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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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Cesarani A, Corte Pause F, Hidalgo J, Garcia A, Degano L, Vicario D, Macciota NPP, Stradaioli G. Genetic background of semen parameters in Italian Simmental bulls. ITALIAN JOURNAL OF ANIMAL SCIENCE 2023. [DOI: 10.1080/1828051x.2022.2160665] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Affiliation(s)
- Alberto Cesarani
- Dipartimento di Agraria, University of Sassari, Sassari, Italy
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Francesca Corte Pause
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
| | - Jorge Hidalgo
- Department of Animal and Dairy Science, University of Georgia, Athens, GA, USA
| | - Andre Garcia
- Angus Genetics Inc. - American Angus Association, Saint Joseph, MO, USA
| | - Lorenzo Degano
- Associazione Nazionale Allevatori Pezzata Rossa Italiana (ANAPRI), Udine, Italy
| | - Daniele Vicario
- Associazione Nazionale Allevatori Pezzata Rossa Italiana (ANAPRI), Udine, Italy
| | | | - Giuseppe Stradaioli
- Department of Agricultural, Food, Environmental and Animal Sciences, University of Udine, Udine, Italy
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Selionova M, Aibazov M, Sermyagin A, Belous A, Deniskova T, Mamontova T, Zharkova E, Zinovieva N. Genome-Wide Association and Pathway Analysis of Carcass and Meat Quality Traits in Karachai Young Goats. Animals (Basel) 2023; 13:3237. [PMID: 37893961 PMCID: PMC10603756 DOI: 10.3390/ani13203237] [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: 08/14/2023] [Revised: 09/26/2023] [Accepted: 09/28/2023] [Indexed: 10/29/2023] Open
Abstract
Goats with diverse economic phenotypic traits play an important role in animal husbandry. However, the genetic mechanisms underlying complex phenotypic traits are unclear in goats. Genomic studies of variations provided a lens to identify functional genes. The work aimed to search for candidate genes related to body measurements and body weight of Karachai goats and develop an experimental PCR-RV test system for genotyping significant SNPs. Comparison of GWAS results for ages 4 and 8 months revealed 58 common SNPs for significant genotypes. 11 common SNPs were identified for body weight, 4 SNPs-for group of traits withers height, rump height, body length, 2 SNPs-for withers height and rump height, 1 SNP-for body length and chest depth. Structural annotation of genomic regions covering a window of ±0.20 Mb showed the presence of 288 genes; 52 of them had the described functions in accordance with gene ontology. The main molecular functions of proteins encoded by these genes are the regulation of transcription, cell proliferation, angiogenesis, body growth, fatty acid and lipid metabolism, nervous system development, and spermatogenesis. SNPs common to body weight and localized within a window of ±200 kb from the structural genes CRADD, HMGA2, MSRB3, FUT8, MAX, and RAB15 were selected to create a test system. The study of meat productivity after slaughter and chemical analysis of muscle tissue in Karachai goats at the age of 8 months of different genotypes according to the identified SNPs revealed that rs268269710 is the most promising for further research and use in breeding. The GG genotype is associated with a larger live weight of animals, a larger carcass yield, the content of the boneless part in it, and the ratio of protein and adipose tissue in meat preferred for dietary nutrition. These results will contribute to the genetic improvement of Karachai goats.
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Affiliation(s)
- Marina Selionova
- Subdepartment of Animal Breeding, Genetics and Biotechnology, Moscow Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Street, 41, 127343 Moscow, Russia; (M.S.); (T.M.)
| | - Magomet Aibazov
- North Caucasian Agrarian Center, Zootechnicheski 15, 355017 Stavropol, Russia;
| | - Alexander Sermyagin
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, 142132 Moscow, Russia; (A.S.); (A.B.); (T.D.); (N.Z.)
| | - Anna Belous
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, 142132 Moscow, Russia; (A.S.); (A.B.); (T.D.); (N.Z.)
| | - Tatiana Deniskova
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, 142132 Moscow, Russia; (A.S.); (A.B.); (T.D.); (N.Z.)
| | - Tatiana Mamontova
- Subdepartment of Animal Breeding, Genetics and Biotechnology, Moscow Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Street, 41, 127343 Moscow, Russia; (M.S.); (T.M.)
| | - Ekaterina Zharkova
- Subdepartment of Animal Breeding, Genetics and Biotechnology, Moscow Timiryazev Agricultural Academy, Russian State Agrarian University, Timiryazevskaya Street, 41, 127343 Moscow, Russia; (M.S.); (T.M.)
| | - Natalia Zinovieva
- L. K. Ernst Federal Research Center for Animal Husbandry, Dubrovitsy 60, 142132 Moscow, Russia; (A.S.); (A.B.); (T.D.); (N.Z.)
