Frank W. Nicholas

A Genome Wide Survey of SNP Variation Reveals the Genetic Structure of Sheep Breeds

The genetic structure of sheep reflects their domestication and subsequent formation into discrete breeds. Understanding genetic structure is essential for achieving genetic improvement through genome-wide association studies, genomic selection and the dissection of quantitative traits. After identifying the first genome-wide set of SNP for sheep, we report on levels of genetic variability both within and between a diverse sample of ovine populations. Then, using cluster analysis and the partitioning of genetic variation, we demonstrate sheep are characterised by weak phylogeographic structure, overlapping genetic similarity and generally low differentiation which is consistent with their short evolutionary history. The degree of population substructure was, however, sufficient to cluster individuals based on geographic origin and known breed history. Specifically, African and Asian populations clustered separately from breeds of European origin sampled from Australia, New Zealand, Europe and North America. Furthermore, we demonstrate the presence of stratification within some, but not all, ovine breeds. The results emphasize that careful documentation of genetic structure will be an essential prerequisite when mapping the genetic basis of complex traits. Furthermore, the identification of a subset of SNP able to assign individuals into broad groupings demonstrates even a small panel of markers may be suitable for applications such as traceability.

The sheep genome illuminates biology of the rumen and lipid metabolism

A genome for ewe and ewe Sheep-specific genetic changes underlie differences in lipid metabolism between sheep and other mammals, and may have contributed to the production of wool. Jiang et al. sequenced the genome of two Texel sheep, a breed that produces high-value meat, milk, and wool. The genome information will provide an important resource for livestock production and aid in the understanding of mammalian evolution. Science, this issue p. 1168 A genomic analysis of sheep explains specializations in digestive system physiology and wool production. 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.

Using comparative genomics to reorder the human genome sequence into a virtual sheep genome

BackgroundIs it possible to construct an accurate and detailed subgene-level map of a genome using bacterial artificial chromosome (BAC) end sequences, a sparse marker map, and the sequences of other genomes?ResultsA sheep BAC library, CHORI-243, was constructed and the BAC end sequences were determined and mapped with high sensitivity and low specificity onto the frameworks of the human, dog, and cow genomes. To maximize genome coverage, the coordinates of all BAC end sequence hits to the cow and dog genomes were also converted to the equivalent human genome coordinates. The 84,624 sheep BACs (about 5.4-fold genome coverage) with paired ends in the correct orientation (tail-to-tail) and spacing, combined with information from sheep BAC comparative genome contigs (CGCs) built separately on the dog and cow genomes, were used to construct 1,172 sheep BAC-CGCs, covering 91.2% of the human genome. Clustered non-tail-to-tail and outsize BACs located close to the ends of many BAC-CGCs linked BAC-CGCs covering about 70% of the genome to at least one other BAC-CGC on the same chromosome. Using the BAC-CGCs, the intrachromosomal and interchromosomal BAC-CGC linkage information, human/cow and vertebrate synteny, and the sheep marker map, a virtual sheep genome was constructed. To identify BACs potentially located in gaps between BAC-CGCs, an additional set of 55,668 sheep BACs were positioned on the sheep genome with lower confidence. A coordinate conversion process allowed us to transfer human genes and other genome features to the virtual sheep genome to display on a sheep genome browser.ConclusionWe demonstrate that limited sequencing of BACs combined with positioning on a well assembled genome and integrating locations from other less well assembled genomes can yield extensive, detailed subgene-level maps of mammalian genomes, for which genomic resources are currently limited.

