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Bitaraf Sani M, Zare Harofte J, Banabazi MH, Esmaeilkhanian S, Shafei Naderi A, Salim N, Teimoori A, Bitaraf A, Zadehrahmani M, Burger PA, Landi V, Silawi M, Taghipour Sheshdeh A, Faghihi MA. Genomic prediction for growth using a low-density SNP panel in dromedary camels. Sci Rep 2021; 11:7675. [PMID: 33828208 PMCID: PMC8027435 DOI: 10.1038/s41598-021-87296-7] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2020] [Accepted: 03/26/2021] [Indexed: 11/29/2022] Open
Abstract
For thousands of years, camels have produced meat, milk, and fiber in harsh desert conditions. For a sustainable development to provide protein resources from desert areas, it is necessary to pay attention to genetic improvement in camel breeding. By using genotyping-by-sequencing (GBS) method we produced over 14,500 genome wide markers to conduct a genome- wide association study (GWAS) for investigating the birth weight, daily gain, and body weight of 96 dromedaries in the Iranian central desert. A total of 99 SNPs were associated with birth weight, daily gain, and body weight (p-value < 0.002). Genomic breeding values (GEBVs) were estimated with the BGLR package using (i) all 14,522 SNPs and (ii) the 99 SNPs by GWAS. Twenty-eight SNPs were associated with birth weight, daily gain, and body weight (p-value < 0.001). Annotation of the genomic region (s) within ± 100 kb of the associated SNPs facilitated prediction of 36 candidate genes. The accuracy of GEBVs was more than 0.65 based on all 14,522 SNPs, but the regression coefficients for birth weight, daily gain, and body weight were 0.39, 0.20, and 0.23, respectively. Because of low sample size, the GEBVs were predicted using the associated SNPs from GWAS. The accuracy of GEBVs based on the 99 associated SNPs was 0.62, 0.82, and 0.57 for birth weight, daily gain, and body weight. This report is the first GWAS using GBS on dromedary camels and identifies markers associated with growth traits that could help to plan breeding program to genetic improvement. Further researches using larger sample size and collaboration of the camel farmers and more profound understanding will permit verification of the associated SNPs identified in this project. The preliminary results of study show that genomic selection could be the appropriate way to genetic improvement of body weight in dromedary camels, which is challenging due to a long generation interval, seasonal reproduction, and lack of records and pedigrees.
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Affiliation(s)
- Morteza Bitaraf Sani
- Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), 8915813155, Yazd, Iran.
| | - Javad Zare Harofte
- Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), 8915813155, Yazd, Iran
| | - Mohammad Hossein Banabazi
- Department of Biotechnology, Animal Science Research Institute of IRAN (ASRI), Agricultural Research, Education & Extension Organization (AREEO), 3146618361, Karaj, Iran
| | - Saeid Esmaeilkhanian
- Department of Biotechnology, Animal Science Research Institute of IRAN (ASRI), Agricultural Research, Education and Extension Organization (AREEO), 3146618361, Karaj, Iran
| | - Ali Shafei Naderi
- Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), 8915813155, Yazd, Iran
| | - Nader Salim
- Organization of Agriculture - Jahad -Yazd, Ministry of Agriculture-Jahad, 8916713449, Yazd, Iran
| | - Abbas Teimoori
- Organization of Agriculture - Jahad -Yazd, Ministry of Agriculture-Jahad, 8916713449, Yazd, Iran
| | - Ahmad Bitaraf
- Animal Science Research Department, Yazd Agricultural and Natural Resources Research and Education Center, Agricultural Research, Education & Extension Organization (AREEO), 8915813155, Yazd, Iran
| | | | - Pamela Anna Burger
- Research Institute of Wildlife Ecology, Vetmeduni Vienna, 1160, Vienna, Austria
| | - Vincenzo Landi
- Departement of Veterinary Medicine, Università Di Bari "Aldo Moro", Bari, Italy
| | - Mohammad Silawi
- Persian BayanGene Research and Training Center, 7134767617, Shiraz, Iran
| | | | - Mohammad Ali Faghihi
- Persian BayanGene Research and Training Center, 7134767617, Shiraz, Iran.,Center for Therapeutic Innovation and Department of Psychiatry and Behavioral Sciences, University of Miami, Miami, FL, 33136, USA
