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Panigrahi M, Kumar H, Saravanan KA, Rajawat D, Sonejita Nayak S, Ghildiyal K, Kaisa K, Parida S, Bhushan B, Dutt T. Trajectory of livestock genomics in South Asia: A comprehensive review. Gene 2022; 843:146808. [PMID: 35973570 DOI: 10.1016/j.gene.2022.146808] [Citation(s) in RCA: 17] [Impact Index Per Article: 8.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/03/2022] [Revised: 08/08/2022] [Accepted: 08/10/2022] [Indexed: 02/07/2023]
Abstract
Livestock plays a central role in sustaining human livelihood in South Asia. There are numerous and distinct livestock species in South Asian countries. Several of them have experienced genetic development in recent years due to the application of genomic technologies and effective breeding programs. This review discusses genomic studies on cattle, buffalo, sheep, goat, pig, horse, camel, yak, mithun, and poultry. The frontiers covered in this review are genetic diversity, admixture studies, selection signature research, QTL discovery, genome-wide association studies (GWAS), and genomic selection. The review concludes with recommendations for South Asian livestock systems to increasingly leverage genomic technologies, based on the lessons learned from the numerous case studies. This paper aims to present a comprehensive analysis of the dichotomy in the South Asian livestock sector and argues that a realistic approach to genomics in livestock can ensure long-term genetic advancements.
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Affiliation(s)
- Manjit Panigrahi
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India.
| | - Harshit Kumar
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - K A Saravanan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Divya Rajawat
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Sonali Sonejita Nayak
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Kanika Ghildiyal
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Kaiho Kaisa
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Subhashree Parida
- Division of Pharmacology & Toxicology, ICAR-Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
| | - Triveni Dutt
- Livestock Production and Management Section, Indian Veterinary Research Institute, Izatnagar, Bareilly 243122, UP, India
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Bello SF, Adeola AC, Nie Q. The study of candidate genes in the improvement of egg production in ducks – a review. Poult Sci 2022; 101:101850. [PMID: 35544958 PMCID: PMC9108513 DOI: 10.1016/j.psj.2022.101850] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/30/2021] [Revised: 03/05/2022] [Accepted: 03/08/2022] [Indexed: 11/01/2022] Open
Abstract
Duck is the second-largest poultry species aside from chicken. The rate of egg production is a major determinant of the economic income of poultry farmers. Among the reproductive organs, the ovary is a major part of the female reproductive system which is highly important for egg production. Based on the importance of this organ, several studies have been carried out to identify candidate genes at the transcriptome level, and also the expression level of these genes at different tissues or egg-laying conditions, and single nucleotide polymorphism (SNPs) of genes associated with egg production in duck. In this review, expression profile and association study analyses at SNPs level of different candidate genes with egg production traits of duck were highlighted. Furthermore, different studies on transcriptome analysis, Quantitative Trait Loci (QTL) mapping, and Genome Wide Association Study (GWAS) approach used to identify potential candidate genes for egg production in ducks were reported. This review would widen our knowledge on molecular markers that are associated or have a positive correlation to improving egg production in ducks, for the increasing world populace.
