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Long M, Wang B, Yang Z, Lu X. Genome-Wide Association Study as an Efficacious Approach to Discover Candidate Genes Associated with Body Linear Type Traits in Dairy Cattle. Animals (Basel) 2024; 14:2181. [PMID: 39123707 PMCID: PMC11311069 DOI: 10.3390/ani14152181] [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: 06/12/2024] [Revised: 07/19/2024] [Accepted: 07/23/2024] [Indexed: 08/12/2024] Open
Abstract
Body shape traits are very important and play a crucial role in the economic development of dairy farming. By improving the accuracy of selection for body size traits, we can enhance economic returns across the dairy industry and on farms, contributing to the future profitability of the dairy sector. Registered body conformation traits are reliable and cost-effective tools for use in national cattle breeding selection programs. These traits are significantly related to the production, longevity, mobility, health, fertility, and environmental adaptation of dairy cows. Therefore, they can be considered indirect indicators of economically important traits in dairy cows. Utilizing efficacious genetic methods, such as genome-wide association studies (GWASs), allows for a deeper understanding of the genetic architecture of complex traits through the identification and application of genetic markers. In the current review, we summarize information on candidate genes and genomic regions associated with body conformation traits in dairy cattle worldwide. The manuscript also reviews the importance of body conformation, the relationship between body conformation traits and other traits, heritability, influencing factors, and the genetics of body conformation traits. The information on candidate genes related to body conformation traits provided in this review may be helpful in selecting potential genetic markers for the genetic improvement of body conformation traits in dairy cattle.
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Affiliation(s)
- Mingxue Long
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (M.L.); (Z.Y.)
| | - Bo Wang
- College of Food Science and Engineering, Yangzhou University, Yangzhou 225009, China;
| | - Zhangping Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (M.L.); (Z.Y.)
| | - Xubin Lu
- College of Animal Science and Technology, Yangzhou University, Yangzhou 225009, China; (M.L.); (Z.Y.)
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Nowak B, Mucha A, Zatoń-Dobrowolska M, Chrostowski G, Kruszyński W. Genetic basis of sow hyperprolificacy and litter size optimization based on a genome-wide association study. Theriogenology 2024; 218:119-125. [PMID: 38325148 DOI: 10.1016/j.theriogenology.2024.01.035] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/30/2023] [Revised: 01/24/2024] [Accepted: 01/25/2024] [Indexed: 02/09/2024]
Abstract
Over the last few decades, there has been a constant increase in sow litter size, the consequences of which include parturition duration extension, an increase in the percentage of stillborn and hypoxic piglets, and increased variation in piglet birth weight, which reduces their vitality. As such, it seems clear that further increasing sow fertility will generate difficulties and costs in rearing numerous litters with low birth weights. Therefore, the current study aimed to analyze the genetic background of sow hyperprolifcacy using a genome-wide association study (GWAS). The research included 144 sows in the maternal component, divided into two equal groups. The first group (control) consisted of females giving birth to the optimal number of piglets in their third and fourth litters (14-16), while the second group (cases) included those with excessive litter size (>16). The analyzed sows were genotyped using Illumina's PorcineSNP60v2 BeadChip microarray, comprising 64,232 single nucleotide polymorphisms (SNPs). Statistical analysis using R included quality control of genotyping data and GWAS analysis based on five logistic regression models (dominant, codominant, overdominant, recessive, and log-additive) with a single SNP marker as the explanatory variable. On this basis, one SNP (SIRI0000069) was identified on chromosome seven within the EFCAB11 (EF-hand calcium binding domain 11) gene that had a statistically significant effect on sow hyperprolificacy. Additionally, ten SNPs (INRA0007631, ALGA0011600, ALGA0043433, ALGA0043428, M1GA0010535 ALGA00443338, ALGA0087116, MARC0056787, ALGA0112928, and ALGA0089047) had a relationship with the analyzed feature at a level close to significance, set at 1-5. These SNPs appear important since they are located on chromosomes on which a large number of quantitative trait loci (QTLs) and SNPs associated with reproductive characteristics, including litter size, have been identified.
