TY - JOUR
T1 - Milk protein polymorphisms and casein haplotypes in Butana cattle
AU - Ahmed, A. Said
AU - Rahmatalla, S.
AU - Bortfeldt, R.
AU - Arends, D.
AU - Reissmann, M.
AU - Brockmann, G. A.
N1 - Funding Information:
A. Said Ahmed was supported by the German Academic Exchange Service (DAAD) and the University of Gezira, Sudan. The authors thank the cattle owners in Sudan for providing samples from Butana cattle, as well as the management team and staff of the Atbara Research Station. We thank Ahmed M. Musa for the help in sample collection.
Publisher Copyright:
© 2016, Institute of Plant Genetics, Polish Academy of Sciences, Poznan.
PY - 2017/5/1
Y1 - 2017/5/1
N2 - Butana is a Bos indicus dairy cattle breed that is well adapted to the local environment of Sudan. The breed has been gradually declining in number due to breed substitution. Therefore, conservation and improvement strategies are required to maintain this breed. The aim of the present study was to assess genetic variation that is characteristic for Butana cattle in the milk protein genes CSN1S1, CSN2, CSN1S2, CSN3, LALBA, and LGB. In a first step, genomic DNA of five unrelated individuals was comparatively sequenced across all exon and flanking sequences. Ninety-three single nucleotide polymorphisms (SNPs) were identified in Butana cattle compared with the Bos taurus reference sequence at Ensembl. We confirmed the recently identified protein variants CSN2*J, CSN2*L, and LALBA*E. Fifty-two SNPs in non-coding regions are novel. Among the novel SNPs, five are located in promoter regions, three of them are in putative transcription factor binding sites (TFBSs) of the CSN1S2 promoter. Fifteen SNPs potentially affect miRNA target sites. In a second step, 50 unrelated Butana cattle were genotyped. This allowed deriving haplotypes for the casein gene cluster on BTA6. The most frequent haplotype was CSN1S1*C-CSN2*A2-CSN1S2*A-CSN3*A (C-A2-A-A, frequency 0.1546). Considering the newly identified CSN1S2 promoter variants, the most frequent haplotype was C-A2-TTC-A-A (0.1046), with TTC as the promoter variant. The information on protein and promoter variants can be used for the development of conservation and breeding strategies for this local breed.
AB - Butana is a Bos indicus dairy cattle breed that is well adapted to the local environment of Sudan. The breed has been gradually declining in number due to breed substitution. Therefore, conservation and improvement strategies are required to maintain this breed. The aim of the present study was to assess genetic variation that is characteristic for Butana cattle in the milk protein genes CSN1S1, CSN2, CSN1S2, CSN3, LALBA, and LGB. In a first step, genomic DNA of five unrelated individuals was comparatively sequenced across all exon and flanking sequences. Ninety-three single nucleotide polymorphisms (SNPs) were identified in Butana cattle compared with the Bos taurus reference sequence at Ensembl. We confirmed the recently identified protein variants CSN2*J, CSN2*L, and LALBA*E. Fifty-two SNPs in non-coding regions are novel. Among the novel SNPs, five are located in promoter regions, three of them are in putative transcription factor binding sites (TFBSs) of the CSN1S2 promoter. Fifteen SNPs potentially affect miRNA target sites. In a second step, 50 unrelated Butana cattle were genotyped. This allowed deriving haplotypes for the casein gene cluster on BTA6. The most frequent haplotype was CSN1S1*C-CSN2*A2-CSN1S2*A-CSN3*A (C-A2-A-A, frequency 0.1546). Considering the newly identified CSN1S2 promoter variants, the most frequent haplotype was C-A2-TTC-A-A (0.1046), with TTC as the promoter variant. The information on protein and promoter variants can be used for the development of conservation and breeding strategies for this local breed.
KW - Bos indicus
KW - Genetic variants
KW - Milk protein
KW - Single nucleotide polymorphism
UR - http://www.scopus.com/inward/record.url?scp=85001544884&partnerID=8YFLogxK
U2 - 10.1007/s13353-016-0381-2
DO - 10.1007/s13353-016-0381-2
M3 - Article
C2 - 27924448
AN - SCOPUS:85001544884
SN - 1234-1983
VL - 58
SP - 261
EP - 271
JO - Journal of Applied Genetics
JF - Journal of Applied Genetics
IS - 2
ER -