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Yang Y, Yang Y, Fan Q, Huang Z, Li J, Wu Q, Tang X, Ding J, Han N, Xu B. Molecular and Biochemical Characterization of Salt-Tolerant Trehalose-6-Phosphate Hydrolases Identified by Screening and Sequencing Salt-Tolerant Clones From the Metagenomic Library of the Gastrointestinal Tract. Front Microbiol 2020; 11:1466. [PMID: 32733411 PMCID: PMC7358406 DOI: 10.3389/fmicb.2020.01466] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/18/2019] [Accepted: 06/04/2020] [Indexed: 11/13/2022] Open
Abstract
The exploration and utilization of microbial salt-tolerant enzymatic and genetic resources are of great significance in the field of biotechnology and for the research of the adaptation of microorganisms to extreme environments. The presence of new salt-tolerant genes and enzymes in the microbial metagenomic library of the gastrointestinal tract has been confirmed through metagenomic technology. This paper aimed to identify and characterize enzymes that confer salt tolerance in the gastrointestinal tract microbe. By screening the fecal metagenomic library, 48 salt-tolerant clones were detected, of which 10 salt-tolerant clones exhibited stronger tolerance to 7% (wt/vol) NaCl and stability in different concentrations of NaCl [5%-9% (wt/vol)]. High-throughput sequencing and biological information analysis showed that 91 potential genes encoded proteins and enzymes that were widely involved in salt tolerance. Furthermore, two trehalose-6-phosphate hydrolase genes, namely, tre_P2 and tre_P3, were successfully cloned and expressed in Escherichia coli BL21 (DE3). By virtue of the substrate of p-nitrophenyl-α-D-glucopyranoside (pNPG) which can be specifically hydrolyzed by trehalose-6-phosphate hydrolase to produce glucose and p-nitrophenol, the two enzymes can act optimally at pH 7.5 and 30°C. Steady-state kinetics with pNPG showed that the K M and K cat values were 15.63 mM and 10.04 s-1 for rTRE_P2 and 12.51 mM and 10.71 s-1 for rTRE_P3, respectively. Characterization of enzymatic properties demonstrated that rTRE_P2 and rTRE_P3 were salt-tolerant. The enzymatic activity increased with increasing NaCl concentration, and the maximum activities of rTRE_P2 and rTRE_P3 were obtained at 4 and 3 M NaCl, respectively. The activities of rTRE_P2 increased by approximately 43-fold even after 24 h of incubation with 5 M NaCl. This study is the first to report the identification as well as molecular and biochemical characterization of salt-tolerant trehalose-6-phosphate hydrolase from the metagenomic library of the gastrointestinal tract. Results indicate the existence of numerous salt-tolerant genes and enzymes in gastrointestinal microbes and provide new insights into the salt-tolerant mechanisms in the gastrointestinal environment.
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Affiliation(s)
- Yanxia Yang
- School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Yunjuan Yang
- School of Life Sciences, Yunnan Normal University, Kunming, China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
| | - Qin Fan
- School of Life Sciences, Yunnan Normal University, Kunming, China
| | - Zunxi Huang
- School of Life Sciences, Yunnan Normal University, Kunming, China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
| | - Junjun Li
- School of Life Sciences, Yunnan Normal University, Kunming, China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
| | - Qian Wu
- School of Life Sciences, Yunnan Normal University, Kunming, China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
| | - Xianghua Tang
- School of Life Sciences, Yunnan Normal University, Kunming, China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
| | - Junmei Ding
- School of Life Sciences, Yunnan Normal University, Kunming, China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
| | - Nanyu Han
- School of Life Sciences, Yunnan Normal University, Kunming, China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
| | - Bo Xu
- School of Life Sciences, Yunnan Normal University, Kunming, China.,Engineering Research Center of Sustainable Development and Utilization of Biomass Energy, Ministry of Education, Kunming, China.,Key Laboratory of Yunnan for Biomass Energy and Biotechnology of Environment, Kunming, China
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Mukherjee S, Cai Z, Mukherjee A, Longkumer I, Mech M, Vupru K, Khate K, Rajkhowa C, Mitra A, Guldbrandtsen B, Lund MS, Sahana G. Whole genome sequence and de novo assembly revealed genomic architecture of Indian Mithun (Bos frontalis). BMC Genomics 2019; 20:617. [PMID: 31357931 PMCID: PMC6664528 DOI: 10.1186/s12864-019-5980-y] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2018] [Accepted: 07/16/2019] [Indexed: 12/20/2022] Open
Abstract
BACKGROUND Mithun (Bos frontalis), also called gayal, is an endangered bovine species, under the tribe bovini with 2n = 58 XX chromosome complements and reared under the tropical rain forests region of India, China, Myanmar, Bhutan and Bangladesh. However, the origin of this species is still disputed and information on its genomic architecture is scanty so far. We trust that availability of its whole genome sequence data and assembly will greatly solve this problem and help to generate many information including phylogenetic status of mithun. Recently, the first genome assembly of gayal, mithun of Chinese origin, was published. However, an improved reference genome assembly would still benefit in understanding genetic variation in mithun populations reared under diverse geographical locations and for building a superior consensus assembly. We, therefore, performed deep sequencing of the genome of an adult female mithun from India, assembled and annotated its genome and performed extensive bioinformatic analyses to produce a superior de novo genome assembly of mithun. RESULTS We generated ≈300 Gigabyte (Gb) raw reads from whole-genome deep sequencing platforms and assembled the sequence data using a hybrid assembly strategy to create a high quality de novo assembly of mithun with 96% recovered as per BUSCO analysis. The final genome assembly has a total length of 3.0 Gb, contains 5,015 scaffolds with an N50 value of 1 Mb. Repeat sequences constitute around 43.66% of the assembly. The genomic alignments between mithun to cattle showed that their genomes, as expected, are highly conserved. Gene annotation identified 28,044 protein-coding genes presented in mithun genome. The gene orthologous groups of mithun showed a high degree of similarity in comparison with other species, while fewer mithun specific coding sequences were found compared to those in cattle. CONCLUSION Here we presented the first de novo draft genome assembly of Indian mithun having better coverage, less fragmented, better annotated, and constitutes a reasonably complete assembly compared to the previously published gayal genome. This comprehensive assembly unravelled the genomic architecture of mithun to a great extent and will provide a reference genome assembly to research community to elucidate the evolutionary history of mithun across its distinct geographical locations.
