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Zhao Q, Huang C, Chen Q, Su Y, Zhang Y, Wang R, Su R, Xu H, Liu S, Ma Y, Zhao Q, Ye S. Genomic Inbreeding and Runs of Homozygosity Analysis of Cashmere Goat. Animals (Basel) 2024; 14:1246. [PMID: 38672394 PMCID: PMC11047310 DOI: 10.3390/ani14081246] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2024] [Revised: 04/15/2024] [Accepted: 04/18/2024] [Indexed: 04/28/2024] Open
Abstract
Cashmere goats are valuable genetic resources which are famous worldwide for their high-quality fiber. Runs of homozygosity (ROHs) have been identified as an efficient tool to assess inbreeding level and identify related genes under selection. However, there is limited research on ROHs in cashmere goats. Therefore, we investigated the ROH pattern, assessed genomic inbreeding levels and examined the candidate genes associated with the cashmere trait using whole-genome resequencing data from 123 goats. Herein, the Inner Mongolia cashmere goat presented the lowest inbreeding coefficient of 0.0263. In total, we identified 57,224 ROHs. Seventy-four ROH islands containing 50 genes were detected. Certain identified genes were related to meat, fiber and milk production (FGF1, PTPRM, RERE, GRID2, RARA); fertility (BIRC6, ECE2, CDH23, PAK1); disease or cold resistance and adaptability (PDCD1LG2, SVIL, PRDM16, RFX4, SH3BP2); and body size and growth (TMEM63C, SYN3, SDC1, STRBP, SMG6). 135 consensus ROHs were identified, and we found candidate genes (FGF5, DVL3, NRAS, KIT) were associated with fiber length or color. These findings enhance our comprehension of inbreeding levels in cashmere goats and the genetic foundations of traits influenced by selective breeding. This research contributes significantly to the future breeding, reservation and use of cashmere goats and other goat breeds.
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Affiliation(s)
- Qian Zhao
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Q.Z.); (C.H.)
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Chang Huang
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Q.Z.); (C.H.)
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Qian Chen
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Yingxiao Su
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Yanjun Zhang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Z.); (R.W.); (R.S.)
| | - Ruijun Wang
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Z.); (R.W.); (R.S.)
| | - Rui Su
- College of Animal Science, Inner Mongolia Agricultural University, Hohhot 010018, China; (Y.Z.); (R.W.); (R.S.)
| | - Huijuan Xu
- Chifeng Hanshan White Cashmere Goat Breeding Farm, Chifeng 024506, China; (H.X.); (S.L.)
| | - Shucai Liu
- Chifeng Hanshan White Cashmere Goat Breeding Farm, Chifeng 024506, China; (H.X.); (S.L.)
| | - Yuehui Ma
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Qianjun Zhao
- State Key Laboratory of Animal Biotech Breeding, Institute of Animal Sciences, Chinese Academy of Agricultural Sciences (CAAS), Beijing 100193, China; (Q.C.); (Y.S.); (Y.M.)
| | - Shaohui Ye
- Department of Animal Breeding and Reproduction, College of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China; (Q.Z.); (C.H.)
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Luigi-Sierra MG, Martínez A, Macri M, Delgado JV, Castelló A, Alvarez JF, Such X, Jordana J, Amills M. Single and longitudinal genome-wide association studies for dairy traits available in goats with three recorded lactations. Anim Genet 2024; 55:257-264. [PMID: 38131417 DOI: 10.1111/age.13391] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2023] [Revised: 12/01/2023] [Accepted: 12/04/2023] [Indexed: 12/23/2023]
Abstract
Milk yield and composition phenotypes are systematically recorded across several lactations in goats, but the majority of genome-wide association studies (GWAS) performed so far have rather ignored the longitudinal nature of such data. Here, we have used two different GWAS approaches to analyse data from three lactations recorded in Murciano-Granadina goats. In Analysis 1, independent GWAS have been carried out for each trait and lactation, while a single longitudinal GWAS, jointly considering all data, has been performed in Analysis 2. In both analyses, genome-wide significant QTL for lactose percentage on chromosome 2 (129.77-131.01 Mb) and for milk protein percentage on the chromosome 6 (74.8-94.6 Mb) casein gene cluster region were detected. In Analysis 1, several QTL were not replicated in all three lactations, possibly due to the existence of lactation-specific genetic determinants. In Analysis 2, we identified several genome-wide significant QTL related to milk yield and protein content that were not uncovered in Analysis 1. The increased number of QTL identified in Analysis 2 suggests that the longitudinal GWAS is particularly well suited for the genetic analysis of dairy traits. Moreover, our data confirm that variability within or close to the casein complex is the main genetic determinant of milk protein percentage in Murciano-Granadina goats.
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Affiliation(s)
- Maria Gracia Luigi-Sierra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Amparo Martínez
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | - Martina Macri
- Departamento de Genética, Universidad de Córdoba, Córdoba, Spain
| | | | - Anna Castelló
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Javier Fernández Alvarez
- Asociación Nacional de Criadores de Caprino de Raza Murciano-Granadina (CAPRIGRAN), Granada, Spain
| | - Xavier Such
- Group of Research in Ruminants (G2R), Department of Animal and Food Science, Universitat Autònoma de Barcelona (UAB), Bellaterra, Spain
| | - Jordi Jordana
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Spain
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra, Spain
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra, Spain
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Selionova M, Trukhachev V, Aibazov M, Sermyagin A, Belous A, Gladkikh M, Zinovieva N. Genome-Wide Association Study of Milk Composition in Karachai Goats. Animals (Basel) 2024; 14:327. [PMID: 38275787 PMCID: PMC10812594 DOI: 10.3390/ani14020327] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/22/2023] [Revised: 01/10/2024] [Accepted: 01/18/2024] [Indexed: 01/27/2024] Open
Abstract
This study is first to perform a genome-wide association study (GWAS) to investigate the milk quality traits in Karachai goats. The objective of the study was to identify candidate genes associated with milk composition traits based on the identification and subsequent analysis of all possible SNPs, both genome-wide (high-confidence) and suggestive (subthreshold significance). To estimate the milk components, 22 traits were determined, including several types of fatty acids. DNA was extracted from ear tissue or blood samples. A total of 167 Karachai goats were genotyped using an Illumina GoatSNP53K BeadChip panel (Illumina Inc., San Diego, CA, USA). Overall, we identified 167 highly significant and subthreshold SNPs associated with the milk components of Karachai goats. A total of 10 SNPs were located within protein-coding genes and 33 SNPs in close proximity to them (±0.2 Mb). The largest number of genome-wide significant SNPs was found on chromosomes 2 and 8 and some of them were associated with several traits. The greatest number of genome-wide significant SNPs was identified for crude protein and lactose (6), and the smallest number-only 1 SNP-for freezing point depression. No SNPs were identified for monounsaturated and polyunsaturated fatty acids. Functional annotation of all 43 SNPs allowed us to identify 66 significant candidate genes on chromosomes 1, 2, 3, 4, 5, 8, 10, 13, 16, 18, 21, 23, 25, 26, and 27. We considered these genes potential DNA markers of the fatty acid composition of Karachai goat milk. Also, we found 12 genes that had a polygenic effect: most of them were simultaneously associated with the dry matter content and fatty acids (METTL, SLC1A 8, PHACTR1, FMO2, ECI1, PGP, ABCA3, AMDHD2). Our results suggest that the genes identified in our study affecting the milk components in Karachai goats differed from those identified in other breeds of dairy goats.
