1
|
Xu W, Wang Z, Tao Z, Li K, Lu L. Discover QTLs for the level of blood components in Shaoxing duck using GWAS and haplotype sharing analysis. Anim Biotechnol 2024; 35:2390940. [PMID: 39137276 DOI: 10.1080/10495398.2024.2390940] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/26/2023] [Accepted: 08/06/2024] [Indexed: 08/15/2024]
Abstract
Blood composition is indicative of health-related traits such as immunity and metabolism. The use of molecular genetics to investigate alterations in these attributes in laying ducks is a novel approach. Our objective was to employ genome - wide association studies (GWAS) and haplotype - sharing analysis to identify genomic regions and potential genes associated with 11 blood components in Shaoxing ducks. Our findings revealed 35 SNPs and 1 SNP associated with low-density lipoprotein cholesterol (LDL) and globulin (GLB), respectively. We identified 36 putative candidate genes for the LDL trait in close proximity to major QTLs and key loci. Based on their biochemical and physiological properties, TRA2A, NPY, ARHGEF26, DHX36, and AADAC are the strongest putative candidate genes. Through linkage disequilibrium analysis and haplotype sharing analysis, we identified three haplotypes and one haplotype, respectively, that were significantly linked with LDL and GLB. These haplotypes could be selected as potential candidate haplotypes for molecular breeding of Shaoxing ducks. Additionally, we utilized a bootstrap test to verify the reliability of GWAS with small experimental samples. The test can be accessed at https://github.com/xuwenwu24/Bootstrap-test.
Collapse
Affiliation(s)
- Wenwu Xu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Science, Hangzhou, China
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zhenzhen Wang
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Zeng Tao
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Science, Hangzhou, China
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| | - Kui Li
- Zhejiang Animal Husbandry Technology Extension and Breeding Livestock & Poultry Testing Station, Hangzhou, Zhejiang, China
| | - Lizhi Lu
- State Key Laboratory for Managing Biotic and Chemical Threats to the Quality and Safety of Agro-Products, Institute of Animal Science and Veterinary, Zhejiang Academy of Agricultural Science, Hangzhou, China
- Institute of Animal Husbandry and Veterinary Medicine, Zhejiang Academy of Agricultural Sciences, Hangzhou, China
| |
Collapse
|
2
|
Song H, Li W, Li Y, Zhai B, Guo Y, Chen Y, Han R, Sun G, Jiang R, Li Z, Yan F, Li G, Liu X, Zhang Y, Tian Y, Kang X. Genome-wide association study of 17 serum biochemical indicators in a chicken F 2 resource population. BMC Genomics 2023; 24:98. [PMID: 36864386 PMCID: PMC9983160 DOI: 10.1186/s12864-023-09206-7] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2022] [Accepted: 02/23/2023] [Indexed: 03/04/2023] Open
Abstract
BACKGROUND Serum biochemical indicators are often regarded as direct reflections of animal metabolism and health. The molecular mechanisms underlying serum biochemical indicators metabolism of chicken (Gallus Gallus) have not been elucidated. Herein, we performed a genome-wide association study (GWAS) to identify the variation associated with serum biochemical indicators. The aim of this research was to broaden the understanding of the serum biochemical indicators in chickens. RESULTS A GWAS of serum biochemical indicators was carried out on 734 samples from an F2 Gushi× Anka chicken population. All chickens were genotyped by sequencing, 734 chickens and 321,314 variants were obtained after quality control. Based on these variants, a total of 236 single-nucleotide polymorphisms (SNPs) on 9 chicken chromosomes (GGAs) were identified to be significantly (-log10(P) > 5.72) associated with eight of seventeen serum biochemical indicators. Ten novel quantitative trait locis (QTLs) were identified for the 8 serum biochemical indicator traits of the F2 population. Literature mining revealed that the ALPL, BCHE, GGT2/GGT5 genes at loci GGA24, GGA9 and GGA15 might affect the alkaline phosphatase (AKP), cholinesterase (CHE) and γ-glutamyl transpeptidase (GGT) traits, respectively. CONCLUSION The findings of the present study may contribute to a better understanding of the molecular mechanisms of chicken serum biochemical indicator regulation and provide a theoretical basis for chicken breeding programs.
