Abstract:
BACKGROUND:Health traits are of significant economic importance to the dairy industry due to their effects on milk production and associated treatment costs. Genome-wide association studies (GWAS) provide a means to identify associated genomic variants and thus reveal insights into the genetic architecture of complex traits and diseases. The objective of this study is to investigate the genetic basis of seven health traits in dairy cattle and to identify potential candidate genes associated with cattle health using GWAS, fine mapping, and analyses of multi-tissue transcriptome data. RESULTS:We studied cow livability and six direct disease traits, mastitis, ketosis, hypocalcemia, displaced abomasum, metritis, and retained placenta, using de-regressed breeding values and more than three million imputed DNA sequence variants. After data edits and filtering on reliability, the number of bulls included in the analyses ranged from 11,880 (hypocalcemia) to 24,699 (livability). GWAS was performed using a mixed-model association test, and a Bayesian fine-mapping procedure was conducted to calculate a posterior probability of causality to each variant and gene in the candidate regions. The GWAS detected a total of eight genome-wide significant associations for three traits, cow livability, ketosis, and hypocalcemia, including the bovine Major Histocompatibility Complex (MHC) region associated with livability. Our fine-mapping of associated regions reported 20 candidate genes with the highest posterior probabilities of causality for cattle health. Combined with transcriptome data across multiple tissues in cattle, we further exploited these candidate genes to identify specific expression patterns in disease-related tissues and relevant biological explanations such as the expression of Group-specific Component (GC) in the liver and association with mastitis as well as the Coiled-Coil Domain Containing 88C (CCDC88C) expression in CD8 cells and association with cow livability. CONCLUSIONS:Collectively, our analyses report six significant associations and 20 candidate genes of cattle health. With the integration of multi-tissue transcriptome data, our results provide useful information for future functional studies and better understanding of the biological relationship between genetics and disease susceptibility in cattle.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Freebern E,Santos DJA,Fang L,Jiang J,Parker Gaddis KL,Liu GE,VanRaden PM,Maltecca C,Cole JB,Ma Ldoi
10.1186/s12864-020-6461-zsubject
Has Abstractpub_date
2020-01-13 00:00:00pages
41issue
1issn
1471-2164pii
10.1186/s12864-020-6461-zjournal_volume
21pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract::ᅟ: Upon publication of the original article [1], the authors had flagged that there was an error in Fig. 1c, as the key in this figure was displaying incorrectly. The colours had not displayed in the key in the final published article, and instead appear as plain white. ...
journal_title:BMC genomics
pub_type: 杂志文章,已发布勘误
doi:10.1186/s12864-018-4614-0
更新日期:2018-04-11 00:00:00
abstract:BACKGROUND:Chemical bioavailability is an important dose metric in environmental risk assessment. Although many approaches have been used to evaluate bioavailability, not a single approach is free from limitations. Previously, we developed a new genomics-based approach that integrated microarray technology and regressi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2541-5
更新日期:2016-03-08 00:00:00
abstract:BACKGROUND:The orphan nuclear receptor TR4 (human testicular receptor 4 or NR2C2) plays a pivotal role in a variety of biological and metabolic processes. With no known ligand and few known target genes, the mode of TR4 function was unclear. RESULTS:We report the first genome-wide identification and characterization o...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-689
更新日期:2010-12-02 00:00:00
abstract:BACKGROUND:Sequencing data from The Cancer Genome Atlas (TGCA), the International Cancer Genome Consortium and other research institutes have revealed the presence of genetic alterations in several tumor types, including gastric cancer. These data have been combined into a catalog of significantly mutated genes for eac...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3166-4
更新日期:2016-10-26 00:00:00
abstract:BACKGROUND:LEF1/TCF transcription factors and their activator β-catenin are effectors of the canonical Wnt pathway. Although Wnt/β-catenin signaling has been implicated in neurodegenerative and psychiatric disorders, its possible role in the adult brain remains enigmatic. To address this issue, we sought to identify th...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-635
更新日期:2012-11-17 00:00:00
abstract:BACKGROUND:Genomic selection based on genotyping-by-sequencing (GBS) data could accelerate alfalfa yield gains, if it displayed moderate ability to predict parent breeding values. Its interest would be enhanced by predicting ability also for germplasm/reference populations other than those for which it was defined. Pre...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2212-y