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Hodge MJ, de Las Heras-Saldana S, Rindfleish SJ, Stephen CP, Pant SD. QTLs and Candidate Genes Associated with Semen Traits in Merino Sheep. Animals (Basel) 2023; 13:2286. [PMID: 37508063 PMCID: PMC10376747 DOI: 10.3390/ani13142286] [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: 06/03/2023] [Revised: 07/06/2023] [Accepted: 07/07/2023] [Indexed: 07/30/2023] Open
Abstract
Ram semen traits play a significant role in conception outcomes, which in turn may influence reproductive efficiency and the overall productivity and profitability of sheep enterprises. Since hundreds of ewes may be inseminated from a single ejaculate, it is important to evaluate semen quality prior to use in sheep breeding programs. Given that semen traits have been found to be heritable, genetic variation likely contributes to the variability observed in these traits. Identifying such genetic variants could provide novel insights into the molecular mechanisms underlying variability in semen traits. Therefore, this study aimed to identify quantitative trait loci (QTLs) associated with semen traits in Merino sheep. A genome-wide association study (GWAS) was undertaken using 4506 semen collection records from 246 Merino rams collected between January 2002 and May 2021. The R package RepeatABEL was used to perform a GWAS for semen volume, gross motility, concentration, and percent post-thaw motility. A total of 35 QTLs, located on 16 Ovis aries autosomes (OARs), were significantly associated with either of the four semen traits in this study. A total of 89, 95, 33, and 73 candidate genes were identified, via modified Bonferroni, within the QTLs significantly associated with volume, gross motility, concentration, and percent post-thaw motility, respectively. Among the candidate genes identified, SORD, SH2B1, and NT5E have been previously described to significantly influence spermatogenesis, spermatozoal motility, and high percent post-thaw motility, respectively. Several candidate genes identified could potentially influence ram semen traits based on existing evidence in the literature. As such, validation of these putative candidates may offer the potential to develop future strategies to improve sheep reproductive efficiency. Furthermore, Merino ram semen traits are lowly heritable (0.071-0.139), and thus may be improved by selective breeding.
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Affiliation(s)
- Marnie J Hodge
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
- Apiam Animal Health, Apiam Genetic Services, Dubbo, NSW 2830, Australia
| | - Sara de Las Heras-Saldana
- Animal Genetics and Breeding Unit, a Joint Venture of NSW Department of Primary Industries and University of New England, Armidale, NSW 2351, Australia
| | | | - Cyril P Stephen
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
- Gulbali Institute, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW 2678, Australia
| | - Sameer D Pant
- School of Agricultural, Environmental and Veterinary Sciences, Charles Sturt University, Wagga Wagga, NSW 2678, Australia
- Gulbali Institute, Charles Sturt University, Boorooma Street, Wagga Wagga, NSW 2678, Australia
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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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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: 8] [Impact Index Per Article: 8.0] [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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Wan X, Jing JN, Wang DF, Lv FH. Whole-genome selective scans detect genes associated with important phenotypic traits in goat ( Capra hircus). Front Genet 2023; 14:1173017. [PMID: 37144124 PMCID: PMC10151485 DOI: 10.3389/fgene.2023.1173017] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2023] [Accepted: 04/03/2023] [Indexed: 05/06/2023] Open
Abstract
Goats with diverse economic phenotypic traits play an important role in animal husbandry. However, the genetic mechanisms underlying complex phenotypic traits are unclear in goats. Genomic studies of variations provided a lens to identify functional genes. In this study, we focused on the worldwide goat breeds with outstanding traits and used whole-genome resequencing data in 361 samples from 68 breeds to detect genomic selection sweep regions. We identified 210-531 genomic regions with six phenotypic traits, respectively. Further gene annotation analysis revealed 332, 203, 164, 300, 205, and 145 candidate genes corresponding with dairy, wool, high prolificacy, poll, big ear, and white coat color traits. Some of these genes have been reported previously (e.g., KIT, KITLG, NBEA, RELL1, AHCY, and EDNRA), while we also discovered novel genes, such as STIM1, NRXN1, LEP, that may be associated with agronomic traits like poll and big ear morphology. Our study found a set of new genetic markers for genetic improvement in goats and provided novel insights into the genetic mechanisms of complex traits.
