Wheat functional genomics and engineering crop improvement

Genetic mapping and determination of the organization of the wheat genome are changing the wheat-breeding process. New initiatives to analyze the expressed portion of the wheat genome and structural analysis of the genomes of Arabidopsis and rice are increasing our knowledge of the genes that are linked to key agronomically important traits

A highly conserved gene island of three genes on chromosome 3B of hexaploid wheat: diverse gene function and genomic structure maintained in a tightly linked block

The complexity of the wheat genome has resulted from waves of retrotransposable element insertions. Gene deletions and disruptions generated by the fast replacement of repetitive elements in wheat have resulted in disruption of colinearity at a micro (sub-megabase) level among the cereals. In view of genomic changes that are possible within a given time span, conservation of genes between species tends to imply an important functional or regional constraint that does not permit a change in genomic structure. The ctg1034 contig completed in this paper was initially studied because it was assigned to the Sr2 resistance locus region, but detailed mapping studies subsequently assigned it to the long arm of 3B and revealed its unusual features

Wheat beta-expansin (EXPB11) genes: Identification of the expressed gene on chromosome 3BS carrying a pollen allergen domain

Background Expansins form a large multi-gene family found in wheat and other cereal genomes that are involved in the expansion of cell walls as a tissue grows. The expansin family can be divided up into two main groups, namely, alpha-expansin (EXPA) and beta-expansin proteins (EXPB), with the EXPB group being of particular interest as group 1-pollen allergens. Results In this study, three beta-expansin genes were identified and characterized from a newly sequenced region of the Triticum aestivum cv. Chinese Spring chromosome 3B physical map at the Sr2 locus (FPC contig ctg11). The analysis of a 357 kb sub-sequence of FPC contig ctg11 identified one beta-expansin genes to be TaEXPB11, originally identified as a cDNA from the wheat cv Wyuna. Through the analysis of intron sequences of the three wheat cv. Chinese Spring genes, we propose that two of these beta-expansin genes are duplications of the TaEXPB11 gene. Comparative sequence analysis with two other wheat cultivars (cv. Westonia and cv. Hope) and a Triticum aestivum var. spelta line validated the identification of the Chinese Spring variant of TaEXPB11. The expression in maternal and grain tissues was confirmed by examining EST databases and carrying out RT-PCR experiments. Detailed examination of the position of TaEXPB11 relative to the locus encoding Sr2 disease resistance ruled out the possibility of this gene directly contributing to the resistance phenotype. Conclusions Through 3-D structural protein comparisons with Zea mays EXPB1, we proposed that variations within the coding sequence of TaEXPB11 in wheats may produce a functional change within features such as domain 1 related to possible involvement in cell wall structure and domain 2 defining the pollen allergen domain and binding to IgE protein. The variation established in this gene suggests it is a clearly identifiable member of a gene family and reflects the dynamic features of the wheat genome as it adapted to a range of different environments and uses

Genomic analysis of Campylobacter fetus subspecies: identification of candidate virulence determinants and diagnostic assay targets

Background: Campylobacter fetus subspecies venerealis is the causative agent of bovine genital campylobacteriosis, asymptomatic in bulls the disease is spread to female cattle causing extensive reproductive loss. The microbiological and molecular differentiation of C. fetus subsp. venerealis from C. fetus subsp. fetus is extremely difficult. This study describes the analysis of the available C. fetus subsp. venerealis AZUL-94 strain genome (~75–80%) to identify elements exclusively found in C. fetus subsp. venerealis strains as potential diagnostic targets and the characterisation of subspecies virulence genes. Results: Eighty Kb of genomic sequence (22 contigs) was identified as unique to C. fetus subsp. venerealis AZUL-94 and consisted of type IV secretory pathway components, putative plasmid genes and hypothetical proteins. Of the 9 PCR assays developed to target C. fetus subsp. venerealis type IV secretion system genes, 4 of these were specific for C. fetus subsp. venerealis biovar venerealis and did not detect C. fetus subsp. venerealis biovar intermedius. Two assays were specific for C. fetus subsp. venerealis AZUL-94 strain, with a further single assay specific for the AZUL-94 strain and C. fetus subsp. venerealis biovar intermedius (and not the remaining C. fetus subsp. venerealis biovar venerealis strains tested). C. fetus subsp. fetus and C. fetus subsp. venerealis were found to share most common Campylobacter virulence factors such as SAP, chemotaxis, flagellar biosynthesis, 2-component systems and cytolethal distending toxin subunits (A, B, C). We did not however, identify in C. fetus the full complement of bacterial adherence candidates commonly found in other Campylobacter spp. Conclusion: The comparison of the available C. fetus subsp. venerealis genome sequence with the C. fetus subsp. fetus genome identified 80 kb of unique C. fetus subsp. venerealis AZUL94 sequence, with subsequent PCR confirmation demonstrating inconsistent amplification of these targets in all other C. fetus subsp. venerealis strains and biovars tested. The assays developed here highlight the complexity of targeting strain specific virulence genes for field studies for the molecular identification and epidemiology of C. fetus