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Affiliation(s)
- Sabyasachi Mukherjee
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland 797106 India
| | - Zexi Cai
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Anupama Mukherjee
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland 797106 India
- Present address: Dairy Cattle Breeding Division, ICAR-National Dairy Research Institute, Karnal, Haryana 132001 India
| | - Imsusosang Longkumer
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland 797106 India
| | - Moonmoon Mech
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland 797106 India
| | - Kezhavituo Vupru
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland 797106 India
| | - Kobu Khate
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland 797106 India
| | - Chandan Rajkhowa
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland 797106 India
| | - Abhijit Mitra
- Animal Genetics and Breeding Lab., ICAR-National Research Centre on Mithun, Medziphema, Nagaland 797106 India
| | - Bernt Guldbrandtsen
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Mogens Sandø Lund
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
| | - Goutam Sahana
- Center for Quantitative Genetics and Genomics, Department of Molecular Biology and Genetics, Aarhus University, 8830 Tjele, Denmark
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5
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Whole-genome sequencing of the endangered bovine species Gayal (Bos frontalis) provides new insights into its genetic features. Sci Rep 2016; 6:19787. [PMID: 26806430 PMCID: PMC4726396 DOI: 10.1038/srep19787] [Citation(s) in RCA: 24] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/06/2015] [Accepted: 12/18/2015] [Indexed: 12/21/2022] Open
Abstract
Gayal (Bos frontalis) is a semi-wild and endangered bovine species that differs from domestic cattle (Bos taurus and Bos indicus), and its genetic background remains unclear. Here, we performed whole-genome sequencing of one Gayal for the first time, with one Red Angus cattle and one Japanese Black cattle as controls. In total, 97.8 Gb of sequencing reads were generated with an average 11.78-fold depth and >98.44% coverage of the reference sequence (UMD3.1). Numerous different variations were identified, 62.24% of the total single nucleotide polymorphisms (SNPs) detected in Gayal were novel, and 16,901 breed-specific nonsynonymous SNPs (BS-nsSNPs) that might be associated with traits of interest in Gayal were further investigated. Moreover, the demographic history of bovine species was first analyzed, and two population expansions and two population bottlenecks were identified. The obvious differences among their population sizes supported that Gayal was not B. taurus. The phylogenic analysis suggested that Gayal was a hybrid descendant from crossing of male wild gaur and female domestic cattle. These discoveries will provide valuable genomic information regarding potential genomic markers that could predict traits of interest for breeding programs of these cattle breeds and may assist relevant departments with future conservation and utilization of Gayal.
