TaqMan allelic discrimination assay for A1 and A2 alleles of the bovine CSN2 gene

Manga, Ivan; Dvořák, Josef

doi:10.17221/89/2009-cjas

Cited by 14 publications

(14 citation statements)

References 19 publications

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“…For instance, a study in Denmark indicated a slight superiority of A1 β-casein for Black-and-White breed (0·550 of total β-casein; Bech & Kristiansen, 1990) and Ehrmann (1997) reported that the situation in Germany was similar (A1 0·573 of total β-casein for Red-and-White). More recently a study from Holstein-Friesian cows in India showed that A2 β-casein was the main β-casein variant (A2 0·559, A1 0·441 of total β-casein; Sodhi et al 2012) and this was also the case in a study in the Czech Republic (A2 0·550, A1 0·450; Manga & Dvořák, 2010). Compared with these studies, the frequency of β-casein A1/A2 alleles in the Chinese Holstein is relatively low, perhaps as a result of natural evolution and crossbreeding.…”

Section: Resultsmentioning

confidence: 88%

Identification of alleles and genotypes of beta-casein with DNA sequencing analysis in Chinese Holstein cow

Dai

Fang²,

Zhao

et al. 2016

Journal of Dairy Research

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The study reported in this Regional Research Communication aimed to analyse the genetic polymorphisms of β-casein in Chinese Holstein cows. β-casein has received considerable research interest in the dairy industry and animal breeding in recent years as a source not only of high quality protein, but also of bioactive peptides that may be linked to health effects. Morever, the polymorphic nature of β-casein and its association with milk production traits, composition, and quality also attracted several efforts in evaluating the allelic distribution of β-casein locus as a potential dairy trait marker. However, few data on beta-casein variants are available for the Chinese Holstein cow. In the present paper, one hundred and thirty three Holstein cows were included in the analysis. Results revealed the presence of 5 variants (A1, A2, A3, B and I), preponderance of the genotype A1A2 (0·353) and superiorities of A1/A2 alleles (0·432 and 0·459, respectively) in the population. Sequence analysis of β-casein gene in the cows showed four nucleotide changes in exon 7. Our study can provide reference and guidance for selection for superior milk for industrial applications and crossbreeding and genetic improvement programmes.

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Section: Resultsmentioning

confidence: 88%

Identification of alleles and genotypes of beta-casein with DNA sequencing analysis in Chinese Holstein cow

Dai

Fang²,

Zhao

et al. 2016

Journal of Dairy Research

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“…During the last decade, SNP assays have been used to identify species-specific polymorphisms in a wide variety of applications (Best et al 2007;Shastry 2007;Manga & Dvorak 2010). Although other DNA-based techniques (e.g.…”

Section: Number Of Fish In Stomachmentioning

confidence: 99%

Novel molecular approach demonstrates that turbid river plumes reduce predation mortality on larval fish

et al. 2014

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Turbidity associated with river plumes is known to affect the search ability of visual predators and thus can drive 'top-down' impacts on prey populations in complex ecosystems; however, traditional quantification of predator-prey relationships (i.e. stomach content analysis) often fails with larval fish due to rapid digestion rates. Herein, we use novel molecular genetic methods to quantify larval yellow perch (YP) in predator stomachs in western Lake Erie to test the hypothesis that turbidity drives variation in larval predation. We characterize predator stomach content DNA to first identify YP DNA (single nucleotide polymorphism) and then quantify larval YP predation (microsatellite allele counting) in two river plumes differing in turbidity. Our results showed elevated larval YP predation in the less turbid river plume, consistent with a top-down impact of turbidity on larval survival. Our analyses highlight novel ecological hypothesis testing using the power of innovative molecular genetic approaches.

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“…Kaminski et al (2007) mentioned the frequency of the A1 allele between 0.402 and 0.472 and the A2 allele between 0.470 and 0.598. Additionally, Manga and Dvorak (2010) Bezdicek (2007) stated that its frequency in the population was 0.094 68. Our observed frequency was 0.095 9.…”

Section: Kappa-casein Csn3_ay380228_13165mentioning

confidence: 99%

Use of SNPs from Illumina BovineSNP50K BeadChip v3 for imputation of microsatellite alleles for parentage verification and QTL reporting

Pribánová¹,

Schröffelová²,

Lipovský³

et al. 2020

CZECH J ANIM SCI

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The present study aimed to test the possibility of avoiding expensive retesting of the whole parental generation for single nucleotide polymorphisms (SNPs), to provide additional analysis of microsatellites in offspring in the transitional period and to analyse the likelihood of imputation of the International Society for Animal Genetics-recommended microsatellite markers from selected SNPs. The imputation and pedigree verification of 9 520 animals (representing 84 dairy bulls, 285 dairy cows, 3 202 beef bulls and 5 949 beef cows) were analysed by the method using 9 410 SNP haplotypes (incorporating an average of 73 SNPs per haplotype). The imputation method was confirmed to allow the parentage verification of up to 87% of the analysed animals without the need for retesting. The most problematic locus was TGLA53, with only 78% successful imputation. Seven loci (BM2113, ETH225, TGLA227, BM1824, SPS115, TGLA122 and TGLA126) had more than 90% imputing accuracy and success of imputation. The success of imputation also depends on the breed and the call rate of the test results. The highest imputation accuracy was found for the Holstein breed; the other six breeds had over 90% successful imputation rates, four breeds had imputation rates between 85.0 and 89.9%, and ten breeds (rarely bred in the Czech Republic) had imputation rates below 85.0%. A call rate of SNP tests lower than 90% indicates problems with haplotype construction and thus deterioration in the success of imputation. The analysis of a possibility of using all possible information from Illumina BovineSNP50K BeadChip v3 showed 109 SNPs encoding 51 quantitative trait loci markers. Haplotypes were designed for interpretation of the most important markers for diseases, exterior and performance. The most important markers for Holstein breeders were chosen as kappa- (variants A, B and E) and beta-casein (variants A1, A2), Holstein haplotypes affecting fertility (HH1, HH3, and HH4) and loci causing genetic defects, bovine leukocyte adhesion deficiency and deficiency of uridine monophosphate synthetase. The results estimated from bovine bead chips corresponded to the expected distribution of the incidence of these traits in the population and were verified by PCR-RFLP tests.

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TaqMan allelic discrimination assay for A1 and A2 alleles of the bovine CSN2 gene

Cited by 14 publications

References 19 publications

Identification of alleles and genotypes of beta-casein with DNA sequencing analysis in Chinese Holstein cow

Identification of alleles and genotypes of beta-casein with DNA sequencing analysis in Chinese Holstein cow

Novel molecular approach demonstrates that turbid river plumes reduce predation mortality on larval fish

Use of SNPs from Illumina BovineSNP50K BeadChip v3 for imputation of microsatellite alleles for parentage verification and QTL reporting

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