The complexity of Rhipicephalus (Boophilus) microplus genome characterised through detailed analysis of two BAC clones

<p>Abstract</p> <p>Background</p> <p><it>Rhipicephalus (Boophilus) microplus (Rmi) </it>a major cattle ectoparasite and tick borne disease vector, impacts on animal welfare and industry productivity. In arthropod research there is an absence of a complete Chelicerate genome, which includes ticks, mites, spiders, scorpions and crustaceans. Model arthropod genomes such as <it>Drosophila </it>and <it>Anopheles </it>are too taxonomically distant for a reference in tick genomic sequence analysis. This study focuses on the <it>de-novo </it>assembly of two <it>R. microplus </it>BAC sequences from the understudied <it>R microplus </it>genome. Based on available <it>R. microplus </it>sequenced resources and comparative analysis, tick genomic structure and functional predictions identify complex gene structures and genomic targets expressed during tick-cattle interaction.</p> <p>Results</p> <p>In our BAC analyses we have assembled, using the correct positioning of BAC end sequences and transcript sequences, two challenging genomic regions. Cot DNA fractions compared to the BAC sequences confirmed a highly repetitive BAC sequence BM-012-E08 and a low repetitive BAC sequence BM-005-G14 which was gene rich and contained short interspersed elements (SINEs). Based directly on the BAC and Cot data comparisons, the genome wide frequency of the SINE Ruka element was estimated. Using a conservative approach to the assembly of the highly repetitive BM-012-E08, the sequence was de-convoluted into three repeat units, each unit containing an 18S, 5.8S and 28S ribosomal RNA (rRNA) encoding gene sequence (rDNA), related internal transcribed spacer and complex intergenic region.</p> <p>In the low repetitive BM-005-G14, a novel gene complex was found between to 2 genes on the same strand. Nested in the second intron of a large 9 Kb <it>papilin </it>gene was a <it>helicase </it>gene. This <it>helicase </it>overlapped in two exonic regions with the <it>papilin</it>. Both these genes were shown expressed in different tick life stage important in ectoparasite interaction with the host. Tick specific sequence differences were also determined for the <it>papilin </it>gene and the protein binding sites of the 18S subunit in a comparison to <it>Bos taurus</it>.</p> <p>Conclusion</p> <p>In the absence of a sequenced reference genome we have assembled two complex BAC sequences, characterised novel gene structure that was confirmed by gene expression and sequencing analyses. This is the first report to provide evidence for 2 eukaryotic genes with exon regions that overlap on the same strand, the first to describe <it>Rhipicephalinae papilin</it>, and the first to report the complete ribosomal DNA repeated unit sequence structure for ticks. The Cot data estimation of genome wide sequence frequency means this research will underpin future efforts for genome sequencing and assembly of the <it>R. microplus </it>genome.</p

Comparison of low molecular weight glutenin subunits identified by SDS-PAGE, 2-DE, MALDI-TOF-MS and PCR in common wheat