A primary assembly of a bovine haplotype block map based on a 15,036-single-nucleotide polymorphism panel genotyped in holstein-friesian cattle

Analysis of data on 1000 Holstein–Friesian bulls genotyped for 15,036 single-nucleotide polymorphisms (SNPs) has enabled genomewide identification of haplotype blocks and tag SNPs. A final subset of 9195 SNPs in Hardy–Weinberg equilibrium and mapped on autosomes on the bovine sequence assembly (release Btau 3.1) was used in this study. The average intermarker spacing was 251.8 kb. The average minor allele frequency (MAF) was 0.29 (0.05–0.5). Following recent precedents in human HapMap studies, a haplotype block was defined where 95% of combinations of SNPs within a region are in very high linkage disequilibrium. A total of 727 haplotype blocks consisting of ≥3 SNPs were identified. The average block length was 69.7 ± 7.7 kb, which is ∼5–10 times larger than in humans. These blocks comprised a total of 2964 SNPs and covered 50,638 kb of the sequence map, which constitutes 2.18% of the length of all autosomes. A set of tag SNPs, which will be useful for further fine-mapping studies, has been identified. Overall, the results suggest that as many as 75,000–100,000 tag SNPs would be needed to track all important haplotype blocks in the bovine genome. This would require ∼250,000 SNPs in the discovery phase.

A physical map of the bovine genome

BackgroundCattle are important agriculturally and relevant as a model organism. Previously described genetic and radiation hybrid (RH) maps of the bovine genome have been used to identify genomic regions and genes affecting specific traits. Application of these maps to identify influential genetic polymorphisms will be enhanced by integration with each other and with bacterial artificial chromosome (BAC) libraries. The BAC libraries and clone maps are essential for the hybrid clone-by-clone/whole-genome shotgun sequencing approach taken by the bovine genome sequencing project.ResultsA bovine BAC map was constructed with HindIII restriction digest fragments of 290,797 BAC clones from animals of three different breeds. Comparative mapping of 422,522 BAC end sequences assisted with BAC map ordering and assembly. Genotypes and pedigree from two genetic maps and marker scores from three whole-genome RH panels were consolidated on a 17,254-marker composite map. Sequence similarity allowed integrating the BAC and composite maps with the bovine draft assembly (Btau3.1), establishing a comprehensive resource describing the bovine genome. Agreement between the marker and BAC maps and the draft assembly is high, although discrepancies exist. The composite and BAC maps are more similar than either is to the draft assembly.ConclusionFurther refinement of the maps and greater integration into the genome assembly process may contribute to a high quality assembly. The maps provide resources to associate phenotypic variation with underlying genomic variation, and are crucial resources for understanding the biology underpinning this important ruminant species so closely associated with humans.

Online Mendelian Inheritance in Animals (OMIA): a comparative knowledgebase of genetic disorders and other familial traits in non-laboratory animals

Online Mendelian Inheritance in Animals (OMIA) provides up-to-date information on inherited disorders and other familial traits in non-laboratory animals. It is freely available online at http://www.angis.org.au/omia. With a strong emphasis on comparative biology, OMIA is modelled on, and reciprocally hyperlinked with, Online Mendelian Inheritance in Man (OMIM). It provides a comprehensive catalog of animal models of human inherited disorders, and also provides comprehensive access to information on potential human homologues of inherited disorders and traits in animals. Because its whole structure is based on comparative biology, it provides phenotypic information in a format that is complementary to all the relevant mapping and sequence databases now existing or being created across the animal kingdom.

Bulldog dwarfism in Dexter cattle is caused by mutations in ACAN

Bulldog dwarfism in Dexter cattle is one of the earliest single-locus disorders described in animals. Affected fetuses display extreme disproportionate dwarfism, reflecting abnormal cartilage development (chondrodysplasia). Typically, they die around the seventh month of gestation, precipitating a natural abortion. Heterozygotes show a milder form of dwarfism, most noticeably having shorter legs. Homozygosity mapping in candidate regions in a small Dexter pedigree suggested aggrecan (ACAN) as the most likely candidate gene. Mutation screening revealed a 4-bp insertion in exon 11 (2266_2267insGGCA) (called BD1 for diagnostic testing) and a second, rarer transition in exon 1 (−198C>T) (called BD2) that cosegregate with the disorder. In chondrocytes from cattle heterozygous for the insertion, mutant mRNA is subject to nonsense-mediated decay, showing only 8% of normal expression. Genotyping in Dexter families throughout the world shows a one-to-one correspondence between genotype and phenotype at this locus. The heterozygous and homozygous-affected Dexter cattle could prove invaluable as a model for human disorders caused by mutations in ACAN.