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Lalsangpuii, Ali MA, Devi LI, Behera P, Ralte L. Effect of age and season on the thyroid hormone activity of Mizoram strain female mithun (Bos frontalis). Vet World 2015; 8:1375-8. [PMID: 27047046 PMCID: PMC4774812 DOI: 10.14202/vetworld.2015.1375-1378] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2015] [Revised: 10/15/2015] [Accepted: 10/25/2015] [Indexed: 11/16/2022] Open
Abstract
AIM The aim of the present study was to generate baseline data on the normal values of the thyroidhormone (TH) activity as well as their correlation with age and season. MATERIALS AND METHODS Blood samples (10 ml) were collected from jugular vein of 30 female mithun's of three different age groups viz. Calves (6 months to 1 year), heifer (1-3 years) and adult (above 3 years) during the three season's viz. Monsoon, winter and spring of a year. The serum was analyzed for thyroid stimulating hormone (TSH), triiodothyronine (T3), and thyroxine (T4) activity. RESULT The result showed a significantly (p<0.05) a higher T3 level in heifers followed by adults and calves and higher T4 level in adults followed by heifers and calves in all the seasons. The TSH level was higher in heifers in all the seasons. The winter season recorded higher level of T3, T4, and TSH as compared to the other seasons of a year. CONCLUSION The TSH and T3 level were the highest for aheifer, whereas T4 level was the highest for adults inall the season. Furthermore, the higher level of TH was observed in winter season. The increased level of the TH during the winter season signifies their calorigenic effect. Similarly in heifers, the increased T3 concentrations show its importance in reproductive physiology and its association with ovarian activity. This indicates that age and season have aprofound effect on TH activity of Mizoram strain female mithun.
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Affiliation(s)
- Lalsangpuii
- Department of Veterinary Physiology and Biochemistry, College of Veterinary Sciences and A.H., Central Agricultural University, Selesih, Aizawl, Mizoram, India
| | - M Ayub Ali
- Department of Veterinary Physiology and Biochemistry, College of Veterinary Sciences and A.H., Central Agricultural University, Selesih, Aizawl, Mizoram, India
| | - L Inaotombi Devi
- Department of Medical Laboratory Technology, Regional Institute of Paramedical and Nursing Sciences, Mizoram, India
| | - Parthasarathi Behera
- Department of Veterinary Physiology and Biochemistry, College of Veterinary Sciences and A.H., Central Agricultural University, Selesih, Aizawl, Mizoram, India
| | - Lalsanglura Ralte
- Department of Medical Laboratory Technology, Regional Institute of Paramedical and Nursing Sciences, Mizoram, India
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Kasuya E. Secretory pattern and regulatory mechanism of growth hormone in cattle. Anim Sci J 2015; 87:178-82. [PMID: 26260675 PMCID: PMC5042056 DOI: 10.1111/asj.12418] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/11/2015] [Revised: 03/02/2015] [Accepted: 03/03/2015] [Indexed: 11/30/2022]
Abstract
The ultradian rhythm of growth hormone (GH) secretion has been known in several animal species for years and has recently been observed in cattle. Although the physiological significance of the rhythm is not yet fully understood, it appears essential for normal growth. In this review, previous studies concerning the GH secretory pattern in cattle, including its ultradian rhythm, are introduced and the regulatory mechanism is discussed on the basis of recent findings.
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Affiliation(s)
- Etsuko Kasuya
- Animal Physiology Research Unit, Division of Animal Sciences, National Institute of Agrobiological Sciences, Tsukuba, Japan
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8
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Sun Y, Zhang X, Xi D, Li G, Wang L, Zheng H, Du M, Gu Z, Yang Y, Yang Y. Isolation and cDNA characteristics of MHC-DRA genes from gayal ( Bos frontalis) and gaytle ( Bos frontalis × Bos taurus). BIOTECHNOL BIOTEC EQ 2015; 29:33-39. [PMID: 26019617 PMCID: PMC4434052 DOI: 10.1080/13102818.2014.986128] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/10/2014] [Accepted: 10/13/2014] [Indexed: 11/12/2022] Open
Abstract
The mammalian major histocompatibility complex (MHC) plays important roles in pathogen recognition and disease resistance. In the present study, the coding sequence and the 5′- and 3′-untranslated regions of MHC class II DR alpha chain (the DRA gene) from rare gayal and gaytle were cloned and analyzed to dissect structural and functional variations. The nucleotide and amino acid sequences for the DRA genes in gayal (Bofr-DRA) and gaytle (Bofr × BoLA-DRA) were almost identical to those for cattle and yak (99%). Compared to yak, two amino acids substitutions in the signal peptide (SP) domain for gayal were found within all Bos animals. Except for only one replacement in the amino acid within the α2 domain of the DRA protein in gayal, the additional residues were highly conserved across the species investigated. The 20 peptide-binding sites (PBS) of Bofr-DRA and Bofr × BoLA-DRA were essentially reserved in the α1 domain among all species investigated. The lesser degree of substitution in Bofr-DRA is concordant with the concept that the DRA gene is highly conserved among all mammals. The very high degree of conservativity of the DRA gene among ruminants, including gayal, suggests its recent evolutionary separation.