Low-molecular-weight glutenin subunits (LMW-GS) play a crucial role in determining end-use quality of common wheat by influencing the viscoelastic properties of dough. Four different methods - sodium dodecyl sulfate polyacrylamide gel electrophoresis (SDS-PAGE), two-dimensional gel electrophoresis (2-DE, IEF × SDS-PAGE), matrix-assisted laser desorption/ionization time-of-flight mass spectrometry (MALDI-TOF-MS) and polymerase chain reaction (PCR), were used to characterize the LMW-GS composition in 103 cultivars from 12 countries

Dynamic modelling of ammonia biofiltration from waste gases

A dynamic model to describe ammonia removal in a gas-phase biofilter was developed. The math-ematical model is based on discretized mass balances and detailed nitrification kinetics that includeinhibitory effects caused by free ammonia (FA) and free nitrous acid (FNA). The model was able to pre-dict experimental results operation under different loading rates (from 3.2 to 13.2 g NH3h-1m-3). In par-ticular the model was capable of reproducing inhibition caused by high inlet ammonia concentrations. Alsoelimination capacity was accurately predicted. Experimental data was also used to optimize certain modelparameters such as the concentration of ammonia- and nitrite-oxidizing biomass.Peer ReviewedPostprint (published version

Crop Updates 2008 - Cereals

This session covers twenty four papers from different authors: WHEAT AGRONOMY 1. Wheat variety performance in the Northern Agricultural Region in 2007, Christine Zaicou, Department of Agriculture and Food 2. Wheat variety performance on the Central Agricultural Region in 2007, Shahajahan Miyan, Department of Agriculture and Food 3. Response of wheat varieties to sowing time in the Great Southern and Lakes Region in 2007, Brenda Shackley and Steve Penny, Department of Agriculture and Food 4. Wheat variety performance in the South Coastal Region in 2007, Sarah Ellis, Department of Agriculture and Food 5. Flowering dates of wheat varieties in Western Australia in 2007, Darshan Sharma, Brenda Shackley and Christine Zaicou, Department of Agriculture and Food BARLEY AGRONOMY 6. Barley variety options for Western Australia, Blakely Paynter, Andrea Hills and Jeff Russell, Department of Agriculture and Food 7. Vlaming A – the newest malting barley variety, Blakely Paynter, Jeff Russell and Andrea Hills, Department of Agriculture and Food 8. Barley yields higher in wide rows with stubble retained in a very dry season at Merredin, Glen Riethmuller, Bill Bowden and Paul Blackwell, Department of Agriculture and Food HERBICIDE TOLERANCE 9. Herbicide tolerance of current/new wheat varieties, Dr Harmohinder Dhammu, Department of Agriculture and Food 10. Herbicide tolerance of new oat varieties, Dr Harmohinder Dhammu, Vince Lambert, and Chris Roberts,Department of Agriculture and Food NUTRITION 11. Managing nitrogen inputs in malting barley, Andrea Hills and Blakely Paynter, Department of Agriculture and Food 12. Decision tools for optimal N on cereal crops, David and Sally Cox, Jeremy Lemon* and Andrea Hills*, *Department of Agriculture and Food 13. Wheat varieties respond differently to potassium application on potassium responsive soils, Paul Damon and Zed Rengel, Faculty of Natural and Agricultural Sciences, University of Western Australia DISEASES 14. Leaf disease management in continuous barley in the northern and central grainbelt of WA, Geoff Thomas, Ciara Beard, Anne Smith, Kith Jayasena and Sean Kelly, Department of Agriculture and Food 15. Temperature and moisture requirements of leaf, stem and stripe rusts of wheat, Geoff Thomas, Rob Loughman and Bill MacLeod, Department of Agriculture and Food 16. Fungicide options for controlling diseases in oats, Raj Malik and Blakely Paynter, Department of Agriculture and Food 17. Survey of wheat root diseases under intensive cereal production in Western Australia during 2005-2007, Ravjit Khangura, William MacLeod, Vivien Vanstone, Colin Hanbury, Mehreteab Aberra, Gordon MacNish and Robert Loughman, Department of Agriculture and Food 18. Epidemiology studies on Wheat Streak Mosaic Virus in 2007, Brenda Coutts, Geoff Strickland, Monica Kehoe, Dustin Severtson and Roger Jones, Department of Agriculture and Food 19. Bacterial diseases that affect WA export hay quality, Dominie Wright and Megan Jordan, Department of Agriculture and Food SOIL 20. Hardpan penetration ability of drought-stressed wheat under pot and field conditions, Xinhua He1, Eli Manyol1, Song-Ai Nio1, Imran Malik1, Tina Botwright-Acuña1,2and Len Wade1,3,1School of Plant Biology, University of Western Australia, 2Tasmanian Institute of Agricultural Research, University of Tasmania, TAS, 3E.H. Graham Centre, Charles Sturt University, NSW HARVEST MANAGEMENT 21. Calculating the risk – the SEPWA Harvest Calculator, Nigel Metz, South East Premium Wheat Growers Association 22. The relationship between grain moisture and atmospheric conditions in cereal crop harvesting on the South Coast of WA, Nigel Metz, South East Premium Wheat Growers Association (SEPWA) MARKETS 23. Varietal accreditation for Australian Barley, Linda Price, Barley Australia STATISTICAL METHODS 24. Applying data mining tools to improve grain quality for growers, Dean Diepeveen1, Leisa Armstrong2, Peter Clarke1, Doug Abrecht1, Rudi Appels2 and Matthew Bellgard3,1Department of Agriculture and Food, Western Australia 2Edith Cowan University, Western Australia, 3Centre of Comparative Genomics, Murdoch Universit