更新日期:2015-12-01 00:00:00
abstract:BACKGROUND:Calcium-dependent protein kinase (CPK) is one of the main Ca2+ combined protein kinase that play significant roles in plant growth, development and response to multiple stresses. Despite an important member of the stress responsive gene family, little is known about the evolutionary history and expression pa...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6501-8
更新日期:2020-01-23 00:00:00
abstract:BACKGROUND:MicroRNAs (miRNAs) are small non-coding RNAs that regulate genes at the post-transcriptional level in spatiotemporal manner. Several miRNAs are identified as prognostic and diagnostic markers in many human cancers. Estimation of the temporal activities of the miRNAs is an important step in the way to underst...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2260-3
更新日期:2015-12-18 00:00:00
abstract:BACKGROUND:Human interfollicular epidermis is sustained by the proliferation of stem cells and their progeny, transient amplifying cells. Molecular characterization of these two cell populations is essential for better understanding of self renewal, differentiation and mechanisms of skin pathogenesis. The purpose of th...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-359
更新日期:2008-07-30 00:00:00
abstract:BACKGROUND:Effector proteins are translocated into host cells by plant-pathogens to undermine pattern-triggered immunity (PTI), the plant response to microbe-associated molecular patterns that interferes with the infection process. Individual effectors are found in variable repertoires where some constituents target th...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2534-4
更新日期:2016-03-14 00:00:00
abstract:BACKGROUND:In mammals, CEACAM1 and closely related members represent paired receptors with similar extracellular ligand-binding regions and cytoplasmic domains with opposing functions. Human CEACAM1 and CEACAM3 which have inhibitory ITIM/ITSM and activating ITAM-like motifs, respectively, in their cytoplasmic regions a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3279-9
更新日期:2016-11-16 00:00:00
abstract:BACKGROUND:The tropical green-lipped mussel Perna viridis is a common biomonitor throughout the Indo-Pacific region that is used for environmental monitoring and ecotoxicological investigations. However, there is limited molecular data available regarding this species. We sought to establish a global transcriptome data...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-804
更新日期:2014-09-19 00:00:00
abstract:BACKGROUND:BCG is the most widely used vaccine of all time and remains the only licensed vaccine for use against tuberculosis in humans. BCG also protects other species such as cattle against tuberculosis, but due to its incompatibility with current tuberculin testing regimens remains unlicensed. BCG's efficacy relates...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5791-1
更新日期:2019-05-28 00:00:00
abstract:BACKGROUND:The genome of the carnivorous marsupial, the Tasmanian devil (Sarcophilus harrisii, Order: Dasyuromorphia), was sequenced in the hopes of finding a cure for or gaining a better understanding of the contagious devil facial tumor disease that is threatening the species' survival. To better understand the Tasma...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-172
更新日期:2012-05-06 00:00:00
abstract:BACKGROUND:Affymetrix GeneChip typically contains multiple probe sets per gene, defined as sibling probe sets in this study. These probe sets may or may not behave similar across treatments. The most appropriate way of consolidating sibling probe sets suitable for analysis is an open problem. We propose the Analysis of...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-188
更新日期:2008-04-24 00:00:00
abstract:BACKGROUND:Banana wilt disease, caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4), is one of the most devastating diseases in banana (Musa spp.). Foc is a soil borne pathogen that causes rot of the roots or wilt of leaves by colonizing the xylem vessels. The dual RNA sequencing is used to simultaneo...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-5902-z
更新日期:2019-06-24 00:00:00
abstract:BACKGROUND:Long non-coding RNAs (lncRNAs) regulate adipose tissue metabolism, however, their function on testosterone deficiency related obesity in humans is less understood. For this research, intact and castrated male pigs are the best model animal because of their similar proportional organ sizes, cardiovascular sys...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3907-z
更新日期:2017-07-19 00:00:00
abstract:BACKGROUND:Theileria parva is an intracellular parasite that causes a lymphoproliferative disease in cattle. It does so by inducing cancer-like phenotypes in the host cells it infects, although the molecular and regulatory mechanisms involved remain poorly understood. RNAseq data, and the resulting updated genome annot...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2444-5