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Affiliation(s)
- Marina Selionova
- Subdepartment of Animal Breeding, Genetics and Biotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Street, 41, 127434 Moscow, Russia (M.G.)
| | - Vladimir Trukhachev
- Subdepartment of Animal Breeding, Genetics and Biotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Street, 41, 127434 Moscow, Russia (M.G.)
| | - Magomet Aibazov
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, 142132 Podolsk, Moscow Region, Russia; (M.A.); (A.S.); (A.B.); (N.Z.)
| | - Alexander Sermyagin
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, 142132 Podolsk, Moscow Region, Russia; (M.A.); (A.S.); (A.B.); (N.Z.)
| | - Anna Belous
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, 142132 Podolsk, Moscow Region, Russia; (M.A.); (A.S.); (A.B.); (N.Z.)
| | - Marianna Gladkikh
- Subdepartment of Animal Breeding, Genetics and Biotechnology, Russian State Agrarian University—Moscow Timiryazev Agricultural Academy, Timiryazevskaya Street, 41, 127434 Moscow, Russia (M.G.)
| | - Natalia Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, 142132 Podolsk, Moscow Region, Russia; (M.A.); (A.S.); (A.B.); (N.Z.)
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Arnal M, Robert-Granié C, Ducrocq V, Larroque H. Validation of single-step genomic BLUP random regression test-day models and SNP effects analysis on milk yield in French Saanen goats. J Dairy Sci 2023:S0022-0302(23)00210-2. [PMID: 37164843 DOI: 10.3168/jds.2022-22550] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2022] [Accepted: 01/04/2023] [Indexed: 05/12/2023]
Abstract
The shape of the lactation curve is linked to an animal's health, feed requirements, and milk production throughout the year. Random regression models (RRM) are widely used for genetic evaluation of total milk production throughout the lactation and for milk yield persistency. Genomic information used with the single-step genomic BLUP method (ssGBLUP) substantially improves the accuracy of genomic prediction of breeding values in the main dairy cattle breeds. The aim of this study was to implement an RRM using ssGBLUP for milk yield in Saanen dairy goats in France. The data set consisted of 7,904,246 test-day records from 1,308,307 lactations of Saanen goats collected in France between 2000 and 2017. The performance of this type of evaluation was assessed by applying a validation step with data targeting candidate bucks. The model was compared with a nongenomic evaluation and a traditional evaluation that use cumulated performance throughout the lactation model (LM). The incorporation of genomic information increased correlations between daughter yield deviations (DYD) and estimated breeding values (EBV) obtained with a partial data set for candidate bucks. The LM and the RRM had similar correlation between DYD and EBV. However, the RRM reduced overestimation of EBV and improved the slope of the regression of DYD on EBV obtained at birth. This study shows that a genomic evaluation from a ssGBLUP RRM is possible in dairy goats in France and that RRM performance is comparable to a LM but with the additional benefit of a genomic evaluation of persistency. Variance of adjacent SNPs was studied with LM and RRM following the ssGBLUP. Both approaches converged on approximately the same regions explaining more than 1% of total variance. Regions associated with persistency were also found.
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Affiliation(s)
- M Arnal
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, 31326 Castanet-Tolosan, France; Institut de l'Elevage, Chemin de Borde Rouge, 31326 Castanet-Tolosan Cedex, France.
| | - C Robert-Granié
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, 31326 Castanet-Tolosan, France
| | - V Ducrocq
- Université Paris-Saclay, INRAE, AgroParisTech, UMR GABI, 78350 Jouy-en-Josas, France
| | - H Larroque
- GenPhySE, Université de Toulouse, INRAE, INPT, ENVT, 31326 Castanet-Tolosan, France
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Brajnik Z, Ogorevc J. Candidate genes for mastitis resistance in dairy cattle: a data integration approach. J Anim Sci Biotechnol 2023; 14:10. [PMID: 36759924 PMCID: PMC9912691 DOI: 10.1186/s40104-022-00821-0] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/11/2022] [Accepted: 12/09/2022] [Indexed: 02/11/2023] Open
Abstract
BACKGROUND Inflammation of the mammary tissue (mastitis) is one of the most detrimental health conditions in dairy ruminants and is considered the most economically important infectious disease of the dairy sector. Improving mastitis resistance is becoming an important goal in dairy ruminant breeding programmes. However, mastitis resistance is a complex trait and identification of mastitis-associated alleles in livestock is difficult. Currently, the only applicable approach to identify candidate loci for complex traits in large farm animals is to combine different information that supports the functionality of the identified genomic regions with respect to a complex trait. METHODS To identify the most promising candidate loci for mastitis resistance we integrated heterogeneous data from multiple sources and compiled the information into a comprehensive database of mastitis-associated candidate loci. Mastitis-associated candidate genes reported in association, expression, and mouse model studies were collected by searching the relevant literature and databases. The collected data were integrated into a single database, screened for overlaps, and used for gene set enrichment analysis. RESULTS The database contains candidate genes from association and expression studies and relevant transgenic mouse models. The 2448 collected candidate loci are evenly distributed across bovine chromosomes. Data integration and analysis revealed overlaps between different studies and/or with mastitis-associated QTL, revealing promising candidate genes for mastitis resistance. CONCLUSION Mastitis resistance is a complex trait influenced by numerous alleles. Based on the number of independent studies, we were able to prioritise candidate genes and propose a list of the 22 most promising. To our knowledge this is the most comprehensive database of mastitis associated candidate genes and could be helpful in selecting genes for functional validation studies.
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Affiliation(s)
- Zala Brajnik
- grid.8954.00000 0001 0721 6013Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Groblje 3, Domzale, SI-1230 Slovenia
| | - Jernej Ogorevc
- Biotechnical Faculty, Department of Animal Science, University of Ljubljana, Groblje 3, Domzale, SI-1230, Slovenia.
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Massender E, Oliveira HR, Brito LF, Maignel L, Jafarikia M, Baes CF, Sullivan B, Schenkel FS. Genome-wide association study for milk production and conformation traits in Canadian Alpine and Saanen dairy goats. J Dairy Sci 2023; 106:1168-1189. [PMID: 36526463 DOI: 10.3168/jds.2022-22223] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/24/2022] [Accepted: 08/09/2022] [Indexed: 12/15/2022]
Abstract
Increasing the productivity of Canadian dairy goats is critical to the competitiveness of the sector; however, little is known about the underlying genetic architecture of economically important traits in these populations. Consequently, the objectives of this study were as follows: (1) to perform a single-step GWAS for milk production traits (milk, protein, and fat yields, and protein and fat percentages in first and later lactations) and conformation traits (body capacity, dairy character, feet and legs, fore udder, general appearance, rear udder, suspensory ligament, and teats) in the Canadian Alpine and Saanen breeds; and (2) to identify positional and functional candidate genes related to these traits. The data available for analysis included 305-d milk production records for 6,409 Alpine and 3,434 Saanen does in first lactation and 5,827 Alpine and 2,632 Saanen does in later lactations; as well as linear type conformation records for 5,158 Alpine and 2,342 Saanen does. Genotypes were available for 833 Alpine and 874 Saanen animals. Both single-breed and multiple-breed GWAS were performed using single-trait animal models. Positional and functional candidate genes were then identified in downstream analyses. The GWAS identified 189 unique SNP that were significant at the chromosomal level, corresponding to 271 unique positional candidate genes within 50 kb up- and downstream, across breeds and traits. This study provides evidence for the economic importance of several candidate genes (e.g., CSN1S1, CSN2, CSN1S2, CSN3, DGAT1, and ZNF16) in the Canadian Alpine and Saanen populations that have been previously reported in other dairy goat populations. Moreover, several novel positional and functional candidate genes (e.g., RPL8, DCK, and MOB1B) were also identified. Overall, the results of this study have provided greater insight into the genetic architecture of milk production and conformation traits in the Canadian Alpine and Saanen populations. Greater understanding of these traits will help to improve dairy goat breeding programs.
