos taurus Cattle, Their Heritability, Potential Genetic Markers, and Associations with Production Traits. Animals (Basel) 2022; 12:ani12192602. [PMID: 36230342 PMCID: PMC9559500 DOI: 10.3390/ani12192602] [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: 09/02/2022] [Revised: 09/21/2022] [Accepted: 09/26/2022] [Indexed: 11/20/2022] Open
Abstract
Simple Summary Cattle have the potential to seriously injure humans and cause damage to property. The risk of cattle reacting in a dangerous manner can be reduced through genetic selection for cattle which have a better temperament. A literature search was undertaken which returned papers which met the criteria of “Bovine”, “Genetics” and “Behaviour” or terms therein. Behavioural traits were grouped and their heritability, genomic associations and correlations with production traits examined. It was found that heritability estimates were more accurate in studies with large populations (n > 1000). Gene associations with behavioural traits were found on all chromosomes except for chromosome 13, with associated SNPs reported on all chromosomes except 5, 13, 17, 18 and 23. Generally, it was found that correlations between behaviour and production traits were low or negligible, suggesting that genetic improvement can be undertaken without negatively affecting production. There was variation between the results of the studies examined, and this underlines that any genetic study is population specific. Thus, to assess the heritability, genetic associations with production and genomic areas of interest for behavioural traits, a large-scale study of the population of interest would be required. Abstract People who work with cattle are at severe risk of serious injury due to the size and strength of the cattle. This risk can be minimised by breeding less dangerous cattle, which have a more favourable reaction to humans. This study provides a systematic review of literature pertaining to cattle genetics relating to behaviour. The review protocol was developed using the Preferred Reporting Items for Systematic reviews and Meta-Analyses (PRISMA) framework, with Population, Exposure and Outcome components identified as Bovine, Genetics and Behaviour respectively. Forty-nine studies were identified in the sifting and assigned non-exclusively to groups of heritability (22), genomic associations (13) and production traits related to behaviour (24). Behavioural traits were clustered into the following groups: “temperament, disposition and/ or docility”, “aggression”, “chute score”, “flight speed”, “milking temperament”, “non-restrained methods” and “restrained methods”. Fourteen papers reported high accuracy (Standard Error ≤ 0.05) estimates of heritability, the majority (n = 12) of these studies measured over 1000 animals. The heritability estimates were found to vary between studies. Gene associations with behavioural traits were found on all chromosomes except for chromosome 13, with associated SNPs reported on all chromosomes except 5, 13, 17, 18 and 23. Generally, it was found that correlations between behaviour and production traits were low or negligible. These studies suggest that additive improvement of behavioural traits in cattle is possible and would not negatively impact performance. However, the variation between studies demonstrates that the genetic relationships are population specific. Thus, to assess the heritability, genetic associations with production and genomic areas of interest for behavioural traits, a large-scale study of the population of interest would be required.
