Publications by authors named "Sean McWilliam"

42 Publications

A low-density SNP genotyping panel for the accurate prediction of cattle breeds.

J Anim Sci 2020 Nov;98(11)

CSIRO Agriculture & Food, Chiswick, New England Highway, Armidale, NSW, Australia.

Genomic tools to better define breed composition in agriculturally important species have sparked scientific and commercial industry interest. Knowledge of breed composition can inform multiple scientifically important decisions of industry application including DNA marker-assisted selection, identification of signatures of selection, and inference of product provenance to improve supply chain integrity. Genomic tools are expensive but can be economized by deploying a relatively small number of highly informative single-nucleotide polymorphisms (SNP) scattered evenly across the genome. Using resources from the 1000 Bull Genomes Project we established calibration (more stringent quality criteria; N = 1,243 cattle) and validation (less stringent; N = 864) data sets representing 17 breeds derived from both taurine and indicine bovine subspecies. Fifteen successively smaller panels (from 500,000 to 50 SNP) were built from those SNP in the calibration data that increasingly satisfied 2 criteria, high differential allele frequencies across the breeds as measured by average Euclidean distance (AED) and high uniformity (even spacing) across the physical genome. Those SNP awarded the highest AED were in or near genes previously identified as important signatures of selection in cattle such as LCORL, NCAPG, KITLG, and PLAG1. For each panel, the genomic breed composition (GBC) of each animal in the validation dataset was estimated using a linear regression model. A systematic exploration of the predictive accuracy of the various sized panels was then undertaken on the validation population using 3 benchmarking approaches: (1) % error (expressed relative to the estimated GBC made from over 1 million SNP), (2) % breed misassignment (expressed relative to each individual's breed recorded), and (3) Shannon's entropy of estimated GBC across the 17 target breeds. Our analyses suggest that a panel of just 250 SNP represents an adequate balance between accuracy and cost-only modest gains in accuracy are made as one increases panel density beyond this point.
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http://dx.doi.org/10.1093/jas/skaa337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8202515PMC
November 2020

Changed Patterns of Genomic Variation Following Recent Domestication: Selection Sweeps in Farmed Atlantic Salmon.

Front Genet 2020 3;11:264. Epub 2020 Apr 3.

CSIRO Agriculture and Food, Brisbane, QLD, Australia.

The introduction of wild Atlantic salmon into captivity, and their subsequent artificial selection for production traits, has caused phenotypic differences between domesticated fish and their wild counterparts. Identification of regions of the genome underling these changes offers the promise of characterizing the early biological consequences of domestication. In the current study, we sequenced a population of farmed European Atlantic salmon and compared the observed patterns of SNP variation to those found in conspecific wild populations. This identified 139 genomic regions that contained significantly elevated SNP homozygosity in farmed fish when compared to their wild counterparts. The most extreme was adjacent to , a gene involved in control of neural crest cell migration. To control for false positive signals, a second and independent dataset of farmed and wild European Atlantic salmon was assessed using the same methodology. A total of 81 outlier regions detected in the first dataset showed significantly reduced homozygosity within the second one, strongly suggesting the genomic regions identified are enriched for true selection sweeps. Examination of the associated genes identified a number previously characterized as targets of selection in other domestic species and that have roles in development, behavior and olfactory system. These include , , and genes. Finally, we searched for evidence of parallel sweeps using a farmed population of North American origin. This failed to detect a convincing overlap to the putative sweeps present in European populations, suggesting the factors that drive patterns of variation under domestication and early artificial selection were largely independent. This is the first analysis on domestication of aquaculture species exploiting whole-genome sequence data and resulted in the identification of sweeps common to multiple independent populations of farmed European Atlantic salmon.
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http://dx.doi.org/10.3389/fgene.2020.00264DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7147387PMC
April 2020

Gene expression identifies metabolic and functional differences between intramuscular and subcutaneous adipocytes in cattle.

BMC Genomics 2020 Jan 28;21(1):77. Epub 2020 Jan 28.

New South Wales Department of Primary Industries, Armidale Livestock Industries Centre, University of New England, Armidale, NSW, 2351, Australia.

Background: This study used a genome-wide screen of gene expression to better understand the metabolic and functional differences between commercially valuable intramuscular fat (IMF) and commercially wasteful subcutaneous (SC) fat depots in Bos taurus beef cattle.

Results: We confirmed many findings previously made at the biochemical level and made new discoveries. The fundamental lipogenic machinery, such as ACACA and FASN encoding the rate limiting Acetyl CoA carboxylase and Fatty Acid synthase were expressed at 1.6-1.8 fold lower levels in IMF, consistent with previous findings. The FA elongation pathway including the rate limiting ELOVL6 was also coordinately downregulated in IMF compared to SC as expected. A 2-fold lower expression in IMF of ACSS2 encoding Acetyl Coenzyme A synthetase is consistent with utilisation of less acetate for lipogenesis in IMF compared to SC as previously determined using radioisotope incorporation. Reduced saturation of fat in the SC depot is reflected by 2.4 fold higher expression of the SCD gene encoding the Δ9 desaturase enzyme. Surprisingly, CH25H encoding the cholesterol 25 hydroxylase enzyme was ~ 36 fold upregulated in IMF compared to SC. Moreover, its expression in whole muscle tissue appears representative of the proportional representation of bovine marbling adipocytes. This suite of observations prompted quantification of a set of oxysterols (oxidised forms of cholesterol) in the plasma of 8 cattle exhibiting varying IMF. Using Liquid Chromatography-Mass Spectrometry (LC-MS) we found the levels of several oxysterols were significantly associated with multiple marbling measurements across the musculature, but (with just one exception) no other carcass phenotypes.

Conclusions: These data build on our molecular understanding of ruminant fat depot biology and suggest oxysterols represent a promising circulating biomarker for cattle marbling.
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http://dx.doi.org/10.1186/s12864-020-6505-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986065PMC
January 2020

Greenlip Abalone () Genome and Protein Analysis Provides Insights into Maturation and Spawning.

G3 (Bethesda) 2019 10 7;9(10):3067-3078. Epub 2019 Oct 7.

School of Science and Education, Genecology Research Center, University of the Sunshine Coast, Maroochydore DC, Queensland, Australia, 4558.

