Computational protocol: Determination of genetic effects of ATF3 and CDKN1A genes on milk yield and compositions in Chinese Holstein population

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Protocol publication

[…] We designed a total of 35 primers (Additional file ) using Primer 3.0 (http://primer3.wi.mit.edu/) and Oligo 6.0 (Molecular Biology Insights, Inc., CO, USA) to amplify the entire coding region and 2000 bp of flanking sequences based on the genomic sequence of the bovine ATF3 (GenBank accession no.: AC_000173.1) and CDKN1A (GenBank accession no.: AC_000180.1) genes, and the primers were synthesized by the Beijing Genomics Institute (BGI, Beijing, China). We randomly divided the DNA samples of the 40 sires into two equal groups, and diluted all the DNA samples into the concentration of 50 ng/μL. Subsequently, we constructed two DNA pools (50 ng/mL) as the templates for the PCR amplification. The amplifications were performed using the PCR system or the touch-down PCR (Additional file ). The purified PCR products were directly sequenced by ABI3730XL DNA analyzer (Applied Biosystems, Foster City, CA, USA), and the sequences were compared by DNAMAN 6.0 (Lynnon Biosoft, USA) and NCBI-BLAST (https://blast.ncbi.nlm.nih.gov/Blast.cgi) to search potential SNPs. The identified SNPs were further individually genotyped for all the 1093 Chinese Holstein cows using the matrix-assisted laser desorption/ionization time of flight mass spectrometry (MALDI-TOF MS, Sequenom MassARRAY, Bioyong Technologies Inc. HK). […]

Pipeline specifications

Software tools Primer3, DNAMAN, BLASTN
Application qPCR
Organisms Bos taurus
Chemicals Amino Acids, Tryptophan