Abstract
Copy number variations (CNVs), which cover many functional genes, are associated with complex diseases, phenotypic diversity and traits that are economically important to raising chickens. The sex-determining region Y-box 6 (Sox6) plays a key role in fast-twitch muscle fiber differentiation of zebrafish and mice, but it is still unknown whether SOX6 plays a role in chicken skeletal muscle development. We identified two copy number polymorphisms (CNPs) which were significantly related to different traits on the genome level in chickens by AccuCopy® and CNVplex® analyses. Notably, five white recessive rock (CN = 1, CN = 3) variant individuals and two Xinghua (CN = 3) variant individuals contain a CNP13 (chromosome5: 10,500,294–10,675,531) which overlaps with SOX6. There is a disordered region in SOX6 proteins 265–579 aa coded by a partial CNV overlapping region. A quantitative real-time polymerase chain reaction showed that the expression level of SOX6 mRNA was positively associated with CNV and highly expressed during the skeletal muscle cell differentiation in chickens. After the knockdown of the SOX6, the expression levels of IGFIR1, MYF6, SOX9, SHOX and CCND1 were significantly down-regulated. All of them directly linked to muscle development. These results suggest that the number of CNVs in the CNP13 is positively associated with the expression level of SOX6, which promotes the proliferation and differentiation of skeletal muscle cells by up-regulating the expression levels of the muscle-growth-related genes in chickens as in other animal species.
Highlights
Copy number variations (CNVs) are defined as large DNA fragments with sizes ranging from base pairs to 3 megabases (Mb) deleted, inserted, duplicated, or translocated in the genome [1], and are a kind of important genomic structure variation
From the analysis of nine chicken families, we found that there were 34 copy number variation region (CNVR) belong to copy number polymorphisms (CNPs)
Combining the genotype frequency of the candidate CNPs, which was detected by three kinds of method (Table 2), with the genetic regularity analysis, we found that some CNPs were unique in the family
Summary
Copy number variations (CNVs) are defined as large DNA fragments with sizes ranging from base pairs (bp) to 3 megabases (Mb) deleted, inserted, duplicated, or translocated in the genome [1], and are a kind of important genomic structure variation. The same region adjacent to and partially overlapping multiple CNVs can be incorporated into a large genomic segment called the copy number variation region (CNVR). A CNVR with a frequency of at least 3% is defined as copy number polymorphism (CNP) [2]. The current research into complex diseases or phenotypic traits is mainly concentrated on association studies with single nucleotide polymorphisms (SNPs), relatively few association studies focus on CNV [3]. With the construction of the chicken genome CNV sketches of different breeds, the researchers found many phenotypic traits associated with chicken CNVs. Genes 2018, 9, 42; doi:10.3390/genes9010042 www.mdpi.com/journal/genes
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