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      Genome-Wide Association Studies Identify Candidate Genes for Coat Color and Mohair Traits in the Iranian Markhoz Goat

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          Abstract

          The Markhoz goat provides an opportunity to study the genetics underlying coat color and mohair traits of an Angora type goat using genome-wide association studies (GWAS). This indigenous Iranian breed is valued for its quality mohair used in ceremonial garments and has the distinction of exhibiting an array of coat colors including black, brown, and white. Here, we performed 16 GWAS for different fleece (mohair) traits and coat color in 228 Markhoz goats sampled from the Markhoz Goat Research Station in Sanandaj, Kurdistan province, located in western Iran using the Illumina Caprine 50K beadchip. The Efficient Mixed Model Linear analysis was used to identify genomic regions with potential candidate genes contributing to coat color and mohair characteristics while correcting for population structure. Significant associations to coat color were found within or near the ASIP, ITCH, AHCY, and RALY genes on chromosome 13 for black and brown coat color and the KIT and PDGFRA genes on chromosome 6 for white coat color. Individual mohair traits were analyzed for genetic association along with principal components that allowed for a broader perspective of combined traits reflecting overall mohair quality and volume. A multitude of markers demonstrated significant association to mohair traits highlighting potential candidate genes of POU1F1 on chromosome 1 for mohair quality, MREG on chromosome 2 for mohair volume, DUOX1 on chromosome 10 for yearling fleece weight, and ADGRV1 on chromosome 7 for grease percentage. Variation in allele frequencies and haplotypes were identified for coat color and differentiated common markers associated with both brown and black coat color. This demonstrates the potential for genetic markers to be used in future breeding programs to improve selection for coat color and mohair traits. Putative candidate genes, both novel and previously identified in other species or breeds, require further investigation to confirm phenotypic causality and potential epistatic relationships.

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          Purification of nucleic acids by extraction with phenol:chloroform.

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            Developmental progress and current status of the Animal QTLdb

            The Animal QTL Database (QTLdb; http://www.animalgenome.org/QTLdb) has undergone dramatic growth in recent years in terms of new data curated, data downloads and new functions and tools. We have focused our development efforts to cope with challenges arising from rapid growth of newly published data and end users’ data demands, and to optimize data retrieval and analysis to facilitate users’ research. Evidenced by the 27 releases in the past 11 years, the growth of the QTLdb has been phenomenal. Here we report our recent progress which is highlighted by addition of one new species, four new data types, four new user tools, a new API tool set, numerous new functions and capabilities added to the curator tool set, expansion of our data alliance partners and more than 20 other improvements. In this paper we present a summary of our progress to date and an outlook regarding future directions.
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              The initial domestication of goats (Capra hircus) in the Zagros mountains 10,000 years ago.

              Initial goat domestication is documented in the highlands of western Iran at 10,000 calibrated calendar years ago. Metrical analyses of patterns of sexual dimorphism in modern wild goat skeletons (Capra hircus aegagrus) allow sex-specific age curves to be computed for archaeofaunal assemblages. A distinct shift to selective harvesting of subadult males marks initial human management and the transition from hunting to herding of the species. Direct accelerator mass spectrometry radiocarbon dates on skeletal elements provide a tight temporal context for the transition.
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                Author and article information

                Contributors
                Journal
                Front Genet
                Front Genet
                Front. Genet.
                Frontiers in Genetics
                Frontiers Media S.A.
                1664-8021
                04 April 2018
                2018
                : 9
                : 105
                Affiliations
                [1] 1Department of Animal Science, College of Agriculture and Natural Resources, University of Tehran , Karaj, Iran
                [2] 2Department of Animal Science, Cornell University , Ithaca, NY, United States
                [3] 3Department of Animal Science, Faculty of Agriculture Engineering, University of Kurdistan , Sanandaj, Iran
                Author notes

                Edited by: Max F. Rothschild, Iowa State University, United States

                Reviewed by: Tosso Leeb, Universität Bern, Switzerland; Brian Kirkpatrick, University of Wisconsin–Madison, United States

                *Correspondence: Hassan Mehrabani-Yeganeh, hmehrbani@ 123456ut.ac.ir Heather J. Huson, hjh3@ 123456cornell.edu

                This article was submitted to Livestock Genomics, a section of the journal Frontiers in Genetics

                Article
                10.3389/fgene.2018.00105
                5893768
                29670642
                5573b8e9-40e8-4c81-8cb4-af0f476f2485
                Copyright © 2018 Nazari-Ghadikolaei, Mehrabani-Yeganeh, Miarei-Aashtiani, Staiger, Rashidi and Huson.

                This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) and the copyright owner are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

                History
                : 27 November 2017
                : 16 March 2018
                Page count
                Figures: 6, Tables: 2, Equations: 0, References: 92, Pages: 15, Words: 0
                Categories
                Genetics
                Original Research

                Genetics
                genome-wide association study,coat color,mohair,fleece,markhoz,goat,angora,wattles
                Genetics
                genome-wide association study, coat color, mohair, fleece, markhoz, goat, angora, wattles

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