Abstract
Simple SummarySrc Homology 2 Domain Containing E (SHE) is a protein coding gene, and member of the SH2 domain-containing family. Sequencing revealed a 2000 bp copy number variation in the SHE gene. There is overlap between SHE copy number variation (CNV) and quantitative trait loci related to milk fat percentage and bone density. A total of 750 sheep, including Chaka sheep (CKS), Hu sheep (HS), Small Tail Han sheep (STHS) and Large Tail Han sheep (LTHS) were available to detect the CNV of the SHE gene and correlate these gene variations with economic traits. The results showed that there were more individuals with SHE copy number loss in CKS and HS than in STHS and LTHS. Association analysis showed that gain and normal copy number types performed better in body length (p < 0.05), circumference of cannon bone (p < 0.05), heart girth (p < 0.05), chest width (p < 0.05) and high at the cross (p < 0.05) in CKS, HS and STHS. Chi-square analyses found significant variation in the CNV of the SHE gene, so it varies greatly between varieties. These findings clarified the relationship between the CNV of the SHE gene and the economic traits in these four kinds of sheep, and provide a reference for sheep breeding.Copy number variation (CNV) caused by gene rearrangement is an important part of genomic structural variation. We found that the copy number variation region of the Src Homology 2 Domain Containing E (SHE) gene correlates with a quantitative trait locus of sheep related to milk fat percentage and bone density. The aim of our study was to detect the copy number variation of the SHE gene in four sheep breeds and to conduct a correlation analysis with economic traits, hoping to provide some reference for sheep breeding. In this study, we examined 750 sheep from four Chinese breeds: Chaka sheep (CKS), Hu sheep (HS), Large Tail Han sheep (LTHS) and Small Tail Han sheep (STHS). We used qPCR to evaluate the copy number of the SHE gene, and then used general linear models to analyze the associations between CNV and economic traits. The results showed that there were more individuals with SHE copy number loss in CKS and HS than in STHS and LTHS individuals. Association analyses showed that gain and normal copy number types were correlated to body length, circumference of cannon bone, heart girth, chest width and high at the cross in CKS, HS and STHS (p < 0.05), but this association was not observed for LTHS. Chi-square values (χ2) found prominent differences in CNV distribution among the studied breeds. Overall, the CNV of the SHE gene may be an important consideration for sheep molecular breeding.
Highlights
A quantitative trait locus (QTL) is a region of DNA that is associated with a particular phenotypic trait, which could be attributed to the effects of multiple genes and their environment
We found that the ANKRD1 gene is present in two gene isinpresent in two copies in both cattle to and sheep according to the animal omics database, sothe we copies both cattle and sheep according the animal omics database, so we selected to use selected to use the
As the main genetic form of submicroscopic structural variation, copy number variation (CNV) are widely distributed in the human genome, and affect gene expression, phenotypic variation and adaptation by interfering with genes and changing gene dosage [16,17,18,19]
Summary
A quantitative trait locus (QTL) is a region of DNA that is associated with a particular phenotypic trait, which could be attributed to the effects of multiple genes and their environment. QTL mapping has been widely used to identify the relationships between genetic markers and quantitative traits of interest. Copy number variation could be an abnormality caused by genome rearrangement. Sized fragments can range from 50 bp to 1 Mb, and mainly arise by genome deletion, insertion, recombination and complex mutations at multiple chromosomal sites [1]. Single nucleotide polymorphisms (SNPs) or copy number variation (CNV). SNPs mainly refer to DNA sequence polymorphism caused by single nucleotide variation at the genome level and are more abundant in genomic variation
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