Wild abalone (Family ) populations have been severely affected by commercial fishing, poaching, anthropogenic pollution, environment and climate changes. These issues have stimulated an increase in aquaculture production; however production growth has been slow due to a lack of genetic knowledge and resources. We have sequenced a draft genome for the commercially important temperate Australian 'greenlip' abalone (, Donovan 1808) and generated 11 tissue transcriptomes from a female adult abalone. Phylogenetic analysis of the greenlip abalone with reference to the Pacific abalone () indicates that these abalone species diverged approximately 71 million years ago. This study presents an in-depth analysis into the features of reproductive dysfunction, where we provide the putative biochemical messenger components (neuropeptides) that may regulate reproduction including gonad maturation and spawning. Indeed, we isolate the egg-laying hormone neuropeptide and under trial conditions induce spawning at 80% efficiency. Altogether, we provide a solid platform for further studies aimed at stimulating advances in abalone aquaculture production. The genome and resources are made available to the public on the abalone 'omics website, http://abalonedb.org.
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http://dx.doi.org/10.1534/g3.119.400388DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6778792PMC
October 2019

Polygenic and sex specific architecture for two maturation traits in farmed Atlantic salmon.

BMC Genomics 2019 Feb 15;20(1):139. Epub 2019 Feb 15.

Commonwealth Scientific and Industrial Research Organisation Agriculture and Food, Queensland Bioscience Precinct, St Lucia Brisbane, 4067, Australia.

Background: A key developmental transformation in the life of all vertebrates is the transition to sexual maturity, whereby individuals are capable of reproducing for the first time. In the farming of Atlantic salmon, early maturation prior to harvest size has serious negative production impacts.

Results: We report genome wide association studies (GWAS) using fish measured for sexual maturation in freshwater or the marine environment. Genotypic data from a custom 50 K single nucleotide polymorphism (SNP) array was used to identify 13 significantly associated SNP for freshwater maturation with the most strongly associated on chromosomes 10 and 11. A higher number of associations (48) were detected for marine maturation, and the two peak loci were found to be the same for both traits. The number and broad distribution of GWAS hits confirmed a highly polygenetic nature, and GWAS performed separately within males and females revealed sex specific genetic behaviour for loci co-located with positional candidate genes phosphatidylinositol-binding clathrin assembly protein-like (picalm) and membrane-associated guanylate kinase, WW and PDZ domain-containing protein 2 (magi2).

Conclusions: The results extend earlier work and have implications for future applied breeding strategies to delay maturation in this important aquaculture species.
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http://dx.doi.org/10.1186/s12864-019-5525-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6377724PMC
February 2019

Genome Sequencing of Blacklip and Greenlip Abalone for Development and Validation of a SNP Based Genotyping Tool.

Front Genet 2018 4;9:687. Epub 2019 Jan 4.

CSIRO Agriculture and Food, Queensland Bioscience Precinct, Brisbane, QLD, Australia.

Abalone breeding in southern Australia often involves the production of interspecies hybrids through crossing blacklip () and greenlip () parental populations. To assist applied breeding and investigate genetic divergence, this study applied genome sequencing and variant detection to develop and validate a SNP genotyping tool. Skim short read Illumina sequencing was performed using 24 individuals from each of the two parental species and a hybrid population. Raw reads were assembled into three population specific pools (each 12-15 fold coverage), before mapping was performed against a draft greenlip abalone reference genome. Variant detection identified 22.4 M raw variants across the three populations (SNP and indels), suggesting they are highly heterozygous. First stage filtering defined a high quality SNP collection of 2.2 M variants independently called in each of the three populations. Second stage filtering identified a much smaller set of variants for assay design and genotyping using a validation set of 191 abalone of known population and pedigree. Comparison of allele frequency data revealed a high proportion of SNP (43%) had divergent allele frequency (< 0.2) between the two parental populations, suggesting they should have utility for parentage assignment. A maximum likelihood approach was used to successfully assign 105 of 105 progeny to their known true parent amongst a set of 86 candidate parents, confirming the genotyping tool has utility for applied breeding. Analysis of pairwise allele sharing successfully discriminated animals into populations, and PCA of genetic distance grouped the hybrid animals with intermediate values between the two parental populations. The findings present a library of DNA polymorphism of utility to breeding and ecological application, and begins to characterize the divergence separating two economically important aquaculture species.
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http://dx.doi.org/10.3389/fgene.2018.00687DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6328477PMC
January 2019

De novo assembly, characterization, functional annotation and expression patterns of the black tiger shrimp (Penaeus monodon) transcriptome.

Sci Rep 2018 09 10;8(1):13553. Epub 2018 Sep 10.

ARC Research Hub for Advanced Prawn Breeding, Townsville, QLD, 4811, Australia.

The black tiger shrimp (Penaeus monodon) remains the second most widely cultured shrimp species globally; however, issues with disease and domestication have seen production levels stagnate over the past two decades. To help identify innovative solutions needed to resolve bottlenecks hampering the culture of this species, it is important to generate genetic and genomic resources. Towards this aim, we have produced the most complete publicly available P. monodon transcriptome database to date based on nine adult tissues and eight early life-history stages (BUSCO - Complete: 98.2% [Duplicated: 51.3%], Fragmented: 0.8%, Missing: 1.0%). The assembly resulted in 236,388 contigs, which were then further segregated into 99,203 adult tissue specific and 58,678 early life-history stage specific clusters. While annotation rates were low (approximately 30%), as is typical for a non-model organisms, annotated transcript clusters were successfully mapped to several hundred functional KEGG pathways. Transcripts were clustered into groups within tissues and early life-history stages, providing initial evidence for their roles in specific tissue functions, or developmental transitions. We expect the transcriptome to provide an essential resource to investigate the molecular basis of commercially relevant-significant traits in P. monodon and other shrimp species.
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http://dx.doi.org/10.1038/s41598-018-31148-4DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6131155PMC
September 2018

Evolution of Sex Determination Loci in Atlantic Salmon.

Sci Rep 2018 04 4;8(1):5664. Epub 2018 Apr 4.

CSIRO Data 61, Canberra, 2601, ACT, Australia.