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Affiliation(s)
- Erin Massender
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada.
| | - Hinayah R Oliveira
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Luiz F Brito
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Laurence Maignel
- Canadian Centre for Swine Improvement Inc., Ottawa, ON, K1A 0C6, Canada
| | - Mohsen Jafarikia
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Canadian Centre for Swine Improvement Inc., Ottawa, ON, K1A 0C6, Canada
| | - Christine F Baes
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada; Institute of Genetics, Vetsuisse Faculty, University of Bern, Bern, 3001, Switzerland
| | - Brian Sullivan
- Canadian Centre for Swine Improvement Inc., Ottawa, ON, K1A 0C6, Canada
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON, N1G 2W1, Canada
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Marina H, Pelayo R, Gutiérrez-Gil B, Suárez-Vega A, Esteban-Blanco C, Reverter A, Arranz JJ. Low-density SNP panel for efficient imputation and genomic selection of milk production and technological traits in dairy sheep. J Dairy Sci 2022; 105:8199-8217. [PMID: 36028350 DOI: 10.3168/jds.2021-21601] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2021] [Accepted: 05/30/2022] [Indexed: 11/19/2022]
Abstract
The present study aimed to ascertain how different strategies for leveraging genomic information enhance the accuracy of estimated breeding values for milk and cheese-making traits and to evaluate the implementation of a low-density (LowD) SNP chip designed explicitly for that aim. Thus, milk samples from a total of 2,020 dairy ewes from 2 breeds (1,039 Spanish Assaf and 981 Churra) were collected and analyzed to determine 3 milk production and composition traits and 2 traits related to milk coagulation properties and cheese yield. The 2 studied populations were genotyped with a customized 50K Affymetrix SNP chip (Affymetrix Inc.) containing 55,627 SNP markers. The prediction accuracies were obtained using different multitrait methodologies, such as the BLUP model based on pedigree information, the genomic BLUP (GBLUP), and the BLUP at the SNP level (SNP-BLUP), which are based on genotypic data, and the single-step GBLUP (ssGBLUP), which combines both sources of information. All of these methods were analyzed by cross-validation, comparing predictions of the whole population with the test population sets. Additionally, we describe the design of a LowD SNP chip (3K) and its prediction accuracies through the different methods mentioned previously. Furthermore, the results obtained using the LowD SNP chip were compared with those based on the 50K SNP chip data sets. Finally, we conclude that implementing genomic selection through the ssGBLUP model in the current breeding programs would increase the accuracy of the estimated breeding values compared with the BLUP methodology in the Assaf (from 0.19 to 0.39) and Churra (from 0.27 to 0.44) dairy sheep populations. The LowD SNP chip is cost-effective and has proven to be an accurate tool for estimating genomic breeding values for milk and cheese-making traits, microsatellite imputation, and parentage verification. The results presented here suggest that the routine use of this LowD SNP chip could potentially increase the genetic gains of the breeding selection programs of the 2 Spanish dairy sheep breeds considered here.
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Affiliation(s)
- H Marina
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - R Pelayo
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - B Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - A Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - C Esteban-Blanco
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - A Reverter
- CSIRO Agriculture & Food, 306 Carmody Rd., St. Lucia, Brisbane, QLD 4067, Australia
| | - J J Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain.
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8
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Massender E, Brito LF, Maignel L, Oliveira HR, Jafarikia M, Baes CF, Sullivan B, Schenkel FS. Single- and multiple-breed genomic evaluations for conformation traits in Canadian Alpine and Saanen dairy goats. J Dairy Sci 2022; 105:5985-6000. [DOI: 10.3168/jds.2021-21713] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/15/2021] [Accepted: 03/10/2022] [Indexed: 11/19/2022]
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9
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Jiang A, Ankersmit-Udy A, Turner SA, Scholtens M, Littlejohn MD, Lopez-Villalobos N, Proser CG, Snell RG, Lehnert K. A Capra hircus chromosome 19 locus linked to milk production influences mammary conformation. J Anim Sci Biotechnol 2022; 13:4. [PMID: 35144696 PMCID: PMC8832686 DOI: 10.1186/s40104-021-00667-y] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/01/2021] [Accepted: 12/09/2021] [Indexed: 11/26/2022] Open
Abstract
Background Economically important milk production traits including milk volume, milk fat and protein yield vary considerably across dairy goats in New Zealand. A significant portion of the variation is attributable to genetic variation. Discovery of genetic markers linked to milk production traits can be utilised to drive selection of high-performance animals. A previously reported genome wide association study across dairy goats in New Zealand identified a quantitative trait locus (QTL) located on chromosome 19. The most significantly associated single nucleotide polymorphism (SNP) marker for this locus is located at position 26,610,610 (SNP marker rs268292132). This locus is associated with multiple milk production traits including fat, protein and volume. The predicted effect of selection for the beneficial haplotype would result in an average production increase of 2.2 kg fat, 1.9 kg protein and 73.6 kg milk yield. An outstanding question was whether selection for the beneficial allele would co-select for any negative pleiotropic effects. An adverse relationship between milk production and udder health traits has been reported at this locus. Therefore, a genome wide association study was undertaken looking for loci associated with udder traits. Results The QTL and production associated marker rs268292132 was identified in this study to also be associated with several goat udder traits including udder depth (UD), fore udder attachment (FUA) and rear udder attachment (RUA). Our study replicates the negative relationship between production and udder traits with the high production allele at position 19:26,610,610 (SNP marker rs268292132) associated with an adverse change in UD, FUA and RUA. Conclusions Our study has confirmed the negative relationship between udder traits and production traits in the NZ goat population. We have found that the frequency of the high production allele is relatively high in the NZ goat population, indicating that its effect on udder conformation is not significantly detrimental on animal health. It will however be important to monitor udder conformation as the chromosome 19 locus is progressively implemented for marker assisted selection. It will also be of interest to determine if the gene underlying the production QTL has a direct effect on mammary gland morphology or whether the changes observed are a consequence of the increased milk volume. Supplementary Information The online version contains supplementary material available at 10.1186/s40104-021-00667-y.
