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Galdino Andrade TE, Scavassini Peña M, Fiorotti J, de Souza Bin R, Rodrigues Caetano A, Connelley T, Ferreira de Miranda Santos IK. Graduate Student Literature Review: The DRB3 gene of the bovine major histocompatibility complex-Discovery, diversity, and distribution of alleles in commercial breeds of cattle and applications for development of vaccines. J Dairy Sci 2024; 107:11324-11341. [PMID: 39004123 DOI: 10.3168/jds.2023-24628] [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] [Received: 12/28/2023] [Accepted: 06/14/2024] [Indexed: 07/16/2024]
Abstract
The bovine major histocompatibility complex (MHC), also known as the bovine leukocyte antigen (BoLA) complex, is the genomic region that encodes the most important molecules for antigen presentation to initiate immune responses. The first evidence of MHC in bovines pointed to a locus containing 2 antigens, one detected by cytotoxic antiserum (MHC class I) and another studied by mixed lymphocyte culture tests (MHC class II). The most studied gene in the BoLA region is the highly polymorphic BoLA-DRB3, which encodes a β chain with a peptide groove domain involved in antigen presentation for T cells that will develop and co-stimulate cellular and humoral effector responses. The BoLA-DRB3 alleles have been associated with outcomes in infectious diseases such as mastitis, trypanosomiasis, and tick loads, and with production traits. To catalog these alleles, 2 nomenclature methods were proposed, and the current use of both systems makes it difficult to list, comprehend and apply these data effectively. In this review we have organized the knowledge available in all of the reports on the frequencies of BoLA-DRB3 alleles. It covers information from studies made in at least 26 countries on more than 30 breeds; studies are lacking in countries that are important producers of cattle livestock. We highlight practical applications of BoLA studies for identification of markers associated with resistance to infectious and parasitic diseases, increased production traits and T cell epitope mapping, in addition to genetic diversity and conservation studies of commercial and Creole and locally adapted breeds. Finally, we provide support for the need of studies to discover new BoLA alleles and uncover unknown roles of this locus in production traits.
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Affiliation(s)
| | - Maurício Scavassini Peña
- Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, SP, Brazil, 14049-900
| | - Jéssica Fiorotti
- Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, SP, Brazil, 14049-900
| | - Renan de Souza Bin
- Ribeirão Preto School of Medicine, University of São Paulo, Ribeirão Preto, SP, Brazil, 14049-900
| | | | - Timothy Connelley
- The Roslin Institute, Royal (Dick) School of Veterinary Studies, University of Edinburgh, Midlothian, United Kingdom, EH25 9RG
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Suprovych TM, Salyha YT, Suprovych MP, Fedorovych EI, Fedorovych VV, Chornyj IO. Genetic Polymorphism of BoLA-DRB3.2 Locus in Ukrainian Cattle Breeds. CYTOL GENET+ 2022. [DOI: 10.3103/s0095452722040089] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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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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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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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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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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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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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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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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Moazemi I, Mohammadabadi MR, Mostafavi A, Esmailizadeh AK, Babenko OI, Bushtruk MV, Tkachenko SV, Stavetska RV, Klopenko NI. Polymorphism of DMRT3 Gene and Its Association with Body Measurements in Horse Breeds. RUSS J GENET+ 2020. [DOI: 10.1134/s1022795420100087] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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Svishcheva G, Babayan O, Lkhasaranov B, Tsendsuren A, Abdurasulov A, Stolpovsky Y. Microsatellite Diversity and Phylogenetic Relationships among East Eurasian Bos taurus Breeds with an Emphasis on Rare and Ancient Local Cattle. Animals (Basel) 2020; 10:E1493. [PMID: 32846979 PMCID: PMC7552156 DOI: 10.3390/ani10091493] [Citation(s) in RCA: 9] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/01/2020] [Revised: 08/10/2020] [Accepted: 08/19/2020] [Indexed: 12/03/2022] Open
Abstract
We report the genetic analysis of 18 population samples of animals, which were taken from cattle (Bos taurus) breeds of European and Asian origins. The main strength of our study is the use of rare and ancient native cattle breeds: the Altai, Ukrainian Grey, Tagil, and Buryat ones. The cattle samples studied have different production purposes, belong to various eco-geographic regions, and consequently have distinct farming conditions. In order to clarify the genetic diversity, phylogenetic relationships and historical origin of the studied breeds, we carried out an analysis of the genetic variation of 14 high-variability microsatellite loci at 1168 genotyped animals. High levels of heterozygosity and allelic richness were identified in four of the ancient local breeds, namely the Kalmyk, Tagil, Kyrgyz native, and Buryat breeds. The greatest phylogenetic distances from a common ancestor were observed for the Yakut and Ukrainian Grey breeds, while the Tagil breed showed the smallest difference. By using clustering approaches, we found that the Altai cattle is genetically close to the Kyrgyz one. Moreover, both the Altai and Kyrgyz breeds exposed genetic divergences from other representatives of the Turano-Mongolian type and genetic relationships with the Brown Swiss and Kostroma breeds. This phenomenon can be explained by the extensive use of the Brown Swiss and Kostroma breeds in the breeding and improvement processes for the Kyrgyz breeds, which have been involved in the process of keeping the Altai cattle. Our results can be valuable for conservation and management purposes.
