Fine Mapping of a Major Backfat QTL Reveals a Causal Regulatory Variant Affecting the CCND2 Gene.

Autor:	Oliveira HC; Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil., Derks MFL; Topigs Norsvin Research Center, Beuningen, Netherlands.; Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands., Lopes MS; Topigs Norsvin Research Center, Beuningen, Netherlands.; Topigs Norsvin, Curitiba, Brazil., Madsen O; Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands., Harlizius B; Topigs Norsvin Research Center, Beuningen, Netherlands., van Son M; Norsvin SA, Hamar, Norway., Grindflek EH; Norsvin SA, Hamar, Norway., Gòdia M; Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands., Gjuvsland AB; Norsvin SA, Hamar, Norway., Otto PI; Department of Animal Science, Universidade Federal de Santa Maria, Santa Maria, Brazil., Groenen MAM; Animal Breeding and Genomics, Wageningen University & Research, Wageningen, Netherlands., Guimaraes SEF; Department of Animal Science, Universidade Federal de Viçosa, Viçosa, Brazil.
Jazyk:	angličtina
Zdroj:	Frontiers in genetics [Front Genet] 2022 May 25; Vol. 13, pp. 871516. Date of Electronic Publication: 2022 May 25 (Print Publication: 2022).
DOI:	10.3389/fgene.2022.871516
Abstrakt:	Backfat is an important trait in pork production, and it has been included in the breeding objectives of genetic companies for decades. Although adipose tissue is a good energy storage, excessive fat results in reduced efficiency and economical losses. A large QTL for backfat thickness on chromosome 5 is still segregating in different commercial pig breeds. We fine mapped this QTL region using a genome-wide association analysis (GWAS) with 133,358 genotyped animals from five commercial populations (Landrace, Pietrain, Large White, Synthetic, and Duroc) imputed to the porcine 660K SNP chip. The lead SNP was located at 5:66103958 (G/A) within the third intron of the CCND2 gene, with the G allele associated with more backfat, while the A allele is associated with less backfat. We further phased the QTL region to discover a core haplotype of five SNPs associated with low backfat across three breeds. Linkage disequilibrium analysis using whole-genome sequence data revealed three candidate causal variants within intronic regions and downstream of the CCND2 gene, including the lead SNP. We evaluated the association of the lead SNP with the expression of the genes in the QTL region (including CCND2 ) in a large cohort of 100 crossbred samples, sequenced in four different tissues (lung, spleen, liver, muscle). Results show that the A allele increases the expression of CCND2 in an additive way in three out of four tissues. Our findings indicate that the causal variant for this QTL region is a regulatory variant within the third intron of the CCND2 gene affecting the expression of CCND2 . Competing Interests: Author ML was employed by Topigs Norsvin. Authors MS, EG and AG were employed by Norsvin SA. The remaining authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest. (Copyright © 2022 Oliveira, Derks, Lopes, Madsen, Harlizius, van Son, Grindflek, Gòdia, Gjuvsland, Otto, Groenen and Guimaraes.)
Databáze:	MEDLINE
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