Bundoora, Australia
Bundoora, Australia

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PubMed | University of New England of Australia, Center for AgriBioscience and Cooperative Research Center for Sheep Industry Innovation
Type: Journal Article | Journal: Animal genetics | Year: 2015

Genotyping sheep for genome-wide SNPs at lower density and imputing to a higher density would enable cost-effective implementation of genomic selection, provided imputation was accurate enough. Here, we describe the design of a low-density (12k) SNP chip and evaluate the accuracy of imputation from the 12k SNP genotypes to 50k SNP genotypes in the major Australian sheep breeds. In addition, the impact of imperfect imputation on genomic predictions was evaluated by comparing the accuracy of genomic predictions for 15 novel meat traits including carcass and meat quality and omega fatty acid traits in sheep, from 12k SNP genotypes, imputed 50k SNP genotypes and real 50k SNP genotypes. The 12k chip design included 12223 SNPs with a high minor allele frequency that were selected with intermarker spacing of 50-475kb. SNPs for parentage and horned or polled tests also were represented. Chromosome ends were enriched with SNPs to reduce edge effects on imputation. The imputation performance of the 12k SNP chip was evaluated using 50k SNP genotypes of 4642 animals from six breeds in three different scenarios: (1) within breed, (2) single breed from multibreed reference and (3) multibreed from a single-breed reference. The highest imputation accuracies were found with scenario 2, whereas scenario 3 was the worst, as expected. Using scenario 2, the average imputation accuracy in Border Leicester, Polled Dorset, Merino, White Suffolk and crosses was 0.95, 0.95, 0.92, 0.91 and 0.93 respectively. Imputation scenario 2 was used to impute 50k genotypes for 10396 animals with novel meat trait phenotypes to compare genomic prediction accuracy using genomic best linear unbiased prediction (GBLUP) with real and imputed 50k genotypes. The weighted mean imputation accuracy achieved was 0.92. The average accuracy of genomic estimated breeding values (GEBVs) based on only 12k data was 0.08 across traits and breeds, but accuracies varied widely. The mean GBLUP accuracies with imputed 50k data more than doubled to 0.21. Accuracies of genomic prediction were very similar for imputed and real 50k genotypes. There was no apparent impact on accuracy of GEBVs as a result of using imputed rather than real 50k genotypes, provided imputation accuracy was >90%.


Daetwyler H.D.,Center for AgriBioscience | Daetwyler H.D.,La Trobe University | Hayden M.J.,Center for AgriBioscience | Hayden M.J.,La Trobe University | And 4 more authors.
Genetics | Year: 2015

Doubled haploids are routinely created and phenotypically selected in plant breeding programs to accelerate the breeding cycle. Genomic selection, which makes use of both phenotypes and genotypes, has been shown to further improve genetic gain through prediction of performance before or without phenotypic characterization of novel germplasm. Additional opportunities exist to combine genomic prediction methods with the creation of doubled haploids. Here we propose an extension to genomic selection, optimal haploid value (OHV) selection, which predicts the best doubled haploid that can be produced from a segregating plant. This method focuses selection on the haplotype and optimizes the breeding program toward its end goal of generating an elite fixed line. We rigorously tested OHV selection breeding programs, using computer simulation, and show that it results in up to 0.6 standard deviations more genetic gain than genomic selection. At the same time, OHV selection preserved a substantially greater amount of genetic diversity in the population than genomic selection, which is important to achieve long-term genetic gain in breeding populations. © 2015 by the Genetics Society of America.


Pandey B.R.,University of Melbourne | Burton W.A.,Seednet Australia | Salisbury P.A.,University of Melbourne | Salisbury P.A.,Center for AgriBioscience | Nicolas M.E.,University of Melbourne
Australian Journal of Crop Science | Year: 2016

Biomass at anthesis is an important trait in predicting yield of Brassica oilseeds in environments where seed filling occurs in dry and warm conditions. This study aimed to compare the ability of non-destructive canopy cover measurements (Sunfleck ceptometer and digital photography) with direct biomass sampling at anthesis to predict the yield of canola-quality B. juncea (juncea canola) hybrids. Field experiments were conducted in the Victorian Mallee (226-248 mm annual rainfall) and the Wimmera (266-407 mm annual rainfall) regions from 2012 to 2014. Nineteen juncea canola genotypes were sown in the first year and 10 to 11 genotypes in the subsequent two years of field experiments. The experimental plots were laid out in a randomized complete block design with three replications. Days to 50% flowering, canopy cover and biomass at 50% flowering and seed yield were recorded. The study concluded that at low rainfall sites (<250 mm annual rainfall), the canopy cover measurements had consistent and significant positive relationships with biomass at anthesis (r2=0.43-0.61 in 2012 and r2=0.72 in 2013) and seed yield (r2=0.25-0.41 in 2012 and r2=0.51 in 2013). Canopy cover also showed a positive and significant relationship with early flowering (r2=0.52 in 2012 and r2=0.60 in 2013) at the relatively low rainfall site. These results suggest that non-destructive canopy cover measurement could replace direct biomass sampling at anthesis in prediction of yield of juncea canola hybrids in low rainfall environments.


