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X chromosome variants were associated to heritable fertility traits, in two bovine populations.
Fortes, Porto-Neto et al. 2019.
Background: Targeting phenotypes related to bull fertility, such as spe... morerm morphology and sperm DNA fragmentation can help identify mutations that limit reproduction capacity. Twenty-five fertility-related phenotypes were measured as indicators of bull fertility (1,099 Brahman bulls and 1,719 Tropical Composite bulls). Measurements included standard bull breeding soundness measures (e.g. sperm motility), scrotal circumference, sperm DNA fragmentation and sperm protamine deficiency. These phenotypes were used in a genome-wide association studies that aimed to detect quantitative trait loci (QTL).
Results: Genomic analyses confirmed some QTL in both breeds (Brahman and Tropical Composites) while others were breed specific. For example, only in Brahman cattle, we identified polymorphisms associated (P < 10-16) with sperm midpiece morphological abnormalities. The QTL identified and mutations occurring only in Bos indicus suggest that the gene A-kinase anchoring protein (AKAP)14 might be related to midpiece abnormalities in Brahman. Associated mutations described herein corroborate with known genes affecting spermatogenesis, including those in the AKAP and testis-expressed gene (TEX) families. Polymorphism associations suggest that AKAP14 and TEX11 are positional and functional candidate genes in chromosome X affecting bull fertility. Most significant variants and QTLs mapped to chromosome X. These results add evidence to a mammalian specialization of X that evolved to harbor genes linked to spermatogenesis, as similarly observed in mice and humans. Some variants in X may affect more than one genetically correlated trait (r2 ~ 0.33–0.51), such as sperm morphology and sperm DNA fragmentation. Correlations and shared QTL support the hypothesis that these phenotypes have the same underlying cause: faulty spermatogenesis. In addition, heritabilities for sperm DNA fragmentation and sperm protamine deficiency were moderate (h2 ~ 0.21–0.47), being the first reported estimates.
Conclusions: Genetic improvement for bull fertility is possible through selective breeding. Genomic selection for bull fertility might be more accurate if the X chromosome mutations that underlie the discovered QTL are included in the analyses. Variants associated with bull fertility accumulate in the X chromosome, as they do in humans and mice, thus, suggesting specialization of this chromosome.
MLA: L.GEN.1818 Bull fertility update: historical data, new cohort and advanced genomics - Livestock genetics and genomics - Published 11 Sep 2019
Unfiltered variants from 935 sheep genomes
Acquired - - Published 26 Jul 2019
High quality variants from 935 sheep genomes
SNP genotypes, collected from 11 populations and 184 Pacific oysters, as part of a published study on genetic diversity. Details of published work are:
"Assessment of genetic diversity and population ... morestructure in cultured Australian Pacific oysters". Animal Genetics (In Press).less
SIP 254 FY18 - Functional Annotation of Salmon Genome - - Published 02 Jul 2019
Data related to Naval-Sanchez et al. 2019 "Selection Signatures in heat-resistant cattle reveal missense mutations in damage response gene HELB".
Whole genome sequences from the 1000 Bull Gen... moreomes Project (Run6, Bos taurus, and Bos indicus) for breeds chosen as a reference for imputation were retrieved (Daetwyler et al. 2014; Hayes and Daetwyler 2018). This results in 440 whole-genome sequences across 18 cattle breeds.
Breeds were grouped in accordance to their phenotypes and reported genomic crosses as taurine (humpless), indicine (with hump), admixed or African sanga, the two latter being stabilized composite breeds (Rege J 1999; Hanotte et al. 2002; Rege J et al. 2007; Mwai et al. 2015; Felius, Marleen et al. 2016).
The dataset contains 186 European Taurine, 102 Asiatic indicine and 80 cross-bred genomes as well as a set of African samples composed of 12 taurine, 41 sanga and 19 indicine.
Genomic Analytics in the Realm of Big Data (OCE Post-Doc) - - Published 17 Jun 2019
Data for the 8-parent MAGIC map, including the genetic map, genetic data for the founding lines and founder population, and the imputed underlying genotypes.
