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ARS Home » Northeast Area » Beltsville, Maryland (BARC) » Beltsville Agricultural Research Center » Animal Genomics and Improvement Laboratory » Research » Publications at this Location » Publication #315013

Research Project: ENHANCING GENETIC MERIT OF RUMINANTS THROUGH GENOME SELECTION AND ANALYSIS

Location: Animal Genomics and Improvement Laboratory

Title: CNV-based genome wide association study reveals additional variants contributing to meat quality in swine

Author
item WANG, LIGANG - Chinese Academy Of Agricultural Sciences
item XU, LINGYANG - University Of Maryland
item LIU, XIN - Chinese Academy Of Agricultural Sciences
item ZHANG, TIAN - Chinese Academy Of Agricultural Sciences
item LI, NA - Chinese Academy Of Agricultural Sciences
item ZHANG, YUEBO - Chinese Academy Of Agricultural Sciences
item YAN, HUA - Chinese Academy Of Agricultural Sciences
item ZHAO, KEBIN - Chinese Academy Of Agricultural Sciences
item Liu, Ge - George
item ZHANG, LONGCHAO - Chinese Academy Of Agricultural Sciences
item WANG, LIXIAN - Chinese Academy Of Agricultural Sciences

Submitted to: Scientific Reports
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 7/2/2015
Publication Date: 8/3/2015
Citation: Wang, L., Xu, L., Liu, X., Zhang, T., Li, N., Zhang, Y., Yan, H., Zhao, K., Liu, G., Zhang, L., Wang, L. 2015. CNV-based genome wide association study reveals additional variants contributing to meat quality in swine. Scientific Reports. 5:12535.

Interpretive Summary: Pork quality is an economically important trait. Using a genome-wide association study based on copy number variations (CNV) we identified 8 CNVs that were significantly associated with pork quality traits. This result provides information to help discover genetic markers which may be suitable for inclusion in a genetic improvement program. Farmers, scientist, and policy planners who need to improve animal health and production based on genome-enabled animal selection will benefit from these results.

Technical Abstract: Pork quality is important both to the meat processing industry and consumers’ purchasing attitudes. Copy number variation (CNV) is a burgeoning kind of variant that may influence meat quality. Herein, a genome-wide association study (GWAS) was performed between CNVs and meat quality traits in swine. After false discovery rate (FDR) correction, a total of 8 CNVs on 6 chromosomes were identified to be significantly associated with at least one meat quality trait. All of the 8 CNVs were verified by next generation sequencing and 6 of them were verified by qPCR. Only the haplotype block containing CNV12 is adjacent to significant SNPs associated with meat quality, suggesting the effects of those CNVs were not likely captured by tag SNPs. The DNA dosage and EST expression of CNV12, which overlap with an obesity related gene Netrin-1 (Ntn1), were consistent with Ntn1 RNA expression, suggesting the CNV12 might be involved in the expression regulation of Ntn1 and finally influence meat quality. We concluded that CNVs may contribute to the genetic variations of meat quality beyond SNPs, and several candidate CNVs associated with meat quality are worthy of further exploration.