Collapse
Affiliation(s)
- Haijie Song
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China
| | - Wenting Li
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China
| | - Yuanfang Li
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China
| | - Bin Zhai
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China
| | - Yujie Guo
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China
| | - Yi Chen
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China
| | - Ruili Han
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China
| | - Guirong Sun
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China
| | - Ruirui Jiang
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China
| | - Zhuanjian Li
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China
| | - Fengbin Yan
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China
| | - Guoxi Li
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China
| | - Xiaojun Liu
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China
| | - Yanhua Zhang
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China.
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China.
| | - Yadong Tian
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China.
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China.
| | - Xiangtao Kang
- College of Animal Science and Technology, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China.
- Henan Key Laboratory for Innovation and Utilization of Chicken Germplasm Resources, Henan Agricultural University, No.15 Longzihu University Area, Zhengzhou New District, 450002, Zhengzhou, China.
| |
Collapse
|
3
|
Bovo S, Ballan M, Schiavo G, Gallo M, Dall'Olio S, Fontanesi L. Haplotype-based genome-wide association studies reveal new loci for haematological and clinical-biochemical parameters in Large White pigs. Anim Genet 2020; 51:601-606. [PMID: 32511786 DOI: 10.1111/age.12959] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/30/2019] [Revised: 02/24/2020] [Accepted: 05/02/2020] [Indexed: 01/21/2023]
Abstract
We report haplotype-based GWASs for 33 blood parameters measured in 843 Italian Large White pigs. In the single-trait analysis, a total of 30 QTL for number of basophils, six erythrocyte traits (haemoglobin, haematocrit, mean corpuscular haemoglobin, mean corpuscular haemoglobin concentration, mean corpuscular volume and red blood cell count) and two clinical-biochemical traits (alkaline phosphatase and Ca2+ contents) were identified. In the multiple-trait analysis, a total of five QTL affected three different clusters of traits. Only four of these QTL were already reported in the single-marker and multi-marker GWASs we previously carried out on the same pig population. QTL on SSC11 and SSC17 showed effects on multiple traits. These results further dissected the genetic architecture of parameters that could be used as proxies in breeding programmes for more complex traits. In addition, these results might help to better define the pig as an animal model for several blood-related biological functions.
Collapse
Affiliation(s)
- S Bovo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, Bologna, 40127, Italy
| | - M Ballan
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, Bologna, 40127, Italy
| | - G Schiavo
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, Bologna, 40127, Italy
| | - M Gallo
- Associazione Nazionale Allevatori Suini, Via Nizza 53, Roma, 00198, Italy
| | - S Dall'Olio
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, Bologna, 40127, Italy
| | - L Fontanesi
- Department of Agricultural and Food Sciences, Division of Animal Sciences, University of Bologna, Viale G. Fanin 46, Bologna, 40127, Italy
| |
Collapse
|
4
|
Reyer H, Oster M, Wittenburg D, Murani E, Ponsuksili S, Wimmers K. Genetic Contribution to Variation in Blood Calcium, Phosphorus, and Alkaline Phosphatase Activity in Pigs. Front Genet 2019; 10:590. [PMID: 31316547 PMCID: PMC6610066 DOI: 10.3389/fgene.2019.00590] [Citation(s) in RCA: 15] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Accepted: 06/04/2019] [Indexed: 12/18/2022] Open
Abstract
Blood values of calcium (Ca), inorganic phosphorus (IP), and alkaline phosphatase activity (ALP) are valuable indicators for mineral status and bone mineralization. The mineral homeostasis is maintained by absorption, retention, and excretion processes employing a number of known and unknown sensing and regulating factors with implications on immunity. Due to the high inter-individual variation of Ca and P levels in the blood of pigs and to clarify molecular contributions to this variation, the genetics of hematological traits related to the Ca and P balance were investigated in a German Landrace population, integrating both single-locus and multi-locus genome-wide association study (GWAS) approaches. Genomic heritability estimates suggest a moderate genetic contribution to the variation of hematological Ca (N = 456), IP (N = 1049), ALP (N = 439), and the Ca/P ratio (N = 455), with values ranging from 0.27 to 0.54. The genome-wide analysis of markers adds a number of genomic regions to the list of quantitative trait loci, some of which overlap with previous results. Despite the gaps in knowledge of genes involved in Ca and P metabolism, genes like THBS2, SHH, PTPRT, PTGS1, and FRAS1 with reported connections to bone metabolism were derived from the significantly associated genomic regions. Additionally, genomic regions included TRAFD1 and genes coding for phosphate transporters (SLC17A1-SLC17A4), which are linked to Ca and P homeostasis. The study calls for improved functional annotation of the proposed candidate genes to derive features involved in maintaining Ca and P balance. This gene information can be exploited to diagnose and predict characteristics of micronutrient utilization, bone development, and a well-functioning musculoskeletal system in pig husbandry and breeding.
