Wheat Research Report: 2015
In this Wheat Research Report we summarise some of the work published by UK wheat researchers in 2015. Given the importance of wheat for both UK and global food security there is plenty of UK work in this area that falls into a number of key areas:
– We highlight three pieces of research undertaken on the genome scale led by the Universities of Liverpool, Bristol and York, which aid to improve knowledge of the highly complex hexaploid wheat genome in order to improve future breeding efforts.
– On the phenotypic level we present studies led by both the John Innes Centre and NIAB that have identified wheat QTLs that are associated either with disease resistance or with the parameters that define grain yield.
– On the gene level researchers from Reading University investigate the role of the TIN gene on the water use efficiency associated with different levels of tillering.
– Elsewhere is a study that mixes digital imaging and field reconstructions with mathematical modeling to develop a methodology to assess the significance of the structure of the wheat canopy in final carbon gain.
– Finally we highlight a study that had high public awareness and that documents the results of a study in which transgenic wheat were generated with the aim of reducing aphid predation by production of a specific pheromone.
March
Griffiths S, Wingen L, Pietragalla J, Garcia G, Hasan A, Miralles D, Calderini DF, Ankleshwaria JB, Waite ML, Simmonds J, Snape J, Reynolds M (2015) Genetic dissection of grain size and grain number trade-offs in CIMMYT wheat germplasm. PLoS One. 10(3):e0118847. http://dx.doi.org/10.1371/journal.pone.0118847 Open Access
This is a collaboration between British, Argentinian, Mexican and Chilean researchers who investigated grain yield in a two CIMMYT varieties. Grain weight (GW) and number per unit area of land (GN) are principle components that determine grain yield and these components often show negative correlation. The CIMMYT varieties were crossed and a QTL loci was identified that showed increased GW but that did not change GN, therefore altering the usual trade off between these parameters. The authors suggest that this loci might be an attractive target for future marker-assisted breeding strategies aimed at developing higher yield wheat varieties.
June
Bruce TJ, Aradottir GI, Smart LE, Martin JL, Caulfield JC, Doherty A, Sparks CA, Woodcock CM, Birkett MA, Napier JA, Jones HD, Pickett JA (2015) The first crop plant genetically engineered to release an insect pheromone for defence. Sci Rep. http://dx.doi.org/10.1038/srep11183 Open Access
This study led by Johnathan Napier, Huw Jones and John Pickett at Rothamstead Research gained a large amount of pubilicity during its trial phase as it drew the attention of anti-GM campaigners. However for many commentators it represents an important point in the ongoing debate surrounding this technology as the public engagement undertaken by these researchers was effective in persuading the public that this was a worthwhile project. This paper reports on the findings from that study wherein hexaploid wheat was genetically engineered to produce a pheromone that aimed to reduce aphid predation. In lab experiments these pheromones were able to repel three species of aphids but in the field experiments these GM wheat showed no alteration in rate of predation. The authors suggest this might be due to erratic climatic conditions or unexpectiedly low overall insect numbers but they recognise that more work needs to be done to identify a class of pheromones that might work in this experimental system. In many ways this study is an important confirmation of the scientific process and should help persuade the general people that GM scientists are undertaking all the necessary controls before organisms with a novel genetic maekup are released into the environment.
October
Burgess AJ, Retkute R, Pound MP, Foulkes J, Preston SP, Jensen OE, Pridmore TP, Murchie EH (2015) High-Resolution Three-Dimensional Structural Data Quantify the Impact of Photoinhibition on Long-Term Carbon Gain in Wheat Canopies in the Field. Plant Physiol. 169(2):1192-204 http://dx.doi.org/10.1104/pp.15.00722 Open Access
This collaboration between crop scientists and mathematicians at the University of Nottingham and those at the University of Manchester investigates the importance of photoinhibition in the overall carbon gain of hexaploid wheat. This parameter has proven difficult to accurately assess due to the lack of data about the detailed architecture of the constantly fluctuating wheat canopy in the field. In this study they compare the canopies of three wheat species using a novel method that involves digital 3D reconstruction. This enables measurement of a range of parameters that subsequently allows an accurate assessment of light distribution throughout the canopy. This data feeds into a mathematical model that predicts that photoinhibition alone can contribute to a substantial reduction in carbon gain. The authors conclude that their model allows them to predict that even moderate changes to leaf angle at the upper levels of the wheat canopy can result in a large number of lower leaves attempting to photosynthesize in a severely light-limited location. When this information is allied to improved field phenotyping it might be possible to select for plants that have a maximal leaf arrangement. When these differences in canopy efficiency are scaled up then the changes in carbon gain will prove to be highly significant in absolute terms.
