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Ilyas I, Nisa FU, Ali MB, Arshad F, Irfan N, Asif M, Amin I. Unveiling genetic variants: Tetra-primer ARMS-PCR diagnosis and structural insights into BLAD, BC, and DUMPS in Pakistani cattle herds. Mol Biol Rep 2024; 51:963. [PMID: 39235569 DOI: 10.1007/s11033-024-09898-4] [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: 06/13/2024] [Accepted: 08/27/2024] [Indexed: 09/06/2024]
Abstract
BACKGROUND Bovine leukocyte adhesion deficiency (BLAD), bovine citrullinemia (BC), and deficiency of Uridine monophosphate synthetase (DUMPS) are the common autosomal recessive disorders affecting the global dairy industry. BLAD leads to poor wound healing and recurrent infections. In BC, ammonia builds up leading to neurological disorders and death. DUMPS results in developmental abnormalities. METHODOLOGY In this study, tetra-primer amplification refractory mutation system polymerase chain reaction (ARMS PCR) based diagnostic tests were optimized for BLAD, BC, and DUMPS. A total of 250 animals (58 indigenous and 192 Holstein Friesian (HF)) were screened from all across Pakistan. In addition to validation of ARMS-PCR results through Sanger sequencing, the protein modeling provided structural insights of the disease-associated reported SNPs. Pathway analysis illustrated gene functions under normal and mutated conditions. Furthermore, haplotype and phylogenetic analysis of ASS1 (Argininosuccinate synthetase) gene were performed on study samples and NCBI retrieved sequences. RESULTS The study's focus was to screen the herds for prevalence of carriers of genetic disorders, as they are the main source of disease dissemination. One animal was found carrier for BC, whereas no carriers were found for BLAD and DUMPS. The protein models corroborated the reported amino acid change in BLAD, and protein truncation in both BC and DUMPS proteins. SNPs found in NCBI retrieved sequences were either silent or missense and had no effect on protein structure. DNA network presented graphical illustration of haplotype interactions and phylogenetic analysis conferred evolutionary landscape of ASS1 gene. The combination of these approaches produced an in-depth genetic picture of BC in Pakistani cattle. CONCLUSION The development of diagnostic tests and identification of the heterozygous BC sample underscores the significance of constant monitoring to avoid the unwanted dissemination of mutant alleles among Pakistani cattle, thereby promoting the general well-being and sustainability of the dairy sector.
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Affiliation(s)
- Iram Ilyas
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, 38000, Pakistan
| | - Fakhar Un Nisa
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, 38000, Pakistan
- Department of Animal Breeding and Genetics, University of Veterinary and Animal Sciences, Lahore, Pakistan
| | - Muhammad Basil Ali
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, 38000, Pakistan
- Senckenberg Biodiversity and Climate Research Institute (SBiK-F), Georg-Voigt-Strasse 14-16, 60325, Frankfurt am Main, Germany
| | - Fazeela Arshad
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, 38000, Pakistan
- The Roslin Institute, University of Edinburgh, Easter Bush campus, Edinburgh, Scotland
| | - Najida Irfan
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, 38000, Pakistan
| | - Muhammad Asif
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, 38000, Pakistan.
| | - Imran Amin
- Agricultural Biotechnology Division, National Institute for Biotechnology and Genetic Engineering (NIBGE), Constituent College of Pakistan Institute of Engineering and Applied Sciences, Jhang Road, Faisalabad, 38000, Pakistan
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Sudhakar A, Nayee N, Saha S, Donthula SK, Poojara HV, Gohil T, Patel AC, Maurya BK. Role of genetic introgression in introducing mutant alleles in Bos indicus cattle and prevalence of lethal genetic disorders in Bos taurus × Bos indicus and Bos indicus cattle in India. Trop Anim Health Prod 2023; 55:399. [PMID: 37940810 DOI: 10.1007/s11250-023-03798-8] [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: 07/09/2022] [Accepted: 10/17/2023] [Indexed: 11/10/2023]
Abstract
Fertility is an important trait associated with reproductive performance and animal welfare concern. Lethal alleles affect fertility through early embryonic death, abortions, and stillbirth depending on the genetic expression of the allele. Holstein Friesian and Jersey are two major Bos taurus breeds used widely for increasing milk yield along with purebreds of Bos indicus breeds like Gir, Kankrej, Sahiwal, and Tharparkar. In the present study, prevalence of lethal mutants in crossbred Holstein Friesian (CBHF, n = 2435), crossbred Jersey (CBJY, n = 2874), Gir (n = 3288), Kankrej (n = 593), Sahiwal (n = 965), and Tharparkar (n = 18) were studied. Heterozygous carrier animals were identified for bovine leukocyte adhesion deficiency (BLAD), Citrullinemia, complex vertebral malformation (CVM), Brachyspina, Holstein Haplotype 1 (HH1), Holstein Haplotype 3 (HH3),Holstein Haplotype 4 (HH4) and Jersey Haplotype 1 (JH1). Breed purity analysis confirmed inheritance of Bos taurus genes contributing to the presence of lethal mutant alleles like BLAD, Citrullinemia, HH1, and JH1 in apparently phenotypic Bos indicus animals. Screening and elimination of heterozygous carrier bulls/cows is essential to control fertility loss associated with lethal alleles.
