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Deng TX, Ma XY, Duan A, Lu XR, Abdel-Shafy H. Genome-wide CNV analysis reveals candidate genes associated with milk production traits in water buffalo (Bubalus bubalis). J Dairy Sci 2024:S0022-0302(24)00802-6. [PMID: 38762109 DOI: 10.3168/jds.2023-24614] [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: 12/24/2023] [Accepted: 03/28/2024] [Indexed: 05/20/2024]
Abstract
Buffaloes are vital contributors to the global dairy industry. Understanding the genetic basis of milk production traits in buffalo populations is essential for breeding programs and improving productivity. In this study, we conducted whole-genome resequencing on 387 buffalo genomes from 29 diverse Asian breeds, including 132 river buffaloes, 129 swamp buffaloes, and 126 crossbred buffaloes. We identified 36,548 copy number variant (CNVs) spanning 133.29 Mb of the buffalo genome, resulting in 2,100 copy number variant regions (CNVRs), with 1,993 shared CNVRs being found within the studied buffalo types. Analyzing CNVRs highlighted distinct genetic differentiation between river and swamp buffalo subspecies, verified by evolutionary tree and principal component analyses. Admixture analysis grouped buffaloes into river and swamp categories, with crossbred buffaloes displaying mixed ancestry. To identify candidate genes associated with milk production traits, we employed 3 approaches. First, we used Vst-based population differentiation, revealing 11 genes within CNVRs that exhibited significant divergence between different buffalo breeds, including genes linked to milk production traits. Second, expression quantitative loci (eQTL) analysis revealed differential expression of CNVR-driven genes (DECGs) associated with milk production traits. Notably, known milk production-related genes were among these DECGs, validating their relevance. Last, a genome-wide association study (GWAS) identified 3 CNVRs significantly linked to peak milk yield. Our study provides comprehensive genomic insights into buffalo populations and identifies candidate genes associated with milk production traits. These findings facilitate genetic breeding programs aimed at increasing milk yield and improving quality in this economically important livestock species.
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Affiliation(s)
- Ting-Xian Deng
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China.
| | - Xiao-Ya Ma
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - Anqin Duan
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - Xing-Rong Lu
- Guangxi Provincial Key Laboratory of Buffalo Genetics, Breeding and Reproduction Technology, Buffalo Research Institute, Chinese Academy of Agricultural Sciences, Nanning 530001, China
| | - Hamdy Abdel-Shafy
- Department of Animal Production, Faculty of Agriculture, Cairo University, 12613, Giza, Egypt
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Andrei CR, Posastiuc FP, Constantin NT, Mitrea IL. New insights into semen separation techniques in buffaloes. Front Vet Sci 2024; 10:1347482. [PMID: 38269362 PMCID: PMC10806153 DOI: 10.3389/fvets.2023.1347482] [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: 11/30/2023] [Accepted: 12/26/2023] [Indexed: 01/26/2024] Open
Abstract
Male infertility is frequently caused by idiopathic or unexplained reasons, resulting in an increase in demand for assisted reproductive technologies. In buffaloes, more than in other animals due to reproductive hardiness, successful fertilization needs spermatozoa to effectively transit the female reproductive system to reach the oocyte. This mechanism naturally picks high-quality sperm cells for conception, but when artificial reproductive technologies such as in vitro fertilization, intracytoplasmic sperm injection, or intrauterine insemination are utilized, alternative techniques of sperm selection are necessary. Currently, technology allows for sperm sorting based on motility, maturity, the lack of apoptotic components, proper morphology, and even sex. This study provides current knowledge on all known techniques of sperm cell sorting in buffaloes, evaluates their efficiency, and discusses the benefits and drawbacks of each approach.