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Affiliation(s)
- Yongke Sun
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Xiaomin Zhang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Dongmei Xi
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Guozhi Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Liping Wang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Huanli Zheng
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Min Du
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Zhaobing Gu
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Yulin Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
| | - Yuai Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming , Yunnan , P.R. China
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9
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Sun Y, Xi D, Li G, Hao T, Chen Y, Yang Y. Genetic characterization of MHC class II DQB exon 2 variants in gayal ( Bos frontalis). BIOTECHNOL BIOTEC EQ 2014; 28:827-833. [PMID: 26019566 PMCID: PMC4434113 DOI: 10.1080/13102818.2014.960787] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/27/2013] [Accepted: 03/07/2014] [Indexed: 11/20/2022] Open
Abstract
In the present study, exon 2 of major histocompatibility complex (MHC) class II DQB gene from 39 gayals (Bos frontalis) was isolated, characterized and compared with previously reported patterns for other bovidae. It was revealed by sequence analyses that there are 36 DQB exon 2 variants among 39 gayals. These variants exhibited a high degree of nucleotide and amino acid substitutions with most amino acid variations occurring at positions forming the peptide-binding sites (PBS). The DQB loci were analysed for patterns of synonymous (dS) and non-synonymous (dN) substitution. The gayals were observed to be under strong balancing selection in the DQB exon 2 PBS (dN = 0.094, P = 0.001). It appears that this variability among gayals could confer the ability to mount immune responses to a wide variety of peptides or pathogens.
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Affiliation(s)
- Yongke Sun
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming 650201 , People's Republic of China
| | - Dongmei Xi
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming 650201 , People's Republic of China
| | - Guozhi Li
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming 650201 , People's Republic of China
| | - Tiantian Hao
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming 650201 , People's Republic of China
| | - Yuhan Chen
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming 650201 , People's Republic of China
| | - Yuai Yang
- Faculty of Animal Science and Technology, Yunnan Agricultural University , Kunming 650201 , People's Republic of China
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10
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Xi D, Liu Q, Huo Y, Sun Y, Leng J, Gou X, Mao H, Deng W. Nucleotide diversity of the melanocortin 1 receptor gene (MC1R) in the gayal (Bos frontalis). Mol Biol Rep 2012; 39:7293-301. [PMID: 22307797 DOI: 10.1007/s11033-012-1559-2] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/18/2011] [Accepted: 01/24/2012] [Indexed: 02/02/2023]
Abstract
The melanocortin 1 receptor gene (MC1R) plays a crucial role in determining coat colour of mammals. To investigate the relationship of polymorphism of the MC1R with coat colour in gayal, the coding sequence (CDS), and the 5'- and 3'-untranslated regions (UTR) of the MC1R were sequenced from 63 samples from the gayal and compared with the sequences of the MC1R from other ruminant species. A sequence of 1,136 bp including the whole CDS (954 bp) and parts of the 5'- and 3'-UTR (164 and 18 bp, respectively) of the gayal MC1R was obtained. A total of nine single nucleotide polymorphisms (SNPs) including four SNPs (c.-129T>C, c.-127A>C, c.-106C>T, c.-1G>A) in the 5'-UTR and five SNPs (c.201C>T, c.583C>T, c.663T>C, c.871A>G and c.876T>C) in the CDS were detected, revealing high genetic diversity. Three novel coding SNPs including c.201C>T, c.583C>T and c.876T>C, which have not been reported previously in bovid species, were retrieved. Within five coding SNPs, c.201C>T, c.663T>C and c.876T>C were silent mutations, while c.583C>T and c.871A>G were mis-sense mutations, resulting in changes in the amino acids located in the fifth (p.L195F) and seventh (p.T291A) transmembrane regions, respectively. The alignment of amino acid sequences was found to be very similar to those for other bovid species. It was demonstrated, using the functional effect prediction, that the p.T291A amino acid replacement could have an effect on MC1R protein function but not for the p.L195F substitution. Using phylogenetic analyses it was revealed that the gayal has a close genetic relationship with the yak. However, three classical bovine MC1R loci the E (D), E (+) and e were not retrieved in the gayal, indicating other genes or factors could affect coat colour in this species.
