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Alipanah M, Mazloom SM, Gharari F. Detection of selective sweep in European wild sheep breeds. 3 Biotech 2024; 14:122. [PMID: 38560387 PMCID: PMC10978567 DOI: 10.1007/s13205-024-03964-1] [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: 03/23/2023] [Accepted: 02/22/2024] [Indexed: 04/04/2024] Open
Abstract
In wild animal populations, there is a differentiation between populations due to natural selection. The direction and pressure of natural selection in the wild sheep are different in the various geographic areas. Linkage disequilibrium studies showed that regions of the genome in whole wild sheep are under natural selection and that natural selection can affect immune or reproductive or metabolic traits. The study aimed to identify genomic regions under natural selection in wild sheep. For this purpose, the genetic information of 24 European wild sheep and 24 Sardinian wild sheep was used. The genotypes were determined using Illumina 50 K SNPChip arrays based on Oar_4.0 version of the sheep genome. After quality control steps, finally, 31,560 SNP markers were analyzed. The value of LD was calculated by calculating the r2 statistic between all pairs of locations through PLINK software. To identify signs of selection based on linkage disequilibrium methods, an extended haplotype homozygosity test of XP-EHH crossing population and iHS intrapopulation was used. The results of iHS studies showed that in European and Sardinian wild sheep, the highest iHS coefficient under natural selection was observed on 3 and 2 chromosome numbers, respectively. Also, the results of XP-EHH studies showed that the largest XP-EHH coefficients under natural selection in European wild sheep compared to Sardinian and vice versa in Sardinian wild sheep compared to European wild sheep were observed on 3 and 16 chromosome numbers, respectively. In addition, the results of gene cycle studies showed that COPB1, SEC24D, ZDHHC17, BBS4, RFX3, SLC26A8, CAMK2D, GRIA1, GRM1, GRID2, PPP2R1A, CPEB4, PLEKHA5 and KIF13A, VPS39, VPS53, DTNBP1, DYNC1I1, FAM91A genes are under natural selection in Sardinian and European wild sheeps, respectively. The direction and selection pressure of natural selection in the two breeds of wild sheep is different due to different geographic conditions.
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Affiliation(s)
- Masoud Alipanah
- Department of Plant Production, University of Torbat Heydarieh, Torbat Heydarieh, 9516168595 Iran
| | - Seyed Mostafa Mazloom
- Department of Animal Science, Ferdowsi University of Mashhad, Mashhad, 9177948974 Iran
| | - Faezeh Gharari
- Department of Plant Production, University of Torbat Heydarieh, Torbat Heydarieh, 9516168595 Iran
- Department of Animal Science, Ferdowsi University of Mashhad, Mashhad, 9177948974 Iran
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Asim M, Saif-Ur Rehman M, Hassan FU, Awan FS. Genetic variants of CSN1S1, CSN2, CSN3, and BLG genes and their association with dairy production traits in Sahiwal cattle and Nili-Ravi buffaloes. Anim Biotechnol 2023; 34:2951-2962. [PMID: 36165734 DOI: 10.1080/10495398.2022.2126365] [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] [Indexed: 11/01/2022]
Abstract
Milk protein genes are associated with milk yield and composition in dairy animals. The present study aimed to identify milk protein genes (CSN1S1, CSN2, CSN3, and BLG) genetic variants and their association with milk yield in Sahiwal cattle and Nili-Ravi buffaloes. One hundred animals from each species were selected to collect blood samples and milk production records. Primers were designed for these milk protein genes for PCR amplification. Sequencing of resultant PCR products revealed a higher number of SNPs (13 vs. 7, 5 vs. 1, and 6 vs. 2) in Sahiwal as compared to Nili-Ravi animals in CSN1S1, CSN2, and CSN3 genes, respectively. However, a single SNP was observed in BLG gene of both species. Association analysis revealed that one SNP in BLG gene of Nili-Ravi was associated (p < 0.05) with 305-day milk yield. Two SNPs at CSN1S1 gene in Sahiwal were associated with dry-period. Similarly, one SNP at CSN1S1 and two SNPs at CSN3 gene showed significant association (p < 0.05) with average calving-interval in Sahiwal while two SNPs in CSN1S1 gene were associated (p < 0.05) with this trait in Nili-Ravi. These SNPs could be helpful as candidate variants for marker-assisted selection in cattle and buffaloes for improvement of lactation performance.
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Affiliation(s)
- Muhammad Asim
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad, Pakistan
| | | | - Faiz-Ul Hassan
- Institute of Animal and Dairy Sciences, University of Agriculture, Faisalabad, Pakistan
| | - Faisal Saeed Awan
- Centre of Agricultural Biochemistry and Biotechnology, University of Agriculture, Faisalabad, Pakistan
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Ardicli S, Dincel D, Samli H, Senturk N, Karalar B, Unlu S, Soyudal B, Kubad E, Balci F. Association of polymorphisms in lipid and energy metabolism-related genes with fattening performance in Simmental cattle. Anim Biotechnol 2023; 34:3428-3440. [PMID: 36459440 DOI: 10.1080/10495398.2022.2152557] [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] [Indexed: 12/04/2022]
Abstract
Lipid and energy metabolism are major constituents of mammal growth and thus fattening performance of cattle. This study was designed to evaluate the effects of polymorphisms in lipid and energy metabolism-related genes including oxidized low-density lipoprotein receptor 1 (OLR1), lactoferrin (LTF), stearoyl-CoA desaturase (SCD), beta-lactoglobulin (LGB), thyroglobulin (TG), annexin A9 (ANXA9), myogenic factor 5 (MYF5), protein kinase AMP-activated non-catalytic subunit gamma 3 (PRKAG3), and pituitary-specific transcriptional factor 1 (PIT1), on fattening performance in Simmental cattle. A total of 72 purebred Simmental bulls with a similar initial age and weight were fattened on the same farm for 10 months. Association analysis was performed using linear mixed models. The OLR1 marker was significantly associated with the final weight (FW), hot carcass weight (HCW), chilled carcass weight (CCW), dressing percentage (DP), and total weight gain (TWG). SCD affected the FW, TWG, and average daily live weight gain (ADWG). The present results clearly demonstrated the significant impact of the TG marker on fattening performance. It was highly significantly associated with the FW, HCW, CCW, and TWG. The SCD × TG and the OLR1 × TG interactions had remarkable effects on the traits analyzed. The GACC and CCCC haplotypes of the SCD × TG and OLR1 × TG, respectively, were found to be powerful markers for fattening performance in Simmentals. Novel associations in this study may be useful for further genetic evaluations to improve beef cattle breeding.
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Affiliation(s)
- Sena Ardicli
- Department of Genetics, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | - Deniz Dincel
- Department of Genetics, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | - Hale Samli
- Department of Genetics, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | - Nursen Senturk
- Department of Molecular Biology and Genetics, Faculty of Science, Istanbul University, Istanbul, Turkey
| | - Beyza Karalar
- Department of Molecular Biology and Genetics, Faculty of Arts and Science, Bursa Uludag University, Bursa, Turkey
| | - Sıla Unlu
- Department of Molecular Biology and Genetics, Faculty of Arts and Science, Yıldız Technical University, Istanbul, Turkey
| | | | - Evrim Kubad
- Department of Animal Nutrition and Nutritional Disease, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
| | - Faruk Balci
- Department of Genetics, Faculty of Veterinary Medicine, Bursa Uludag University, Bursa, Turkey
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Helal M, Ali MA, Nadrin AH, Awad YI, Younis NK, Alasyed BM, Jamal M, Eid DH, Soliman HA, Eissa SA, Ragab M. Association between IRS-1, PPAR-γ and LEP genes polymorphisms and growth traits in rabbits. Anim Biotechnol 2023; 34:2391-2399. [PMID: 35767350 DOI: 10.1080/10495398.2022.2092743] [Citation(s) in RCA: 3] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
Single nucleotide polymorphisms are commonly associated with changes in quantitative traits, and have been considered useful markers for improving different traits in livestock. The current study aimed to explore the effect of three SNPs located in Insulin receptor substrate (IRS-1), Peroxisome proliferator-activated receptor γ (PPAR-γ), and Leptin (LEP) genes on the growth traits of rabbits. Individuals from three rabbit breeds were genotyped using RFLP-PCR. The IRS-1 variant (c.189T > G) was associated with post-weaning body weight, and body weight gains, However, the effect on growth rates was insignificant in Baladi Red and V-line rabbits. The PPAR-γ variant (c.207A > C) was significantly associated with 8-wk body weights in V-line rabbits, 10-wk body weights, and growth rates from 8 to 10 weeks of age in New Zealand rabbits. However, the differences between genotypes were insignificant for body weight gains and average daily gain. The LEP gene mutation (g.16079636C > G) had significant effects on body weights at 6 and 8 weeks of age in New Zealand White rabbits and 8 weeks of age in Baladi Red rabbits were associated with the presence of the C allele. Concludingly, the results stressed the importance of the IRS-1 gene in post-weaning growth and suggested the existence of breed-specific effects for PPAR-γ and LEP.
