ORCID Profile
0000-0002-1584-7605
Current Organisations
AgriBio
,
CSIRO Queensland Bioscience Precinct
,
University of Adelaide
,
University of Melbourne
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Publisher: Springer Science and Business Media LLC
Date: 07-2021
DOI: 10.1038/S42003-021-02340-6
Abstract: To further the understanding of the evolution of transcriptional regulation, we profiled genome-wide transcriptional start sites ( TSSs ) in two sub-species, Bos taurus taurus and Bos taurus indicus , that erged approximately 500,000 years ago. Evolutionary and developmental-stage differences in TSSs were detected across the sub-species, including translocation of dominant TSS and changes in TSS distribution. The 16% of all SNPs located in significant differentially used TSS clusters across sub-species had significant shifts in allele frequency (472 SNPs), indicating they may have been subject to selection. In spleen and muscle, a higher relative TSS expression was observed in Bos indicus than Bos taurus for all heat shock protein genes, which may be responsible for the tropical adaptation of Bos indicus .
Publisher: Springer Science and Business Media LLC
Date: 19-10-2020
DOI: 10.1186/S12864-020-07018-7
Abstract: Mutations in the mitochondrial genome have been implicated in mitochondrial disease, often characterized by impaired cellular energy metabolism. Cellular energy metabolism in mitochondria involves mitochondrial proteins (MP) from both the nuclear ( Nu MP) and mitochondrial ( Mt MP) genomes. The expression of MP genes in tissues may be tissue specific to meet varying specific energy demands across the tissues. Currently, the characteristics of MP gene expression in tissues of dairy cattle are not well understood. In this study, we profile the expression of MP genes in 29 adult and six foetal tissues in dairy cattle using RNA sequencing and gene expression analyses: particularly differential gene expression and co-expression network analyses. MP genes were differentially expressed (DE over-expressed or under-expressed) across tissues in cattle. All 29 tissues showed DE Nu MP genes in varying proportions of over-expression and under-expression. On the other hand, DE of Mt MP genes was observed in 50% of tissues and notably Mt MP genes within a tissue was either all over-expressed or all under-expressed. A high proportion of Nu MP (up to 60%) and Mt MP (up to 100%) genes were over-expressed in tissues with expected high metabolic demand heart, skeletal muscles and tongue, and under-expressed (up to 45% of Nu MP, 77% of Mt MP genes) in tissues with expected low metabolic rates leukocytes, thymus, and lymph nodes. These tissues also invariably had the expression of all Mt MP genes in the direction of dominant Nu MP genes expression. The Nu MP and Mt MP genes were highly co-expressed across tissues and co-expression of genes in a cluster were non-random and functionally enriched for energy generation pathway. The differential gene expression and co-expression patterns were validated in independent cow and sheep datasets. The results of this study support the concept that there are biological interaction of MP genes from the mitochondrial and nuclear genomes given their over-expression in tissues with high energy demand and co-expression in tissues. This highlights the importance of considering MP genes from both genomes in future studies related to mitochondrial functions and traits related to energy metabolism.
Publisher: Research Square Platform LLC
Date: 26-09-2023
Publisher: Elsevier BV
Date: 07-2017
DOI: 10.1016/J.PLACENTA.2017.04.009
Abstract: Placental function impacts growth and development with lifelong consequences for performance and health. We provide novel insights into placental development in bovine, an important agricultural species and biomedical model. Concepti with defined genetics and sex were recovered from nulliparous dams managed under standardized conditions to study placental gross morphological and histomorphological parameters at the late embryo (Day48) and early accelerated fetal growth (Day153) stages. Placentome number increased 3-fold between Day48 and Day153. Placental barrier thickness was thinner, and volume of placental components, and surface areas and densities were higher at Day153 than Day48. We confirmed two placentome types, flat and convex. At Day48, there were more convex than flat placentomes, and convex placentomes had a lower proportion of maternal connective tissue (P < 0.01). However, this was reversed at Day153, where convex placentomes were lower in number and had greater volume of placental components (P < 0.01- P < 0.001) and greater surface area (P < 0.001) than flat placentomes. Importantly, embryo (r = 0.50) and fetal (r = 0.30) weight correlated with total number of convex but not flat placentomes. Extensive remodelling of the placenta increases capacity for nutrient exchange to support rapidly increasing embryo-fetal weight from Day48 to Day153. The cellular composition of convex placentomes, and exclusive relationships between convex placentome number and embryo-fetal weight, provide strong evidence for these placentomes as drivers of prenatal growth. The difference in proportion of maternal connective tissue between placentome types at Day48 suggests that this tissue plays a role in determining placentome shape, further highlighting the importance of early placental development.