Salisbury P.A.,University of Melbourne | Salisbury P.A.,Center for AgriBioscience | Cowling W.A.,University of Western Australia | Potter T.D.,Yeruga Crop Research
Crop and Pasture Science | Year: 2016

Innovation has been integral in the development of the current Australian canola (Brassica napus L.) industry. From the initial introduction of poorly adapted Canadian germplasm, Australian breeders have developed high yielding, high quality, disease-resistant canola cultivars. The Australian canola industry has transitioned from being reliant on imports to becoming one of the world's major exporters of canola. This review details the progressive innovations in the Australian canola breeding programs from the initial introduction of rapeseed to more recent developments including herbicide resistance, hybrid cultivars, speciality oil types and genetically modified canola. © CSIRO 2016.


Sudheesh S.,Center for AgriBioscience | Sudheesh S.,La Trobe University | Sawbridge T.I.,Center for AgriBioscience | Sawbridge T.I.,La Trobe University | And 5 more authors.
BMC Genomics | Year: 2015

Background: Field pea (Pisum sativum L.) is a cool-season grain legume that is cultivated world-wide for both human consumption and stock-feed purposes. Enhancement of genetic and genomic resources for field pea will permit improved understanding of the control of traits relevant to crop productivity and quality. Advances in second-generation sequencing and associated bioinformatics analysis now provide unprecedented opportunities for the development of such resources. The objective of this study was to perform transcriptome sequencing and characterisation from two genotypes of field pea that differ in terms of seed and plant morphological characteristics. Results: Transcriptome sequencing was performed with RNA templates from multiple tissues of the field pea genotypes Kaspa and Parafield. Tissue samples were collected at various growth stages, and a total of 23 cDNA libraries were sequenced using Illumina high-throughput sequencing platforms. A total of 407 and 352 million paired-end reads from the Kaspa and Parafield transcriptomes, respectively were assembled into 129,282 and 149,272 contigs, which were filtered on the basis of known gene annotations, presence of open reading frames (ORFs), reciprocal matches and degree of coverage. Totals of 126,335 contigs from Kaspa and 145,730 from Parafield were subsequently selected as the reference set. Reciprocal sequence analysis revealed that c. 87 % of contigs were expressed in both cultivars, while a small proportion were unique to each genotype. Reads from different libraries were aligned to the genotype-specific assemblies in order to identify and characterise expression of contigs on a tissue-specific basis, of which 87 % were expressed in more than one tissue, while others showed distinct expression patterns in specific tissues, providing unique transcriptome signatures. Conclusion: This study provided a comprehensive assembled and annotated transcriptome set for field pea that can be used for development of genetic markers, in order to assess genetic diversity, construct linkage maps, perform trait-dissection and implement whole-genome selection strategies in varietal improvement programs, as well to identify target genes for genetic modification approaches on the basis of annotation and expression analysis. In addition, the reference field pea transcriptome will prove highly valuable for comparative genomics studies and construction of a finalised genome sequence. © 2015 Sudheesh et al.


De Groef B.,La Trobe University | De Groef B.,Center for AgriBioscience | Grommen S.V.H.,La Trobe University | Grommen S.V.H.,Center for AgriBioscience | Darras V.M.,Catholic University of Leuven
Frontiers in Endocrinology | Year: 2013

A major life stage transition in birds and other oviparous sauropsids is the hatching of the cleidoic egg. Not unlike amphibian metamorphosis, hatching in these species can be regarded as a transition from a relatively well-protected "aqueous" environment to a more hazardous and terrestrial life outside the egg, a transition in which thyroid hormones (THs) (often in concert with glucocorticoids) play an important role. In precocial birds such as the chicken, the perihatch period is characterized by peak values of THs. THs are implicated in the control of muscle development, lung maturation and the switch from chorioallantoic to pulmonary respiration, yolk sac retraction, gut development and induction of hepatic genes to accommodate the change in dietary energy source, initiation of thermoregulation, and the final stages of brain maturation as well as early post-hatch imprinting behavior. There is evidence that, at least for some of these processes, THs may have similar roles in non-avian sauropsids. In altricial birds such as passerines on the other hand, THs do not rise significantly until well after hatching and peak values coincide with the development of endothermy. It is not known how hatching-associated processes are regulated by hormones in these animals or how this developmental mode evolved from TH-dependent precocial hatching. Apart from being key metabolic hormones, thyroid hormones (THs) play an important role in development by controlling the growth and differentiation of almost every organ in the vertebrate body. The first clear evidence for the need of THs in vertebrate development came from frogs, where THs, in synergy with corticosteroids, control the transition from an aquatic larva to a terrestrial juvenile during metamorphosis. Superficially, hatching in birds and other oviparous sauropsids resembles anuran metamorphosis in that it marks a transition from an "aqueous" environment, to some extent protected against desiccation and predation by the eggshell, to a more exposed terrestrial life. The similarity is more striking when the endocrinology of hatching is considered, at least in precocial birds. In all precocial bird species studied to date, hatching is accompanied by and dependent on a rise in THs (and corticosteroids). We will first discuss these hormonal changes in precocial species and compare them to what is known in altricial birds and other oviparous sauropsids. Secondly, we will briefly review the role of THs in hatching and hatching-associated processes such as lung and gut maturation, the development of endothermy, and imprinting behavior. © 2013 De Groef, Grommen and Darras.