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Affiliation(s)
- Mostafa Helal
- Department of Animal Production, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mahmoud A Ali
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Amira H Nadrin
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Yomna I Awad
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Nada K Younis
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Basant M Alasyed
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mohnad Jamal
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Dima H Eid
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Hagar A Soliman
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Sara A Eissa
- Biotechnology Program, Faculty of Agriculture, Cairo University, Giza, Egypt
| | - Mohamed Ragab
- Department of Poultry Production, Kafr El-Sheikh University, Kafr EL-Sheikh, Egypt
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Sonali, Bhardwaj A, Unnati, Nayan V, Legha RA, Bhattacharya TK, Pal Y, Giri SK. Identification and characterization of single nucleotide polymorphisms in DMRT3 gene in Indian horse ( Equus caballus) and donkey ( Equus asinus) populations. Anim Biotechnol 2023; 34:4910-4920. [PMID: 37149793 DOI: 10.1080/10495398.2023.2206866] [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] [Indexed: 05/08/2023]
Abstract
Equines' ability in racing and riding as well as gaitedness have influenced the human civilization. Aim of this study was to identify and characterize the novel polymorphisms or SNPs in DMRT3 gene in Indian horse and donkey breeds. In this study, the DMRT3 gene was sequenced and characterized in 72 Indian horses' and 33 Indian donkeys' samples. One SNP (A > C) at 878 was found in studied horses while identical SNPs (A > C) at two different nucleotide positions i.e., 878 and 942 in DMRT3 gene (chromosome 23) were observed in studied Indian donkey breeds. Horses and donkeys both have a non-synonymous mutation (A > C) at nucleotide 878 (codon 61) that converts a Stop codon (TAG > TCG) to coding codon Serine, whereas donkeys have a synonymous mutation at nucleotide 942 (codon 82) that converts Serine (TCA > TCC) into Serine. A phylogenetic tree indicated that the DMRT3 gene was equally distributed among the equine breeds. Most of the donkey breeds have been shown high levels of genetic diversity while horse breeds and Halari donkey showed the least genetic diversity. Mutation in DMRT3 has a major impact on gaitedness in horses and is presented at a high frequency in gaited breeds and in horses breed for harness racing.
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Affiliation(s)
- Sonali
- ICAR-National Research Centre on Equines, Hisar, Haryana, India
- Department of Biotechnology (SBAS), Maharaja Agrasen University, Baddi, (Solan) HP, India
| | | | - Unnati
- ICAR-National Research Centre on Equines, Hisar, Haryana, India
| | - Varij Nayan
- ICAR-Central Institute for Research on Buffaloes, Hisar, Haryana, India
| | | | | | - Yash Pal
- ICAR-National Research Centre on Equines, Hisar, Haryana, India
| | - Shiv Kumar Giri
- Department of Biotechnology (SBAS), Maharaja Agrasen University, Baddi, (Solan) HP, India
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Cai W, Xu Y, Bai Z, Lin G, Wang L, Dou X, Han D, Wang Z, Wang J, Zhang X, Zhang Y, Qin Y, Gu M, Sun Y, Wu Y, Chen R, Wang Z. Association analysis for SNPs of BAAT and COL1A1 genes with cashmere production performance and other production traits in Liaoning cashmere goats. Anim Biotechnol 2023; 34:2324-2335. [PMID: 35749728 DOI: 10.1080/10495398.2022.2088550] [Citation(s) in RCA: 5] [Impact Index Per Article: 5.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/09/2023]
Abstract
This study aimed to investigate the relationship between the polymorphism of bile acid-CoA: amino acid N-acyltransferase (BAAT) and collagen type I alpha 1 chain (COL1A1) genes and the production performance of Liaoning Cashmere goat (LCG). The potential single nucleotide polymorphisms (SNPs) of LCG were detected by sequence comparison of BAAT and COL1A1 genes and PCR-Seq polymorphism, and the effect of SNPs on production performance was analyzed by SPSS software. The results showed that three SNPs loci were detected in BAAT gene: G7900A, T7967C, C7998T, and one SNP locus T6716C was detected in COL1AL gene. At G7900A locus, the dominant genotype for cashmere performance was GG, and the dominant genotype for body measurement traits and milk production traits was AG. At T7967C locus, the dominant genotype for cashmere performance was TT, and the dominant genotype for body measurement traits and milk production traits was CC. At C7998T locus, TT was the dominant genotype for cashmere performance, body measurement traits, and milk production traits. At the T6716C locus, TT was the dominant genotype for cashmere performance, body measurement traits, and milk production traits. H1H1: AACC is the dominant haplotype combination. Therefore, this study will provide a reliable reference for future research on cashmere production performance, body measurement traits, and milk production traits of LCG.
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Affiliation(s)
- Weidong Cai
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanan Xu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zhixian Bai
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Guangyu Lin
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Lingling Wang
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Xingtang Dou
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Di Han
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Zhanhong Wang
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Jiaming Wang
- Liaoning Province Modern Agricultural Production Base Construction Engineering Center, Shenyang, China
| | - Xinjiang Zhang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yu Zhang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yuting Qin
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Ming Gu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yinggang Sun
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Yanzhi Wu
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Rui Chen
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
| | - Zeying Wang
- College of Animal Science & Veterinary Medicine, Shenyang Agricultural University, Shenyang, China
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Hengwei Y, Raza SHA, Wang S, Khan R, Ayari-Akkari A, El Moneim Ahmed DA, Ahmad I, Shaoib M, Abd El-Aziz AH, Rahman SU, Jahejo AR, Zan L. The growth curve determination and economic trait correlation for Qinchuan bull population. Anim Biotechnol 2023; 34:2649-2656. [PMID: 35980325 DOI: 10.1080/10495398.2022.2111309] [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] [Indexed: 11/01/2022]
Abstract
Carcass weight, as a measure of meat yield, and body measurements are directly correlated traits in livestock. However, longitudinally collected phenotype records of local breeds are not comprehensive. The research was performed on Qinchuan bull population to understand their growth and development, and data from Qinchuan bull that was weighed and measured at birth, 6, 12, 18, and 24 months of age was analyzed. Furthermore, Logistic, Brody, Gompertz, and Bertallanffy were used to fit the growth curves for weight and body size traits. The results showed that the four curve models have good fitting degrees for the weight and body size (R2 > 0.99), and the Bertallanffy model exhibited a good fit to the measured data of body weight, and the model estimated the inflection point of body weight as (5.43 months of age, 122.01 kg). Particularly, the limited mature body weight can reach 557.8 kg by the Brody model. Body weight was significantly positively correlated with body height, hip height, body length, chest circumference, abdominal girth, and calf girth (p < 0.0001), and the correlation between body weight and body length was the highest (r = 0.975). The regression equation predicting body weight was Y = -275.691 + 3.28 X3 + 1.311 X4 - 0.397 X5.
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Affiliation(s)
- Yu Hengwei
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | | | - Sihu Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
| | - Rajwali Khan
- Department of Livestock Management, Breeding and Genetic, The University of Agriculture Peshawar, Peshawar, Pakistan
| | - Amel Ayari-Akkari
- Biology Department, College of Sciences, King Khaled University, Abha, Saudi Arabia
- Laboratory of Diversity, Management and Conservation of Biological Systems, Faculty of Sciences of Tunis, University of Tunis El Manar, Tunis, Tunisia
| | | | - Ijaz Ahmad
- Department of Livestock Management, Breeding and Genetic, The University of Agriculture Peshawar, Peshawar, Pakistan
| | - Muhammad Shaoib
- College of Veterinary Science, The University of Agriculture Peshawar, Peshawar, Pakistan
| | - Ayman H Abd El-Aziz
- Department of Animal and Poultry Production, Faculty of Agriculture, Damanhour University, Damanhour, Egypt
| | - Siddiq Ur Rahman
- Department of Computer science and Bioinformatics, Khushal Khan Khattak University, Karak, Pakistan
| | - Ali Raza Jahejo
- College of Veterinary Medicine, Shanxi Agricultural University, Jinzhong, China
| | - Linsen Zan
- College of Animal Science and Technology, Northwest A&F University, Yangling, China
- National Beef Cattle Improvement Center, Yangling, China
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Teferedegn EY, Can H, Erkunt Alak S, Ün C. Low frequency of protective variants at regulatory region of PRNP gene indicating the genetically high risk of BSE in Ethiopian Bos indicus and Bos taurus africanus. Anim Biotechnol 2023; 34:1931-1936. [PMID: 35400314 DOI: 10.1080/10495398.2022.2058007] [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] [Indexed: 11/01/2022]
Abstract
Susceptibility to classical bovine spongiform encephalopathy (BSE) has been linked to 23 bp indel in promoter and 12 bp indel in the first intron of cattle prion protein gene. This study aimed to investigate 23/12 bp indel polymorphisms in the polymorphisms in cattle prion protein (PRNP) gene to reveal the risk of BSE in Ethiopian cattle. Also, frequency of each polymorphism was compared to the other Bos taurus and Bos indicus breeds. According to results, the insertion variant was detected at a low frequency in all of the study populations at both loci. The 23 bp insertion allele in Fogera breed was relatively lower than Borona and Arsi and the same allele at the same locus in Afar breed was higher than the rest of the breeds (0.16). Due to high linkage disequilibrium (LD) of the deletion allele in Bos taurus, the frequencies of deletion allele at 23 bp (0.84) and 12 bp (0.86) loci in Afar breed were relatively closer than the rest of the breeds. In addition, DD/DD was found as the highly frequent diplotype in all of the breeds. The low frequency of insertion alleles at 23 and 12 bp indel sites demonstrate that Ethiopian cattle have a genetically high risk for BSE.