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Affiliation(s)
- Crina Raluca Andrei
- Faculty of Veterinary Medicine of Bucharest, University of Agronomic Sciences and Veterinary Medicine, Bucharest, Romania
| | - Florin Petrișor Posastiuc
- Faculty of Veterinary Medicine of Bucharest, University of Agronomic Sciences and Veterinary Medicine, Bucharest, Romania
- Faculty of Veterinary Medicine, Ghent University, Merelbeke, Belgium
| | - Nicolae Tiberiu Constantin
- Faculty of Veterinary Medicine of Bucharest, University of Agronomic Sciences and Veterinary Medicine, Bucharest, Romania
- Research and Development Institute for Bovine Balotești, Balotești, Romania
| | - Ioan Liviu Mitrea
- Faculty of Veterinary Medicine of Bucharest, University of Agronomic Sciences and Veterinary Medicine, Bucharest, Romania
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Saravanan KA, Rajawat D, Kumar H, Nayak SS, Bhushan B, Dutt T, Panigrahi M. Signatures of selection in riverine buffalo populations revealed by genome-wide SNP data. Anim Biotechnol 2023; 34:3343-3354. [PMID: 36384399 DOI: 10.1080/10495398.2022.2145292] [Citation(s) in RCA: 10] [Impact Index Per Article: 10.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
The detection of selection signatures assists in understanding domestication, evolution, and the identification of genomic regions related to adaptation and production traits in buffaloes. The emergence of high-throughput technologies like Next Generation Sequencing and SNP genotyping had expanded our ability to detect these signatures of selection. In this study, we sought to identify signatures of selection in five buffalo populations (Brazilian Murrah, Bulgarian Murrah, Indian Murrah, Nili-Ravi, and Kundi) using Axiom Buffalo 90 K Genotyping Array data. Using seven different methodologies (Tajima's D, CLR, ROH, iHS, FST, FLK and hapFLK), we identified selection signatures in 374 genomic regions, spanning a total of 381 genes and 350 quantitative trait loci (QTLs). Among these, several candidate genes were associated with QTLs for milk production, reproduction, growth and carcass traits. The genes and QTLs reported in this study provide insight into selection signals shaping the genome of buffalo breeds. Our findings can aid in further genomic association studies, genomic prediction, and the implementation of breeding programmes in Indian buffaloes.
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Affiliation(s)
- K A Saravanan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
| | - Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly, India
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Genetic Diversity Relationship in Azakheli Buffalo Inferred from mtDNA and MC1R Sequences Comparison. BIOMED RESEARCH INTERNATIONAL 2022; 2022:5770562. [PMID: 36601617 PMCID: PMC9806686 DOI: 10.1155/2022/5770562] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/22/2022] [Revised: 11/22/2022] [Accepted: 11/29/2022] [Indexed: 12/15/2022]
Abstract
Azakheli is relatively smaller riverine breed with a very peculiar characteristics kept under unique traditional husbandry practices in comparison with rest of the Pakistani buffalo breeds; however, milk production is comparable. The present study was conducted to evaluate the genetic diversity of Azakheli breed. A total of sixty-six blood samples were collected for the amplification of mtDNA D-loop region and MC1R gene sequencing analysis. Median-joining network analysis of 191 mtDNA D-loop sequences of Azakheli and eight Indian riverine buffalo breeds clustered into three clades. Ancient Azakheli Region 1 clade was the oldest with the highest mutation steps and was present close to the root of UPGMA phylogenetic tree. There was 5 mutated lines distance between Pakistan buffalo and Indian riverine buffaloes. The populations of neighboring countries did not share any haplotypes with Azakheli buffalo of Pakistan. Possibly, residing for so long in the cold atmosphere and high elevation regions caused the mutation in mtDNA D-loop, though these conditions did not affect the overall performance of Azakheli as milch buffalo breed of Pakistan. MC1R analyses showed high mutations in Azakheli of Albino phenotype and all the black phenotype individuals of Azakheli buffalo share haplotypes with dominant Chinese and Indian black phenotypes buffaloes in MC1R median-joining network, indicating the reason of black coat color is due to MC1R gene. The haplotype diversity and nucleotide diversity was (H. 0.923, Pi: 0.00895) in Azakheli. Current results illustrated Asian ancestry for Azakheli buffalo, and mtDNA and MC1R analyses provided further evidence. Additional genetic analyses and archeological studies may provide further insight into the domestication period and history of Azakheli buffalo breed. The further studies are required on different coat colors with different genes on Azakheli buffalo to understand the phenotype variation.