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Affiliation(s)
- Błażej Nowak
- Department of Genetics, Wrocław University of Environmental and Life Sciences, Kożuchowska 7, 51-631, Wrocław, Poland.
| | - Anna Mucha
- Department of Genetics, Wrocław University of Environmental and Life Sciences, Kożuchowska 7, 51-631, Wrocław, Poland
| | - Magdalena Zatoń-Dobrowolska
- Department of Genetics, Wrocław University of Environmental and Life Sciences, Kożuchowska 7, 51-631, Wrocław, Poland
| | - Grzegorz Chrostowski
- Department of Genetics, Wrocław University of Environmental and Life Sciences, Kożuchowska 7, 51-631, Wrocław, Poland
| | - Wojciech Kruszyński
- Department of Genetics, Wrocław University of Environmental and Life Sciences, Kożuchowska 7, 51-631, Wrocław, Poland
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Jalata B, Goshu HA, Mediksa T, Bekele D, Aliye M. Reproductive performance of Horro and Horro-crossbred dairy cows in Ethiopia's subhumid tropical environments. Trop Anim Health Prod 2023; 55:323. [PMID: 37749411 DOI: 10.1007/s11250-023-03718-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/19/2023] [Accepted: 09/12/2023] [Indexed: 09/27/2023]
Abstract
Estrus detection, timing of insemination, feeding, and health care practices are all factors that can significantly affect cattle breeding efficiency and lifetime production. In Ethiopia's subhumid environment, the age at first calving, number of days open, duration from calving to first heat, and number of services per conception are economic traits that affect reproductive performance of Horro and Horro-crossbred dairy cows. Data collected at Ethiopia's Bako Agricultural Research Center between 1980-2019 was used to study the reproductive performance of Horro and Horro-crosses with Holstein Friesian and Jersey dairy cows. We identified overall mean ± standard error values of factors that affect reproductive performance, including age at first service (AFS) (29.2 ± 0.2 months), age at first calving (AFC) (39.8 ± 0.2 months), number of services per conception (NSC) (1.76 ± 0.4 months), calving interval (CI) (13.2 ± 0.3 months), days open (DO) (94.3 ± 4.3 days), conception rate (CR) (75.0 ± 1.3%), and replacement rate (RR) (28.4 ± 0.3%). The odds ratios of the 60-day and 90-day nonreturn rates (NRR) were 0.22 and 0.96, respectively. Sire and dam breed and birth period had significant (P < 0.001) effects on AFS and AFC, while season and dam parity had significant effects on CI and DO. Inconsistencies regarding feeding, heat detection, inseminator skills, insemination timing, animal health, and other husbandry practices may extend periods of AFS, AFC, CI, and DO. To optimize reproductive performance in Horro cows and Horro crossbreeds in Ethiopia's subhumid environments, improving management practices should be a priority.
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Affiliation(s)
| | - Habtamu Abera Goshu
- Bio and Emerging Technology Institute (BETin) and Ministry of Innovation and Technology, PO Box 5954, Addis Ababa, Ethiopia.
| | - Tesfaye Mediksa
- Bako Agricultural Research Center, P.O. Box 03, Bako, Ethiopia
| | - Dereje Bekele
- Bako Agricultural Research Center, P.O. Box 03, Bako, Ethiopia
| | - Mohammed Aliye
- Jimma University College of Agriculture and Veterinary Medicine, P.O. Box 3, Jimma, Ethiopia
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Identification of candidate genomic regions for egg yolk moisture content based on a genome-wide association study. BMC Genomics 2023; 24:110. [PMID: 36918797 PMCID: PMC10015838 DOI: 10.1186/s12864-023-09221-8] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/30/2022] [Accepted: 03/01/2023] [Indexed: 03/15/2023] Open
Abstract