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Affiliation(s)
- Eden Yitna Teferedegn
- Department of Biology Molecular Biology Section, Faculty of Science, Ege University, İzmir, Turkey
| | - Hüseyin Can
- Department of Biology Molecular Biology Section, Faculty of Science, Ege University, İzmir, Turkey
| | - Sedef Erkunt Alak
- Department of Biology Molecular Biology Section, Faculty of Science, Ege University, İzmir, Turkey
| | - Cemal Ün
- Department of Biology Molecular Biology Section, Faculty of Science, Ege University, İzmir, Turkey
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Ahlawat S, Sharma U, Arora R, Sharma R, Chhabra P, Veer Singh K, Vijh RK. Mitogenomic phylogeny reveals the predominance of the Nubian lineage of African wild ass in Indian donkeys. Gene 2023:147627. [PMID: 37429369 DOI: 10.1016/j.gene.2023.147627] [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: 05/18/2023] [Revised: 06/27/2023] [Accepted: 07/06/2023] [Indexed: 07/12/2023]
Abstract
To contribute to the knowledge of maternal genetic diversity in domestic donkeys, this study investigated the mitochondrial DNA variations and analyzed the genetic structure in Indian donkeys based on 31 mitogenome sequences representing four breeds/populations (Agra, Halari, Kachchhi and Spiti). A total of 27 haplotypes with a haplotype diversity value of 0.989 were evident in the donkey genetic resources of India. The genetic differentiation between the investigated populations was evaluated using population pairwise FST values, which showed maximum differentiation between Kachchhi and Halari donkeys. The Neighbor-Joining (NJ) tree based on the whole mitogenome sequence and the Median-Joining (MJ) network for partial D-loop fragment showed clear demarcation of Indian donkeys into Nubian and Somali clades, substantiating African maternal origin of Indian domestic donkeys. The topology of the MJ network excluded the Asian wild asses as the possible progenitors of Indian donkeys. Halari and Agra donkeys showed conformity exclusively to the Nubian lineage of the African wild asses. However, representation of both the Nubian and Somali lineages was observed in Kachchhi and Spiti donkeys. Comprehensive analysis carried out by retrieving D-loop sequences from different countries representing Asia, Africa, Europe and South America revealed existence of shared haplotypes across geographically isolated regions of the globe. This observation is indicative of utility of donkeys as pack animals across inter-continental trading routes during development of human civilizations. Our results represent a valuable contribution to maternal genetic diversity of Indian donkeys and provide insights into the worldwide spread of the species following initial domestication in Africa.
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Affiliation(s)
- Sonika Ahlawat
- ICAR-National Bureau of Animal Genetic Resources, Karnal.
| | - Upasna Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | - Reena Arora
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | - Rekha Sharma
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | - Pooja Chhabra
- ICAR-National Bureau of Animal Genetic Resources, Karnal
| | | | - R K Vijh
- ICAR-National Bureau of Animal Genetic Resources, Karnal
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Norasi E, Rastegar M, Hosseini SD, Aghcheli B, Tahamtan A. Prevalence of CCR5 Delta 32 Genetic Variant in the Turkmen Population of Golestan Province, Northeast of Iran. BIOMED RESEARCH INTERNATIONAL 2023; 2023:8823863. [PMID: 37388364 PMCID: PMC10307026 DOI: 10.1155/2023/8823863] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 04/30/2023] [Revised: 05/23/2023] [Accepted: 06/14/2023] [Indexed: 07/01/2023]
Abstract
The 32 bp deletion in the chemokine receptor (C-C motif) 5 gene (CCR5Δ32) is a natural loss of function polymorphism that prevents the protein from locating on the cell surface. This genetic variation acts as a double-edge sword in the pathogenesis/defense mechanism of different health conditions, such as viral infections, autoimmune diseases, and cancers. Here, we evaluated the prevalence of the CCR5Δ32 polymorphism in the Turkmen population of Golestan province, northeast of Iran. Blood samples were collected from 400 randomly selected Turkmen populations (199 women and 201 men), and genomic DNA was extracted. Characterization of CCR5Δ32 genotypes was performed by PCR using primers flanking the 32-nucleotide deletion in the CCR5 gene. The amplified DNA fragments were visualized on 2% agarose gel electrophoresis with cybergreen staining under UV light. All individuals were of Turkmen ethnicity and lived in the Golestan province, northeast of Iran. The mean age of all participants was 35.46 years, with a 20-45 year range. All the studied subjects were healthy without any severe conditions such as autoimmune disease and viral infections. All individuals had no history of HIV infection. The PCR product visualization showed that all the samples are at the 330 bp size, which means the CCR5Δ32 allele was utterly absent from the study population. The presence of the CCR5Δ32 allele among Turkmens may be attributed to the admixture with European descent people. We conclude that the CCR5Δ32 polymorphism may be absent in the Iranian Turkmen population, and further studies with a large population are needed.
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Affiliation(s)
- Elmira Norasi
- School of International, Golestan University of Medical Sciences, Gorgan, Iran
| | - Mostafa Rastegar
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | | | - Bahman Aghcheli
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
| | - Alireza Tahamtan
- Department of Microbiology, Faculty of Medicine, Golestan University of Medical Sciences, Gorgan, Iran
- Infectious Diseases Research Center, Golestan University of Medical Sciences, Gorgan, Iran
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El-Mansy SA, Naiel MA, Abu El-Naser IA, De Waard M, Babalghith AO, Ogaly HA, El-Saber Batiha G, Ghazy AA. The growth hormone gene polymorphism and its relationship to performance and carcass features in Egyptian Awassi lambs. Heliyon 2023; 9:e14194. [PMID: 36938391 PMCID: PMC10015200 DOI: 10.1016/j.heliyon.2023.e14194] [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: 08/31/2022] [Revised: 02/18/2023] [Accepted: 02/23/2023] [Indexed: 03/06/2023] Open
Abstract
The main purpose of the existing experiment was to assess the allelic and genotypic polymorphisms of the Growth hormone (GH) gene and its correlation with growth indices, efficiency of consumed feed, some body indices and carcass traits of the Egyptian Awassi sheep. Forty Egyptian Awassi male lambs were selected for their growing indices (post-weaning daily gain, marketing weight, and weaning weight), feed efficiency (consumed feed and of consumed feed), body conformational indicators (skeletal muscle index, relative body index, body mass index, and body index), and carcass features (dressing %, hot carcass weight, fore-legs %, neck %, loin %, ribs %, abdominal fat %, Tail % and hind-legs %). The polymerase chain reaction-restricted fragment length polymorphism (PCR-RFLP) tool was applied to detect the genotypic and allelic GH gene polymorphisms properties. The PCR-RFLP analysis identified three main genotypes (AA, AB and BB) and two main alleles (A and B). The GH genotype (AA or AB) exhibited moderate significant influence (P < 0.05) on marketing weight, Loin% and Tail%. Also, genotype (AB or BB) of expressed GH gene significantly (P < 0.01) influence on consumed feed, post-weaning daily gain, neck% and body mass index, whereas, it had no influence on the phenotypic values of the other characteristics investigated. The presence of the A allele in the genotype was markedly associated (P < 0.01) with consumed feed, body mass index and post-weaning daily growth; conversely, the presence of the B allele in the genotype was significantly related (P < 0.05) with marketing weight, loin %, and tail %. While, GH gene expression was revealed to be highly significant (P < 0.01) in relation to post-weaning daily growth, feed intake, and neck %. According to the findings, determining the associations between GH gene variation and growth, efficiency of consumed feed, body measurements, and carcass features of Egyptian Awassi sheep and applying marker assisted selection with the GH gene to improve these traits is warranted and will be of significant economic value to sheep production.
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Affiliation(s)
- Salah A. El-Mansy
- Department of Animal Production, Faculty of Agriculture, Zagazig University, Zagazig, 44519, Egypt
| | - Mohammed A.E. Naiel
- Department of Animal Production, Faculty of Agriculture, Zagazig University, Zagazig, 44519, Egypt
- Corresponding author.
| | | | - Michel De Waard
- FranceSmartox Biotechnology, 6 Rue Des Platanes, F-38120 Saint-Egrève, France
- L’institut du Thorax, INSERM, CNRS, UNIV NANTES, F-44007 Nantes, France
- LabEx Ion Channels, Science & Therapeutics, Université de Nice Sophia-Antipolis, F-06560 Valbonne, France
| | - Ahmad O. Babalghith
- Medical Genetics Department, College of Medicine, Umm Al-Qura University, Saudi Arabia
| | - Hanan A. Ogaly
- Chemistry Department, College of Science, King Khalid University, Abha, 61421, Saudi Arabia
- Biochemistry and Molecular Biology Department, Faculty of Veterinary Medicine, Cairo University, Giza, 12211, Egypt
| | - Gaber El-Saber Batiha
- Department of Pharmacology and Therapeutics, Faculty of Veterinary Medicine, Damanhour University, Damanhour, 22511, AlBeheira, Egypt
| | - Abdullah A. Ghazy
- Department of Animal Production, Faculty of Agriculture, Suez Canal University, 41522, Ismailia, Egypt
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12
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Ramya P, Beena V, Radhika G, Shynu M, Jayavardhanan K. Molecular characterisation of coding regions of HIF-1a gene in Vechur cattle by cDNA sequencing. Heliyon 2022; 8:e12578. [PMID: 36601432 PMCID: PMC9806684 DOI: 10.1016/j.heliyon.2022.e12578] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/16/2022] [Revised: 11/09/2022] [Accepted: 12/15/2022] [Indexed: 12/25/2022] Open
Abstract
Hypoxia-inducible factor (HIF)-1α is a transcription factor stabilized by hypoxia by inducing or suppressing the homeostatic regulatory gene expression, enabling tissues and cells to survive despite fluctuations in environmental circumstances. As the name implies, hypoxia-inducible factor-1 is secreted not only as a cellular response to hypoxia but also in heat stress and oxidative stress. The goal of this work was to determine the molecular characterisation of the HIF-1α gene coding region as well as the differences in HIF-1αprotein primary structure between Vechur cattle and other cattle breeds in the online databases. Total RNA was isolated from blood samples of 6 Vechur cattle using the trizol reagent method, and full-length c sequences of the HIF-1α gene were sequenced. The base pair length of composite HIF-1αcDNA of Vechur cattle and encoding ORFis 3956 bp and 2469 bp respectively. The 5'UTR was recognized to be 279 bp in length. The start codon was identified at nucleotide 280-282, the stop codon UGA at 2746-2748 bp and a 1208 bp 3'UTR which included a poly-A tail of 27 adenine residues. In a comparative analysis of the cDNA, point transitions causing guanine to adenine (G>A) changes at 1211th and 2699th positions were noticed as a heterozygous condition in the whole 3956 bp sequence. These two SNVs in the coding regions were responsible for two amino acid changes in the deduced 823 amino acid sequence. Since the predicted amino acid arginine had been replaced with lysine at 311th and 807th positions, it showed 99.76 percent sequence identity with Bos taurus. The phylogenetic tree revealed that the HIF-1α protein of Vechur cattle had a lesser evolutionary distance from the same gene of related species emphasising the highly conserved nature of this particular protein. This structural variation observed in the present study should be evaluated on a larger population to assess its functional relevance for thermo-tolerance.