Teleost fish exhibit a remarkable diversity in the control of sex determination, offering the opportunity to identify novel differentiation mechanisms and their ecological consequences. Here, we perform GWAS using 4715 fish and 46,501 SNP to map sex determination to three separate genomic locations in Atlantic salmon (Salmo salar). To characterize each, whole genome sequencing was performed to 30-fold depth of coverage using 20 fish representing each of three identified sex lineages. SNP polymorphism reveals male fish carry a single copy of the male specific region, consistent with an XX/XY or male heterogametric sex system. Haplotype analysis revealed deep divergence between the putatively ancestral locus on chromosome 2, compared with loci on chromosomes 3 and 6. Haplotypes in fish carrying either the chromosome 3 or 6 loci were nearly indistinguishable, indicating a founding event that occurred following the speciation event that defined Salmo salar from other salmonids. These findings highlight the evolutionarily fluid state of sex determination systems in salmonids, and resolve to the sequence level differences in animals with divergent sex lineages.
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http://dx.doi.org/10.1038/s41598-018-23984-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5884791PMC
April 2018

Sheep genome functional annotation reveals proximal regulatory elements contributed to the evolution of modern breeds.

Nat Commun 2018 02 28;9(1):859. Epub 2018 Feb 28.

CSIRO Agriculture and Food, 306 Carmody Road, St. Lucia, 4067, QLD, Australia.

Domestication fundamentally reshaped animal morphology, physiology and behaviour, offering the opportunity to investigate the molecular processes driving evolutionary change. Here we assess sheep domestication and artificial selection by comparing genome sequence from 43 modern breeds (Ovis aries) and their Asian mouflon ancestor (O. orientalis) to identify selection sweeps. Next, we provide a comparative functional annotation of the sheep genome, validated using experimental ChIP-Seq of sheep tissue. Using these annotations, we evaluate the impact of selection and domestication on regulatory sequences and find that sweeps are significantly enriched for protein coding genes, proximal regulatory elements of genes and genome features associated with active transcription. Finally, we find individual sites displaying strong allele frequency divergence are enriched for the same regulatory features. Our data demonstrate that remodelling of gene expression is likely to have been one of the evolutionary forces that drove phenotypic diversification of this common livestock species.
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http://dx.doi.org/10.1038/s41467-017-02809-1DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5830443PMC
February 2018

Genomic correlation: harnessing the benefit of combining two unrelated populations for genomic selection.

Genet Sel Evol 2015 Nov 2;47:84. Epub 2015 Nov 2.

CSIRO Agriculture, Queensland Bioscience Precinct, St. Lucia, QLD, 4067, Australia.

Background: The success of genomic selection in animal breeding hinges on the availability of a large reference population on which genomic-based predictions of additive genetic or breeding values are built. Here, we explore the benefit of combining two unrelated populations into a single reference population.

Methods: The datasets consisted of 1829 Brahman and 1973 Tropical Composite cattle with measurements on five phenotypes relevant to tropical adaptation and genotypes for 71,726 genome-wide single nucleotide polymorphisms (SNPs). The underlying genomic correlation for the same phenotype across the two breeds was explored on the basis of consistent linkage disequilibrium (LD) phase and marker effects in both breeds.

Results: The proportion of genetic variance explained by the entire set of SNPs ranged from 37.5 to 57.6 %. Estimated genomic correlations were drastically affected by the process used to select SNPs and went from near 0 to more than 0.80 for most traits when using the set of SNPs with significant effects and the same LD phase in the two breeds. We found that, by carefully selecting the subset of SNPs, the missing heritability can be largely recovered and accuracies in genomic predictions can be improved six-fold. However, the increases in accuracy might come at the expense of large biases.

Conclusions: Our results offer hope for the effective implementation of genomic selection schemes in situations where the number of breeds is large, the sample size within any single breed is small and the breeding objective includes many phenotypes.
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http://dx.doi.org/10.1186/s12711-015-0162-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4630892PMC
November 2015

Whole-genome resequencing uncovers molecular signatures of natural and sexual selection in wild bighorn sheep.

Mol Ecol 2015 Nov 6;24(22):5616-32. Epub 2015 Nov 6.

CSIRO Agriculture, 306 Carmody Road, St Lucia, Brisbane, Qld, 4067, Australia.

The identification of genes influencing fitness is central to our understanding of the genetic basis of adaptation and how it shapes phenotypic variation in wild populations. Here, we used whole-genome resequencing of wild Rocky Mountain bighorn sheep (Ovis canadensis) to >50-fold coverage to identify 2.8 million single nucleotide polymorphisms (SNPs) and genomic regions bearing signatures of directional selection (i.e. selective sweeps). A comparison of SNP diversity between the X chromosome and the autosomes indicated that bighorn males had a dramatically reduced long-term effective population size compared to females. This probably reflects a long history of intense sexual selection mediated by male-male competition for mates. Selective sweep scans based on heterozygosity and nucleotide diversity revealed evidence for a selective sweep shared across multiple populations at RXFP2, a gene that strongly affects horn size in domestic ungulates. The massive horns carried by bighorn rams appear to have evolved in part via strong positive selection at RXFP2. We identified evidence for selection within individual populations at genes affecting early body growth and cellular response to hypoxia; however, these must be interpreted more cautiously as genetic drift is strong within local populations and may have caused false positives. These results represent a rare example of strong genomic signatures of selection identified at genes with known function in wild populations of a nonmodel species. Our results also showcase the value of reference genome assemblies from agricultural or model species for studies of the genomic basis of adaptation in closely related wild taxa.
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http://dx.doi.org/10.1111/mec.13415DOI Listing
November 2015

Non-synonymous mutations mapped to chromosome X associated with andrological and growth traits in beef cattle.

BMC Genomics 2015 May 15;16:384. Epub 2015 May 15.

Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, QLD, 4067, Australia.

Background: Previous genome-wide association analyses identified QTL regions in the X chromosome for percentage of normal sperm and scrotal circumference in Brahman and Tropical Composite cattle. These traits are important to be studied because they are indicators of male fertility and are correlated with female sexual precocity and reproductive longevity. The aim was to investigate candidate genes in these regions and to identify putative causative mutations that influence these traits. In addition, we tested the identified mutations for female fertility and growth traits.

Results: Using a combination of bioinformatics and molecular assay technology, twelve non-synonymous SNPs in eleven genes were genotyped in a cattle population. Three and nine SNPs explained more than 1% of the additive genetic variance for percentage of normal sperm and scrotal circumference, respectively. The SNPs that had a major influence in percentage of normal sperm were mapped to LOC100138021 and TAF7L genes; and in TEX11 and AR genes for scrotal circumference. One SNP in TEX11 was explained ~13% of the additive genetic variance for scrotal circumference at 12 months. The tested SNP were also associated with weight measurements, but not with female fertility traits.

