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Lee J, Cho K, Weigel KA, White HM, Do C, Choi I. Identification of genomic regions and genes associated with subclinical ketosis in periparturient dairy cows. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2024; 66:567-576. [PMID: 38975580 PMCID: PMC11222121 DOI: 10.5187/jast.2023.e97] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Subscribe] [Scholar Register] [Received: 06/09/2023] [Revised: 08/16/2023] [Accepted: 09/12/2023] [Indexed: 07/09/2024]
Abstract
Subclinical ketosis (SCK) is a prevalent metabolic disorder that occurs during the transition to lactation period. It is defined as a high blood concentration of ketone bodies (beta-hydroxybutyric acid f ≥ 1.2 mmol/L) within the first few weeks of lactation, and often presents without clinical signs. SCK is mainly caused by negative energy balance (NEB). The objective of this study is to identify single nucleotide polymorphisms (SNPs) associated with SCK using genome-wide association studies (GWAS), and to predict the biological functions of proximal genes using gene-set enrichment analysis (GSEA). Blood samples were collected from 112 Holstein cows between 5 and 18 days postpartum to determine the incidence of SCK. Genomic DNA extracted from both SCK and healthy cows was examined using the Illumina Bovine SNP50K BeadChip for genotyping. GWAS revealed 194 putative SNPs and 163 genes associated with those SNPs. Additionally, GSEA showed that the genes retrieved by Database for Annotation, Visualization, and Integrated Discovery (DAVID) belonged to calcium signaling, starch and sucrose, immune network, and metabolic pathways. Furthermore, the proximal genes were found to be related to germ cell and early embryo development. In summary, this study proposes several feasible SNPs and genes associated with SCK through GWAS and GSEA. These candidates can be utilized in selective breeding programs to reduce the genetic risk for SCK and subfertility in high-performance dairy cows.
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Affiliation(s)
- Jihwan Lee
- Dairy Science Division, National Institute
of Animal Science, RDA, Cheon 31000, Korea
| | - KwangHyeon Cho
- Department of Beef and Dairy Science,
Korea National College of Agriculture and Fisheries, Jeonju
54874, Korea
| | - Kent A. Weigel
- Department of Animal and Dairy Sciences,
University of Wisconsin, Madison 53706, USA
| | - Heather M. White
- Department of Animal and Dairy Sciences,
University of Wisconsin, Madison 53706, USA
| | - ChangHee Do
- Department of Animal and Dairy Sciences,
Chungnam National University, Daejeon 34134, Korea
| | - Inchul Choi
- Department of Animal and Dairy Sciences,
Chungnam National University, Daejeon 34134, Korea
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Zhou S, Shi X, Song C, Wang Y, Lai M, Chen X, Zhang C, Chen H, Fang X. SNP discovery of PRKAB1 gene and their associations with growth traits in goats. Anim Biotechnol 2022; 33:1613-1619. [PMID: 34106801 DOI: 10.1080/10495398.2021.1920426] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
Abstract
AMPK plays an important role in regulating the metabolism of carbohydrate, lipid and protein in an organism, and is considered to be a key regulator of cellular energy homeostasis. In recent years, attention has been drawn to AMPK subunit polymorphisms and their association with economical traits of domestic animals and fowls. PRKAB1 encodes the β1 regulatory subunit of AMPK, and it has been reported that PRKAB1 may be applied in breeding programs of meat-type chicken. To date, the polymorphism of goat PRKAB1 gene and its associations remain unknown. In this paper, the polymorphism of PRKAB1 gene was detected in 316 goats of three breeds. A total of four novel single nucleotide polymorphisms (SNPs) of PRKAB1 gene were revealed by sequence analysis. Among them, three were in the coding region (285 C > A, 297 C > A, 309 C > T), and they were all synonymous. One was in the intron (229 A > G). The associations between polymorphic loci and the growth traits of Xuhuai and Haimen goats were analyzed, and significant associations were found in body length index and trunk index (p < 0.05) for Xuhuai breed, while no significant associations in Haimen breed. Our results provide useful information for the improvement and breeding of Chinese native goats.
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Affiliation(s)
- Shengliang Zhou
- College of Health Sciences, Jiangsu Normal University, Xuzhou, China
| | - Xiuying Shi
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, China
| | - Chengchuang Song
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, China
| | - Yanhong Wang
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, China
| | - Min Lai
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, China
| | - Xi Chen
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, China
| | - Chunlei Zhang
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, China
| | - Hong Chen
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, China
| | - Xingtang Fang
- Institute of Cellular and Molecular Biology, Jiangsu Normal University, Xuzhou, China
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Cai W, Li C, Li J, Song J, Zhang S. Integrated Small RNA Sequencing, Transcriptome and GWAS Data Reveal microRNA Regulation in Response to Milk Protein Traits in Chinese Holstein Cattle. Front Genet 2021; 12:726706. [PMID: 34712266 PMCID: PMC8546187 DOI: 10.3389/fgene.2021.726706] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2021] [Accepted: 09/21/2021] [Indexed: 01/04/2023] Open
Abstract
Milk protein is one of the most important economic traits in the dairy industry. Yet, the regulatory network of miRNAs for the synthesis of milk protein in mammary is poorly understood. Samples from 12 Chinese Holstein cows with three high ( ≥ 3.5%) and three low ( ≤ 3.0%) phenotypic values for milk protein percentage in lactation and non-lactation were examined through deep small RNA sequencing. We characterized 388 known and 212 novel miRNAs in the mammary gland. Differentially expressed analysis detected 28 miRNAs in lactation and 52 miRNAs in the non-lactating period with a highly significant correlation with milk protein concentration. Target prediction and correlation analysis identified some key miRNAs and their targets potentially involved in the synthesis of milk protein. We analyzed for enrichments of GWAS signals in miRNAs and their correlated targets. Our results demonstrated that genomic regions harboring DE miRNA genes in lactation were significantly enriched with GWAS signals for milk protein percentage traits and that enrichments within DE miRNA targets were significantly higher than in random gene sets for the majority of milk production traits. This integrated study on the transcriptome and posttranscriptional regulatory profiles between significantly differential phenotypes of milk protein concentration provides new insights into the mechanism of milk protein synthesis, which should reveal the regulatory mechanisms of milk secretion.