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Affiliation(s)
- P.R. Ramya
- Department of Veterinary Biochemistry, College of Veterinary and Animal Sciences, Mannuthy, Thrissur District, Kerala State, 680651, India
| | - V. Beena
- Department of Veterinary Physiology, Kerala Veterinary and Animal Sciences University, Mannuthy, Kerala State, 680651, India
| | - G. Radhika
- Department of Animal Breeding and Genetics, Kerala Veterinary and Animal Sciences University, Pookkod, Wayanad District, 673576, Kerala State, India
| | - M. Shynu
- Department of Veterinary Biochemistry, Kerala Veterinary and Animal Sciences University, Pookkod, Wayanad District, 673576, Kerala State, India
| | - K.K. Jayavardhanan
- Department of Veterinary Biochemistry, College of Veterinary and Animal Sciences, Mannuthy, Thrissur District, 680651, Kerala State, India
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13
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Wang Q, You L, Li Z, Zhang L, Li X, Yang X. Influence of AGTR1 and ABCB1 Gene Polymorphism on the Curative Effect of Irbesartan. Int J Hypertens 2022; 2022:4278675. [PMID: 36404948 PMCID: PMC9668479 DOI: 10.1155/2022/4278675] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/09/2022] [Revised: 09/23/2022] [Accepted: 10/18/2022] [Indexed: 08/30/2023] Open
Abstract
The interindividual heterogeneity in response to the antihypertensive effect of irbesartan has received considerable attention because of gene polymorphism. In this study, we investigated the new combinational influences of AGTR1 and ABCB1 gene polymorphism on the therapeutic effect of irbesartan among Chinese hypertensive patients. A total of 353 samples including 168 normal people and 185 hypertensive patients were adopted, and genotypes comprise ABCB1 (CC, CT, and TT) and AGTR1 (AA and AC) in this study. The results of multiple linear regression models showed that no statistically significant differences were observed in blood pressure change following irbesartan administration in each genotype from either ABCB1 (CC, CT, and TT) or AGTR1 (AA and AC). However, spline smoothing analysis demonstrated that the blood pressure therapeutic responses of irbesartan presented a noticeable difference among different ABCB1 genotypes when irbesartan doses reached over 300 ng/mL. Eventually, we assumed that the different drug responses of irbesartan among various AGTR1 genotypes were due to the diversity of the irbesartan-conjugated protein, which is responsible for crossing-coupled intracellular G-protein-coupled receptors (GPCRs).
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Affiliation(s)
- Qiao Wang
- Department of Cardiovascular Medicine, The Fourth Affiliated Hospital of Harbin Medical University, Harbin 116000, China
- Department of Cardiovascular Medicine, Dalian University Affiliated Xinhua Hospital, Dalian 116021, China
| | - Lingsen You
- Division of Histology and Embryology, Joint Laboratory for Embryonic Development & Prenatal Medicine, Medical College, Jinan University, Guangzhou 510632, China
| | - Zeyu Li
- Division of Histology and Embryology, Joint Laboratory for Embryonic Development & Prenatal Medicine, Medical College, Jinan University, Guangzhou 510632, China
| | - Leiyi Zhang
- Department of Cardiovascular Medicine, The First Affiliated Hospital of Jiamusi Medical University, Jiamusi 114003, China
| | - Xueqi Li
- Department of Cardiovascular Medicine, The Fourth Affiliated Hospital of Harbin Medical University, Harbin 116000, China
| | - Xuesong Yang
- Division of Histology and Embryology, Joint Laboratory for Embryonic Development & Prenatal Medicine, Medical College, Jinan University, Guangzhou 510632, China
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JASMINE AJEMIMA, SARKAR UTTAM, ROY MANORANJAN, DATTA SANJOY. Influence of genetic and non-genetic factors on growth performance in Black Bengal goats under field condition in West Bengal. THE INDIAN JOURNAL OF ANIMAL SCIENCES 2022. [DOI: 10.56093/ijans.v92i10.124645] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/05/2022]
Abstract
Data on 10148 Black Bengal kids recorded from 2008 to 2019 and maintained at farmer’s fields at different agroclimatic clusters of West Bengal under the project “AICRP on Goat Improvement, Black Bengal Field Unit- Kolkata” were used to study the effect of non-genetic factors on body weight from birth to 12 months of age. The data were analysed using least squares analysis technique. The average birth weights of Black Bengal goats obtained under four different agro-climatic clusters revealed that there was a significant variation in body weight (kg) of all ages. The effect of year of kidding, influence of season and parity of the dam on body weight of Black Bengal kids at different ages were significant. But a non-significant result was found at the body weight in all the seasons as well as in all the parities at 9 and 12 months of age. Sex of the kid and type of birth had significant effect on body weights from birth to 12 months of age. Significantly higher body weight at birth was recorded in single born kid, followed by twin and triplets. The study concluded that it is possible to improve non-genetic elements in the field, particularly by providing excellent housing, reducing stress, having access to grazing pasture, and doing routine deworming and vaccinations. The findings supported the need for environmental changes that can aid in the development of management strategies and decision making regarding the selection.
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15
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Wang C, Yang Y, Liu Y, Zhang Y, Chen S, Li G, Wang X, Wang H, Song J, Gong S, Lin Z, He D. Novel IGF2BP1 splice variants, expression and their association with growth traits in goose. Br Poult Sci 2022; 63:804-812. [PMID: 35766314 DOI: 10.1080/00071668.2022.2094220] [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: 11/02/2022]
Abstract
1. The gene IGF2BP1 has been reported as being related to the body size and body weight in ducks, goats and chickens. However, this potential growth-related gene has not yet been reported in geese.2. The goose IGF2BP1 cDNA (IGF2BP1-X1) is 2,925 bp in length, containing an open reading frame (ORF) of 1,731 bp that encodes a protein of 576 amino acids. Six IGF2BP1 transcripts (IGF2BP1-X2∼IGF2BP1-X7) were identified due to the alternative splicing of different exons within the IGF2BP1-X1 transcript.3. RT-qPCR analysis indicated that the goose IGF2BP1 mRNA was differentially expressed in the examined tissues of the female embryos (28 d of development), adult (70 d of age) and laying (270 d of age) of Zhedong White geese.4. In total, 16 single nucleotide polymorphisms (SNPs) and three insertion/deletion (InDel) variants were detected in several introns and 3'-untranslated regions of the goose IGF2BP1 gene. The 17-bp InDel within IGF2BP1 intron 14 was significantly associated with body weight at six weeks old (BW6, P<0.05), and extremely significantly associated with the BW8 and BW10 (P<0.01) of Zhedong White geese.
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Affiliation(s)
- Cui Wang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, P.R. China
| | - Yunzhou Yang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, P.R. China
| | - Yi Liu
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, P.R. China
| | - Yuting Zhang
- Shanghai Ocean University, College of Fisheries and Life Science, Shanghai 201306, P.R. China
| | - Shufang Chen
- NingBo Academy of Agricultural Sciences, Ningbo 315040, P.R. China
| | - Guangquan Li
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, P.R. China
| | - Xianze Wang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, P.R. China
| | - Huiying Wang
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, P.R. China
| | - Jiawei Song
- Xiangshan Animal Husbandry and Veterinary General Station, Ningbo 315700, P.R. China
| | - Shaoming Gong
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, P.R. China
| | - Zhenping Lin
- Shantou Baisha Research Institute of Original Species of Poultry and Stock, Shantou 515100, P.R. China
| | - Daqian He
- Institute of Animal Husbandry and Veterinary Science, Shanghai Academy of Agricultural Sciences, Shanghai 201106, P.R. China
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16
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Abd El Fattah EM, Behour TS, Ashour AF, Amin AMS. Association analysis of prolactin and prolactin receptor genes with selected productive and reproductive traits in Egyptian buffalo. Anim Biotechnol 2022:1-9. [PMID: 35148254 DOI: 10.1080/10495398.2022.2028160] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/01/2022]
Abstract
A total of 266 records of buffalo raised in two experimental herds in Egypt were assessed to detect prolactin (PRL) and prolactin receptor (PRLR) genes' polymorphism using PCR-Single Strand Conformational Polymorphism (SSCP) and PCR-Restricted Fragment Length Polymorphism (RFLP) techniques as well as to investigate their association with calf birth weight (BW), weaning weight (WW), lactation period (LP), total milk yield (TMY), stillbirth, calving ease (CE), gestation length (GL), postpartum interval to pregnancy (PPIP), calving interval (CI), and age at first calving (AFC). Predicted breeding values were estimated and used in the association with detected genotypes. A monomorphic pattern of the studied PRL 156 bp segment was recorded and absence of its polymorphism in buffalo was corroborated. We also determined polymorphism of PRLR reflected in three loci: PRLR2, PRLR4, and PRLR9. Significant differences among PRLP9 genotypes (AA, AB, and BB) were displayed for all studied traits as well as among PRLR2 genotypes, except for CE, while PRLR4 genotypes significantly differed only in BW, WW, TMY, stillbirth, GL, and AFC. In practice, strong associations among genotypes of the PRLR gene and the traits of interest candidate this gene to be selective in Egyptian buffalo breeding for improving both productive and reproductive traits.
