Development of PCR based assays for detection of lethal Holstein haplotype 1, 3 and 4 in Holstein Friesian cattle

Kumar, Amarjeet; Gupta, I. D.; Mohan, G. Krishna; Vineeth, M R; Kumar, Dinesh; Jayakumar, S.; Niranjan, S. K.

doi:10.1016/j.mcp.2019.101503

Cited by 11 publications

(12 citation statements)

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“…In comparison with Kumar and collaborators' ( 6 ) protocol, our protocol has few differences, the sizes of amplicon fragments [189 bp for outer primers, 140 bp for inner (C), and 105 bp for inner (T) ( 6 ) vs. 430 bp for outer primers, 286 bp for inner (C), and 198 bp for inner (T)] and the amplification conditions [initial denaturation at 95°C for 3 min, followed by 35 cycles of 94°C for 30 s, 60° C for 30 s, 72°C for 1 min, and a final extension at 72°C for 10 min ( 6 ) vs. initial denaturation at 95°C for 10 min, followed by 35 cycles of 95°C for 45 s, 60.1° C for 1 min, 72°C for 45 s, and a final extension at 72°C for 10 min].…”

Section: Discussionmentioning

confidence: 79%

“…The diagnosis is made by the polymerase chain reaction (PCR) test and genetic sequencing of the animal, besides that, other tests like single-stranded conformation PCR ( 4 ), allelic specific PCR ( 5 ), and amplification refractory mutation system ( ARMS -PCR) ( 6 ) were also used. The ARMS -PCR is considered a simple and low-cost method to determine SNP with no need for genetic sequencing of the animal genome ( 7 ), and it has been recently validated to determine the HH1 in Holstein cattle ( 6 ).…”

Section: Introductionmentioning

confidence: 99%

“…Studies performed in the United States ( 6 , 8 ), France ( 9 ), Russia ( 10 – 12 ), Japan ( 5 ), and Poland ( 4 ) demonstrated that the prevalence of the mutation varies from 1.48% to 65%. However, according to known literature, there are no studies about this mutation in Brazil.…”

Section: Introductionmentioning

confidence: 99%

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Allele Frequency of APAF1 Mutation in Holstein Cattle in Brazil

et al. 2022

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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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Section: Discussionmentioning

confidence: 79%

Section: Introductionmentioning

confidence: 99%

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Allele Frequency of APAF1 Mutation in Holstein Cattle in Brazil

et al. 2022

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“…The direct detection of carriers at the DNA level is possible for a defect with a known molecular basis. Different molecular methods have been applied to identify heterozygous individuals with some defects, such as PCR‐RFLP for HH4 (Fritz et al., 2013; Kumar et al., 2020), TaqMan for CVM and BLAD (Zhang et al., 2012) and allele‐specific PCR for BS (Charlier et al., 2012; Fang et al., 2013), HCD (Kipp et al., 2016; Li et al., 2018; Menzi et al., 2016; Schütz et al., 2016) and HH5 (Schütz et al., 2016). The Kompetitive allele‐specific PCR (KASP) assay based on an allele‐specific PCR followed by bi‐allelic scoring has been validated as an efficient and reliable genotyping strategy flexible for different types of variants, including single nucleotide polymorphism (SNP) and insertion or deletion (He et al., 2014; Ren et al., 2019; Semagn et al., 2014).…”

Section: Introductionmentioning

confidence: 99%

Prevalence of nine genetic defects in Chinese Holstein cattle

Khan

Omar

et al. 2021

Veterinary Medicine & Sci

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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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“…The 10 animals previously sequenced by NGS had their genotypes 100% confirmed by the protocol developed in this study. The tetra-primer ARMS-PCR genotyping technique was also successfully used to genotype lethal haplotype 1 in Holstein Friesian cattle (Kumar et al, 2020) and AGPAT6 gene, associated with milk fat content in Karan Fries Breeding Bulls (Upadhyay et al, 2019).…”

mentioning

confidence: 99%