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Affiliation(s)
- Xing Wan
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jia-Nan Jing
- College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Dong-Feng Wang
- CAS Key Laboratory of Animal Ecology and Conservation Biology, Institute of Zoology, Chinese Academy of Sciences (CAS), Beijing, China
- University of Chinese Academy of Sciences (UCAS), Beijing, China
| | - Feng-Hua Lv
- College of Animal Science and Technology, China Agricultural University, Beijing, China
- *Correspondence: Feng-Hua Lv,
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Zhu X, Ni P, Sturrock M, Wang Y, Ding J, Chang Y, Hu J, Bao Z. Fine-mapping and association analysis of candidate genes for papilla number in sea cucumber, Apostichopus japonicus. MARINE LIFE SCIENCE & TECHNOLOGY 2022; 4:343-355. [PMID: 37073167 PMCID: PMC10077181 DOI: 10.1007/s42995-022-00139-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/17/2022] [Accepted: 06/03/2022] [Indexed: 05/03/2023]
Abstract
The papilla number is one of the most economically important traits of sea cucumber in the China marketing trade. However, the genetic basis for papilla number diversity in holothurians is still scarce. In the present study, we conducted genome-wide association studies (GWAS) for the trait papilla number of sea cucumbers utilizing a set of 400,186 high-quality SNPs derived from 200 sea cucumbers. Two significant trait-associated SNPs that passed Bonferroni correction (P < 1.25E-7) were located in the intergenic region near PATS1 and the genic region of EIF4G, which were reported to play a pivotal role in cell growth and proliferation. The fine-mapping regions around the top two lead SNPs provided precise causative loci/genes related to papilla formation and cellular activity, including PPP2R3C, GBP1, and BCAS3. Potential SNPs with P < 1E-4 were acquired for the following GO and KEGG enrichment analysis. Moreover, the two lead SNPs were verified in another population of sea cucumber, and the expressive detection of three potential candidate genes PATS1, PPP2R3C, and EIF4G that near or cover the two lead SNPs was conducted in papilla tissue of TG (Top papilla number group) and BG (Bottom papilla number group) by qRT-PCR. We found the significantly higher expression profile of PATS1 (3.34-fold), PPP2R3C (4.90-fold), and EIF4G (4.23-fold) in TG, implying their potential function in papilla polymorphism. The present results provide valuable information to decipher the phenotype differences of the papilla trait and will provide a scientific basis for selective breeding in sea cucumbers. Supplementary Information The online version contains supplementary material available at 10.1007/s42995-022-00139-w.
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Affiliation(s)
- Xinghai Zhu
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Ping Ni
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Marc Sturrock
- Department of Physiology and Medical Physics, Royal College of Surgeons in Ireland, Dublin, D02 YN77 Ireland
| | - Yangfan Wang
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
| | - Jun Ding
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023 China
| | - Yaqing Chang
- College of Fisheries and Life Science, Dalian Ocean University, Dalian, 116023 China
| | - Jingjie Hu
- Laboratory of Tropical Marine Germplasm Resources and Breeding Engineering, Sanya Oceanographic Institution, Ocean University of China, Sanya, 572000 China
| | - Zhenmin Bao
- Ministry of Education Key Laboratory of Marine Genetics and Breeding, College of Marine Life Sciences, Ocean University of China, Qingdao, 266003 China
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Gu B, Sun R, Fang X, Zhang J, Zhao Z, Huang D, Zhao Y, Zhao Y. Genome-Wide Association Study of Body Conformation Traits by Whole Genome Sequencing in Dazu Black Goats. Animals (Basel) 2022; 12:ani12050548. [PMID: 35268118 PMCID: PMC8908837 DOI: 10.3390/ani12050548] [Citation(s) in RCA: 9] [Impact Index Per Article: 4.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2021] [Revised: 02/15/2022] [Accepted: 02/19/2022] [Indexed: 02/07/2023] Open
Abstract
Simple Summary Body conformation traits are economically important in the goat meat industry. Good growth performance in goats, including an accelerated growth rate, can improve carcass weight and meat yield. The identification of genetic variants associated with these traits provides a basis for the genetic improvement of growth performance. In this study, we measured six body conformation traits, including body height, body length, cannon circumference, chest depth, chest width, and heart girth. By a genome-wide association study of a Chinese meat goat breed, 53 significant single nucleotide polymorphisms and 42 candidate genes associated with these traits were detected. These findings improve our understanding of the genetic basis of body conformation traits in goats. Abstract Identifying associations between genetic markers and economic traits has practical benefits for the meat goat industry. To better understand the genomic regions and biological pathways contributing to body conformation traits of meat goats, a genome-wide association study was performed using Dazu black goats (DBGs), a Chinese indigenous goat breed. In particular, 150 DBGs were genotyped by whole-genome sequencing, and six body conformation traits, including body height (BH), body length (BL), cannon circumference (CC), chest depth (CD), chest width (CW), and heart girth (HG), were examined. In total, 53 potential SNPs were associated with these body conformation traits. A bioinformatics analysis was performed to evaluate the genes located close to the significant SNPs. Finally, 42 candidate genes (e.g., PSTPIP2, C7orf57, CCL19, FGF9, SGCG, FIGN, and SIPA1L) were identified as components of the genetic architecture underlying body conformation traits. Our results provide useful biological information for the improvement of growth performance and have practical applications for genomic selection in goats.