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Affiliation(s)
- A Sudhakar
- National Dairy Development Board (NDDB), Anand, 388001, Gujarat, India.
| | - Nilesh Nayee
- National Dairy Development Board (NDDB), Anand, 388001, Gujarat, India
| | - Sujit Saha
- National Dairy Development Board (NDDB), Anand, 388001, Gujarat, India
| | | | - Hardik V Poojara
- National Dairy Development Board (NDDB), Anand, 388001, Gujarat, India
| | - Tejas Gohil
- Sabarmati Ashram Gaushala ( Genomics lab), Anand, 388001, Gujarat, India
| | - Aashish C Patel
- College of Veterinary Science and Animal Husbandry, KU, Anand, 388001, Gujarat, India
| | - Brijesh K Maurya
- National Dairy Development Board (NDDB), Anand, 388001, Gujarat, India
- NDDB CALF Ltd., Anand, 388001, Gujarat, India
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Alyethodi RR, Singh U, Kumar S, Deb R, Alex R, Sharma S, Sengar GS, Prakash B. Development of a fast and economical genotyping protocol for bovine leukocyte adhesion deficiency (BLAD) in cattle. SPRINGERPLUS 2016; 5:1442. [PMID: 27652018 PMCID: PMC5005226 DOI: 10.1186/s40064-016-3148-7] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 06/06/2016] [Accepted: 08/24/2016] [Indexed: 11/26/2022]
Abstract
Fast and economical means of assaying SNP's are important in diagnostic assays, especially when a large number of animals have to be screened for a genetic disease. This study was aimed at the development of a fast and economical screening assay for bovine leukocyte adhesion deficiency (BLAD) which is an important genetic disease of cattle industry. Four primers were designed where the outer primers amplify a 354 bp amplicon of CD18 gene carrying the polymorphism responsible for BLAD. The specifically designed inner primers in conjunction with the modified reaction mixture and cyclic conditions ensured amplification of either of wild or mutated alleles. Together with outer primers, the inner primers generated typical banding pattern in agarose gel which discriminated the normal animal against the carrier. We successfully used this protocol in 200 bulls for genotyping the BLAD allele which confirmed by sequencing, showing a cent percentage concordance. With the developed assay the need for restriction digestion or use of costly equipment viz. real time PCR was eliminated. This genotyping assay ensured fast and economical genotyping and could be adopted in every laboratory with a minimum equipment requirement of thermocycler and gel documentation system.