BACKGROUND Eggs represent important sources of protein and are widely loved by consumers. Egg yolk taste is an important index for egg selection, and the moisture content of the egg yolk affects the taste. To understand the molecular mechanism underlying egg yolk moisture content, this study determined the phenotype and heritability of egg yolk water content and conducted a genome-wide association study (GWAS) using a mixed linear model. RESULTS We determined the phenotype and heritability of thermogelled egg yolk water content (TWC) and found that the average TWC was 47.73%. Moreover, significant variations occurred (41.06-57.12%), and the heritability was 0.11, which indicates medium-low heritability. Through the GWAS, 48 single nucleotide polymorphisms (SNPs) related to TWC (20 significantly, 28 suggestively) were obtained, and they were mainly located on chromosomes 10 and 13. We identified 36 candidate genes based on gene function and found that they were mainly involved in regulating fat, protein, and water content and embryonic development. FGF9, PIAS1, FEM1B, NOX5, GLCE, VDAC1, IGFBP7, and THOC5 were involved in lipid formation and regulation; AP3S2, GNPDA1, HSPA4, AP1B1, CABP7, EEF1D, SYTL3, PPP2CA, SKP1, and UBE2B were involved in protein folding and hydrolysis; and CSF2, SOWAHA, GDF9, FSTL4, RAPGEF6, PAQR5, and ZMAT5 were related to embryonic development and egg production. Moreover, MICU2, ITGA11, WDR76, BLM, ANPEP, TECRL, EWSR1, and P4HA2 were related to yolk quality, while ITGA11, WDR76, BLM, and ANPEP were potentially significantly involved in egg yolk water content and thus deserve further attention and research. In addition, this study identified a 19.31-19.92 Mb genome region on GGA10, and a linkage disequilibrium analysis identified strong correlations within this region. Thus, GGA10 may represent a candidate region for TWC traits. CONCLUSION The molecular genetic mechanism involved in TWC was revealed through heritability measurements and GWAS, which identified a series of SNPs, candidate genes, and candidate regions related to TWC. These results provide insights on the molecular mechanism of egg yolk moisture content and may aid in the development of new egg traits.
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Lan Q, Deng Q, Qi S, Zhang Y, Li Z, Yin S, Li Y, Tan H, Wu M, Yin Y, He J, Liu M. Genome-Wide Association Analysis Identified Variants Associated with Body Measurement and Reproduction Traits in Shaziling Pigs. Genes (Basel) 2023; 14:522. [PMID: 36833449 PMCID: PMC9957351 DOI: 10.3390/genes14020522] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2023] [Revised: 02/09/2023] [Accepted: 02/16/2023] [Indexed: 02/22/2023] Open
Abstract
With the increasing popularity of genomic sequencing, breeders pay more attention to identifying the crucial molecular markers and quantitative trait loci for improving the body size and reproduction traits that could affect the production efficiency of pig-breeding enterprises. Nevertheless, for the Shaziling pig, a well-known indigenous breed in China, the relationship between phenotypes and their corresponding genetic architecture remains largely unknown. Herein, in the Shaziling population, a total of 190 samples were genotyped using the Geneseek Porcine 50K SNP Chip, obtaining 41857 SNPs for further analysis. For phenotypes, two body measurement traits and four reproduction traits in the first parity from the 190 Shaziling sows were measured and recorded, respectively. Subsequently, a genome-wide association study (GWAS) between the SNPs and the six phenotypes was performed. The correlation between body size and reproduction phenotypes was not statistically significant. A total of 31 SNPs were found to be associated with body length (BL), chest circumference (CC), number of healthy births (NHB), and number of stillborns (NSB). Gene annotation for those candidate SNPs identified 18 functional genes, such as GLP1R, NFYA, NANOG, COX7A2, BMPR1B, FOXP1, SLC29A1, CNTNAP4, and KIT, which exert important roles in skeletal morphogenesis, chondrogenesis, obesity, and embryonic and fetal development. These findings are helpful to better understand the genetic mechanism for body size and reproduction phenotypes, while the phenotype-associated SNPs could be used as the molecular markers for the pig breeding programs.
