Detection of copy number variation and selection signatures on the X chromosome in Chinese indigenous sheep with different types of tail

Objective Chinese indigenous sheep breeds can be classified into the following three categories by their tail morphology: fat-tailed, fat-rumped and thin-tailed sheep. The typical sheep breeds corresponding to fat-tailed, fat-rumped, and thin-tailed sheep are large-tailed Han, Altay, and Tibetan sheep, respectively. Detection of copy number variation (CNV) and selection signatures provides information on the genetic mechanisms underlying the phenotypic differences of the different sheep types. Methods In this study, PennCNV software and F-statistics (FST) were implemented to detect CNV and selection signatures, respectively, on the X chromosome in three Chinese indigenous sheep breeds using ovine high-density 600K single nucleotide polymorphism arrays. Results In large-tailed Han, Altay, and Tibetan sheep, respectively, a total of six, four and 22 CNV regions (CNVRs) with lengths of 1.23, 0.93, and 7.02 Mb were identified on the X chromosome. In addition, 49, 34, and 55 candidate selection regions with respective lengths of 27.49, 16.47, and 25.42 Mb were identified in large-tailed Han, Altay, and Tibetan sheep, respectively. The bioinformatics analysis results indicated several genes in these regions were associated with fat, including dehydrogenase/reductase X-linked, calcium voltage-gated channel subunit alpha1 F, and patatin like phospholipase domain containing 4. In addition, three other genes were identified from this analysis: the family with sequence similarity 58 member A gene was associated with energy metabolism, the serine/arginine-rich protein specific kinase 3 gene was associated with skeletal muscle development, and the interleukin 2 receptor subunit gamma gene was associated with the immune system. Conclusion The results of this study indicated CNVRs and selection regions on the X chromosome of Chinese indigenous sheep contained several genes associated with various heritable traits.

[1]  Caiye Zhu,et al.  Detection of Selection Signatures on the X Chromosome in Three Sheep Breeds , 2015, International journal of molecular sciences.

[2]  John J. Stainton,et al.  Detecting signatures of selection in nine distinct lines of broiler chickens. , 2015, Animal genetics.

[3]  Qin Zhang,et al.  Identification of Selection Footprints on the X Chromosome in Pig , 2014, PloS one.

[4]  Ronald A. DePinho,et al.  Deletion of Hepatic FoxO1/3/4 Genes in Mice Significantly Impacts on Glucose Metabolism through Downregulation of Gluconeogenesis and Upregulation of Glycolysis , 2013, PloS one.

[5]  I. Jackson,et al.  Signatures of Diversifying Selection in European Pig Breeds , 2013, PLoS genetics.

[6]  Xiangdong Ding,et al.  Genome-wide detection of copy number variations using high-density SNP genotyping platforms in Holsteins , 2013, BMC Genomics.

[7]  A. M. Barrio,et al.  Strong signatures of selection in the domestic pig genome , 2012, Proceedings of the National Academy of Sciences.

[8]  M. Amills,et al.  Copy number variation in the genomes of domestic animals. , 2012, Animal genetics.

[9]  A. Nejati-Javaremi,et al.  Genomic scan of selective sweeps in thin and fat tail sheep breeds for identifying of candidate regions associated with fat deposition , 2012, BMC Genetics.

[10]  M. Lei,et al.  Molecular characterization and expression patterns of serine/arginine-rich specific kinase 3 (SPRK3) in porcine skeletal muscle , 2011, Molecular Biology Reports.

[11]  Alfonso Valencia,et al.  Assessment of copy number variation using the Illumina Infinium 1M SNP‐array: a comparison of methodological approaches in the Spanish Bladder Cancer/EPICURO study , 2011, Human mutation.

[12]  Kenny Q. Ye,et al.  Mapping copy number variation by population scale genome sequencing , 2010, Nature.

[13]  Raquel E. Gur,et al.  Strong synaptic transmission impact by copy number variations in schizophrenia , 2010, Proceedings of the National Academy of Sciences.

[14]  Xiao-yu Zhou,et al.  Gene expression profiles of adipose tissue of high-fat diet-induced obese rats by cDNA microarrays , 2010, Molecular Biology Reports.

[15]  Laure Ségurel,et al.  Looking for signatures of sex-specific demography and local adaptation on the X chromosome , 2010, Genome Biology.

[16]  P. Stankiewicz,et al.  Structural variation in the human genome and its role in disease. , 2010, Annual review of medicine.

[17]  Susumu Goto,et al.  KEGG for representation and analysis of molecular networks involving diseases and drugs , 2009, Nucleic Acids Res..

[18]  J. McEwan,et al.  An examination of positive selection and changing effective population size in Angus and Holstein cattle populations (Bos taurus) using a high density SNP genotyping platform and the contribution of ancient polymorphism to genomic diversity in Domestic cattle , 2009, BMC Genomics.

[19]  B. Browning,et al.  A unified approach to genotype imputation and haplotype-phase inference for large data sets of trios and unrelated individuals. , 2009, American journal of human genetics.

[20]  M. Zamiri,et al.  Relationships of fat-tail dimensions with fat-tail weight and carcass characteristics at different slaughter weights of Torki-Ghashghaii sheep. , 2008, Meat science.

[21]  Zachary A. Szpiech,et al.  Genotype, haplotype and copy-number variation in worldwide human populations , 2008, Nature.

[22]  Joseph T. Glessner,et al.  PennCNV: an integrated hidden Markov model designed for high-resolution copy number variation detection in whole-genome SNP genotyping data. , 2007, Genome research.

[23]  D. Conrad,et al.  Global variation in copy number in the human genome , 2006, Nature.

[24]  L. Andersson,et al.  A large duplication associated with dominant white color in pigs originated by homologous recombination between LINE elements flanking KIT , 2002, Mammalian Genome.

[25]  M. Ashburner,et al.  Gene Ontology: tool for the unification of biology , 2000, Nature Genetics.

[26]  B. Weir,et al.  ESTIMATING F‐STATISTICS FOR THE ANALYSIS OF POPULATION STRUCTURE , 1984, Evolution; international journal of organic evolution.