PubMed | Center for AgriBioscience and Grains Innovation Park
Type: | Journal: Frontiers in plant science | Year: 2015

Field pea (Pisum sativum L.) is an important grain legume consumed both as human food and animal feed. However, productivity in low rainfall regions can be significantly reduced by inferior soils containing high levels of boron and/or salinity. Furthermore, powdery mildew (PM) (Erysiphe pisi) disease also causes significant yield loss in warmer regions. Breeding for tolerance to these abiotic and biotic stresses are major aims for pea breeding programs and the application of molecular markers for these traits could greatly assist in developing improved germplasm at a faster rate. The current study reports the evaluation of a near diagnostic marker, PsMlo, associated with PM resistance and boron (B) tolerance as well as linked markers associated with salinity tolerance across a diverse set of pea germplasm. The PsMlo1 marker predicted the PM and B phenotypic responses with high levels of accuracy (>80%) across a wide range of field pea genotypes, hence offers the potential to be widely adapted in pea breeding programs. In contrast, linked markers for salinity tolerance were population specific; therefore, application of these markers would be suitable to relevant crosses within the program. Our results also suggest that there are possible new sources of salt tolerance present in field pea germplasm that could be further exploited.


PubMed | CNR Institute of Neuroscience, Berghan Carrick Consulting, University of Queensland, Center for AgriBioscience and 2 more.
Type: Journal Article | Journal: BMC genomics | Year: 2016

Polymorphisms underlying complex traits often explain a small part (less than 1%) of the phenotypic variance (Quantitative trait loci (QTL) were identified using 11,527 Holstein cattle with milk production records and up to 444 cows with milk composition traits. There were eight regions that contained QTL for both milk production and a composition trait, including four novel regions. One region on BTAU1 affected both milk yield and phosphorous concentration in milk. The QTL interval included the gene SLC37A1, a phosphorous antiporter. The most significant imputed sequence variants in this region explained 0.001 Milk production traits in dairy cows are typical complex traits where polymorphisms explain only a small portion of the phenotypic variance. However, here we show that these mutations can have larger effects on secondary traits, such as concentrations of minerals, proteins and sugars in the milk, and expression levels of genes in mammary tissue. These larger effects were used to successfully map variants for milk production traits. Genetically simple traits also provide a direct biological link between possible causal mutations and the effect of these mutations on milk production.


PubMed | Murdoch University, Justus Liebig University, University of Rostock and Center for AgriBioscience
Type: | Journal: Plant, cell & environment | Year: 2016

Roots, the hidden half of crop plants, are essential for resource acquisition. However, knowledge about the genetic control of below-ground plant development in wheat, one of the most important small-grain crops in the world, is very limited. The molecular interactions connecting root and shoot development and growth, and thus modulating the plants demand for water and nutrients along with its ability to access them, are largely unexplored. Here we demonstrate that linkage drag in European bread wheat, driven by strong selection for a haplotype variant controlling heading date, has eliminated a specific combination of two flanking, highly conserved, haplotype variants whose interaction confers increased root biomass. Reversing this inadvertent consequence of selection could recover root diversity that may prove essential for future food production in fluctuating environments. Highly conserved synteny to rice across this chromosome segment suggests that adaptive selection has shaped the diversity landscape of this locus across different, globally-important cereal crops. By mining wheat gene expression data we identified root-expressed genes within the region of interest that could help breeders to select positive variants adapted to specific target soil environments.


PubMed | Center for AgriBioscience and Cooperative Research Center for Sheep Industry Innovation
Type: | Journal: BMC genomics | Year: 2016

Genetic variation in both the composition and distribution of fat and muscle in the body is important to human health as well as the healthiness and value of meat from cattle and sheep. Here we use detailed phenotyping and a multi-trait approach to identify genes explaining variation in body composition traits.A multi-trait genome wide association analysis of 56 carcass composition traits measured on 10,613 sheep with imputed and real genotypes on 510,174 SNPs was performed. We clustered 71 significant SNPs into five groups based on their pleiotropic effects across the 56 traits. Among these 71 significant SNPs, one group of 11 SNPs affected the fatty acid profile of the muscle and were close to 8 genes involved in fatty acid or triglyceride synthesis. Another group of 23 SNPs had an effect on mature size, based on their pattern of effects across traits, but the genes near this group of SNPs did not share any obvious function. Many of the likely candidate genes near SNPs with significant pleiotropic effects on the 56 traits are involved in intra-cellular signalling pathways. Among the significant SNPs were some with a convincing candidate gene due to the function of the gene (e.g. glycogen synthase affecting glycogen concentration) or because the same gene was associated with similar traits in other species.Using a multi-trait analysis increased the power to detect associations between SNP and body composition traits compared with the single trait analyses. Detailed phenotypic information helped to identify a convincing candidate in some cases as did information from other species.

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