A First-Generation Metric Linkage Disequilibrium Map of Bovine Chromosome 6

We constructed a metric linkage disequilibrium (LD) map of bovine chromosome 6 (BTA6) on the basis of data from 220 SNPs genotyped on 433 Australian dairy bulls. This metric LD map has distances in LD units (LDUs) that are analogous to centimorgans in linkage maps. The LD map of BTA6 has a total length of 8.9 LDUs. Within the LD map, regions of high LD (represented as blocks) and regions of low LD (steps) are observed, when plotted against the integrated map in kilobases. At the most stringent block definition, namely a set of loci with zero LDU increase over the span of these markers, BTA6 comprises 40 blocks, accounting for 41% of the chromosome. At a slightly lower stringency of block definition (a set of loci covering a maximum of 0.2 LDUs on the LD map), up to 81% of BTA6 is spanned by 46 blocks and with 13 steps that are likely to reflect recombination hot spots. The mean swept radius (the distance over which LD is likely to be useful for mapping) is 13.3 Mb, confirming extensive LD in Holstein–Friesian dairy cattle, which makes such populations ideal for whole-genome association studies.

OMIA (Online Mendelian Inheritance in Animals): an enhanced platform and integration into the Entrez search interface at NCBI

Online Mendelian Inheritance in Animals (OMIA) is a comprehensive, annotated catalogue of inherited disorders and other familial traits in animals other than humans and mice. Structured as a comparative biology resource, OMIA is a comprehensive resource of phenotypic information on heritable animal traits and genes in a strongly comparative context, relating traits to genes where possible. OMIA is modelled on and is complementary to Online Mendelian Inheritance in Man (OMIM). OMIA has been moved to a MySQL database at the Australian National Genomic Information Service (ANGIS) and can be accessed at . It has also been integrated into the Entrez search interface at the National Center for Biotechnology Information (NCBI; ). Curation of OMIA data by researchers working on particular species and disorders has also been enabled.

Disease resistance in Merino sheep. III. Genetic variation in resistance to footrot following challenge and subsequent vaccination with an homologous rDNA pilus vaccine under both induced and natural conditions