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Affiliation(s)
- Andrew Jiang
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | - Alex Ankersmit-Udy
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
| | | | | | - Mathew D Littlejohn
- AL Rae Centre of Genetics and Breeding, Massey University, Hamilton, New Zealand
| | - Nicolas Lopez-Villalobos
- Dairy Cattle Breeding and Genetics, School of Agriculture & Environment, Massey University, Hamilton, New Zealand
| | | | - Russell G Snell
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand.
| | - Klaus Lehnert
- Applied Translational Genetics Group, School of Biological Sciences, The University of Auckland, Auckland, New Zealand
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Zhang Y, Li M, Yu B, Lu S, Zhang L, Zhu S, Yu Z, Xia T, Huang H, Jiang W, Zhang S, Sun L, Ye Q, Sun J, Zhu H, Huang P, Hong H, Yu S, Li W, Ai D, Fan J, Li W, Song H, Xu L, Chen X, Chen T, Zhou M, Ou J, Yang J, Li W, Hu Y, Wu W. Cold protection allows local cryotherapy in a clinical-relevant model of traumatic optic neuropathy. eLife 2022; 11:75070. [PMID: 35352678 PMCID: PMC9068221 DOI: 10.7554/elife.75070] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2021] [Accepted: 03/29/2022] [Indexed: 11/24/2022] Open
Abstract
Therapeutic hypothermia (TH) is potentially an important therapy for central nervous system (CNS) trauma. However, its clinical application remains controversial, hampered by two major factors: (1) Many of the CNS injury sites, such as the optic nerve (ON), are deeply buried, preventing access for local TH. The alternative is to apply TH systemically, which significantly limits the applicable temperature range. (2) Even with possible access for 'local refrigeration', cold-induced cellular damage offsets the benefit of TH. Here we present a clinically translatable model of traumatic optic neuropathy (TON) by applying clinical trans-nasal endoscopic surgery to goats and non-human primates. This model faithfully recapitulates clinical features of TON such as the injury site (pre-chiasmatic ON), the spatiotemporal pattern of neural degeneration, and the accessibility of local treatments with large operating space. We also developed a computer program to simplify the endoscopic procedure and expand this model to other large animal species. Moreover, applying a cold-protective treatment, inspired by our previous hibernation research, enables us to deliver deep hypothermia (4 °C) locally to mitigate inflammation and metabolic stress (indicated by the transcriptomic changes after injury) without cold-induced cellular damage, and confers prominent neuroprotection both structurally and functionally. Intriguingly, neither treatment alone was effective, demonstrating that in situ deep hypothermia combined with cold protection constitutes a breakthrough for TH as a therapy for TON and other CNS traumas.
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Affiliation(s)
- Yikui Zhang
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical UniversityWenzhouChina
| | - Mengyun Li
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical UniversityWenzhouChina
| | - Bo Yu
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical UniversityWenzhouChina
| | - Shengjian Lu
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical UniversityWenzhouChina
| | - Lujie Zhang
- Beijing Engineering Research Center of Mixed Reality and Advanced Display, School of Optics and Photonics, Beijing Institute of TechnologyBeijingChina
| | - Senmiao Zhu
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical UniversityWenzhouChina
| | - Zhonghao Yu
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical UniversityWenzhouChina
| | - Tian Xia
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical UniversityWenzhouChina
| | - Haoliang Huang
- Department of Ophthalmology, Stanford University School of MedicinePalo AltoUnited States
| | - WenHao Jiang
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical UniversityWenzhouChina
| | - Si Zhang
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical UniversityWenzhouChina
| | - Lanfang Sun
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical UniversityWenzhouChina
| | - Qian Ye
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical UniversityWenzhouChina
| | - Jiaying Sun
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical UniversityWenzhouChina
| | - Hui Zhu
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical UniversityWenzhouChina
| | - Pingping Huang
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical UniversityWenzhouChina
| | - Huifeng Hong
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical UniversityWenzhouChina
| | - Shuaishuai Yu
- School of Laboratory Medicine and Life Sciences, Wenzhou Medical UniversityWenzhouChina
| | - Wenjie Li
- Beijing Engineering Research Center of Mixed Reality and Advanced Display, School of Optics and Photonics, Beijing Institute of TechnologyBeijingChina
| | - Danni Ai
- Beijing Engineering Research Center of Mixed Reality and Advanced Display, School of Optics and Photonics, Beijing Institute of TechnologyBeijingChina
| | - Jingfan Fan
- Beijing Engineering Research Center of Mixed Reality and Advanced Display, School of Optics and Photonics, Beijing Institute of TechnologyBeijingChina
| | - Wentao Li
- School of Computer Science & Technology, Beijing Institute of TechnologyBeijingChina
| | - Hong Song
- School of Computer Science & Technology, Beijing Institute of TechnologyBeijingChina
| | - Lei Xu
- Medical Radiology Department, 2nd Affiliated Hospital, Wenzhou Medical UniversityWenzhouChina
| | - Xiwen Chen
- Animal Facility Center, Wenzhou Medical UniversityWenzhouChina
| | - Tongke Chen
- Animal Facility Center, Wenzhou Medical UniversityWenzhouChina
| | - Meng Zhou
- School of Biomedical Engineering, The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical UniversityWenzhouChina
| | - Jingxing Ou
- Department of Hepatic Surgery and Liver Transplantation Center of the Third Affiliated, Hospital, Guangdong Province Engineering Laboratory for Transplantation MedicineGuangzhouChina,Guangdong Key Laboratory of Liver Disease Research, the Third Affiliated Hospital of Sun Yat-sen UniversityGuangzhouChina
| | - Jian Yang
- Beijing Engineering Research Center of Mixed Reality and Advanced Display, School of Optics and Photonics, Beijing Institute of TechnologyBeijingChina
| | - Wei Li
- Retinal Neurophysiology Section, National Eye Institute, National Institute of Health, NIHBethesdaUnited States
| | - Yang Hu
- Department of Ophthalmology, Stanford University School of MedicinePalo AltoUnited States
| | - Wencan Wu
- The Eye Hospital, School of Ophthalmology & Optometry, Wenzhou Medical UniversityWenzhouChina
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11
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Marina H, Chitneedi P, Pelayo R, Suárez-Vega A, Esteban-Blanco C, Gutiérrez-Gil B, Arranz JJ. Study on the concordance between different SNP-genotyping platforms in sheep. Anim Genet 2021; 52:868-880. [PMID: 34515357 DOI: 10.1111/age.13139] [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] [Accepted: 08/28/2021] [Indexed: 12/12/2022]
Abstract
Different SNP genotyping technologies are commonly used in multiple studies to perform QTL detection, genotype imputation, and genomic predictions. Therefore, genotyping errors cannot be ignored, as they can reduce the accuracy of different procedures applied in genomic selection, such as genomic imputation, genomic predictions, and false-positive results in genome-wide association studies. Currently, whole-genome resequencing (WGR) also offers the potential for variant calling analysis and high-throughput genotyping. WGR might overshadow array-based genotyping technologies due to the larger amount and precision of the genomic information provided; however, its comparatively higher price per individual still limits its use in larger populations. Thus, the objective of this work was to evaluate the accuracy of the two most popular SNP-chip technologies, namely, Affymetrix and Illumina, for high-throughput genotyping in sheep considering high-coverage WGR datasets as references. Analyses were performed using two reference sheep genome assemblies, the popular Oar_v3.1 reference genome and the latest available version Oar_rambouillet_v1.0. Our results demonstrate that the genotypes from both platforms are suggested to have high concordance rates with the genotypes determined from reference WGR datasets (96.59% and 99.51% for Affymetrix and Illumina technologies, respectively). The concordance results provided in the current study can pinpoint low reproducible markers across multiple platforms used for sheep genotyping data. Comparing results using two reference genome assemblies also informs how genome assembly quality can influence genotype concordance rates among different genotyping platforms. Moreover, we describe an efficient pipeline to test the reliability of markers included in sheep SNP-chip panels against WGR datasets available on public databases. This pipeline may be helpful for discarding low-reliability markers before exploiting genomic information for gene mapping analyses or genomic prediction.