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Integrative QTL mapping and selection signatures in Groningen White Headed cattle inferred from whole-genome sequences. PLoS One 2022; 17:e0276309. [PMID: 36288367 PMCID: PMC9605288 DOI: 10.1371/journal.pone.0276309] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2021] [Accepted: 10/04/2022] [Indexed: 11/04/2022] Open
Abstract
Here, we aimed to identify and characterize genomic regions that differ between Groningen White Headed (GWH) breed and other cattle, and in particular to identify candidate genes associated with coat color and/or eye-protective phenotypes. Firstly, whole genome sequences of 170 animals from eight breeds were used to evaluate the genetic structure of the GWH in relation to other cattle breeds by carrying out principal components and model-based clustering analyses. Secondly, the candidate genomic regions were identified by integrating the findings from: a) a genome-wide association study using GWH, other white headed breeds (Hereford and Simmental), and breeds with a non-white headed phenotype (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel, Dutch Belted, and Holstein Friesian); b) scans for specific signatures of selection in GWH cattle by comparison with four other Dutch traditional breeds (Dutch Friesian, Deep Red, Meuse-Rhine-Yssel and Dutch Belted) and the commercial Holstein Friesian; and c) detection of candidate genes identified via these approaches. The alignment of the filtered reads to the reference genome (ARS-UCD1.2) resulted in a mean depth of coverage of 8.7X. After variant calling, the lowest number of breed-specific variants was detected in Holstein Friesian (148,213), and the largest in Deep Red (558,909). By integrating the results, we identified five genomic regions under selection on BTA4 (70.2-71.3 Mb), BTA5 (10.0-19.7 Mb), BTA20 (10.0-19.9 and 20.0-22.7 Mb), and BTA25 (0.5-9.2 Mb). These regions contain positional and functional candidate genes associated with retinal degeneration (e.g., CWC27 and CLUAP1), ultraviolet protection (e.g., ERCC8), and pigmentation (e.g. PDE4D) which are probably associated with the GWH specific pigmentation and/or eye-protective phenotypes, e.g. Ambilateral Circumocular Pigmentation (ACOP). Our results will assist in characterizing the molecular basis of GWH phenotypes and the biological implications of its adaptation.
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Buffalo Milk as a Source of Probiotic Functional Products. Microorganisms 2021; 9:microorganisms9112303. [PMID: 34835429 PMCID: PMC8620832 DOI: 10.3390/microorganisms9112303] [Citation(s) in RCA: 6] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/23/2021] [Revised: 10/26/2021] [Accepted: 11/03/2021] [Indexed: 01/02/2023] Open
Abstract
In the past two decades, consumption of food has been accruing due to its health claims which include gastrointestinal health, improved immunity, and well-being. Currently, the dairy industry is the sector where probiotics are most widely used, especially in fermented milk, cheese, yoghurt, butter, and dairy beverages. Although, it is still necessary to face many challenges regarding their stability and functionality in food. Considering the increasing demand for healthy products, it is necessary to develop strategies that aim to increase the consumption of functional foods in order to meet probiotic usefulness criteria and the consumer market. This review aimed to promote the utilization of buffalo milk considering its probiotic effects as a functional food and natural remedy to various ailments, emphasizing the potential of innovation and the importance of milk-based products as health promoters. The intake of probiotics plays an important role in modulating the health of the host, as a result of a balanced intestinal microbiota, reducing the risk of development of various diseases such as cancer, colitis, lactose intolerance, heart diseases, and obesity, among other disorders. However, further studies should be carried out to deepen the knowledge on the relationship between raw buffalo milk, its dairy products microbiota and consumer’s health beneficial effects, as well as to implement a strategy to increase the variety and availability of its products as a functional food in the market.
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