Conclusions: The strong association of SNPs located in X chromosome genes with male fertility traits validates the QTL. The implicated genes became good candidates to be used for genetic evaluation, without detrimentally influencing female fertility traits.
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http://dx.doi.org/10.1186/s12864-015-1595-0DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4432507PMC
May 2015

Transcriptome profiles of Penaeus (Marsupenaeus) japonicus animal and vegetal half-embryos: identification of sex determination, germ line, mesoderm, and other developmental genes.

Mar Biotechnol (NY) 2015 Jun 30;17(3):252-65. Epub 2015 Jan 30.

CSIRO Agriculture Flagship, Integrated Sustainable Aquaculture, Dutton Park, Qld, 4102, Australia,

There is virtually no knowledge of the molecular events controlling early embryogenesis in Penaeid shrimp. A combination of controlled spawning environment, shrimp embryo micro-dissection techniques, and next-generation sequencing was used to produce transcriptome EST datasets of Penaeus japonicus animal and vegetal half-embryos. Embryos were collected immediately after spawning, and then blastomeres were separated at the two-cell stage and allowed to develop to late gastrulation, then pooled for RNA isolation and cDNA synthesis. Ion Torrent sequencing of cDNA from approximately 500 pooled animal and vegetal half-embryos from multiple spawnings resulted in 560,516 and 493,703 reads, respectively. Reads from each library were assembled and Gene Ontogeny analysis produced 3479 annotated animal contigs and 4173 annotated vegetal contigs, with 159/139 hits for developmental processes in the animal/vegetal contigs, respectively. Contigs were subject to BLAST for selected developmental toolbox genes. Some of the genes found included the sex determination genes sex-lethal and transformer; the germ line genes argonaute 1, boule, germ cell-less, gustavus, maelstrom, mex-3, par-1, pumilio, SmB, staufen, and tudor; the mesoderm genes brachyury, mef2, snail, and twist; the axis determination/segmentation genes β-catenin, deformed, distal-less, engrailed, giant, hairy, hunchback, kruppel, orthodenticle, patched, tailless, and wingless/wnt-8c; and a number of cell-cycle regulators. Animal and vegetal contigs were computationally subtracted from each other to produce sets unique to either half-embryo library. Genes expressed only in the animal half included bmp1, kruppel, maelstrom, and orthodenticle. Genes expressed only in the vegetal half included boule, brachyury, deformed, dorsal, engrailed, hunchback, spalt, twist, and wingless/wnt-8c.
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http://dx.doi.org/10.1007/s10126-015-9613-4DOI Listing
June 2015

SNP discovery in nonmodel organisms: strand bias and base-substitution errors reduce conversion rates.

Mol Ecol Resour 2015 Jul 23;15(4):723-36. Epub 2014 Nov 23.

School of Biological and Biomedical Sciences, Durham University, Durham, DH1 3LE, UK.

Single nucleotide polymorphisms (SNPs) have become the marker of choice for genetic studies in organisms of conservation, commercial or biological interest. Most SNP discovery projects in nonmodel organisms apply a strategy for identifying putative SNPs based on filtering rules that account for random sequencing errors. Here, we analyse data used to develop 4723 novel SNPs for the commercially important deep-sea fish, orange roughy (Hoplostethus atlanticus), to assess the impact of not accounting for systematic sequencing errors when filtering identified polymorphisms when discovering SNPs. We used SAMtools to identify polymorphisms in a velvet assembly of genomic DNA sequence data from seven individuals. The resulting set of polymorphisms were filtered to minimize 'bycatch'-polymorphisms caused by sequencing or assembly error. An Illumina Infinium SNP chip was used to genotype a final set of 7714 polymorphisms across 1734 individuals. Five predictors were examined for their effect on the probability of obtaining an assayable SNP: depth of coverage, number of reads that support a variant, polymorphism type (e.g. A/C), strand-bias and Illumina SNP probe design score. Our results indicate that filtering out systematic sequencing errors could substantially improve the efficiency of SNP discovery. We show that BLASTX can be used as an efficient tool to identify single-copy genomic regions in the absence of a reference genome. The results have implications for research aiming to identify assayable SNPs and build SNP genotyping assays for nonmodel organisms.
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http://dx.doi.org/10.1111/1755-0998.12343DOI Listing
July 2015

Exploiting genomic data to identify proteins involved in abalone reproduction.

J Proteomics 2014 Aug 12;108:337-53. Epub 2014 Jun 12.

CSIRO Food Futures Flagship, 5 Julius Avenue, North Ryde, New South Wales 2113, Australia; CSIRO Animal, Food and Health Sciences, Queensland Bioscience Precinct, 306 Carmody Road, St Lucia, Queensland 4067, Australia. Electronic address:

Unlabelled: Aside from their critical role in reproduction, abalone gonads serve as an indicator of sexual maturity and energy balance, two key considerations for effective abalone culture. Temperate abalone farmers face issues with tank restocking with highly marketable abalone owing to inefficient spawning induction methods. The identification of key proteins in sexually mature abalone will serve as the foundation for a greater understanding of reproductive biology. Addressing this knowledge gap is the first step towards improving abalone aquaculture methods. Proteomic profiling of female and male gonads of greenlip abalone, Haliotis laevigata, was undertaken using liquid chromatography-mass spectrometry. Owing to the incomplete nature of abalone protein databases, in addition to searching against two publicly available databases, a custom database comprising genomic data was used. Overall, 162 and 110 proteins were identified in females and males respectively with 40 proteins common to both sexes. For proteins involved in sexual maturation, sperm and egg structure, motility, acrosomal reaction and fertilization, 23 were identified only in females, 18 only in males and 6 were common. Gene ontology analysis revealed clear differences between the female and male protein profiles reflecting a higher rate of protein synthesis in the ovary and higher metabolic activity in the testis.

Biological Significance: A comprehensive mass spectrometry-based analysis was performed to profile the abalone gonad proteome providing the foundation for future studies of reproduction in abalone. Key proteins involved in both reproduction and energy balance were identified. Genomic resources were utilised to build a database of molluscan proteins yielding >60% more protein identifications than in a standard workflow employing public protein databases.
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http://dx.doi.org/10.1016/j.jprot.2014.06.001DOI Listing
August 2014

The sheep genome illuminates biology of the rumen and lipid metabolism.

Science 2014 Jun;344(6188):1168-1173

Human Genome Sequencing Center, Baylor College of Medicine, Houston, TX 77030, USA.

