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Ma X, Ying F, Li Z, Bai L, Wang M, Zhu D, Liu D, Wen J, Zhao G, Liu R. New insights into the genetic loci related to egg weight and age at first egg traits in broiler breeder. Poult Sci 2024; 103:103613. [PMID: 38492250 PMCID: PMC10959720 DOI: 10.1016/j.psj.2024.103613] [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: 12/19/2023] [Revised: 02/29/2024] [Accepted: 02/29/2024] [Indexed: 03/18/2024] Open
Abstract
Egg weight (EW) and age at first egg (AFE) are economically important traits in breeder chicken production. The genetic basis of these traits, however, is far from understood, especially for broiler breeders. In this study, genetic parameter estimation, genome-wide association analysis, meta-analysis, and selective sweep analysis were carried out to identify genetic loci associated with EW and AFE in 6,842 broiler breeders. The study found that the heritability of EW ranged from 0.42 to 0.44, while the heritability of AFE was estimated at 0.33 in the maternal line. Meta-analysis and selective sweep analysis identified two colocalized regions on GGA4 that significantly influenced EW at 32 wk (EW32W) and at 43 wk (EW43W) with both paternal and maternal lines. The genes AR, YIPF6, and STARD8 were located within the significant region (GGA4: 366.86-575.50 kb), potentially affecting EW through the regulation of follicle development, cell proliferation, and lipid transfer etc. The promising genes LCORL and NCAPG were positioned within the significant region (GGA4:75.35-75.42 Mb), potentially influencing EW through pleiotropic effects on growth and development. Additionally, 3 significant regions were associated with AFE on chromosomes GGA7, GGA19, and GGA27. All of these factors affected the AFE by influencing ovarian development. In our study, the genomic information from both paternal and maternal lines was used to identify genetic regions associated with EW and AFE. Two genomic regions and eight genes were identified as the most likely candidates affecting EW and AFE. These findings contribute to a better understanding of the genetic basis of egg production traits in broiler breeders and provide new insights into future technology development.
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Affiliation(s)
- Xiaochun Ma
- State Key Laboratory of Animal Biotech Breeding; State Key Laboratory of Animal Nutrition and Feeding; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Fan Ying
- Foshan Gaoming Xinguang Agricultural and Animal Industrials Corporation, Foshan 528515, China
| | - Zhengda Li
- State Key Laboratory of Animal Biotech Breeding; State Key Laboratory of Animal Nutrition and Feeding; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Lu Bai
- State Key Laboratory of Animal Biotech Breeding; State Key Laboratory of Animal Nutrition and Feeding; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Mengjie Wang
- State Key Laboratory of Animal Biotech Breeding; State Key Laboratory of Animal Nutrition and Feeding; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Dan Zhu
- Foshan Gaoming Xinguang Agricultural and Animal Industrials Corporation, Foshan 528515, China
| | - Dawei Liu
- Foshan Gaoming Xinguang Agricultural and Animal Industrials Corporation, Foshan 528515, China
| | - Jie Wen
- State Key Laboratory of Animal Biotech Breeding; State Key Laboratory of Animal Nutrition and Feeding; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Guiping Zhao
- State Key Laboratory of Animal Biotech Breeding; State Key Laboratory of Animal Nutrition and Feeding; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China
| | - Ranran Liu
- State Key Laboratory of Animal Biotech Breeding; State Key Laboratory of Animal Nutrition and Feeding; Key Laboratory of Animal (Poultry) Genetics Breeding and Reproduction, Ministry of Agriculture; Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing 100193, China.
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Berghof TVL, Bedere N, Peeters K, Poppe M, Visscher J, Mulder HA. The genetics of resilience and its relationships with egg production traits and antibody traits in chickens. Genet Sel Evol 2024; 56:20. [PMID: 38504219 PMCID: PMC10953135 DOI: 10.1186/s12711-024-00888-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2023] [Accepted: 03/06/2024] [Indexed: 03/21/2024] Open
Abstract
BACKGROUND Resilience is the capacity of an animal to be minimally affected by disturbances or to rapidly return to its initial state before exposure to a disturbance. Resilient livestock are desired because of their improved health and increased economic profit. Genetic improvement of resilience may also lead to trade-offs with production traits. Recently, resilience indicators based on longitudinal data have been suggested, but they need further evaluation to determine whether they are indeed predictive of improved resilience, such as disease resilience. This study investigated different resilience indicators based on deviations between expected and observed egg production (EP) by exploring their genetic parameters, their possible trade-offs with production traits, and their relationships with antibody traits in chickens. METHODS Egg production in a nucleus breeding herd environment based on 1-week-, 2-week-, or 3-week-intervals of two purebred chicken lines, a white egg-laying (33,825 chickens) and a brown egg-laying line (34,397 chickens), were used to determine deviations between observed EP and expected average batch EP, and between observed EP and expected individual EP. These deviations were used to calculate three types of resilience indicators for two life periods of each individual: natural logarithm-transformed variance (ln(variance)), skewness, and lag-one autocorrelation (autocorrelation) of deviations from 25 to 83 weeks of age and from 83 weeks of age to end of life. Then, we estimated their genetic correlations with EP traits and with two antibody traits. RESULTS The most promising resilience indicators were those based on 1-week-intervals, as they had the highest heritability estimates (0.02-0.12) and high genetic correlations (above 0.60) with the same resilience indicators based on longer intervals. The three types of resilience indicators differed genetically from each other, which indicates that they possibly capture different aspects of resilience. Genetic correlations of the resilience indicator traits based on 1-week-intervals with EP traits were favorable or zero, which means that trade-off effects were marginal. The resilience indicator traits based on 1-week-intervals also showed no genetic correlations with the antibody traits, which suggests that they are not informative for improved immunity or vice versa in the nucleus environment. CONCLUSIONS This paper gives direction towards the evaluation and implementation of resilience indicators, i.e. to further investigate resilience indicator traits based on 1-week-intervals, in breeding programs for selecting genetically more resilient layer chickens.
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Affiliation(s)
- Tom V L Berghof
- Wageningen University & Research Animal Breeding and Genomics, PO Box 338, 6700 AH, Wageningen, The Netherlands.
- Reproductive Biotechnology, TUM School of Life Sciences, Technical University of Munich, Liesel-Beckmann-Strasse 1, 85354, Freising, Germany.
| | - Nicolas Bedere
- PEGASE, INRAE, Institut Agro, 35590, Saint Gilles, France
| | - Katrijn Peeters
- Hendrix Genetics B.V., P.O. Box 114, 5830 AC, Boxmeer, The Netherlands
| | - Marieke Poppe
- Wageningen University & Research Animal Breeding and Genomics, PO Box 338, 6700 AH, Wageningen, The Netherlands
- CRV B.V., Wassenaarweg 20, Arnhem, The Netherlands
| | - Jeroen Visscher
- Hendrix Genetics B.V., P.O. Box 114, 5830 AC, Boxmeer, The Netherlands
| | - Han A Mulder
- Wageningen University & Research Animal Breeding and Genomics, PO Box 338, 6700 AH, Wageningen, The Netherlands.
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3
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Richter J, Hidalgo J, Bussiman F, Breen V, Misztal I, Lourenco D. Temporal dynamics of genetic parameters and SNP effects for performance and disorder traits in poultry undergoing genomic selection. J Anim Sci 2024; 102:skae097. [PMID: 38576313 PMCID: PMC11044709 DOI: 10.1093/jas/skae097] [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: 11/09/2023] [Accepted: 04/03/2024] [Indexed: 04/06/2024] Open
Abstract
Accurate genetic parameters are crucial for predicting breeding values and selection responses in breeding programs. Genetic parameters change with selection, reducing additive genetic variance and changing genetic correlations. This study investigates the dynamic changes in genetic parameters for residual feed intake (RFI), gain (GAIN), breast percentage (BP), and femoral head necrosis (FHN) in a broiler population that undergoes selection, both with and without the use of genomic information. Changes in single nucleotide polymorphism (SNP) effects were also investigated when including genomic information. The dataset containing 200,093 phenotypes for RFI, 42,895 for BP, 203,060 for GAIN, and 63,349 for FHN was obtained from 55 mating groups. The pedigree included 1,252,619 purebred broilers, of which 154,318 were genotyped with a 60K Illumina Chicken SNP BeadChip. A Bayesian approach within the GIBBSF90 + software was applied to estimate the genetic parameters for single-, two-, and four-trait models with sliding time intervals. For all models, we used genomic-based (GEN) and pedigree-based approaches (PED), meaning with or without genotypes. For GEN (PED), heritability varied from 0.19 to 0.2 (0.31 to 0.21) for RFI, 0.18 to 0.11 (0.25 to 0.14) for GAIN, 0.45 to 0.38 (0.61 to 0.47) for BP, and 0.35 to 0.24 (0.53 to 0.28) for FHN, across the intervals. Changes in genetic correlations estimated by GEN (PED) were 0.32 to 0.33 (0.12 to 0.25) for RFI-GAIN, -0.04 to -0.27 (-0.18 to -0.27) for RFI-BP, -0.04 to -0.07 (-0.02 to -0.08) for RFI-FHN, -0.04 to 0.04 (0.06 to 0.2) for GAIN-BP, -0.17 to -0.06 (-0.02 to -0.01) for GAIN-FHN, and 0.02 to 0.07 (0.06 to 0.07) for BP-FHN. Heritabilities tended to decrease over time while genetic correlations showed both increases and decreases depending on the traits. Similar to heritabilities, correlations between SNP effects declined from 0.78 to 0.2 for RFI, 0.8 to 0.2 for GAIN, 0.73 to 0.16 for BP, and 0.71 to 0.14 for FHN over the eight intervals with genomic information, suggesting potential epistatic interactions affecting genetic trait architecture. Given rapid genetic architecture changes and differing estimates between genomic and pedigree-based approaches, using more recent data and genomic information to estimate variance components is recommended for populations undergoing genomic selection to avoid potential biases in genetic parameters.
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Affiliation(s)
- Jennifer Richter
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA
| | - Jorge Hidalgo
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA
| | - Fernando Bussiman
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA
| | - Vivian Breen
- Cobb-Vantress, Inc., Siloam Springs, AR 72761, USA
| | - Ignacy Misztal
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA
| | - Daniela Lourenco
- Department of Animal and Dairy Science, University of Georgia, Athens, GA 30602, USA
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Alboali H, Moradi MH, Khaltabadi Farahani AH, Mohammadi H. Genome-wide association study for body weight and feed consumption traits in Japanese quail using Bayesian approaches. Poult Sci 2024; 103:103208. [PMID: 37980758 PMCID: PMC10663954 DOI: 10.1016/j.psj.2023.103208] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/23/2023] [Revised: 10/12/2023] [Accepted: 10/13/2023] [Indexed: 11/21/2023] Open
Abstract
The aim of this study was to perform a genome-wide association study (GWAS) based on Bayes A and Bayes B statistical methods to identify genomic loci and candidate genes associated with body weight gain, feed intake, and feed conversion ratio in Japanese quail. For this purpose, genomic data obtained from Illumina iSelect 4K quail SNP chip were utilized. After implementing various quality control steps, genotype data from a total of 875 birds for 2,015 SNP markers were used for subsequent analyses. The Bayesian analyses were performed using hibayes package in R (version 4.3.1) and Gibbs sampling algorithm. The results of the analyses showed that Bayes A accounted for 11.43, 11.65, and 11.39% of the phenotypic variance for body weight gain, feed intake, and feed conversion ratio, respectively, while the variance explained by Bayes B was 7.02, 8.61, and 6.48%, respectively. Therefore, in the current study, results obtained from Bayes A were used for further analyses. In order to perform the gene enrichment analysis and to identify the functional pathways and classes of genes that are over-represented in a large set of genes associated with each trait, all markers that accounted for more than 0.1% of the phenotypic variance for each trait were used. The results of this analysis revealed a total of 23, 38, and 14 SNP markers associated with body weight gain, feed intake, and feed conversion ratio in Japanese quail, respectively. The results of the gene enrichment analysis led to the identification of biological pathways (and candidate genes) related to lipid phosphorylation (TTC7A gene) and cell junction (FGFR4 and FLRT2 genes) associated with body weight gain, calcium signaling pathway (ADCY2 and CAMK1D genes) associated with feed intake, and glycerolipid metabolic process (LIPC gene), lipid metabolic process (ADGRF5 and ESR1 genes), and glutathione transferase (GSTK1 gene) associated with feed conversion ratio. Overall, the findings of this study can provide valuable insights into the genetic architecture of growth and feed consumption traits in Japanese quail.
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Affiliation(s)
- Hassan Alboali
- Department of Animal Science, Faculty of Agriculture and Environment, Arak University, 38156-8-8349 Arak, Iran
| | - Mohammad Hossein Moradi
- Department of Animal Science, Faculty of Agriculture and Environment, Arak University, 38156-8-8349 Arak, Iran.
| | | | - Hossein Mohammadi
- Department of Animal Science, Faculty of Agriculture and Environment, Arak University, 38156-8-8349 Arak, Iran
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Haqani MI, Nakano M, Nagano AJ, Nakamura Y, Tsudzuki M. Association analysis of production traits of Japanese quail (Coturnix japonica) using restriction-site associated DNA sequencing. Sci Rep 2023; 13:21307. [PMID: 38042890 PMCID: PMC10693557 DOI: 10.1038/s41598-023-48293-0] [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: 01/06/2023] [Revised: 10/10/2023] [Accepted: 11/24/2023] [Indexed: 12/04/2023] Open
Abstract
This study was designed to perform an association analysis and identify SNP markers associated with production traits of Japanese quail using restriction-site-associated DNA sequencing. Weekly body weight data from 805 quail were collected from hatching to 16 weeks of age. A total number of 3990 eggs obtained from 399 female quail were used to assess egg quality traits. Egg-related traits were measured at the beginning of egg production (first stage) and at 12 weeks of age (second stage). Five eggs were analyzed at each stage. Traits, such as egg weight, egg length and short axes, eggshell strength and weight, egg equator thickness, yolk weight, diameter, and colour, albumen weight, age of first egg, total number of laid eggs, and egg production rate, were assessed. A total of 383 SNPs and 1151 associations as well as 734 SNPs and 1442 associations were identified in relation to quail production traits using general linear model (GLM) and mixed linear model (MLM) approaches, respectively. The GLM-identified SNPs were located on chromosomes 1-13, 15, 17-20, 24, 26-28, and Z, underlying phenotypic traits, except for egg and albumen weight at the first stage and yolk yellowness at the second stage. The MLM-identified SNPs were positioned on defined chromosomes associated with phenotypic traits except for the egg long axis at the second stage of egg production. Finally, 35 speculated genes were identified as candidate genes for the targeted traits based on their nearest positions. Our findings provide a deeper understanding and allow a more precise genetic improvement of production traits of Galliformes, particularly in Japanese quail.