SUMMARY Eight traits representing clinical indicators of resistance to footrot were examined in 1562 Merino sheep, representing the progeny from 162 sires in four major bloodlines. Over a 4-year period, sheep were exposed to virulent isolates of Dicbelobacter nodosus under both an experimental challenge in which footrot was induced, and a separate natural challenge involving a different isolate of D. nodosus. Five footrot traits and three healing traits were each recorded on seven occasions following induced challenge, and on five occasions following natural challenge. All sheep were vaccinated with a primary and booster injection of an homologous rDNA pilus vaccine, 9 and 6 weeks after initiation of the induced and natural challenge respectively. The major fixed effects which influenced variation in resistance were (in order of importance) time of inspection after challenge, year and group in which sheep were challenged, and sex of the animal. Date of birth, birth-rearing type and age or dam were unimportant in the expression of footrot. Half-sib heritability estimates of resistance to footrot were low to moderate for single observations recorded pre-vaccination (0.07-0.22), and slightly lower for inspections made after vaccination (0.07-0.15). Repeatability estimates for footrot traits during a challenge ranged from 0.31 to 0.70 for inspections pre-vaccination, and 0.19 to 0.35 for inspections post-vaccination. Genetic correlations among footrot traits recorded at repeat inspections were high for observations pre-vaccination (range 0.87-1.00) and slightly lower for observations made after vaccination (0.52-1.00). Heritability estimates derived from repeat measurements approached 0.30 for most traits, except for traits describing healing, which had a heritability of almost zero. Heritability estimates of liability to footrot ranged between 0.09 and 0.41 depending on the time after challenge when the inspections were made. The genetic correlation between induced and natural footrot ranged from 0.14 to 0.95, depending on the period over which inspections were made, with an average of 0.67. In addition to within-flock genetic variation in resistance to footrot, significant differences were observed between different bloodlines within the experimental flock. It was concluded that there is substantial genetic variation in resistance to challenge with virulent isolates of D. nodosus. However, practical restrictions of exploiting available genetic variation may limit the widespread adoption of direct selection. ZUSAMMENFASSUNG: Krankheitsresistenz in Merinos III. Genetische Variabilität in Moderhinke Resistenz nach Infektion und folgender Impfung mit homologer rDNA pilus Vakzine unter induzierten und natürlichen Bedingungen Acht Merkmale, die als klinische Hinweise auf Moderhinkeresistenz betrachtet werden, wurden in 1562 Merino Schafen aus 162 Vatertieren von vier wichtigen Linien untersucht. Über eine 4-Jahresperiode wurden die Schafe virulenten Isolaten von Dichelobacter nodosus unter Versuchsbedingungen ausgesetzt und eine getrennte natürliche Infektion mit verschiedenen Isolaten von D. nodosus durchgeführt. Fünf Moderhinkemerkmale und drei Gesundungsmerkmale wurden nach Infektion bei sieben Gelegenheiten festgehalten und an fünf nach natürlicher Infektion. Alle Schafe wurden mit einer primären und einer booster Injektion homologer rDNA pilus Vakzine geimpft, 9 und 6 Wochen nach der induzierten und natiirlichen Infektion. Die wichtigsten fixen Effekte, welche die Variabilität der Resistenz beeinflussen, waren, nach Wichtigkeit gereint, Zeit der Prüfung nach Impfung, Jahr und Gruppe in welcher Schafe geimpft wurden und Geschlecht. Geburtsdatum, Aufzuchttyp und Mutterschaf-alter waren im Hinblick auf Moderhinke unwichtig. Halbgeschwister-Heritabilitätsschätzungen ihrer Resistenz waren niedrig bis mittel für Einzelbeobachtungen vor der Impfung (0,07-0,22) und geringfügig geringer für Beurteilung nach Impfung (0,07-0,15). Wiederholbarkeitsschätzungen für Moderhinkemerkmale bewegten sich von 0,31 bis 0,70 für Inspektionen vor und 0,19-0,35 für Inspektionen nach Impfung. Genetische Korrelationen zwischen Moderhinkemerkmalen bei verschiedenen Untersuchungen waren fur Beobachtungen vor der Impfung hoch (0,87-1) und geringfügig niedriger nachher (0,52-1). Heritabilitätsschätzungen von wiederholten Messungen erreichten 0,30 für die meisten Merkmale außer für jene, welche Heilung beschreiben, die nahezu keine Heritabilität zeigen. Heritabilitätsschätzungen für Moderhinkeempfindlichkeit variierten zwischen 0,09 und 0,41 in Abhängigkeit von der Untersuchungszeit nach den Impfungen. Die genetische Korrelation zwischen induzierter und natürlicher Moderhinke schwankte von 0,14 bis 0,95 in Abhängikeit von der Dauer der Beobachtungsperiode, durschnittlich 0,67. Zusätzlich zur genetischen Variabilität innerhalb der Herde wurden signifikante Unterschiede zwischen verschiedenen Linien innerhalb der Versuchsherde gefunden. Darauf wird es geschlossen, daß substantielle genetische Variabilität für Resistenz gegenüber virulenten Isolaten von D. nodosus existiert. Allerdings können praktische Hindernisse die Ausnutzung der vorhandenen genetischen Variabilität durch direkte Selektion einschränken.