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Affiliation(s)
- H Marina
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
| | - P Chitneedi
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
| | - R Pelayo
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
| | - A Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
| | - C Esteban-Blanco
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
| | - B Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
| | - J J Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León, 24071, Spain
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12
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Marina H, Pelayo R, Suárez-Vega A, Gutiérrez-Gil B, Esteban-Blanco C, Arranz JJ. Genome-wide association studies (GWAS) and post-GWAS analyses for technological traits in Assaf and Churra dairy breeds. J Dairy Sci 2021; 104:11850-11866. [PMID: 34454756 DOI: 10.3168/jds.2021-20510] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2021] [Accepted: 07/05/2021] [Indexed: 12/30/2022]
Abstract
This study aimed to perform a GWAS to identify genomic regions associated with milk and cheese-making traits in Assaf and Churra dairy sheep breeds; second, it aimed to identify possible positional and functional candidate genes and their interactions through post-GWAS studies. For 2,020 dairy ewes from 2 breeds (1,039 Spanish Assaf and 981 Churra), milk samples were collected and analyzed to determine 6 milk production and composition traits and 6 traits related to milk coagulation properties and cheese yield. The genetic profiles of the ewes were obtained using a genotyping chip array that included 50,934 SNP markers. For both milk and cheese-making traits, separate single-breed GWAS were performed using GCTA software. The set of positional candidate genes identified via GWAS was subjected to guilt-by-association-based prioritization analysis with ToppGene software. Totals of 84 and 139 chromosome-wise significant associations for the 6 milk traits and the 6 cheese-making traits were identified in this study. No significant SNPs were found in common between the 2 studied breeds, possibly due to their genetic heterogeneity of the phenotypes under study. Additionally, 63 and 176 positional candidate genes were located in the genomic intervals defined as confidence regions in relation to the significant SNPs identified for the analyzed traits for Assaf and Churra breeds. After the functional prioritization analysis, 71 genes were identified as promising positional and functional candidate genes and proposed as targets of future research to identify putative causative variants in relation to the traits under examination. In addition, this multitrait study allowed us to identify variants that have a pleiotropic effect on both milk production and cheese-related traits. The incorporation of variants among the proposed functional and positional candidate genes into genomic selection strategies represent an interesting approach for achieving rapid genetic gains, specifically for those traits difficult to measure, such as cheese-making traits.
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Affiliation(s)
- H Marina
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - R Pelayo
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - A Suárez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - B Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - C Esteban-Blanco
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - J J Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain.
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13
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Association of Breed of Sheep or Goats with Somatic Cell Counts and Total Bacterial Counts of Bulk-Tank Milk. APPLIED SCIENCES-BASEL 2021. [DOI: 10.3390/app11167356] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/06/2023]
Abstract
The objective was to describe potential associations of somatic cell counts (SCC) and total bacterial counts (TBC) in bulk-tank milk from sheep and goat farms with breeds of these animals in Greece. In total, 325 dairy sheep flocks and 119 dairy goat herds were visited for the collection of milk; the breed of animals in farms was evaluated for a potential association with SCC or TBC. The most frequently seen sheep breeds were the Lacaune (95 flocks) and the Chios (44 flocks). The most frequently seen goat breeds were the indigenous Greek (Capra prisca) (50 herds) and the Murciano-Granadina (13 herds). In a multivariable analysis, the breed and the application of machine-milking in sheep flocks, and the breed and the management system in goat herds emerged as significant factors for increased SCC (>0.75 × 106 cells mL−1) in bulk-tank milk. Further, the month of lactation at sampling in sheep flocks emerged a significant factor for increased TBC (>1500 × 103 cfu mL−1) in bulk-tank milk.
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14
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Talouarn E, Teissier M, Bardou P, Larroque H, Clément V, Palhière I, Tosser-Klopp G, Rupp R, Robert-Granié C. Using sequence variants of a QTL region improves the accuracy of genomic evaluation in French Saanen goats. J Dairy Sci 2020; 104:588-601. [PMID: 33131807 DOI: 10.3168/jds.2020-18837] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/04/2020] [Accepted: 08/11/2020] [Indexed: 11/19/2022]
Abstract
The enhanced availability of sequence data in livestock provides an opportunity for more accurate predictions in routine genomic evaluations. Such evaluations would therefore no longer rely only on the linkage disequilibrium between a chip marker and the causal mutation. The objective of this study was to assess the usefulness of sequence data in Saanen goats (n = 33) to better capture a quantitative trait locus (QTL) on chromosome 19 (CHI19) and improve the accuracy of predictions for 3 milk production traits, 5 type traits, and somatic cell scores. All 1,207 50K genotypes were imputed to the sequence level. Four scenarios, each using a subset of CHI19 imputed variants, were then tested. Sequence-derived information included all CHI19 variants (529,576), all variants in the QTL region (22,269), 178 variants selected in the QTL region and added to an updated chip, or 178 randomly selected variants on CHI19. Two genomic evaluation models were applied: single-step genomic BLUP and weighted single-step genomic BLUP. All scenarios were compared with single-step genomic BLUP using 50K genotypes. Best overall results were obtained using single-step genomic BLUP on 50K genotypes completed with all variants in the QTL region of chromosome 19 (6.2% average increase in accuracy for 9 traits) with the highest accuracy gain for fat yield (17.9%), significant increases for milk (13.7%) and protein yields (12.5%), and type traits associated with CHI19. Despite its association with the QTL region of chromosome 19, the somatic cell score showed decreased accuracy in every alternative scenario. Using all CHI19 variants led to an overall decrease of 4.8% in prediction accuracy. The updated chip was efficient and improved genomic evaluations by 3.1 to 6.4% on average, depending on the scenario. Indeed, information from only a few carefully selected variants increased accuracies for traits of interest when used in a single-step genomic BLUP model. In conclusion, using QTL region variants imputed from sequence data in single-step genomic evaluations represents a promising perspective for such evaluations in dairy goats. Furthermore, using only a limited number of selected variants in QTL regions, as available on SNP chip updates, significantly increases the accuracy for QTL-associated traits without deteriorating the evaluation accuracy for other traits. The latter approach is interesting, as it avoids time-consuming imputation and data formatting processes and provides reliable genotypes.