Collapse
|
10
|
Zare M, Atashi H, Hostens M. Genome-Wide Association Study for Lactation Performance in the Early and Peak Stages of Lactation in Holstein Dairy Cows. Animals (Basel) 2022; 12:ani12121541. [PMID: 35739877 PMCID: PMC9219502 DOI: 10.3390/ani12121541] [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: 04/03/2022] [Revised: 05/27/2022] [Accepted: 06/10/2022] [Indexed: 11/24/2022] Open
Abstract
Simple Summary Although genome-wide association studies (GWAS) have been carried out within a variety of cattle breeds, they are mainly based on the accumulated 305-day lactation yield traits estimated by summing the test-day recorded every day during the lactation period, or combining the weekly or monthly test-day records by linear interpolation. Since the additive genetic variance for milk yield and composition changes during lactation, the genetic effects of QTL related to these traits are not constant during the lactation period. Therefore, a better understanding of the genetic architecture of milk production traits in different lactation stages (e.g., beginning, peak, and end stages of lactation) is needed. The aim of this study was to detect genomic loci associated with lactation performance during 9 to 50 days in milk (DIM) in Holstein dairy cows. Candidate genes identified for milk production traits showed contrasting results between the EARLY and PEAK stages of lactation. Based on the results of this study, it can be concluded that in any genomic study it should be taken into account that the genetic effects of genes related to the lactation performance are not constant during the lactation period. Abstract This study aimed to detect genomic loci associated with the lactation performance during 9 to 50 days in milk (DIM) in Holstein dairy cows. Daily milk yield (MY), fat yield (FY), and protein yield (PY) during 9 to 50 DIM were recorded on 134 multiparous Holstein dairy cows distributed in four research herds. Fat- and protein-corrected milk (FPCM), fat-corrected milk (FCM), and energy-corrected milk (ECM) were predicted. The records collected during 9 to 25 DIM were put into the early stage of lactation (EARLY) and those collected during 26 to 50 DIM were put into the peak stage of lactation (PEAK). Then, the mean of traits in each cow included in each lactation stage (EARLY and PEAK) were estimated and used as phenotypic observations for the genome-wide association study. The included animals were genotyped with the Illumina BovineHD Genotyping BeadChip (Illumina Inc., San Diego, CA, USA) for a total of 777,962 single nucleotide polymorphisms (SNPs). After quality control, 585,109 variants were analyzed using GEMMA software in a mixed linear model. Although there was no SNP associated with traits included at the 5% genome-wide significance threshold, 18 SNPs were identified to be associated with milk yield and composition at the suggestive genome-wide significance threshold. Candidate genes identified for milk production traits showed contrasting results between the EARLY and PEAK stages of lactation. This suggests that differential sets of candidate genes underlie the phenotypic expression of the considered traits in the EARLY and PEAK stages of lactation. Although further functional studies are needed to validate our findings in independent populations, it can be concluded that in any genomic study it should be taken into account that the genetic effects of genes related to the lactation performance are not constant during the lactation period.
Collapse
Affiliation(s)
- Mahsa Zare
- Department of Animal Science, Shiraz University, Shiraz 7144113131, Iran; (M.Z.); (H.A.)
| | - Hadi Atashi
- Department of Animal Science, Shiraz University, Shiraz 7144113131, Iran; (M.Z.); (H.A.)
| | - Miel Hostens
- Department of Population Health Sciences, University of Utrecht, Yalelaan 7, 3584 CL Utrecht, The Netherlands
- Correspondence: ; Tel.: +31-30-253-1820
| |
Collapse
|
11
|
Chen SY, Schenkel FS, Melo ALP, Oliveira HR, Pedrosa VB, Araujo AC, Melka MG, Brito LF. Identifying pleiotropic variants and candidate genes for fertility and reproduction traits in Holstein cattle via association studies based on imputed whole-genome sequence genotypes. BMC Genomics 2022; 23:331. [PMID: 35484513 PMCID: PMC9052698 DOI: 10.1186/s12864-022-08555-z] [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: 08/05/2021] [Accepted: 04/12/2022] [Indexed: 02/06/2023] Open
Abstract
Background Genetic progress for fertility and reproduction traits in dairy cattle has been limited due to the low heritability of most indicator traits. Moreover, most of the quantitative trait loci (QTL) and candidate genes associated with these traits remain unknown. In this study, we used 5.6 million imputed DNA sequence variants (single nucleotide polymorphisms, SNPs) for genome-wide association studies (GWAS) of 18 fertility and reproduction traits in Holstein cattle. Aiming to identify pleiotropic variants and increase detection power, multiple-trait analyses were performed using a method to efficiently combine the estimated SNP effects of single-trait GWAS based on a chi-square statistic. Results There were 87, 72, and 84 significant SNPs identified for heifer, cow, and sire traits, respectively, which showed a wide and distinct distribution across the genome, suggesting that they have relatively distinct polygenic nature. The biological functions of immune response and fatty acid metabolism were significantly enriched for the 184 and 124 positional candidate genes identified for heifer and cow traits, respectively. No known biological function was significantly enriched for the 147 positional candidate genes found for sire traits. The most important chromosomes that had three or more significant QTL identified are BTA22 and BTA23 for heifer traits, BTA8 and BTA17 for cow traits, and BTA4, BTA7, BTA17, BTA22, BTA25, and BTA28 for sire traits. Several novel and biologically important positional candidate genes were strongly suggested for heifer (SOD2, WTAP, DLEC1, PFKFB4, TRIM27, HECW1, DNAH17, and ADAM3A), cow (ANXA1, PCSK5, SPESP1, and JMJD1C), and sire (ELMO1, CFAP70, SOX30, DGCR8, SEPTIN14, PAPOLB, JMJD1C, and NELL2) traits. Conclusions These findings contribute to better understand the underlying biological mechanisms of fertility and reproduction traits measured in heifers, cows, and sires, which may contribute to improve genomic evaluation for these traits in dairy cattle. Supplementary Information The online version contains supplementary material available at 10.1186/s12864-022-08555-z.