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Affiliation(s)
- Qun Lan
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Qiuchun Deng
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Shijin Qi
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Yuebo Zhang
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Zhi Li
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Shishu Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Yulian Li
- Xiang Dong Experiment Station, Hunan Provincial Pig Industrial Technology System, Xiangtan 411100, China
| | - Hong Tan
- Xiang Dong Experiment Station, Hunan Provincial Pig Industrial Technology System, Xiangtan 411100, China
| | - Maisheng Wu
- Xiang Dong Experiment Station, Hunan Provincial Pig Industrial Technology System, Xiangtan 411100, China
| | - Yulong Yin
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Key Laboratory of Agro-Ecological Processes in Subtropical Region, Institute of Subtropical Agriculture, Chinese Academy of Sciences; Hunan Provincial Engineering Research Center for Healthy Livestock and Poultry Production; Scientific Observing and Experimental Station of Animal Nutrition and Feed Science in South-Central, Ministry of Agriculture, Changsha 410125, China
| | - Jun He
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
| | - Mei Liu
- College of Animal Science and Technology, Hunan Agricultural University, Changsha 410128, China
- Kunpeng Institute of Modern Agriculture at Foshan, Foshan 528226, China
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Martino NA, Picardi E, Ciani E, D’Erchia AM, Bogliolo L, Ariu F, Mastrorocco A, Temerario L, Mansi L, Palumbo V, Pesole G, Dell’Aquila ME. Cumulus Cell Transcriptome after Cumulus-Oocyte Complex Exposure to Nanomolar Cadmium in an In Vitro Animal Model of Prepubertal and Adult Age. BIOLOGY 2023; 12:biology12020249. [PMID: 36829526 PMCID: PMC9953098 DOI: 10.3390/biology12020249] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Revised: 01/25/2023] [Accepted: 02/02/2023] [Indexed: 02/09/2023]
Abstract
Cadmium (Cd), a highly toxic pollutant, impairs oocyte fertilization, through oxidative damage on cumulus cells (CCs). This study analysed the transcriptomic profile of CCs of cumulus-oocyte complexes (COCs) from adult and prepubertal sheep, exposed to Cd nanomolar concentration during in vitro maturation. In both age-groups, CCs of matured oocytes underwent RNA-seq, data analysis and validation. Differentially expressed genes (DEGs) were identified in adult (n = 99 DEGs) and prepubertal (n = 18 DEGs) CCs upon Cd exposure. Transcriptomes of adult CCs clustered separately between Cd-exposed and control samples, whereas prepubertal ones did not as observed by Principal Component Analysis. The transcriptomic signature of Cd-induced CC toxicity was identified by gene annotation and literature search. Genes associated with previous studies on ovarian functions and/or Cd effects were confirmed and new genes were identified, thus implementing the knowledge on their involvement in such processes. Enrichment and validation analysis showed that, in adult CCs, Cd acted as endocrine disruptor on DEGs involved in hormone biosynthesis, cumulus expansion, regulation of cell signalling, growth and differentiation and oocyte maturation, whereas in prepubertal CCs, Cd affected DEGs involved in CC development and viability and CC-oocyte communications. In conclusion, these DEGs could be used as valuable non-invasive biomarkers for oocyte competence.
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Affiliation(s)
- Nicola Antonio Martino
- Department of Biosciences, Biotechnologies & Environment, University of Bari Aldo Moro, Via Edoardo Orabona, 70125 Bari, Italy
- Correspondence: ; Tel.: +39-0805443888
| | - Ernesto Picardi
- Department of Biosciences, Biotechnologies & Environment, University of Bari Aldo Moro, Via Edoardo Orabona, 70125 Bari, Italy
| | - Elena Ciani
- Department of Biosciences, Biotechnologies & Environment, University of Bari Aldo Moro, Via Edoardo Orabona, 70125 Bari, Italy
| | - Anna Maria D’Erchia
- Department of Biosciences, Biotechnologies & Environment, University of Bari Aldo Moro, Via Edoardo Orabona, 70125 Bari, Italy
| | - Luisa Bogliolo
- Department of Veterinary Medicine, University of Sassari, Via Vienna n. 2, 07100 Sassari, Italy
| | - Federica Ariu
- Department of Veterinary Medicine, University of Sassari, Via Vienna n. 2, 07100 Sassari, Italy
| | - Antonella Mastrorocco
- Department of Biosciences, Biotechnologies & Environment, University of Bari Aldo Moro, Via Edoardo Orabona, 70125 Bari, Italy