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Affiliation(s)
- Mohammad Ibrahim Haqani
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8525, Japan.
| | - Michiharu Nakano
- Faculty of Agriculture and Marine Sciences, Kochi University, Nankoku, Kochi, 783-8502, Japan
| | - Atsushi J Nagano
- Faculty of Agriculture, Ryukoku University, Otsu, Shiga, 520-2194, Japan
- Institute for Advanced Biosciences, Keio University, Yamagata, 997-0017, Japan
| | - Yoshiaki Nakamura
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8525, Japan
- Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8525, Japan
| | - Masaoki Tsudzuki
- Graduate School of Integrated Sciences for Life, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8525, Japan.
- Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima, 739-8525, Japan.
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Wolc A, Dekkers JCM. Application of Bayesian genomic prediction methods to genome-wide association analyses. Genet Sel Evol 2022; 54:31. [PMID: 35562659 PMCID: PMC9103490 DOI: 10.1186/s12711-022-00724-8] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2022] [Accepted: 04/27/2022] [Indexed: 11/19/2022] Open
Abstract
Background Bayesian genomic prediction methods were developed to simultaneously fit all genotyped markers to a set of available phenotypes for prediction of breeding values for quantitative traits, allowing for differences in the genetic architecture (distribution of marker effects) of traits. These methods also provide a flexible and reliable framework for genome-wide association (GWA) studies. The objective here was to review developments in Bayesian hierarchical and variable selection models for GWA analyses. Results By fitting all genotyped markers simultaneously, Bayesian GWA methods implicitly account for population structure and the multiple-testing problem of classical single-marker GWA. Implemented using Markov chain Monte Carlo methods, Bayesian GWA methods allow for control of error rates using probabilities obtained from posterior distributions. Power of GWA studies using Bayesian methods can be enhanced by using informative priors based on previous association studies, gene expression analyses, or functional annotation information. Applied to multiple traits, Bayesian GWA analyses can give insight into pleiotropic effects by multi-trait, structural equation, or graphical models. Bayesian methods can also be used to combine genomic, transcriptomic, proteomic, and other -omics data to infer causal genotype to phenotype relationships and to suggest external interventions that can improve performance. Conclusions Bayesian hierarchical and variable selection methods provide a unified and powerful framework for genomic prediction, GWA, integration of prior information, and integration of information from other -omics platforms to identify causal mutations for complex quantitative traits.
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Affiliation(s)
- Anna Wolc
- Department of Animal Science, Iowa State University, 806 Stange Road, 239 Kildee Hall, Ames, IA, 50010, USA.,Hy-Line International, 2583 240th Street, Dallas Center, IA, 50063, USA
| | - Jack C M Dekkers
- Department of Animal Science, Iowa State University, 806 Stange Road, 239 Kildee Hall, Ames, IA, 50010, USA.
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Bedere N, Berghof TVL, Peeters K, Pinard-van der Laan MH, Visscher J, David I, Mulder HA. Using egg production longitudinal recording to study the genetic background of resilience in purebred and crossbred laying hens. Genet Sel Evol 2022; 54:26. [PMID: 35439920 PMCID: PMC9020098 DOI: 10.1186/s12711-022-00716-8] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/19/2021] [Accepted: 03/28/2022] [Indexed: 12/02/2022] Open
Abstract
Background There is growing interest in using genetic selection to obtain more resilient farm animals (i.e. that are minimally affected by disturbances or rapidly recover from them). The aims of this study were to: (i) estimate the genetic parameters of resilience indicator traits based on egg production data, (ii) assess whether these traits are genetically correlated in purebreds and crossbreds, and (iii) assess the genetic correlations of these traits with egg production (EP) as total number of eggs between 25 and 83 weeks. Purebred hens (33,825 from a White Leghorn (WA) line and 34,397 from a Rhode Island (BD) line were housed in individual cages, while crossbred hens were housed in collective cages of 6 to 8 paternal half-sibs (12,852 WA and 3898 BD crossbred groups, where the name of the group refers to the line used as the sire). Deviations of a hen’s weekly egg production from the average of the corresponding batch were calculated. Resilience indicator traits investigated were the natural logarithm of the variance (LNVAR), the skewness (SKEW), and the lag-one autocorrelation (AUTO-R) of these deviations. Results In both purebred lines, EP was estimated to be lowly heritable (WA: 0.11 and BD: 0.12). Resilience indicators were also estimated to be lowly heritable in both lines (LNVAR: 0.10 and 0.12, SKEW: 0.04 and 0.02, AUTO-R: 0.06 and 0.08 in WA and BD, respectively). In both crossbred groups, EP, AUTO-R, and SKEW were estimated to be less heritable than in purebreds (EP: \documentclass[12pt]{minimal}
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\begin{document}$$h^{2}$$\end{document}h2 ≤ 0.07; and resilience indicator traits: \documentclass[12pt]{minimal}
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\begin{document}$$h^{2}$$\end{document}h2 ≤ 0.03), while LNVAR had an \documentclass[12pt]{minimal}
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\begin{document}$$h^{2}$$\end{document}h2 estimate that was similar to or higher in crossbreds (\documentclass[12pt]{minimal}
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\begin{document}$$h^{2}$$\end{document}h2 ranged from 0.13 to 0.21) than in purebreds. In both purebreds and crossbreds, resilience indicator traits were estimated to have favorable genetic correlations with EP and between each other. For all traits and in both lines, estimates of genetic correlations between purebreds and crossbreds (\documentclass[12pt]{minimal}
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\begin{document}$$r_{pc}$$\end{document}rpc) differed from 1 and ranged from 0.16 to 0.63. Conclusions These results show that selection for resilience based on EP data can be considered in breeding programs for layers. Genetic improvement of resilience in crossbreds can be achieved by using information on purebreds, but would be greatly enhanced by the integration of information on crossbreds in breeding programs. Supplementary Information The online version contains supplementary material available at 10.1186/s12711-022-00716-8.
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Affiliation(s)
- Nicolas Bedere
- PEGASE, INRAE, Institut Agro, 35590, Saint Gilles, France.
| | - Tom V L Berghof
- Wageningen University & Research Animal Breeding & Genomics, P.O. Box 338, 6700 AH, Wageningen, The Netherlands.,Reproductive Biotechnology, TUM School of Life Sciences, Technical University of Munich, Liesel‑Beckmann‑Strasse 1, 85354, Freising, Germany
| | - Katrijn Peeters
- Hendrix Genetics B.V., P.O. Box 114, 5830 AC, Boxmeer, The Netherlands
| | | | - Jeroen Visscher
- Hendrix Genetics B.V., P.O. Box 114, 5830 AC, Boxmeer, The Netherlands
| | - Ingrid David
- GenPhySE, Université de Toulouse, INRAE, ENVT, 31320, Castanet Tolosan, France
| | - Han A Mulder
- Wageningen University & Research Animal Breeding & Genomics, P.O. Box 338, 6700 AH, Wageningen, The Netherlands
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Li J, Wang Z, Lubritz D, Arango J, Fulton J, Settar P, Rowland K, Cheng H, Wolc A. Genome-wide association studies for egg quality traits in White Leghorn layers using low-pass sequencing and SNP chip data. J Anim Breed Genet 2022; 139:380-397. [PMID: 35404478 DOI: 10.1111/jbg.12679] [Citation(s) in RCA: 4] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/31/2021] [Revised: 03/05/2022] [Accepted: 03/27/2022] [Indexed: 12/24/2022]
Abstract
Low-pass sequencing data have been proposed as an alternative to single nucleotide polymorphism (SNP) chips in genome-wide association studies (GWAS) of several species. However, it has not been used in layer chickens yet. This study aims at comparing the GWAS results of White Leghorn chickens using low-pass sequencing data (1×) and 54 k SNP chip data. Ten commercially relevant egg quality traits including albumen height, shell strength, shell colour, egg weight and yolk weight collected from up to 1,420 White Leghorn chickens were analysed. The results showed that the genomic heritability estimates based on low-pass sequencing data were higher than those based on SNP chip data. Although two GWAS analyses showed similar overall landscape for most traits, low-pass sequencing captured some significant SNPs that were not on the SNP chip. In GWAS analysis using 54 k SNP chip data, after including more individuals (up to 5,700), additional significant SNPs not detected by low-pass sequencing data were found. In conclusion, GWAS using low-pass sequencing data showed similar results to those with SNP chip data and may require much larger sample sizes to show measurable advantages.
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Affiliation(s)
- Jinghui Li
- Department of Animal Science, University of California, Davis, California, USA
| | - Zigui Wang
- Department of Animal Science, University of California, Davis, California, USA
| | | | | | | | | | | | - Hao Cheng
- Department of Animal Science, University of California, Davis, California, USA
| | - Anna Wolc
- Hy-Line International, Dallas Center, Iowa, USA.,Department of Animal Science, Iowa State University, Ames, Iowa, USA
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Sell-Kubiak E, Knol EF, Lopes M. Evaluation of the phenotypic and genomic background of variability based on litter size of Large White pigs. Genet Sel Evol 2022; 54:1. [PMID: 34979897 PMCID: PMC8722267 DOI: 10.1186/s12711-021-00692-5] [Citation(s) in RCA: 8] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2021] [Accepted: 12/15/2021] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND The genetic background of trait variability has captured the interest of ecologists and animal breeders because the genes that control it could be involved in buffering various environmental effects. Phenotypic variability of a given trait can be assessed by studying the heterogeneity of the residual variance, and the quantitative trait loci (QTL) that are involved in the control of this variability are described as variance QTL (vQTL). This study focuses on litter size (total number born, TNB) and its variability in a Large White pig population. The variability of TNB was evaluated either using a simple method, i.e. analysis of the log-transformed variance of residuals (LnVar), or the more complex double hierarchical generalized linear model (DHGLM). We also performed a single-SNP (single nucleotide polymorphism) genome-wide association study (GWAS). To our knowledge, this is only the second study that reports vQTL for litter size in pigs and the first one that shows GWAS results when using two methods to evaluate variability of TNB: LnVar and DHGLM. RESULTS Based on LnVar, three candidate vQTL regions were detected, on Sus scrofa chromosomes (SSC) 1, 7, and 18, which comprised 18 SNPs. Based on the DHGLM, three candidate vQTL regions were detected, i.e. two on SSC7 and one on SSC11, which comprised 32 SNPs. Only one candidate vQTL region overlapped between the two methods, on SSC7, which also contained the most significant SNP. Within this vQTL region, two candidate genes were identified, ADGRF1, which is involved in neurodevelopment of the brain, and ADGRF5, which is involved in the function of the respiratory system and in vascularization. The correlation between estimated breeding values based on the two methods was 0.86. Three-fold cross-validation indicated that DHGLM yielded EBV that were much more accurate and had better prediction of missing observations than LnVar. CONCLUSIONS The results indicated that the LnVar and DHGLM methods resulted in genetically different traits. Based on their validation, we recommend the use of DHGLM over the simpler method of log-transformed variance of residuals. These conclusions can be useful for future studies on the evaluation of the variability of any trait in any species.
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Affiliation(s)
- Ewa Sell-Kubiak
- Department of Genetics and Animal Breeding, Poznan University of Life Sciences, Poznań, Poland.
| | - Egbert F Knol
- Topigs Norsvin Research Centre, Beuningen, The Netherlands
| | - Marcos Lopes
- Topigs Norsvin Research Centre, Beuningen, The Netherlands.,Topigs Norsvin, Curitiba, Brazil
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10
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Cheng H, Xu K, Li J, Abraham KJ. Optimizing Sequencing Resources in Genotyped Livestock Populations Using Linear Programming. Front Genet 2021; 12:740340. [PMID: 34745214 PMCID: PMC8570094 DOI: 10.3389/fgene.2021.740340] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/12/2021] [Accepted: 09/20/2021] [Indexed: 11/13/2022] Open
Abstract
Low-cost genome-wide single-nucleotide polymorphisms (SNPs) are routinely used in animal breeding programs. Compared to SNP arrays, the use of whole-genome sequence data generated by the next-generation sequencing technologies (NGS) has great potential in livestock populations. However, sequencing a large number of animals to exploit the full potential of whole-genome sequence data is not feasible. Thus, novel strategies are required for the allocation of sequencing resources in genotyped livestock populations such that the entire population can be imputed, maximizing the efficiency of whole genome sequencing budgets. We present two applications of linear programming for the efficient allocation of sequencing resources. The first application is to identify the minimum number of animals for sequencing subject to the criterion that each haplotype in the population is contained in at least one of the animals selected for sequencing. The second application is the selection of animals whose haplotypes include the largest possible proportion of common haplotypes present in the population, assuming a limited sequencing budget. Both applications are available in an open source program LPChoose. In both applications, LPChoose has similar or better performance than some other methods suggesting that linear programming methods offer great potential for the efficient allocation of sequencing resources. The utility of these methods can be increased through the development of improved heuristics.
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Affiliation(s)
- Hao Cheng
- Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Keyu Xu
- Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Jinghui Li
- Department of Animal Science, University of California, Davis, Davis, CA, United States
| | - Kuruvilla Joseph Abraham
- Department of Economics, FEARP, University of São-Paulo, Ribeirão Preto, Brazil.,Department of Computer Science-ICMC, University of São Paulo, São Carlos, Brazil
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11
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Identification and Validation of Marketing Weight-Related SNP Markers Using SLAF Sequencing in Male Yangzhou Geese. Genes (Basel) 2021; 12:genes12081203. [PMID: 34440377 PMCID: PMC8393582 DOI: 10.3390/genes12081203] [Citation(s) in RCA: 9] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2021] [Revised: 07/27/2021] [Accepted: 07/29/2021] [Indexed: 11/17/2022] Open
Abstract
Growth performance is a complex economic trait for avian production. The swan goose (Anser cygnoides) has never been exploited genetically like chickens or other waterfowl species such as ducks. Traditional phenotypic selection is still the main method for genetic improvement of geese body weight. In this study, specific locus amplified fragment sequencing (SLAF-seq) with bulked segregant analysis (BSA) was conducted for discovering and genotyping single nucleotide polymorphisms (SNPs) associated with marketing weight trait in male geese. A total of 149,045 SNPs were obtained from 427,093 SLAF tags with an average sequencing depth of 44.97-fold and a Q30 value of 93.26%. After SNPs' filtering, a total of 12,917 SNPs were included in the study. The 31 highest significant SNPs-which had different allelic frequencies-were further validated by individual-based AS-PCR genotyping in two populations. The association between 10 novel SNPs and the marketing weight of male geese was confirmed. The 10 significant SNPs were involved in linear regression model analysis, which confirmed single-SNP associations and revealed three types of SNP networks for marketing weight. The 10 significant SNPs were located within or close to 10 novel genes, which were identified. The qPCR analysis showed significant difference between genotypes of each SNP in seven genes. Developed SLAF-seq and identified genes will enrich growth performance studies, promoting molecular breeding applications to boost the marketing weight of Chinese geese.