Publisher: Wiley
Date: 20-10-2014
DOI: 10.1002/JBMR.2263
Abstract: Parent-of-origin-dependent (epi)genetic factors are important determinants of prenatal development that program adult phenotype. However, data on magnitude and specificity of maternal and paternal genome effects on fetal bone are lacking. We used an outbred bovine model to dissect and quantify effects of parental genomes, fetal sex, and nongenetic maternal effects on the fetal skeleton and analyzed phenotypic and molecular relationships between fetal muscle and bone. Analysis of 51 bone morphometric and weight parameters from 72 fetuses recovered at day 153 gestation (54% term) identified six principal components (PC1-6) that explained 80% of the variation in skeletal parameters. Parental genomes accounted for most of the variation in bone wet weight (PC1, 72.1%), limb ossification (PC2, 99.8%), flat bone size (PC4, 99.7%), and axial skeletal growth (PC5, 96.9%). Limb length showed lesser effects of parental genomes (PC3, 40.8%) and a significant nongenetic maternal effect (gestational weight gain, 29%). Fetal sex affected bone wet weight (PC1, p < 0.0001) and limb length (PC3, p < 0.05). Partitioning of variation explained by parental genomes revealed strong maternal genome effects on bone wet weight (74.1%, p < 0.0001) and axial skeletal growth (93.5%, p < 0.001), whereas paternal genome controlled limb ossification (95.1%, p < 0.0001). Histomorphometric data revealed strong maternal genome effects on growth plate height (98.6%, p < 0.0001) and trabecular thickness (85.5%, p < 0.0001) in distal femur. Parental genome effects on fetal bone were mirrored by maternal genome effects on fetal serum 25-hydroxyvitamin D (96.9%, p < 0.001) and paternal genome effects on alkaline phosphatase (90.0%, p < 0.001) and their correlations with maternally controlled bone wet weight and paternally controlled limb ossification, respectively. Bone wet weight and flat bone size correlated positively with muscle weight (r = 0.84 and 0.77, p < 0.0001) and negatively with muscle H19 expression (r = -0.34 and -0.31, p < 0.01). Because imprinted maternally expressed H19 regulates growth factors by miRNA interference, this suggests muscle-bone interaction via epigenetic factors.
Publisher: AIP Publishing
Date: 02-09-2004
DOI: 10.1063/1.1781762
Abstract: We present neutron and synchrotron powder-diffraction investigations as well as ab initio calculations to elucidate delicate structural features in doped skutterudites. S les with assumed Fe doping were investigated (FeyCo4Sb12, y=0.4, 0.8, 1.0, and 1.6), as well as s les with formal Ni substitution (Co4−xNixSb12, x=0, 0.4, 0.8, and 1.2). The present study serves as a case story for the determination of fine structural details of thermoelectric skutterudites by diffraction methods in combination with ab initio calculations. We illustrate the problem of fluorescence in the conventional x-ray powder diffraction on the Fe-doped s les by a comparison with the neutron powder-diffraction data. On the series of the Ni-substituted s les, the neutron powder-diffraction data were collected to investigate the exact sitting of the Ni. The s le with the highest Ni substitution (Co2.8Ni1.2Sb12) was also used for high resolution, high-energy synchrotron powder diffraction measurements. These revealed that the s le consists of two skutterudite phases. A complete description of the Ni-substituted s les was obtained in tandem with ab initio calculations, which show that the system contains a Ni-rich (Co0.38Ni3.62Sb12) and a Ni-poor (Co3.76Ni0.24Sb12)) skutterudite phases.
Publisher: Springer Science and Business Media LLC
Date: 23-08-2017
DOI: 10.1038/S41598-017-09788-9
Abstract: While single nucleotide polymorphisms (SNPs) associated with multiple phenotype have been reported, the knowledge of pleiotropy of uncorrelated phenotype is minimal. Principal components (PCs) and uncorrelated Cholesky transformed traits (CT) were constructed using 25 raw traits (RTs) of 2841 dairy bulls. Multi-trait meta-analyses of single-trait genome-wide association studies for RT, PC and CT in bulls were validated in 6821 cows. Most PCs and CTs had substantial estimates of heritability, suggesting that genes affect phenotype via erse pathways. Phenotypic orthogonalizations did not eliminate pleiotropy: the meta-analysis achieved an agreement of significant pleiotropic SNPs ( p 1 × 10 −5 , n = 368) between RTs (416), PCs (466) and CTs (425). From this overlap we identified 21 lead SNPs with 100% validation rate containing two clusters: one consisted of DGAT1 (chr14:1.8 M+), MGST1 (chr5:93 M+), PAEP (chr11:103 M+) and GPAT4 (chr27:36 M+) affecting protein, milk and fat yield and the other included CSN2 (chr6:87 M+), MUC1 (chr3:15.6 M), GHR (chr20:31.2 M+) and SDC2 (chr14:70 M+) affecting protein and milk yield. Combining beef cattle data identified correlated SNPs representing CAPN1 (chr29:44 M+) and CAST (chr 7:96 M+) loci affecting beef tenderness, showing pleiotropic effects in dairy cattle. Our findings show that SNPs with a large effect on one trait are likely to have small effects on other uncorrelated traits.