Collapse
Affiliation(s)
- Henry Reyer
- Genomics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Michael Oster
- Genomics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Dörte Wittenburg
- Biomathematics and Bioinformatics Unit, Institute of Genetics and Biometry, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Eduard Murani
- Genomics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Siriluck Ponsuksili
- Functional Genome Analysis Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany
| | - Klaus Wimmers
- Genomics Unit, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology, Dummerstorf, Germany.,Department of Animal Breeding and Genetics, Faculty of Agricultural and Environmental Sciences, University of Rostock, Rostock, Germany
| |
Collapse
|
5
|
Zhu F, Cui QQ, Yang YZ, Hao JP, Yang FX, Hou ZC. Genome-wide association study of the level of blood components in Pekin ducks. Genomics 2019; 112:379-387. [PMID: 30818062 DOI: 10.1016/j.ygeno.2019.02.017] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/12/2018] [Revised: 01/12/2019] [Accepted: 02/22/2019] [Indexed: 12/29/2022]
Abstract
Blood components are considered to reflect nutrient metabolism and immune activity in both humans and animals. In this study, we measured 12 blood components in Pekin ducks and performed genome-wide association analysis to identify the QTLs (quantitative trait locus) using a genotyping-by-sequencing strategy. A total of 54 QTLs were identified for blood components. One genome-wide significant QTL for alkaline phosphatase was identified within the intron-region of the OTOG gene (P = 1.31E-07). Moreover, 21 genome-wide significant SNPs for the level of serum cholinesterase were identified on six different scaffolds. In addition, for serum calcium, one genome-wide significant QTL was identified in the upstream region of gene RAB11B. These results provide new markers for functional studies in Pekin ducks, and several candidate genes were identified, which may provide additional insights into specific mechanisms for blood metabolism in ducks and their potential application for duck breeding programs.
Collapse
Affiliation(s)
- Feng Zhu
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Qian-Qian Cui
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China
| | - Yu-Ze Yang
- Beijing General Station of Animal Husbandry, Beijing 100107, China
| | | | | | - Zhuo-Cheng Hou
- National Engineering Laboratory for Animal Breeding and Key Laboratory of Animal Genetics, Breeding and Reproduction, MARA, Department of Animal Genetics and Breeding, China Agricultural University, Beijing 100193, China.
| |
Collapse
|
6
|
Just F, Reyer H, Muráni E, Ponsuksili S, Oster M, Wimmers K. Genetic variants of major genes contributing to phosphate and calcium homeostasis and their association with serum parameters in pigs. J Appl Genet 2018; 59:325-333. [PMID: 29931419 PMCID: PMC6061000 DOI: 10.1007/s13353-018-0449-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/26/2017] [Revised: 04/12/2018] [Accepted: 06/08/2018] [Indexed: 12/29/2022]
Abstract
Calcium and phosphorus are irreplaceable components of life. Tracking the fate of calcium and phosphorus in organisms deserves high attention due to their relevance in bone metabolism and subsequently animal health. Indeed, bone serves as reservoir for calcium and phosphorus, whose formation and resorption follow specific molecular routes including hormones, receptors, and transcription factors. The objective of the study was to analyze the genetic variation of major components driving mineral utilization such as calcitonin receptor, calcium sensing receptor, fibroblast growth factor 23 (FGF23), parathyroid hormone receptor, osteopontin, stanniocalcin 1, RAF-type zinc finger domain containing 1 (TRAFD1), and vitamin D receptor. A German Landrace pig population (n = 360) was used to perform an association analysis between selected single nucleotide polymorphisms (SNP) and relevant serum parameters (calcium, phosphorus, calcium/phosphorus ratio, alkaline phosphatase). Analyzed SNPs in FGF23 (rs710498025) and TRAFD1 (rs345195312) were significantly (p ≤ 0.05) associated with the serum calcium/phosphorus ratio and serum phosphorus levels, respectively. This might represent a modulation of the homeostatic balance between calcium and phosphorus. Furthermore, TRAFD1 is known to be involved in skeletal disorders which emphasize its link to phosphorus utilization and immune system. However, none of the analyzed genetic variants of these major regulators of phosphate and calcium homeostasis showed significant associations after correction for multiple testing (q value > 0.05). Thus, minor contributors as well as unknown and yet to be elucidated regulators of mineral homeostasis need to be characterized towards the implementation of improved phosphorus efficiency in pig breeding programs.