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Affiliation(s)
- Estelle Talouarn
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet-Tolosan, France.
| | - Marc Teissier
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet-Tolosan, France
| | | | - Hélène Larroque
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet-Tolosan, France
| | | | - Isabelle Palhière
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet-Tolosan, France
| | | | - Rachel Rupp
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet-Tolosan, France
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15
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Luigi-Sierra MG, Landi V, Guan D, Delgado JV, Castelló A, Cabrera B, Mármol-Sánchez E, Alvarez JF, Gómez-Carpio M, Martínez A, Such X, Jordana J, Amills M. A genome-wide association analysis for body, udder, and leg conformation traits recorded in Murciano-Granadina goats. J Dairy Sci 2020; 103:11605-11617. [PMID: 33069406 DOI: 10.3168/jds.2020-18461] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/02/2020] [Accepted: 08/03/2020] [Indexed: 02/02/2023]
Abstract
Morphological traits are of great importance to dairy goat production given their effect on phenotypes of economic interest. However, their underlying genomic architecture has not yet been extensively characterized. Herein, we aimed to identify genomic regions associated with body, udder, and leg conformation traits recorded in 825 Murciano-Granadina goats. We genotyped this resource population using the GoatSNP50 BeadChip (Illumina Inc., San Diego, CA) and performed genome-wide association analyses using the GEMMA software. We found 2 genome-wide significant associations between markers rs268273468 [Capra hircus (CHI) 16:69617700] and rs268249346 (CHI 28:18321523) and medial suspensory ligament. In contrast, we did not detect any genome-wide significant associations for body and leg traits. Moreover, we found 12, 19, and 7 chromosome-wide significant associations for udder, body, and leg traits, respectively. Comparison of our data with previous studies revealed a low level of positional concordance between regions associated with morphological traits. In addition to technical factors, this lack of concordance could be due to a substantial level of genetic heterogeneity among breeds or to the strong polygenic background of morphological traits, which makes it difficult to detect genetic factors that have small phenotypic effects.
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Affiliation(s)
- Maria Gracia Luigi-Sierra
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Vincenzo Landi
- Departamento de Genética, Universidad de Córdoba, Córdoba 14071, Spain; Department of Veterinary Medicine, University of Bari "Aldo Moro," SP. 62 per Casamassima km. 3, 70010 Valenzano (BA), Italy
| | - Dailu Guan
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | | | - Anna Castelló
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Betlem Cabrera
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Emilio Mármol-Sánchez
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Javier Fernández Alvarez
- Asociación Nacional de Criadores de Caprino de Raza Murciano-Granadina (CAPRIGRAN), 18340 Granada, Spain
| | | | - Amparo Martínez
- Departamento de Genética, Universidad de Córdoba, Córdoba 14071, Spain
| | - Xavier Such
- Group of Research in Ruminants (G2R), Department of Animal and Food Science, Universitat Autònoma de Barcelona (UAB), Bellaterra, Barcelona 08193, Spain
| | - Jordi Jordana
- Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain
| | - Marcel Amills
- Centre for Research in Agricultural Genomics (CRAG), CSIC-IRTA-UAB-UB, Campus Universitat Autònoma de Barcelona, Bellaterra 08193, Spain; Departament de Ciència Animal i dels Aliments, Facultat de Veterinària, Universitat Autònoma de Barcelona, Bellaterra 08193, Spain.
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16
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Teissier M, Larroque H, Brito LF, Rupp R, Schenkel FS, Robert-Granié C. Genomic predictions based on haplotypes fitted as pseudo-SNP for milk production and udder type traits and SCS in French dairy goats. J Dairy Sci 2020; 103:11559-11573. [PMID: 33041034 DOI: 10.3168/jds.2020-18662] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/06/2020] [Accepted: 07/27/2020] [Indexed: 12/18/2022]
Abstract
The development of statistical methods aiming to improve the accuracy of genomic predictions is of utmost value for dairy goat breeding programs. In this context, the use of haplotypes, instead of individual SNP, could improve the accuracy of genomic predictions by better capturing the effect of causal variants, instead of relying solely on linkage disequilibrium with individual SNP. Haplotypes can be included in genomic evaluation models in various ways, such as fitting them as pseudo-SNP (i.e., haplotypes converted into biallelic SNP format). This can be easily incorporated in the software already available for single-step genomic predictions (ssGBLUP). Therefore, the aim of this study was to compare the predictive performances of ssGBLUP and weighted ssGBLUP (WssGBLUP) based on individual SNP or on haplotypes fitted as pseudo-SNP. Performance was compared in terms of accuracy, bias, and weights for SNP versus pseudo-SNP. Genomic predictions were performed on 5 milk production traits, 5 udder type traits, and somatic cell score (SCS). The training population was formed by 307 Alpine and 247 Saanen progeny-tested bucks, genotyped using the Illumina Goat SNP50 BeadChip (Illumina, San Diego, CA). The validation population included 205 Alpine and 146 Saanen young bucks. The accuracy of genomic predictions was evaluated in the validation population as the Pearson correlation between genomic estimated breeding values (GEBV), predicted based on various methods, and daughter deviation (DD) based on the official genetic evaluation of January 2016. Haplotype-based models were shown to improve the performance of genomic predictions for some traits. Gains in accuracy of up to +19% (0.310 to 0.368 for fat yield) in Alpine and up to +3% (0.361 to 0.373 for udder shape) in Saanen were observed with ssGBLUP. The ssGBLUP accuracies averaged across all traits and methods were equal to 0.467 (SNP) versus 0.471 (pseudo-SNP) in Alpine and 0.528 (SNP) versus 0.523 (pseudo-SNP) in Saanen. With WssGBLUP, gains in accuracy of up to 24% (0.298 to 0.370 for fat yield) in Alpine and 14% (0.431 to 0.490 for SCS) in Saanen were observed with WssGBLUP. Accuracies of WssGBLUP averaged across all traits and methods were equal to 0.455 (SNP and pseudo-SNP) in Alpine and 0.542 (SNP) versus 0.528 (pseudo-SNP) in Saanen. The average (±SD) slope of the regression of DD on GEBV for the validation animals, across all breeds, traits and scenarios, were equal to 0.82 ± 0.20 (SNP) and 0.83 ± 0.18 (pseudo-SNP) for ssGBLUP and 0.67 ± 0.16 (SNP) and 0.65 ± 0.16 (pseudo-SNP) for WssGBLUP, which suggest that haplotype-based models and ssGBLUPSNP were similarly biased. However, WssGBLUP was more biased than ssGBLUP, and its gains in accuracies were limited to milk production traits. Despite the fact that genomic predictions based on haplotypes require additional steps and time, the observed gains in GEBV predictive performance indicate that haplotype-based methods could be recommended for some traits.