Collapse
Affiliation(s)
- Shi-Yi Chen
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA.,Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Ana L P Melo
- Department of Reproduction and Animal Evaluation, Rural Federal University of Rio de Janeiro, Seropédica, RJ, 23897-000, Brazil
| | - Hinayah R Oliveira
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA.,Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
| | - Victor B Pedrosa
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA.,Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa, PR, 84030-900, Brazil
| | - Andre C Araujo
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA
| | - Melkaye G Melka
- Department of Animal and Food Science, University of Wisconsin River Falls, River Falls, WI, 54022, USA
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, 270 S. Russell Street, West Lafayette, IN, 47907-2041, USA. .,Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
| |
Collapse
|
12
|
Genome-Wide Genomic and Functional Association Study for Workability and Calving Traits in Holstein Cattle. Animals (Basel) 2022; 12:ani12091127. [PMID: 35565554 PMCID: PMC9102336 DOI: 10.3390/ani12091127] [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: 02/11/2022] [Revised: 04/25/2022] [Accepted: 04/26/2022] [Indexed: 02/04/2023] Open
Abstract
The goal of our study was to identify the SNPs, metabolic pathways (KEGG), and gene ontology (GO) terms significantly associated with calving and workability traits in dairy cattle. We analysed direct (DCE) and maternal (MCE) calving ease, direct (DSB) and maternal (MSB) stillbirth, milking speed (MSP), and temperament (TEM) based on a Holstein-Friesian dairy cattle population consisting of 35,203 individuals. The number of animals, depending on the trait, ranged from 22,301 bulls for TEM to 30,603 for DCE. We estimated the SNP effects (based on 46,216 polymorphisms from Illumina BovineSNP50 BeadChip Version 2) using a multi-SNP mixed model. The SNP positions were mapped to genes and the GO terms/KEGG pathways of the corresponding genes were assigned. The estimation of the GO term/KEGG pathway effects was based on a mixed model using the SNP effects as dependent variables. The number of significant SNPs comprised 59 for DCE, 25 for DSB and MSP, 17 for MCE and MSB, and 7 for TEM. Significant KEGG pathways were found for MSB (2), TEM (2), and MSP (1) and 11 GO terms were significant for MSP, 10 for DCE, 8 for DSB and TEM, 5 for MCE, and 3 for MSB. From the perspective of a better understanding of the genomic background of the phenotypes, traits with low heritabilities suggest that the focus should be moved from single genes to the metabolic pathways or gene ontologies significant for the phenotype.