Collapse
Affiliation(s)
- Franziska Just
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Henry Reyer
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Eduard Muráni
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Siriluck Ponsuksili
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Michael Oster
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany
| | - Klaus Wimmers
- Institute of Genome Biology, Leibniz Institute for Farm Animal Biology, Wilhelm-Stahl-Allee 2, 18196, Dummerstorf, Germany. .,Faculty of Agricultural and Environmental Sciences, University Rostock, 18059, Rostock, Germany.
| |
Collapse
|
7
|
Ponsuksili S, Reyer H, Trakooljul N, Murani E, Wimmers K. Single- and Bayesian Multi-Marker Genome-Wide Association for Haematological Parameters in Pigs. PLoS One 2016; 11:e0159212. [PMID: 27434032 PMCID: PMC4951017 DOI: 10.1371/journal.pone.0159212] [Citation(s) in RCA: 18] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/31/2016] [Accepted: 06/28/2016] [Indexed: 12/15/2022] Open
Abstract
Haematological traits are important traits that show associations with immune and metabolic status, as well as diseases in humans and animals. Mapping genome regions that affect the blood cell traits can contribute to the identification of genomic features useable as biomarkers for immune, disease and metabolic status. A genome-wide association study (GWAS) was conducted using PorcineSNP60 BeadChips. Single-marker and Bayesian multi-marker approaches were integrated to identify genomic regions and corresponding genes overlapping for both methods. GWAS was performed for haematological traits of 591 German Landrace pig. Heritability estimates for haematological traits were medium to high. In total 252 single SNPs associated with 12 haematological traits were identified (NegLog10 of p-value > 5). The Bayesian multi-marker approach revealed 102 QTL regions across the genome, indicated by 1-Mb windows with contribution to additive genetic variance above 0.5%. The integration of both methods resulted in 24 overlapping QTL regions. This study identified overlapping QTL regions from single- and multi-marker approaches for haematological traits. Identifying candidate genes that affect blood cell traits provides the first step towards the understanding of the molecular basis of haematological phenotypes.
Collapse
Affiliation(s)
- Siriluck Ponsuksili
- Research Unit ‘Functional Genome Analyses’, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany
| | - Henry Reyer
- Research Unit ‘Genomics’, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany
| | - Nares Trakooljul
- Research Unit ‘Genomics’, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany
| | - Eduard Murani
- Research Unit ‘Genomics’, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany
| | - Klaus Wimmers
- Research Unit ‘Genomics’, Institute for Genome Biology, Leibniz Institute for Farm Animal Biology (FBN), Wilhelm-Stahl-Allee 2, D-18196, Dummerstorf, Germany
- * E-mail:
| |
Collapse
|
8
|
Bovo S, Schiavo G, Mazzoni G, Dall'Olio S, Galimberti G, Calò DG, Scotti E, Bertolini F, Buttazzoni L, Samorè AB, Fontanesi L. Genome-wide association study for the level of serum electrolytes in Italian Large White pigs. Anim Genet 2016; 47:597-602. [DOI: 10.1111/age.12459] [Citation(s) in RCA: 10] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Accepted: 04/19/2016] [Indexed: 01/15/2023]
Affiliation(s)
- S. Bovo
- Department of Agricultural and Food Sciences; Division of Animal Sciences; University of Bologna; Viale Fanin 46 40127 Bologna Italy
| | - G. Schiavo
- Department of Agricultural and Food Sciences; Division of Animal Sciences; University of Bologna; Viale Fanin 46 40127 Bologna Italy
| | - G. Mazzoni
- Department of Agricultural and Food Sciences; Division of Animal Sciences; University of Bologna; Viale Fanin 46 40127 Bologna Italy
| | - S. Dall'Olio
- Department of Agricultural and Food Sciences; Division of Animal Sciences; University of Bologna; Viale Fanin 46 40127 Bologna Italy
| | - G. Galimberti
- Department of Statistical Sciences “Paolo Fortunati”; University of Bologna; Via delle Belle Arti 41 40126 Bologna Italy
| | - D. G. Calò
- Department of Statistical Sciences “Paolo Fortunati”; University of Bologna; Via delle Belle Arti 41 40126 Bologna Italy
| | - E. Scotti
- Department of Agricultural and Food Sciences; Division of Animal Sciences; University of Bologna; Viale Fanin 46 40127 Bologna Italy
| | - F. Bertolini
- Department of Agricultural and Food Sciences; Division of Animal Sciences; University of Bologna; Viale Fanin 46 40127 Bologna Italy
| | - L. Buttazzoni
- Centro di Ricerca per la Produzione delle Carni e il Miglioramento Genetico; Consiglio per la Ricerca in agricoltura e l'analisi dell'Economia Agraria (CREA); Via Salaria 31 00015 Monterotondo (RM) Italy
| | - A. B. Samorè