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Affiliation(s)
- Eman Mohamed Abd El Fattah
- Animal Reproduction Research Institute (ARRI), Agricultural Research Center, Ministry of Agriculture and Land Reclamation, Giza, Egypt
| | - Tahani Salama Behour
- Animal Reproduction Research Institute (ARRI), Agricultural Research Center, Ministry of Agriculture and Land Reclamation, Giza, Egypt
| | - Ayman Fouad Ashour
- Animal Production Research Institute (APRI), Agricultural Research Center, Ministry of Agriculture and Land Reclamation, Dokki, Giza, Egypt
| | - Amin Mohamed Said Amin
- Animal Production Research Institute (APRI), Agricultural Research Center, Ministry of Agriculture and Land Reclamation, Dokki, Giza, Egypt
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17
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Facioli FL, da Silva AN, Dos Santos ED, de Camargo J, Warpechowski MB, da Oliveira Cruz J, Lof LM, Zanella R. From Mendel laws to whole genetic association study to decipher the swine mulefoot phenotype. Res Vet Sci 2021; 143:58-65. [PMID: 34974356 DOI: 10.1016/j.rvsc.2021.12.009] [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: 08/18/2021] [Revised: 11/24/2021] [Accepted: 12/16/2021] [Indexed: 11/28/2022]
Abstract
The swine mulefoot (SM) is a rare condition characterized by a non-cloven hoof due to the partial or total fusion of the phalanges. No comprehensive study has been conducted to identify associated markers with this phenotype until now. We aimed to characterize the association between SNP and the mulefoot phenotype using a Genome-Wide Association Study (GWAS). An experimental population was produced using a half-sib mating where the male had the mulefoot phenotype and the females (n = 6) had cloven hoofs. The cross resulted in 27 (47%) animals with the mulefoot characteristic and 30 (53%) normal animals, indicating the possible dominant gene action. Animals were further genotyped using the Illumina PorcineSNP50k BeadChip, and SNPs were tested for associations. Twenty-nine SNPs located on the SSC15, SSC4, and SSCX were associated with the mulefoot phenotype (p-value <5 × 10-5). Six markers were found in the intronic regions of VWC2L, CATIP, PDK3, PCYT1B, and POLA1 genes. The marker rs81277626, on SSC15:116,886,110 bp, is located in the Von Willebrand Factor C Domain (VWC2L), a possible functional candidate gene. The VWC2L is part of a biological process involved with the bone morphogenetic protein (BMP) signaling pathway, previously associated with syndactyly in other species. In conclusion, the identified markers suggest the involvement of the VWC2L gene in the SM phenotype in this population.
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Affiliation(s)
- Fernanda Luiza Facioli
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil
| | - Arthur Nery da Silva
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil
| | - Ezequiel Davi Dos Santos
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil
| | - Janine de Camargo
- Programa de Pós Graduação em Bioexperimentação, Faculdade de Agronomia e Medicina Veterinária,Universidade de Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil
| | - Marson Bruck Warpechowski
- Departamento de Zootecnia, Setor de Ciências Agrárias, Universidade Federal do Paraná, Curitiba, Paraná, Brazil
| | - Juliano da Oliveira Cruz
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil
| | - Lucas Mallmann Lof
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil
| | - Ricardo Zanella
- Faculdade de Agronomia e Medicina Veterinária, Curso de Medicina Veterinária, Universidade de Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil; Programa de Pós Graduação em Bioexperimentação, Faculdade de Agronomia e Medicina Veterinária,Universidade de Passo Fundo, Passo Fundo, Rio Grande do Sul, Brazil.
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18
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Guo S, Bai Y, Zhang Q, Zhang H, Fan Y, Han H, Liu Y. Associations of CALM1 and DRD1 polymorphisms, and their expression levels, with Taihang chicken egg-production traits. Anim Biotechnol 2021:1-11. [PMID: 34890302 DOI: 10.1080/10495398.2021.2008948] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/04/2023]
Abstract
Egg production by hens is an important reproductive performance index in the poultry industry. To investigate the effects of the CALM1 and DRD1 genes on egg production in chicken, their mRNA expression and single nucleotide polymorphisms (SNP) levels were investigated, and bioinformatics and egg-production association analyses were performed. Three SNPs (g.44069941G > A and g.44069889A > G in CALM1 and g.10742639C > T in DRD1) were detected in the exons and introns of CALM1 and DRD1 in 400 Taihang chickens. Among them, g.44069941G > A was significantly associated with Taihang chicken egg production on the 500th day (p < 0.05), whereas g.10742639C > T was significantly associated with the 300th day (p < 0.05). The expression levels of CALM1 and DRD1 in ovarian tissues of a high-yielding Taihang group were greater than in a low-yielding group (p < 0.05). The bioinformatics analysis revealed that the mutations influenced the mRNA secondary structures of CALM1 and DRD1. This study provides new insights into the potential effects of CALM1 and DRD1 polymorphisms on chicken egg production. The two SNPs g.44069941G > A and g.10742639C > T are potential molecular markers for improving the reproductive traits of Taihang chicken.
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Affiliation(s)
- Siwu Guo
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
| | - Ying Bai
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
| | - Qingyang Zhang
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
| | - Hui Zhang
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
| | - Yekai Fan
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
| | - Haiyin Han
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
| | - Yufang Liu
- College of Life Sciences and Food Engineering, Hebei University of Engineering, Handan, China
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19
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Parasar P, Bhushan B, Panigrahi M, Kumar H, Kaisa K, Dutt T. Characterization of BoLA class II DQA and DQB by PCR-RFLP, cloning, and sequencing reveals sequence diversity in crossbred cattle. Anim Biotechnol 2021:1-11. [PMID: 34813716 DOI: 10.1080/10495398.2021.2006205] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/08/2023]
Abstract
The BoLA class II DQA and DQB genes in crossbred cattle were studied using PCR-RFLP, cloning, and sequencing techniques. Seventy-two crossbred cattle (Vrindavani) were used in the current study. HaeIII and XbaI restriction enzymes digested DQA exon 2-3, revealing seven (HaeIII-A-G) and three (XbaI A-C) motifs, respectively. The BoLA-DQB gene was analyzed using PCR-RFLP with PstI and TaqI restriction enzymes, yielding five restriction motifs for each restriction enzyme (PstI-A-E and TaqI-A-E). In crossbred cattle, addition, deletion, and substitutions were observed in distinct sequences, resulting in variations in overall gene length. Changes in nucleotides at positions 64-80, 110-200, and 207-264 were largely responsible for polymorphism in DQA exon 2. The phylogenetic analysis predicted a high degree of nucleotide and amino acid changes in DQA exon 2-3 and DQB exon 2. DQA genes had a nucleotide dissimilarity of 0.3-25.4 percent, while DQB genes had a nucleotide dissimilarity of 1.5-14.3 percent. We cloned and sequenced 20 genotypes based on PCR-RFLP of the DQA and DQB genes. The current study observed variation in the DQA and DQB genes and will serve as a foundation for future research on the BoLA DQA and DQB genes.
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Affiliation(s)
- Parveen Parasar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Bharat Bhushan
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Manjit Panigrahi
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Harshit Kumar
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Kaiho Kaisa
- Division of Animal Genetics, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
| | - Triveni Dutt
- Livestock Production and Management Section, ICAR-Indian Veterinary Research Institute, Bareilly, Uttar Pradesh, India
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20
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Ali A, Javed K, Zahoor I, Anjum KM, Sharif N. Identification of polymorphisms in the MSTN and ADRB3 genes associated with growth and ultrasound carcass traits in Kajli sheep. Anim Biotechnol 2021:1-16. [PMID: 34775903 DOI: 10.1080/10495398.2021.2000428] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The aim of this investigation was to find single nucleotide polymorphisms (SNPs) in the myostatin (MSTN) and the beta-3 adrenergic receptor (ADRB3) genes associated with growth and ultrasound carcass traits in Kajli sheep. The five growth traits were birth weight (BWT-EBV), 120-day weight (120DWT-EBV), 180-day weight (180DWT-EBV), 270-day weight (270DWT-EBV), and 365-day weight (365DWT-EBV). The three ultrasound carcass traits were width (WLD) and depth of longissimus dorsi (DLD) and back fat thickness (BFT). The analysis of the MSTN sequence revealed one non-synonymous substitution (c.197T > A) in exon 1, one single nucleotide substitution (c.373 + 18G > T) in intron 1, and one synonymous substitution (c.861T > A) in exon 3. However, there were four single nucleotide synonymous substitutions (c.130C > T, c.294C > G, c.579G > T, and c.654C > G) in exon 1 of the ADRB3 gene. All the SNPs in the MSTN gene, except for c.373 + 18G > T, were in Hardy-Weinberg Equilibrium (HWE). Conversely, none of the SNPs found in ADRB3 were in HWE. Two of the MSTN SNPs (c.197T > A and c.373 + 18G > T) had significant associations with all evaluated growth and ultrasound carcass traits. The SNPs c.130C > T and c.294C > G in ADRB3 were significantly associated with 180DWT-EBV. Collectively, these findings indicate that several SNPs in the studied genes were significantly related to growth and carcass traits in Kajli sheep.
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Affiliation(s)
- Asad Ali
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Khalid Javed
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Imran Zahoor
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Khalid Mahmood Anjum
- Department of Wildlife & Ecology, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Numan Sharif
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
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21
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S Balamurugan T, Kumar P, Shrivastava K, Prakash O, Kumar A, Chauhan A, Sahoo NR, Bhushan B, Kaveriyappan I, Velusamy S. Genetic polymorphism of microsatellite loci in MHC class II exon 2 gene and its association with endoparasitic infestation, predominantly Haemonchus contortus in Salem black goat. Anim Biotechnol 2021:1-9. [PMID: 34749570 DOI: 10.1080/10495398.2021.1998088] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
MHC gene is highly polymorphic and plays central molecule in immune system in recognition of pathogens and parasites. The present study examined the variability of MHC class II DRB exon 2 gene using microsatellite analysis, and its association with Haemonchus contortus infestation in Salem Black goat population. Animals were naturally exposed to mixed infestation of endoparasites, predominantly Haemonchus contortus. Pooled fecal coproculture and larval identification showed predominant presence of haemonchus (L3) larva. Fecal egg count (FEC) and packed cell volume (PCV) were used as indicator traits. All the three studied loci, OarCP73, DYA, and ODRB1.2, were polymorphic having three, four, and four alleles and four, eight, and nine genotypes, respectively. The loci showed low to moderate values of polymorphic information content. The mean fecal egg count estimates were 477.12 ± 34.14 eggs per gram of feces and the mean PCV values were within the normal range; however, they showed negative correlation with FEC values. All the three microsatellite loci and the effect of genotypes on indicator traits were found to be statistically significant (p ≤ 0.05). The present study will be helpful in selection and breeding of goats for Haemonchosis resistance.