Publisher: Elsevier BV
Date: 12-2019
Publisher: Cold Spring Harbor Laboratory
Date: 31-05-2022
DOI: 10.1101/2022.05.30.494093
Abstract: Many quantitative trait loci (QTL) are located in non-coding genomic regions. Therefore, QTL are assumed to affect gene regulation. Gene expression and RNA splicing are primary steps of transcription so QTL changing gene expression (eQTL) or RNA splicing (sQTL) are expected to significantly contribute to phenotypic variations. Here, we quantify the contribution of eQTL and sQTL detected from 16 tissues (N~5,000) to 37 complex traits of ~120k cattle. Using Bayesian methods, we show that including more regulatory variants in the model explains larger proportions of heritability. Across traits, cis and trans eQTL and sQTL detected from 16 tissues jointly explain ~70% (SE=0.5%) of heritability, 44% more than expected from the same number of random variants, where trans e/sQTL contribute 24% (14% more than expected). Multi-tissue cis and trans e/sQTL also explain 71% (SE=0.3%) of heritability for the metabolome, demonstrating the essential role of proximal and distal regulatory variants in shaping mammalian phenotypes.
Publisher: Proceedings of the National Academy of Sciences
Date: 09-09-2019
Abstract: Many genome variants shaping mammalian phenotype are hypothesized to regulate gene transcription and/or to be under selection. However, most of the evidence to support this hypothesis comes from human studies. Systematic evidence for regulatory and evolutionary signals contributing to complex traits in a different mammalian model is needed. Sequence variants associated with gene expression (expression quantitative trait loci [eQTLs]) and concentration of metabolites (metabolic quantitative trait loci [mQTLs]) and under histone-modification marks in several tissues were discovered from multiomics data of over 400 cattle. Variants under selection and evolutionary constraint were identified using genome databases of multiple species. These analyses defined 30 sets of variants, and for each set, we estimated the genetic variance the set explained across 34 complex traits in 11,923 bulls and 32,347 cows with 17,669,372 imputed variants. The per-variant trait heritability of these sets across traits was highly consistent ( r 0.94) between bulls and cows. Based on the per-variant heritability, conserved sites across 100 vertebrate species and mQTLs ranked the highest, followed by eQTLs, young variants, those under histone-modification marks, and selection signatures. From these results, we defined a Functional-And-Evolutionary Trait Heritability (FAETH) score indicating the functionality and predicted heritability of each variant. In additional 7,551 cattle, the high FAETH-ranking variants had significantly increased genetic variances and genomic prediction accuracies in 3 production traits compared to the low FAETH-ranking variants. The FAETH framework combines the information of gene regulation, evolution, and trait heritability to rank variants, and the publicly available FAETH data provide a set of biological priors for cattle genomic selection worldwide.
Publisher: Frontiers Media SA
Date: 20-08-2018
Publisher: Springer Science and Business Media LLC
Date: 08-02-2021
DOI: 10.1038/S41467-021-21001-0
Abstract: The difficulty in finding causative mutations has h ered their use in genomic prediction. Here, we present a methodology to fine-map potentially causal variants genome-wide by integrating the functional, evolutionary and pleiotropic information of variants using GWAS, variant clustering and Bayesian mixture models. Our analysis of 17 million sequence variants in 44,000+ Australian dairy cattle for 34 traits suggests, on average, one pleiotropic QTL existing in each 50 kb chromosome-segment. We selected a set of 80k variants representing potentially causal variants within each chromosome segment to develop a bovine XT-50K genotyping array. The custom array contains many pleiotropic variants with biological functions, including splicing QTLs and variants at conserved sites across 100 vertebrate species. This biology-informed custom array outperformed the standard array in predicting genetic value of multiple traits across populations in independent datasets of 90,000+ dairy cattle from the USA, Australia and New Zealand.
Publisher: Springer Science and Business Media LLC
Date: 11-08-2022
DOI: 10.1038/S41588-022-01153-5
Abstract: Characterization of genetic regulatory variants acting on livestock gene expression is essential for interpreting the molecular mechanisms underlying traits of economic value and for increasing the rate of genetic gain through artificial selection. Here we build a Cattle Genotype-Tissue Expression atlas (CattleGTEx) as part of the pilot phase of the Farm animal GTEx (FarmGTEx) project for the research community based on 7,180 publicly available RNA-sequencing (RNA-seq) s les. We describe the transcriptomic landscape of more than 100 tissues/cell types and report hundreds of thousands of genetic associations with gene expression and alternative splicing for 23 distinct tissues. We evaluate the tissue-sharing patterns of these genetic regulatory effects, and functionally annotate them using multiomics data. Finally, we link gene expression in different tissues to 43 economically important traits using both transcriptome-wide association and colocalization analyses to decipher the molecular regulatory mechanisms underpinning such agronomic traits in cattle.
