Genotyping of DLY Pig Ear Tissues

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)].

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Li H., Xu C., Meng F., Yao Z., Fan Z., Yang Y., Meng X., Zhan Y., Sun Y., Ma F., Yang J., Yang M., Yang J., Wu Z., Cai G, & Zheng E. (2022). Genome-Wide Association Studies for Flesh Color and Intramuscular Fat in (Duroc × Landrace × Large White) Crossbred Commercial Pigs. Genes, 13(11), 2131.

Publication 2022

GeneSeek Porcine 50K SNP chip

Agarose gel electrophoresis Chip Chloroform Light Phenol Porcine Quality Sex chromosomes Shenhua Snps Tissues

Corresponding Organization : South China Agricultural University

Other organizations : Guangdong Academy of Agricultural Sciences, Zhongkai University of Agriculture and Engineering, Key Laboratory of Guangdong Province

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Variable analysis

independent variables

Genotyping method as described by Ding et al. [27]
GeneSeek Porcine 50K SNP chip (Neogen, Lincoln, NE, USA)

dependent variables

Heritability of the traits

control variables

Quality filtering using PLINK v1.90: 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)
Exclusion of markers located on sex chromosomes and unmapped regions

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