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12
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Zhang Y, Song Y, Gao J, Zhang H, Yang N, Yang R. Hierarchical mixed-model expedites genome-wide longitudinal association analysis. Brief Bioinform 2021; 22:6217728. [PMID: 33834187 DOI: 10.1093/bib/bbab096] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/20/2020] [Revised: 03/02/2021] [Accepted: 03/03/2021] [Indexed: 11/13/2022] Open
Abstract
A hierarchical random regression model (Hi-RRM) was extended into a genome-wide association analysis for longitudinal data, which significantly reduced the dimensionality of repeated measurements. The Hi-RRM first modeled the phenotypic trajectory of each individual using a RRM and then associated phenotypic regressions with genetic markers using a multivariate mixed model (mvLMM). By spectral decomposition of genomic relationship and regression covariance matrices, the mvLMM was transformed into a multiple linear regression, which improved computing efficiency while implementing mvLMM associations in efficient mixed-model association expedited (EMMAX). Compared with the existing RRM-based association analyses, the statistical utility of Hi-RRM was demonstrated by simulation experiments. The method proposed here was also applied to find the quantitative trait nucleotides controlling the growth pattern of egg weights in poultry data.
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Affiliation(s)
- Ying Zhang
- College of Animal Science and Veterinary Medicine, Heilongjiang Bayi Agricultural University, People's Republic of China
| | - Yuxin Song
- Wuxi Fisheries College, Nanjing Agricultural University, People's Republic of China
| | - Jin Gao
- Wuxi Fisheries College, Nanjing Agricultural University, People's Republic of China
| | - Hengyu Zhang
- Department of Information and Computing Science, Heilongjiang Bayi Agricultural University, People's Republic of China
| | - Ning Yang
- College of Animal Science and Technology, China Agricultural University, People's Republic of China
| | - Runqing Yang
- Research Centre for Aquatic biotechnology, Chinese Academy of Fishery Sciences, People's Republic of China
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13
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Li F, Liu J, Liu W, Gao J, Lei Q, Han H, Yang J, Li H, Cao D, Zhou Y. Genome-wide association study of body size traits in Wenshang Barred chickens based on the specific-locus amplified fragment sequencing technology. Anim Sci J 2021; 92:e13506. [PMID: 33398896 DOI: 10.1111/asj.13506] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Revised: 11/04/2020] [Accepted: 11/16/2020] [Indexed: 12/12/2022]
Abstract
Chicken body size (BS) is an economically important trait, which has been assessed in many studies for genetic selection. However, previous reports detected functional chromosome mutations or regions using gene chips. The present study used the specific-locus amplified fragment sequencing (SLAF-seq) technology to perform a genome-wide association study (GWAS) of purebred Wenshang Barred chickens. A total of 250 one-day-old male chickens were assessed in this study. Body size in individual birds was measured at 56 days. SLAF-seq was used to genotype and GWAS analysis was carried out using the general linear model (GLM) of the TASSEL program. A total of 1,286,715 single-nucleotide polymorphisms (SNPs) were detected, of which 175,211 were tested as candidate SNPs for genome-wide association analysis using the TASSEL general linear model. Three SNPs markers reached genome-wide significance. Of these, chrZ:81729634, chrZ:81841715, and chrZ:81954149 at 81,729,634, 81,841,715, and 81,954,149 bp of GGA Z were significantly associated with body diagonal length at 56 days (BDL56); and tibia length at 56 days (TL56). These SNPs were close to three genes, including ZCCHC7, PAX5, and MELK. These results open new horizons for studies on BS and should promote the use of Chinese chickens, especially Wenshang Barred chickens.
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Affiliation(s)
- Fuwei Li
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| | - Jie Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| | - Wei Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| | - Jinbo Gao
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| | - Qiuxia Lei
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| | - Haixia Han
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| | - Jingchao Yang
- Shandong Animal Husbandry General Station, Ji'nan, P. R. China
| | - Huimin Li
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| | - Dingguo Cao
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
| | - Yan Zhou
- Poultry Institute, Shandong Academy of Agricultural Sciences, Ji'nan, P. R. China.,Poultry Breeding Engineering Technology Center of Shandong Province, Ji'nan, P. R. China.,The Key Lab of Poultry Disease Diagnosis and Immunology of Shandong Province, Ji'nan, P. R. China
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14
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Estimation of Variance Components and Genomic Prediction for Individual Birth Weight Using Three Different Genome-Wide SNP Platforms in Yorkshire Pigs. Animals (Basel) 2020; 10:ani10122219. [PMID: 33256056 PMCID: PMC7761447 DOI: 10.3390/ani10122219] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2020] [Revised: 11/20/2020] [Accepted: 11/23/2020] [Indexed: 11/17/2022] Open
Abstract
Simple Summary The individual birth weight (IBW) of pigs is an important trait regarding its relevance to mortality at weaning, sow prolificacy, and growth performance. This study investigates the variance component estimation, informative window regions, and the efficiency of genomic predictions associated with IBW traits in Yorkshire pigs. The low heritability (0.13) is estimated on the basis of a full model including individual genetic, sow genetic, and common environmental effects. Two common window regions of the genome are identified under three different genotyping platforms found within the ARAP2 and TSN genes concerning the IBW trait. The genomic prediction ability is improved using deregressed estimated breeding values including parental information as a response variable despite Bayesian methods and genotyping platforms for the IBW trait in Korean Yorkshire pigs. Abstract This study estimates the individual birth weight (IBW) trait heritability and investigates the genomic prediction efficiency using three types of high-density single nucleotide polymorphism (SNP) genotyping panels in Korean Yorkshire pigs. We use 38,864 IBW phenotypic records to identify a suitable model for statistical genetics, where 698 genotypes match our phenotypic records. During our genomic analysis, the deregressed estimated breeding values (DEBVs) and their reliabilities are used as derived response variables from the estimated breeding values (EBVs). Bayesian methods identify the informative regions and perform the genomic prediction using the IBW trait, in which two common significant window regions (SSC8 27 Mb and SSC15 29 Mb) are identified using the three genotyping platforms. Higher prediction ability is observed using the DEBV-including parent average as a response variable, regardless of the SNP genotyping panels and the Bayesian methods, relative to the DEBV-excluding parent average. Hence, we suggest that fine-mapping studies targeting the identified informative regions in this study are necessary to find the causal mutations to improve the IBW trait’s prediction ability. Furthermore, studying the IBW trait using a genomic prediction model with a larger genomic dataset may improve the genomic prediction accuracy in Korean Yorkshire pigs.
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15
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Scholtens M, Jiang A, Smith A, Littlejohn M, Lehnert K, Snell R, Lopez-Villalobos N, Garrick D, Blair H. Genome-wide association studies of lactation yields of milk, fat, protein and somatic cell score in New Zealand dairy goats. J Anim Sci Biotechnol 2020; 11:55. [PMID: 32489662 PMCID: PMC7247195 DOI: 10.1186/s40104-020-00453-2] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/26/2019] [Accepted: 04/01/2020] [Indexed: 12/12/2022] Open
Abstract
Background Identifying associations between genetic markers and traits of economic importance will provide practical benefits for the dairy goat industry, enabling genomic prediction of the breeding value of individuals, and facilitating discovery of the underlying genes and mutations. Genome-wide association studies were implemented to detect genetic regions that are significantly associated with effects on lactation yields of milk (MY), fat (FY), protein (PY) and somatic cell score (SCS) in New Zealand dairy goats. Methods A total of 4,840 goats were genotyped with the Caprine 50 K SNP chip (Illumina Inc., San Diego, CA). After quality filtering, 3,732 animals and 41,989 SNPs were analysed assuming an additive linear model. Four GWAS models were performed, a single-SNP additive linear model and three multi-SNP BayesC models. For the single-SNP GWAS, SNPs were fitted individually as fixed covariates, while the BayesC models fit all SNPs simultaneously as random effects. A cluster of significant SNPs were used to define a haplotype block whose alleles were fitted as covariates in a Bayesian model. The corresponding diplotypes of the haplotype block were then fit as class variables in another Bayesian model. Results Across all four traits, a total of 43 genome-wide significant SNPs were detected from the SNP GWAS. At a genome-wide significance level, the single-SNP analysis identified a cluster of variants on chromosome 19 associated with MY, FY, PY, and another cluster on chromosome 29 associated with SCS. Significant SNPs mapped in introns of candidate genes (45%), in intergenic regions (36%), were 0-5 kb upstream or downstream of the closest gene (14%) or were synonymous substitutions (5%). The most significant genomic window was located on chromosome 19 explaining up to 9.6% of the phenotypic variation for MY, 8.1% for FY, 9.1% for PY and 1% for SCS. Conclusions The quantitative trait loci for yield traits on chromosome 19 confirms reported findings in other dairy goat populations. There is benefit to be gained from using these results for genomic selection to improve milk production in New Zealand dairy goats.
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Affiliation(s)
- Megan Scholtens
- AL Rae Centre for Genetics and Breeding, School of Agriculture, Massey University, Palmerston North, New Zealand
| | - Andrew Jiang
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Ashley Smith
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Mathew Littlejohn
- Research and Development, Livestock Improvement Corporation, Ruakura Road, Hamilton, New Zealand
| | - Klaus Lehnert
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Russell Snell
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Nicolas Lopez-Villalobos
- AL Rae Centre for Genetics and Breeding, School of Agriculture, Massey University, Palmerston North, New Zealand
| | - Dorian Garrick
- AL Rae Centre for Genetics and Breeding, School of Agriculture, Massey University, Palmerston North, New Zealand
| | - Hugh Blair
- AL Rae Centre for Genetics and Breeding, School of Agriculture, Massey University, Palmerston North, New Zealand
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16
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Genome-Wide Association Study Using Fix-Length Haplotypes and Network Analysis Revealed New Candidate Genes for Nematode Resistance and Body Weight in Blackface Lambs. ANNALS OF ANIMAL SCIENCE 2020. [DOI: 10.2478/aoas-2020-0028] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/20/2022]
Abstract
Abstract
The objectives of this study were to identify genomic regions by Bayesian methods (BayesA, BayesB, or BayesN) that fit fixed-length haplotypes or SNPs using GenSel. Covariates for haplo-type alleles of five lengths (125, 250, 500 kb, 1 or 2 Mb) were generated, and rare haplotypes were removed at three thresholds (1, 5, or 10%). Subsequently, we performed gene network analyses to investigate the biological processes shared by genes that were identified for the same across traits. Genotypes at 41,034 SNPs that were common on OvineSNP50 panel were phased for 751 Scottish Blackface (SBF) lambs. This is the first study to quantify the proportion of genetic variance using haplotypes across the whole genome in an SBF population. The genetic variance explained of haplotype-based GWAS was higher than that of SNP-based GWAS in across traits studied. In this population, fitting 500kb haplotypes with a 1% frequency threshold resulted in the highest proportion of genetic variance explained for nematode resistance and fitting 2Mb haplotypes with a 10% frequency threshold improved genetic variance explained for body weight comparable to fitting SNPs by BayesB. Candidate genes, including CXCR4, STAT4, CCL1, CCL2, CCL3, CCL5, CCL8, CCL16, CCL18, CARMIL2, and HSPA14 were identified for nematode resistance and ADH5, PPP3CA, and FABP4 for body weight traits. Network analysis provided annotation results linking to all identified candidate genes. This study supported previous results from GWAS of nematode resistance and body weight and revealed additional regions in the ovine genome associated with these economically important traits. These results suggest that network analysis can provide new information regarding biological mechanisms and genes leading to complex phenotypes, like nematode resistance and body weight of lamb.
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17
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Barrett NW, Rowland K, Schmidt CJ, Lamont SJ, Rothschild MF, Ashwell CM, Persia ME. Effects of acute and chronic heat stress on the performance, egg quality, body temperature, and blood gas parameters of laying hens. Poult Sci 2020; 98:6684-6692. [PMID: 31573614 PMCID: PMC8914008 DOI: 10.3382/ps/pez541] [Citation(s) in RCA: 50] [Impact Index Per Article: 12.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2019] [Accepted: 09/09/2019] [Indexed: 12/29/2022] Open
Abstract
The goal of this experiment was to measure the physiological response of individual laying hens exposed to heat stress (HS). Performance, egg quality, body temperature (BT), and blood chemistry of laying hens were individually recorded before and after various intervals of daily cyclic HS. In total, 407 18-week-old W-36 parent-line laying hens (Hy-Line International, Dallas Center, IA) were housed individually in battery cages. After an acclimation period, baseline data were collected from 22 to 24-wk before the hens were subjected to a daily cyclic HS consisting of 7 h at 35°C returning to 30°C for the remaining 17 h/D from 24 to 28-wk of age. Eggs were collected and individually weighed daily. Feed intake (FI), egg production (EP), egg weights, egg mass, BW, and feed efficiency (FE) (g egg/kg FI) were calculated over 2-wk time periods. Eggs were collected for quality assessment the day before HS began, the 2nd day of HS, and on a weekly basis throughout the 4-wk HS. Blood was collected and BT measured the day before heat HS was initiated, on the first day of HS, and again at 2 and 4-wk of HS. Blood PCO2 and iCa decreased, and blood pH increased within 4 to 6 h of HS (P ≤ 0.01). Shell weights decreased with acute HS, possibly due to the reduction in blood iCa (P ≤ 0.01). After 4-wk of HS the blood pH returned to pre-HS levels but iCa remained decreased (P ≤ 0.01). Shell weights remained low and Haugh units decreased after 2 and 4-wk of HS (P ≤ 0.01). Feed efficiency was increased and FI, EP, and BW decreased by 2-wk of HS and remained low through 4-wk (P ≤ 0.01). The cyclic HS had a significant effect on the performance, egg quality, and blood chemistry over the 4-wk HS.
