ORCID Profile
0000-0002-7614-7207
Current Organisations
University of California Davis
,
Princeton University
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Publisher: Springer Science and Business Media LLC
Date: 28-04-2021
DOI: 10.1186/S12711-021-00633-2
Abstract: Nellore cattle ( Bos indicus ) are well-known for their adaptation to warm and humid environments. Hair length and coat color may impact heat tolerance. The Nellore breed has been strongly selected for white coat, but bulls generally exhibit darker hair ranging from light grey to black on the head, neck, hump, and knees. Given the potential contribution of coat color variation to the adaptation of cattle populations to tropical and sub-tropical environments, our aim was to map positional and functional candidate genetic variants associated with darkness of hair coat (DHC) in Nellore bulls. We performed a genome-wide association study (GWAS) for DHC using data from 432 Nellore bulls that were genotyped for more than 777 k single nucleotide polymorphism (SNP) markers. A single major association signal was detected in the vicinity of the agouti signaling protein gene ( ASIP ). The analysis of whole-genome sequence (WGS) data from 21 bulls revealed functional variants that are associated with DHC, including a structural rearrangement involving ASIP ( ASIP -SV1). We further characterized this structural variant using Oxford Nanopore sequencing data from 13 Australian Brahman heifers, which share ancestry with Nellore cattle we found that this variant originates from a 1155-bp deletion followed by an insertion of a transposable element of more than 150 bp that may impact the recruitment of ASIP non-coding exons. Our results indicate that the variant ASIP sequence causes darker coat pigmentation on specific parts of the body, most likely through a decreased expression of ASIP and consequently an increased production of eumelanin.
Publisher: Public Library of Science (PLoS)
Date: 12-01-2012
Publisher: Public Library of Science (PLoS)
Date: 17-01-2013
Publisher: Oxford University Press (OUP)
Date: 31-05-2016
DOI: 10.1093/JNEN/NLW042
Publisher: Springer Science and Business Media LLC
Date: 27-07-2017
Publisher: Wiley
Date: 05-09-2019
DOI: 10.1111/AGE.12834
Publisher: Public Library of Science (PLoS)
Date: 30-01-2013
Publisher: Public Library of Science (PLoS)
Date: 23-03-2015
Publisher: Public Library of Science (PLoS)
Date: 03-04-2014
Publisher: Wiley
Date: 12-07-2021
DOI: 10.1111/AGE.13117
Abstract: Genotype imputation using a reference panel that combines high‐density array data and publicly available whole genome sequence consortium variant data is potentially a cost‐effective method to increase the density of extant lower‐density array datasets. In this study, three datasets (two Border Collie one Italian Spinone) generated using a legacy array (Illumina CanineHD, 173 662 SNPs) were utilised to assess the feasibility and accuracy of this approach and to gather additional evidence for the efficacy of canine genotype imputation. The cosmopolitan reference panels used to impute genotypes comprised dogs of 158 breeds, mixed breed dogs, wolves and Chinese indigenous dogs, as well as breed‐specific in iduals genotyped using the Axiom Canine HD array. The two Border Collie reference panels comprised 808 in iduals including 79 Border Collies and 426 326 or 426 332 SNPs and the Italian Spinone reference panel comprised 807 in iduals including 38 Italian Spinoni and 476 313 SNPs. A high accuracy for imputation was observed, with the lowest accuracy observed for one of the Border Collie datasets (mean R 2 = 0.94) and the highest for the Italian Spinone dataset (mean R 2 = 0.97). This study’s findings demonstrate that imputation of a legacy array study set using a reference panel comprising both breed‐specific array data and multi‐breed variant data derived from whole genomes is effective and accurate. The process of canine genotype imputation, using the valuable growing resource of publicly available canine genome variant datasets alongside breed‐specific data, is described in detail to facilitate and encourage use of this technique in canine genetics.
Publisher: Public Library of Science (PLoS)
Date: 09-03-2020
No related grants have been discovered for Danika Bannasch.