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Haque MA, Lee YM, Ha JJ, Jin S, Park B, Kim NY, Won JI, Kim JJ. Genomic Predictions in Korean Hanwoo Cows: A Comparative Analysis of Genomic BLUP and Bayesian Methods for Reproductive Traits. Animals (Basel) 2023; 14:27. [PMID: 38200758 PMCID: PMC10778388 DOI: 10.3390/ani14010027] [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: 11/03/2023] [Revised: 12/07/2023] [Accepted: 12/18/2023] [Indexed: 01/12/2024] Open
Abstract
This study aimed to predict the accuracy of genomic estimated breeding values (GEBVs) for reproductive traits in Hanwoo cows using the GBLUP, BayesB, BayesLASSO, and BayesR methods. Accuracy estimates of GEBVs for reproductive traits were derived through fivefold cross-validation, analyzing a dataset comprising 11,348 animals and employing an Illumina Bovine 50K SNP chip. GBLUP showed an accuracy of 0.26 for AFC, while BayesB, BayesLASSO, and BayesR demonstrated values of 0.28, 0.29, and 0.29, respectively. For CI, GBLUP attained an accuracy of 0.19, whereas BayesB, BayesLASSO, and BayesR scored 0.21, 0.24, and 0.25, respectively. The accuracy for GL was uniform across GBLUP, BayesB, and BayesR at 0.31, whereas BayesLASSO showed a slightly higher accuracy of 0.33. For NAIPC, GBLUP showed an accuracy of 0.24, while BayesB, BayesLASSO, and BayesR recorded 0.22, 0.27, and 0.30, respectively. The variation in genomic prediction accuracy among methods indicated Bayesian approaches slightly outperformed GBLUP. The findings suggest that Bayesian methods, notably BayesLASSO and BayesR, offer improved predictive capabilities for reproductive traits. Future research may explore more advanced genomic approaches to enhance predictive accuracy and genetic gains in Hanwoo cattle breeding programs.
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Affiliation(s)
- Md Azizul Haque
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (M.A.H.); (Y.-M.L.)
| | - Yun-Mi Lee
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (M.A.H.); (Y.-M.L.)
| | - Jae-Jung Ha
- Gyeongbuk Livestock Research Institute, Yeongju 36052, Republic of Korea;
| | - Shil Jin
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang 25340, Republic of Korea; (S.J.); (B.P.); (N.-Y.K.)
| | - Byoungho Park
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang 25340, Republic of Korea; (S.J.); (B.P.); (N.-Y.K.)
| | - Nam-Young Kim
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang 25340, Republic of Korea; (S.J.); (B.P.); (N.-Y.K.)
| | - Jeong-Il Won
- Hanwoo Research Institute, National Institute of Animal Science, Pyeongchang 25340, Republic of Korea; (S.J.); (B.P.); (N.-Y.K.)
| | - Jong-Joo Kim
- Department of Biotechnology, Yeungnam University, Gyeongsan 38541, Republic of Korea; (M.A.H.); (Y.-M.L.)
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Chen C, Hu X, Ahmad MJ, Niu K, Ye T, Liang A, Yang L. Novel Insight into the Role of Squalene Epoxidase ( SQLE) Gene in Determining Milk Production Traits in Buffalo. Int J Mol Sci 2023; 24:ijms24032436. [PMID: 36768756 PMCID: PMC9916492 DOI: 10.3390/ijms24032436] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/19/2022] [Revised: 01/13/2023] [Accepted: 01/17/2023] [Indexed: 01/28/2023] Open
Abstract
Understanding the genetic mechanisms underlying milk production traits contribute to improving the production potential of dairy animals. Squalene epoxidase (SQLE) is one of the rate-limiting enzymes for cholesterol biosynthesis and was highly expressed in the buffalo mammary. The objectives of the present study were to detect the polymorphisms within SQLE in buffalo, the genetic effects of these mutations on milk production traits, and to understand the gene regulatory effects on buffalo mammary epithelial cells (BuMECs). A total of five SNPs were identified by sequencing, g.18858G > A loci were significantly associated with fat yield, and g.22834C > T loci were significantly associated with peak milk yield, milk yield, fat yield, and protein yield. Notably, linkage disequilibrium analysis indicated that 2 SNPs (g.18858G > A and g.22834C > T) formed one haplotype block, which was found to be significantly associated with milk fat yield, fat percentage, and protein yield. Furthermore, expression of SQLE was measured in different tissues of buffalo and was found to be higher in the mammary. Knockdown of SQLE gene expression significantly affected the growth of BuMECs, including proliferation, cell cycle, and apoptosis, and significantly downregulated the expression of related genes MYC, PCNA, and P21. In addition, knockdown of the SQLE gene significantly reduces triglyceride concentrations and the signal intensity of oil red O staining. In addition, silencing of SQLE was also found to regulate the synthesis and secretion of β-casein and κ-casein negatively. Furthermore, SQLE knockdown is accompanied by the downregulation of critical genes (RPS6KB1, JAK2, eIF4E, and SREBP1) related to milk fat and protein synthesis. The current study showed the potential of the SQLE gene as a candidate for buffalo milk production traits. It provides a new understanding of the physiological mechanisms underlying buffalo milk production regulation.