| | - Letizia Temerario
- Department of Biosciences, Biotechnologies & Environment, University of Bari Aldo Moro, Via Edoardo Orabona, 70125 Bari, Italy
| | - Luigi Mansi
- Department of Biosciences, Biotechnologies & Environment, University of Bari Aldo Moro, Via Edoardo Orabona, 70125 Bari, Italy
| | - Valeria Palumbo
- Department of Biosciences, Biotechnologies & Environment, University of Bari Aldo Moro, Via Edoardo Orabona, 70125 Bari, Italy
| | - Graziano Pesole
- Department of Biosciences, Biotechnologies & Environment, University of Bari Aldo Moro, Via Edoardo Orabona, 70125 Bari, Italy
| | - Maria Elena Dell’Aquila
- Department of Biosciences, Biotechnologies & Environment, University of Bari Aldo Moro, Via Edoardo Orabona, 70125 Bari, Italy
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Zlobin AS, Volkova NA, Zinovieva NA, Iolchiev BS, Bagirov VA, Borodin PM, Axenovich TI, Tsepilov YA. Loci Associated with Negative Heterosis for Viability and Meat Productivity in Interspecific Sheep Hybrids. Animals (Basel) 2023; 13:ani13010184. [PMID: 36611792 PMCID: PMC9817718 DOI: 10.3390/ani13010184] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/26/2022] [Revised: 12/15/2022] [Accepted: 12/19/2022] [Indexed: 01/05/2023] Open
Abstract
Negative heterosis can occur on different economically important traits, but the exact biological mechanisms of this phenomenon are still unknown. The present study focuses on determining the genetic factors associated with negative heterosis in interspecific hybrids between domestic sheep (Ovis aries) and argali (Ovis ammon). One locus (rs417431015) associated with viability and two loci (rs413302370, rs402808951) associated with meat productivity were identified. One gene (ARAP2) was prioritized for viability and three for meat productivity (PDE2A, ARAP1, and PCDH15). The loci associated with meat productivity were demonstrated to fit the overdominant inheritance model and could potentially be involved int negative heterosis mechanisms.
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Affiliation(s)
- Alexander S. Zlobin
- Kurchatov Genomic Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences SB RAS, 630090 Novosibirsk, Russia
| | - Natalia A. Volkova
- L.K. Ernst Federal Science Center for Animal Husbandry, 101000 Moscow, Russia
| | | | - Baylar S. Iolchiev
- L.K. Ernst Federal Science Center for Animal Husbandry, 101000 Moscow, Russia
| | - Vugar A. Bagirov
- L.K. Ernst Federal Science Center for Animal Husbandry, 101000 Moscow, Russia
| | - Pavel M. Borodin
- Institute of Cytology and Genetics, SB RAS, 630090 Novosibirsk, Russia
| | | | - Yakov A. Tsepilov
- Kurchatov Genomic Center, Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences SB RAS, 630090 Novosibirsk, Russia
- Correspondence:
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Sun Y, Wu X, Ma Y, Liu D, Lu X, Zhao T, Yang Z. Molecular Marker-Assisted Selection of ABCG2, CD44, SPP1 Genes Contribute to Milk Production Traits of Chinese Holstein. Animals (Basel) 2022; 13:ani13010089. [PMID: 36611698 PMCID: PMC9817805 DOI: 10.3390/ani13010089] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/19/2022] [Revised: 12/18/2022] [Accepted: 12/23/2022] [Indexed: 12/28/2022] Open
Abstract
Based on our results of genome-wide association analysis, we performed gene ontology (GO) annotation and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway enrichment analysis; three candidate genes (ABCG2, CD44, SPP1) were screened in this study for SNPs association analysis with production traits in 999 Holstein cattle. In this research, flight mass spectrometry genotyping was used to detect the polymorphism of SNP seats. It was shown that four, four, and two single nucleotide polymorphisms (SNP) loci were detected for the ABCG2, CD44, and SPP1 genes, respectively, and the different genotypes of these 10 SNPs significantly affected the milk production performance of Chinese Holstein cattle in terms of milk yield, milk fat percentage, milk protein percentage, somatic cell score, and urea nitrogen content. Among them, ABCG2-G.80952G > T locus, ABCG2-G.120017G > A locus and CD44-G.2294G > C locus had significant effects on somatic cell score (p < 0.01). Cows with GG genotypes at ABCG2-G.80952G > T locus, AA and GG genotypes at ABCG2-G.120017G > A locus, and GG genotypes at CD44-G.2294G > C locus had lower somatic cell scores. The present study elucidated that ABCG2, CD44, and SPP1 could be selected for marker-assisted selection and will benefit for future precise molecular breeding.