Sheep (Ovis aries) are a major source of meat, milk, and fiber in the form of wool and represent a distinct class of animals that have a specialized digestive organ, the rumen, that carries out the initial digestion of plant material. We have developed and analyzed a high-quality reference sheep genome and transcriptomes from 40 different tissues. We identified highly expressed genes encoding keratin cross-linking proteins associated with rumen evolution. We also identified genes involved in lipid metabolism that had been amplified and/or had altered tissue expression patterns. This may be in response to changes in the barrier lipids of the skin, an interaction between lipid metabolism and wool synthesis, and an increased role of volatile fatty acids in ruminants compared with nonruminant animals.
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http://dx.doi.org/10.1126/science.1252806DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4157056PMC
June 2014

Variation in genes involved in epigenetic processes offers insights into tropically adapted cattle diversity.

Front Genet 2014 22;5:89. Epub 2014 Apr 22.

CSIRO Food Futures Flagship and CSIRO Animal, Health and Food Sciences Brisbane, QLD, Australia.

We evaluated the relevance of the BovineHD Illumina SNP chip with respect to genes involved in epigenetic processes. Genotypes for 729,068 SNP on two tropical cattle breeds of Australia were used: Brahman (n = 2112) and Tropical Composite (n = 2550). We used data mining approaches to compile a list of bovine protein-coding genes involved in epigenetic processes. These genes represent 9 functional categories that contain between one (histone demethylases) and 99 (chromatin remodeling factors) genes. A total of 3091 SNP mapped to positions within 3000 bp of the 193 coding regions of those genes, including 113 SNP in transcribed regions, 2738 in intronic regions and 240 in up- or down-stream regions. For all these SNP categories, we observed differences in the allelic frequencies between Brahman and Tropical Composite cattle. These differences were larger than those observed for the entire set of 729,068 SNP (P = 1.79 x 10(-5)). A multidimensional scaling analysis using only the 113 SNP in transcribed regions allowed for the separation of the two populations and this separation was comparable to the one obtained with a random set of 113 SNP (Principal Component 1 r (2) > 0.84). To further characterize the differences between the breeds we defined a gene-differentiation metric based on the average genotypic frequencies of SNP connected to each gene and compared both cattle populations. The 10% most differentiated genes were distributed across 10 chromosomes, with significant (P < 0.05) enrichment on BTA 3 and 10. The 10% most conserved genes were located in 12 chromosomes. We conclude that there is variation between cattle populations in genes connected to epigenetic processes, and this variation can be used to differentiate cattle breeds. More research is needed to fully characterize the use of these SNP and its potential as means to further our understanding of biological variation and epigenetic processes.
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http://dx.doi.org/10.3389/fgene.2014.00089DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4001012PMC
May 2014

Information compression exploits patterns of genome composition to discriminate populations and highlight regions of evolutionary interest.

BMC Bioinformatics 2014 Mar 7;15:66. Epub 2014 Mar 7.

Computational and Systems Biology, CSIRO Animal, Food and Health Sciences, St, Lucia, Brisbane, QLD 4067, Australia.

Background: Genomic information allows population relatedness to be inferred and selected genes to be identified. Single nucleotide polymorphism microarray (SNP-chip) data, a proxy for genome composition, contains patterns in allele order and proportion. These patterns can be quantified by compression efficiency (CE). In principle, the composition of an entire genome can be represented by a CE number quantifying allele representation and order.

Results: We applied a compression algorithm (DEFLATE) to genome-wide high-density SNP data from 4,155 human, 1,800 cattle, 1,222 sheep, 81 dogs and 49 mice samples. All human ethnic groups can be clustered by CE and the clusters recover phylogeography based on traditional fixation index (FST) analyses. CE analysis of other mammals results in segregation by breed or species, and is sensitive to admixture and past effective population size. This clustering is a consequence of individual patterns such as runs of homozygosity. Intriguingly, a related approach can also be used to identify genomic loci that show population-specific CE segregation. A high resolution CE 'sliding window' scan across the human genome, organised at the population level, revealed genes known to be under evolutionary pressure. These include SLC24A5 (European and Gujarati Indian skin pigmentation), HERC2 (European eye color), LCT (European and Maasai milk digestion) and EDAR (Asian hair thickness). We also identified a set of previously unidentified loci with high population-specific CE scores including the chromatin remodeler SCMH1 in Africans and EDA2R in Asians. Closer inspection reveals that these prioritised genomic regions do not correspond to simple runs of homozygosity but rather compositionally complex regions that are shared by many individuals of a given population. Unlike FST, CE analyses do not require ab initio population comparisons and are amenable to the hemizygous X chromosome.

Conclusions: We conclude with a discussion of the implications of CE for a complex systems science view of genome evolution. CE allows one to clearly visualise the evolution of individual genomes and populations through a formal, mathematically-rigorous information space. Overall, CE makes a set of biological predictions, some of which are unique and await functional validation.
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http://dx.doi.org/10.1186/1471-2105-15-66DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4015654PMC
March 2014

Evidence for positive selection of taurine genes within a QTL region on chromosome X associated with testicular size in Australian Brahman cattle.

BMC Genet 2014 Jan 10;15. Epub 2014 Jan 10.

Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, The University of Queensland, Brisbane, Qld 4072, Australia.

Background: Previous genome-wide association studies have identified significant regions of the X chromosome associated with reproductive traits in two Bos indicus-influenced breeds: Brahman cattle and Tropical Composites. Two QTL regions on this chromosome were identified in both breeds as strongly associated with scrotal circumference measurements, a reproductive trait previously shown to be useful for selection of young bulls. Scrotal circumference is genetically correlated with early age at puberty in both male and female offspring. These QTL were located at positions 69-77 and 81-92 Mb respectively, large areas each to which a significant number of potential candidate genes were mapped.

Results: To further characterise these regions, a bioinformatic approach was undertaken to identify novel non-synonymous SNP within the QTL regions of interest in Brahman cattle. After SNP discovery, we used conventional molecular assay technologies to perform studies of two candidate genes in both breeds. Non-synonymous SNP mapped to Testis-expressed gene 11 (Tex11) were associated (P < 0.001) with scrotal circumference in both breeds, and associations with percentage of normal sperm cells were also observed (P < 0.05). Evidence for recent selection was found as Tex11 SNP form a haplotype segment of Bos taurus origin that is retained within Brahman and Tropical Composite cattle with greatest reproductive potential.