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Affiliation(s)
- Wentao Cai
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China.,Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China.,Department of Animal and Avian Science, University of Maryland, College Park, MD, United States
| | - Cong Li
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Junya Li
- Laboratory of Molecular Biology and Bovine Breeding, Institute of Animal Science, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jiuzhou Song
- Department of Animal and Avian Science, University of Maryland, College Park, MD, United States
| | - Shengli Zhang
- Key Laboratory of Animal Genetics, Breeding and Reproduction, Ministry of Agriculture & National Engineering Laboratory for Animal Breeding, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Wu C, Sirard MA. Parental Effects on Epigenetic Programming in Gametes and Embryos of Dairy Cows. Front Genet 2020; 11:557846. [PMID: 33173533 PMCID: PMC7591718 DOI: 10.3389/fgene.2020.557846] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2020] [Accepted: 09/18/2020] [Indexed: 12/11/2022] Open
Abstract
The bovine represents an important agriculture species and dairy breeds have experienced intense genetic selection over the last decades. The selection of breeders focused initially on milk production, but now includes feed efficiency, health, and fertility, although these traits show lower heritability. The non-genetic paternal and maternal effects on the next generation represent a new research topic that is part of epigenetics. The evidence for embryo programming from both parents is increasing. Both oocytes and spermatozoa carry methylation marks, histones modifications, small RNAs, and chromatin state variations. These epigenetic modifications may remain active in the early zygote and influence the embryonic period and beyond. In this paper, we review parental non-genetic effects retained in gametes on early embryo development of dairy cows, with emphasis on parental age (around puberty), the metabolism of the mother at the time of conception and in vitro culture (IVC) conditions. In our recent findings, transcriptomic signatures and DNA methylation patterns of blastocysts and gametes originating from various parental and IVC conditions revealed surprisingly similar results. Embryos from all these experiments displayed a metabolic signature that could be described as an "economy" mode where protein synthesis is reduced, mitochondria are considered less functional. In the absence of any significant phenotype, these results indicated a possible similar adaptation of the embryo to younger parental age, post-partum metabolic status and IVC conditions mediated by epigenetic factors.
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Affiliation(s)
| | - Marc-André Sirard
- Centre de Recherche en Reproduction, Développement et Santé Intergénérationnelle (CRDSI), Département des Sciences Animales, Faculté des Sciences de l’Agriculture et de l’Alimentation, Université Laval, Québec City, QC, Canada
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Expression of genes involved in BMP and estrogen signaling and AMPK production can be important factors affecting total number of antral follicles in ewes. Theriogenology 2016; 91:36-43. [PMID: 28215684 DOI: 10.1016/j.theriogenology.2016.12.023] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2016] [Revised: 12/16/2016] [Accepted: 12/21/2016] [Indexed: 11/24/2022]
Abstract
Follicular growth and ovulation of healthy oocytes is a complicated process which is regulated by several endocrine and paracrine factors as well as cross-talk between the oocyte and its surrounding somatic cells. This study compared the expression profile of some candidate genes involved in BMP signaling as well as estrogen and AMPK production in cumulus-oocyte complex (COC) of small and large antral follicles and their associated somatic cell layers in ovaries from ewes with high- and low-antral follicle count (AFC). Expression of GDF9 was increased by increasing the size of antral follicles, while BMP15 expression was decreased by follicular size. It should be noteworthy that transcription of both GDF9 and BMP15 was also detected in the adjacent cellular layers under the follicles. There was a very strong positive correlation between BMP15 and BMPR2 in ovary tissues. Expression of GDF9 was highly correlated with BMP15, BMPR1B, and BMPR2 in large antral follicles. Expression of BMP7 in small antral follicles and BMPR2 in ovary tissues was significantly increased in the high-AFC group. Expression of ESR1 and ESR2 involved in estrogen production as well as PRKAA1 which involved in AMPK production were significantly greater in large antral follicles of high-AFC. There was a very high correlation between Cyp19 and ESR1 in large antral follicles and ovary tissues. Expression of Cyp19 and PRKAA1 were positively correlated with GDF9, BMP15, and BMP7 in large follicles. In conclusion, this study suggests that apart from the BMP signaling, genes involved in AMPK and estrogen production can be pivotal players in ewe's follicular development process. In addition, a strong cross-talk can exist among AMPK, BMP signaling, and estrogen synthesis systems in ewe ovary.
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