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Affiliation(s)
- Thirunavukkarasu S Balamurugan
- Division of Animal Genetics, Molecular Genetics Lab, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, UP, India
| | - Pushpendra Kumar
- Division of Animal Genetics, Molecular Genetics Lab, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, UP, India
| | - Kush Shrivastava
- Division of Animal Genetics, Molecular Genetics Lab, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, UP, India
| | - Om Prakash
- Division of Animal Genetics, Molecular Genetics Lab, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, UP, India
| | - Amit Kumar
- Division of Animal Genetics, Molecular Genetics Lab, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, UP, India
| | - Anuj Chauhan
- Division of Animal Genetics, Molecular Genetics Lab, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, UP, India
| | - Nihar Ranjan Sahoo
- Division of Animal Genetics, Molecular Genetics Lab, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, UP, India
| | - Bharat Bhushan
- Division of Animal Genetics, Molecular Genetics Lab, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, UP, India
| | - Ilayakumar Kaveriyappan
- Division of Animal Genetics, Molecular Genetics Lab, ICAR-Indian Veterinary Research Institute (IVRI), Bareilly, UP, India
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Yao R, Lu T, Liu J, Li W, Weng X, Yue X, Li F. Variants of ADPGK gene and its effect on the male reproductive organ parameters and sperm count in Hu sheep. Anim Biotechnol 2021:1-8. [PMID: 34730075 DOI: 10.1080/10495398.2021.1995400] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
ADP-dependent glucokinase (ADPGK) plays an important role instead of hexokinase in regulating energy metabolism via the Embden-Meyerhof-Parnas Pathway. And energy provided via glycolysis promotes testis development and spermatogenesis. In this study, 466 Hu sheep were screened for mutations in the ADPGK gene to examine the association of the ADPGK gene polymorphisms with the testis traits and spermatogenesis. The NC_056060.1: g.31295 C > T SNP was found in the 3'-UTR region, resulting in two genotypes CC and TC type with genotypic frequencies of 0.66 and 0.34, respectively. This mutation was significantly associated with testis weight, testis long circumference, testis short girth, epididymis weight, and sperm concentration (p < 0.05). Moreover, TC genotype individuals had an increased tendency in the expression of the ADPGK gene and had significant reproductive performance advantages compared with CC genotype individuals in the study. And compared with the small testes (<50 g), the ADPGK gene expression of big testes (>160 g) increased significantly. This indicates an association between the ADPGK gene and reproductive organ parameters and sperm count in selected Hu sheep breed, and this SNP may serve as an effective DNA molecular marker for marker-assisted selection in Hu sheep breeding programs.
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Affiliation(s)
- Rongyu Yao
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Tingting Lu
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Jiamei Liu
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Wanhong Li
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiuiu Weng
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Xiangpeng Yue
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China
| | - Fadi Li
- Key Laboratory of Grassland Livestock Industry Innovation, Ministry of Agriculture and Rural Affairs, Engineering Research Center of Grassland Industry, Ministry of Education, State Key Laboratory of Grassland Agro-ecosystems, College of Pastoral Agriculture Science and Technology, Lanzhou University, Lanzhou, China.,Gansu Runmu Biological Engineering Co., Ltd., Yongchang, China.,Biotechnology Engineering Laboratory of Gansu Meat Sheep Breeding, Minqin, China
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Ibrahim AHM, Megaley AFM, Sallam AMA. Variation in the ovine FOXP3 gene and its effect on growth traits in Egyptian Barki sheep. Anim Biotechnol 2021:1-7. [PMID: 34727013 DOI: 10.1080/10495398.2021.1996387] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/19/2022]
Abstract
The aim of the present study was to detect the FOXP3 gene polymorphisms in Barki sheep at a variable region covering exon 13, intron 13 and the coding sequence in exon 14 and to test the association of these polymorphisms with growth traits. 122 Barki lambs were phenotyped for various growth traits, viz., birth weight (BW), weaning weight (WW), pre-weaning daily gain in weight (ADG1), post-weaning daily gain in weight (ADG2) and marketing bodyweight (MW). The polymerase chain reaction - single-strand conformational polymorphisms (PCR-SSCP) and DNA sequencing methods were used to identify the genetic variants in the FOXP3 gene. The associations between the variation in FOXP3 gene and growth traits were tested using a general linear model. Two variants (F1 and F2 with gene frequencies of 0.64 and 0.36, respectively), and three genotypes (F1F1, F1F2 and F2F2 with frequencies of 0.37, 0.53 and 0.10, respectively) were detected. The association of FOXP3 genotype was significant (p < 0.05) with ADG2 and MW. It is concluded that FOXP3 genotype might be helpful for sheep breeders to produce fast-growing lambs. However, further studies are needed in a large population to confirm the association we found.
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Affiliation(s)
- Adel H M Ibrahim
- Department of Animal Breeding, Desert Research Center, Cairo, Egypt
| | | | - Ahmed M A Sallam
- Department of Animal Breeding, Desert Research Center, Cairo, Egypt
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24
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Yi X, He S, Wang S, Zhao H, Wu M, Liu S, Pan Y, Zhang Y, Sun X. Expression of different genotypes of bovine TRDMT1 gene and its polymorphisms association with body measures in Qinchuan cattle (Bos Taurus). Anim Biotechnol 2021:1-11. [PMID: 34629027 DOI: 10.1080/10495398.2021.1984248] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
DNA methyltransferase 2 (DNMT2) was renamed as tRNA aspartic acid methyltransferase 1 (TRDMT1) by catalyzing the methylation of tRNAAsp anti-codon loop C38. The development of sequencing of nucleic acids and protein detection techniques have prompted the demonstration that TRDMT1 mediated tRNA modification affects protein synthesis efficiency. This process affects the growth and development of animals. The DNA of 224 Qinchuan cattles aged 2-4 years old was collected in this experiment. The genetic variations of TRDMT1 exon and some intron regions were detected by mixed pool sequencing technology. qRT-PCR and Western Blot were used to detect the expression levels of mRNA and protein produced with the combination of different genetic variant loci. Three haplotypes were detected and the distribution ratios were different. Muscle tissue mRNA and protein testing showed that there were differences in mRNA expression levels among different genotypes (P < 0.05) and the protein expression levels between different genotypes show the same trend as mRNA. This study provides potential molecular materials for the improvement of Qinchuan cattle reproductivity and provides theoretical support for studying the effects of livestock TRDMT1 on animal growth and development.
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Affiliation(s)
- Xiaohua Yi
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuai He
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Shuhui Wang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Haidong Zhao
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Mingli Wu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Shirong Liu
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yun Pan
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Yu Zhang
- College of Animal Science and Technology, Northwest A&F University, Yangling, Shaanxi, China
| | - Xiuzhu Sun
- College of Grassland Agriculture, Northwest A&F University, Yangling, Shaanxi, China
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Mi T, Liu K, Guo T, Li L, Wang Y, Li C, Cui Y, Dai J, Zhang Y, Hu S. Analysis of the eighth intron polymorphism of NR6A1 gene in sheep and its correlation with lumbar spine number. Anim Biotechnol 2021; 34:218-224. [PMID: 34346290 DOI: 10.1080/10495398.2021.1954529] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
For revealing molecular markers related to the traits of multiple lumbar vertebrae in sheep, we analyze the relationship between NR6A1 gene polymorphism and lumbar vertebrae number traits in Xinjiang Kazakh sheep. Lumbar muscle tissues were collected from 6-lumbar spine (L6) Kazak sheep and 7-lumbar spine (L7) Kazak sheep and the intron-8 of NR6A1 gene was amplified by PCR. The SNP locus was detected by the PCR-SSCP method. One-Way ANOVA and an Independent Chi-square Test is adopted to analyze the genotype association with lumbar spine number variation. There were two SNP loci in the intron-8 of the NR6A1 gene: IVS8-188 and IVS8-281. One-Way ANOVA and Independent Chi-square Test indicated a significant association between IVS8-281 and lumbar spine number. The SNP locus of NR6A1 gene intron 8 (IVS8-281G > A) could play a certain role in the variation of lumbar spine number in Xinjiang Kazakh sheep and demonstrates potential to accelerate the sheep breeding of selection process.
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Affiliation(s)
- Taotao Mi
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Xinjiang, China.,College of Life Sciences, Shihezi University, Shihezi, China
| | - Kaiping Liu
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Tao Guo
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Lei Li
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Yue Wang
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Cunyuan Li
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Yuying Cui
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Jihong Dai
- College of Life Sciences, Shihezi University, Shihezi, China
| | - Yunfeng Zhang
- State Key Laboratory of Sheep Genetic Improvement and Healthy Production, Xinjiang Academy of Agricultural and Reclamation Science, Xinjiang, China
| | - Shengwei Hu
- College of Life Sciences, Shihezi University, Shihezi, China
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Mandefro A, Sisay T, Edea Z, Uzzaman MR, Kim KS, Dadi H. Genetic assessment of BoLA-DRB3 polymorphisms by comparing Bangladesh, Ethiopian, and Korean cattle. JOURNAL OF ANIMAL SCIENCE AND TECHNOLOGY 2021; 63:248-261. [PMID: 33987601 PMCID: PMC8071750 DOI: 10.5187/jast.2021.e37] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 11/26/2020] [Revised: 01/03/2021] [Accepted: 01/10/2021] [Indexed: 12/20/2022]
Abstract
Attributable to their major function in pathogen recognition, the use of bovine
leukocyte antigens (BoLA) as disease markers in immunological traits in cattle
is well established. However, limited report exists on polymorphism of the BoLA
gene in zebu cattle breeds by high resolution typing methods. Thus, we used a
polymerase chain reaction sequence-based typing (PCR-SBT) method to sequence
exon 2 of the BoLA class II DRB3 gene from 100 animals (Boran, n = 13; Sheko, n
= 20; Fogera, n = 16; Horro, n = 19), Hanwoo cattle (n = 18) and Bangladesh Red
Chittagong zebu (n = 14). Out of the 59 detected alleles, 43 were already
deposited under the Immuno Polymorphism Database for major histocompatibility
complex (IPD-MHC) while 16 were unique to this study. Assessment of the level of
genetic variability at the population and sequence levels with genetic distance
in the breeds considered in this study showed that Zebu breeds had a gene
diversity score greater than 0.752, nucleotide diversity score greater than
0.152, and mean number of pairwise differences higher than 14, being very
comparable to those investigated for other cattle breeds. Regarding neutrality
tests analyzed, we investigated that all the breeds except Hanwoo had an excess
number of alleles and could be expected from a recent population expansion or
genetic hitchhiking. Howbeit, the observed heterozygosity was not significantly
(p < 0.05) higher than the expected heterozygosity.