- Department of Agricultural and Food Sciences; Division of Animal Sciences; University of Bologna; Viale Fanin 46 40127 Bologna Italy
| | - L. Fontanesi
- Department of Agricultural and Food Sciences; Division of Animal Sciences; University of Bologna; Viale Fanin 46 40127 Bologna Italy
| |
Collapse
|
9
|
Van Goor A, Ashwell CM, Persia ME, Rothschild MF, Schmidt CJ, Lamont SJ. Quantitative trait loci identified for blood chemistry components of an advanced intercross line of chickens under heat stress. BMC Genomics 2016; 17:287. [PMID: 27076351 PMCID: PMC4831167 DOI: 10.1186/s12864-016-2601-x] [Citation(s) in RCA: 23] [Impact Index Per Article: 2.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/26/2016] [Accepted: 03/22/2016] [Indexed: 12/25/2022] Open
Abstract
BACKGROUND Heat stress in poultry results in considerable economic losses and is a concern for both animal health and welfare. Physiological changes occur during periods of heat stress, including changes in blood chemistry components. A highly advanced intercross line, created from a broiler (heat susceptible) by Fayoumi (heat resistant) cross, was exposed to daily heat cycles for seven days starting at 22 days of age. Blood components measured pre-heat treatment and on the seventh day of heat treatment included pH, pCO2, pO2, base excess, HCO3, TCO2, K, Na, ionized Ca, hematocrit, hemoglobin, sO2, and glucose. A genome-wide association study (GWAS) for these traits and their calculated changes was conducted to identify quantitative trait loci (QTL) using a 600 K SNP panel. RESULTS There were significant increases in pH, base excess, HCO3, TCO2, ionized Ca, hematocrit, hemoglobin, and sO2, and significant decreases in pCO2 and glucose after 7 days of heat treatment. Heritabilities ranged from 0.01-0.21 for pre-heat measurements, 0.01-0.23 for measurements taken during heat, and 0.00-0.10 for the calculated change due to heat treatment. All blood components were highly correlated within measurement days, but not correlated between measurement days. The GWAS revealed 61 QTL for all traits, located on GGA (Gallus gallus chromosome) 1, 3, 6, 9, 10, 12-14, 17, 18, 21-28, and Z. A functional analysis of the genes in these QTL regions identified the Angiopoietin pathway as significant. The QTL that co-localized for three or more traits were on GGA10, 22, 26, 28, and Z and revealed candidate genes for birds' response to heat stress. CONCLUSIONS The results of this study contribute to our knowledge of levels and heritabilities of several blood components of chickens under thermoneutral and heat stress conditions. Most components responded to heat treatment. Mapped QTL may serve as markers for genomic selection to enhance heat tolerance in poultry. The Angiopoietin pathway is likely involved in the response to heat stress in chickens. Several candidate genes were identified, giving additional insight into potential mechanisms of physiologic response to high ambient temperatures.
Collapse
Affiliation(s)
| | | | - Michael E Persia
- Department of Animal and Poultry Sciences, Virginia Polytechnic Institute and State University, Blacksburg, VA, USA
| | - Max F Rothschild
- Department of Animal Science, Iowa State University, Ames, IA, USA
| | - Carl J Schmidt
- Department of Animal and Food Sciences, University of Delaware, Newark, DE, USA
| | - Susan J Lamont
- Department of Animal Science, Iowa State University, Ames, IA, USA.
| |
Collapse
|
10
|
Hofmaier F, Dinger K, Braun R, Sterner-Kock A. Range of blood lactate values in farm pigs prior to experimental surgery. Lab Anim 2013; 47:130-2. [PMID: 23479774 DOI: 10.1177/0023677213476857] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/21/2023]
Abstract
In biomedical research the pig is widely used as an animal model for experimental surgery. Feasible monitoring tools during anaesthesia are pivotal for successful and reliable research outcome. Blood lactate values are a monitoring tool and prognostic indicator during surgery both in humans and animals. Lactate levels in pigs might be influenced by various parameters including stressful handling, breed and weight differences. To determine blood lactate levels present prior to experimental surgery, values of 124 female farm pigs were measured in venous blood samples. Pigs presented with blood lactate concentrations ranging from 0.5 to 5.5 mmol/L (median, 1.2 mmol/L; interquartile range [IQR] 1.2). Considering genetic background, Rheinhybrid/Pietrain pigs (n = 51; median, 1.4 mmol/L; IQR, 1) had significantly higher blood lactate levels compared with Landrace/Pietrain crossbred animals (n = 73; median, 1.1 mmol/L; IQR, 1; P < 0.05). Body weight had no significant effect on blood lactate levels within the evaluated range. This report can benefit research projects monitoring blood lactate values in farm pigs during experimental surgery.