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Affiliation(s)
- Marc Teissier
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet-Tolosan, France.
| | - Hélène Larroque
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet-Tolosan, France
| | - Luiz F Brito
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada; Department of Animal Sciences, Purdue University, West Lafayette, IN 47907
| | - Rachel Rupp
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326 Castanet-Tolosan, France
| | - Flavio S Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, Ontario, N1G 2W1, Canada
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17
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Biffani S, Tiezzi F, Fresi P, Stella A, Minozzi G. Genetic parameters of weeping teats in Italian Saanen and Alpine dairy goats and their relationship with milk production and somatic cell score. J Dairy Sci 2020; 103:9167-9176. [PMID: 32713699 DOI: 10.3168/jds.2020-18175] [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: 01/08/2020] [Accepted: 04/14/2020] [Indexed: 01/26/2023]
Abstract
This paper reports a quantitative genetics analysis of weeping teats (WT), an abnormality of the mammary gland in goats. Weeping teats are characterized by milk oozing out of the teat or by the presence of multiple cysts near its base. This abnormality has been routinely recorded in Italian Alpine and Saanen goats since 2000 using a score of 0 or 1 (0 = defect not present, 1 = defect present). No information is available on the genetic background of WT or its relationship with production or other udder-related traits. Data obtained by the Italian National Sheep and Goat Breeders Association (Rome, Italy) were used to estimate both heritability of WT and its genetic correlation with milk yield, somatic cell score, and udder traits. The final data set used in the analysis included 2,178 Saanen and 2,309 Alpine primiparous goats kidding from 2009 to 2014. The pedigree data included 7,333 Saanen and 7,421 Alpines, respectively. A threshold-linear multivariate animal model was used to estimate variance and covariance components. A genealogical data analysis was also implemented, including genealogical data completeness, inbreeding, and identification of possible most recent common ancestors. On average, around 4 and 13% of primiparous Saanen and Alpine females kidding from 2009 to 2014 showed mammary gland abnormality, respectively. Weeping teats heritability was 0.27 and 0.26 for Saanen and Alpine, respectively. Genetic correlations between milk production or somatic cell score ranged from -0.16 in Saanen to 0.43 in Alpine, but the standard error of the estimates was very large. Positive genetic correlations were observed among WT and teat characteristics in both Saanen and Alpine. The average inbreeding of abnormality carriers was 2.4 and 5.1 for Saanen and Alpine, respectively. The genealogical data analysis identified 4 common ancestors of affected does in Saanen and 2 in Alpine. These results indicate that WT have a possible genetic background. A genome-wide association study might help in understanding the polygenic or monogenic determination of this abnormality.
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Affiliation(s)
- Stefano Biffani
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Biologia e Biotecnologia Agraria (IBBA), 20133 Milano, Italy.
| | - Francesco Tiezzi
- Department of Animal Science, North Carolina State University, Raleigh 27695
| | | | - Alessandra Stella
- Consiglio Nazionale delle Ricerche (CNR), Istituto di Biologia e Biotecnologia Agraria (IBBA), 20133 Milano, Italy
| | - Giulietta Minozzi
- Department of Veterinary Medicine, University of Milan, 20133 Milan, Italy
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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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Talouarn E, Bardou P, Palhière I, Oget C, Clément V, Tosser-Klopp G, Rupp R, Robert-Granié C. Genome wide association analysis on semen volume and milk yield using different strategies of imputation to whole genome sequence in French dairy goats. BMC Genet 2020; 21:19. [PMID: 32085723 PMCID: PMC7035711 DOI: 10.1186/s12863-020-0826-9] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/28/2019] [Accepted: 02/13/2020] [Indexed: 01/17/2023] Open
Abstract
Background Goats were domesticated 10,500 years ago to supply humans with useful resources. Since then, specialized breeds that are adapted to their local environment have been developed and display specific genetic profiles. The VarGoats project is a 1000 genomes resequencing program designed to cover the genetic diversity of the Capra genus. In this study, our main objective was to assess the use of sequence data to detect genomic regions associated with traits of interest in French Alpine and Saanen breeds. Results Direct imputation from the GoatSNP50 BeadChip genotypes to sequence level was investigated in these breeds using FImpute and different reference panels: within-breed, all Capra hircus sequenced individuals, European goats and French mainland goats. The best results were obtained with the French goat panel with allele and genotype concordance rates reaching 0.86 and 0.75 in the Alpine and 0.86 and 0.73 in the Saanen breed respectively. Mean correlations tended to be low in both breeds due to the high proportion of variants with low frequencies. For association analysis, imputation was performed using FImpute for 1129 French Alpine and Saanen males using within-breed and French panels on 23,338,436 filtered variants. The association results of both imputation scenarios were then compared. In Saanen goats, a large region on chromosome 19 was significantly linked to semen volume and milk yield in both scenarios. Significant variants for milk yield were annotated for 91 genes on chromosome 19 in Saanen goats. For semen volume, the annotated genes include YBOX2 which is related to azoospermia or oligospermia in other species. New signals for milk yield were detected on chromosome 2 in Alpine goats and on chromosome 5 in Saanen goats when using a multi-breed panel. Conclusion Even with very small reference populations, an acceptable imputation quality can be achieved in French dairy goats. GWAS on imputed sequences confirmed the existence of QTLs and identified new regions of interest in dairy goats. Adding identified candidates to a genotyping array and sequencing more individuals might corroborate the involvement of identified regions while removing potential imputation errors.
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Affiliation(s)
- Estelle Talouarn
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet Tolosan, France.
| | - Philippe Bardou
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet Tolosan, France.,Sigenae, INRAE, 31326, Castanet-Tolosan, France
| | - Isabelle Palhière
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet Tolosan, France
| | - Claire Oget
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet Tolosan, France
| | | | | | - Gwenola Tosser-Klopp
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet Tolosan, France
| | - Rachel Rupp
- GenPhySE, Université de Toulouse, INRAE, ENVT, F-31326, Castanet Tolosan, France
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20
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Oget C, Teissier M, Astruc JM, Tosser-Klopp G, Rupp R. Alternative methods improve the accuracy of genomic prediction using information from a causal point mutation in a dairy sheep model. BMC Genomics 2019; 20:719. [PMID: 31533617 PMCID: PMC6751880 DOI: 10.1186/s12864-019-6068-4] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/03/2019] [Accepted: 08/29/2019] [Indexed: 11/13/2022] Open
Abstract
Background Genomic evaluation is usually based on a set of markers assumed to be linked with causal mutations. Selection and precise management of major genes and the remaining polygenic component might be improved by including causal polymorphisms in the evaluation models. In this study, various methods involving a known mutation were used to estimate prediction accuracy. The SOCS2 gene, which influences body growth, milk production and somatic cell scores, a proxy for mastitis, was studied as an example in dairy sheep. Methods The data comprised 1,503,148 phenotypes and 9844 54K SNPs genotypes. The SOCS2 SNP was genotyped for 4297 animals and imputed in the above 9844 animals. Breeding values and their accuracies were estimated for each of nine traits by using single-step approaches. Pedigree-based BLUP, single-step genomic BLUP (ssGBLUP) involving the 54K ovine SNPs chip, and four weighted ssGBLUP (WssGBLUP) methods were compared. In WssGBLUP methods, weights are assigned to SNPs depending on their effect on the trait. The ssGBLUP and WssGBLUP methods were again tested after including the SOCS2 causal mutation as a SNP. Finally, the Gene Content approach was tested, which uses a multiple-trait model that considers the SOCS2 genotype as a trait. Results EBV accuracies were increased by 14.03% between the pedigree-based BLUP and ssGBLUP methods and by 3.99% between ssGBLUP and WssGBLUP. Adding the SOCS2 SNP to ssGBLUP methods led to an average gain of 0.26%. Construction of the kinship matrix and estimation of breeding values was generally improved by placing emphasis on SNPs in regions with a strong effect on traits. In the absence of chip data, the Gene Content method, compared to pedigree-based BLUP, efficiently accounted for partial genotyping information on SOCS2 as accuracy was increased by 6.25%. This method also allowed dissociation of the genetic component due to the major gene from the remaining polygenic component. Conclusions Causal mutations with a moderate to strong effect can be captured with conventional SNP chips by applying appropriate genomic evaluation methods. The Gene Content method provides an efficient way to account for causal mutations in populations lacking genome-wide genotyping. Electronic supplementary material The online version of this article (10.1186/s12864-019-6068-4) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Claire Oget
- GenPhySE, Université de Toulouse, INRA, ENVT, Castanet-Tolosan, France.