Conclusions: Association of non-synonymous SNP presented here are a first step to functional genetic studies. Bovine species may serve as a model for studying the role of Tex11 in male fertility, warranting further in-depth molecular characterisation.
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http://dx.doi.org/10.1186/1471-2156-15-6DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3893399PMC
January 2014

Next-generation sequencing: a challenge to meet the increasing demand for training workshops in Australia.

Brief Bioinform 2013 Sep 29;14(5):563-74. Epub 2013 Mar 29.

The Australian Centre for Plant Functional Genomics, University of Adelaide, SA 5064, Australia.

The widespread adoption of high-throughput next-generation sequencing (NGS) technology among the Australian life science research community is highlighting an urgent need to up-skill biologists in tools required for handling and analysing their NGS data. There is currently a shortage of cutting-edge bioinformatics training courses in Australia as a consequence of a scarcity of skilled trainers with time and funding to develop and deliver training courses. To address this, a consortium of Australian research organizations, including Bioplatforms Australia, the Commonwealth Scientific and Industrial Research Organisation and the Australian Bioinformatics Network, have been collaborating with EMBL-EBI training team. A group of Australian bioinformaticians attended the train-the-trainer workshop to improve training skills in developing and delivering bioinformatics workshop curriculum. A 2-day NGS workshop was jointly developed to provide hands-on knowledge and understanding of typical NGS data analysis workflows. The road show-style workshop was successfully delivered at five geographically distant venues in Australia using the newly established Australian NeCTAR Research Cloud. We highlight the challenges we had to overcome at different stages from design to delivery, including the establishment of an Australian bioinformatics training network and the computing infrastructure and resource development. A virtual machine image, workshop materials and scripts for configuring a machine with workshop contents have all been made available under a Creative Commons Attribution 3.0 Unported License. This means participants continue to have convenient access to an environment they had become familiar and bioinformatics trainers are able to access and reuse these resources.
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http://dx.doi.org/10.1093/bib/bbt022DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3771231PMC
September 2013

Transcriptomics of a giant freshwater prawn (Macrobrachium rosenbergii): de novo assembly, annotation and marker discovery.

PLoS One 2011 8;6(12):e27938. Epub 2011 Dec 8.

Biogeosciences, Queensland University of Technology, Brisbane, Queensland, Australia.

Background: Giant freshwater prawn (Macrobrachium rosenbergii or GFP), is the most economically important freshwater crustacean species. However, as little is known about its genome, 454 pyrosequencing of cDNA was undertaken to characterise its transcriptome and identify genes important for growth.

Methodology And Principal Findings: A collection of 787,731 sequence reads (244.37 Mb) obtained from 454 pyrosequencing analysis of cDNA prepared from muscle, ovary and testis tissues taken from 18 adult prawns was assembled into 123,534 expressed sequence tags (ESTs). Of these, 46% of the 8,411 contigs and 19% of 115,123 singletons possessed high similarity to sequences in the GenBank non-redundant database, with most significant (E value < 1e(-5)) contig (80%) and singleton (84%) matches occurring with crustacean and insect sequences. KEGG analysis of the contig open reading frames identified putative members of several biological pathways potentially important for growth. The top InterProScan domains detected included RNA recognition motifs, serine/threonine-protein kinase-like domains, actin-like families, and zinc finger domains. Transcripts derived from genes such as actin, myosin heavy and light chain, tropomyosin and troponin with fundamental roles in muscle development and construction were abundant. Amongst the contigs, 834 single nucleotide polymorphisms, 1198 indels and 658 simple sequence repeats motifs were also identified.

Conclusions: The M. rosenbergii transcriptome data reported here should provide an invaluable resource for improving our understanding of this species' genome structure and biology. The data will also instruct future functional studies to manipulate or select for genes influencing growth that should find practical applications in aquaculture breeding programs.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0027938PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3234237PMC
April 2012

Using regulatory and epistatic networks to extend the findings of a genome scan: identifying the gene drivers of pigmentation in merino sheep.

PLoS One 2011 20;6(6):e21158. Epub 2011 Jun 20.

Livestock Industries, Commonwealth Scientific and Industrial Research Organisation (CSIRO), Brisbane, Queensland, Australia.

Extending genome wide association analysis by the inclusion of gene expression data may assist in the dissection of complex traits. We examined piebald, a pigmentation phenotype in both human and Merino sheep, by analysing multiple data types using a systems approach. First, a case control analysis of 49,034 ovine SNP was performed which confirmed a multigenic basis for the condition. We combined these results with gene expression data from five tissue types analysed with a skin-specific microarray. Promoter sequence analysis of differentially expressed genes allowed us to reverse-engineer a regulatory network. Likewise, by testing two-loci models derived from all pair-wise comparisons across piebald-associated SNP, we generated an epistatic network. At the intersection of both networks, we identified thirteen genes with insulin-like growth factor binding protein 7 (IGFBP7), platelet-derived growth factor alpha (PDGFRA) and the tetraspanin platelet activator CD9 at the kernel of the intersection. Further, we report a number of differentially expressed genes in regions containing highly associated SNP including ATRN, DOCK7, FGFR1OP, GLI3, SILV and TBX15. The application of network theory facilitated co-analysis of genetic variation with gene expression, recapitulated aspects of the known molecular biology of skin pigmentation and provided insights into the transcription regulation and epistatic interactions involved in piebald Merino sheep.
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http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0021158PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3119053PMC
October 2011

Analysis of copy number variants in the cattle genome.

Gene 2011 Aug 18;482(1-2):73-7. Epub 2011 May 18.

CSIRO Livestock Industries, Level 5 Queensland Bioscience Precinct, 306 Carmody Road, St Lucia 4067, Australia.

Copy number variation (CNV) is likely to be an important component of heritable variation in livestock. To characterise CNVs in cattle, we performed a genome wide survey to determine the number, location and gene content of these genomic features. A tiling oligonucleotide array with ~385,000 probes was used for comparative genomic hybridisation of both taurine and zebu cattle. Using a conservative set of calling criteria, a total of 51 CNV were detected that collectively spanned approximately half of one percent of the bovine genome. The size of the average CNV within each animal ranged from 213 kb up to 335 kb. Half of the CNV were detected in a single animal only, whilst the remainder was independently identified in multiple individuals. Analysis was performed to determine the gene content for each CNV region. This revealed that the majority of CNV (82%) spanned at least one gene, with a number of CNV containing genes which are known to control aspects of phenotypic variation in cattle. Whilst additional studies are required to determine the impact of individual CNV, this study confirmed them as an important class of genomic variation in cattle.
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http://dx.doi.org/10.1016/j.gene.2011.04.011DOI Listing
August 2011

Bovine proteins containing poly-glutamine repeats are often polymorphic and enriched for components of transcriptional regulatory complexes.

