Copy number variation-based genome wide association study reveals additional variants contributing to meat quality in Swine

As a global food source, pork has unquestionable significant implications on the livelihood of human beings. Pork quality is important to the meat processing industry and consumers’ purchasing attitude1, thus, it is one of the main selection objective in breeding plans for most of the pig breeding organizations and enterprises2. Meat quality traits are complex and usually influenced by multiple genes or QTLs, therefore, the genetic improvement of these traits is rather slow. However, genome-wide association studies (GWAS), linkage mapping, and selective sweep analysis have been successfully employed to investigate significant gene markers for pH, tenderness, meat color, intramuscular fat (IMF) content1,2,3,4,5,6,7,8,9. To date, a total of 12,618 QTLs from 461 publications have been recorded in PigQTLdb (http://www.animalgenome.org/cgi-bin/QTLdb/SS/index, released at Feb 11, 2015)10. Among these QTLs, more than half (7,014) were associated with meat and carcass quality traits. However, the limited density of microsatellite (SSR) markers resulted in inaccurate QTL mapping (Some segments are larger than 20 cM11, even cover a whole chromosome12). Long-term fine mapping experiments are needed to refine their locations and investigate causative variants13. Additionally, although genome wide association studies identified significant SNPs associated with meat quality traits, these SNPs explain a small portion of the genetic variance2,4. Alternative variances, which could explain the “missing heritability” of meat quality traits, were urgently needed14. Copy number variations (CNVs) are currently accepted as a common source of genetic variation, and the “missing heritability” could partially be explained by CNVs as reported in several human studies15,16,17,18,19. In animals, there is strong evidence of the effects CNVs may have on disease resistance and economically important traits, such as milk production13, gastrointestinal nematodes resistance20, residual feed intake21, Marek’s disease-resistance22, late-feathering23, and squamous cell carcinoma of the digit24. Min pig is well known in China for its excellent meat quality (with 5% IMF in LM at 240-day-old) and good cold resistance capacity, and Large-white pig is a normal lean meat type breed with normal meat quality. The intercross of Min × Large-white is a good model to analyze the genetics of meat quality2. The objective of this work was to perform systematic CNV association analysis with meat quality traits using the Porcine SNP60 Genotyping BeadChip (Illumina, San Diego, CA, USA), analyze the joint or independent effects of CNVs and SNPs, and provide some helpful information to identify genetic markers that may be suitable for inclusion in genetic improvement program.