Collapse
Affiliation(s)
- F Hofmaier
- Experimentelle Medizin, Uniklinik Köln, University of Cologne, Robert-Koch-Strasse 10, Building 51 A, 50931 Cologne, Germany.
| | | | | | | |
Collapse
|
11
|
Zhou X, Jiang T, Du X, Zhou P, Jiang Z, Michal JJ, Liu B. Molecular characterization of porcine SARM1 and its role in regulating TLRs signaling during highly pathogenic porcine reproductive and respiratory syndrome virus infection in vivo. DEVELOPMENTAL AND COMPARATIVE IMMUNOLOGY 2013; 39:117-126. [PMID: 22366489 DOI: 10.1016/j.dci.2012.02.001] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/08/2011] [Revised: 02/07/2012] [Accepted: 02/08/2012] [Indexed: 05/31/2023]
Abstract
Toll-like receptors (TLRs) are important pattern-recognition receptors (PRRs) that trigger innate immune response and mediate acquired immunity. Evidence has shown that SARM1 (sterile-α and TIR motif containing protein 1) is one of five TIR domain-containing adaptor proteins involved in TLRs signaling transduction. In the present study, a full-length cDNA sequence was cloned for the porcine SARM1 gene, which contains nine exons. Using the radiation hybrid mapping approach, we assigned the porcine gene to SSC12 q13. Under the normal condition, porcine SARM1 was highly expressed in brain and spleen. Polyinosinic-polycytidylic acid (poly (I:C)) weakly induced the porcine SARM1 expression in the early stimulation. We found that porcine SARM1 protein is localized in mitochondria and attenuates NF-κB activation induced by stimulation and infection. The quantitative real-time PCR (Q-PCR) analysis showed that the expression of porcine SARM1 significantly decreased in several tissues of Tongcheng pigs infected with highly pathogenic porcine reproductive and respiratory syndrome virus (HP-PRRSV). Gene-interaction network analysis for porcine SARM1 in porcine alveolar macrophages (PAMs) showed that down-regulation of SARM1 gene in infected Tongcheng pig may modulate TRIF-depend TLRs signaling and regulate the expression of disease-resistant genes and inflammatory genes. Our findings provide evidence that porcine SARM1 may play an important role in immune regulation with PRRSV infection.
Collapse
Affiliation(s)
- Xiang Zhou
- Key Lab of Agricultural Animal Genetics, Breeding, and Reproduction of Ministry of Education & Key Lab of Swine Genetics and Breeding of Ministry of Agriculture, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070 Hubei, PR China
| | | | | | | | | | | | | |
Collapse
|
12
|
A missense mutation (c.1963A<G) of the complementary component 2 (C2) gene is associated with serum Ca⁺⁺ concentrations in pigs. Mol Biol Rep 2012; 39:9291-7. [PMID: 22763733 DOI: 10.1007/s11033-012-1679-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/24/2011] [Accepted: 06/05/2012] [Indexed: 10/28/2022]
Abstract
Serum Ca(++) levels play important roles in the humoral immunity. The aim of this study was to detect quantitative trait loci and the associated positional candidate genes affecting baseline serum Ca(++) concentrations. A genome-wide association study was conducted in an F(2) intercross population between Landrace and Korean native pigs using the porcine single nucleotide polymorphism (SNP) 60 K beadchip and the PLINK program based on linear regression. Data used in the study included 410 F(2) pigs. All experimental animals were genotyped with 36,613 SNP markers located throughout the pig autosomes. We identified a strong association between a SNP marker on chromosome 7 and serum Ca(++) levels (DIAS0002191, genomic control-corrected P = 7.7 × 10(-5)). The position of DIAS0002191 was closely located to SLA class III region containing the C2 gene encoding the complementary component 2 protein, a protein which is important in the humoral immune responses. De novo sequencing of the porcine C2 gene revealed a missense mutation [c.1963A<G (N655D)] and this missense mutation was also strongly associated with serum Ca(++) concentrations (genomic control-corrected P = 5.9 × 10(-5)). Further studies are necessary to investigate the effect of this missense mutation at a functional-molecular level. In conclusion, the missense mutation of the C2 gene identified in this study may help in elucidating the genetic factors underlying humoral immune reactions.