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Affiliation(s)
- Gulnara Svishcheva
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
- Institute of Cytology and Genetics, Siberian Branch of the Russian Academy of Sciences, 630090 Novosibirsk, Russia
| | - Olga Babayan
- Gordiz Ltd., Skolkovo Innovation Centre, 121205 Moscow, Russia
| | | | - Ariuntuul Tsendsuren
- Institute of General and Experimental Biology, The Mongolian Academy of Sciences, Ulaanbaatar 210351, Mongolia
| | - Abdugani Abdurasulov
- Department of Agriculture, Faculty of Natural Sciences and Geography, Osh State University, 723500 Osh, Kyrgyzstan
| | - Yurii Stolpovsky
- Vavilov Institute of General Genetics, Russian Academy of Sciences, 119333 Moscow, Russia
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Intrabreed and interbreed variation of the BOLA-DRB3.2 gene in the Kostroma and Yaroslavl indigenous Russian cattle breeds. Immunogenetics 2020; 72:355-366. [DOI: 10.1007/s00251-020-01173-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2020] [Accepted: 06/30/2020] [Indexed: 10/23/2022]
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Hao D, Thomsen B, Bai J, Peng S, Lan X, Huang Y, Wang X, Chen H. Expression profiles of the MXD3 gene and association of sequence variants with growth traits in Xianan and Qinchuan cattle. Vet Med Sci 2020; 6:399-409. [PMID: 32141244 PMCID: PMC7397896 DOI: 10.1002/vms3.251] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/18/2019] [Revised: 01/07/2020] [Accepted: 01/24/2020] [Indexed: 01/17/2023] Open
Abstract
Max dimerization protein 3 (MXD3) belongs to the MYC superfamily of basic helix‐loop‐helix leucine zipper transcription factors, and MXD3‐MAX heterodimers can bind to promoters of target genes to modulate their expression. The aim of this study was to determine the MXD3 mRNA expression levels in various cattle tissues comprising heart, liver, spleen, lung, kidney, Longissimus dorsi muscle and subcutaneous fat in Chinese Qinchuan and Xianan cattle breeds. The RT‐qPCR data showed that the MXD3 gene was variably expressed between all tissues and at levels that were significantly different between two breeds (p < .05). We used the polymerase chain reaction‐restriction fragment length polymorphism (PCR‐RFLP) method to investigate the possible association between single‐nucleotide polymorphisms (SNP) within the MXD3 gene and five different growth traits in cattle. We found two intronic SNPs (g.2694 C>T and g.3801 T>C) and one SNP in 3′untranslated region (3′UTR) (g.6263 G>A) of MXD3 gene. Association analysis revealed strong associations between pairwise and triple SNP combinations and the growth traits. Based on these results, we suggest that MXD3 polymorphisms could be useful as molecular markers in the Chinese beef cattle breeding program.