Publisher: Wiley
Date: 20-08-2004
Abstract: The experimental electron density of the high-performance thermoelectric material Zn4Sb3 has been determined by maximum entropy (MEM) analysis of short-wavelength synchrotron powder diffraction data. These data are found to be more accurate than conventional single-crystal data due to the reduction of common systematic errors, such as absorption, extinction and anomalous scattering. Analysis of the MEM electron density directly reveals interstitial Zn atoms and a partially occupied main Zn site. Two types of Sb atoms are observed: a free spherical ion (Sb3-) and Sb2(4-) dimers. Analysis of the MEM electron density also reveals possible Sb disorder along the c axis. The disorder, defects and vacancies are all features that contribute to the drastic reduction of the thermal conductivity of the material. Topological analysis of the thermally smeared MEM density has been carried out. Starting with the X-ray structure ab initio computational methods have been used to deconvolute structural information from the space-time data averaging inherent to the XRD experiment. The analysis reveals how interstitial Zn atoms and vacancies affect the electronic structure and transport properties of beta-Zn4Sb3. The structure consists of an ideal A12Sb10 framework in which point defects are distributed. We propose that the material is a 0.184:0.420:0.396 mixture of A12Sb10, A11BCSb10 and A10BCDSb10 cells, in which A, B, C and D are the four Zn sites in the X-ray structure. Given the similar density of states (DOS) of the A12Sb10, A11BCSb10 and A10BCDSb10 cells, one may electronically model the defective stoichiometry of the real system either by n-doping the 12-Zn atom cell or by p-doping the two 13-Zn atom cells. This leads to similar calculated Seebeck coefficients for the A12Sb10, A11BCSb10 and A10BCDSb10 cells (115.0, 123.0 and 110.3 microV K(-1) at T=670 K). The model system is therefore a p-doped semiconductor as found experimentally. The effect is dramatic if these cells are doped differently with respect to the experimental electron count. Thus, 0.33 extra electrons supplied to either kind of cell would increase the Seebeck coefficient to about 260 microV K(-1). Additional electrons would also lower sigma, so the resulting effect on the thermoelectric figure of merit of Zn4Sb3 challenges further experimental work.
Publisher: Springer Science and Business Media LLC
Date: 04-07-2018
Publisher: Springer Science and Business Media LLC
Date: 21-11-2019
DOI: 10.1186/S12864-019-6228-6
Abstract: DNA methylation has been shown to be involved in many biological processes, including X chromosome inactivation in females, paternal genomic imprinting, and others. Based on the correlation patterns of methylation levels of neighboring CpG sites among 28 sperm whole genome bisulfite sequencing (WGBS) data (486 × coverage), we obtained 31,272 methylation haplotype blocks (MHBs). Among them, we defined conserved methylated regions (CMRs), variably methylated regions (VMRs) and highly variably methylated regions (HVMRs) among in iduals, and showed that HVMRs might play roles in transcriptional regulation and function in complex traits variation and adaptive evolution by integrating evidence from traditional and molecular quantitative trait loci (QTL), and selection signatures. Using a weighted correlation network analysis (WGCNA), we also detected a co-regulated module of HVMRs that was significantly associated with reproduction traits, and enriched for glycosyltransferase genes, which play critical roles in spermatogenesis and fertilization. Additionally, we identified 46 VMRs significantly associated with reproduction traits, nine of which were regulated by cis-SNPs, implying the possible intrinsic relationships among genomic variations, DNA methylation, and phenotypes. These significant VMRs were co-localized (± 10 kb) with genes related to sperm motility and reproduction, including ZFP36L1 , CRISP2 and HGF . We provided further evidence that rs109326022 within a predominant QTL on BTA18 might influence the reproduction traits through regulating the methylation level of nearby genes JOSD2 and ASPDH in sperm. In summary, our results demonstrated associations of sperm DNA methylation with reproduction traits, highlighting the potential of epigenomic information in genomic improvement programs for cattle.
Publisher: The Company of Biologists
Date: 2018
DOI: 10.1242/JCS.213678
Abstract: Fibroblast growth factor receptors (FGFRs) are a family of receptor tyrosine kinases that control a erse range of biological processes during development and in adult tissues. We recently reported that somatic FGFR2 mutations are associated with shorter survival in endometrial cancer. However, little is known about how these FGFR2 mutations contribute to endometrial cancer metastasis. Here, we report that expression of the activating mutations FGFR2
Publisher: Springer Science and Business Media LLC
Date: 07-07-2020
Publisher: Springer Science and Business Media LLC
Date: 23-03-2021
DOI: 10.1038/S41467-021-22100-8
Abstract: Gene regulatory elements are central drivers of phenotypic variation and thus of critical importance towards understanding the genetics of complex traits. The Functional Annotation of Animal Genomes consortium was formed to collaboratively annotate the functional elements in animal genomes, starting with domesticated animals. Here we present an expansive collection of datasets from eight erse tissues in three important agricultural species: chicken ( Gallus gallus ), pig ( Sus scrofa ), and cattle ( Bos taurus ). Comparative analysis of these datasets and those from the human and mouse Encyclopedia of DNA Elements projects reveal that a core set of regulatory elements are functionally conserved independent of ergence between species, and that tissue-specific transcription factor occupancy at regulatory elements and their predicted target genes are also conserved. These datasets represent a unique opportunity for the emerging field of comparative epigenomics, as well as the agricultural research community, including species that are globally important food resources.
