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Khan MYA, Dai D, Su X, Tian J, Zhou J, Ma L, Wang Y, Wen W, Zhang Y. Multiplex fluorescent amplification-refractory mutation system PCR method for the detection of 10 genetic defects in Holstein cattle and its comparison with the KASP genotyping assay. Anim Genet 2024; 55:457-464. [PMID: 38622758 DOI: 10.1111/age.13432] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2023] [Revised: 02/27/2024] [Accepted: 04/05/2024] [Indexed: 04/17/2024]
Abstract
The common deleterious genetic defects in Holstein cattle include haplotypes 1-6 (HH1-HH6), haplotypes for cholesterol deficiency (HCD), bovine leukocyte adhesion deficiency (BLAD), complex vertebral malformation (CVM) and brachyspina syndrome (BS). Recessive inheritance patterns of these genetic defects permit the carriers to function normally, but homozygous recessive genotypes cause embryo loss or neonatal death. Therefore, rapid detection of the carriers is essential to manage these genetic defects. This study was conducted to develop a single-tube multiplex fluorescent amplification-refractory mutation system (mf-ARMS) PCR method for efficient genotyping of these 10 genetic defects and to compare its efficiency with the kompetitive allele specific PCR (KASP) genotyping assay. The mf-ARMS PCR method introduced 10 sets of tri-primers optimized with additional mismatches in the 3' end of wild and mutant-specific primers, size differentiation between wild and mutant-specific primers, fluorescent labeling of universal primers, adjustment of annealing temperatures and optimization of primer concentrations. The genotyping of 484 Holstein cows resulted in 16.12% carriers with at least one genetic defect, while no homozygous recessive genotype was detected. This study found carrier frequencies ranging from 0.0% (HH6) to 3.72% (HH3) for individual defects. The mf-ARMS PCR method demonstrated improved detection, time and cost efficiency compared with the KASP method for these defects. Therefore, the application of mf-ARMS PCR for genotyping Holstein cattle is anticipated to decrease the frequency of lethal alleles and limit the transmission of these genetic defects.
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Affiliation(s)
- Md Yousuf Ali Khan
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
- Bangladesh Livestock Research Institute, Dhaka, Bangladesh
| | - Dongmei Dai
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Xin Su
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Jia Tian
- Laboratory of Dairy Herd Improvement, NingXia Animal Husbandry Station, Yinchuan, China
| | - Jiamin Zhou
- Laboratory of Dairy Herd Improvement, NingXia Animal Husbandry Station, Yinchuan, China
| | - Liqin Ma
- Laboratory of Dairy Herd Improvement, NingXia Animal Husbandry Station, Yinchuan, China
| | - Yachun Wang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wan Wen
- Laboratory of Dairy Herd Improvement, NingXia Animal Husbandry Station, Yinchuan, China
| | - Yi Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Surati U, Niranjan SK. Development of PCR-based genetic test for detection of TTF1 mutation causing abortion in Holstein Friesian cattle. Reprod Domest Anim 2024; 59:e14581. [PMID: 38698693 DOI: 10.1111/rda.14581] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/30/2024] [Revised: 03/18/2024] [Accepted: 04/20/2024] [Indexed: 05/05/2024]
Abstract
A stop-gain mutation (rs715966442; BTA11: 1,02,463,944 nucleotide position) in transcription termination factor, RNA polymerase I (TTF1) gene causes abortion in Holstein Friesian (HF) cattle. A PCR-restriction fragment length polymorphism (PCR-RFLP)-based genetic test has been developed and validated to screen the TTF1 mutation locus in HF cattle. The mutation locus was screened in 80 HF and HF crossbreds using the protocol, which revealed two animals as carriers of the mutant TTF1 allele. The test employed is cost-effective, rapid and precise and can be utilized as an effective tool for the screening of TTF1 mutation carriers in HF cattle population.