SIP 8: MAGIC and HIF development and an - - Published 27 Dec 2018
Genome, annotation and raw data for publication titled: "Genomic changes associated with adaptation to arid environments in cactophilic Drosophila species "
Legacy data - - Published 12 Dec 2018
Legacy data - - Published 02 Nov 2018
We sequenced small RNAs from the following five conditions: germinated spores (3 replicates), ungerminated spores (1 replicate), uninfected wheat (3 replicates) and infected wheat at 3dpi, 5dpi and 7d... morepi (3 replicates each). less
Characterisation of non-coding RNA cross talk mechanisms between fungal pathogens and plants and investigation of their role in pathogenicity - - Published 31 Oct 2018
The files used in the real data analyses of the paper entitled "Eagle: Making multiple-locus association mapping on a genome-wide scale routine". The original data comes from Nicod et al. (2016) Natu... morere Genetics who collected SNP dosages (continuous scores from 0 to1). We transformed these dosages into SNP genotypes (0,1,2).
Input files suitable for analysis by Eagle. The data were obtained from a large genome-wide association study (GWAS) performed in outbred mice and published on the Heterogeneous Stock Mouse web site. The data were reorganized to make it suitable for input into Eagle.
Acquired - Development of Statistical Methods - Published 12 Oct 2018
Transcriptome reads and assembly from multiple life stages of the Queensland Fruit Fly (Bactrocera tryoni).
HAL Diet medicated RNAi Sterile Insect T - - Published 28 Sep 2018
125 bp paired-end Illumina HiSeq 2500 v4.0 NGS sequence reads for 72 individually indexed Cinclosoma specimens (by mitochondrial data composed of C. castanotum , C. clarum , C. fordianum , ... moreand one each of C. punctatum and C. cinnamomeum alisteri as outgroups). This sequence data forms the basis of a biogeographic population genomics study of Cinclosoma across Australia's semi-arid south and west. less
OCE Postdoc Evolutionary Rescue a - Quail-thrush Population Genomics and Biogeography - Published 13 Aug 2018
Assembled genomic and tissue-specific transcriptomic data resources for two genetically distinct lines of Cowpea (Vigna unguiculata (L.) Walp). For each of two varieties of cowpea (IT97K-499-35, IT86D... more-1010) this collections contains the following datasets :
i) genomic survey assemblies based on Illumina sequencing
ii) transcriptome assemblies
iii) raw DNA and RNA sequence data feeding into the above assemblies
iv) In-silico gene predictions and predicted gene sequences derived from IT86D-1010 and IT97K-499-35
v) Mapping to the Vigna unguiculata v1.0 reference genome (http://phytozome.jgi.doe.gov/)
Capturing Heterosis for Smallholders, OPP1076280 - Crop genomics - Published 06 Jun 2018
A collection of raw and analysed sequence resources of three ovule cell types; enlarging aposporous initial cells, early aposporous embryo sacs and somatic ovule cells in apomictic Hieracium praealtum... more. This collection was generated by the Asexual Seed Formation research team in CSIRO led by Anna Koltunow. This data collection supports the publication : Asexual female gametogenesis involves contact with a sexually-fated megaspore in apomictic Hieracium Martina Juranić, Matthew R. Tucker , Carolyn J. Schultz, Neil J. Shirley, Jennifer M. Taylor, Andrew Spriggs, Susan D. Johnson, Vincent Bulone and Anna M.G. Koltunow* Plant Physiology 2018less
OCE, PDF, KOL014-RAB018, Switching betwe - Development and Characterisation of Hieracium Genomics Resource - Published 31 May 2018
raw sequence and variant files from genome sequencing of Abalone species.
Jade Tiger Abalone selective breeding program: Enhancing genetic gains and securing program sustainability - - Published 29 May 2018
Raw single nucleotide polymorphism (SNP) genotypes obtained from samples collected in the Kimberley region of Western Australia. Genotypes derived from a "reduced representation" sequencing method as ... moreprovided by Diversity Arrays PTY LTD.
Also, covariates associated with each individual:
WAMSI-Kim 1.1.3 Ecological connectivity - DArTseq genotyping - Published 08 Feb 2018
Supplementary Data9: Allele Frequencies for 14 million SNPs MAF>0.05
OCE Post Doc - Conseq Animal Domesticati - - Published 06 Feb 2018
SNPs discovered in 20 farmed Tasmanian salmon from high covergae sequence analysis, SNps present in double haploid reference animal removed.
SIP 52 Salmon Genome & Tailored tools fo - - Published 29 Jan 2018
In the absence of detailed functional annotation for any livestock genome, we used comparative genomics to predict ovine regulatory elements using human data. Reciprocal liftOver was used to predict t... morehe ovine genome location of ENCODE promoters and enhancers, along with 12 chromatin states built using 127 diverse epigenome.