Collapse
|
13
|
Araujo AC, Carneiro PLS, Alvarenga AB, Oliveira HR, Miller SP, Retallick K, Brito LF. Haplotype-Based Single-Step GWAS for Yearling Temperament in American Angus Cattle. Genes (Basel) 2021; 13:17. [PMID: 35052358 PMCID: PMC8775055 DOI: 10.3390/genes13010017] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Revised: 12/14/2021] [Accepted: 12/18/2021] [Indexed: 01/23/2023] Open
Abstract
Behavior is a complex trait and, therefore, understanding its genetic architecture is paramount for the development of effective breeding strategies. The objective of this study was to perform traditional and weighted single-step genome-wide association studies (ssGWAS and WssGWAS, respectively) for yearling temperament (YT) in North American Angus cattle using haplotypes. Approximately 266 K YT records and 70 K animals genotyped using a 50 K single nucleotide polymorphisms (SNP) panel were used. Linkage disequilibrium thresholds (LD) of 0.15, 0.50, and 0.80 were used to create the haploblocks, and the inclusion of non-LD-clustered SNPs (NCSNP) with the haplotypes in the genomic models was also evaluated. WssGWAS did not perform better than ssGWAS. Cattle YT was found to be a highly polygenic trait, with genes and quantitative trait loci (QTL) broadly distributed across the whole genome. Association studies using LD-based haplotypes should include NCSNPs and different LD thresholds to increase the likelihood of finding the relevant genomic regions affecting the trait of interest. The main candidate genes identified, i.e., ATXN10, ADAM10, VAX2, ATP6V1B1, CRISPLD1, CAPRIN1, FA2H, SPEF2, PLXNA1, and CACNA2D3, are involved in important biological processes and metabolic pathways related to behavioral traits, social interactions, and aggressiveness in cattle. Future studies should further investigate the role of these candidate genes.
Collapse
Affiliation(s)
- Andre C. Araujo
- Graduate Program in Animal Sciences, State University of Southwestern Bahia, Itapetinga 45700-000, Brazil;
- Department of Animal Science, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.)
| | - Paulo L. S. Carneiro
- Department of Biology, State University of Southwest Bahia, Jequié 45205-490, Brazil;
| | - Amanda B. Alvarenga
- Department of Animal Science, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.)
| | - Hinayah R. Oliveira
- Department of Animal Science, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.)
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G2W1, Canada
| | - Stephen P. Miller
- American Angus Association, Angus Genetics Inc., 3201 Frederick Ave, St. Joseph, MO 64506, USA; (S.P.M.); (K.R.)
| | - Kelli Retallick
- American Angus Association, Angus Genetics Inc., 3201 Frederick Ave, St. Joseph, MO 64506, USA; (S.P.M.); (K.R.)
| | - Luiz F. Brito
- Department of Animal Science, Purdue University, West Lafayette, IN 47907, USA; (A.B.A.); (H.R.O.)
| |
Collapse
|
14
|
Pedrosa VB, Schenkel FS, Chen SY, Oliveira HR, Casey TM, Melka MG, Brito LF. Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data. Genes (Basel) 2021; 12:genes12111830. [PMID: 34828436 PMCID: PMC8624223 DOI: 10.3390/genes12111830] [Citation(s) in RCA: 37] [Impact Index Per Article: 12.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/13/2021] [Accepted: 11/17/2021] [Indexed: 12/22/2022] Open
Abstract
Lactation persistency and milk production are among the most economically important traits in the dairy industry. In this study, we explored the association of over 6.1 million imputed whole-genome sequence variants with lactation persistency (LP), milk yield (MILK), fat yield (FAT), fat percentage (FAT%), protein yield (PROT), and protein percentage (PROT%) in North American Holstein cattle. We identified 49, 3991, 2607, 4459, 805, and 5519 SNPs significantly associated with LP, MILK, FAT, FAT%, PROT, and PROT%, respectively. Various known associations were confirmed while several novel candidate genes were also revealed, including ARHGAP35, NPAS1, TMEM160, ZC3H4, SAE1, ZMIZ1, PPIF, LDB2, ABI3, SERPINB6, and SERPINB9 for LP; NIM1K, ZNF131, GABRG1, GABRA2, DCHS1, and SPIDR for MILK; NR6A1, OLFML2A, EXT2, POLD1, GOT1, and ETV6 for FAT; DPP6, LRRC26, and the KCN gene family for FAT%; CDC14A, RTCA, HSTN, and ODAM for PROT; and HERC3, HERC5, LALBA, CCL28, and NEURL1 for PROT%. Most of these genes are involved in relevant gene ontology (GO) terms such as fatty acid homeostasis, transporter regulator activity, response to progesterone and estradiol, response to steroid hormones, and lactation. The significant genomic regions found contribute to a better understanding of the molecular mechanisms related to LP and milk production in North American Holstein cattle.