The Hardy Weinberg equilibrium (HWE) analysis revealed non-significant excess of
heterozygote animals, indicative of plausible over-dominant selection. The
pairwise FST values suggested a low genetic variation among all the breeds (FST
= 0.056; p < 0.05), besides the rooting from the
evolutionary or domestication history of the cattle. No detached clade was
observed in the evolutionary divergence study of the BoLA-DRB3 gene, inferred
from the phylogenetic tree based on the maximum likelihood model. The
investigation herein indicated the clear differences in BoLA-DRB3 gene
variability between African and Asian cattle breeds.
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Affiliation(s)
- Ayele Mandefro
- Department of Biotechnology, Addis Ababa Science and Technology University, Addis Ababa 16417, Ethiopia
| | - Tesfaye Sisay
- Institute of Biotechnology, Addis Ababa University, Addis Ababa 1176, Ethiopia
| | - Zewdu Edea
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
| | - Md Rasel Uzzaman
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
| | - Kwan-Suk Kim
- Department of Animal Science, Chungbuk National University, Cheongju 28644, Korea
| | - Hailu Dadi
- Ethiopian Biotechnology Institute, Addis Ababa 5954, Ethiopia
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Suprovych TM, Suprovych MP, Mokhnachova NB, Biriukova OD, Strojanovska LV, Chepurna VA. Genetic variability and biodiversity of Ukrainian Gray cattle by the BoLA-DRB3 gene. REGULATORY MECHANISMS IN BIOSYSTEMS 2021. [DOI: 10.15421/022106] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/05/2022] Open
Abstract
At the current stage of genetic studies of cattle, more and more attention is being drawn to autochthonous breeds. Native cattle have a number of prominent phenotypic traits and have preserved unique genes and their combinations lost by modern commercial breeds, which would be valuable to use in selective programs. We surveyed polymorphism of the Ukrainian autochthonous Gray breed according to alleles of exon 2 of the BoLA-DRB3 gene. The uniqueness of the gene lies in the broad variability of its allele variants. Significant informativeness at DNA level is quite important for genetic studies. We surveyed allele polymorphism using the PCR-RLFP method on DNA isolated from 88 samples of blood of cows and 5 samples of sperm. We identified 28 alleles, of which 23 variants were nomenclature ones and 5 (jba, *jab, *jbb, *nad and *nda) were “without established nomenclature”, their share accounting for 8.9%. Four alleles *06, *12, *16 and *jba had a frequency above 5% and occupied 69.9% of the breed’s allele fund overall. The commonest allele was BoLA-DRB3.2*16 (44.1%). In total, we found 40 genotypes. Considering the significant dominance of variant *16, as expected, 5 genotypes with its inclusion occurred: *16/*16, *12/*16, *06/*16, *16/*24 and *jba/*16. It was present in the genotype of two out three studied animals. Parameters of heterozygosity, effective number of alleles, Shannon and Pielou indices indicate that Ukrainian Gray cattle are characterized by lowest level of genetic variability and biodiversity according to the BoLA-DRB3 gene compared with other breeds. Due to significant dominance of allele *16, the breed has no inbred motifs. We noted deviation toward increase in homozygosity without deviations from the norm of the distribution according to Hardy-Weinberg equilibrium. The obtained results will be used for genetic-populational programs with the purpose of improving the genetic potential of cattle breeds in terms of economically beneficial traits and diseases of cattle.
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Abdelgadir AZ, Musa LMA, Jawasreh KI, Saleem AO, El-Hag F, Ahmed MKA. G1 point mutation in growth differentiation factor 9 gene affects litter size in Sudanese desert sheep. Vet World 2021; 14:104-112. [PMID: 33642793 PMCID: PMC7896890 DOI: 10.14202/vetworld.2021.104-112] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/12/2020] [Accepted: 12/03/2020] [Indexed: 11/29/2022] Open
Abstract
BACKGROUND AND AIM Sudanese desert sheep encompass different sheep breeds named according to the different Sudanese tribes that rear them such as the Dubasi, Shugor, and Watish sheep. The objectives of this study were to screen for G1 point mutation in the polymorphic growth differentiation factor 9 (GDF9) gene, investigate its association with litter size, and construct the phylogeny of the different tribal breeds that belong to the Sudanese Desert sheep tribal types. MATERIALS AND METHODS Genomic DNA was extracted from whole blood of three tribal Desert sheep breeds (Dubasi, Watish, and Shugor) using the guanidine chloride method. Polymerase chain reaction-restriction fragment length polymorphism with HhaI restriction enzyme and sequencing techniques was used for genotyping the GDF9 locus for possible mutations associated with litter size in the three desert sheep tribal types. RESULTS G1 mutation in GDF9 caused the replacement of Arginine by Histidine at residue 87. The wild type allele (A) had the highest frequency, whereas the mutant type allele (a) had the lowest in all the sequenced subtypes. The genotype frequencies of the wild type ewes (AA) were higher than the heterozygous (Aa) and the mutant type (aa) frequencies in the three studied desert sheep types. No significant differences were found in the allele frequency between the three tribal types. Litter size was significantly influenced by the genotypes of GDF9 gene, parities, and subtypes (p≤0.01, 0.01, and 0.05, respectively). In the Watish sheep type, heterozygous sheep in their second parity recorded the highest litter size. Sequence alignment of GDF9 gene samples with the database entry indicated that all three tribal types were similar and identical to the reference sequence. The phylogenetic tree revealed that Shugor is the common ancestor of the studied types and Watish is more closely related to Shugor than Dubasi. This result mi ght partly explain the lower reproductive performance of Dubasi compared to Watish and Shugor. CONCLUSION The presence of one copy of GDF9 gene increased litter size in the studied Sudanese Desert sheep. This locus may be used as a biomarker for litter size improvement through genotypic selection and allele or gene introgression.
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Affiliation(s)
- Amani Z. Abdelgadir
- Department of Animal Production, Faculty of Agriculture, Omdurman Islamic University, Sudan
| | - Lutfi M. A. Musa
- Department of Animal Breeding and Genetics, Faculty of Animal Production, University of Khartoum, Sudan
- Arab Center for Studies of Arid Zones and Dry Land, The League of Arab states, Syria
| | - Khaleel I. Jawasreh
- Department of Animal Productions, Faculty of Agriculture – Jordan University of Science and Technology, Jordan
| | - Aubai O. Saleem
- Department of Bioinformatics, Africa City of technology, Sudan
| | - Faisal El-Hag
- Arid Land Research Center (ALRC), Tottori University, 1390 Hamasaka, Tottori 680-0001, Japan
| | - Mohamed-Khair A. Ahmed
- Department of Animal Breeding and Genetics, Faculty of Animal Production, University of Khartoum, Sudan
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Pillai HB, Thirupathy Venkatachalapathy R. Association of inhibin alpha gene polymorphism with litter size and growth in Malabari goats of India. Small Rumin Res 2020. [DOI: 10.1016/j.smallrumres.2020.106188] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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Kułaj D, Pokorska J, Ormian M, Dusza M. Short Communication: New alleles at the BoLA-DQA1 locus in Holstein–Fresian cattle. CANADIAN JOURNAL OF ANIMAL SCIENCE 2015. [DOI: 10.4141/cjas-2014-147] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/17/2022]
Abstract
Kułajaj, D., Pokorska, J., Ormian, M. and Dusza, M. 2015. Short Communication: New alleles at the BoLA-DQA1 locus in Holstein Fresian cattle. Can. J. Anim. Sci. 95: 161–164. The aim of the study was to analyze genetic polymorphism at locus BoLA-DQA1 in Polish Holstein-Friesian cattle, using next generation sequencing technology (Miseq sequencer – Illumina). In the studied cattle population we identified 14 alleles, of which three were determined for the first time (BoLA-DQA1*0106, BoLA-DQA1*3201, BoLA-DQA1*3301). The frequencies of these alleles were respectively: 0.0423, 0.0282, 0.0282. At locus BoLA-DQA1 the highest frequency was found for the BoLA-DQA1*10011 and BoLA-DQA1*0101 alleles and their frequencies were respectively: 0.3592 and 0.2606. The frequencies of other alleles identified in the studied population ranged from 0.0070 to 0.0704. The results obtained in this study indicate that the BoLA-DQA1 locus is highly polymorphic and new alleles are still identifiable.
