Applied Biotechnologies Achievements

• Biometrician Dr David Baird made a major contribution to the statistics package,GenStat Release 9.1. His analysis pipeline for DNA electrophoresis gels was used by our BioControl & BioSecurity Section.

• Dr Ken Dodd released two publications about genetic evaluation using parentage information from genetic markers.

• Dr Roger Littlejohn carried out significant work and released publications on Hidden Markov models.

• Dr Paul Shorten and Dr Tanya Soboleva's work on gene spread was published – attracting considerable overseas interest. Dr Shorten also published material about modelling microbial growth.

• Scientist Tony Pleasant has completed his work on a probabilistic model of sheep eating quality for Meat and Livestock Australia. This model is being applied throughout the sheep meat industry.

• We characterised the bovine Bactericidal permeability Increasing (BPI) – like locus in cattle. This included sequencing, assembling and annotating this region using Bioinformatics techniques. BPI and associated genes are of interest to AgResearch due to their putative antimicrobial role. The work has been written for publication in a journal titled: “Expansion of the Bactericidal/permeability increasing-like (BPI-like) protein locus in cattle”

• Nauman Maqbool's work with Animal Genomics Scientists John McEwan and Richard Hall on the interspecies QTL project for deer growth and body shape. This work has been accepted for publication in the Journal Animal Genetics, titled: “A QTL Study of Growth and Body Shape in the Inter-Species Hybrid of Père David’s deer (Elaphurus davidianus) and Red deer (Cervus elaphus)”.

• Jonathan Warren's and Nauman Maqbool's work on GBrowse for plants and cattle.To maximise gains from the recently finished genomic sequence assembly of cattle, the genome was made available to AgResearch scientists in-house through a generic genome browser called GBrowse. The in-silico annotation of the bovine genome with known genes and AgResearch’s proprietary data makes it possible for scientists to look at their favourite gene(s), obtain the genomic sequence, and plan further experiments without putting their proprietary data on to the public websites. The in-house GBrowse also gives us the flexibility to further extensively annotate the regions of interest for AgResearch scientists.

• Anar Khan's and Zaneta Park-Ng’s work with the Advanced Fungal Technologies group on designing the first custom AgResearch Affymetrix chip. We have designed a NimbleExpress Affymetrix GeneChip® representing a subset of genes from two species, perennial ryegrass and the fungal endophyte Neotyphodium lolii, which form a mutualistic association that is significant to New Zealand pastoral farming. Endophyte infection confers a number of advantages upon ryegrass, including resistance to insects and nematodes, and resistance to drought. The molecular basis underlying their symbiosis is largely uncharacterised. This custom microarray chip will allow us to gain new insights into genes and processes that play an important role in symbiosis, in a high-throughput manner. This is one of the first dual species Affymetrix microarray studies worldwide, and the first to focus on endophyte-grass symbiosis.

• We have developed an oral vaccine for possums that provides significant protection against infection with tuberculosis, in collaboration with the University of Otago and the Animal Health Board.

• At the Mystery Creek Fieldays, we launched (with PGG-Wrightson) the new AR37 ryegrass endophyte strain. AR37 is a major advance on AR1 that was itself a major breakthrough. Both strains offer plants protection against black beetle, pasture mealy bug and the Argentine stem weevil. AR37 also protects against root aphid and probably porina caterpillar, as well as standing up better to black beetle, a major pest in the north of New Zealand. Development of AR37 was greatly assisted by funding from Meat & Wool New Zealand.

• We are developing techniques which could see health-promoting long chain omega-3 polyunsaturated fatty acids entering the human diet through meat and dairy products instead of fish. The Forage Biotechnology Section is working to protect polyunsaturated fats in the leaves of plants like ryegrass, allowing the delivery of omega-3 into animals’ diets.

• Characterised and patented key endophyte alkaloid gene clusters with Massey University, one of which, peramine, was expressed by re-introducing the gene into a knockout endophyte. Currently working on engineering plants to produce the insect feeding deterrent directly.

• Developed OBodies - artificial antibodies which could replace traditional antibody production using laboratory animals for application in the areas of therapeutics, clinical diagnostics and molecular biology tools.

• Developed an inducible flowering 'switch' which enables us to trigger flowering in modified plants following chemical application.

• Our Forage Biotechnology and Forage Improvement Sections have developed Direct Infusion Mass Spectrometry. This is a tool for unbiased metabolite analysis that has been used to identify QTL associated with endophyte and alkaloid concentrations in ryegrass

• Developed and patented the expression of stable and functional ion channels in a novel biomimetic membrane system. Potential applications include medical diagnostics, pharmaceuticals/agrochemicals and bio-sensors.

• Pastoral Genomics developed Trifolium occidentale as a plant model system to underpin future genomic approaches directed at white clover improvement. Capabilities include a mutant population, molecular map and plant transformation capabilities.

• Established and incorporated PhytaGro, a plant science IP development company in collaboration with Finistere Partners in the United States. Our strategy is to partner with US industry leaders to jointly implement affiliate programmes

• Identified and patented PEAPOD, a gene that limits cell proliferation during leaf development and regulates lamina size. When disrupted in clover, plants with enlarged leaves but normal stems are obtained indicating that this gene could influence harvest index. Opportunities in other dicotyledonous species are also under investigation.