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Affiliation(s)
- Dan Hao
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, Yangling, Shaanxi, China.,Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Bo Thomsen
- Department of Molecular Biology and Genetics, Aarhus University, Aarhus C, Denmark
| | - Jiangsong Bai
- College of Veterinary Medicine, China Agricultural University, Beijing, China.,Beijing Zhongnongtongchuang (ZNTC) Biotechnology Co., Ltd, Beijing, China
| | - Shujun Peng
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, Yangling, Shaanxi, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, Yangling, Shaanxi, China
| | - Yongzhen Huang
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, Yangling, Shaanxi, China
| | - Xiao Wang
- Department of Applied Mathematics and Computer Science, Technical University of Denmark, Kongens Lyngby, Denmark
| | - Hong Chen
- College of Animal Science and Technology, Northwest A&F University, Shaanxi Key Laboratory of Animal Genetics, Breeding and Reproduction, Yangling, Shaanxi, China
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Silpa M, Naicy T, Aravindakshan T, Radhika G, Venkatachalapathy R, Kurian E. Sirtuin3 gene tissue expression profiling, SNP detection and its association with body conformation traits in goats. Small Rumin Res 2020. [DOI: 10.1016/j.smallrumres.2019.11.003] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
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18
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Wang K, Kang Z, Jiang E, Yan H, Zhu H, Liu J, Qu L, Lan X, Pan C. Genetic effects of DSCAML1 identified in genome-wide association study revealing strong associations with litter size and semen quality in goat (Capra hircus). Theriogenology 2020; 146:20-25. [PMID: 32036056 DOI: 10.1016/j.theriogenology.2020.01.079] [Citation(s) in RCA: 47] [Impact Index Per Article: 11.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/16/2019] [Revised: 01/30/2020] [Accepted: 01/30/2020] [Indexed: 01/31/2023]
Abstract
The down syndrome cell adhesion molecule like 1 (DSCAML1), is associated with the development of the nervous system and neurologic diseases. Previous Genome-wide association studies have shown that it is associated with sperm morphology, suggesting it has a critical role in fecundity. In this study, expression profiles of goat DSCAML1 mRNA were analyzed. The results showed that its expression in the testis differ significantly between the mitotic stage and meiotic stage. Three insertion/deletion (indel) variants of goat DSCAML1 were determined in the Shaanbei White Cashmere Goat (SWCG, n = 2162). Based on the association analysis, two indels (P2-16bp, P14-15bp) were significantly related to sperm quality (sperm motility and sperm density) in male goat and three loci were markedly related to the first-birth litter size in female goat (P = 4.0 × 10-6; P = 1.0 × 10-6; P = 4.7 × 10-2). In male goats, the different genotypes of P2-16bp and P14-15bp revealed a noticeable effect on the expression of DSCAML1. Moreover, the effects observed in the first-birth litter followed a similar trend, which may provide the basis for further research of DSCAML1 gene function and marker assisted selection (MAS) programs to improve reproductive traits.
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Affiliation(s)
- Ke Wang
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, Ministry of Agriculture, No. 22 Xinong Road, Yangling, Shaanxi, 712100, China.
| | - Zihong Kang
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, Ministry of Agriculture, No. 22 Xinong Road, Yangling, Shaanxi, 712100, China.
| | - Enhui Jiang
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, Ministry of Agriculture, No. 22 Xinong Road, Yangling, Shaanxi, 712100, China.
| | - Hailong Yan
- Department of Neurology, Institute of Brain Science, Medical School, Shanxi Datong University, Datong, 037000, China
| | - Haijing Zhu
- Life Science Research Center, Yulin University, Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin, 719000, China
| | - Jinwang Liu
- Life Science Research Center, Yulin University, Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin, 719000, China
| | - Lei Qu
- Life Science Research Center, Yulin University, Shaanxi Provincial Engineering and Technology Research Center of Cashmere Goats, Yulin, 719000, China
| | - Xianyong Lan
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, Ministry of Agriculture, No. 22 Xinong Road, Yangling, Shaanxi, 712100, China
| | - Chuanying Pan
- College of Animal Science and Technology, Northwest A&F University, Key Laboratory of Animal Genetics, Breeding and Reproduction of Shaanxi Province, Key Laboratory of Animal Biotechnology, Ministry of Agriculture, No. 22 Xinong Road, Yangling, Shaanxi, 712100, China.
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Al-Shuhaib MBS, Al-Kafajy FR, Al-Jashami GS. A computational approach for explaining the effect of the prl gene polymorphism on prolactin structure and biological activity in Japanese quails. Anim Biotechnol 2019; 32:273-281. [PMID: 31661660 DOI: 10.1080/10495398.2019.1683568] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
Abstract
Prolactin is a versatile hormone with multiple activities, including a negative control on egg production. This study was conducted to genotype all the coding portions of the prl gene using PCR-SSCP-sequencing, and to investigate the effects of amino acid substitutions of the prl gene on the structure and function of prolactin in quails using in silico approach. Though all genotyped exons exerted homogenous PCR-SSCP patterns, a total of 12 novel SNPs were detected in the investigated exons, including three SNPs in exon-1, 8 SNPs in exon-2, and one SNP in exon-4. Three adjacent missense SNPs were detected in exon-2, namely H69P, T70P, and S71F. Computational tools indicated obvious deleterious effects of T70P, with less extent to H69P and S71F on prolactin functions and activity, which may lead to limited participation of this hormone in the negative control of egg production. In conclusion, the introduction of in silico prediction has suggested an alternative solution for the breeders to evaluate the effect of each witnessed nsSNP in protein structure and function. The current study suggests three nsSNPs, T70P, T70P, and S71F as strong candidates for the negative effect on prolactin biological activity with a consequent reversal positive effect on egg productivity traits.