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Affiliation(s)
- Rafeeque R. Alyethodi
- ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut Cantt, Meerut, UP 250001 India
| | - Umesh Singh
- ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut Cantt, Meerut, UP 250001 India
| | - Sushil Kumar
- ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut Cantt, Meerut, UP 250001 India
| | - Rajib Deb
- ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut Cantt, Meerut, UP 250001 India
| | - Rani Alex
- ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut Cantt, Meerut, UP 250001 India
| | - Sheetal Sharma
- ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut Cantt, Meerut, UP 250001 India
| | - Gyanendra S. Sengar
- ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut Cantt, Meerut, UP 250001 India
| | - B. Prakash
- ICAR-Central Institute for Research on Cattle, Grass Farm Road, Meerut Cantt, Meerut, UP 250001 India
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Khade AS, Doiphode AY, Umrikar UD, Sawane MP, Pawar VD. Genotyping of the Holstein-Friesian crossbred cattle for CD18 gene using PCR-RFLP. Vet World 2014. [DOI: 10.14202/vetworld.2014.360-362] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/16/2022] Open
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Şahin E, Karslı T, Galiç A, Balcıoğlu MS. Identification of bovine leukocyte adhesion deficiency (BLAD) and bovine citrullinaemia (BC) alleles in Holstein cows reared in Antalya region. JOURNAL OF APPLIED ANIMAL RESEARCH 2013. [DOI: 10.1080/09712119.2012.738221] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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Sharma D, Kumar S, Deb SM, Mitra A, Niranjan SK, Naskar S, Sharma A. Identification of novel allelic variants of integrin beta 2 (ITGB2) gene and screening for Bubaline leukocyte adhesion deficiency syndrome in Indian water buffaloes (Bubalus bubalis). Anim Biotechnol 2009; 20:156-60. [PMID: 19544212 DOI: 10.1080/10495390902895883] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/20/2022]
Abstract
A fragment of 570 bp corresponding to exon 5 and 6 of integrin beta 2 (ITGB2) gene was amplified for screening D128G mutation in one hundred and fifty two buffaloes (Bubalus bubalis) which causes bovine leukocyte adhesion deficiency syndrome (BLAD) in cattle, as well as to ascertain polymorphism. TaqI PCR-RFLP revealed no such mutation thus indicating the absence of bubaline leukocyte adhesion deficiency (BuLAD) allele in animals under study. However, the polymorphism studies using MspI restriction enzyme revealed two genotypic patterns viz. AA pattern (bands of 293, 141, 105, and 31 bp) and BB pattern (bands of 293, 105, 77, 64, and 31 bp). The sequences of A and B alleles were submitted to the GenBank (EU853307 and AY821799).
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Affiliation(s)
- Deepak Sharma
- Animal Genetics Division, Indian Veterinary Research Institute, Indian Council of Agricultural Research, Izatnagar, Bareilly (UP), India
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Nasreen F, Altaf Malik N, Naeem Riaz M, Anver Qureshi J. Detection and screening of bovine leukocyte adhesion deficiency in Pakistan using molecular methods. Hereditas 2009; 146:74-8. [DOI: 10.1111/j.1601-5223.2009.02093.x] [Citation(s) in RCA: 9] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/28/2022] Open
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Schütz E, Scharfenstein M, Brenig B. Implication of complex vertebral malformation and bovine leukocyte adhesion deficiency DNA-based testing on disease frequency in the Holstein population. J Dairy Sci 2009; 91:4854-9. [PMID: 19038961 DOI: 10.3168/jds.2008-1154] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/19/2022]
Abstract
Two inherited lethal disorders, bovine leukocyte adhesion deficiency (BLAD) and complex vertebral malformation (CVM), play a major role in breeding of Holstein cattle. Both inherited diseases are based on single nucleotide polymorphisms that have been known for 12 and 7 yr, respectively. A total of 25,753 cattle were genotyped for BLAD (18,200 tests) and CVM (14,493 tests) in our laboratory since the beginning of the genotyping programs for these diseases. Based on founder effects, the CVM mutation is thought to be linked to milk production. The BLAD was genotyped using RFLP until 2001; then a fluorescence resonance energy transfer assay on a LightCycler was used, as for CVM genotyping. By using single nucleotide polymorphism-aided breeding, the allelic frequency of the BLAD and CVM mutations in the active sire population was reduced from 9.4% in 1997 to 0.3% in 2007 (BLAD) and from 8.3% in 2002 to 2.3% in 2007 (CVM), with calculated half-life of the mutant allele of 2.1 yr for BLAD and 3.6 yr for CVM. An observed increase of BLAD frequency in 1999 could be attributed to the massive use of a BLAD-positive sire tested falsely negative in another laboratory. These data show that marker-assisted selection is capable of substantially reducing the frequency of a mutation within a period of not more than 5 yr. The different selection strategies against the lethal recessive allele in CVM and BLAD are reflected in the different reduction rates of the specific allele frequencies.
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Affiliation(s)
- E Schütz
- Institute of Veterinary Medicine, Georg-August-University of Göttingen, Burckhardtweg 2, 37077 Göttingen, Germany
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Patel RK, Soni KJ, Chauhan JB, Singh KM, Sambasiva Rao KR. Factor XI deficiency in Indian Bos taurus, Bos indicus, Bos taurus x Bos indicus crossbreds and Bubalus bubalis. Genet Mol Biol 2007. [DOI: 10.1590/s1415-47572007000400013] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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