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Affiliation(s)
| | - Kaylee Rowland
- Department of Animal Science, Iowa State University, Ames 50011
| | - Carl J Schmidt
- Department of Animal and Food Sciences, University of Delaware, Newark 19716
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames 50011
| | | | - Chris M Ashwell
- Prestage Department of Poultry Science, North Carolina State University, Raleigh 27695
| | - Michael E Persia
- Department of Animal and Poultry Sciences, Virginia Tech, Blacksburg 24061
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18
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Hess AS, Trible BR, Hess MK, Rowland RR, Lunney JK, Plastow GS, Dekkers JCM. Genetic relationships of antibody response, viremia level, and weight gain in pigs experimentally infected with porcine reproductive and respiratory syndrome virus1. J Anim Sci 2020; 96:3565-3581. [PMID: 29905795 DOI: 10.1093/jas/sky229] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2018] [Accepted: 06/13/2018] [Indexed: 12/16/2022] Open
Abstract
Genetic and antigenic variability between Porcine Reproductive and Respiratory Syndrome Virus (PRRSV) isolates has encumbered vaccine development. Here, the genetic basis of PRRSV antibody response was assessed using data from experimental infection trials of commercial crossbred weaner pigs across with one of two distinct PRRSV isolates, NVSL-97-7895 (~750 pigs) and KS-2006-72109 (~450 pigs). Objectives were to estimate the genetic parameters of antibody response, measured as the sample to positive ratio (S:P) of PRRSV N-protein specific IgG in serum at 42 d post infection (dpi); assess the relationship of S:P at 42 dpi with serum viremia and growth under infection; and identify genomic regions associated with S:P at 42 dpi. Estimates of heritability of S:P at 42 dpi for NVSL and KS06 were 0.31 ± 0.09 and 0.40 ± 0.10 and appeared to be under similar genetic control (genetic correlation 0.73 ± 0.39). Estimates of genetic correlations of S:P were generally weak with viral load (NVSL: -0.20 ± 0.18; KS06: -0.69 ± 0.20), measured as area under the curve of log10 serum viremia from 0 to 21 dpi, and with weight gain (WG) from 0 to 42 dpi (NVSL: -0.38 ± 0.19; KS06: -0.08 ± 0.25). However, genetic correlations of S:P at 42 dpi with daily serum viremia and with 3-d WG revealed dynamic relationships, with S:P at 42 dpi having the strongest negative genetic correlations with daily viremia when IgG production starts (10-20 dpi), and negative genetic correlations with WG early after infection but positive later on. This suggests that animals that placed more emphasis on immune response early in infection reaped benefits of that later in infection by more effectively clearing the virus. The WUR10000125 SNP on SSC4, previously associated with response to PRRSV, did not have a significant effect on S:P at 42 dpi (P > 0.05) but genotype-specific genetic correlations of S:P with daily viremia and 3-d WG suggested that the lower WG of pigs with the unfavorable AA WUR10000125 genotype may be due to their utilization of a more energetically costly host response compared to pigs with the favorable genotype. Genome-wide association studies identified three SNPs in the Major Histocompatibility Complex associated with S:P that explained ~10 (NVSL) and 45% (KS06) of the genetic variance but were not associated with viremia or WG. In conclusion, antibody response to PRRSV infection is a possible biomarker for improved host response to PRRSV infection.
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Affiliation(s)
- Andrew S Hess
- Department of Animal Science, Iowa State University, Ames, IA
| | - Ben R Trible
- College of Veterinary Medicine, Kansas State University, Manhattan, KS
| | - Melanie K Hess
- Department of Animal Science, Iowa State University, Ames, IA
| | - Raymond R Rowland
- College of Veterinary Medicine, Kansas State University, Manhattan, KS
| | - Joan K Lunney
- Animal Parasitic Diseases Laboratory, USDA, ARS, BARC, Beltsville, MD
| | - Graham S Plastow
- Department of Agriculture, Food and Nutritional Sciences, University of Alberta, Edmonton, Alberta, Canada
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19
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Beral A, Rincent R, Le Gouis J, Girousse C, Allard V. Wheat individual grain-size variance originates from crop development and from specific genetic determinism. PLoS One 2020; 15:e0230689. [PMID: 32214360 PMCID: PMC7098578 DOI: 10.1371/journal.pone.0230689] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/17/2019] [Accepted: 03/05/2020] [Indexed: 11/19/2022] Open
Abstract
Wheat grain yield is usually decomposed in the yield components: number of spikes / m2, number of grains / spike, number of grains / m2 and thousand kernel weight (TKW). These are correlated one with another due to yield component compensation. Under optimal conditions, the number of grains per m2 has been identified as the main determinant of yield. However, with increasing occurrences of post-flowering abiotic stress associated with climate change, TKW may become severely limiting and hence a target for breeding. TKW is usually studied at the plot scale as it represents the average mass of a grain. However, this view disregards the large intra-genotypic variance of individual grain mass and its effect on TKW. The aim of this study is to investigate the determinism of the variance of individual grain size. We measured yield components and individual grain size variances of two large genetic wheat panels grown in two environments. We also carried out a genome-wide association study using a dense SNPs array. We show that the variance of individual grain size partly originates from the pre-flowering components of grain yield; in particular it is driven by canopy structure via its negative correlation with the number of spikes per m2. But the variance of final grain size also has a specific genetic basis. The genome-wide analysis revealed the existence of QTL with strong effects on the variance of individual grain size, independently from the other yield components. Finally, our results reveal some interesting drivers for manipulating individual grain size variance either through canopy structure or through specific chromosomal regions.
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Affiliation(s)
- Aurore Beral
- UMR 1095 GDEC, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Renaud Rincent
- UMR 1095 GDEC, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Jacques Le Gouis
- UMR 1095 GDEC, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Christine Girousse
- UMR 1095 GDEC, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
| | - Vincent Allard
- UMR 1095 GDEC, INRAE, Université Clermont Auvergne, Clermont-Ferrand, France
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20
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Wolc A, Drobik-Czwarno W, Jankowski T, Arango J, Settar P, Fulton JE, Fernando RL, Garrick DJ, Dekkers JCM. Accuracy of genomic prediction of shell quality in a White Leghorn line. Poult Sci 2020; 99:2833-2840. [PMID: 32475416 PMCID: PMC7597664 DOI: 10.1016/j.psj.2020.01.019] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Revised: 01/13/2020] [Accepted: 01/20/2020] [Indexed: 11/16/2022] Open
Abstract
Several genomic methods were applied for predicting shell quality traits recorded at 4 different hen ages in a White Leghorn line. The accuracies of genomic prediction of single-step GBLUP and single-trait Bayes B were compared with predictions of breeding values based on pedigree-BLUP under single-trait or multitrait models. Breaking strength (BS) and dynamic stiffness (Kdyn) measurements were collected on 18,524 birds from 3 consecutive generations, of which 4,164 animals also had genotypes from an Affymetrix 50K panel containing 49,591 SNPs after quality control edits. All traits had low to moderate heritability, ranging from 0.17 for BS to 0.34 for Kdyn. The highest accuracies of prediction were obtained for the multitrait single-step model. The use of marker information resulted in higher prediction accuracies than pedigree-based models for almost all traits. A genome-wide association study based on a Bayes B model was conducted to detect regions explaining the largest proportion of genetic variance. Across all 8 shell quality traits analyzed, 7 regions each explaining over 2% of genetic variance and 54 regions each explaining over 1% of genetic variance were identified. The windows explaining a large proportion of genetic variance overlapped with several potential candidate genes with biological functions linked to shell formation. A multitrait repeatability model using a single-step method is recommended for genomic evaluation of shell quality in layer chickens.
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Affiliation(s)
- A Wolc
- Department of Animal Sciences, Iowa State University, Ames, IA 50011-1178, USA; Hy-Line International, Dallas Center, IA 50063, USA.
| | - W Drobik-Czwarno
- Department of Animal Genetics and Conservation, Institute of Animal Science, Warsaw University of Life Sciences, 02-787 Warsaw, Poland
| | | | - J Arango
- Hy-Line International, Dallas Center, IA 50063, USA
| | - P Settar
- Hy-Line International, Dallas Center, IA 50063, USA
| | - J E Fulton
- Hy-Line International, Dallas Center, IA 50063, USA
| | - R L Fernando
- Department of Animal Sciences, Iowa State University, Ames, IA 50011-1178, USA
| | - D J Garrick
- Department of Animal Sciences, Iowa State University, Ames, IA 50011-1178, USA
| | - J C M Dekkers
- Department of Animal Sciences, Iowa State University, Ames, IA 50011-1178, USA
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21
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Li JJ, Zhang L, Ren P, Wang Y, Yin LQ, Ran JS, Zhang XX, Liu YP. Genotype frequency distributions of 28 SNP markers in two commercial lines and five Chinese native chicken populations. BMC Genet 2020; 21:12. [PMID: 32019486 PMCID: PMC7001339 DOI: 10.1186/s12863-020-0815-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2019] [Accepted: 01/27/2020] [Indexed: 11/18/2022] Open
Abstract
Background Modern breeding in the poultry industry mainly aims to produce high-performance poultry lines and breeds in two main directions of productivity, meat and eggs. To understand more about the productive potential of lowly selected Chinese native chicken populations, we selected 14 representative SNP markers strongly associated with growth traits or carcass traits and 14 SNP markers strongly associated with egg laying traits through previous reports. By using the MassArray technology, we detected the genotype frequency distributions of these 28 SNP markers in seven populations including four lowly selected as well as one moderately selected Sichuan native chicken populations, one commercial broiler line and one commercial layer line. Results Based on the genotype frequency distributions of these 28 SNP markers in 5 native chicken populations and 2 commercial lines, the results suggested that these Chinese indigenous chicken populations have a relatively close relationship with the commercial broiler line but a marked distinction from the commercial layer line. Two native chicken breeds, Shimian Caoke Chicken and Daheng Broilers, share similar genetic structure with the broiler line. Conclusions Our observations may help us to better select and breed superior domestic chickens and provide new clues for further study of breeding programs in local chicken populations.
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Affiliation(s)
- Jing-Jing Li
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Long Zhang
- Institute of Ecology, Key Laboratory of Southwest China Wildlife Resources Conservation (Ministry of Education), China West Normal University, Nanchong, 637009, Sichuan, China
| | - Peng Ren
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ye Wang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Ling-Qian Yin
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Jin-Shan Ran
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Xian-Xian Zhang
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China
| | - Yi-Ping Liu
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, Sichuan Agricultural University, Chengdu, 611130, Sichuan, China.
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22
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Pierce C, Speidel S, Coleman S, Enns R, Bailey D, Medrano J, Cánovas A, Meiman P, Howery L, Mandeville W, Thomas M. Genome-wide association studies of beef cow terrain-use traits using Bayesian multiple-SNP regression. Livest Sci 2020. [DOI: 10.1016/j.livsci.2019.103900] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/11/2023]
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23
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Berghof TVL, Bovenhuis H, Mulder HA. Body Weight Deviations as Indicator for Resilience in Layer Chickens. Front Genet 2019; 10:1216. [PMID: 31921285 PMCID: PMC6923720 DOI: 10.3389/fgene.2019.01216] [Citation(s) in RCA: 36] [Impact Index Per Article: 7.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2019] [Accepted: 11/04/2019] [Indexed: 02/04/2023] Open
Abstract
Resilience is the capacity of an animal to be minimally affected by disturbances or to rapidly return to the state pertained before exposure to a disturbance. Less resilient animals are expected to be more susceptible to environmental perturbations, such as diseases, and will consequently show more and/or greater fluctuations in production than more resilient animals. Natural antibodies (NAb) are antibodies recognizing antigens without previous exposure to these, and are hypothesized to be an indication of general disease resistance. The objective of this research was to investigate genetic parameters of resilience indicators based on standardized body weight (BW) deviations and to investigate its relation with immunity (i.e. NAb) and disease resistance. Keyhole limpet hemocyanin-binding NAb were measured in layer chickens, which were selectively bred for high and low keyhole limpet hemocyanin-binding NAb levels during six generations. In addition, BW data of these layers were collected on a four-weekly interval from 4 weeks of age until 32 weeks of age. Standardized deviations of BW from an individual were compared to lines’ average BW (i.e. across individuals), and these were used to calculate resilience indicators: natural logarithm-transformed variance [ln(variance)], skewness, and lag-one autocorrelation of deviations (i.e. all within an individual). Heritabilities of resilience indicators were between 0.09 and 0.11. Genetic correlations between the three resilience indicators were between -0.20 and 0.40 (with high SE), which might suggest that the resilience indicators capture different aspects of resilience. Genetic correlations between resilience indicators and NAb were close to zero, which suggests that the resilience indicators and NAb capture different aspects of immunity. This might indicate that, in this dataset, environmental perturbations are only to a small extent affected by disease incidence, possibly due to a lack of disease occurrence. However, a lower estimated breeding value for ln(variance) was predictive for lower lesion scores after an avian pathogenic Escherichia coli inoculation and vice versa. In conclusion, this study shows that there is genetic variation in resilience indicators based on BW deviations in layer chickens, which opens up possibilities to improve resilience by means of selective breeding.
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Affiliation(s)
- Tom V L Berghof
- Wageningen University & Research Animal Breeding and Genomics, Wageningen, Netherlands
| | - Henk Bovenhuis
- Wageningen University & Research Animal Breeding and Genomics, Wageningen, Netherlands
| | - Han A Mulder
- Wageningen University & Research Animal Breeding and Genomics, Wageningen, Netherlands
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24
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Iung LHDS, Carvalheiro R, Neves HHDR, Mulder HA. Genetics and genomics of uniformity and resilience in livestock and aquaculture species: A review. J Anim Breed Genet 2019; 137:263-280. [PMID: 31709657 DOI: 10.1111/jbg.12454] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2019] [Revised: 10/15/2019] [Accepted: 10/16/2019] [Indexed: 01/29/2023]
Abstract
Genetic control of residual variance offers opportunities to increase uniformity and resilience of livestock and aquaculture species. Improving uniformity and resilience of animals will improve health and welfare of animals and lead to more homogenous products. Our aims in this review were to summarize the current models and methods to study genetic control of residual variance, genetic parameters and genomic results for residual variance and discuss future research directions. Typically, the genetic coefficient of variation is high (median = 0.27; range 0-0.86) and the heritability of residual variance is low (median = 0.01; range 0-0.10). Higher heritabilities can be achieved when increasing the number of records per animal. Divergent selection experiments have supported the feasibility of selecting for high or low residual variance. Genomic studies have revealed associations in regions related to stress, including those from the heat shock protein family. Although the number of studies is growing, genetic control of residual variance is still poorly understood, but big data and genomics offer great opportunities.