Shifting the limits in wheat research and breeding using a fully annotated reference genome

Introduction: Wheat (Triticum aestivum L.) is the most widely cultivated crop on Earth, contributing about a fifth of the total calories consumed by humans. Consequently, wheat yields and production affect the global economy, and failed harvests can lead to social unrest. Breeders continuously strive to develop improved varieties by fine-tuning genetically complex yield and end-use quality parameters while maintaining stable yields and adapting the crop to regionally specific biotic and abiotic stresses. Rationale: Breeding efforts are limited by insufficient knowledge and understanding of wheat biology and the molecular basis of central agronomic traits. To meet the demands of human population growth, there is an urgent need for wheat research and breeding to accelerate genetic gain as well as to increase and protect wheat yield and quality traits. In other plant and animal species, access to a fully annotated and ordered genome sequence, including regulatory sequences and genome-diversity information, has promoted the development of systematic and more time-efficient approaches for the selection and understanding of important traits. Wheat has lagged behind, primarily owing to the challenges of assembling a genome that is more than five times as large as the human genome, polyploid, and complex, containing more than 85% repetitive DNA. To provide a foundation for improvement through molecular breeding, in 2005, the International Wheat Genome Sequencing Consortium set out to deliver a high-quality annotated reference genome sequence of bread wheat. Results: An annotated reference sequence representing the hexaploid bread wheat genome in the form of 21 chromosome-like sequence assemblies has now been delivered, giving access to 107,891 high-confidence genes, including their genomic context of regulatory sequences. This assembly enabled the discovery of tissue- and developmental stage–related gene coexpression networks using a transcriptome atlas representing all stages of wheat development. The dynamics of change in complex gene families involved in environmental adaptation and end-use quality were revealed at subgenome resolution and contextualized to known agronomic single-gene or quantitative trait loci. Aspects of the future value of the annotated assembly for molecular breeding and research were exemplarily illustrated by resolving the genetic basis of a quantitative trait locus conferring resistance to abiotic stress and insect damage as well as by serving as the basis for genome editing of the flowering-time trait. Conclusion: This annotated reference sequence of wheat is a resource that can now drive disruptive innovation in wheat improvement, as this community resource establishes the foundation for accelerating wheat research and application through improved understanding of wheat biology and genomics-assisted breeding. Importantly, the bioinformatics capacity developed for model-organism genomes will facilitate a better understanding of the wheat genome as a result of the high-quality chromosome-based genome assembly. By necessity, breeders work with the genome at the whole chromosome level, as each new cross involves the modification of genome-wide gene networks that control the expression of complex traits such as yield. With the annotated and ordered reference genome sequence in place, researchers and breeders can now easily access sequence-level information to precisely define the necessary changes in the genomes for breeding programs. This will be realized through the implementation of new DNA marker platforms and targeted breeding technologies, including genome editing