Genome-Wide Detection of Copy Number Variations and Their Association With Distinct Phenotypes in the World's Sheep.

Frontiers in Genetics
Hosein Salehian-DehkordiFeng-Hua Lv

Abstract

Copy number variations (CNVs) are a major source of structural variation in mammalian genomes. Here, we characterized the genome-wide CNV in 2059 sheep from 67 populations all over the world using the Ovine Infinium HD (600K) SNP BeadChip. We tested their associations with distinct phenotypic traits by conducting multiple independent genome-wide tests. In total, we detected 7547 unique CNVs and 18,152 CNV events in 1217 non-redundant CNV regions (CNVRs), covering 245 Mb (∼10%) of the whole sheep genome. We identified seven CNVRs with frequencies correlating to geographical origins and 107 CNVRs overlapping 53 known quantitative trait loci (QTLs). Gene ontology and pathway enrichment analyses of CNV-overlapping genes revealed their common involvement in energy metabolism, endocrine regulation, nervous system development, cell proliferation, immune, and reproduction. For the phenotypic traits, we detected significantly associated (adjusted P < 0.05) CNVRs harboring functional candidate genes, such as SBNO2 for polycerate; PPP1R11 and GABBR1 for tail weight; AKT1 for supernumerary nipple; CSRP1, WNT7B, HMX1, and FGFR3 for ear size; and NOS3 and FILIP1 in Wadi sheep; SNRPD3, KHDRBS2, and SDCCAG3 in Hu sheep; NOS3, BMP1, and SLC19A1...Continue Reading

References

Dec 13, 2002·Fertility and Sterility·Lukas A HeflerClemens B Tempfer
Dec 3, 2004·The Biochemical Journal·Ana DinarinaAngel R Nebreda
Nov 24, 2006·Nature·Richard RedonMatthew E Hurles
Dec 30, 2006·PLoS Genetics·Nick PattersonDavid Reich
Sep 5, 2007·Nature Genetics·Stephen W SchererLars Feuk
Nov 21, 2007·The Journal of Immunology : Official Journal of the American Association of Immunologists·Karim C El KasmiPeter J Murray
Jun 13, 2008·Nature Protocols·Thomas D Schmittgen, Kenneth J Livak
May 19, 2009·Nature Reviews. Genetics·Michael E Goddard, Ben J Hayes
Sep 1, 2009·Annual Review of Genomics and Human Genetics·Feng ZhangJames R Lupski
Oct 9, 2009·Nature·Donald F ConradMatthew E Hurles
Jan 12, 2010·Methods : a Companion to Methods in Enzymology·Barbara D'haeneJan Hellemans
May 22, 2010·Proceedings of the National Academy of Sciences of the United States of America·Joseph T GlessnerHakon Hakonarson
May 14, 2011·Molecular Ecology Resources·Shuhua XuLi Jin
Feb 22, 2012·PLoS Biology·James W KijasUNKNOWN International Sheep Genomics Consortium Members
May 12, 2012·Bioinformatics·Shane NephJohn A Stamatoyannopoulos
Jan 8, 2013·Nucleic Acids Research·Joseph T GlessnerHakon Hakonarson
Jul 22, 2014·Animal Genetics·James W KijasUNKNOWN International Sheep Genomics Consortium
Jul 23, 2014·Asian-Australasian Journal of Animal Sciences·Hyeonju AhnHeebal Kim
Sep 25, 2014·Molecular Biology and Evolution·Feng-Hua LvPaolo Ajmone Marsan
Jun 10, 2016·BMC Genomics·Gemma M JenkinsJohn C McEwan
Aug 18, 2017·Physiological Reviews·Kazuo OkamotoHiroshi Takayanagi

❮ Previous
Next ❯

Software Mentioned

Primer
SmartPCA
BEDOPS
Admixture
InsertPlinkPvalues
Bedtools
PEAS
Illumina GenomeStudio
UCSC liftOver
PennCNV

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.