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Affiliation(s)
- Laiza Helena de Souza Iung
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil.,CRV Lagoa, Sertãozinho, Brazil
| | - Roberto Carvalheiro
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Jaboticabal, Brazil.,National Council for Scientific and Technological Development (CNPq), Brasília, Brazil
| | | | - Herman Arend Mulder
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, The Netherlands
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25
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Moreira GCM, Poleti MD, Pértille F, Boschiero C, Cesar ASM, Godoy TF, Ledur MC, Reecy JM, Garrick DJ, Coutinho LL. Unraveling genomic associations with feed efficiency and body weight traits in chickens through an integrative approach. BMC Genet 2019; 20:83. [PMID: 31694549 PMCID: PMC6836328 DOI: 10.1186/s12863-019-0783-3] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2019] [Accepted: 10/11/2019] [Indexed: 12/25/2022] Open
Abstract
Background Feed efficiency and growth rate have been targets for selection to improve chicken production. The incorporation of genomic tools may help to accelerate selection. We genotyped 529 individuals using a high-density SNP chip (600 K, Affymetrix®) to estimate genomic heritability of performance traits and to identify genomic regions and their positional candidate genes associated with performance traits in a Brazilian F2 Chicken Resource population. Regions exhibiting selection signatures and a SNP dataset from resequencing were integrated with the genomic regions identified using the chip to refine the list of positional candidate genes and identify potential causative mutations. Results Feed intake (FI), feed conversion ratio (FC), feed efficiency (FE) and weight gain (WG) exhibited low genomic heritability values (i.e. from 0.0002 to 0.13), while body weight at hatch (BW1), 35 days-of-age (BW35), and 41 days-of-age (BW41) exhibited high genomic heritability values (i.e. from 0.60 to 0.73) in this F2 population. Twenty unique 1-Mb genomic windows were associated with BW1, BW35 or BW41, located on GGA1–4, 6–7, 10, 14, 24, 27 and 28. Thirty-eight positional candidate genes were identified within these windows, and three of them overlapped with selection signature regions. Thirteen predicted deleterious and three high impact sequence SNPs in these QTL regions were annotated in 11 positional candidate genes related to osteogenesis, skeletal muscle development, growth, energy metabolism and lipid metabolism, which may be associated with body weight in chickens. Conclusions The use of a high-density SNP array to identify QTL which were integrated with whole genome sequence signatures of selection allowed the identification of candidate genes and candidate causal variants. One novel QTL was detected providing additional information to understand the genetic architecture of body weight traits. We identified QTL for body weight traits, which were also associated with fatness in the same population. Our findings form a basis for further functional studies to elucidate the role of specific genes in regulating body weight and fat deposition in chickens, generating useful information for poultry breeding programs.
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Affiliation(s)
| | - Mirele Daiana Poleti
- University of São Paulo (USP) / College of Animal Science and Food Engineering (FZEA), Pirassununga, São Paulo, Brazil
| | - Fábio Pértille
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | - Clarissa Boschiero
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - Thaís Fernanda Godoy
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil
| | | | - James M Reecy
- Department of Animal Science, Iowa State University (ISU), Ames, Iowa, USA
| | - Dorian J Garrick
- School of Agriculture, Massey University, Ruakura, Hamilton, New Zealand
| | - Luiz Lehmann Coutinho
- Department of Animal Science, University of São Paulo, Piracicaba, SP, 13418-900, Brazil.
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26
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Shrestha M, Solé M, Ducro BJ, Sundquist M, Thomas R, Schurink A, Eriksson S, Lindgren G. Genome-wide association study for insect bite hypersensitivity susceptibility in horses revealed novel associated loci on chromosome 1. J Anim Breed Genet 2019; 137:223-233. [PMID: 31489730 DOI: 10.1111/jbg.12436] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2019] [Revised: 08/08/2019] [Accepted: 08/09/2019] [Indexed: 01/10/2023]
Abstract
Equine insect bite hypersensitivity (IBH) is a pruritic skin allergy caused primarily by biting midges, Culicoides spp. IBH susceptibility has polygenic inheritance and occurs at high frequencies in several horse breeds worldwide, causing increased costs and reduced welfare of affected horses. The aim of this study was to identify and validate single nucleotide polymorphisms (SNPs) associated with equine IBH susceptibility. After quality control, 33,523 SNPs were included in a Bayesian genome-wide association study on 177 affected and 178 unaffected Icelandic horses. We report associated regions in E. caballus (ECA) 1, 3, 15 and 18, overlapping with known IBH QTLs in horses, and novel regions containing several genes, together explaining 11.46% of the total genetic variance. For validation, three SNPs on ECA 1 and ECA X (explaining the largest percentage of genetic variance) within 1-mb genomic windows for IBH were genotyped in an independent population of 280 Exmoor ponies. The associated genomic region (152-153 mb) on ECA 1 was confirmed in Exmoor ponies and contains the AQR gene involved in splicing processes and a long non-coding RNA. This study confirms the polygenic nature of IBH susceptibility and suggests a role of transcriptional regulatory mechanisms (e.g., alternative splicing) for IBH predisposition in these horse breeds.
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Affiliation(s)
- Merina Shrestha
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Animal Breeding and Genomics, Wageningen University and Research, Wageningen, the Netherlands
| | - Marina Solé
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Bart J Ducro
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, the Netherlands
| | | | - Ruth Thomas
- The Exmoor Pony Society, Woodmans, Deveon, UK
| | - Anouk Schurink
- Animal Breeding and Genomics, Wageningen University and Research, Wageningen, the Netherlands
| | - Susanne Eriksson
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden
| | - Gabriella Lindgren
- Department of Animal Breeding and Genetics, Swedish University of Agricultural Sciences, Uppsala, Sweden.,Department of Biosystems, KU Leuven, Leuven, Belgium
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27
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Lokapirnasari WP, Pribadi TB, Arif AA, Soeharsono S, Hidanah S, Harijani N, Najwan R, Huda K, Wardhani HCP, Rahman NFN, Yulianto AB. Potency of probiotics Bifidobacterium spp. and Lactobacillus casei to improve growth performance and business analysis in organic laying hens. Vet World 2019; 12:860-867. [PMID: 31440006 PMCID: PMC6661486 DOI: 10.14202/vetworld.2019.860-867] [Citation(s) in RCA: 19] [Impact Index Per Article: 3.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2019] [Accepted: 05/13/2019] [Indexed: 12/03/2022] Open
Abstract
Aim: This study aimed to determine the use of probiotics Bifidobacterium spp. and Lactobacillus casei as alternative antibiotic growth promoters (AGPs) to improve growth performance and business analysis. Materials and Methods: This study used a completely randomized factorial design. The first factor was the time of administration (1, 2, 3, and 4 weeks) and the second was the use of probiotics (control without probiotics; 0.1% AGP and 0.5% Bifidobacterium spp. + 0.25% L. casei). One hundred and eighty laying hens (Lohmann strain), of 30 weeks old, were divided into 12 treatment groups, composed of five replicates, each consisting of three laying hens. Results: The results showed that using 0.5% Bifidobacterium spp. + 0.25% L. casei in weeks 1 and 2 showed the lowest feed intake (FI) (112.11-112.19 g/day), the highest egg weight (60.28 g) in the 1st week, the lowest feed conversion ratio (FCR) (2.21-2.23), and highest feed efficiency (44.75-45.25%) for 3-4 weeks, and the highest hen-day production (86.66-86.90%) for 3-4 weeks and the most profitable business analysis (IDR. 30,353). Conclusions: Based on the results, it can be concluded that the addition of 0.5% Bifidobacterium spp. + 25% L. casei probiotics can be used as a substitute for AGP; it can reduce the FI and FCR, increasing egg weight, feed efficiency, and hen-day production, as well as illustrating the results of the most profitable business analysis.
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Affiliation(s)
- Widya Paramita Lokapirnasari
- Department of Animal Husbandry, Faculty of Veterinary Medicine, Universitas Airlangga, Jl. Mulyorejo, Kampus C, Universitas Airlangga, Surabaya, Indonesia.,Halal Research Center, Universitas Airlangga, Jl. Mulyorejo, Kampus C, Universitas Airlangga, Surabaya, Indonesia
| | - Teguh Bagus Pribadi
- Magister of Veterinary Agribusiness, Faculty of Veterinary Medicine, Universitas Airlangga, Indonesia
| | - Anam Al Arif
- Department of Animal Husbandry, Faculty of Veterinary Medicine, Universitas Airlangga, Jl. Mulyorejo, Kampus C, Universitas Airlangga, Surabaya, Indonesia
| | - Soeharsono Soeharsono
- Department of Veterinary Anatomy, Faculty of Veterinary Medicine, Universitas Airlangga, Indonesia
| | - Sri Hidanah
- Department of Animal Husbandry, Faculty of Veterinary Medicine, Universitas Airlangga, Jl. Mulyorejo, Kampus C, Universitas Airlangga, Surabaya, Indonesia
| | - Nenny Harijani
- Department of Veterinary Public Health, Faculty of Veterinary Medicine, Universitas Airlangga, Indonesia
| | - Rifqy Najwan
- Magister of Veterinary Agribusiness, Faculty of Veterinary Medicine, Universitas Airlangga, Indonesia
| | - Khoirul Huda
- Magister of Veterinary Agribusiness, Faculty of Veterinary Medicine, Universitas Airlangga, Indonesia
| | | | - Nabil Fariz Noor Rahman
- Magister of Veterinary Agribusiness, Faculty of Veterinary Medicine, Universitas Airlangga, Indonesia
| | - Andreas Berny Yulianto
- Sains Veteriner, Faculty of Veterinary Medicine, Universitas Airlangga, Surabaya, Indonesia
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28
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Corty RW, Valdar W. QTL Mapping on a Background of Variance Heterogeneity. G3 (BETHESDA, MD.) 2018; 8:3767-3782. [PMID: 30389794 DOI: 10.1101/276980] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/28/2023]
Abstract
Standard QTL mapping procedures seek to identify genetic loci affecting the phenotypic mean while assuming that all individuals have the same residual variance. But when the residual variance differs systematically between groups, perhaps due to a genetic or environmental factor, such standard procedures can falter: in testing for QTL associations, they attribute too much weight to observations that are noisy and too little to those that are precise, resulting in reduced power and and increased susceptibility to false positives. The negative effects of such "background variance heterogeneity" (BVH) on standard QTL mapping have received little attention until now, although the subject is closely related to work on the detection of variance-controlling genes. Here we use simulation to examine how BVH affects power and false positive rate for detecting QTL affecting the mean (mQTL), the variance (vQTL), or both (mvQTL). We compare linear regression for mQTL and Levene's test for vQTL, with tests more recently developed, including tests based on the double generalized linear model (DGLM), which can model BVH explicitly. We show that, when used in conjunction with a suitable permutation procedure, the DGLM-based tests accurately control false positive rate and are more powerful than the other tests. We also find that some adverse effects of BVH can be mitigated by applying a rank inverse normal transform. We apply our novel approach, which we term "mean-variance QTL mapping", to publicly available data on a mouse backcross and, after accommodating BVH driven by sire, detect a new mQTL for bodyweight.
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Affiliation(s)
- Robert W Corty
- Department of Genetics
- Bioinformatics and Computational Biology Curriculum
| | - William Valdar
- Department of Genetics
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
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29
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Corty RW, Valdar W. QTL Mapping on a Background of Variance Heterogeneity. G3 (BETHESDA, MD.) 2018; 8:3767-3782. [PMID: 30389794 PMCID: PMC6288843 DOI: 10.1534/g3.118.200790] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 02/27/2018] [Accepted: 10/28/2018] [Indexed: 12/21/2022]
Abstract
Standard QTL mapping procedures seek to identify genetic loci affecting the phenotypic mean while assuming that all individuals have the same residual variance. But when the residual variance differs systematically between groups, perhaps due to a genetic or environmental factor, such standard procedures can falter: in testing for QTL associations, they attribute too much weight to observations that are noisy and too little to those that are precise, resulting in reduced power and and increased susceptibility to false positives. The negative effects of such "background variance heterogeneity" (BVH) on standard QTL mapping have received little attention until now, although the subject is closely related to work on the detection of variance-controlling genes. Here we use simulation to examine how BVH affects power and false positive rate for detecting QTL affecting the mean (mQTL), the variance (vQTL), or both (mvQTL). We compare linear regression for mQTL and Levene's test for vQTL, with tests more recently developed, including tests based on the double generalized linear model (DGLM), which can model BVH explicitly. We show that, when used in conjunction with a suitable permutation procedure, the DGLM-based tests accurately control false positive rate and are more powerful than the other tests. We also find that some adverse effects of BVH can be mitigated by applying a rank inverse normal transform. We apply our novel approach, which we term "mean-variance QTL mapping", to publicly available data on a mouse backcross and, after accommodating BVH driven by sire, detect a new mQTL for bodyweight.
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Affiliation(s)
- Robert W Corty
- Department of Genetics
- Bioinformatics and Computational Biology Curriculum
| | - William Valdar
- Department of Genetics
- Lineberger Comprehensive Cancer Center, University of North Carolina, Chapel Hill, NC
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30
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Moreira GCM, Boschiero C, Cesar ASM, Reecy JM, Godoy TF, Pértille F, Ledur MC, Moura ASAMT, Garrick DJ, Coutinho LL. Integration of genome wide association studies and whole genome sequencing provides novel insights into fat deposition in chicken. Sci Rep 2018; 8:16222. [PMID: 30385857 PMCID: PMC6212401 DOI: 10.1038/s41598-018-34364-0] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/20/2018] [Accepted: 10/12/2018] [Indexed: 02/07/2023] Open
Abstract
Excessive fat deposition is a negative factor for poultry production because it reduces feed efficiency, increases the cost of meat production and is a health concern for consumers. We genotyped 497 birds from a Brazilian F2 Chicken Resource Population, using a high-density SNP array (600 K), to estimate the genomic heritability of fat deposition related traits and to identify genomic regions and positional candidate genes (PCGs) associated with these traits. Selection signature regions, haplotype blocks and SNP data from a previous whole genome sequencing study in the founders of this chicken F2 population were used to refine the list of PCGs and to identify potential causative SNPs. We obtained high genomic heritabilities (0.43-0.56) and identified 22 unique QTLs for abdominal fat and carcass fat content traits. These QTLs harbored 26 PCGs involved in biological processes such as fat cell differentiation, insulin and triglyceride levels, and lipid biosynthetic process. Three of these 26 PCGs were located within haplotype blocks there were associated with fat traits, five overlapped with selection signature regions, and 12 contained predicted deleterious variants. The identified QTLs, PCGs and potentially causative SNPs provide new insights into the genetic control of fat deposition and can lead to improved accuracy of selection to reduce excessive fat deposition in chickens.