• Synthesised the first Affymetrix Nimble Express dual genome (endophyte/ryegrass) microarray which will enable the identification of genes involved in symbiosis, signalling, iron homeostasis, and secondary metabolism.

• 'Crusader' white clover won the NIAB Cup in the UK for outstanding cultivar of the year for any crop.

• The ancestral genomes of white clover were distinguished and identified using molecular cytogenetic procedures.

• Several new inter-specific hybrids in Trifolium were created and we demonstrated outstanding potential of hybrids between T. repens and T. uniflorum.

• We established that the genetically-controlled variation in carbohydrate:protein ratio of white clover affected skatole content - an important flavour compound - in milk

• The resistance to clover cyst nematode Heterodera trifolii of clover lines we had developed was shown to be based on a hypersensitive response. Field trials validated the efficacy of nematode resistance in enhancing persistence of white clover.

• We identified QTL for herbage mass and root form in ryegrass. We validated QTL for seed production traits in white clover and began applying them in breeding.

• The lolitriol ELISA assay was refined and effectively deployed as the standard quality control test for AR1.

• We completed identification and characterisation of epoxy-janthitrem I, the most abundant of the active factors in AR37 endophyte. A related compound was found to be active against porina larvae.

• A novel sperm activation method has improved bovine somatic cloning efficiency to term from 7% to 18%.

• Aggregating Nuclear Transfer embryos have significantly increased embryonic cloning efficiency to weaning from 8% to 20%.

• Techniques to investigate histone modifications as epigenetic marks are now complete and can be used for further analysis of clonal cell lines.

• We have identified the epigenetic status of 3 imprinted genes - IGF2, P57Kip2 and H19 during early development. This could be useful as early embryonic markers for aberrant pregnancies.

• We have established a new collaboration with Hematech USA that focuses on developing markers for hydrops susceptibility during cloning. The goal is to decrease the incidence of hydrops in cloned pregnancies.

• The establishment of EPIGEN - a new consortium to investigate epigenetic markers that can detect aberrant growth, differentiation, embryogenesis and genotypes that are valuable to the agricultural sector.

• We have achieved proof of concept that transgenic cells for recombinant human myelin-basic protein were successfully cloned in the bovine and that the cows then secrete this protein in milk. We also have an ongoing collaboration with Pharming NV to generate a herd of transgenic animals that secrete recombinant human Lactoferrin in their milk.

• A fertility model to look at successful pregnancy outcomes in humans has been completed and is being investigated for market potential.

• We have developed a unique method to freeze shellfish sperm and embryos - a collaboration with the Cawthron Institute. This has significant economic implications for New Zealand aquaculture.

• We assisted in successfully hosting the 10th International Ruminant Reproduction Symposium in Wellington – a prestigious conference that focused on the reproduction of mainly sheep and cattle.

• Senior Scientist Dr Chris Morris receives a prestigious Royal Society Science and Technology Silver Medal for his contribution to the advancement of New Zealand science over the past 31 years.

• Genomnz, our commercial unit that is New Zealand's leading DNA parentage and single gene testing service in deer, cattle, sheep and salmon, processed more than 100,000 commercial livestock samples in the past year.

• The Animal Genomics Section obtained a license from a USA Genomics company, enabling evaluation of more trait tests for the New Zealand beef industry.

• Catapult®, a spin out company from the Ovita consortia in which AgR is 25% shareholder, commercially released two tests resulting from Animal Genomics research, MyoMax® and i-Scan®.

• A Meat Quality industry trial demonstrated that colour stability in meat is highly heritable, meaning it is likely to find genes underlying this trait. A genome scan is underway for this.

• The Bovine Genome sequence was released. Senior Scientist John McEwan represented New Zealand in this international effort that is a major resource for genomic studies in cattle, sheep and deer.

• The Cattle Facial Eczema programme has successfully validated and fine-mapped the chromosomal region associated with resistance to facial eczema. This will enter validation trials in 2007.

• The meat traceability programme filed three patents for composite meat products. This is likely to be a high growth area, with an increasing number of countries interested in pursuing country-of-origin assurances.

• A lamb survival programme has completed analysis of a large industry data set and developed three areas where gains can be made in reducing early lamb losses.

• The peramine biosynthetic gene cluster has been isolated. These genes are required to make the broad spectrum insect feeding deterrent, peramine. Modification and transformation of this cluster into plants offers great potential to enhance insect resistance in commercial crops.

• A saturated white clover genetic linkage map based on high throughput Single Sequence Repeat markers has been published. This map will underpin subsequent searches for genes that have a major influence of desirable and undesirable clover traits. Several regions containing such genes (QTL or quantitative trait loci) have been discovered.

• Isolation of transgenic bovine cells without the use of antibiotic selection markers was successfully demonstrated. This could help address perceived public concerns that use of antibiotic selection markers in creation of transgenic organisms may enhance evolution of antibiotic-resistant “super-bugs”.

• Flowering switches that enable controlled suppression or induction of flowering have been patented. Such a technology could offer advantages to a range of plant-based industries, including synchronising crop harvesting or maintaining pasture quality by suppressing seeding.

• AgResearch scientists led a workshop on dairy cow fertility at Ruakura to develop a novel and compelling method to model the complex biological interactions involved in ovulation and conception.

• Five new ryegrass cultivars were developed and three white clover cultivars were released in the USA (Durana and Patriot) and Australasia (Tribute).