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Affiliation(s)
- Utsav Surati
- ICAR-National Bureau of Animal Genetic Resources, Karnal, Haryana, India
- ICAR-National Dairy Research Institute, Karnal, Haryana, India
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Shormanova M, Makhmutov A, Shormanova A, Muslimova Z, Ussenbekov Y. Development of alternative diagnosis of HH1, HH3, HH5 and HCD fertility haplotypes and subfertility syndrome in cattle. Reprod Domest Anim 2024; 59:e14533. [PMID: 38268216 DOI: 10.1111/rda.14533] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/20/2023] [Revised: 12/13/2023] [Accepted: 01/03/2024] [Indexed: 01/26/2024]
Abstract
The increasing prevalence of hereditary anomalies in Holstein cattle populations presents a pressing issue, leading to concerns such as embryonic mortality and the birth of non-viable offspring. This study addresses the urgency of managing harmful genetic mutations in Holstein cattle by developing alternative diagnostic methods. The research aims to devise effective means to diagnose fertility haplotypes HH1, HH3, HH5, HCD and BY and subfertility syndrome in cattle. To achieve this goal, a range of molecular genetic techniques were employed, including Tetra-Primer ARMS-PCR methods, PCR-RFLP analysis and allele-specific PCR. These methods facilitated the identification of heterozygous carriers of various fertility haplotypes and subfertility syndrome in Holstein cows and servicing bulls. The study reveals the prevalence of these genetic defects within the Republic of Kazakhstan's cattle population. HH1, HH3, HH5, HCD and BY fertility haplotypes were found to have occurrence rates ranging from 1.4% to 16.6%, with subfertility syndrome detected in 4.5% of Simmental bulls. The practical significance of this research lies in its contribution to genetic monitoring and management strategies for Holstein cattle populations. By introducing affordable, rapid and accurate diagnostic methods, such as the T-ARMS-PCR, the study provides a valuable tool for controlling and mitigating the spread of harmful genetic mutations, ultimately improving the overall genetic health and productivity of Holstein cattle in the region. This research addresses a critical need in the cattle breeding industry and underscores the importance of genetic monitoring to ensure the long-term viability and sustainability of Holstein cattle populations.
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Affiliation(s)
- Marzhan Shormanova
- Department of Obstetrics, Surgery and Biotechnology of Animal Reproduction, Kazakh National Agrarian Research University, Almaty, Republic of Kazakhstan
| | - Abzal Makhmutov
- Department of Obstetrics, Surgery and Biotechnology of Animal Reproduction, Kazakh National Agrarian Research University, Almaty, Republic of Kazakhstan
| | - Aizhamal Shormanova
- Institute of Botany and Phytointroduction, Kazakh National Agrarian Research University, Almaty, Republic of Kazakhstan
| | - Zhadyra Muslimova
- Department of Obstetrics, Surgery and Biotechnology of Animal Reproduction, Kazakh National Agrarian Research University, Almaty, Republic of Kazakhstan
| | - Yessengali Ussenbekov
- Department of Obstetrics, Surgery and Biotechnology of Animal Reproduction, Kazakh National Agrarian Research University, Almaty, Republic of Kazakhstan
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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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Albertino LG, Albuquerque ALH, Ferreira JF, Oliveira JPM, Borges AS, Patelli THC, Oliveira-Filho JP. Allele Frequency of APAF1 Mutation in Holstein Cattle in Brazil. Front Vet Sci 2022; 9:822224. [PMID: 35280144 PMCID: PMC8904897 DOI: 10.3389/fvets.2022.822224] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/25/2021] [Accepted: 01/10/2022] [Indexed: 11/30/2022] Open
Abstract
APAF1 is an autosomal recessive inherited mutation, associated with Holstein haplotype 1 (HH1) and characterized by a substitution of cytosine for a thymine (c.1741C>T) in chromosome 5. The mutation causes fetal and embryonic loss, between 60 and 200 days of gestation, and reduced conception rate. The ARMS-PCR is considered a simple and low-cost method to determine single nucleotide polymorphism (SNP) with no need for genetic sequencing of the animal genome. This study aimed to verify the allelic frequency of APAF1 mutation in Brazilian Holstein cattle. A total of 248 Holstein DNA samples (210 cows and 38 bulls) were analyzed, and synthetic genes were manufactured to validate the primers developed by the authors. All animals assessed in this study were classified as wild-type for APAF1 mutation. The primers and protocol developed for the ARMS-PCR technique work with 100% specificity and efficiency since the amplicon formations are as expected according to the genotypes. In conclusion, the mutation responsible for APAF1 was not detected in the Brazilian Holstein cattle population assessed in this prevalence study, although it is not possible to affirm that APAF1 does not occur in Brazilian Holstein animals. The tetra-primer ARMS-PCR protocol for APAF1 mutation that has been validated here may be a relatively simple and economical method to determine the animals' genotype.
