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Chagne D.,The New Zealand Institute for Plant and Food Research Ltd | Crowhurst R.N.,Mount Albert Research Center | Pindo M.,Instituto Agrario San Michele allAdige Research and Innovation Center | Thrimawithana A.,Mount Albert Research Center | And 39 more authors.
PLoS ONE | Year: 2014

We present a draft assembly of the genome of European pear (Pyrus communis) 'Bartlett'. Our assembly was developed employing second generation sequencing technology (Roche 454), from single-end, 2 kb, and 7 kb insert paired-end reads using Newbler (version 2.7). It contains 142,083 scaffolds greater than 499 bases (maximum scaffold length of 1.2 Mb) and covers a total of 577.3 Mb, representing most of the expected 600 Mb Pyrus genome. A total of 829,823 putative single nucleotide polymorphisms (SNPs) were detected using re-sequencing of 'Louise Bonne de Jersey' and 'Old Home'. A total of 2,279 genetically mapped SNP markers anchor 171 Mb of the assembled genome. Ab initio gene prediction combined with prediction based on homology searching detected 43,419 putative gene models. Of these, 1219 proteins (556 clusters) are unique to European pear compared to 12 other sequenced plant genomes. Analysis of the expansin gene family provided an example of the quality of the gene prediction and an insight into the relationships among one class of cell wall related genes that control fruit softening in both European pear and apple (Malusxdomestica). The 'Bartlett' genome assembly v1.0 (http://www.rosaceae.org/species/pyrus/ pyrus-communis/genome-v1.0) is an invaluable tool for identifying the genetic control of key horticultural traits in pear and will enable the wide application of marker-assisted and genomic selection that will enhance the speed and efficiency of pear cultivar development. © 2014 Chagné et al.


Bassett S.A.,Agresearch Ltd. | Johnson R.D.,Agresearch Ltd. | Simpson W.R.,Agresearch Ltd. | Laugraud A.,Lincoln Research Center | And 2 more authors.
FEMS Microbiology Letters | Year: 2016

Secreted proteins, those involved in cell wall biogenesis, are likely to play a role in communication in the symbiotic interaction between the fungal endophyte Epichloë festucae with perennial ryegrass (Lolium perenne), particularly given the close association between fungal hyphae and the plant cell wall. Our hypothesis was that secreted proteins are likely to be responsible for establishing and maintaining a normal symbiotic relationship. We analyzed an endophyte EST database for genes with predicted signal peptide sequences. Here, we report the identification and characterization of rhgA; a gene involved in the regulation of hyphal growth in planta. In planta analysis of ΔrhgA mutants showed that disruption of rhgA resulted in extensive unregulated hyphal growth. This phenotype was fully complemented by insertion of the rhgA gene and suggests that rhgA is important for maintaining normal hyphal growth during symbiosis. © FEMS 2016. All rights reserved.


PubMed | Lincoln Research Center, Victoria University of Wellington and Agresearch Ltd.
Type: Journal Article | Journal: FEMS microbiology letters | Year: 2016

Secreted proteins, those involved in cell wall biogenesis, are likely to play a role in communication in the symbiotic interaction between the fungal endophyte Epichlo festucae with perennial ryegrass (Lolium perenne), particularly given the close association between fungal hyphae and the plant cell wall. Our hypothesis was that secreted proteins are likely to be responsible for establishing and maintaining a normal symbiotic relationship. We analyzed an endophyte EST database for genes with predicted signal peptide sequences. Here, we report the identification and characterization of rhgA; a gene involved in the regulation of hyphal growth in planta In planta analysis of rhgA mutants showed that disruption of rhgA resulted in extensive unregulated hyphal growth. This phenotype was fully complemented by insertion of the rhgA gene and suggests that rhgA is important for maintaining normal hyphal growth during symbiosis.


Pal P.,Lincoln University at Christchurch | Clough T.J.,Lincoln University at Christchurch | Kelliher F.M.,Lincoln University at Christchurch | Kelliher F.M.,Lincoln Research Center | And 2 more authors.
Journal of Environmental Quality | Year: 2012

Th e rationale for this study came from observing grazing dairy cattle dropping freshly harvested plant material onto the soil surface, hereafter called litter-fall. Th e Intergovernmental Panel on Climate Change (IPCC) guidelines include N 2O emissions during pasture renewal but do not consider N 2O emissions that may result from litter-fall. Th e objectives of this study were to determine litter-fall rates and to assess indicative N 2O emission factors (EFs) for the dominant pasture species (perennial ryegrass [Lolium perenne L.] and white clover [Trifolium repens L.]). Herbage was vacuumed from intensively managed dairy pastures before and after 30 different grazing events when cows (84 cows ha -1) grazed for 24 h according to a rotational system; the interval between grazing events ranged from 21 to 30 d. A laboratory incubation study was performed to assess potential EF values for the pasture species at two soil moisture contents. Finely ground pasture material was incubated under controlled laboratory conditions with soil, and the N 2O emissions were measured until rates returned to control levels. On average, pre- and postgrazing dry matter yields per grazing event were 2516 ± 636 and 1167 ± 265 kg DM ha -1 (±SD), respectively. Pregrazing litter was absent, whereas postgrazing fresh and senesced litter-fall rates were 53 ± 24 and 19 ± 18 kg DM ha -1, respectively. Annually, the rotational grazing system resulted in 12 grazing events where fresh litter-fall equaed to 16 kg N ha -1 yr -1 to the soil. Emission factors in the laboratory experiment indicated that the EF for perennial ryegrass and white clover ranged from 0.7 to 3.1%. If such EF values should also occur under field conditions, then we estimate that litter-fall induces an N 2O emission rate of 0.3 kg N 2O ha -1 yr -1. Litter-fall as a source of N 2O in grazed pastures requires further assessment. © 2012 by the American Society of Agronomy, Crop Science Society of America, and Soil Science Society of America.


Swaminathan J.,Lincoln Research Center | van Koten C.,Lincoln Research Center | Henderson H.V.,Ruakura Research Center | Jackson T.A.,Lincoln Research Center | Wilson M.J.,Ruakura Research Center
Journal of Applied Microbiology | Year: 2016

Aims: We aimed to evaluate different formulations for their ability to adhere Trichoderma atroviridae spores to wheat seeds, and promote survival during storage at a range of temperatures and relative humidities (RH). Methods and Results: We tested a range of formulations for their ability to adhere T. atroviridae spores to wheat seeds. Treated seeds were stored for 6 months at a range of temperatures and RH, and spore viability among formulation was compared over time. Spore survival within formulations interacted significantly with environmental conditions. Notably, under optimum conditions (low temperatures and RH) best spore survival was recorded with a xanthan-gum-based formulation. Conversely under suboptimum conditions (high temperatures and RH), survival of spores was best in a waxy-starch formulation, but very poor in the xanthan-gum formulation. Conclusions: These results indicate that T. atroviridae spores can be effectively delivered on to seeds and that a xanthan-gum formulation is promising when optimal storage conditions can be maintained. Significance and Impact of the Study: Most published formulation papers/patents only report survival of organisms over time at a single or limited number of temperatures and RH. For the first time, this study shows how different formulations are better suited to certain temperature and RH combinations. © 2016 The Society for Applied Microbiology.

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