Collapse
Affiliation(s)
- Victor B. Pedrosa
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa 84030-900, Brazil
| | - Flavio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G2W1, Canada;
| | - Shi-Yi Chen
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G2W1, Canada;
| | - Theresa M. Casey
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
| | - Melkaye G. Melka
- Department of Animal and Food Science, University of Wisconsin River Falls, River Falls, WI 54022, USA;
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
- Correspondence:
| |
Collapse
|
15
|
Falchi L, Gaspa G, Cesarani A, Correddu F, Degano L, Vicario D, Lourenco D, Macciotta NPP. Investigation of β-hydroxybutyrate in early lactation of Simmental cows: Genetic parameters and genomic predictions. J Anim Breed Genet 2021; 138:708-718. [PMID: 34180560 PMCID: PMC8518359 DOI: 10.1111/jbg.12637] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/21/2021] [Accepted: 05/28/2021] [Indexed: 11/28/2022]
Abstract
Genomic information allows for a more accurate calculation of relationships among animals than the pedigree information, leading to an increase in accuracy of breeding values. Here, we used pedigree-based and single-step genomic approaches to estimate variance components and breeding values for β-hydroxybutyrate milk content (BHB). Additionally, we performed a genome-wide association study (GWAS) to depict its genetic architecture. BHB concentrations within the first 90 days of lactation, estimated from milk medium infrared spectra, were available for 30,461 cows (70,984 records). Genotypes at 42,152 loci were available for 9,123 animals. Low heritabilities were found for BHB using pedigree-based (0.09 ± 0.01) and genomic (0.10 ± 0.01) approaches. Genetic correlation between BHB and milk traits ranged from -0.27 ± 0.06 (BHB and protein percentage) to 0.13 ± 0.07 (BHB and fat-to-protein ratio) using pedigree and from -0.26 ± 0.05 (BHB and protein percentage) to 0.13 ± 0.06 (BHB and fat-to-protein ratio) using genomics. Breeding values were validated for 344 genotyped cows using linear regression method. The genomic EBV (GEBV) had greater accuracy (0.51 vs. 0.45) and regression coefficient (0.98 vs. 0.95) compared to EBV. The correlation between two subsequent evaluations, without and with phenotypes for validation cows, was 0.85 for GEBV and 0.82 for EBV. Predictive ability (correlation between (G)EBV and adjusted phenotypes) was greater when genomic information was used (0.38) than in the pedigree-based approach (0.31). Validation statistics in the pairwise two-trait models (milk yield, fat and protein percentage, urea, fat/protein ratio, lactose and logarithmic transformation of somatic cells count) were very similar to the ones highlighted for the single-trait model. The GWAS allowed discovering four significant markers located on BTA20 (57.5-58.2 Mb), where the ANKH gene is mapped. This gene has been associated with lactose, alpha-lactalbumin and BHB. Results of this study confirmed the usefulness of genomic information to provide more accurate variance components and breeding values, and important insights about the genomic determination of BHB milk content.