Publisher: Springer Science and Business Media LLC
Date: 14-12-2016
DOI: 10.1038/SREP39022
Abstract: Ruminants obtain nutrients from microbial fermentation of plant material, primarily in their rumen, a multilayered forestomach. How the different layers of the rumen wall respond to diet and influence microbial fermentation, and how these process are regulated, is not well understood. Gene expression correlation networks were constructed from full thickness rumen wall transcriptomes of 24 sheep fed two different amounts and qualities of a forage and measured for methane production. The network contained two major negatively correlated gene sub-networks predominantly representing the epithelial and muscle layers of the rumen wall. Within the epithelium sub-network gene clusters representing lipid/oxo-acid metabolism, general metabolism and proliferating and differentiating cells were identified. The expression of cell cycle and metabolic genes was positively correlated with dry matter intake, ruminal short chain fatty acid concentrations and methane production. A weak correlation between lipid/oxo-acid metabolism genes and methane yield was observed. Feed consumption level explained the majority of gene expression variation, particularly for the cell cycle genes. Many known stratified epithelium transcription factors had significantly enriched targets in the epithelial gene clusters. The expression patterns of the transcription factors and their targets in proliferating and differentiating skin is mirrored in the rumen, suggesting conservation of regulatory systems.
Publisher: Public Library of Science (PLoS)
Date: 14-01-2013
Publisher: Springer Science and Business Media LLC
Date: 02-12-2021
DOI: 10.1038/S42003-021-02874-9
Abstract: Mutant alleles (MAs) that have been classically recognised have large effects on phenotype and tend to be deleterious to traits and fitness. Is this the case for mutations with small effects? We infer MAs for 8 million sequence variants in 113k cattle and quantify the effects of MA on 37 complex traits. Heterozygosity for variants at genomic sites conserved across 100 vertebrate species increase fertility, stature, and milk production, positively associating these traits with fitness. MAs decrease stature and fat and protein concentration in milk, but increase gestation length and somatic cell count in milk (the latter indicative of mastitis). However, the frequency of MAs decreasing stature and fat and protein concentration, increasing gestation length and somatic cell count were lower than the frequency of MAs with the opposite effect. These results suggest bias in the mutations direction of effect (e.g. towards reduced protein in milk), but selection operating to reduce the frequency of these MAs. Taken together, our results imply two classes of genomic sites subject to long-term selection: sites conserved across vertebrates show hybrid vigour while sites subject to less long-term selection show a bias in mutation towards undesirable alleles.
Publisher: Frontiers Media SA
Date: 23-06-2021
DOI: 10.3389/FGENE.2021.664379
Abstract: Genetic variants which affect complex traits (causal variants) are thought to be found in functional regions of the genome. Identifying causal variants would be useful for predicting complex trait phenotypes in dairy cows, however, functional regions are poorly annotated in the bovine genome. Functional regions can be identified on a genome-wide scale by assaying for post-translational modifications to histone proteins (histone modifications) and proteins interacting with the genome (e.g., transcription factors) using a method called Chromatin immunoprecipitation followed by sequencing (ChIP-seq). In this study ChIP-seq was performed to find functional regions in the bovine genome by assaying for four histone modifications (H3K4Me1, H3K4Me3, H3K27ac, and H3K27Me3) and one transcription factor (CTCF) in 6 tissues (heart, kidney, liver, lung, mammary and spleen) from 2 to 3 lactating dairy cows. Eighty-six ChIP-seq s les were generated in this study, identifying millions of functional regions in the bovine genome. Combinations of histone modifications and CTCF were found using ChromHMM and annotated by comparing with active and inactive genes across the genome. Functional marks differed between tissues highlighting areas which might be particularly important to tissue-specific regulation. Supporting the cis-regulatory role of functional regions, the read counts in some ChIP peaks correlated with nearby gene expression. The functional regions identified in this study were enriched for putative causal variants as seen in other species. Interestingly, regions which correlated with gene expression were particularly enriched for potential causal variants. This supports the hypothesis that complex traits are regulated by variants that alter gene expression. This study provides one of the largest ChIP-seq annotation resources in cattle including, for the first time, in the mammary gland of lactating cows. By linking regulatory regions to expression QTL and trait QTL we demonstrate a new strategy for identifying causal variants in cattle.