| | - Marc Teissier
- GenPhySE, Université de Toulouse, INRA, ENVT, Castanet-Tolosan, France
| | | | | | - Rachel Rupp
- GenPhySE, Université de Toulouse, INRA, ENVT, Castanet-Tolosan, France
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21
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Gipson TA. Recent advances in breeding and genetics for dairy goats. ASIAN-AUSTRALASIAN JOURNAL OF ANIMAL SCIENCES 2019; 32:1275-1283. [PMID: 31357268 PMCID: PMC6668855 DOI: 10.5713/ajas.19.0381] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Accepted: 07/03/2019] [Indexed: 12/27/2022]
Abstract
Goats (Capra hircus) were domesticated during the late Neolithic, approximately 10,500 years ago, and humans exerted minor selection pressure until fairly recently. Probably the largest genetic change occurring over the millennia happened via natural selection and random genetic drift, the latter causing genes to be fixed in small and isolated populations. Recent human-influenced genetic changes have occurred through biometrics and genomics. For the most part, biometrics has concentrated upon the refining of estimates of heritabilities and genetic correlations. Heritabilities are instrumental in the calculation of estimated breeding values and genetic correlations are necessary in the construction of selection indices that account for changes in multiple traits under selection at one time. Early genomic studies focused upon microsatellite markers, which are short tandem repeats of nucleic acids and which are detected using polymerase chain reaction primers flanking the microsatellite. Microsatellite markers have been very important in parentage verification, which can impact genetic progress. Additionally, microsatellite markers have been a useful tool in assessing genetic diversity between and among breeds, which is important in the conservation of minor breeds. Single nucleotide polymorphisms are a new genomic tool that have refined classical BLUP methodology (biometric) to provide more accurate genomic estimated breeding values, provided a large reference population is available.
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Affiliation(s)
- Terry A Gipson
- American Institute for Goat Research, Langston University, Langston, OK 73050, USA
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22
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Teissier M, Larroque H, Robert-Granie C. Accuracy of genomic evaluation with weighted single-step genomic best linear unbiased prediction for milk production traits, udder type traits, and somatic cell scores in French dairy goats. J Dairy Sci 2019; 102:3142-3154. [PMID: 30712939 DOI: 10.3168/jds.2018-15650] [Citation(s) in RCA: 24] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2018] [Accepted: 12/05/2018] [Indexed: 01/17/2023]
Abstract
Genomic evaluation of French dairy goats is routinely conducted using the single-step genomic BLUP (ssGBLUP) method. This method has the advantage of simultaneously using all phenotypes, pedigrees, and genotypes. However, ssGBLUP assumes that all SNP explain the same amount of genetic variance, which is unlikely in the case of traits whose major genes or QTL are segregating. In this study, we investigated the effect of weighted ssGBLUP and its alternatives, which give more weight to SNP associated with the trait, on the accuracy of genomic evaluation of milk production, udder type traits, and somatic cell scores. The data set included 2,955 genotyped animals and 2,543,680 pedigree animals. The number of phenotypes varied with the trait. The accuracy of genomic evaluation was assessed on 205 genotyped Alpine and 146 genotyped Saanen goats born between 2009 and 2012. For traits with unknown QTL, weighted ssGBLUP was less accurate than, or as accurate as, ssGBLUP. For traits with identified QTL (i.e., QTL only present in the Saanen breed), weighted ssGBLUP outperformed ssGBLUP by between 2 and 14%.
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Affiliation(s)
- M Teissier
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 31326 Castanet-Tolosan, France.
| | - H Larroque
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 31326 Castanet-Tolosan, France
| | - C Robert-Granie
- GenPhySE, Université de Toulouse, INRA, INPT, ENVT, 31326 Castanet-Tolosan, France
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Gutiérrez-Gil B, Esteban-Blanco C, Suarez-Vega A, Arranz JJ. Detection of quantitative trait loci and putative causal variants affecting somatic cell score in dairy sheep by using a 50K SNP chip and whole-genome sequencing. J Dairy Sci 2018; 101:9072-9088. [PMID: 30100503 DOI: 10.3168/jds.2018-14736] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2018] [Accepted: 06/21/2018] [Indexed: 12/12/2022]
Abstract
This study presents a scan of the ovine genome to identify quantitative trait loci (QTL) influencing the somatic cell score (SCS), a classical indicator of subclinical mastitis in sheep, and a subsequent high-resolution analysis of one of the identified QTL regions based on the analysis of whole-genome sequence data sets. A half-sib commercial population of Churra sheep genotyped with a 50K SNP chip was analyzed using linkage analysis (LA) and combined linkage and linkage disequilibrium analysis (LDLA). By LA, 2 5% chromosome-wide significant QTL on OAR5 and OAR25 and one 5% genome-wide significant QTL on ovine chromosome 20 (OAR20) were detected, whereas 22 significant associations were identified by LDLA. Two of the associations detected by LDLA replicated LA-detected effects (OAR20, OAR25). We compared the detected associations with previously reported QTL in sheep and cattle, and functional candidate genes were identified within the estimated confidence intervals. We then performed a high-resolution analysis of the OAR20 QTL region, the most significant QTL region identified by LA that replicated a QTL previously described in Churra sheep for SCS using microsatellite markers. For that, 2 segregating trios of 2 segregating families for the OAR20 QTL (each including the Qq sire and 2 daughters, QQ and qq) were selected for whole-genome sequencing. The bioinformatic analysis of the 6 sequenced samples performed across the genomic interval considered (14.2-41.7 Mb) identified a total of 227,030 variants commonly identified by 2 independent software packages. For the 3 different concordance tests considered, due to discrepancies regarding the QTL peak in the segregating families, the list of mutations concordant with the QTL segregating pattern was processed to identify the variants identified in immune-related genes that show a moderate/high impact on the encoded protein function. Among a list of 85 missense variants concordant with the QTL segregation pattern that were within candidate immune-related genes, 13 variants distributed across 7 genes [PKHD1, NOTCH4, AGER, ENSOARG00000009395 (HLA-C, Homo sapiens), ENSOARG00000015002 (HLA-B, H. sapiens), MOG, and ENSOARG00000018075 (BoLA, Bos taurus, orthologous to human HLA-A] were predicted to cause deleterious effects on protein function. Future studies should assess the possible associations of the candidate variants identified herein in commercial populations with indicator traits of udder inflammation (SCS, clinical mastitis).
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Affiliation(s)
- B Gutiérrez-Gil
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain.
| | - C Esteban-Blanco
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - A Suarez-Vega
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
| | - J J Arranz
- Departamento de Producción Animal, Facultad de Veterinaria, Universidad de León, Campus de Vegazana s/n, León 24071, Spain
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