Collapse
|
13
|
Yoo CK, Cho IC, Lee JB, Jung EJ, Lim HT, Han SH, Lee SS, Ko MS, Kang T, Hwang JH, Park YS, Park HB. QTL analysis of clinical-chemical traits in an F₂ intercross between Landrace and Korean native pigs. Physiol Genomics 2012; 44:657-68. [PMID: 22496488 DOI: 10.1152/physiolgenomics.00172.2011] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/02/2023] Open
Abstract
Clinical-chemical traits are essential when examining the health status of individuals. The aim of this study was to identify quantitative trait loci (QTL) and the associated positional candidate genes affecting clinical-chemical traits in a reciprocal F(2) intercross between Landrace and Korean native pigs. Following an overnight fast, 25 serum phenotypes related to clinical-chemical traits (e.g., hepatic function parameters, renal function parameters, electrolyte, lipids) were measured in >970 F(2) progeny. All experimental samples were subjected to genotyping analysis using 165 microsatellite markers located across the genome. We identified eleven genome-wide significant QTL in six chromosomal regions (SSC 2, 7, 8, 13, 14, and 15) and 59 suggestive QTL in 17 chromosomal regions (SSC 1, 2, 3, 4, 5, 6, 7, 8, 9, 10, 12, 13, 14, 15, 16, 17, and 18). We also observed significant effects of reciprocal crosses on some of the traits, which would seem to result from maternal effect, QTL on sex chromosomes, imprinted genes, or genetic difference in mitochondrial DNA. The role of genomic imprinting in clinical-chemical traits also was investigated. Genome-wide analysis revealed a significant evidence for an imprinted QTL in SSC4 affecting serum amylase levels. Additionally, a series of bivariate linkage analysis provided strong evidence that QTL in SSC 2, 13, 15, and 18 have a pleiotropic effect on clinical-chemical traits. In conclusion, our study detected both novel and previously reported QTL influencing clinical-chemical traits in pigs. The identified QTL together with the positional candidate genes identified here could play an important role in elucidating the genetic structure of clinical-chemical phenotype variation in humans and swine.
Collapse
Affiliation(s)
- Chae-Kyoung Yoo
- Animal Science Major, Division of Applied Life Science (Brain Korea 21 Program) Gyeongsang National University, Jinju, Korea
| | | | | | | | | | | | | | | | | | | | | | | |
Collapse
|
14
|
Nielson CM, Zmuda JM, Carlos AS, Wagoner WJ, Larson EA, Orwoll ES, Klein RF. Rare coding variants in ALPL are associated with low serum alkaline phosphatase and low bone mineral density. J Bone Miner Res 2012; 27:93-103. [PMID: 21956185 PMCID: PMC3810303 DOI: 10.1002/jbmr.527] [Citation(s) in RCA: 34] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Submit a Manuscript] [Subscribe] [Scholar Register] [Received: 05/24/2011] [Revised: 09/12/2011] [Accepted: 09/22/2011] [Indexed: 12/17/2022]
Abstract
Alkaline phosphatase (ALP) plays an essential role in the regulation of tissue mineralization, and its activity is highly heritable. Guided by genetic associations discovered in a murine model, we hypothesized a role for rare coding variants in determining serum ALP level and bone mineral density (BMD) in humans. We sequenced the coding regions of the ALP gene (ALPL) in men with low and normal serum ALP activity levels. Single-nucleotide ALPL variants, including 19 rare nonsynonymous variants (minor allele frequency <1%), were much more frequent among the low ALP group (33.8%) than the normal group (1.4%, p = 1 × 10(-11)). Within the low ALP group, men with a rare, nonsynonymous variant had 11.2% lower mean serum ALP (p = 3.9 × 10(-4)), 6.7% lower BMD (p = 0.03), and 11.1% higher serum phosphate (p = 0.002) than those without. In contrast, common nonsynonymous variants had no association with serum ALP, phosphate, or BMD. Multiple rare ALPL coding variants are present in the general population, and nonsynonymous coding variants may be responsible for heritable differences in mineralization and thus BMD.