BMC Genomics 2010 Nov 23;11:654. Epub 2010 Nov 23.

CSIRO Livestock Industries, Queensland Bioscience Precinct, 306 Carmody Rd, St Lucia, Queensland 4067, Australia.

Background: About forty human diseases are caused by repeat instability mutations. A distinct subset of these diseases is the result of extreme expansions of polymorphic trinucleotide repeats; typically CAG repeats encoding poly-glutamine (poly-Q) tracts in proteins. Polymorphic repeat length variation is also apparent in human poly-Q encoding genes from normal individuals. As these coding sequence repeats are subject to selection in mammals, it has been suggested that normal variations in some of these typically highly conserved genes are implicated in morphological differences between species and phenotypic variations within species. At present, poly-Q encoding genes in non-human mammalian species are poorly documented, as are their functions and propensities for polymorphic variation.

Results: The current investigation identified 178 bovine poly-Q encoding genes (Q ≥ 5) and within this group, 26 genes with orthologs in both human and mouse that did not contain poly-Q repeats. The bovine poly-Q encoding genes typically had ubiquitous expression patterns although there was bias towards expression in epithelia, brain and testes. They were also characterised by unusually large sizes. Analysis of gene ontology terms revealed that the encoded proteins were strongly enriched for functions associated with transcriptional regulation and many contributed to physical interaction networks in the nucleus where they presumably act cooperatively in transcriptional regulatory complexes. In addition, the coding sequence CAG repeats in some bovine genes impacted mRNA splicing thereby generating unusual transcriptional diversity, which in at least one instance was tissue-specific. The poly-Q encoding genes were prioritised using multiple criteria for their likelihood of being polymorphic and then the highest ranking group was experimentally tested for polymorphic variation within a cattle diversity panel. Extensive and meiotically stable variation was identified.

Conclusions: Transcriptional diversity can potentially be generated in poly-Q encoding genes by the impact of CAG repeat tracts on mRNA alternative splicing. This effect, combined with the physical interactions of the encoded proteins in large transcriptional regulatory complexes suggests that polymorphic variations of proteins in these complexes have strong potential to affect phenotype.
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http://dx.doi.org/10.1186/1471-2164-11-654DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3014979PMC
November 2010

Using paired-end sequences to optimise parameters for alignment of sequence reads against related genomes.

BMC Genomics 2010 Aug 3;11:458. Epub 2010 Aug 3.

CSIRO Livestock Industries, 306 Carmody Road, St, Lucia, QLD 4067, Australia.

Background: The advent of cheap high through-put sequencing methods has facilitated low coverage skims of a large number of organisms. To maximise the utility of the sequences, assembly into contigs and then ordering of those contigs is required. Whilst sequences can be assembled into contigs de novo, using assembled genomes of closely related organisms as a framework can considerably aid the process. However, the preferred search programs and parameters that will optimise the sensitivity and specificity of the alignments between the sequence reads and the framework genome(s) are not necessarily obvious. Here we demonstrate a process that uses paired-end sequence reads to choose an optimal program and alignment parameters.

Results: Unlike two single fragment reads, in paired-end sequence reads, such as BAC-end sequences, the two sequences in the pair have a known positional relationship in the original genome. This provides an additional level of confidence over match scores and e-values in the accuracy of the positional assignment of the reads in the comparative genome. Three commonly used sequence alignment programs: MegaBLAST, Blastz and PatternHunter were used to align a set of ovine BAC-end sequences against the equine genome assembly. A range of different search parameters, with a particular focus on contiguous and discontiguous seeds, were used for each program. The number of reads with a hit and the number of read pairs with hits for the two end sequences in the tail-to-tail paired-end configuration were plotted relative to the theoretical maximum expected curve. Of the programs tested, MegaBLAST with short contiguous seed lengths (word size 8-11) performed best in this particular task. In addition the data also provides estimates of the false positive and false negative rates, which can be used to determine the appropriate values of additional parameters, such as score cut-off, to balance sensitivity and specificity. To determine whether the approach also worked for the alignment of shorter reads, the first 240 bases of each BAC end sequence were also aligned to the equine genome. Again, contiguous MegaBLAST performed the best in optimising the sensitivity and specificity with which sheep BAC end reads map to the equine and bovine genomes.

Conclusions: Paired-end reads, such as BAC-end sequences, provide an efficient mechanism to optimise sequence alignment parameters, for example for comparative genome assemblies, by providing an objective standard to evaluate performance.
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http://dx.doi.org/10.1186/1471-2164-11-458DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC3091654PMC
August 2010

Skeletal muscle specific genes networks in cattle.

Funct Integr Genomics 2010 Nov 4;10(4):609-18. Epub 2010 Jun 4.

Departamento de Mejora Genética Animal, Instituto Nacional de Investigación y Tecnología Agraria y Alimentaria, Ctra de A Coruña km 7.5, 28040 Madrid, Spain.

While physiological differences across skeletal muscles have been described, the differential gene expression underlying them and the discovery of how they interact to perform specific biological processes are largely to be elucidated. The purpose of the present study was, firstly, to profile by cDNA microarrays the differential gene expression between two skeletal muscle types, Psoas major (PM) and Flexor digitorum (FD), in beef cattle and then to interpret the results in the context of a bovine gene coexpression network, detecting possible changes in connectivity across the skeletal muscle system. Eighty four genes were differentially expressed (DE) between muscles. Approximately 54% encoded metabolic enzymes and structural-contractile proteins. DE genes were involved in similar processes and functions, but the proportion of genes in each category varied within each muscle. A correlation matrix was obtained for 61 out of the 84 DE genes from a gene coexpression network. Different groups of coexpression were observed, the largest one having 28 metabolic and contractile genes, up-regulated in PM, and mainly encoding fast-glycolytic fibre structural components and glycolytic enzymes. In FD, genes related to cell support seemed to constitute its identity feature and did not positively correlate to the rest of DE genes in FD. Moreover, changes in connectivity for some DE genes were observed in the different gene ontologies. Our results confirm the existence of a muscle dependent transcription and coexpression pattern and suggest the necessity of integrating different muscle types to perform comprehensive networks for the transcriptional landscape of bovine skeletal muscle.
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http://dx.doi.org/10.1007/s10142-010-0175-2DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2990504PMC
November 2010

A genomics-informed, SNP association study reveals FBLN1 and FABP4 as contributing to resistance to fleece rot in Australian Merino sheep.