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Affiliation(s)
| | - Fadhil R Al-Kafajy
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, Iraq
| | - Ghadeer S Al-Jashami
- Department of Animal Production, College of Agriculture, Al-Qasim Green University, Al-Qasim, Babil, Iraq
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Mostafavi A, Fozi MA, Koshkooieh AE, Mohammadabadi M, Babenko OI, Klopenko NI. Effect of LCORL gene polymorphism on body size traits in horse populations. ACTA SCIENTIARUM: ANIMAL SCIENCES 2019. [DOI: 10.4025/actascianimsci.v42i1.47483] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
Abstract
The aim of this study was to determine polymorphism of LCORL gene in horse breeds and its association with body size. PCR-RFLP technique was performed using AluI for genotyping of 306 horses. Results showed that C is the rare allele in Iranian Breeds, because these horses have been used since ancient times as a courier and for war and archery, hence selection has done to benefit of spiky horses with medium body that need less food and are tireless. While, for foreign breeds; frequency of C allele was high that can be concluded these breeds used in fields, forests, and mines. A UPGMA dendrogram based on the Nei's standard genetic distance among studied breeds showed separate clusters for Iranian native and exotic breeds. Statistical association analysis of three observed genotypes with body size showed that there is an association between this polymorphism and body size criteria (p < 0.01). Overall, it can be concluded that studied mutation in LCORL gene can be used as candidate marker for improving body weight in horse.
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Bosewell A, Naicy T, Aravindakshan T, Kurian E. Sequence characterization, structural analysis, SNP detection and expression profiling of SLC11A1 gene in Indian goats. Small Rumin Res 2018. [DOI: 10.1016/j.smallrumres.2018.04.012] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/15/2022]
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22
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Naicy T, Venkatachalapathy T, Aravindakshan T, Bosewell A, Silpa M. Association of a SacII polymorphism in the Nerve Growth Factor (NGF) gene exon 3 with growth traits in Indian goats. Small Rumin Res 2018. [DOI: 10.1016/j.smallrumres.2017.11.009] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/18/2022]
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qPCR and HRM-based diagnosis of SNPs on growth differentiation factor 9 (GDF9), a gene associated with sheep (Ovis aries) prolificacy. 3 Biotech 2017; 7:204. [PMID: 28667646 DOI: 10.1007/s13205-017-0837-z] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/15/2017] [Accepted: 05/26/2017] [Indexed: 10/19/2022] Open
Abstract
Prolificacy is a desirable trait for genetic improvement of sheep flocks, since it holds the potential to improve productivity. Animals carrying single-nucleotide polymorphisms (SNPs) in genes associated with this trait can be identified and employed to increase prolificacy in flocks. In this study, we report a diagnostic method based on quantitative PCR and high-resolution melting curves to detect different SNPs in the prolificacy-associated gene growth differentiation factor 9 (GDF9). The diagnostic method was validated using artificial sequences representing known SNPs in GDF9, then applied to a real flock comprising four breeds and admixed animals (n = 306). Five different SNPs were identified in this flock, as was a low or null frequency of occurrence of SNPs positively associated with prolificacy. This indicates a need to implement a breeding strategy for recovering or reintroducing such SNPs. Our method provides a genotyping strategy for identifying individuals with SNPs of interest for prolificacy, which will help producers plan a breeding strategy for this trait. This method can be adapted and expanded for the diagnosis of other traits of interest.