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Affiliation(s)
| | - Clarissa Boschiero
- Department of Animal Science, University of São Paulo, Piracicaba, SP, Brazil
| | | | - James M Reecy
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | | | - Fábio Pértille
- Department of Animal Science, University of São Paulo, Piracicaba, SP, Brazil
| | | | | | - Dorian J Garrick
- School of Agriculture, Massey University, Ruakura, Hamilton, New Zealand
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31
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Iung LHDS, Mulder HA, Neves HHDR, Carvalheiro R. Genomic regions underlying uniformity of yearling weight in Nellore cattle evaluated under different response variables. BMC Genomics 2018; 19:619. [PMID: 30115034 PMCID: PMC6097312 DOI: 10.1186/s12864-018-5003-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/24/2018] [Accepted: 08/08/2018] [Indexed: 02/22/2023] Open
Abstract
BACKGROUND In livestock, residual variance has been studied because of the interest to improve uniformity of production. Several studies have provided evidence that residual variance is partially under genetic control; however, few investigations have elucidated genes that control it. The aim of this study was to identify genomic regions associated with within-family residual variance of yearling weight (YW; N = 423) in Nellore bulls with high density SNP data, using different response variables. For this, solutions from double hierarchical generalized linear models (DHGLM) were used to provide the response variables, as follows: a DGHLM assuming non-null genetic correlation between mean and residual variance (rmv ≠ 0) to obtain deregressed EBV for mean (dEBVm) and residual variance (dEBVv); and a DHGLM assuming rmv = 0 to obtain two alternative response variables for residual variance, dEBVv_r0 and log-transformed variance of estimated residuals (ln_[Formula: see text]). RESULTS The dEBVm and dEBVv were highly correlated, resulting in common regions associated with mean and residual variance of YW. However, higher effects on variance than the mean showed that these regions had effects on the variance beyond scale effects. More independent association results between mean and residual variance were obtained when null rmv was assumed. While 13 and 4 single nucleotide polymorphisms (SNPs) showed a strong association (Bayes Factor > 20) with dEBVv and ln_[Formula: see text], respectively, only suggestive signals were found for dEBVv_r0. All overlapping 1-Mb windows among top 20 between dEBVm and dEBVv were previously associated with growth traits. The potential candidate genes for uniformity are involved in metabolism, stress, inflammatory and immune responses, mineralization, neuronal activity and bone formation. CONCLUSIONS It is necessary to use a strategy like assuming null rmv to obtain genomic regions associated with uniformity that are not associated with the mean. Genes involved not only in metabolism, but also stress, inflammatory and immune responses, mineralization, neuronal activity and bone formation were the most promising biological candidates for uniformity of YW. Although no clear evidence of using a specific response variable was found, we recommend consider different response variables to study uniformity to increase evidence on candidate regions and biological mechanisms behind it.
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Affiliation(s)
- Laiza Helena de Souza Iung
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Via de Acesso Prof. Paulo Donato Castelane, S/N, Vila Industrial, FCAV/UNESP, Jaboticabal, São Paulo, 14884-900 Brazil
| | - Herman Arend Mulder
- Wageningen University & Research Animal Breeding and Genomics, P.O. Box 338, 6700 AH Wageningen, The Netherlands
| | | | - Roberto Carvalheiro
- School of Agricultural and Veterinarian Sciences, São Paulo State University (Unesp), Via de Acesso Prof. Paulo Donato Castelane, S/N, Vila Industrial, FCAV/UNESP, Jaboticabal, São Paulo, 14884-900 Brazil
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Li F, Han H, Lei Q, Gao J, Liu J, Liu W, Zhou Y, Li H, Cao D. Genome-wide association study of body weight in Wenshang Barred chicken based on the SLAF-seq technology. J Appl Genet 2018; 59:305-312. [PMID: 29946990 DOI: 10.1007/s13353-018-0452-7] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/06/2017] [Revised: 06/13/2018] [Accepted: 06/19/2018] [Indexed: 12/19/2022]
Abstract
Chicken body weight (BW) is an economically important trait, and many studies have been conducted on genetic selection for BW. However, previous studies have detected functional chromosome mutations or regions using gene chips. The present study used the specific-locus amplified fragment sequencing (SLAF-seq) technology to perform a genome-wide association study (GWAS) on purebred Wengshang Barred chicken. A total of 1,286,715 single-nucleotide polymorphisms (SNPs) were detected, and 175,211 SNPs were selected as candidate SNPs for genome-wide association analysis using TASSEL general linear models. Six SNP markers reached genome-wide significance. Of these, rs732048524, rs735522839, rs738991545, and rs15837818 were significantly associated with body weight at 28 days (BW28), while rs314086457 and rs315694878 were significantly associated with BW120. These SNPs are close to seven genes (PRSS23, ME3, FAM181B, NABP1, SDPR, TSSK6L2, and RBBP8). Moreover, 24 BW-associated SNPs reached "suggestive" genome-wide significance. Of these, 6, 13, 1, and 4 SNPs were associated with BW28, BW56, BW80, and BW120, respectively. These results would enrich the studies on BW and promote the use of Chinese chicken, especially the Wenshang Barred chicken.
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Affiliation(s)
- Fuwei Li
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Haixia Han
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Qiuxia Lei
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Jinbo Gao
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Jie Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Wei Liu
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Yan Zhou
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Huimin Li
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China.,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China
| | - Dingguo Cao
- Poultry Institute, Shandong Academy of Agricultural Sciences, Jinan, 250023, People's Republic of China. .,Poultry Breeding Engineering Technology Center of Shandong Province, Jinan, 250023, Shandong, China.
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Villanueva S, Ali ABA, Campbell DLM, Siegford JM. Nest use and patterns of egg laying and damage by 4 strains of laying hens in an aviary system. Poult Sci 2018; 96:3011-3020. [PMID: 28431049 PMCID: PMC5850654 DOI: 10.3382/ps/pex104] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/08/2016] [Accepted: 03/26/2017] [Indexed: 11/20/2022] Open
Abstract
Laying hens are strongly motivated to use nests for egg laying, and alternative production systems (e.g., aviaries) provide artificial sites to meet this need and ensure efficient collection of clean, undamaged eggs. However, nests are typically not provided to allow simultaneous use by all hens; therefore, competition or mislaid eggs can result. To understand the influence of strain on laying eggs outside nests and damage to eggs, we compared daily patterns of nests use and egg laying among 4 laying hen strains (Hy-Line Brown (HB), Bovans Brown (BB), DeKalb White (DW), and Hy-Line W36 (W36)). Hens were observed over 3 consecutive days in aviaries with colony nests in the enclosure's top tier (2 nests/unit, 4 aviary units/strain, 144 hens/unit). The number and location of hens in nests and the number, location and condition of eggs throughout aviaries were recorded. Most eggs (90 to 95%) were laid in nests; however, brown hens consistently laid more non-nest eggs and damaged more eggs than white hens (P ≤ 0.05). Higher nest occupancy by brown hens was correlated with more non-nest and damaged eggs (P ≤ 0.05). In the morning, brown hens occupied more nest space and laid more nest eggs than white hens (e.g., HB vs. DW: 82.97 and 34.66% of space; 91.35 and 68.73% of nest eggs; P ≤ 0.05). At midday, white hens occupied more nest space and laid more nest eggs than brown hens (e.g., HB vs. DW: 28.47 and 15.81% of space; 27.39 and 8.29% of nest eggs; P ≤ 0.05). Brown hens preferred right nest compartments and laid more eggs there, whereas white hens preferred left compartments and W36 laid more eggs there (P ≤ 0.05). These findings indicate that different strains of hens have different patterns of nest use and laying behavior. In brown hens, heavy morning nest use was related to laying eggs outside nests and more damaged eggs, suggesting insufficient space for oviposition in nests. Specific facility design should be matched to hens’ preferences to accommodate behavioral needs of different strains.
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Affiliation(s)
- S Villanueva
- Animal Behavior and Welfare Group, Department of Animal Science, Michigan State University, East Lansing, MI
| | - A B A Ali
- Animal Behavior and Welfare Group, Department of Animal Science, Michigan State University, East Lansing, MI
| | - D L M Campbell
- Animal Behavior and Welfare Group, Department of Animal Science, Michigan State University, East Lansing, MI
| | - J M Siegford
- Animal Behavior and Welfare Group, Department of Animal Science, Michigan State University, East Lansing, MI.
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Metodiev S, Thekkoot D, Young J, Onteru S, Rothschild M, Dekkers J. A whole-genome association study for litter size and litter weight traits in pigs. Livest Sci 2018. [DOI: 10.1016/j.livsci.2018.03.004] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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35
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Liu Z, Sun C, Yan Y, Li G, Wu G, Liu A, Yang N. Genome-Wide Association Analysis of Age-Dependent Egg Weights in Chickens. Front Genet 2018; 9:128. [PMID: 29755503 PMCID: PMC5932955 DOI: 10.3389/fgene.2018.00128] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/12/2017] [Accepted: 03/29/2018] [Indexed: 12/22/2022] Open
Abstract
Egg weight (EW) is an economically-important trait and displays a consecutive increase with the hen's age. Because extremely large eggs cause a range of problems in the poultry industry, we performed a genome-wide association study (GWAS) in order to identify genomic variations that are associated with EW. We utilized the Affymetrix 600 K high density SNP array in a population of 1,078 hens at seven time points from day at first egg to 80 weeks age (EW80). Results reveal that a 90 Kb genomic region (169.42 Mb ~ 169.51 Mb) in GGA1 is significantly associated with EW36 and is also potentially associated with egg weight at 28, 56, and 66 week of age. The leading SNP could account for 3.66% of the phenotypic variation, while two promising genes (DLEU7 and MIR15A) can be mapped to this narrow significant region and may affect EW in a pleiotropic manner. In addition, one gene (CECR2 on GGA1) and two genes (MEIS1 and SPRED2 on GGA3), which involved in the processes of embryogenesis and organogenesis, were also considered to be candidates related to first egg weight (FEW) and EW56, respectively. Findings in our study could provide worthy theoretical basis to generate eggs of ideal size based on marker assisted breeding selection.
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Affiliation(s)
- Zhuang Liu
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Congjiao Sun
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yiyuan Yan
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.,Beijing Engineering Research Center of Layer, Beijing, China
| | - Guangqi Li
- Beijing Engineering Research Center of Layer, Beijing, China
| | - Guiqin Wu
- Beijing Engineering Research Center of Layer, Beijing, China
| | - Aiqiao Liu
- Beijing Engineering Research Center of Layer, Beijing, China
| | - Ning Yang
- National Engineering Laboratory for Animal Breeding and MOA Key Laboratory of Animal Genetics and Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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36
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Cross AJ, Keel BN, Brown-Brandl TM, Cassady JP, Rohrer GA. Genome-wide association of changes in swine feeding behaviour due to heat stress. Genet Sel Evol 2018; 50:11. [PMID: 29573750 PMCID: PMC5866911 DOI: 10.1186/s12711-018-0382-1] [Citation(s) in RCA: 21] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2017] [Accepted: 02/26/2018] [Indexed: 12/20/2022] Open
Abstract
Background Heat stress has a negative impact on pork production, particularly during the grow-finish phase. As temperature increases, feeding behaviour changes in order for pigs to decrease heat production. The objective of this study was to identify genetic markers associated with changes in feeding behaviour due to heat stress. Feeding data were collected on 1154 grow-finish pigs using an electronic feeding system from July 2011 to March 2016. In this study, days were classified based on the maximum temperature humidity index (THI) during the day as “Normal” (< 23.33 °C), “Alert” (23.33 °C ≤ × < 26.11 °C), “Danger” (26.11 °C ≤ × < 28.88 °C), and “Emergency” (≥ 28.88 °C). Six hundred and eighty-one pigs that experienced more than one THI category were genotyped using a variety of SNP platforms, with final genotypes imputed to approximately 60,000 markers. Results A genome-wide association study (GWAS) for change in feeding behaviour between each pair of THI categories (six pairs) was conducted. Estimates of heritability for differences in feeding activity between each of the THI categories were low (0.02 ± 0.03) to moderate (0.21 ± 0.04). Sixty-six associations which explained more than 1% of the genomic variation for a trait were detected across the six GWAS, with the smallest number of associations detected in comparisons with Emergency THI. Gene ontology enrichment analysis showed that biological processes related to immune response and function were over-represented among the genes located in these regions. Conclusions Genetic differences exist for changes in feeding behaviour induced by elevated ambient temperatures in grow-finish pigs. Selection for heat-tolerant grow-finish pigs should improve production efficiency during warm months in commercial production. Genetic variation in heat shock, stress response and immune function genes may be responsible for the observed differences in performance during heat stress events.
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Affiliation(s)
- Amanda J Cross
- Department of Animal Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Brittney N Keel
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA
| | | | - Joseph P Cassady
- Department of Animal Science, South Dakota State University, Brookings, SD, 57007, USA
| | - Gary A Rohrer
- USDA, ARS, U.S. Meat Animal Research Center, Clay Center, NE, 68933, USA.
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Hardie L, VandeHaar M, Tempelman R, Weigel K, Armentano L, Wiggans G, Veerkamp R, de Haas Y, Coffey M, Connor E, Hanigan M, Staples C, Wang Z, Dekkers J, Spurlock D. The genetic and biological basis of feed efficiency in mid-lactation Holstein dairy cows. J Dairy Sci 2017; 100:9061-9075. [DOI: 10.3168/jds.2017-12604] [Citation(s) in RCA: 47] [Impact Index Per Article: 6.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/16/2017] [Accepted: 07/12/2017] [Indexed: 12/16/2022]
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38
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Wang YM, Xu HB, Wang MS, Otecko NO, Ye LQ, Wu DD, Zhang YP. Annotating long intergenic non-coding RNAs under artificial selection during chicken domestication. BMC Evol Biol 2017; 17:192. [PMID: 28810830 PMCID: PMC5558714 DOI: 10.1186/s12862-017-1036-6] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/17/2017] [Accepted: 08/04/2017] [Indexed: 12/18/2022] Open
Abstract
Background Numerous biological functions of long intergenic non-coding RNAs (lincRNAs) have been identified. However, the contribution of lincRNAs to the domestication process has remained elusive. Following domestication from their wild ancestors, animals display substantial changes in many phenotypic traits. Therefore, it is possible that diverse molecular drivers play important roles in this process. Results We analyzed 821 transcriptomes in this study and annotated 4754 lincRNA genes in the chicken genome. Our population genomic analysis indicates that 419 lincRNAs potentially evolved during artificial selection related to the domestication of chicken, while a comparative transcriptomic analysis identified 68 lincRNAs that were differentially expressed under different conditions. We also found 47 lincRNAs linked to special phenotypes. Conclusions Our study provides a comprehensive view of the genome-wide landscape of lincRNAs in chicken. This will promote a better understanding of the roles of lincRNAs in domestication, and the genetic mechanisms associated with the artificial selection of domestic animals. Electronic supplementary material The online version of this article (doi:10.1186/s12862-017-1036-6) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Yun-Mei Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hai-Bo Xu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ming-Shan Wang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Newton Otieno Otecko
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Ling-Qun Ye
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China.,University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Dong-Dong Wu
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
| | - Ya-Ping Zhang
- State Key Laboratory of Genetic Resources and Evolution, Kunming Institute of Zoology, Chinese Academy of Sciences, Kunming, 650223, China. .,University of Chinese Academy of Sciences, Beijing, 100049, China.