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Affiliation(s)
- Dominika Kułaj
- University of Agriculture in Krakow, Department of Cattle Breeding, al. Mickiewicza 24/28, 30-059 Krakow, Poland
- University of Agriculture in Krakow, Department of Cattle Breeding, al. Mickiewicza 24/28, 30-059 Krakow, Poland
| | - Joanna Pokorska
- University of Agriculture in Krakow, Department of Cattle Breeding, al. Mickiewicza 24/28, 30-059 Krakow, Poland
- University of Agriculture in Krakow, Department of Cattle Breeding, al. Mickiewicza 24/28, 30-059 Krakow, Poland
| | - Marian Ormian
- University of Agriculture in Krakow, Department of Cattle Breeding, al. Mickiewicza 24/28, 30-059 Krakow, Poland
- University of Agriculture in Krakow, Department of Cattle Breeding, al. Mickiewicza 24/28, 30-059 Krakow, Poland
| | - Magdalena Dusza
- University of Agriculture in Krakow, Department of Cattle Breeding, al. Mickiewicza 24/28, 30-059 Krakow, Poland
- University of Agriculture in Krakow, Department of Cattle Breeding, al. Mickiewicza 24/28, 30-059 Krakow, Poland
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Mosafer J, Heydarpour M, Manshad E, Russell G, Sulimova GE. Distribution of BoLA-DRB3 allelic frequencies and identification of two new alleles in Iranian buffalo breed. ScientificWorldJournal 2012; 2012:863024. [PMID: 22454612 PMCID: PMC3289872 DOI: 10.1100/2012/863024] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/12/2011] [Accepted: 11/13/2011] [Indexed: 12/03/2022] Open
Abstract
The role of the major histocompatibility complex (MHC) in the immune response makes it an attractive candidate gene for associations with disease resistance and susceptibility. This study describes genetic variability in the BoLA-DRB3 in Iranian buffaloes. Heminested PCR-RFLP method was used to identify the frequency of BoLA-DRB3 alleles. The BoLA-DRB3 locus is highly polymorphic in the study herd (12 alleles). Almost 63.50% of the alleles were accounted for by four alleles (BoLA-DRB3.2 ∗48, ∗20, ∗21, and obe) in Iranian buffalo. The DRB3.2 ∗48 allele frequency (24.20%) was higher than the others. The frequencies of the DRB3.2 ∗20 and DRB3.2 ∗21 are 14.52 and 14.00, respectively, and obe and gbb have a new pattern. Significant distinctions have been found between Iranian buffalo and other cattle breed studied. In the Iranian buffaloes studied alleles associated with resistance to various diseases are found.
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Affiliation(s)
- J Mosafer
- Department of Animal Science, Ferdowsi University of Mashhad, P.O. Box 91775-1163, 9177948974 Mashhad, Iran. mosafer
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Ruzina MN, Shtyfurko TA, Mohammadabadi MR, Gendzhieva OB, Tsedev T, Sulimova GE. Polymorphism of the BoLA-DRB3 gene in the Mongolian, Kalmyk, and Yakut cattle breeds. RUSS J GENET+ 2010. [DOI: 10.1134/s1022795410040113] [Citation(s) in RCA: 28] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Pashmi M, Qanbari S, Ghorashi SA, Sharifi AR, Simianer H. Analysis of relationship between bovine lymphocyte antigen DRB3.2 alleles, somatic cell count and milk traits in Iranian Holstein population. J Anim Breed Genet 2010; 126:296-303. [PMID: 19630880 DOI: 10.1111/j.1439-0388.2008.00783.x] [Citation(s) in RCA: 15] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
The major histocompatibility complex (MHC) is a gene complex closely linked to the vertebrate immune system due to its importance in antigen recognition and immune response to pathogens. To improve our understanding of the MHC and disease resistance in dairy cattle, we gathered 5119 test day records of somatic cell count (SCC) and performance traits of 262 Holstein dairy cows to determine whether the DRB region of the MHC contains alleles that are associated with elevated SCC, milk yield, protein and fat percent of milk. To this purpose, genotyping of animals for DRB3 gene was investigated by polymerase chain reaction-based restriction fragment length polymorphism (PCR-RFLP) assay. A two-step PCR was carried out so as to amplify a 284 base-pair fragment of exon 2 of the target gene. Second PCR products were treated with three restriction endonuclease enzymes RsaI, BstYI and HaeIII. Twenty-eight BoLA-DRB3 alleles were identified including one novel allele (*40). The results in general are in good accordance with allele frequencies of Holstein cattle populations reported by previous studies. Analyses of associations were modeled based on repeated measurement anova and generalized logistic linear methods for production traits and SCC data, respectively. The results of this study showed a significant relationship between the elevated SCC reflecting an increased probability of occurrence to subclinical mastitis and DRB3.2 allele *8 (p < 0.03). The results also revealed significant positive relationships of alleles*22 (p < 0.01) and allele*11 (p < 0.05) with milk fat percent as well as of alleles*24 (p < 0.03) and *22 (p < 0.05) with protein percent. The present study failed to find any association between milk yield and tested alleles. Because of the lack of consistency among results of similar studies, we suggest further investigations to determine the precise nature of these associations with the high polymorphic bovine MHC region to be performed based on haplotypes.
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Affiliation(s)
- M Pashmi
- Department of Animal Science, Abhar Azad University, Abhar, Iran
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34
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Mohammadi A, Nassiry MR, Mosafer J, Mohammadabadi MR, Sulimova GE. Distribution of BoLA-DRB3 allelic frequencies and identification of a new allele in the Iranian cattle breed Sistani (Bos indicus). RUSS J GENET+ 2009. [DOI: 10.1134/s1022795409020100] [Citation(s) in RCA: 35] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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35
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Juliarena M, Poli M, Ceriani C, Sala L, Rodríguez E, Gutierrez S, Dolcini G, Odeon A, Esteban E. Antibody response against three widespread bovine viruses is not impaired in Holstein cattle carrying bovine leukocyte antigen DRB3.2 alleles associated with bovine leukemia virus resistance. J Dairy Sci 2009; 92:375-81. [DOI: 10.3168/jds.2008-1143] [Citation(s) in RCA: 11] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
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36
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Juliarena MA, Poli M, Sala L, Ceriani C, Gutierrez S, Dolcini G, Rodrguez EM, Mario B, Rodrguez-Dubra C, Esteban EN. Association of BLV infection profiles with alleles of theBoLA-DRB3.2gene. Anim Genet 2008; 39:432-8. [DOI: 10.1111/j.1365-2052.2008.01750.x] [Citation(s) in RCA: 83] [Impact Index Per Article: 5.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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37
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Behl JD, Verma NK, Behl R, Mukesh M, Ahlawat SPS. Characterization of genetic polymorphism of the bovine lymphocyte antigen DRB3.2 locus in Kankrej cattle (Bos indicus). J Dairy Sci 2007; 90:2997-3001. [PMID: 17517741 DOI: 10.3168/jds.2006-547] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Bovine lymphocyte antigen DRB 3.2 (BoLA-DRB3.2) gene encodes for the beta chain of the major histocompatibility complex (MHC) class II molecule in cattle, which is a glycoprotein present on the surface of antigen-presenting cells. This locus shows extensive polymorphism in it. The objective of the present study was to genotype the BoLA-DRB3.2 locus in Kankrej cattle (n = 50) by PCR-RFLP. Bovine DNA was isolated from aliquots of whole blood. Primers specific for exon 2 of the bovine lymphocyte antigen (BoLA)-DRB3 gene were used to amplify the region. The 304-bp amplified product of the DRB3 gene was separately digested with restriction endonucleases RsaI, BstYI, and Hae III. Twenty-four BoLA-DRB 3.2 alleles were identified with frequencies ranging from 1 to 22.0%. Twenty-one alleles of the total 24 alleles were similar to those reported earlier; 3 alleles were new and had not been reported previously. The allele BoLA-DRB3.2*34 occurred at the highest frequency of 22% (approx.) in the Kankrej animals studied. Six alleles (BoLA-DRB3.2 *34, *15, *06, *20, *37, and *20) accounted for almost 71% of the total alleles observed to be present in the Kankrej animals. All the new alleles observed were present at frequencies of 1%. The results obtained in the present study demonstrated that the BoLA DRB3.2 locus is highly polymorphic in the Kankrej cattle.
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Affiliation(s)
- J D Behl
- National Bureau of Animal Genetic Resources, P.O. Box No. 129, G.T. Bypass Road, Karnal, Haryana, India.
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38
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Morris CA. A review of genetic resistance to disease in Bos taurus cattle. Vet J 2006; 174:481-91. [PMID: 17095270 DOI: 10.1016/j.tvjl.2006.09.006] [Citation(s) in RCA: 36] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/08/2006] [Revised: 09/14/2006] [Accepted: 09/20/2006] [Indexed: 10/23/2022]
Abstract
Cattle show considerable variability in their responses to a wide range of disease challenges, and much of the variability is genetic. This review highlights genetic variation in disease susceptibility in Bos taurus cattle, with variation found at the breed level and also within breeds. Disease challenges come from bacteria and viruses, parasites and feed-borne toxins. For an animal to survive, it needs its own mechanisms for resisting these challenges, or for being resilient to them, or it must be protected artificially from them. Disease challenges have been classified as 'diseases from without', but there is also another class of genetic diseases resulting from inborn errors of metabolism, which might be called 'diseases from within'. Degrees of inheritance (heritabilities) are reviewed for a range of economically important traits including resistance to mastitis, ketosis, lameness, nematode parasites, external parasites, eye disease, respiratory disorders, tuberculosis, brucellosis, Johne's disease, foot-and-mouth disease, bovine spongiform encephalopathy, metabolic disorders caused by toxins found on the feed, and threshold levels of minerals and metabolites. Many, but not all, of the above require an immune response as part of the fight against an external challenge, and measurements have been made of general immune response as a way of describing or predicting how an animal will respond. There are now some examples of industry or breed societies applying selection for resistance to one or more diseases as part of a complete breeding objective in dairy cattle, beef cattle or dual purpose livestock. In most cases, industry and breed societies are in the early stages of applying effective selection pressure for resistance to specific cattle diseases, with the notable exceptions of Scandinavian cattle schemes, which lead the world in this respect.
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Affiliation(s)
- C A Morris
- AgResearch, Ruakura Research Centre, PB 3123, Hamilton 2001, New Zealand.
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