Collapse
Affiliation(s)
- Laura Falchi
- Department of Agricultural SciencesUniversity of SassariSassariItaly
| | - Giustino Gaspa
- Department of Agricultural, Forest and Food SciencesUniversity of TorinoTorinoItaly
| | - Alberto Cesarani
- Department of Agricultural SciencesUniversity of SassariSassariItaly
- Department of Animal and Dairy ScienceUniversity of GeorgiaAthensGAUSA
| | - Fabio Correddu
- Department of Agricultural SciencesUniversity of SassariSassariItaly
| | - Lorenzo Degano
- Associazione Nazionale Allevatori Pezzata Rossa (ANAPRI)UdineItaly
| | - Daniele Vicario
- Associazione Nazionale Allevatori Pezzata Rossa (ANAPRI)UdineItaly
| | - Daniela Lourenco
- Department of Animal and Dairy ScienceUniversity of GeorgiaAthensGAUSA
| | | |
Collapse
|
16
|
Hollifield MK, Lourenco D, Bermann M, Howard JT, Misztal I. Determining the stability of accuracy of genomic estimated breeding values in future generations in commercial pig populations. J Anim Sci 2021; 99:6176311. [PMID: 33733277 PMCID: PMC8051850 DOI: 10.1093/jas/skab085] [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: 11/30/2020] [Accepted: 03/15/2021] [Indexed: 01/08/2023] Open
Abstract
Genomic information has a limited dimensionality (number of independent chromosome segments [Me]) related to the effective population size. Under the additive model, the persistence of genomic accuracies over generations should be high when the nongenomic information (pedigree and phenotypes) is equivalent to Me animals with high accuracy. The objective of this study was to evaluate the decay in accuracy over time and to compare the magnitude of decay with varying quantities of data and with traits of low and moderate heritability. The dataset included 161,897 phenotypic records for a growth trait (GT) and 27,669 phenotypic records for a fitness trait (FT) related to prolificacy in a population with dimensionality around 5,000. The pedigree included 404,979 animals from 2008 to 2020, of which 55,118 were genotyped. Two single-trait models were used with all ancestral data and sliding subsets of 3-, 2-, and 1-generation intervals. Single-step genomic best linear unbiased prediction (ssGBLUP) was used to compute genomic estimated breeding values (GEBV). Estimated accuracies were calculated by the linear regression (LR) method. The validation population consisted of single generations succeeding the training population and continued forward for all generations available. The average accuracy for the first generation after training with all ancestral data was 0.69 and 0.46 for GT and FT, respectively. The average decay in accuracy from the first generation after training to generation 9 was −0.13 and −0.19 for GT and FT, respectively. The persistence of accuracy improves with more data. Old data have a limited impact on the predictions for young animals for a trait with a large amount of information but a bigger impact for a trait with less information.
Collapse
Affiliation(s)
| | - Daniela Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Matias Bermann
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | | | - Ignacy Misztal
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| |
Collapse
|
17
|
Schmidtmann C, Schönherz A, Guldbrandtsen B, Marjanovic J, Calus M, Hinrichs D, Thaller G. Assessing the genetic background and genomic relatedness of red cattle populations originating from Northern Europe. Genet Sel Evol 2021; 53:23. [PMID: 33676402 PMCID: PMC7936461 DOI: 10.1186/s12711-021-00613-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/20/2020] [Accepted: 02/08/2021] [Indexed: 12/20/2022] Open
Abstract
Background Local cattle breeds need special attention, as they are valuable reservoirs of genetic diversity. Appropriate breeding decisions and adequate genomic management of numerically smaller populations are required for their conservation. At this point, the analysis of dense genome-wide marker arrays provides encompassing insights into the genomic constitution of livestock populations. We have analyzed the genetic characterization of ten cattle breeds originating from Germany, The Netherlands and Denmark belonging to the group of red dairy breeds in Northern Europe. The results are intended to provide initial evidence on whether joint genomic breeding strategies of these populations will be successful. Results Traditional Danish Red and Groningen White-Headed were the most genetically differentiated breeds and their populations showed the highest levels of inbreeding. In contrast, close genetic relationships and shared ancestry were observed for the populations of German Red and White Dual-Purpose, Dutch Meuse-Rhine-Yssel, and Dutch Deep Red breeds, reflecting their common histories. A considerable amount of gene flow from Red Holstein to German Angler and to German Red and White Dual-Purpose was revealed, which is consistent with frequent crossbreeding to improve productivity of these local breeds. In Red Holstein, marked genomic signatures of selection were reported on chromosome 18, suggesting directed selection for important breeding goal traits. Furthermore, tests for signatures of selection between Red Holstein, Red and White Dual-Purpose, and Meuse-Rhine-Yssel uncovered signals for all investigated pairs of populations. The corresponding genomic regions, which were putatively under different selection pressures, harboured various genes which are associated with traits such as milk and beef production, mastitis and female fertility. Conclusions This study provides comprehensive knowledge on the genetic constitution and genomic connectedness of divergent red cattle populations in Northern Europe. The results will help to design and optimize breeding strategies. A joint genomic evaluation including some of the breeds studied here seems feasible.