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Affiliation(s)
- Dongmei Xi
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
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11
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Xi D, Wu M, Fan Y, Liu Q, Leng J, Gou X, Mao H, Deng W. Polymorphisms of the insulin-like growth factor-binding protein 3 gene (IGFBP3) in gayal (Bos frontalis). Gene 2012; 497:98-102. [PMID: 22310386 DOI: 10.1016/j.gene.2012.01.051] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2011] [Revised: 12/15/2011] [Accepted: 01/21/2012] [Indexed: 10/14/2022]
Abstract
The gene coding for insulin-like growth factor-binding protein 3 (IGFBP3) is important for regulation of growth, development and metabolism in mammals. The present investigation was conducted to study nucleotide polymorphism of the IGFBP3 in gayal (Bos frontalis) and to compare the variations with those which occur in other ruminants. A fragment of 645 base pairs of the IGFBP3 covering a part of exon 2, the complete intron 2 and exon 3 and a part of intron 3 was amplified, sequenced (n=46) and digested (n=79) with HaeIII restriction enzyme from 125 collected gayal samples. Nine single nucleotide polymorphisms (SNPs) [C14T, A122C, C137T, G144C, C155T, G213A, C279A, G334A and G460A] were identified and located in intron 2, revealing high genetic variability. The alignment of nucleotide sequences was found to be very similar to those for other bovid species. Sequencing and HaeIII digestion showed that frequency of alleles C and A [consisting of fragments of sizes 56, 64, 228, 264, 282, 298 and 497 bp (CC genotype)] was 0.96 and 0.04 for the SNP C279A. Moreover, the genotype frequency of the SNP C279A in gayal was compared with that in other ruminants and it appears that this polymorphism may be associated with low fat content and rapid growth in this rare species.
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Affiliation(s)
- Dongmei Xi
- Faculty of Animal Science and Technology, Yunnan Agricultural University, Kunming 650201, China
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Genetic variability of the coding region for the prion protein gene (PRNP) in gayal (Bos frontalis). Mol Biol Rep 2011; 39:2011-20. [PMID: 21633886 DOI: 10.1007/s11033-011-0948-2] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/14/2011] [Accepted: 05/26/2011] [Indexed: 10/18/2022]
Abstract
The gayal (Bos frontalis) is a rare semi-wild bovid species in which bovine spongiform encephalopathy (BSE) has not been reported. Polymorphisms of the prion protein gene (PRNP) have been correlated significantly with resistance to BSE. In this study, the coding region of PRNP was cloned and characterized in samples from 125 gayal. A total of ten single nucleotide polymorphisms (SNPs), including six silent mutations (C60T, G75A, A108T, G126A, C357T and C678T) and four mis-sense mutations (C8A, G145A, G461A and C756G), corresponding to amino acids T3K, G49S9, N154S and I252M were identified, revealing high genetic diversity. Three novel SNPs including C60T, G145A and C756G, which have not been reported previously in bovid species, were retrieved. There also was one insertion-deletion (187Del24) at the N-terminal octapeptide repeat region. Alignment of nucleotide and amino acid sequences showed a high degree of similarity with other bovid species. Using phylogenetic analyses it was revealed that gayal has a close genetic relationship with Zebu cattle. In short, preliminary information is provided about genotypes of the PRNP in gayal. This could assist with the study of the pathogenesis of transmissible spongiform encephalopathies and cross species transmission as well as a molecular breeding project for gayal in China.