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Parameters and genetic associations of visual scores and weights in Hereford and Braford breeds. Livest Sci 2020. [DOI: 10.1016/j.livsci.2020.104216] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Ge F, Jia C, Bao P, Wu X, Liang C, Yan P. Accuracies of Genomic Prediction for Growth Traits at Weaning and Yearling Ages in Yak. Animals (Basel) 2020; 10:E1793. [PMID: 33023134 PMCID: PMC7650705 DOI: 10.3390/ani10101793] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/06/2020] [Revised: 09/26/2020] [Accepted: 09/28/2020] [Indexed: 12/20/2022] Open
Abstract
Genomic selection is a promising breeding strategy that has been used in considerable numbers of breeding projects due to its highly accurate results. Yak are rare mammals that are remarkable because of their ability to survive in the extreme and harsh conditions predominantly at the so-called "roof of the world"-the Qinghai-Tibetan Plateau. In the current study, we conducted an exploration of the feasibility of genomic evaluation and compared the predictive accuracy of early growth traits with five different approaches. In total, four growth traits were measured in 354 yaks, including body weight, withers height, body length, and chest girth in two early stages of development (weaning and yearling). Genotyping was implemented using the Illumina BovineHD BeadChip. The predictive accuracy was calculated through five-fold cross-validation in five classical statistical methods including genomic best linear unbiased prediction (GBLUP) and four Bayesian methods. Body weights at 30 months in the same yak population were also measured to evaluate the prediction at 6 months. The results indicated that the predictive accuracy for the early growth traits of yak ranged from 0.147 to 0.391. Similar performance was found for the GBLUP and Bayesian methods for most growth traits. Among the Bayesian methods, Bayes B outperformed Bayes A in the majority of traits. The average correlation coefficient between the prediction at 6 months using different methods and observations at 30 months was 0.4. These results indicate that genomic prediction is feasible for early growth traits in yak. Considering that genomic selection is necessary in yak breeding projects, the present study provides promising reference for future applications.
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Affiliation(s)
| | | | | | | | - Chunnian Liang
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (F.G.); (C.J.); (P.B.); (X.W.)
| | - Ping Yan
- Key Laboratory of Yak Breeding Engineering of Gansu Province, Lanzhou Institute of Husbandry and Pharmaceutical Sciences, Chinese Academy of Agricultural Sciences, Lanzhou 730050, China; (F.G.); (C.J.); (P.B.); (X.W.)
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Takeda M, Uemoto Y, Satoh M. Effect of genotyped bulls with different numbers of phenotyped progenies on quantitative trait loci detection and genomic evaluation in a simulated cattle population. Anim Sci J 2020; 91:e13432. [PMID: 32779330 PMCID: PMC7507195 DOI: 10.1111/asj.13432] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Revised: 06/18/2020] [Accepted: 07/01/2020] [Indexed: 02/02/2023]
Abstract
The objective of this study was to assess the effect of genotyped bulls with different numbers of phenotyped progenies on quantitative trait loci (QTL) detection and genomic evaluation using a simulated cattle population. Twelve generations (G1–G12) were simulated from the base generation (G0). The recent population had different effective population sizes, heritability, and number of QTL. G0–G4 were used for pedigree information. A total of 300 genotyped bulls from G5–G10 were randomly selected. Their progenies were generated in G6–G11 with different numbers of progeny per bull. Scenarios were considered according to the number of progenies and whether the genotypes were possessed by the bulls or the progenies. A genome‐wide association study and genomic evaluation were performed with a single‐step genomic best linear unbiased prediction method to calculate the power of QTL detection and the genomic estimated breeding value (GEBV). We found that genotyped bulls could be available for QTL detection depending on conditions. Additionally, using a reference population, including genotyped bulls, which had more progeny phenotypes, enabled a more accurate prediction of GEBV. However, it is desirable to have more than 4,500 individuals consisting of both genotypes and phenotypes for practical genomic evaluation.
