Study of the copy number variation on the sex chromosome in some Iranian sheep breeds

Document Type : Research Paper

Authors

1 Department of Animal Science, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, Sari, Iran

2 Department of Animal Science, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, SARI-IRAN, Iran

3 Department of Animal Science, Faculty of Animal Science and Fisheries, Sari Agricultural Sciences and Natural Resources University, Iran

4 Department of Animal Science, Faculty of Agriculture and Natural Resources, Arak university, ARAK-IRAN, Iran

Abstract

Copy number variation (CNVs) is one of the most important structural variations in the genome which play an important role in the genetic variance of economic traits. In this study, CNVs and copy number variation regions (CNVRs) on the sex chromosome were investigated in three native Iranian sheep breeds, including fat-tailed Baluchi and Lori-Bakhtiari breeds and thin-tailed Zel breed. 50K genotyped samples were obtained and CNVs were identified for each individual using PennCNV software. After identifying CNVs in each individual, the quality control of CNVs was performed with different filters, and CNVRs were identified by using the overlapping regions of CNVs using CNVRuler software. In total, 37, 11 and 4 CNVs of gain events were identified on the X chromosome of Baluchi, Zel and Lori-Bakhtiari sheep, respectively. The minimum, maximum and average length of identified CNVs were 94477, 1293154 and 447694 bp in Baluchi breed, 271819, 906644 and 674854 bp in Zel breed and 99705, 306525 and 167913 bp in Lori Bakhtiari breed, respectively. After merging the CNVs, 30, 10 and 4 CNVRs were identified in these three breeds, respectively, all of which were of the gain events. The analysis of genes in CNVR regions showed that some of these genes (VEGF, VAM21, TRPC5, NDUFA1, APLN and TNMD) were related to fat metabolism. Annotations of genes for molecular function were significantly enriched in the pathway of arylsulfatase activity, which plays a role in reproduction. Further studies on these CNV regions can help identify genes affecting fat metabolism in sheep.

Keywords

Main Subjects

Extended Abstract

Introduction

Copy number variations (CNV), with a minimum size of 50 base-pairs, is one of the most important sources of genetic variation, which together with SNP data provides informative genomic structural data. Several studies have shown that some CNVs play significant role in the phenotypic diversity of economically important traits and the development of disease resistance or susceptibility in sheep. Genome-wide copy-number association studies provide new facilities to identify the genetic mechanisms underlying complex traits in sheep breeds. Since the X chromosome has a remarkable number of genes, it is a valuable study target for the identification of CNVs at the genome level. Several studies have reported the presence of CNVs and selection signatures on the sheep X chromosome. In this study, CNVs and copy number variation regions on the sex chromosome were investigated in three native Iranian sheep breeds, including fat-tailed Baluchi and Lori-Bakhtiari breeds and thin-tailed Zel breed.

 

Materials and Methods

To identify the copy number variation on the X chromosome, the genomic data of 96 Baluchi sheep, 47 Lori-Bakhtiari sheep and 47 Zel sheep, genotyped using Illumina Ovine SNP50 Bead Chip array, were used. The quality control steps were as follows: animals with more than 5% of missing genotypes, SNPs with MAF of less than 5% and SNPs with genotyping call rate of less than 5% and deviation from Hardy-Weinberg equilibrium (p<1×10-6) were discarded from the further study. To identify CNVs, signal intensity ratios (LRR) and B allele frequencies (BAF) files were obtained for each marker. The population B allele frequency was estimated based on the BAF of each marker in the population. The GC model file was created by considering the GC content of the regions surrounding one million base pairs (500 kb each side). Also, to compare and investigate the effect of considering the GC file, the analyzes were also performed without considering the gcmodel. Finally, CNVs were identified for each individual using PennCNV software. After identifying CNVs in each individual, the quality control and filtering of CNVs were performed: samples with standard deviation of log R ratio (LRR) less than 0.3, BAF drift less than 0.01, wave factor less than 0.05 and confidence score less than 15 (less than 10 for gain events) were excluded. Also, CNVs must had at least 3 consecutive SNPs. To identify CNVs on the X chromosome, lastchr --chrx argument in PennCNV was used. Identification of CNVRs was performed using the overlapping regions of CNVs in different animals using CNVRuler software. The UCSC genome browser tool (version 4) was used to identify the gene content located in CNVRs. Finally, gene ontology (GO) analysis was performed for the identified genes using the DAVID.

 

Results and discussion

In this study, X chromosome-linked CNVs and CNVRs were investigated in three Iranian breeds including two fat-tailed breeds (Baluchi and Lori-Bakhtiari) and one thin-tailed breed (Zel). The results showed that considering quality control for GC content, as in previous studies, led to a reduction in the number of CNVs. The minimum, maximum and average length of identified CNVs were 94477, 1293154 and 447694 bp in Baluchi breed, 271819, 906644 and 674854 bp in Zel breed and 99705, 306525 and 167913 bp in Lori Bakhtiari breed, respectively. After merging the CNVs, 30, 10 and 4 CNVRs were identified in these three breeds, respectively, all of which were of the gain events. The analysis of genes in CNVR regions showed that some of these genes (VEGF, VAM21, TRPC5, NDUFA1, APLN and TNMD) were related to fat metabolism. Annotations of genes for molecular function were significantly enriched in the pathway of arylsulfatase activity, which plays a role in reproduction. Further studies on these CNV regions can help identify genes affecting fat metabolism in sheep.

 

Conclusion

In general, more CNVs and CNVRs were identified in the thin- tailed Zell breed compared to the studied fat-tailed breeds. Several genes were identified in the CNVR regions, which were reported to be associated with fat metabolism in previous studies. Therefore, with more detailed studies of these genes, useful information regarding the underlying mechanism of fat metabolism in sheep can be obtained.

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Iranian Journal of animal Science
Volume 54, Issue 3
October 2023
Pages 253-266

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History

  • Receive Date: 27 July 2022
  • Revise Date: 17 November 2022
  • Accept Date: 28 November 2022

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