DNA was extracted from each sample of ear tissue following the standard phenol/chloroform extraction method. All DNA samples were qualified and normalized to a final concentration of 50 ng/μL. DNA quality was assessed on the basis of the ratios of light absorption (A260/280 and A260/230) and electrophoresis. The quality and concentration of each genomic DNA sample met the requirements for the Illumina SNP genotyping platform. The 390 individuals were genotyped using the porcine SNP60K Beadchip of Illumina (San Diego, CA, USA) [12 (link)]. Quality control was performed using PLINK v 1.07 software [17 (link)]. SNP markers with genotype missing rates >0.05, call rate <95%, minor allele frequencies <0.01, and Hardy–Weinberg p≤10E-06 were excluded. Unmapped SNPS and SNPs located on sex chromosomes were removed in accordance with the Sus scrofa10.2 assembly of the reference genome [18 (link)]. Samples and SNPs that passed the filter were selected for subsequent GWA analysis.
Protocol detail
Porcine SNP Genotyping and Quality Control
Partial Protocol Preview
This section provides a glimpse into the protocol.
The remaining content is hidden due to licensing restrictions, but the full text is available at the following link:
Access Free Full Text.
Corresponding Organization :
Other organizations : South China Agricultural University, Wen's Food Group (China)
Top 5 similar protocols
Variable analysis
independent variables
- DNA extraction method (phenol/chloroform extraction)
- DNA normalization to 50 ng/μL
- SNP genotyping
- Genotype quality control (missing rates, call rate, minor allele frequencies, Hardy-Weinberg equilibrium)
- DNA quality assessment (A260/280, A260/230, electrophoresis)
- Illumina SNP genotyping platform requirements
Annotations
Based on most similar protocols
Etiam vel ipsum. Morbi facilisis vestibulum nisl. Praesent cursus laoreet felis. Integer adipiscing pretium orci. Nulla facilisi. Quisque posuere bibendum purus. Nulla quam mauris, cursus eget, convallis ac, molestie non, enim. Aliquam congue. Quisque sagittis nonummy sapien. Proin molestie sem vitae urna. Maecenas lorem.
Sign up for free or login to display all annotations
As authors may omit details in methods from publication, our AI will look for missing critical information across the 5 most similar protocols.
About PubCompare
Our mission is to provide scientists with the largest repository of trustworthy protocols and intelligent analytical tools, thereby offering them extensive information to design robust protocols aimed at minimizing the risk of failures.
We believe that the most crucial aspect is to grant scientists access to a wide range of reliable sources and new useful tools that surpass human capabilities.
However, we trust in allowing scientists to determine how to construct their own protocols based on this information, as they are the experts in their field.
Ready to get started?
Sign up for free.
Registration takes 20 seconds.
Available from any computer
No download required
Revolutionizing how scientists
search and build protocols!