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Leng J, Xie L, Zhu R, Yang S, Gou X, Li S, Mao H. Dominant bacterial communities in the rumen of Gayals (Bos frontalis), Yaks (Bos grunniens) and Yunnan Yellow Cattle (Bos taurs) revealed by denaturing gradient gel electrophoresis. Mol Biol Rep 2010; 38:4863-72. [DOI: 10.1007/s11033-010-0627-8] [Citation(s) in RCA: 23] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/15/2010] [Accepted: 11/29/2010] [Indexed: 11/28/2022]
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Yang S, Ma S, Chen J, Mao H, He Y, Xi D, Yang L, He T, Deng W. Bacterial diversity in the rumen of Gayals (Bos frontalis), Swamp buffaloes (Bubalus bubalis) and Holstein cow as revealed by cloned 16S rRNA gene sequences. Mol Biol Rep 2009; 37:2063-73. [DOI: 10.1007/s11033-009-9664-6] [Citation(s) in RCA: 41] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/02/2009] [Accepted: 07/24/2009] [Indexed: 11/28/2022]
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Mondal M, Rajkhowa C, Prakash BS. Diurnal Changes in Blood Metabolites and Their Relation to Plasma Growth Hormone and Time of Feeding in Mithun Heifers (Bos frontalis). Chronobiol Int 2009; 22:807-16. [PMID: 16298769 DOI: 10.1080/07420520500263359] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
Abstract
The aim of the present study was to investigate what, if any, diurnal changes occur in blood metabolites in relation to plasma growth hormone (GH) and feeding time among mithun (Bos frontalis), a semi-wild ruminant. Blood samples were collected at hourly intervals during a 24 h span from 6 mithun heifers (averaging 2.5 yr of age and averaging 230 kg in weight) that were fed twice a day at 11:00 and 16:00 h. Samples were assayed for plasma GH and blood metabolites, non-esterified fatty acids (NEFA), glucose, and alpha-amino nitrogen. The total sampling period was divided into a 1) postprandial (after meal) period (period I: 11:00 to 21:00 h) and 2) interprandial period (period II: 22:00 to 10:00 h) and also into night (20:00 to 05:00 h) and day (06:00 to 10:00 h) periods for statistical analysis. Plasma glucose and alpha-amino nitrogen levels increased (p<0.01), and plasma NEFA and GH decreased (p<0.01) after each meal. No diurnal rhythmicity was detected in plasma glucose or alpha-amino nitrogen levels. Interestingly, plasma NEFA and GH levels were higher (p<0.01) during the interprandial (period II) and night periods, indicating an energy deficit that occurred progressively during the interprandial period of nocturnal feed deprivation. In twice-daily-fed mithuns we conclude that: 1) plasma metabolites and GH exhibited a definite pattern of change with time of feeding; 2) concentrations of plasma NEFA were higher nocturnally due to an energy deficit and that GH levels were higher during the interprandial period after the second meal; 3) the interprandial period after the second feeding may be considered to constitute a short-term food deprivation; 4) the longer interprandial period of 19 h in this study between the second and subsequent morning meal may be changed into equally divided feedings to minimize the short-term energy deficit; and 5) blood sampling for blood metabolites in mithuns should be conducted at a fixed time of day with special emphasis on time of feeding.
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Affiliation(s)
- Mohan Mondal
- Animal Endocrinology Laboratory, National Research Centre on Mithun (ICAR), Jharnapani, Medziphema, Nagaland, India.
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Prakash BS, Sarkar M, Mondal M. An Update on Reproduction in Yak and Mithun. Reprod Domest Anim 2008; 43 Suppl 2:217-23. [DOI: 10.1111/j.1439-0531.2008.01165.x] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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Mondal M, Rajkhowa C, Prakash BS. Twenty-four-hour rhythmicity of growth hormone in captive adult mithuns (Bos frontalis). BIOL RHYTHM RES 2005. [DOI: 10.1080/09291010500101884] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
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Mondal M, Rajkhowa C, Prakash B. Standardization and validation of a simple, sensitive, second antibody format enzyme immunoassay for growth hormone determination in mithun (Bos frontalis) plasma. Zoo Biol 2005. [DOI: 10.1002/zoo.20069] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/11/2022]
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