Collapse
Affiliation(s)
- Christin Schmidtmann
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, 24098, Kiel, Germany.
| | - Anna Schönherz
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark.,Department of Animal Science, Aarhus University, 8830, Tjele, Denmark
| | - Bernt Guldbrandtsen
- Department of Molecular Biology and Genetics, Center for Quantitative Genetics and Genomics, Aarhus University, 8830, Tjele, Denmark.,Department of Animal Sciences, Department of Animal Breeding and Husbandry, University of Bonn, 53115, Bonn, Germany
| | - Jovana Marjanovic
- Animal Breeding and Genomics, Wageningen University and Research, 6700AH, Wageningen, The Netherlands
| | - Mario Calus
- Animal Breeding and Genomics, Wageningen University and Research, 6700AH, Wageningen, The Netherlands
| | - Dirk Hinrichs
- Department of Animal Breeding, University of Kassel, 37213, Witzenhausen, Germany
| | - Georg Thaller
- Institute of Animal Breeding and Husbandry, Christian-Albrechts-University Kiel, 24098, Kiel, Germany
| |
Collapse
|
18
|
Lázaro SF, Tonhati H, Oliveira HR, Silva AA, Nascimento AV, Santos DJA, Stefani G, Brito LF. Genomic studies of milk-related traits in water buffalo (Bubalus bubalis) based on single-step genomic best linear unbiased prediction and random regression models. J Dairy Sci 2021; 104:5768-5793. [PMID: 33685677 DOI: 10.3168/jds.2020-19534] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/27/2020] [Accepted: 01/02/2021] [Indexed: 01/14/2023]
Abstract
Genomic selection has been widely implemented in many livestock breeding programs, but it remains incipient in buffalo. Therefore, this study aimed to (1) estimate variance components incorporating genomic information in Murrah buffalo; (2) evaluate the performance of genomic prediction for milk-related traits using single- and multitrait random regression models (RRM) and the single-step genomic best linear unbiased prediction approach; and (3) estimate longitudinal SNP effects and candidate genes potentially associated with time-dependent variation in milk, fat, and protein yields, as well as somatic cell score (SCS) in multiple parities. The data used to estimate the genetic parameters consisted of a total of 323,140 test-day records. The average daily heritability estimates were moderate (0.35 ± 0.02 for milk yield, 0.22 ± 0.03 for fat yield, 0.42 ± 0.03 for protein yield, and 0.16 ± 0.03 for SCS). The highest heritability estimates, considering all traits studied, were observed between 20 and 280 d in milk (DIM). The genetic correlation estimates at different DIM among the evaluated traits ranged from -0.10 (156 to 185 DIM for SCS) to 0.61 (36 to 65 DIM for fat yield). In general, direct selection for any of the traits evaluated is expected to result in indirect genetic gains for milk yield, fat yield, and protein yield but also increase SCS at certain lactation stages, which is undesirable. The predicted RRM coefficients were used to derive the genomic estimated breeding values (GEBV) for each time point (from 5 to 305 DIM). In general, the tuning parameters evaluated when constructing the hybrid genomic relationship matrices had a small effect on the GEBV accuracy and a greater effect on the bias estimates. The SNP solutions were back-solved from the GEBV predicted from the Legendre random regression coefficients, which were then used to estimate the longitudinal SNP effects (from 5 to 305 DIM). The daily SNP effect for 3 different lactation stages were performed considering 3 different lactation stages for each trait and parity: from 5 to 70, from 71 to 150, and from 151 to 305 DIM. Important genomic regions related to the analyzed traits and parities that explain more than 0.50% of the total additive genetic variance were selected for further analyses of candidate genes. In general, similar potential candidate genes were found between traits, but our results suggest evidence of differential sets of candidate genes underlying the phenotypic expression of the traits across parities. These results contribute to a better understanding of the genetic architecture of milk production traits in dairy buffalo and reinforce the relevance of incorporating genomic information to genetically evaluate longitudinal traits in dairy buffalo. Furthermore, the candidate genes identified can be used as target genes in future functional genomics studies.