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Affiliation(s)
- Yujia Sun
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Xinyi Wu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Yaoyao Ma
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Dingding Liu
- Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Xubin Lu
- Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Tianqi Zhao
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
| | - Zhangping Yang
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, The Ministry of Education of China, Institutes of Agricultural Science and Technology Development, Yangzhou University, Yangzhou 225009, China
- Key Laboratory of Animal Genetics & Breeding and Molecular Design of Jiangsu Province, Yangzhou University, Yangzhou 225009, China
- Correspondence: ; Tel.: +86-0514-87979230
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Čítek J, Brzáková M, Bauer J, Tichý L, Sztankóová Z, Vostrý L, Steyn Y. Genome-Wide Association Study for Body Conformation Traits and Fitness in Czech Holsteins. Animals (Basel) 2022; 12:ani12243522. [PMID: 36552441 PMCID: PMC10375906 DOI: 10.3390/ani12243522] [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: 09/27/2022] [Revised: 12/07/2022] [Accepted: 12/12/2022] [Indexed: 12/15/2022] Open
Abstract
The aim of this study was a genome-wide association study (GWAS) on conformation traits using 25,486 genotyped Czech Holsteins, with 35,227 common SNPs for each genotype. Linear trait records were collected between 1995 and 2020. The Interbull information from Multiple Across Country Evaluation (MACE) was included for bulls that mostly had daughter records in a foreign country. When using the Bonferroni correction, the number of SNPs that were either significant or approached the significance threshold was low-dairy capacity composite on BTA4, feet and legs composite BTA21, total score BTA10, stature BTA24, body depth BTA6, angularity BTA20, fore udder attachment BTA10. Without the Bonferroni correction, the total number of significant or near of significance SNPs was 32. The SNPs were localized on BTA1,2,4,5,6,7,8,18,22,25,26,28 for dairy capacity composite, BTA15,21 for feet and legs composite, BTA10 for total score, BTA24 stature, BTA6,23 body depth, BTA20 angularity, BTA2 rump angle, BTA9,10 rear legs rear view, BTA2,19 rear legs side view, BTA10 fore udder attachment, BTA2 udder depth, BTA10 rear udder height, BTA12 central alignment, BTA24 rear teat placement, BTA8,29 rear udder width. The results provide biological information for the improvement of body conformation and fitness in the Holstein population.
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Affiliation(s)
- Jindřich Čítek
- Department of Genetics and Agricultural Biotechnology, Faculty of Agriculture, University of South Bohemia in České Budějovice, Studentská 1668, 370 05 České Budějovice, Czech Republic
- Veterinary Research Institute, Hudcova 296, 621 00 Brno, Czech Republic
| | - Michaela Brzáková
- Institute of Animal Science, Přátelství 815, 104 00 Praha, Czech Republic
| | - Jiří Bauer
- Czech Moravian Breeders' Corporation, Benešovská 123, 252 09 Hradištko, Czech Republic
| | - Ladislav Tichý
- Institute of Animal Science, Přátelství 815, 104 00 Praha, Czech Republic
- Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Praha, Czech Republic
| | - Zuzana Sztankóová
- Institute of Animal Science, Přátelství 815, 104 00 Praha, Czech Republic
| | - Luboš Vostrý
- Faculty of Agrobiology, Food and Natural Resources, Czech University of Life Sciences Prague, 165 00 Praha, Czech Republic
| | - Yvette Steyn
- Department of Animal and Dairy Science, University of Georgia, 425 River Road, Athens, GA 30602, USA
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de Souza TC, de Souza TC, da Cruz VAR, Mourão GB, Pedrosa VB, Rovadoscki GA, Coutinho LL, de Camargo GMF, Costa RB, de Carvalho GGP, Pinto LFB. Estimates of heritability and candidate genes for primal cuts and dressing percentage in Santa Ines sheep. Livest Sci 2022. [DOI: 10.1016/j.livsci.2022.105048] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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11
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Zhu JY, Guang-Xin E, Wang JB, Xu SS, yang X. Single nucleotide polymorphisms in the 3′ UTR of follistatin-like 4 and scavenger receptor class B member 1 are associated with Dazu black goat litter size. CANADIAN JOURNAL OF ANIMAL SCIENCE 2022. [DOI: 10.1139/cjas-2020-0170] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The untranslated regions (UTR) of genes play crucial roles in regulating gene expression at the post-transcriptional level such as affecting mRNA stabilization. In this study, 26 single nucleotide polymorphisms (SNPs) and one deletion located in UTR were genotyped from 186 Dazu black goats via SNaPshot, and the correlation between genotype and litter size was analyzed. Results indicated that two SNP loci, SNP_chr17-20182525 and SNP_chr7-65652612, which are located at the 3′UTR of scavenger receptor class B member 1 and follistatin-like 4, are significantly (p<0.05) correlated with the litter size of first parity goats. SNP_chr7-65652612 is also significantly associated with the total litter size of first and second parity offspring (p<0.05). In conclusion, SNP_chr7-65652612 and SNP_chr17-20182525 have correlation with the litter size of Dazu black goat and they are potential genetic markers for litter size breeding.