BMC Vet Res 2010 May 26;6:27. Epub 2010 May 26.

CSIRO Livestock Industries, 306 Carmody Rd, St Lucia, QLD 4067, Australia.

Background: Fleece rot (FR) and body-strike of Merino sheep by the sheep blowfly Lucilia cuprina are major problems for the Australian wool industry, causing significant losses as a result of increased management costs coupled with reduced wool productivity and quality. In addition to direct effects on fleece quality, fleece rot is a major predisposing factor to blowfly strike on the body of sheep. In order to investigate the genetic drivers of resistance to fleece rot, we constructed a combined ovine-bovine cDNA microarray of almost 12,000 probes including 6,125 skin expressed sequence tags and 5,760 anonymous clones obtained from skin subtracted libraries derived from fleece rot resistant and susceptible animals. This microarray platform was used to profile the gene expression changes between skin samples of six resistant and six susceptible animals taken immediately before, during and after FR induction. Mixed-model equations were employed to normalize the data and 155 genes were found to be differentially expressed (DE). Ten DE genes were selected for validation using real-time PCR on independent skin samples. The genomic regions of a further 5 DE genes were surveyed to identify single nucleotide polymorphisms (SNP) that were genotyped across three populations for their associations with fleece rot resistance.

Results: The majority of the DE genes originated from the fleece rot subtracted libraries and over-representing gene ontology terms included defense response to bacterium and epidermis development, indicating a role of these processes in modulating the sheep's response to fleece rot. We focused on genes that contribute to the physical barrier function of skin, including keratins, collagens, fibulin and lipid proteins, to identify SNPs that were associated to fleece rot scores.

Conclusions: We identified FBLN1 (fibulin) and FABP4 (fatty acid binding protein 4) as key factors in sheep's resistance to fleece rot. Validation of these markers in other populations could lead to vital tests for marker assisted selection that will ultimately increase the natural fleece rot resistance of Merino sheep.
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http://dx.doi.org/10.1186/1746-6148-6-27DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2886023PMC
May 2010

Analysis of the complement and molecular evolution of tRNA genes in cow.

BMC Genomics 2009 Apr 24;10:188. Epub 2009 Apr 24.

CSIRO Livestock Industries, Queensland Biosciences Precinct, St Lucia, QLD, Australia.

Background: Detailed information regarding the number and organization of transfer RNA (tRNA) genes at the genome level is becoming readily available with the increase of DNA sequencing of whole genomes. However the identification of functional tRNA genes is challenging for species that have large numbers of repetitive elements containing tRNA derived sequences, such as Bos taurus. Reliable identification and annotation of entire sets of tRNA genes allows the evolution of tRNA genes to be understood on a genomic scale.

Results: In this study, we explored the B. taurus genome using bioinformatics and comparative genomics approaches to catalogue and analyze cow tRNA genes. The initial analysis of the cow genome using tRNAscan-SE identified 31,868 putative tRNA genes and 189,183 pseudogenes, where 28,830 of the 31,868 predicted tRNA genes were classified as repetitive elements by the RepeatMasker program. We then used comparative genomics to further discriminate between functional tRNA genes and tRNA-derived sequences for the remaining set of 3,038 putative tRNA genes. For our analysis, we used the human, chimpanzee, mouse, rat, horse, dog, chicken and fugu genomes to predict that the number of active tRNA genes in cow lies in the vicinity of 439. Of this set, 150 tRNA genes were 100% identical in their sequences across all nine vertebrate genomes studied. Using clustering analyses, we identified a new tRNA-GlyCCC subfamily present in all analyzed mammalian genomes. We suggest that this subfamily originated from an ancestral tRNA-GlyGCC gene via a point mutation prior to the radiation of the mammalian lineages. Lastly, in a separate analysis we created phylogenetic profiles for each putative cow tRNA gene using a representative set of genomes to gain an overview of common evolutionary histories of tRNA genes.

Conclusion: The use of a combination of bioinformatics and comparative genomics approaches has allowed the confident identification of a set of cow tRNA genes that will facilitate further studies in understanding the molecular evolution of cow tRNA genes.
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http://dx.doi.org/10.1186/1471-2164-10-188DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2680898PMC
April 2009

Genome-wide survey of SNP variation uncovers the genetic structure of cattle breeds.

Science 2009 Apr;324(5926):528-32

The imprints of domestication and breed development on the genomes of livestock likely differ from those of companion animals. A deep draft sequence assembly of shotgun reads from a single Hereford female and comparative sequences sampled from six additional breeds were used to develop probes to interrogate 37,470 single-nucleotide polymorphisms (SNPs) in 497 cattle from 19 geographically and biologically diverse breeds. These data show that cattle have undergone a rapid recent decrease in effective population size from a very large ancestral population, possibly due to bottlenecks associated with domestication, selection, and breed formation. Domestication and artificial selection appear to have left detectable signatures of selection within the cattle genome, yet the current levels of diversity within breeds are at least as great as exists within humans.
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http://dx.doi.org/10.1126/science.1167936DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2735092PMC
April 2009

The genome sequence of taurine cattle: a window to ruminant biology and evolution.

Science 2009 Apr;324(5926):522-8

To understand the biology and evolution of ruminants, the cattle genome was sequenced to about sevenfold coverage. The cattle genome contains a minimum of 22,000 genes, with a core set of 14,345 orthologs shared among seven mammalian species of which 1217 are absent or undetected in noneutherian (marsupial or monotreme) genomes. Cattle-specific evolutionary breakpoint regions in chromosomes have a higher density of segmental duplications, enrichment of repetitive elements, and species-specific variations in genes associated with lactation and immune responsiveness. Genes involved in metabolism are generally highly conserved, although five metabolic genes are deleted or extensively diverged from their human orthologs. The cattle genome sequence thus provides a resource for understanding mammalian evolution and accelerating livestock genetic improvement for milk and meat production.
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http://dx.doi.org/10.1126/science.1169588DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC2943200PMC
April 2009
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