Here we make available the following files:
a) Sheep_epigenome_predicted_features.tar.gz: contains the final reciprocal best alignment from ENCODE proximal as well as chromHMM ROADMAP features. The result of reciprocal liftOver.
b) liftOver_sheep_temporary_files.tar.gz: We have
added a new tar file with liftOver temporary files
i) LiftOver temporary files mapping human to sheep,
ii) LiftOver temporary files mapping sheep back to human and
iii) Dictionary files containing the link between human to sheep coordinates for exact best-reciprocal files.
OCE Post Doc - Conseq Animal Domesticati - - Published 09 Nov 2017
This data set contains the genomes of Helicoverpa armigera and Helicoverpa zea and the relevant annotations.
Genomic innovations, transcriptional plasticity and gene loss underlying the evolution an... mored divergence of two highly polyphagous and invasive Helicoverpa pest species
Legacy data - Insect genomics - Published 11 Aug 2017
A collection of raw and analysed sequence resources across several Hieracium species and genotypes related to the study of apomixis. This collection was generated by the Asexual Seed Formation researc... moreh team in CSIRO led by Anna Koltunow.
This data collection supports the publication : Generation of an integrated Hieracium genomic and transcriptome resource enables exploration of small RNA pathways during apomixis initiation
David S. Rabiger, Jennifer M. Taylor, Andrew Spriggs, Melanie L. Hand, Steven T. Henderson, Susan D. Johnson, Karsten Oelkers1, Maria Hrmova, Keisuke Saito, Go Suzuki, Yasuhiko Mukai, Bernard J. Carroll and Anna M.G. Koltunow*
BMC Biology 2016
OCE, PDF, KOL014-RAB018, Switching betwe - Development and Characterisation of Hieracium Genomics Resource - Published 28 Apr 2017
Files associated with this project:
== MiSeq PE and Mitochrondrial reads ==
== HiSeq PE Data ==
= Mitochondrial genome =
... more- A_hancockii_mito_complete.fa (complete mitochrondrial genome)
= Nuclear genome =
- FRR3425_A_hancockii_noMITO_min_200.fasta (contigs > 200bp)
- FRR3425_A_hancockii_noMITO_belowCutoff_200.fasta (contigs < 200bp)
**Gene Calls (AUGUSTUS)**
- FRR3425.outfile (GFF)
- FRR3425.outfile.aa (Amino acid calls for genes)
- FRR3425.outfile.cdexons (Exons)
- FRR3425.outfile.codingseq (Coding seqs)
Legacy data - Fungal genomics - Published 07 Mar 2017
Draft genome assemblies of 380 Bradyrhizobium isolates collected from soil samples at the base of Acacia acuminata trees in Southwest Australia
Biodiversity Eco Know & Serv - Awards & - Survey of rhizobia in soils of South-West Australia - Published 03 Mar 2017
Reproduction and recruitment underlie the maintenance of biological communities. For most marine organisms the ocean environment provides the potential for widespread dispersal of organisms during var... moreious life cycle stages via currents, tides and wind.
Within the Kimberley region, key biological communities have a range of reproductive modes. Understanding patterns of larval connectivity is critical to managing the exposure of biological communities to disturbances in space and time.
KSN Project 1.1.3 employed genomic tools (microsatellite DNA markers and single nucleotide polymorphisms) and microchemistry to provide the first comprehensive measurements of the distances moved by marine organisms between Kimberley reefs, and how frequently organisms move between the Kimberley and other regions (e.g. offshore shoals, the Pilbara). The research also identified potential barriers to movement. Seven organisms (two
hard corals, two seagrasses, a mollusc, two fishes) were chosen as models for exploring connectivity in the Kimberley at both fine and broad scales.
This metadata record applies to three of the seven species investigated as part of project WAMSI 2 KSN 1.1.3. The data held is Raw SNP genotype. Metadata records associated with other species and lodged by AIMS, WA Museum, Curtin University, Department of Fisheries (WA) and Edith Cowan University can be accessed via Pawsey.
WAMSI-Kim 1.1.3 Ecological connectivity - Survey - Published 05 Dec 2016
The DEW pipeline is a one command line solution that aligns reads, corrects expression biases (eXpress), TMM normalizes (edgeR) and produces FPKM values that are then visualized with pretty ggplot gra... morephics.
This BZ2-compressed tar archive provides the software and licensing statements. DEW is written in Perl and requires a SQLite database and is supported for Linux 64-bit computers. The homepage of the software can be found at http://dew.sourceforge.net.less
Cont to TCP01 Dissecting Adaptive - transcriptomics software development - Published 06 Jan 2015