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Affiliation(s)
- Ji-Yuan Zhu
- Northeast Agricultural University, 12430, College of Animal Science and Technology, Harbin, Heilongjiang, China,
| | - E Guang-Xin
- Southwest University, 26463, Chongqing, China
| | - Jia-Bo Wang
- Southwest Minzu University, 66336, Chengdu, China
| | - Shan-Shan Xu
- Heilongjiang Academy of Agricultural Sciences, 74727, Harbin, China
| | - xiuqin yang
- Northeast Agricultural University, 12430, Harbin, China
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Lu X, Arbab AAI, Abdalla IM, Liu D, Zhang Z, Xu T, Su G, Yang Z. Genetic Parameter Estimation and Genome-Wide Association Study-Based Loci Identification of Milk-Related Traits in Chinese Holstein. Front Genet 2022; 12:799664. [PMID: 35154251 PMCID: PMC8836289 DOI: 10.3389/fgene.2021.799664] [Citation(s) in RCA: 7] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/21/2021] [Accepted: 12/07/2021] [Indexed: 11/22/2022] Open
Abstract
Accurately estimating the genetic parameters and revealing more genetic variants underlying milk production and quality are conducive to the genetic improvement of dairy cows. In this study, we estimate the genetic parameters of five milk-related traits of cows-namely, milk yield (MY), milk fat percentage (MFP), milk fat yield (MFY), milk protein percentage (MPP), and milk protein yield (MPY)-based on a random regression test-day model. A total of 95,375 test-day records of 9,834 cows in the lower reaches of the Yangtze River were used for the estimation. In addition, genome-wide association studies (GWASs) for these traits were conducted, based on adjusted phenotypes. The heritability, as well as the standard errors, of MY, MFP, MFY, MPP, and MPY during lactation ranged from 0.22 ± 0.02 to 0.31 ± 0.04, 0.06 ± 0.02 to 0.15 ± 0.03, 0.09 ± 0.02 to 0.28 ± 0.04, 0.07 ± 0.01 to 0.16 ± 0.03, and 0.14 ± 0.02 to 0.27 ± 0.03, respectively, and the genetic correlations between different days in milk (DIM) within lactations decreased as the time interval increased. Two, six, four, six, and three single nucleotide polymorphisms (SNPs) were detected, which explained 5.44, 12.39, 8.89, 10.65, and 7.09% of the phenotypic variation in MY, MFP, MFY, MPP, and MPY, respectively. Ten Kyoto Encyclopedia of Genes and Genomes pathways and 25 Gene Ontology terms were enriched by analyzing the nearest genes and genes within 200 kb of the detected SNPs. Moreover, 17 genes in the enrichment results that may play roles in milk production and quality were selected as candidates, including CAMK2G, WNT3A, WNT9A, PLCB4, SMAD9, PLA2G4A, ARF1, OPLAH, MGST1, CLIP1, DGAT1, PRMT6, VPS28, HSF1, MAF1, TMEM98, and F7. We hope that this study will provide useful information for in-depth understanding of the genetic architecture of milk production and quality traits, as well as contribute to the genomic selection work of dairy cows in the lower reaches of the Yangtze River.
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Affiliation(s)
- Xubin Lu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
- Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
| | | | | | - Dingding Liu
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Zhipeng Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Tianle Xu
- Joint International Research Laboratory of Agriculture and Agri-Product Safety, Yangzhou University, Yangzhou, China
| | - Guosheng Su
- Center for Quantitative Genetics and Genomics, Aarhus University, Tjele, Denmark
| | - Zhangping Yang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
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