Collapse
Affiliation(s)
- Carrie M Nielson
- Public Health and Preventive Medicine, Oregon Health & Science University, Portland, OR, USA
- Bone and Mineral Research Unit, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Joseph M Zmuda
- Department of Epidemiology, University of Pittsburgh, Pittsburgh, PA, USA
- Department of Human Genetics, University of Pittsburgh, Pittsburgh, PA, USA
| | - Amy S Carlos
- Bone and Mineral Research Unit, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Wendy J Wagoner
- Bone and Mineral Research Unit, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Emily A Larson
- Bone and Mineral Research Unit, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Eric S Orwoll
- Bone and Mineral Research Unit, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
| | - Robert F Klein
- Bone and Mineral Research Unit, Department of Medicine, Oregon Health & Science University, Portland, OR, USA
- Portland Veterans Affairs Medical Center, Portland, OR, USA
| |
Collapse
|
15
|
Lunney JK, Chen H. Genetic control of host resistance to porcine reproductive and respiratory syndrome virus (PRRSV) infection. Virus Res 2010; 154:161-9. [PMID: 20709118 DOI: 10.1016/j.virusres.2010.08.004] [Citation(s) in RCA: 59] [Impact Index Per Article: 4.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2010] [Accepted: 08/05/2010] [Indexed: 12/30/2022]
Abstract
This manuscript focuses on the advances made using genomic approaches to identify biomarkers that define genes and pathways that are correlated with swine resistance to infection with porcine reproductive and respiratory syndrome virus (PRRSV), the most economically important swine viral pathogen worldwide. International efforts are underway to assess resistance and susceptibility to infectious pathogens using tools such as gene arrays, single nucleotide polymorphisms (SNPs) chips, genome-wide association studies (GWAS), proteomics, and advanced bioinformatics. These studies should identify new candidate genes and biological pathways associated with host PRRS resistance and alternate viral disease processes and mechanisms; they may unveil biomarkers that account for genetic control of PRRS or, alternately, that reveal new targets for therapeutics or vaccines. Previous genomic approaches have expanded our understanding of quantitative trait loci (QTL) controlling traits of economic importance in pig production, e.g., feed efficiency, meat production, leanness; only recently have these included health traits and disease resistance. Genomic studies should have substantial impact for the pig industry since it is now possible to include the use of biomarkers for basic health traits alongside broader set of markers utilized for selection of pigs for improved performance and reproductive traits, as well as pork quality. Additionally these studies may reveal alternate PRRS control mechanisms that can be exploited for novel drugs, biotherapeutics and vaccine designs.
Collapse
Affiliation(s)
- Joan K Lunney
- Animal Parasitic Diseases Laboratory, ANRI, ARS, USDA, BARC-East, Beltsville, MD 20705, USA.
| | | |
Collapse
|
16
|
Reiner G, Clemens N, Lohner E, Willems H. SNPs in the porcine GOT1 gene improve a QTL for serum aspartate aminotransferase activity on SSC14. Anim Genet 2009; 41:319-23. [PMID: 19968637 DOI: 10.1111/j.1365-2052.2009.01997.x] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Abstract
Clinical-chemical traits are essential parameters to quantify the health status of individuals and herds, but the knowledge about their genetic architecture is sparse, especially in swine. We have recently described three QTL for serum aspartate aminotransferase activity (sAST), and one of these maps to a region on SSC14 where the aspartate aminotransferase coding gene GOT1 is located. This QTL was only apparent under the acute burden of a model disease. The aim of the present study was to characterize GOT1 as a candidate gene and to test the effects of different GOT1 SNPs as potential quantitative trait nucleotides (QTNs) for sAST. Nine SNPs within GOT1 were identified, and SNP c.-793C>G significantly increased the QTL effects and narrowed the confidence interval from 90 to 15 cM. Additionally, we found a significant association of SNP c.-793C>G in a commercial outbred line, but with reversed phase. We conclude that GOT1 is a putative candidate gene for the sAST QTL on SSC14, and that SNP c.-793C>G is close to the responsible QTN.
Collapse
Affiliation(s)
- G Reiner
- Department of Veterinary Clinical Sciences, Justus-Liebig-University, D-35392 Giessen, Germany.
| | | | | | | |
Collapse
|
17
|
Reiner G, Köhler F, Berge T, Fischer R, Hübner-Weitz K, Scholl J, Willems H. Mapping of quantitative trait loci affecting behaviour in swine. Anim Genet 2009; 40:366-76. [DOI: 10.1111/j.1365-2052.2008.01847.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/15/2023]
|