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Affiliation(s)
- Masayuki Takeda
- National Livestock Breeding Center, Nishigo, Japan.,Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Yoshinobu Uemoto
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
| | - Masahiro Satoh
- Graduate School of Agricultural Science, Tohoku University, Sendai, Japan
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Alvarenga AB, Veroneze R, Oliveira HR, Marques DBD, Lopes PS, Silva FF, Brito LF. Comparing Alternative Single-Step GBLUP Approaches and Training Population Designs for Genomic Evaluation of Crossbred Animals. Front Genet 2020; 11:263. [PMID: 32328083 PMCID: PMC7162606 DOI: 10.3389/fgene.2020.00263] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/27/2019] [Accepted: 03/05/2020] [Indexed: 02/06/2023] Open
Abstract
As crossbreeding is extensively used in some livestock species, we aimed to evaluate the performance of single-step GBLUP (ssGBLUP) and weighted ssGBLUP (WssGBLUP) methods to predict Genomic Estimated Breeding Values (GEBVs) of crossbred animals. Different training population scenarios were evaluated: (SC1) ssGBLUP based on a single-trait model considering purebred and crossbred animals in a joint training population; (SC2) ssGBLUP based on a multiple-trait model to enable considering phenotypes recorded in purebred and crossbred training animals as different traits; (SC3) WssGBLUP based on a single-trait model considering purebred and crossbred animals jointly in the training population (both populations were used for SNP weights' estimation); (SC4) WssGBLUP based on a single-trait model considering only purebred animals in the training population (crossbred population only used for SNP weights' estimation); (SC5) WssGBLUP based on a single-trait model and the training population characterized by purebred animals (purebred population used for SNP weights' estimation). A complex trait was simulated assuming alternative genetic architectures. Different scaling factors to blend the inverse of the genomic (G -1) and pedigree (A 22 - 1 ) relationship matrices were also tested. The predictive performance of each scenario was evaluated based on the validation accuracy and regression coefficient. The genetic correlations across simulated populations in the different scenarios ranged from moderate to high (0.71-0.99). The scenario mimicking a completely polygenic trait (h Q T L 2 = 0) yielded the lowest validation accuracy (0.12; for SC3 and SC4). The simulated scenarios assuming 4,500 QTLs affecting the trait andh Q T L 2 = h 2 resulted in the greatest GEBV accuracies (0.47; for SC1 and SC2). The regression coefficients ranged from 0.28 (for SC3 assuming polygenic effect) to 1.27 (for SC2 considering 4,500 QTLs). In general, SC3 and SC5 resulted in inflated GEBVs, whereas other scenarios yielded deflated GEBVs. The scaling factors used to combine G -1 andA 22 - 1 had a small influence on the validation accuracies, but a greater effect on the regression coefficients. Due to the complexity of multiple-trait models and WssGBLUP analyses, and a similar predictive performance across the methods evaluated, SC1 is recommended for genomic evaluation in crossbred populations with similar genetic structures [moderate-to-high (0.71-0.99) genetic correlations between purebred and crossbred populations].