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Chen C, Steibel JP, Tempelman RJ. Genome-Wide Association Analyses Based on Broadly Different Specifications for Prior Distributions, Genomic Windows, and Estimation Methods. Genetics 2017; 206:1791-1806. [PMID: 28637709 PMCID: PMC5560788 DOI: 10.1534/genetics.117.202259] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2017] [Accepted: 06/19/2017] [Indexed: 11/18/2022] Open
Abstract
A currently popular strategy (EMMAX) for genome-wide association (GWA) analysis infers association for the specific marker of interest by treating its effect as fixed while treating all other marker effects as classical Gaussian random effects. It may be more statistically coherent to specify all markers as sharing the same prior distribution, whether that distribution is Gaussian, heavy-tailed (BayesA), or has variable selection specifications based on a mixture of, say, two Gaussian distributions [stochastic search and variable selection (SSVS)]. Furthermore, all such GWA inference should be formally based on posterior probabilities or test statistics as we present here, rather than merely being based on point estimates. We compared these three broad categories of priors within a simulation study to investigate the effects of different degrees of skewness for quantitative trait loci (QTL) effects and numbers of QTL using 43,266 SNP marker genotypes from 922 Duroc-Pietrain F2-cross pigs. Genomic regions were based either on single SNP associations, on nonoverlapping windows of various fixed sizes (0.5-3 Mb), or on adaptively determined windows that cluster the genome into blocks based on linkage disequilibrium. We found that SSVS and BayesA lead to the best receiver operating curve properties in almost all cases. We also evaluated approximate maximum a posteriori (MAP) approaches to BayesA and SSVS as potential computationally feasible alternatives; however, MAP inferences were not promising, particularly due to their sensitivity to starting values. We determined that it is advantageous to use variable selection specifications based on adaptively constructed genomic window lengths for GWA studies.
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Affiliation(s)
- Chunyu Chen
- Department of Animal Science, Michigan State University, East Lansing, Michigan 48824
| | - Juan P Steibel
- Department of Animal Science, Michigan State University, East Lansing, Michigan 48824
| | - Robert J Tempelman
- Department of Animal Science, Michigan State University, East Lansing, Michigan 48824
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Sollero BP, Junqueira VS, Gomes CCG, Caetano AR, Cardoso FF. Tag SNP selection for prediction of tick resistance in Brazilian Braford and Hereford cattle breeds using Bayesian methods. Genet Sel Evol 2017; 49:49. [PMID: 28619006 PMCID: PMC5471684 DOI: 10.1186/s12711-017-0325-2] [Citation(s) in RCA: 23] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2016] [Accepted: 05/31/2017] [Indexed: 01/01/2023] Open
Abstract
BACKGROUND Cattle resistance to ticks is known to be under genetic control with a complex biological mechanism within and among breeds. Our aim was to identify genomic segments and tag single nucleotide polymorphisms (SNPs) associated with tick-resistance in Hereford and Braford cattle. The predictive performance of a very low-density tag SNP panel was estimated and compared with results obtained with a 50 K SNP dataset. RESULTS BayesB (π = 0.99) was initially applied in a genome-wide association study (GWAS) for this complex trait by using deregressed estimated breeding values for tick counts and 41,045 SNP genotypes from 3455 animals raised in southern Brazil. To estimate the combined effect of a genomic region that is potentially associated with quantitative trait loci (QTL), 2519 non-overlapping 1-Mb windows that varied in SNP number were defined, with the top 48 windows including 914 SNPs and explaining more than 20% of the estimated genetic variance for tick resistance. Subsequently, the most informative SNPs were selected based on Bayesian parameters (model frequency and t-like statistics), linkage disequilibrium and minor allele frequency to propose a very low-density 58-SNP panel. Some of these tag SNPs mapped close to or within genes and pseudogenes that are functionally related to tick resistance. Prediction ability of this SNP panel was investigated by cross-validation using K-means and random clustering and a BayesA model to predict direct genomic values. Accuracies from these cross-validations were 0.27 ± 0.09 and 0.30 ± 0.09 for the K-means and random clustering groups, respectively, compared to respective values of 0.37 ± 0.08 and 0.43 ± 0.08 when using all 41,045 SNPs and BayesB with π = 0.99, or of 0.28 ± 0.07 and 0.40 ± 0.08 with π = 0.999. CONCLUSIONS Bayesian GWAS model parameters can be used to select tag SNPs for a very low-density panel, which will include SNPs that are potentially linked to functional genes. It can be useful for cost-effective genomic selection tools, when one or a few key complex traits are of interest.
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Affiliation(s)
- Bruna P. Sollero
- Embrapa Pecuária Sul, Caixa Postal 242 - BR 153 - Km 633, Bagé, Rio Grande do Sul 96.401-970 Brazil
| | - Vinícius S. Junqueira
- Departamento de Zootecnia, Universidade Federal de Viçosa, Avenida Peter Henry Rolfs, s/n - Campus Universitário, Viçosa, Minas Gerais 36.570-000 Brazil
| | - Cláudia C. G. Gomes
- Embrapa Pecuária Sul, Caixa Postal 242 - BR 153 - Km 633, Bagé, Rio Grande do Sul 96.401-970 Brazil
| | - Alexandre R. Caetano
- Embrapa Recursos Genéticos e Biotecnologia, Parque Estacao Biologica Final Av. W/5 Norte, Brasilia-DF, C.P. 02372, Brasília, Distrito Federal 70770-917 Brazil
| | - Fernando F. Cardoso
- Embrapa Pecuária Sul, Caixa Postal 242 - BR 153 - Km 633, Bagé, Rio Grande do Sul 96.401-970 Brazil
- Universidade Federal de Pelotas, Capão do Leão, Rio Grande do Sul 96.000-010 Brazil
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Thekkoot DM, Young JM, Rothschild MF, Dekkers JCM. Genomewide association analysis of sow lactation performance traits in lines of Yorkshire pigs divergently selected for residual feed intake during grow-finish phase. J Anim Sci 2017; 94:2317-31. [PMID: 27285909 DOI: 10.2527/jas.2015-0258] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Lactation is an economically and biologically important phase in the life cycle of sows. Short generation intervals in nucleus herds and low heritability of traits associated with lactation along with challenges associated with collecting accurate lactation performance phenotypes emphasize the importance of using genomic tools to examine the underlying genetics of these traits. We report the first genomewide association study (GWAS) on traits associated with lactation and efficiency in 2 lines of Yorkshire pigs that were divergently selected for residual feed intake during grow-finish phase. A total of 862 farrowing records from 2 parities were analyzed using a Bayesian whole genome variable selection model (Bayes B) to locate 1-Mb regions that were most strongly associated with each trait. The GWAS was conducted separately for parity 1 and 2 records. Marker-based heritabilities ranged from 0.03 to 0.39 for parity 1 traits and from 0.06 to 0.40 for parity 2 traits. For all traits studied, around 90% of genetic variance came from a large number of genomic regions with small effects, whereas genomic regions with large effects were found to be different for the same trait measured in parity 1 and 2. The highest percentage of genetic variance explained by a 1-Mb window for each trait ranged from 0.4% for feed intake during lactation to 4.2% for back fat measured at farrowing in parity 1 sows and from 0.2% for lactation feed intake to 5.4% for protein mass loss during lactation in parity 2 sows. A total of thirteen 1-Mb nonoverlapping windows were found to explain more than 1.5% of genetic variance for either a single trait or across multiple traits. These 1-Mb windows were on chromosomes 2, 3, 6, 7, 8, 11, 14, 15, 17, and 18. The major positional candidate genes within 1 Mb upstream and downstream of these windows were , (SSC2), (SSC6) (SSC7), (SSC8), (SSC11), (SSC14), (SSC17). Further validation studies on larger populations are required to validate these findings and to improve our understanding of the biology and complex genetic architecture of traits associated with sow lactation performance.
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Lien CY, Tixier-Boichard M, Wu SW, Wang WF, Ng CS, Chen CF. Detection of QTL for traits related to adaptation to sub-optimal climatic conditions in chickens. Genet Sel Evol 2017; 49:39. [PMID: 28427323 PMCID: PMC5399330 DOI: 10.1186/s12711-017-0314-5] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2016] [Accepted: 03/31/2017] [Indexed: 02/06/2023] Open
Abstract
BACKGROUND Growth traits can be used as indicators of adaptation to sub-optimal conditions. The current study aimed at identifying quantitative trait loci (QTL) that control performance under variable temperature conditions in chickens. METHODS An F2 population was produced by crossing the Taiwan Country chicken L2 line (selected for body weight, comb area, and egg production) with an experimental line of Rhode Island Red layer R- (selected for low residual feed consumption). A total of 844 animals were genotyped with the 60 K Illumina single nucleotide polymorphism (SNP) chip. Whole-genome interval linkage mapping and a genome-wide association study (GWAS) were performed for body weight at 0, 4, 8, 12, and 16 weeks of age, shank length at 8 weeks of age, size of comb area at 16 weeks of age, and antibody response to sheep red blood cells at 11 weeks of age (7 and 14 days after primary immunization). Relevant genes were identified based on functional annotation of candidate genes and potentially relevant SNPs were detected by comparing whole-genome sequences of several birds between the parental lines. RESULTS Whole-genome QTL analysis revealed 47 QTL and 714 effects associated with 178 SNPs were identified by GWAS with 5% Bonferroni genome-wide significance. Little overlap was observed between the QTL and GWAS results, with only two chromosomal regions detected by both approaches, i.e. one on GGA24 (GGA for Gallus gallus chromosome) for BW04 and one on GGAZ for six growth-related traits. Based on whole-genome sequence, differences between the parental lines based on several birds were screened in the genome-wide QTL regions and in a region detected by both methods, resulting in the identification of 106 putative candidate genes with a total of 15,443 SNPs, of which 41 were missense and 1698 were not described in the dbSNP archive. CONCLUSIONS The QTL detected in this study for growth and morphological traits likely influence adaptation of chickens to sub-tropical climate. Using whole-genome sequence data, we identified candidate SNPs for further confirmation of QTL in the F2 design. A strong QTL effect found on GGAZ underlines the importance of sex-linked inheritance for growth traits in chickens.
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Affiliation(s)
- Ching-Yi Lien
- GABI, INRA, AgroParisTech, Université Paris-Saclay, 78350, Jouy-en-Josas, France.,Department of Animal Science, National Chung Hsing University, 145 Xingda Rd., South District, Taichung, 40227, Taiwan.,Livestock Research Institute, Council of Agriculture, Executive Yuan, 112 Muchang, Xinhua District, Tainan, 71246, Taiwan
| | | | - Shih-Wen Wu
- Fonghuanggu Bird and Ecology Park, National Museum of Natural Science, 1-9 Renyi Rd., Lugu Township, Nantou County, 55841, Taiwan
| | - Woei-Fuh Wang
- Biodiversity Research Center, Academia Sinica, 128 Academia Rd., Section 2, Nankang, Taipei, 11529, Taiwan
| | - Chen Siang Ng
- Institute of Molecular and Cellular Biology, National Tsing Hua University, No. 101, Section 2, Kuang-Fu Rd., Hsinchu, 30013, Taiwan
| | - Chih-Feng Chen
- Department of Animal Science, National Chung Hsing University, 145 Xingda Rd., South District, Taichung, 40227, Taiwan. .,Center for the Integrative and Evolutionary Galliformes Genomics, National Chung Hsing University, No. 250, Guoguang Rd., South District, Taichung, 40227, Taiwan.
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Application of Whole-Genome Prediction Methods for Genome-Wide Association Studies: A Bayesian Approach. JOURNAL OF AGRICULTURAL BIOLOGICAL AND ENVIRONMENTAL STATISTICS 2017. [DOI: 10.1007/s13253-017-0277-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
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44
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Goto T, Tsudzuki M. Genetic Mapping of Quantitative Trait Loci for Egg Production and Egg Quality Traits in Chickens: a Review. J Poult Sci 2017; 54:1-12. [PMID: 32908402 PMCID: PMC7477176 DOI: 10.2141/jpsa.0160121] [Citation(s) in RCA: 16] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2016] [Accepted: 10/24/2016] [Indexed: 12/11/2022] Open
Abstract
Chickens display a wide spectrum of phenotypic variations in quantitative traits such as egg-related traits. Quantitative trait locus (QTL) analysis is a statistical method used to understand the relationship between phenotypic (trait measurements) and genotypic data (molecular markers). We have performed QTL analyses for egg-related traits using an original resource population based on the Japanese Large Game (Oh-Shamo) and the White Leghorn breeds of chickens. In this article, we summarize the results of our extensive QTL analyses for 11 and 66 traits for egg production and egg quality, respectively. We reveal that at least 30 QTL regions on 17 different chromosomes affect phenotypic variation in egg-related traits. Each locus had an age-specific effect on traits, and a variety in effects was also apparent, such as additive, dominance, and epistatic-interaction effects. Although genome-wide association study (GWAS) is suitable for gene-level resolution mapping of GWAS loci with additive effects, QTL mapping studies enable us to comprehensively understand genetic control, such as chromosomal regions, genetic contribution to phenotypic variance, mode of inheritance, and age-specificity of both common and rare alleles. QTL analyses also describe the relationship between genotypes and phenotypes in experimental populations. Accumulation of QTL information, including GWAS loci, is also useful for studies of population genomics approached without phenotypic data in order to validate the identified genomic signatures of positive selection. The combination of QTL studies and next-generation sequencing techniques with uncharacterized genetic resources will enhance current understanding of the relationship between genotypes and phenotypes in livestock animals.