Publisher: American Dairy Science Association
Date: 08-2019
Abstract: The aim of this study was to investigate the feasibility of using mid-infrared (MIR) spectroscopy analysis of milk s les to increase the power and precision of genome-wide association studies (GWAS) for milk composition and to better distinguish linked quantitative trait loci (QTL). To achieve this goal, we analyzed phenotypic data of milk composition traits, related MIR spectra, and genotypic data comprising 626,777 SNP on 5,202 Holstein, Jersey, and crossbred cows. We performed a conventional GWAS on protein, lactose, fat, and fatty acid concentrations in milk, a GWAS on in idual MIR wavenumbers, and a partial least squares regression (PLS), which is equivalent to a multi-trait GWAS, exploiting MIR data simultaneously to predict SNP genotypes. The PLS detected most of the QTL identified using single-trait GWAS, usually with a higher significance value, as well as previously undetected QTL for milk composition. Each QTL tends to have a different pattern of effects across the MIR spectrum and this explains the increased power. Because SNP tracking different QTL tend to have different patterns of effect, it was possible to distinguish closely linked QTL. Overall, the results of this study suggest that using MIR data through either GWAS or PLS analysis applied to genomic data can provide a powerful tool to distinguish milk composition QTL.
Publisher: Cold Spring Harbor Laboratory
Date: 04-02-2021
DOI: 10.1101/2021.02.04.429719
Abstract: Climate change and resilience to warming climates have implications for humans, livestock, and wildlife. The genetic mechanisms that confer thermotolerance to mammals are still not well characterized. We used dairy cows as a model to study heat tolerance because they are lactating, and therefore often prone to thermal stress. The data comprised almost 0.5 million milk records (milk, fat, and proteins) of 29,107 Australian Holsteins, each having around 15 million imputed sequence variants. Dairy animals often reduce their milk production when temperature and humidity rise thus, the phenotypes used to measure an in idual’s heat tolerance were defined as the rate of milk production decline (slope traits) with a rising temperature-humidity index. With these slope traits, we performed a genome-wide association study (GWAS) using different approaches, including conditional analyses, to correct for the relationship between heat tolerance and level of milk production. The results revealed multiple novel loci for heat tolerance, including 61 potential functional variants at sites highly conserved across vertebrate species. Moreover, it was interesting that specific candidate variants and genes are related to the neuronal system ( ITPR1, ITPR2, and GRIA4 ) and neuroactive ligand-receptor interaction functions for heat tolerance ( NPFFR2, CALCR, and GHR ), providing a novel insight that can help to develop genetic and management approaches to combat heat stress. While understanding the genetic basis of heat tolerance is crucial in the context of global warming’s effect on humans, livestock, and wildlife, the specific genetic variants and biological features that confer thermotolerance in animals are still not well characterized. The ability to tolerate heat varies across in iduals, with substantial genetic control of this complex trait. Dairy cattle are excellent model in which to find genes associated with in idual variations in heat tolerance since they significantly suffer from heat stress due to the metabolic heat of lactation. By genome-wide association studies of more than 29,000 cows with 15 million sequence variants and controlled phenotype measurements, we identify many new loci associated with heat tolerance. The biological functions of these loci are linked to the neuronal system and neuroactive ligand-receptor interaction functions. Also, several putative causal mutations for heat tolerance are at genomic sites that are otherwise evolutionarily conserved across 100 vertebrate species. Overall, our findings provide new insight into the molecular and biological basis of heat tolerance that can help to develop genetic and management approaches to combat heat stress.
Publisher: Springer Science and Business Media LLC
Date: 27-06-2004
DOI: 10.1038/NMAT1154
Publisher: CSIRO Publishing
Date: 21-07-2021
DOI: 10.1071/AN21061
Abstract: Context Functional genomics studies have highlighted genomic regions with regulatory and evolutionary significance. Such information independent of association analysis may benefit fine-mapping and genomic selection of economically important traits. However, systematic evaluation of the use of functional information in mapping, and genomic selection of cattle traits, is lacking. Also, single-nucleotide polymorphisms (SNPs) from the high-density (HD) panel are known to tag informative variants, but the performance of genomic prediction using HD SNPs together with variants supported by different functional genomics is unknown. Aims We selected six sets of functionally important variants and modelled each set together with HD SNPs in Bayesian models to map and predict protein, fat and milk yield as well as mastitis, somatic cell count and temperament of dairy cattle. Methods Two models were used, namely (1) BayesR, which includes priors of four distribution of variant effects, and (2) BayesRC, which includes additional priors of different functional classes of variants. Bayesian models were trained in three breeds of 28 000 cows of Holstein, Jersey and Australian Red and predicted into 2600 independent bulls. Key results Adding functionally important variants significantly increased the enrichment of genetic variance explained for mapped variants, suggesting improved genome-wide mapping precision. Such improvement was significantly higher when the same set of variants was modelled by BayesRC than by BayesR. Combining functional variant sets with HD SNPs improves genomic prediction accuracy in the majority of the cases and such improvement was more common and stronger for non-Holstein breeds and traits such as mastitis, somatic cell count and temperament. In contrast, adding a large number of random sequence variants to HD SNPs reduces mapping precision and has a worse or similar prediction accuracy, compared with using HD SNPs alone to map or predict. While BayesRC tended to have better genomic prediction accuracy than did BayesR, the overall difference in prediction accuracy between the two models was insignificant. Conclusions Our findings demonstrated the usefulness of functional data in genomic mapping and prediction. Implications We have highlighted the need for effective tools exploiting complex functional datasets to improve genomic prediction.