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Affiliation(s)
- Chao Chen
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Xiangwei Hu
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Muhammad Jamil Ahmad
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Kaifeng Niu
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Tingzhu Ye
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
| | - Aixin Liang
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Province’s Engineering Research Center in Buffalo Breeding and Products, Wuhan 430070, China
| | - Liguo Yang
- National Center for International Research on Animal Genetics, Breeding and Reproduction (NCIRAGBR), College of Animal Science and Technology, Huazhong Agricultural University, Wuhan 430070, China
- Hubei Province’s Engineering Research Center in Buffalo Breeding and Products, Wuhan 430070, China
- Correspondence:
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Fathoni A, Boonkum W, Chankitisakul V, Duangjinda M. An Appropriate Genetic Approach for Improving Reproductive Traits in Crossbred Thai-Holstein Cattle under Heat Stress Conditions. Vet Sci 2022; 9:vetsci9040163. [PMID: 35448661 PMCID: PMC9031002 DOI: 10.3390/vetsci9040163] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/01/2022] [Revised: 03/19/2022] [Accepted: 03/26/2022] [Indexed: 01/16/2023] Open
Abstract
Thailand is a tropical country affected by global climate change and has high temperatures and humidity that cause heat stress in livestock. A temperature−humidity index (THI) is required to assess and evaluate heat stress levels in livestock. One of the livestock types in Thailand experiencing heat stress due to extreme climate change is crossbred dairy cattle. Genetic evaluations of heat tolerance in dairy cattle have been carried out for reproductive traits. Heritability values for reproductive traits are generally low (<0.10) because environmental factors heavily influence them. Consequently, genetic improvement for these traits would be slow compared to production traits. Positive and negative genetic correlations were found between reproductive traits and reproductive traits and yield traits. Several selection methods for reproductive traits have been introduced, i.e., the traditional method, marker-assisted selection (MAS), and genomic selection (GS). GS is the most promising technique and provides accurate results with a high genetic gain. Single-step genomic BLUP (ssGBLUP) has higher accuracy than the multi-step equivalent for fertility traits or low-heritability traits.
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Affiliation(s)
- Akhmad Fathoni
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (A.F.); (W.B.); (V.C.)
- Department of Animal Breeding and Reproduction, Faculty of Animal Science, Universitas Gadjah Mada, Yogyakarta 55281, Indonesia
| | - Wuttigrai Boonkum
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (A.F.); (W.B.); (V.C.)
- Network Center for Animal Breeding and OMICS Research, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Vibuntita Chankitisakul
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (A.F.); (W.B.); (V.C.)
- Network Center for Animal Breeding and OMICS Research, Khon Kaen University, Khon Kaen 40002, Thailand
| | - Monchai Duangjinda
- Department of Animal Science, Faculty of Agriculture, Khon Kaen University, Khon Kaen 40002, Thailand; (A.F.); (W.B.); (V.C.)