Collapse
Affiliation(s)
- Sirlene F Lázaro
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907; Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Humberto Tonhati
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Hinayah R Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907; Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, N1G 2W1, ON, Canada
| | - Alessandra A Silva
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - André V Nascimento
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Daniel J A Santos
- Department of Animal and Avian Science, University of Maryland, College Park 20742
| | - Gabriela Stefani
- Department of Animal Science, College of Agricultural and Veterinary Sciences, São Paulo State University (UNESP), Jaboticabal, 14884-900, SP, Brazil
| | - Luiz F Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907.
| |
Collapse
|
19
|
Cesarani A, Garcia A, Hidalgo J, Degano L, Vicario D, Macciotta NPP, Lourenco D. Genomic information allows for more accurate breeding values for milkability in dual-purpose Italian Simmental cattle. J Dairy Sci 2021; 104:5719-5727. [PMID: 33612221 DOI: 10.3168/jds.2020-19838] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2020] [Accepted: 12/14/2020] [Indexed: 02/01/2023]
Abstract
Milkability is a trait related to the milking efficiency of an animal, and it is a component of the herd profitability. Due to its economic importance, milkability is currently included in the selection index of the Italian Simmental cattle breed with a weight of 7.5%. This lowly heritable trait is measured on a subjective scale from 1 to 3 (1 = slow, 3 = fast), and genetic evaluations are performed by pedigree-based BLUP. Genomic information is now available for some animals in the Italian Simmental population, and its inclusion in the genetic evaluation system could increase accuracy of breeding values and genetic progress for milkability. The aim of this study was to test the feasibility and advantages of having a genomic evaluation for this trait in the Italian Simmental population. Phenotypes were available for 131,308 cows. A total of 9,526 animals had genotypes for 42,152 loci; among the genotyped animals, 2,455 were cows with phenotypes, and the other were their relatives. The youngest cows with both phenotypes and genotypes (n = 900) were identified as selection candidates. Variance components and heritability were estimated using pedigree information, whereas genetic and genomic evaluations were carried out using BLUP and single-step genomic BLUP (ssGBLUP), respectively. In addition, a weighted ssGBLUP was assessed using genomic regions from a genome-wide association study. Evaluation models were validated using theoretical and realized accuracies. The estimated heritability for milkability was 0.12 ± 0.01. The mean theoretical accuracies for selection candidates were 0.43 ± 0.08 (BLUP) and 0.53 ± 0.06 (ssGBLUP). The mean realized accuracies based on linear regression statistics were 0.29 (BLUP) and 0.40 (ssGBLUP). No genomic regions were significantly associated with milkability, thus no improvements in accuracy were observed when using weighted ssGBLUP. Results indicated that genomic information could improve the accuracy of breeding values and increase genetic progress for milkability in Italian Simmental.
Collapse
Affiliation(s)
- A Cesarani
- Department of Animal and Dairy Science, University of Georgia, Athens, 30602.
| | - A Garcia
- Department of Animal and Dairy Science, University of Georgia, Athens, 30602
| | - J Hidalgo
- Department of Animal and Dairy Science, University of Georgia, Athens, 30602
| | - L Degano
- Associazione Nazionale Allevatori Pezzata Rossa Italiana (ANAPRI), 33100 Udine, Italy
| | - D Vicario
- Associazione Nazionale Allevatori Pezzata Rossa Italiana (ANAPRI), 33100 Udine, Italy
| | - N P P Macciotta
- Department of Agricultural Sciences, University of Sassari, 07100 Sassari, Italy
| | - D Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, 30602
| |
Collapse
|