Publisher: Cold Spring Harbor Laboratory
Date: 15-07-2022
DOI: 10.1101/2022.07.13.499886
Abstract: To complete the genome-to-phenome map, transcriptome-wide association studies (TWAS) are performed to correlate genetically predicted gene expression with observed phenotypic measurements. However, the relatively small training population assayed with gene expression could limit the accuracy of TWAS. We propose Genetic Score Omics Regression (GSOR) correlating observed gene expression with genetically predicted phenotype, i.e., genetic score. The score, calculated using variants near genes with assayed expression, provides a powerful association test between cis- effects on gene expression and the trait. In simulated and real data, GSOR outperforms TWAS in detecting causal/informative genes. Applying GSOR to transcriptomes of 16 tissue (N∼5000) and 37 traits in ∼120,000 cattle, multi-trait meta-analyses of omics-associations (MTAO) found that, on average, each significant gene expression and splicing mediates cis -genetic effects on 8∼10 traits. Supported by Mendelian Randomisation, MTAO prioritised genes/splicing show increased evolutionary constraints. Many newly discovered genes/splicing regions underlie previously thought single-gene loci to influence multiple traits.
Publisher: Springer Science and Business Media LLC
Date: 18-01-2021
DOI: 10.1186/S12711-021-00602-9
Abstract: Variants that regulate transcription, such as expression quantitative trait loci (eQTL), have shown enrichment in genome-wide association studies (GWAS) for mammalian complex traits. However, no study has reported eQTL in sheep, although it is an important agricultural species for which many GWAS of complex meat traits have been conducted. Using RNA sequence data produced from liver and muscle from 149 sheep and imputed whole-genome single nucleotide polymorphisms (SNPs), our aim was to dissect the genetic architecture of the transcriptome by associating sheep genotypes with three major molecular phenotypes including gene expression (geQTL), exon expression (eeQTL) and RNA splicing (sQTL). We also examined these three types of eQTL for their enrichment in GWAS of multi-meat traits and fatty acid profiles. Whereas a relatively small number of molecular phenotypes were significantly heritable (h 2 0, P 0.05), their mean heritability ranged from 0.67 to 0.73 for liver and from 0.71 to 0.77 for muscle. Association analysis between molecular phenotypes and SNPs within ± 1 Mb identified many significant cis-eQTL (false discovery rate, FDR 0.01). The median distance between the eQTL and transcription start sites (TSS) ranged from 68 to 153 kb across the three eQTL types. The number of common variants between geQTL, eeQTL and sQTL within each tissue, and the number of common variants between liver and muscle within each eQTL type were all significantly ( P 0.05) larger than expected by chance. The identified eQTL were significantly ( P 0.05) enriched in GWAS hits associated with 56 carcass traits and fatty acid profiles. For ex le, several geQTL in muscle mapped to the FAM184B gene, hundreds of sQTL in liver and muscle mapped to the CAST gene, and hundreds of sQTL in liver mapped to the C6 gene. These three genes are associated with body composition or fatty acid profiles. We detected a large number of significant eQTL and found that the overlap of variants between eQTL types and tissues was prevalent. Many eQTL were also QTL for meat traits. Our study fills a gap in the knowledge on the regulatory variants and their role in complex traits for the sheep model.
Publisher: Elsevier BV
Date: 08-2023
Publisher: Springer Science and Business Media LLC
Date: 17-08-2021
DOI: 10.1038/S41598-021-95816-8
Abstract: While understanding the genetic basis of heat tolerance is crucial in the context of global warming’s effect on humans, livestock, and wildlife, the specific genetic variants and biological features that confer thermotolerance in animals are still not well characterized. We used dairy cows as a model to study heat tolerance because they are lactating, and therefore often prone to thermal stress. The data comprised almost 0.5 million milk records (milk, fat, and proteins) of 29,107 Australian Holsteins, each having around 15 million imputed sequence variants. Dairy animals often reduce their milk production when temperature and humidity rise thus, the phenotypes used to measure an in idual’s heat tolerance were defined as the rate of milk production decline (slope traits) with a rising temperature–humidity index. With these slope traits, we performed a genome-wide association study (GWAS) using different approaches, including conditional analyses, to correct for the relationship between heat tolerance and level of milk production. The results revealed multiple novel loci for heat tolerance, including 61 potential functional variants at sites highly conserved across 100 vertebrate species. Moreover, it was interesting that specific candidate variants and genes are related to the neuronal system ( ITPR1, ITPR2, and GRIA4 ) and neuroactive ligand–receptor interaction functions for heat tolerance ( NPFFR2, CALCR, and GHR ), providing a novel insight that can help to develop genetic and management approaches to combat heat stress.
