Geneseek porcine 50k snp chip

A total of 1518 ear tissues from the DLY pig was collected. Extraction of DNA from the ear tissues was completed using the traditional standard phenol/chloroform method, and the quality of the DNA samples was assessed using the light absorption ratio (A260/280) of a spectrophotometer (Guangzhou Shenhua Biotechnology Co., Ltd., Guangzhou, China) and agarose gel electrophoresis [25 (link),26 (link)]. Genotyping was performed according to the method described by Ding et al. [27 (link)]. According to the manufacturer’s requirements, 1518 pigs were genotyped with the GeneSeek Porcine 50K SNP chip (Neogen, Lincoln, NE, USA) and quality filtering was completed using PLINK v1.90 [28 (link)]. Individuals with call rates of > 95% and markers with call rates of > 99%, a minor allele frequency (MAF) of > 99%, and a Hardy–Weinberg test p-value of > 10⁻⁶ were retained. In addition, all markers located on sex chromosomes and unmapped regions were excluded from analysis [29 (link),30 (link)]. Briefly, a total of 28,066 SNPs were finally obtained for subsequent analysis after data editing. Furthermore, the heritability of the traits was estimated using GCTA v1.92 software in this study [31 (link)].

Genotyping was performed as described by Ding et al. (2017) (link). Briefly, genomic DNA was extracted from ear tissue samples using the phenol–chloroform method. Genotyping was performed using the Geneseek Porcine 50K SNP Chip (Neogen, Lincoln, NE, United States), which contains 50,703 SNPs across autosomes and sex chromosomes. Quality control of the SNP data was performed using PLINK software (Purcell et al., 2007 (link)). Animals with call rates > 0.95, and SNPs with call rates > 0.99, minor allele frequency > 0.01, and P-value > 10^-6 for the Hardy–Weinberg equilibrium test were included. Only autosomal SNPs were considered for subsequent analyses.

Genomic DNA was extracted from ear tissues using an animal tissue DNA extraction kit (Generay Biotech Co., Ltd., Shanghai, China) following the manufacturer’s protocol. DNA quality was detected using a NanoDrop ND-1000 (Peqlab Biotechnology) and agarose gel electrophoresis. The DNA concentration of the samples was adjusted to 50 ng/μl. Samples were genotyped with the GeneSeek Porcine 50 K SNP Chip (Neogen, Lincoln, NE, United States) (Ding et al., 2018 (link)). Quality control (QC) was carried out using PLINK v1.07 (Purcell et al., 2007 (link)) software. SNPs with call rates lower than 95%, ambiguous locations, and minor allele frequencies less than 0.01 were discarded. SNPs that failed the Hardy–Weinberg equilibrium test (p < 10^–6) and unmapped or located on the sex chromosomes were also removed.

Collected ear tissues were used to extract genomic DNA by applying standard protocols. In this study, all animals were still raised until elimination after phenotypic measurement and ear tissue collection. These animals were not anesthetized during the ear tissue collection. Genotyping was conducted as described by Ding et al. [34 (link)]. DNA quality was measured by electrophoresis and a light absorption ratio (A260/280). All DNA samples were diluted to a concentration of 50 ng/μL. After DNA QC, 5860 Duroc and pigs were genotyped with the Geneseek Porcine 50 K SNP chip (Neogen, Lincoln, NE, United States). The genotype QC was conducted by PLINK v 1.9 [35 (link)]. The following criteria were used to filter SNPs prior to conducting association analysis: animal call rates < 95%, SNPs with call rates of < 90%, minorallele frequency < 1%, and P-value < 10^− 6 for the Hardy-Weinberg equilibrium test were excluded. This study excluded the SNPs located on the sex chromosomes and unmapped regions. In addition, the two Duroc pig populations follow the same QC criteria. In the meta-analysis of GWAS, a common set of SNPs that passed QC across the two populations were later used.

In this study, loin muscle depth (LMD) from the 10^th rib to 11^th rib of pigs was measured in Yorkshire pigs with the weight of 100 ± 5 kg by an Aloka 500V SSD B ultrasound. In total, LMD of 16,533 pigs was recorded in the years from March 2014 to January 2018. The pedigrees of these measured pigs could be traced back at least five generations with a total of 42,245 pigs included in these pedigrees. Genomic selection was started late in 2016 and finished at the end of 2018 due to the outbreak of African swine fever. Ear tissues were collected by the criterion of at least 2 males and 2 females in each litter. A total of 2,733 Yorkshire (YY) pigs provided both LMD recordings and ear tissue samples simultaneously.
Total DNA was extracted from these 2,733 pigs and genotyped using the Geneseek Porcine 50K SNP Chip (Neogen, Lincoln, NE, United States), and 50,703 SNP markers across the genome were obtained. SNPs were mapped to the Sscrofa11.1 pig genome assembly. Quality control (QC) was carried out with the following parameters set: individual call rate≥90%; SNP call rate≥90%; minor allele frequency≥0.01; Hardy-Weinberg equilibrium P-value≥10⁻⁶. After quality control, a total of 42,772 SNPs were obtained from each of 2,733 pigs, and these SNPs were used for subsequent genome-wide association analysis.

Ear tissue was collected from all animals, and genomic DNA was extracted from ear tissue by the standard phenol-chloroform method. DNA quality was assessed by ratios of light absorption (A260/280 and A260/230) and electrophoresis. Qualified DNA concentration was diluted to 50ng/μl. All animals were genotyped with the GeneSeek Porcine 50K SNP chip (Neogen, Lincoln, NE, United States) that contains 50,703 SNP across the whole genome. The quality control (QC) was performed by PLINK v 1.9 (14 (link)). Briefly, individuals with call rates more than 95% and SNPs with call rates more than 99%, minor allele frequency more than 1%, and Hardy-Weinberg P-value more than 10⁻⁶. Moreover, SNPs unmapped regions and located on the sex chromosomes were filtered. Notably, the two Duroc pig populations obey the same QC criteria. After genotype QC, the qualified individuals and SNPs were used for subsequent single-trait and multi-trait GWAS analyses (Supplementary Table 1).