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Macneil MD, Alexander LJ, Kantanen J, Ammosov IA, Ivanova ZI, Popov RG, Ozerov M, Millbrooke A, Cronin MA. Potential emigration of Siberian cattle germplasm on Chirikof Island, Alaska. J Genet 2017; 96:47-51. [PMID: 28360389 DOI: 10.1007/s12041-016-0739-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
Abstract
Feral cattle residing in Chirikof Island, Alaska, are relatively distinct from breeds used in commercial production in North America. However, preliminary evidence suggested that they exhibit substantial genetic relationship with cattle from Yakutian region of Siberia. Thus, our objective was to further elucidate quantify the origins, admixture and divergence of the Chirikof Island cattle relative to cattle from Siberia and USA. Subject animals were genotyped at 15 microsatellite loci. Compared with Turano-Mongolian and North American cattle, Chirikof Island cattle had similar variation, with slightly less observed heterozygosity, fewer alleles per locus and a positive fixation index. Analysis of the genetic distances revealed two primary clusters; one that contained the North American breeds and the Kazakh White head, and a second that contained the Yakutian and Kalmyk breeds, and the Chirikof population. Thus, it is suggested that Chirikof Island cattle may be a composite of British breeds emanating from North America and Turano-Mongolian cattle. A potential founder effect, consistent with historical records of the Russian-American period, may contribute to the adaptation of the Chirikof Island cattle to their harsh high-latitude environment. Further study of adaptive mechanisms manifest by these cattle is warranted.
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Affiliation(s)
- M D Macneil
- Delta G, 145 Ice Cave Rd, Miles City, MT 59301, USA.
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25
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Shamsalddini S, Mohammadabadi MR, Esmailizadeh AK. Polymorphism of the prolactin gene and its effect on fiber traits in goat. RUSS J GENET+ 2016. [DOI: 10.1134/s1022795416040098] [Citation(s) in RCA: 20] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
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26
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Das DN, Sri Hari VG, Hatkar DN, Rengarajan K, Saravanan R, Suryanarayana VVS, Murthy LK. Genetic diversity and population genetic analysis of bovine MHC class II DRB3.2 locus in three Bos indicus cattle breeds of Southern India. Int J Immunogenet 2012; 39:508-19. [PMID: 22607523 DOI: 10.1111/j.1744-313x.2012.01126.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
The present study was performed to evaluate the genetic polymorphism of BoLA-DRB3.2 locus in Malnad Gidda, Hallikar and Ongole South Indian Bos indicus cattle breeds, employing the PCR-RFLP technique. In Malnad Gidda population, 37 BoLA-DRB3.2 alleles were detected, including one novel allele DRB3*2503 (GenBank: HM031389) that was observed in the frequency of 1.87%. In Hallikar and Ongole populations, 29 and 21 BoLA-DRB3.2 alleles were identified, respectively. The frequencies of the most common BoLA-DRB3.2 alleles (with allele frequency > 5%), in Malnad Gidda population, were DRB3.2*15 (10.30%), DRB3*5702 (9.35%), DRB3.2*16 (8.41%), DRB3.2*23 (7.01%) and DRB3.2*09 (5.61%). In Hallikar population, the most common alleles were DRB3.2*11 (13.00%), DRB3.2*44 (11.60%), DRB3.2*31 (10.30%), DRB3.2*28 (5.48%) and DRB3.2*51 (5.48%). The most common alleles in Ongole population were DRB3.2*15 (22.50%), DRB3.2*06 (20.00%), DRB3.2*13 (13.30%), DRB3.2*12 (9.17%) and DRB3.2*23 (7.50%). A high degree of heterozygosity observed in Malnad Gidda (H(O) = 0.934, H(E) = 0.955), Hallikar (H(O) = 0.931, H(E) = 0.943) and Ongole (H(O) = 0.800, H(E) = 0.878) populations, along with F(IS) values close to F(IS) zero (Malnad Gidda: F(IS) = 0.0221, Hallikar: F(IS) = 0.0127 and Ongole: F(IS) = 0.0903), yielded nonsignificant P-values with respect to Hardy-Weinberg equilibrium probabilities revealing, no perceptible inbreeding, greater genetic diversity and characteristic population structure being preserved in the three studied cattle populations. The phylogenetic tree constructed based on the frequencies of BoLA-DRB3.2 alleles observed in 10 Bos indicus and Bos taurus cattle breeds revealed distinct clustering of specific Bos indicus cattle breeds, along with unique genetic differentiation observed among them. The results of this study demonstrated that the BoLA-DRB3.2 is a highly polymorphic locus, with significant breed-specific genetic diversities being present amongst the three studied cattle breeds. The population genetics and phylogenetic analysis have revealed pivotal information about the population structure and importance of the presently studied three Bos indicus cattle breeds as unique animal genetic resources, which have to be conserved for maintaining native cattle genetic diversity.
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Affiliation(s)
- D N Das
- Department of Animal Genetics and Breeding, National Dairy Research Institute, Southern Regional Station, Adugodi, Bangalore, India
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