Publisher: Springer Science and Business Media LLC
Date: 2006
DOI: 10.1557/PROC-0945-FF07-05
Abstract: The stability of high performance thermoelectric Zn 4 Sb 3 has been studied, by using synchrotron powder diffraction to establish differences in phase transition temperatures of two s les. High resolution multi temperature diffraction data has been collected, with a time interval of 13 months, and the phase transition temperature was determined based on the results of Rietveld refinements. The refinements show a difference in transition temperature from data collected the first time till data collected the second time. Furthermore the s les showed impurity peaks after being exposed to air for 13 months, indicating that the s le decomposes over time.
Publisher: American Physical Society (APS)
Date: 13-04-2005
Publisher: Springer Science and Business Media LLC
Date: 28-02-2020
DOI: 10.1038/S42003-020-0823-6
Abstract: In genome-wide association studies (GWAS), variants showing consistent effect directions across populations are considered as true discoveries. We model this information in an E ffect D irection ME ta-analysis (EDME) to quantify pleiotropy using GWAS of 34 Cholesky-decorrelated traits in 44,000+ cattle with sequence variants. The effect-direction agreement between independent bull and cow datasets was used to quantify the false discovery rate by effect direction (FDRed) and the number of affected traits for prioritised variants. Variants with multi-trait p 1e–6 affected 1∼22 traits with an average of 10 traits. EDME assigns pleiotropic variants to each trait which informs the biology behind complex traits. New pleiotropic loci are identified, including signals from the cattle FTO locus mirroring its bystander effects on human obesity. When validated in the 1000-Bull Genome database, the prioritized pleiotropic variants consistently predicted expected phenotypic differences between dairy and beef cattle. EDME provides robust approaches to control GWAS FDR and quantify pleiotropy.
Publisher: PeerJ
Date: 08-03-2016
DOI: 10.7717/PEERJ.1762
Abstract: Background. Ruminants are successful herbivorous mammals, in part due to their specialized forestomachs, the rumen complex, which facilitates the conversion of feed to soluble nutrients by micro-organisms. Is the rumen complex a modified stomach expressing new epithelial (cornification) and metabolic programs, or a specialised stratified epithelium that has acquired new metabolic activities, potentially similar to those of the colon? How has the presence of the rumen affected other sections of the gastrointestinal tract (GIT) of ruminants compared to non-ruminants? Methods. Transcriptome data from 11 tissues covering the sheep GIT, two stratified epithelial and two control tissues, was analysed using principal components to cluster tissues based on gene expression profile similarity. Expression profiles of genes along the sheep GIT were used to generate a network to identify genes enriched for expression in different compartments of the GIT. The data from sheep was compared to similar data sets from two non-ruminants, pigs (closely related) and humans (more distantly related). Results. The rumen transcriptome clustered with the skin and tonsil, but not the GIT transcriptomes, driven by genes from the epidermal differentiation complex, and genes encoding stratified epithelium keratins and innate immunity proteins. By analysing all of the gene expression profiles across tissues together 16 major clusters were identified. The strongest of these, and consistent with the high turnover rate of the GIT, showed a marked enrichment of cell cycle process genes ( P = 1.4 E−46), across the whole GIT, relative to liver and muscle, with highest expression in the caecum followed by colon and rumen. The expression patterns of several membrane transporters (chloride, zinc, nucleosides, amino acids, fatty acids, cholesterol and bile acids) along the GIT was very similar in sheep, pig and humans. In contrast, short chain fatty acid uptake and metabolism appeared to be different between the species and different between the rumen and colon in sheep. The importance of nitrogen and iodine recycling in sheep was highlighted by the highly preferential expression of SLC14A1 -urea (rumen), RHBG-ammonia (intestines) and SLC5A5- iodine (abomasum). The gene encoding a poorly characterized member of the maltase-glucoamylase family (MGAM2), predicted to play a role in the degradation of starch or glycogen, was highly expressed in the small and large intestines. Discussion. The rumen appears to be a specialised stratified cornified epithelium, probably derived from the oesophagus, which has gained some liver-like and other specialized metabolic functions, but probably not by expression of pre-existing colon metabolic programs. Changes in gene transcription downstream of the rumen also appear have occurred as a consequence of the evolution of the rumen and its effect on nutrient composition flowing down the GIT.
No related grants have been discovered for Ruidong Xiang.