更新日期:2016-02-20 00:00:00
abstract:BACKGROUND:Ramularia collo-cygni is a newly important, foliar fungal pathogen of barley that causes the disease Ramularia leaf spot. The fungus exhibits a prolonged endophytic growth stage before switching life habit to become an aggressive, necrotrophic pathogen that causes significant losses to green leaf area and he...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2928-3
更新日期:2016-08-09 00:00:00
abstract:BACKGROUND:Large amounts of mammalian protein-protein interaction (PPI) data have been generated and are available for public use. From a systems biology perspective, Proteins/genes interactions encode the key mechanisms distinguishing disease and health, and such mechanisms can be uncovered through network analysis. A...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-325
更新日期:2012-07-20 00:00:00
abstract:BACKGROUND:RNA-seq has shown huge potential for phylogenomic inferences in non-model organisms. However, error, incompleteness, and redundant assembled transcripts for each gene in de novo assembly of short reads cause noise in analyses and a large amount of missing data in the aligned matrix. To address these problems...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-328
更新日期:2013-05-14 00:00:00
abstract:BACKGROUND:Exosomes, endosome-derived membrane microvesicles, contain specific RNA transcripts that are thought to be involved in cell-cell communication. These RNA transcripts have great potential as disease biomarkers. To characterize exosomal RNA profiles systemically, we performed RNA sequencing analysis using thre...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-319
更新日期:2013-05-10 00:00:00
abstract:BACKGROUND:New gene emergence is so far assumed to be mostly driven by duplication and divergence of existing genes. The possibility that entirely new genes could emerge out of the non-coding genomic background was long thought to be almost negligible. With the increasing availability of fully sequenced genomes across ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-117
更新日期:2013-02-21 00:00:00
abstract:BACKGROUND:Understanding the underlying genetic structure of human populations is of fundamental interest to both biological and social sciences. Advances in high-throughput genotyping technology have markedly improved our understanding of global patterns of human genetic variation. The most widely used methods for col...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5168-x
更新日期:2018-10-29 00:00:00
abstract:BACKGROUND:In many microbial genomes, a strong preference for a small number of codons can be observed in genes whose products are needed by the cell in large quantities. This codon usage bias (CUB) improves translational accuracy and speed and is one of several factors optimizing cell growth. Whereas CUB and the overr...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-617
更新日期:2010-11-04 00:00:00
abstract::We describe an emerging initiative - the 'Functional Annotation of All Salmonid Genomes' (FAASG), which will leverage the extensive trait diversity that has evolved since a whole genome duplication event in the salmonid ancestor, to develop an integrative understanding of the functional genomic basis of phenotypic var...
journal_title:BMC genomics
pub_type: 社论
doi:10.1186/s12864-017-3862-8
更新日期:2017-06-27 00:00:00
abstract:BACKGROUND:Major secondary metabolites, including flavonoids, caffeine, and theanine, are important components of tea products and are closely related to the taste, flavor, and health benefits of tea. Secondary metabolite biosynthesis in Camellia sinensis is differentially regulated in different tissues during growth a...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1773-0
更新日期:2015-07-29 00:00:00
abstract:BACKGROUND:The study and analysis of gene expression measurements is the primary focus of functional genomics. Once expression data is available, biologists are faced with the task of extracting (new) knowledge associated to the underlying biological phenomenon. Most often, in order to perform this task, biologists exe...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-S6-S2
更新日期:2013-10-25 00:00:00
abstract:BACKGROUND:Mycoviruses are viruses that naturally infect and replicate in fungi. Aspergillus fumigatus, an opportunistic pathogen causing fungal lung diseases in humans and animals, was recently shown to harbour several different types of mycoviruses. A well-characterised defence against virus infection is RNA silencin...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3773-8
更新日期:2017-05-30 00:00:00
abstract:BACKGROUND:The availability of fully sequenced genomes and the implementation of transcriptome technologies have increased the studies investigating the expression profiles for a variety of tissues, conditions, and species. In this study, using RNA-seq data for three distinct tissues (brain, liver, and muscle), we inve...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-511
更新日期:2011-10-17 00:00:00