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Affiliation(s)
- Amanda B. Alvarenga
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Department of Animal Science, Federal University of Viçosa, Viçosa, Brazil
| | - Renata Veroneze
- Department of Animal Science, Federal University of Viçosa, Viçosa, Brazil
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
- Department of Animal Biosciences, Centre for Genetic Improvement of Livestock, University of Guelph, Guelph, ON, Canada
| | | | - Paulo S. Lopes
- Department of Animal Science, Federal University of Viçosa, Viçosa, Brazil
| | - Fabyano F. Silva
- Department of Animal Science, Federal University of Viçosa, Viçosa, Brazil
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN, United States
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Piccoli ML, Brito LF, Braccini J, Oliveira HR, Cardoso FF, Roso VM, Sargolzaei M, Schenkel FS. Comparison of genomic prediction methods for evaluation of adaptation and productive efficiency traits in Braford and Hereford cattle. Livest Sci 2020. [DOI: 10.1016/j.livsci.2019.103864] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/29/2022]
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Moré DD, Cardoso FF, Mudadu MA, Malagó-Jr W, Gulias-Gomes CC, Sollero BP, Ibelli AMG, Coutinho LL, Regitano LCA. Network analysis uncovers putative genes affecting resistance to tick infestation in Braford cattle skin. BMC Genomics 2019; 20:998. [PMID: 31856720 PMCID: PMC6923859 DOI: 10.1186/s12864-019-6360-3] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2018] [Accepted: 12/01/2019] [Indexed: 12/13/2022] Open
Abstract
Background Genetic resistance in cattle is considered a suitable way to control tick burden and its consequent losses for livestock production. Exploring tick-resistant (R) and tick-susceptible (S) hosts, we investigated the genetic mechanisms underlying the variation of Braford resistance to tick infestation. Skin biopsies from four-times-artificially infested R (n = 20) and S (n = 19) hosts, obtained before the first and 24 h after the fourth tick infestation were submitted to RNA-Sequencing. Differential gene expression, functional enrichment, and network analysis were performed to identify genetic pathways and transcription factors (TFs) affecting host resistance. Results Intergroup comparisons of hosts before (Rpre vs. Spre) and after (Rpost vs. Spost) tick infestation found 51 differentially expressed genes (DEGs), of which almost all presented high variation (TopDEGs), and 38 were redundant genes. Gene expression was consistently different between R and S hosts, suggesting the existence of specific anti-tick mechanisms. In the intragroup comparisons, Rpost vs. Rpre and Spost vs. Spre, we found more than two thousand DEGs in response to tick infestation in both resistance groups. Redundant and non-redundant TopDEGs with potential anti-tick functions suggested a role in the development of different levels of resistance within the same breed. Leukocyte chemotaxis was over-represented in both hosts, whereas skin degradation and remodeling were only found in TopDEGs from R hosts. Also, these genes indicated the participation of cytokines, such as IL6 and IL22, and the activation of Wingless (WNT)-signaling pathway. A central gene of this pathway, WNT7A, was consistently modulated when hosts were compared. Moreover, the findings based on a genome-wide association study (GWAS) corroborate the prediction of the WNT-signaling pathway as a candidate mechanism of resistance. The regulation of immune response was the most relevant pathway predicted for S hosts. Members of Ap1 and NF-kB families were the most relevant TFs predicted for R and S, respectively. Conclusion This work provides indications of genetic mechanisms presented by Braford cattle with different levels of resistance in response to tick infestation, contributing to the search of candidate genes for tick resistance in bovine.
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Affiliation(s)
| | - Fernando F Cardoso
- EMBRAPA Pecuária Sul, Bagé, Rio Grande do Sul, Brazil.,Federal University of Pelotas, Capão do Leão, Rio Grande do Sul, Brazil
| | | | | | | | | | | | - Luiz L Coutinho
- Luiz de Queiroz College of Agriculture, University of São Paulo, Piracicaba, São Paulo, Brazil
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Piccoli ML, Brito LF, Braccini J, Brito FV, Cardoso FF, Cobuci JA, Sargolzaei M, Schenkel FS. A comprehensive comparison between single- and two-step GBLUP methods in a simulated beef cattle population. CANADIAN JOURNAL OF ANIMAL SCIENCE 2018. [DOI: 10.1139/cjas-2017-0176] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The statistical methods used in the genetic evaluations are a key component of the process and can be best compared by using simulated data. The latter is especially true in grazing beef cattle production systems, where the number of proven bulls with highly reliable estimated breeding values is limited to allow for a trustworthy validation of genomic predictions. Therefore, we simulated data for 4980 beef cattle aiming to compare single-step genomic best linear unbiased prediction (ssGBLUP), which simultaneously incorporates pedigree, phenotypic, and genomic data into genomic evaluations, and two-step GBLUP (tsGBLUP) procedures and genomic estimated breeding values (GEBVs) blending methods. The greatest increases in GEBV accuracies compared with the parents’ average estimated breeding values (EBVPA) were 0.364 and 0.341 for ssGBLUP and tsGBLUP, respectively. Direct genomic value and GEBV accuracies when using ssGBLUP and tsGBLUP procedures were similar, except for the GEBV accuracies using Hayes’ blending method in tsGBLUP. There was no significant or slight bias in genomic predictions from ssGBLUP or tsGBLUP (using VanRaden’s blending method), indicating that these predictions are on the same scale compared with the true breeding values. Overall, genetic evaluations including genomic information resulted in gains in accuracy >100% compared with the EBVPA. In addition, there were no significant differences between the selected animals (10% males and 50% females) by using ssGBLUP or tsGBLUP.