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Affiliation(s)
- Lukas Garrido Albertino
- São Paulo State University (UNESP), School of Veterinary Medicine and Animal Science, Botucatu, Brazil
| | | | - Julia Franco Ferreira
- São Paulo State University (UNESP), School of Veterinary Medicine and Animal Science, Botucatu, Brazil
| | | | - Alexandre Secorun Borges
- São Paulo State University (UNESP), School of Veterinary Medicine and Animal Science, Botucatu, Brazil
| | | | - José Paes Oliveira-Filho
- São Paulo State University (UNESP), School of Veterinary Medicine and Animal Science, Botucatu, Brazil
- *Correspondence: José Paes Oliveira-Filho
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Khan MYA, Omar AI, He Y, Chen S, Zhang S, Xiao W, Zhang Y. Prevalence of nine genetic defects in Chinese Holstein cattle. Vet Med Sci 2021; 7:1728-1735. [PMID: 33991412 PMCID: PMC8464240 DOI: 10.1002/vms3.525] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2020] [Revised: 03/22/2021] [Accepted: 04/22/2021] [Indexed: 11/06/2022] Open
Abstract
Worldwide use of elite sires has caused inbreeding accumulation and high frequencies of genetic defects in dairy cattle populations. In recent years, several genetic defect genes or haplotypes have been identified in Holstein cattle. A rapid and reliable microfluidic chip with Kompetitive allele-specific PCR (KASP) assay was developed in our previous study for the detection of heterozygotes at eight genetic defect loci of bovine leukocyte adhesion deficiency (BLAD), Brachyspina syndrome (BS), complex vertebral malformation (CVM), Holstein haplotype 1 (HH1), Holstein haplotype 3 (HH3), Holstein haplotype 4 (HH4), Holstein haplotype 5 (HH5) and haplotype for cholesterol deficiency (HCD). This study aimed to extend that assay to include a newly identified genetic defect of Holstein haplotype 6 (HH6) and to estimate the frequencies of carriers for each of the nine genetic defects in six Chinese Holstein herds. Of the 1633 cows, carrier frequencies of the genetic defects were 6.92%, 5.76%, 4.46%, 4.30%, 3.62%, 2.94%, 1.86% and 0.37% for HH1, HH3, CVM, HH5, HCD, BS, HH6 and BLAD, respectively. No carrier was found for HH4. Notably, 27.43% of cows carried at least one genetic defect, while 2.27% and 0.12% of cows carried double and triple genetic defect alleles, respectively. The existence of genetic defects calls for routine molecular testing and effective management of genetic defects by avoiding carrier-to-carrier mating in production herds and eliminating or at least reducing the frequency of the defective alleles through marker-assisted selection in breeding herds.
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Affiliation(s)
- Md Yousuf Ali Khan
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Abdullah I Omar
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Yuwei He
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Shaohu Chen
- Dairy Data Center of China Dairy Association, Beijing, China
| | - Shengli Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
| | - Wei Xiao
- Beijing Animal Husbandry Station, Beijing, China
| | - Yi Zhang
- National Engineering Laboratory for Animal Breeding, Key Laboratory of Animal Genetics, Breeding and Reproduction of Ministry of Agriculture and Rural Affairs, College of Animal Science and Technology, China Agricultural University, Beijing, China
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Faza D, Pereira H, Egito A, Torres Júnior R, Kim E, Sonstegard T, Martins M, Panetto J, Silva M, Machado M. Development of tetra-primer ARMS-PCR protocol to genotype the prolactin receptor SNP 39136666 and assessment of this SNP in Brazilian locally adapted cattle breeds. ARQ BRAS MED VET ZOO 2021. [DOI: 10.1590/1678-4162-12104] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022] Open
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8
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Kumar A, Gupta ID, Mohan G, M R V, D RK, S J, Kataria RS, Niranjan SK. Alternate PCR assays for screening of JH1 mutation associated with embryonic death in Jersey cattle. Mol Cell Probes 2020; 55:101688. [PMID: 33279530 DOI: 10.1016/j.mcp.2020.101688] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/29/2020] [Revised: 12/01/2020] [Accepted: 12/01/2020] [Indexed: 10/22/2022]
Abstract
Jersey haplotype (JH) 1, a stop-gain lethal mutation in the CWC15 gene, causes embryonic losses in Jersey cattle. Two PCR based assays using Amplification Refractory Mutation System (T-ARMS-PCR) and restriction fragment length polymorphism (PCR-RFLP) were developed for screening of the JH1 in cattle. During the screening, seven among 30 Indian Jersey bulls were identified as carriers of the mutant JH1 allele, the first time in the country. These PCR assays are economical, rapid and accurate; and can be used separately or in combination for screening and cross-validation of the JH1 carriers in Jersey cattle.
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Affiliation(s)
- Anshuman Kumar
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India; ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | | | - Govind Mohan
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India; ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Vineeth M R
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India; ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Ravi Kumar D
- ICAR-National Dairy Research Institute, Karnal, 132001, Haryana, India
| | - Jayakumar S
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Ranjit Singh Kataria
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India
| | - Saket Kumar Niranjan
- ICAR-National Bureau of Animal Genetic Resources, Karnal, 132001, Haryana, India.
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