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Affiliation(s)
- Tatsuhiko Goto
- Genetics, Ecology and Evolution, School of Life Sciences, University of Nottingham, University Park, Nottingham NG7 2RD, UK
- Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
- Present address: Department of Life Science and Agriculture, Obihiro University of Agriculture and Veterinary Medicine, Inada-cho, Obihiro, Hokkaido 080-8555, Japan
| | - Masaoki Tsudzuki
- Japanese Avian Bioresource Project Research Center, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
- Graduate School of Biosphere Science, Hiroshima University, Higashi-Hiroshima, Hiroshima 739-8528, Japan
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Ali ABA, Campbell DLM, Karcher DM, Siegford JM. Influence of genetic strain and access to litter on spatial distribution of 4 strains of laying hens in an aviary system. Poult Sci 2016; 95:2489-2502. [PMID: 27444438 PMCID: PMC5049101 DOI: 10.3382/ps/pew236] [Citation(s) in RCA: 34] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 05/27/2016] [Indexed: 11/25/2022] Open
Abstract
Many laying hen producers are transitioning from conventional cages to new housing systems including multi-tier aviaries. Aviary resources, such as litter areas, are intended to encourage hens’ expression of natural behaviors to improve their welfare. Little research has examined the influence of laying hen strain on distribution and behavior inside aviaries, yet differences could influence a strain's suitability for an aviary design. This research examined how laying hens of 4 strains (Hy-Line Brown [HB], Bovans Brown [BB], DeKalb White [DW], and Hy-Line W36) distributed themselves among 3 enclosed aviary tiers and 2 litter areas at peak lay (25 to 28 wk of age) and after gaining access to litter on the floor (26 wk). Observations of hens’ spatial distribution were conducted immediately before and after, and 3 wk after hens gained access to litter. More HB and BB hens were in upper tiers in morning compared to DW and W36 (all P ≤ 0.05). However, DW and W36 hens roosted in upper tiers in larger numbers than HB and BB during evening (all P ≤ 0.05). More DW and W36 hens were on litter compared to BB and HB, particularly when litter was first accessible (all P ≤ 0.05). The number of hens on litter increased over time for all strains (P ≤ 0.06). White hens on litter occupied open areas in higher numbers (P ≤ 0.05), while more brown hens occupied litter under the aviary after acclimation (P ≤ 0.05). In the dark period, W36 and DW hens were present in higher numbers in upper tiers than HB and BB, while HB and BB showed higher tier-to-tier movement than DW and W36 (P ≤ 0.05). In general, more white hens roosted higher at night and explored litter sooner, while more brown hens were near or in nests in the morning and moved at night. Distinct strain differences indicate that attention should be paid to the match between configuration of the aviary design and strain of laying hen.
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Affiliation(s)
- A B A Ali
- Department of Animal Science, Michigan State University, East Lansing, MI
| | - D L M Campbell
- Department of Animal Science, Michigan State University, East Lansing, MI
| | - D M Karcher
- Department of Animal Science, Michigan State University, East Lansing, MI
| | - J M Siegford
- Department of Animal Science, Michigan State University, East Lansing, MI
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Wang Z, Meng G, Li N, Yu M, Liang X, Min Y, Liu F, Gao Y. The association of very low-density lipoprotein receptor (VLDLR) haplotypes with egg production indicates VLDLR is a candidate gene for modulating egg production. Genet Mol Biol 2016; 39:380-91. [PMID: 27560838 PMCID: PMC5004830 DOI: 10.1590/1678-4685-gmb-2015-0206] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/13/2015] [Accepted: 02/20/2016] [Indexed: 11/21/2022] Open
Abstract
The very low-density lipoprotein receptor (VLDLR) transports egg yolk precursors into oocytes. However, our knowledge of the distribution patterns of VLDLR variants among breeds and their relationship to egg production is still incomplete. In this study, eight single nucleotide polymorphisms (SNPs) that account for 87% of all VLDLR variants were genotyped in Nick Chick (NC, n=91), Lohmann Brown (LohB, n=50) and Lueyang (LY, n=381) chickens, the latter being an Chinese indigenous breed. Egg production by NC and LY chickens was recorded from 17 to 50 weeks. Only four similar haplotypes were found in NC and LohB, of which two accounted for 100% of all NC haplotypes and 92.5% of LohB haplotypes. In contrast, there was considerable haplotypic diversity in LY. Comparison of egg production in LY showed that hens with NC-like haplotypes had a significantly higher production (p < 0.05) than those without the haplotypes. However, VLDLR expression was not significantly different between the haplotypes. These findings indicate a divergence in the distribution of VLDLR haplotypes between selected and non-selected breeds and suggest that the near fixation of VLDLR variants in NC and LohB is compatible with signature of selection. These data also support VLDLR as a candidate gene for modulating egg production.
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Affiliation(s)
- ZhePeng Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - GuoHua Meng
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Na Li
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - MingFen Yu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - XiaoWei Liang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - YuNa Min
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - FuZhu Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - YuPeng Gao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
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Mulder HA, Visscher J, Fablet J. Estimating the purebred-crossbred genetic correlation for uniformity of eggshell color in laying hens. Genet Sel Evol 2016; 48:39. [PMID: 27151311 PMCID: PMC4857450 DOI: 10.1186/s12711-016-0212-2] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2015] [Accepted: 04/01/2016] [Indexed: 11/30/2022] Open
Abstract
Background Uniformity of eggs is an important aspect for retailers because consumers prefer homogeneous products. One of these characteristics is the color of the eggshell, especially for brown eggs. Existence of a genetic component in environmental variance would enable selection for uniformity of eggshell color. Therefore, the objective of this study was to quantify the genetic variance in environmental variance of eggshell color in purebred and crossbred laying hens, to estimate the genetic correlation between environmental variance of eggshell color in purebred and crossbred laying hens and to estimate genetic correlations between environmental variance at different times of the laying period. Methods We analyzed 167,651 and 79,345 eggshell color records of purebred and crossbred laying hens, respectively. The purebred and crossbred laying hens originated mostly from the same sires. Since eggshell color records of crossbred laying hens were collected per cage, these records could be related only to cage and sire family. A double hierarchical generalized linear sire model was used to estimate the genetic variance of the mean of eggshell color and its environmental variance. Approximate standard errors for heritability and the genetic coefficient of variation for environmental variance were derived. Results The genetic variance in environmental variance at the log scale was equal to 0.077 and 0.067, for purebred and crossbred laying hens, respectively. The genetic coefficient of variation for environmental variance was equal to 0.28 and 0.26, for purebred and crossbred laying hens, respectively. A genetic correlation of 0.70 was found between purebred and crossbred environmental variance of eggshell color, which indicates that there is some reranking of sires for environmental variance of eggshell color in purebred and crossbred laying hens. Genetic correlations between environmental variance of eggshell color in different laying periods were generally higher than 0.85, except between early laying and mid or late laying periods. Conclusions Our results indicate that genetic selection can be efficient to improve uniformity of eggshell color in purebreds and crossbreds, ideally by applying combined crossbred and purebred selection. This methodology can be used to estimate genetic correlations between purebred and crossbred lines for uniformity of other traits and species. Electronic supplementary material The online version of this article (doi:10.1186/s12711-016-0212-2) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Han A Mulder
- Animal Breeding and Genomics Centre, Wageningen University & Research, PO Box 338, 6700 AH, Wageningen, The Netherlands.
| | - Jeroen Visscher
- Institut de Sélection Animale B.V., Hendrix Genetics, PO Box 114, 5830 AC, Boxmeer, The Netherlands
| | - Julien Fablet
- Institut de Sélection Animale S.A.S., Hendrix Genetics, 22440, Ploufragan, France
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Ros-Freixedes R, Gol S, Pena RN, Tor M, Ibáñez-Escriche N, Dekkers JCM, Estany J. Genome-Wide Association Study Singles Out SCD and LEPR as the Two Main Loci Influencing Intramuscular Fat Content and Fatty Acid Composition in Duroc Pigs. PLoS One 2016; 11:e0152496. [PMID: 27023885 PMCID: PMC4811567 DOI: 10.1371/journal.pone.0152496] [Citation(s) in RCA: 67] [Impact Index Per Article: 8.4] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/02/2015] [Accepted: 03/15/2016] [Indexed: 11/23/2022] Open
Abstract
Intramuscular fat (IMF) content and fatty acid composition affect the organoleptic quality and nutritional value of pork. A genome-wide association study was performed on 138 Duroc pigs genotyped with a 60k SNP chip to detect biologically relevant genomic variants influencing fat content and composition. Despite the limited sample size, the genome-wide association study was powerful enough to detect the association between fatty acid composition and a known haplotypic variant in SCD (SSC14) and to reveal an association of IMF and fatty acid composition in the LEPR region (SSC6). The association of LEPR was later validated with an independent set of 853 pigs using a candidate quantitative trait nucleotide. The SCD gene is responsible for the biosynthesis of oleic acid (C18:1) from stearic acid. This locus affected the stearic to oleic desaturation index (C18:1/C18:0), C18:1, and saturated (SFA) and monounsaturated (MUFA) fatty acids content. These effects were consistently detected in gluteus medius, longissimus dorsi, and subcutaneous fat. The association of LEPR with fatty acid composition was detected only in muscle and was, at least in part, a consequence of its effect on IMF content, with increased IMF resulting in more SFA, less polyunsaturated fatty acids (PUFA), and greater SFA/PUFA ratio. Marker substitution effects estimated with a subset of 65 animals were used to predict the genomic estimated breeding values of 70 animals born 7 years later. Although predictions with the whole SNP chip information were in relatively high correlation with observed SFA, MUFA, and C18:1/C18:0 (0.48–0.60), IMF content and composition were in general better predicted by using only SNPs at the SCD and LEPR loci, in which case the correlation between predicted and observed values was in the range of 0.36 to 0.54 for all traits. Results indicate that markers in the SCD and LEPR genes can be useful to select for optimum fatty acid profiles of pork.
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Affiliation(s)
- Roger Ros-Freixedes
- Departament de Ciència Animal, Universitat de Lleida–Agrotecnio Center, Lleida, Catalonia, Spain
- * E-mail: (RRF); (JE)
| | - Sofia Gol
- Departament de Ciència Animal, Universitat de Lleida–Agrotecnio Center, Lleida, Catalonia, Spain
| | - Ramona N. Pena
- Departament de Ciència Animal, Universitat de Lleida–Agrotecnio Center, Lleida, Catalonia, Spain
| | - Marc Tor
- Departament de Ciència Animal, Universitat de Lleida–Agrotecnio Center, Lleida, Catalonia, Spain
| | - Noelia Ibáñez-Escriche
- Departament de Ciència Animal, Universitat de Lleida–Agrotecnio Center, Lleida, Catalonia, Spain
- IRTA, Genètica i Millora Animal, Lleida, Catalonia, Spain
| | - Jack C. M. Dekkers
- Department of Animal Science, Iowa State University, Ames, Iowa, United States of America
| | - Joan Estany
- Departament de Ciència Animal, Universitat de Lleida–Agrotecnio Center, Lleida, Catalonia, Spain
- * E-mail: (RRF); (JE)
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Wolc A, Arango J, Settar P, Fulton JE, O’Sullivan NP, Dekkers JCM, Fernando R, Garrick DJ. Mixture models detect large effect QTL better than GBLUP and result in more accurate and persistent predictions. J Anim Sci Biotechnol 2016; 7:7. [PMID: 26870325 PMCID: PMC4750167 DOI: 10.1186/s40104-016-0066-z] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/09/2015] [Accepted: 01/27/2016] [Indexed: 11/24/2022] Open
Abstract
BACKGROUND Accurate evaluation of SNP effects is important for genome wide association studies and for genomic prediction. The genetic architecture of quantitative traits differs widely, with some traits exhibiting few if any quantitative trait loci (QTL) with large effects, while other traits have one or several easily detectable QTL with large effects. METHODS Body weight in broilers and egg weight in layers are two examples of traits that have QTL of large effect. A commonly used method for genome wide association studies is to fit a mixture model such as BayesB that assumes some known proportion of SNP effects are zero. In contrast, the most commonly used method for genomic prediction is known as GBLUP, which involves fitting an animal model to phenotypic data with the variance-covariance or genomic relationship matrix among the animals being determined by genome wide SNP genotypes. Genotypes at each SNP are typically weighted equally in determining the genomic relationship matrix for GBLUP. We used the equivalent marker effects model formulation of GBLUP for this study. We compare these two classes of models using egg weight data collected over 8 generations from 2,324 animals genotyped with a 42 K SNP panel. RESULTS Using data from the first 7 generations, both BayesB and GBLUP found the largest QTL in a similar well-recognized QTL region, but this QTL was estimated to account for 24 % of genetic variation with BayesB and less than 1 % with GBLUP. When predicting phenotypes in generation 8 BayesB accounted for 36 % of the phenotypic variation and GBLUP for 25 %. When using only data from any one generation, the same QTL was identified with BayesB in all but one generation but never with GBLUP. Predictions of phenotypes in generations 2 to 7 based on only 295 animals from generation 1 accounted for 10 % phenotypic variation with BayesB but only 6 % with GBLUP. Predicting phenotype using only the marker effects in the 1 Mb region that accounted for the largest effect on egg weight from generation 1 data alone accounted for almost 8 % variation using BayesB but had no predictive power with GBLUP. CONCLUSIONS In conclusion, In the presence of large effect QTL, BayesB did a better job of QTL detection and its genomic predictions were more accurate and persistent than those from GBLUP.
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Affiliation(s)
- Anna Wolc
- />Department of Animal Science, Iowa State University, 225D Kildee Hall, Ames, IA 50011 USA
- />Hy-Line International, Dallas Center, IA USA
| | | | | | | | | | - Jack C. M. Dekkers
- />Department of Animal Science, Iowa State University, 225D Kildee Hall, Ames, IA 50011 USA
| | - Rohan Fernando
- />Department of Animal Science, Iowa State University, 225D Kildee Hall, Ames, IA 50011 USA
| | - Dorian J. Garrick
- />Department of Animal Science, Iowa State University, 225D Kildee Hall, Ames, IA 50011 USA
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Quantitative Trait Locus and Genetical Genomics Analysis Identifies Putatively Causal Genes for Fecundity and Brooding in the Chicken. G3-GENES GENOMES GENETICS 2015; 6:311-9. [PMID: 26637433 PMCID: PMC4751551 DOI: 10.1534/g3.115.024299] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
Life history traits such as fecundity are important to evolution because they make up components of lifetime fitness. Due to their polygenic architectures, such traits are difficult to investigate with genetic mapping. Therefore, little is known about their molecular basis. One possible way toward finding the underlying genes is to map intermediary molecular phenotypes, such as gene expression traits. We set out to map candidate quantitative trait genes for egg fecundity in the chicken by combining quantitative trait locus mapping in an advanced intercross of wild by domestic chickens with expression quantitative trait locus mapping in the same birds. We measured individual egg fecundity in 232 intercross chickens in two consecutive trials, the second one aimed at measuring brooding. We found 12 loci for different aspects of egg fecundity. We then combined the genomic confidence intervals of these loci with expression quantitative trait loci from bone and hypothalamus in the same intercross. Overlaps between egg loci and expression loci, and trait–gene expression correlations identify 29 candidates from bone and five from hypothalamus. The candidate quantitative trait genes include fibroblast growth factor 1, and mitochondrial ribosomal proteins L42 and L32. In summary, we found putative quantitative trait genes for egg traits in the chicken that may have been affected by regulatory variants under chicken domestication. These represent, to the best of our knowledge, some of the first candidate genes identified by genome-wide mapping for life history traits in an avian species.
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