Genomic DNA was extracted from fresh leaves of field grown non-infected plants at seedling stage using the CTAB method [52 (link)]. The association mapping population was genotyped from the wheat Illumina 90 K iSelect array with 81,587 SNPs (Wang et al. 2014) at the Biotechnology Center, Department of Plant Sciences, University of California, USA, using the Illumina SNP genotyping platform and BeadArray Microbead Chip [53 (link)]. To avoid spurious marker-trait associations (MTAs), SNP markers with minor allele frequencies (MAF) < 0.05 and missing data > 10% were excluded from subsequent analyses. The physical positions of SNP markers were obtained from Chinese Spring reference genome sequences at the International Wheat Genome Sequencing Consortium website (IWGSC, http://www.wheatgenome.org/ ).
Snp genotyping platform
Manufactured by Illumina
The SNP genotyping platform is a laboratory equipment designed for the analysis of single nucleotide polymorphisms (SNPs) in DNA samples. It provides a high-throughput and accurate method for identifying and quantifying specific genetic variants within a given sample.
Automatically generated - may contain errors
3 protocols using snp genotyping platform
1
Wheat Genome Genotyping Protocol
2
Porcine SNP Genotyping and Quality Control
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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.
3
Porcine Genomic DNA Genotyping
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A standard phenol/chloroform method was used to extract genomic DNA from muscle samples for all the pigs. The quality and concentration of genomic DNA fulfilled the requirements for the Illumina SNP genotyping platform. Samples were genotyped with GeneSeek Genomic Profiler Porcine HD BeadChip (Neogen Corporation, Lansing, MI, USA) according to the manufacturer’s protocol and genotypes were called using GenomeStudio (version 2011.1; Illumina Inc., San Diego, CA, USA).
Quality controls were implemented by Plink v1.07 [13 (link)] according to the following filtering. Firstly, SNPs with GC score below 0.2 were considered failed genotypes, and Fimpute [14 (link)] was used to impute the failed loci. Then, SNPs were excluded from the data set if i) SNPs without genome location based on the pig genome assembly Sus scrofa Build 10.2 or located on Y chromosome, ii) its minor allele frequency was <5%, or iii) it departed severely from Hardy–Weinberg equilibrium with a p-value lower than 106.
Quality controls were implemented by Plink v1.07 [13 (link)] according to the following filtering. Firstly, SNPs with GC score below 0.2 were considered failed genotypes, and Fimpute [14 (link)] was used to impute the failed loci. Then, SNPs were excluded from the data set if i) SNPs without genome location based on the pig genome assembly Sus scrofa Build 10.2 or located on Y chromosome, ii) its minor allele frequency was <5%, or iii) it departed severely from Hardy–Weinberg equilibrium with a p-value lower than 106.
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