- Network Center for Animal Breeding and OMICS Research, Khon Kaen University, Khon Kaen 40002, Thailand
- Correspondence: ; Tel.: +66-81-872-4207
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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: 37] [Impact Index Per Article: 12.3] [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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Shao B, Sun H, Ahmad MJ, Ghanem N, Abdel-Shafy H, Du C, Deng T, Mansoor S, Zhou Y, Yang Y, Zhang S, Yang L, Hua G. Genetic Features of Reproductive Traits in Bovine and Buffalo: Lessons From Bovine to Buffalo. Front Genet 2021; 12:617128. [PMID: 33833774 PMCID: PMC8021858 DOI: 10.3389/fgene.2021.617128] [Citation(s) in RCA: 12] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/14/2020] [Accepted: 02/25/2021] [Indexed: 11/13/2022] Open
Abstract
Bovine and buffalo are important livestock species that have contributed to human lives for more than 1000 years. Improving fertility is very important to reduce the cost of production. In the current review, we classified reproductive traits into three categories: ovulation, breeding, and calving related traits. We systematically summarized the heritability estimates, molecular markers, and genomic selection (GS) for reproductive traits of bovine and buffalo. This review aimed to compile the heritability and genome-wide association studies (GWASs) related to reproductive traits in both bovine and buffalos and tried to highlight the possible disciplines which should benefit buffalo breeding. The estimates of heritability of reproductive traits ranged were from 0 to 0.57 and there were wide differences between the populations. For some specific traits, such as age of puberty (AOP) and calving difficulty (CD), the majority beef population presents relatively higher heritability than dairy cattle. Compared to bovine, genetic studies for buffalo reproductive traits are limited for age at first calving and calving interval traits. Several quantitative trait loci (QTLs), candidate genes, and SNPs associated with bovine reproductive traits were screened and identified by candidate gene methods and/or GWASs. The IGF1 and LEP pathways in addition to non-coding RNAs are highlighted due to their crucial relevance with reproductive traits. The distribution of QTLs related to various traits showed a great differences. Few GWAS have been performed so far on buffalo age at first calving, calving interval, and days open traits. In addition, we summarized the GS studies on bovine and buffalo reproductive traits and compared the accuracy between different reports. Taken together, GWAS and candidate gene approaches can help to understand the molecular genetic mechanisms of complex traits. Recently, GS has been used extensively and can be performed on multiple traits to improve the accuracy of prediction even for traits with low heritability, and can be combined with multi-omics for further analysis.
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Affiliation(s)
- Baoshun Shao
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Hui Sun
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Muhammad Jamil Ahmad
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Nasser Ghanem
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Hamdy Abdel-Shafy
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Chao Du
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
| | - Tingxian Deng
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning, China
| | - Shahid Mansoor
- National Institute for Biotechnology and Genetic Engineering (NIBGE), Faisalabad, Pakistan
| | - Yang Zhou
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- International Joint Research Centre for Animal Genetics, Breeding and Reproduction, Wuhan, China
- Hubei Province’s Engineering Research Center in Buffalo Breeding and Products, Wuhan, China
| | - Yifen Yang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Shujun Zhang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- International Joint Research Centre for Animal Genetics, Breeding and Reproduction, Wuhan, China
- Hubei Province’s Engineering Research Center in Buffalo Breeding and Products, Wuhan, China
| | - Liguo Yang
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- International Joint Research Centre for Animal Genetics, Breeding and Reproduction, Wuhan, China
- Hubei Province’s Engineering Research Center in Buffalo Breeding and Products, Wuhan, China
| | - Guohua Hua
- Key Lab of Agricultural Animal Genetics, Breeding and Reproduction of Ministry of Education, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, China
- International Joint Research Centre for Animal Genetics, Breeding and Reproduction, Wuhan, China
- Hubei Province’s Engineering Research Center in Buffalo Breeding and Products, Wuhan, China
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Paiva JT, Peixoto MGCD, Bruneli FAT, Alvarenga AB, Oliveira HR, Silva AA, Silva DA, Veroneze R, Silva FF, Lopes PS. Genetic parameters, genome-wide association and gene networks for milk and reproductive traits in Guzerá cattle. Livest Sci 2020. [DOI: 10.1016/j.livsci.2020.104273] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/08/2023]
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Petrini J, Souza Iung LH, Petersen Rodriguez MA, Salvian M, Alberto Rovadoscki G, Colonia SRR, Cassoli LD, Lehmann Coutinho L, Fernando Machado P, Wiggans G, Mourão GB. Assessing the accuracy of prediction for milk fatty acids by using a small reference population of tropical Holstein cows. J Anim Breed Genet 2019; 136:453-463. [DOI: 10.1111/jbg.12434] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/18/2019] [Revised: 08/01/2019] [Accepted: 08/05/2019] [Indexed: 11/28/2022]
Affiliation(s)
- Juliana Petrini
- Department of Animal Science University of São Paulo Piracicaba Brazil
- Department of Statistics, Institute of Exact Sciences Federal University of Alfenas Alfenas Brazil
| | | | | | - Mayara Salvian
- Department of Animal Science University of São Paulo Piracicaba Brazil
| | | | | | | | | | | | - George Wiggans
- Animal Genomics and Improvement Laboratory, Agricultural Research Service USDA Beltsville Maryland
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