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Affiliation(s)
- Mario L. Piccoli
- Departamento de Zootecnia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91540-000, Brazil
- GenSys Consultores Associados S/S, Porto Alegre, RS 90460-060, Brazil
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - Luiz F. Brito
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
| | - José Braccini
- Departamento de Zootecnia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91540-000, Brazil
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brasília, DF 71605-001, Brazil
| | - Fernanda V. Brito
- GenSys Consultores Associados S/S, Porto Alegre, RS 90460-060, Brazil
| | - Fernando F. Cardoso
- Conselho Nacional de Desenvolvimento Científico e Tecnológico, Brasília, DF 71605-001, Brazil
- Embrapa Pecuária Sul, Bagé, RS 96401-970, Brazil
| | - Jaime A. Cobuci
- Departamento de Zootecnia, Universidade Federal do Rio Grande do Sul, Porto Alegre, RS 91540-000, Brazil
| | - Mehdi Sargolzaei
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
- The Semex Alliance, Guelph, ON N1H 6J2, Canada
| | - Flávio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G 2W1, Canada
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van Marle-Köster E, Visser C. Genetic Improvement in South African Livestock: Can Genomics Bridge the Gap Between the Developed and Developing Sectors? Front Genet 2018; 9:331. [PMID: 30190725 PMCID: PMC6115519 DOI: 10.3389/fgene.2018.00331] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/09/2018] [Accepted: 07/31/2018] [Indexed: 11/13/2022] Open
Abstract
South Africa (SA) holds a unique position on the African continent with a rich diversity in terms of available livestock resources, vegetation, climatic regions and cultures. The livestock sector has been characterized by a dual system of a highly developed commercial sector using modern technology vs. a developing sector including emerging and smallholder farmers. Emerging farmers typically aim to join the commercial sector, but lag behind with regard to the use of modern genetic technologies, while smallholder farmers use traditional practices aimed at subsistence. Several factors influence potential application of genomics by the livestock industries, which include available research funding, socio-economic constraints and extension services. State funded Beef and Dairy genomic programs have been established with the aim of building reference populations for genomic selection with most of the potential beneficiaries in the well-developed commercial sector. The structure of the beef, dairy and small stock industries is fragmented and the outcomes of selection strategies are not perceived as an advantage by the processing industry or the consumer. The indigenous and local composites represent approximately 40% of the total beef and sheep populations and present valuable genetic resources. Genomic research has mostly provided insight on genetic biodiversity of these resources, with limited attention to novel phenotypes associated with adaptation or disease tolerance. Genetic improvement of livestock through genomic technology needs to address the role of adapted breeds in challenging environments, increasing reproductive and growth efficiency. National animal recording schemes contributed significantly to progress in the developed sector with regard to genetic evaluations and estimated breeding values (EBV) as a selection tool over the past three decades. The challenge remains on moving the focus to novel traits for increasing efficiency and addressing welfare and environmental issues. Genetic research programs are required that will be directed to bridge the gap between the elite breeders and the developing livestock sector. The aim of this review was to provide a perspective on the dichotomy in the South African livestock sector arguing that a realistic approach to the use of genomics in beef, dairy and small stock is required to ensure sustainable long term genetic progress.
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Affiliation(s)
- Esté van Marle-Köster
- Department of Animal and Wildlife Sciences, Faculty of Natural and Agricultural Science, University of Pretoria, Pretoria, South Africa
| | - Carina Visser
- Department of Animal and Wildlife Sciences, Faculty of Natural and Agricultural Science, University of Pretoria, Pretoria, South Africa
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Teixeira B, MacNeil M, da Costa R, Dionello N, Yokoo M, Cardoso F. Genetic parameters and trends for traits of the Hereford and Braford breeds in Brazil. Livest Sci 2018. [DOI: 10.1016/j.livsci.2017.12.008] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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