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Affiliation(s)
- Bowen Gu
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (B.G.); (R.S.); (X.F.); (J.Z.); (Z.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing 400715, China
| | - Ruifan Sun
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (B.G.); (R.S.); (X.F.); (J.Z.); (Z.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing 400715, China
| | - Xingqiang Fang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (B.G.); (R.S.); (X.F.); (J.Z.); (Z.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing 400715, China
| | - Jipan Zhang
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (B.G.); (R.S.); (X.F.); (J.Z.); (Z.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing 400715, China
| | - Zhongquan Zhao
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (B.G.); (R.S.); (X.F.); (J.Z.); (Z.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing 400715, China
| | - Deli Huang
- Tengda Animal Husbandry Co., Ltd., Chongqing 402360, China;
| | - Yuanping Zhao
- Dazu County Agriculture and Rural Committee, Chongqing 402360, China;
| | - Yongju Zhao
- College of Animal Science and Technology, Southwest University, Chongqing 400715, China; (B.G.); (R.S.); (X.F.); (J.Z.); (Z.Z.)
- Chongqing Key Laboratory of Herbivore Science, Chongqing 400715, China
- Chongqing Engineering Research Center for Herbivores Resource Protection and Utilization, Chongqing 400715, China
- Correspondence:
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Pedrosa VB, Schenkel FS, Chen SY, Oliveira HR, Casey TM, Melka MG, Brito LF. Genomewide Association Analyses of Lactation Persistency and Milk Production Traits in Holstein Cattle Based on Imputed Whole-Genome Sequence Data. Genes (Basel) 2021; 12:genes12111830. [PMID: 34828436 PMCID: PMC8624223 DOI: 10.3390/genes12111830] [Citation(s) in RCA: 27] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2021] [Revised: 11/13/2021] [Accepted: 11/17/2021] [Indexed: 12/22/2022] Open
Abstract
Lactation persistency and milk production are among the most economically important traits in the dairy industry. In this study, we explored the association of over 6.1 million imputed whole-genome sequence variants with lactation persistency (LP), milk yield (MILK), fat yield (FAT), fat percentage (FAT%), protein yield (PROT), and protein percentage (PROT%) in North American Holstein cattle. We identified 49, 3991, 2607, 4459, 805, and 5519 SNPs significantly associated with LP, MILK, FAT, FAT%, PROT, and PROT%, respectively. Various known associations were confirmed while several novel candidate genes were also revealed, including ARHGAP35, NPAS1, TMEM160, ZC3H4, SAE1, ZMIZ1, PPIF, LDB2, ABI3, SERPINB6, and SERPINB9 for LP; NIM1K, ZNF131, GABRG1, GABRA2, DCHS1, and SPIDR for MILK; NR6A1, OLFML2A, EXT2, POLD1, GOT1, and ETV6 for FAT; DPP6, LRRC26, and the KCN gene family for FAT%; CDC14A, RTCA, HSTN, and ODAM for PROT; and HERC3, HERC5, LALBA, CCL28, and NEURL1 for PROT%. Most of these genes are involved in relevant gene ontology (GO) terms such as fatty acid homeostasis, transporter regulator activity, response to progesterone and estradiol, response to steroid hormones, and lactation. The significant genomic regions found contribute to a better understanding of the molecular mechanisms related to LP and milk production in North American Holstein cattle.
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Affiliation(s)
- Victor B. Pedrosa
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
- Department of Animal Sciences, State University of Ponta Grossa, Ponta Grossa 84030-900, Brazil
| | - Flavio S. Schenkel
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G2W1, Canada;
| | - Shi-Yi Chen
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
- Farm Animal Genetic Resources Exploration and Innovation Key Laboratory of Sichuan Province, College of Animal Science & Technology, Sichuan Agricultural University, Chengdu 611130, China
| | - Hinayah R. Oliveira
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
- Centre for Genetic Improvement of Livestock, Department of Animal Biosciences, University of Guelph, Guelph, ON N1G2W1, Canada;
| | - Theresa M. Casey
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
| | - Melkaye G. Melka
- Department of Animal and Food Science, University of Wisconsin River Falls, River Falls, WI 54022, USA;
| | - Luiz F. Brito
- Department of Animal Sciences, Purdue University, West Lafayette, IN 47907, USA; (V.B.P.); (S.-Y.C.); (H.R.O.); (T.M.C.)
- Correspondence:
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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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