Understanding functional implication of β-casein gene variants in four cattle breeds characterized using AmpliSeq approach.
AmpliSeq
Cattle
Next generation sequencing
Single nucleotide polymorphism
β-Casein
Journal
3 Biotech
ISSN: 2190-572X
Titre abrégé: 3 Biotech
Pays: Germany
ID NLM: 101565857
Informations de publication
Date de publication:
Sep 2020
Sep 2020
Historique:
received:
11
07
2020
accepted:
21
08
2020
entrez:
28
9
2020
pubmed:
29
9
2020
medline:
29
9
2020
Statut:
ppublish
Résumé
Here, we designed a custom panel targeting whole β-casein gene SNPs of zebu and taurine cattle breeds to identify variants and applicability in dairy cattle genotyping. We sequenced two libraries consisting of different pools of primer sets from 95 individuals on the Illumina MiSeq. Consequently, over 92% target regions were amplified and 71 SNPs were available after quality filtering. Only three intronic variants were novel while majority of the identified variants were catalogued in dbSNP as known variants. Identified missense SNPs lead to variant A1/A2, B, F and A3, located in exon 7 only. For confirmation, A1/A2 locus was genotyped using PCR-RFLP. Variant B was observed in all animals, either in homozygous or in heterozygous form. Variants A1, F and A3 predicted to have a deleterious effect on protein function by decreasing the structural stability. Additionally, SIFT score revealed that the A1 variant might affect the protein function.
Identifiants
pubmed: 32983825
doi: 10.1007/s13205-020-02410-2
pii: 2410
pmc: PMC7468016
doi:
Types de publication
Journal Article
Langues
eng
Pagination
414Informations de copyright
© King Abdulaziz City for Science and Technology 2020.
Déclaration de conflit d'intérêts
Conflict of interestNone of the authors has any financial or personal relationship that could inappropriately influence or bias the content of the paper.
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