Hendriks PW, Kirkegaard JA, Lilley JM, Gregory PJ, Rebetzke GJ (2015) A tillering inhibition gene influences root-shoot carbon partitioning and pattern of water use to improve wheat productivity in rainfed environments. J Exp Bot. http://dx.doi.org/10.1093/jxb/erv457 Open Access
Peter Gregory (Reading) is the UK lead on this UK-Australian collaboration where researchers investigate the role of the wheat TILLING INHIBITION (TIN) gene during measurements of water-use in rainfed environments. They used near-isogenic lines (NILs) that varied in expression of TIN to show that the root-shoot ratio increased two-fold following tillering in plants with expression of TIN. Following a range of measurements the authors are able to conclude that water use efficiency was increased in TIN-containing lines, resulting in increases in grain yield. Although TIN was associated with increased biomass, the significant influence of both genetics and environment means that the requirement remains for careful assessment of TIN-containing progeny.
Winfield MO, Allen AM, Burridge AJ, Barker GL, Benbow HR, Wilkinson PA, Coghill J, Waterfall C, Davassi A, Scopes G, Pirani A, Webster T, Brew F, Bloor C, King J, West C, Griffiths S, King I, Bentley AR, Edwards KJ (2015) High-density SNP genotyping array for hexaploid wheat and its secondary and tertiary gene pool Plant Biotechnol J. http://dx.doi.org/10.1111/pbi.12485 Open Access
This wheat SNP genotyping project involves researchers from Bristol and Nottingham Universities alongside those from the JIC and NIAB together with industrial assistance from Affymetrix. This highly descriptive study identifies a large number of SNPs useful for subsequent genotyping of hexaploid wheat and for SNP-tracking following introgression from different genetic stocks. Following initial sequencing, markers have been validated using an ultra-high-density genome array. In the spirit of open access, all the sequence information defined by this project is available at:
http://goo.gl/e4oEhs (Putative varietal SNPs from CerealDBs)
http://goo.gl/VdN5NW (Putative SNP probes from CerealDBs)
Harper AL, Trick M, He Z, Clissold L, Fellgett A, Griffiths S, Bancroft I (2015) Genome distribution of differential homoeologue contributions to leaf gene expression in bread wheat. Plant Biotechnol J. http://dx.doi.org/10.1111/pbi.12486 Open Access
Ian Bancroft at the University of York is corresponding author on this work that is a collaboration between his own lab and that of Simon Griffiths at the JIC. They have used de novo expression data together with a new genetic linkage map to develop an ordered set of nonredundant transcripts for each of the three A,B D subgenomes of hexaploid wheat (between 40K-60K unigenes from each sub-genome). An RNAseq dataset obtained from young leaf tissue was mapped to this reference sequence in order to define the relative expression of each homoeologues variant. This showed no dominance for a particular sub-genome but rather the most highly transcribed genes were distributed throughout each sub-genome. Assessment of wider genome areas was able to define regions where one genome was dominant over the other two as well as regions where one genome was repressed compared to the other two. This study offers further insights into the expression relationships between each sub-genome and adds to the other recent methylation data (outlined below) that offers a different insight into the nature of the hexaploid wheat genome.
December
Gardiner LJ, Quinton-Tulloch M, Olohan L, Price J, Hall N, Hall A (2015) A genome-wide survey of DNA methylation in hexaploid wheat Genome Biol 16(1):273 http://dx.doi.org/10.1186/s13059-015-0838-3 Open Access
Anthony Hall leads this University of Liverpool study that analyses the wheat genome by bisulfite sequencing to identify the differential methylation that occurs throughout the three sub-genomes of allohexaploid wheat. The authors correlate sub-genome specific promoter methylation with altered expression from each particular sub-genomes. They also conduct an experiment demonstrating that temperature has an impact on gene expression across all of the sub-genomes. Although there is significant variation between sub-genomes the authors show that patterns of methylation in the D-genome is conserved with regions in its diploid progenitor Aegilops tauschii.
Gordon A, Basler R, Bansept-Basler P,, Fanstone V, Harinarayan L,, Grant PK, Birchmore R, Bayles RA,, Boyd LA, O’Sullivan DM (2015) The identification of QTL controlling ergot sclerotia size in hexaploid wheat implicates a role for the Rht dwarfing alleles Theor Appl Genet. 128(12):2447-60 http://dx.doi.org/10.1007/s00122-015-2599-5
This academic-industry collaboration is led by researchers at NIAB and the University of Reading and tackles an aspect of plant biology that is of great interest to those interested in developing disease resistance wheat varieties. This study looks at infection success of Claviceps purpurea, which is fungal pathogen that infects a range of temperate grasses and is therefore economically important. Claviceps infection produces a sclerotia within the seed and, when ingested, can cause significant illness in mammals. Two varieties of winter hexaploid wheat were identified that showed more resistance to Claviceps so these were crossed to produce a doubled haploid mapping population. Following phenotypic assessment of sclerotia development, QTLs were identified that mapped to reduced height (Rht) loci and therefore indicates that semi-dwarf varieties may display resistance to Claviceps infection.
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