Identification of Genomic Characteristics and Selective Signals in a Du'an Goat Flock

Animals : an Open Access Journal From MDPI
Qiuming ChenChu-Zhao Lei

Abstract

The Du'an goat is one of the most important farm animals in the Guangxi Autonomous Region of China, but the genetic basis underlying its adaptive traits has still not been investigated. Firstly, in this study, the genomes of 15 Du'an goats from a breeding farm were sequenced (mean depth: 9.50X) to analyze the patterns of genetic variation. A comparable diversity (17.3 million single nucleotide polymorphisms and 2.1 million indels) was observed to be associated with a lower runs of homozygosity-based inbreeding coefficient and smaller effective population size in comparison with other breeds. From selective sweep and gene set enrichment analyses, we revealed selective signals related to adaptive traits, including immune resistance (serpin cluster, INFGR1, TLR2, and immune-related pathways), body size (HMGA2, LCOR, ESR1, and cancer-related pathways) and heat tolerance (MTOR, ABCG2, PDE10A, and purine metabolism pathway). Our findings uncovered the unique diversity at the genomic level and will provide the opportunities for improvement of productivity in the Du'an goat.

References

Nov 1, 1988·Clinical Allergy·K ChenJ T Zhang
Mar 1, 1984·American Journal of Epidemiology·J BrissonP Cole
Aug 24, 2002·Epidemiologic Reviews·D GunnellJ M Holly
Dec 12, 2002·Chemical Reviews·Peter G W Gettins
Jan 16, 2007·Archives de pédiatrie : organe officiel de la Sociéte française de pédiatrie·M MuszlakC Picard
May 20, 2009·Bioinformatics·Heng Li, Richard Durbin
Jul 6, 2010·Nucleic Acids Research·Kai WangHakon Hakonarson
Jan 11, 2011·The Veterinary Clinics of North America. Food Animal Practice·Apostolos D Galatos
Jan 12, 2011·The Journal of Physiological Sciences : JPS·Ryo KakigiShizuo Katamoto
Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
May 5, 2012·Comparative Biochemistry and Physiology. Part A, Molecular & Integrative Physiology·Christopher P BonvillainChristopher C Green
Jul 19, 2012·PloS One·Shokouh Makvandi-NejadNathan B Sutter
Nov 22, 2012·Acta Physiologica·T YoshiharaS Katamoto
Apr 4, 2014·Bioinformatics·Anthony M BolgerBjoern Usadel
Jul 13, 2014·Molecular Biology and Evolution·Zachary A Szpiech, Ryan D Hernandez
Aug 8, 2015·Journal of Animal Physiology and Animal Nutrition·I Belhadj SlimenM Abdrrabba
May 7, 2016·Bioinformatics·Michael DeGiorgioRasmus Nielsen
Jun 2, 2016·EMBO Molecular Medicine·Mohammed K HankirWiebke K Fenske
Sep 8, 2016·Scientific Reports·Lucía Sánchez Di MaggioPatricia Berasain
Nov 20, 2018·Genetics, Selection, Evolution : GSE·Francesca BertoliniUNKNOWN AdaptMap consortium
Nov 7, 2019·Animals : an Open Access Journal From MDPI·Qingqing NingChuzhao Lei
Jul 17, 2020·Science Advances·Zhuqing ZhengYu Jiang
Sep 17, 2020·Science Advances·Zhuqing ZhengYu Jiang

❮ Previous
Next ❯

Citations


❮ Previous
Next ❯

Software Mentioned

sweepfinder2
PLINK
custom
VCFtools
perl script
Beagle
selscan
HaplotypeCaller
SNeP
KOBAS

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.