Palmerston North, New Zealand
Palmerston North, New Zealand

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Tomer N.,Plant & Food Research | McGlone A.,Plant & Food Research | Kunnemeyer R.,University of Waikato
Computers and Electronics in Agriculture | Year: 2017

We have compared simulations of the diffuse optical transport in fresh whole brown onions (Allium cepa) with real measurements. To ensure the accuracy of the computer simulations, a structured light scanner was used to record the three dimensional shape of the produce as well as the locations of light source and detectors. The light transport within the produce was simulated by the NIRFast finite element method using the mesh created by the 3D scanner. Results collected from 10 fresh onions showed general agreement between experiments and simulations when appropriate absorption and scattering values were used with the computer mesh models. Onion tissue absorption coefficients measured by the inverse adding doubling method are five times larger than those required to recreate the experimental transmission readings. The absorption values used are close to those reported in the literature using different measurement methods, such as time-resolved reflectance spectroscopy on apples. Simulations using mesh models with internal regions suggested inhomogeneous optical property distributions influenced the transport of light within the onions. © 2017 Elsevier B.V.

News Article | May 5, 2017

New Zealand scientists have managed to successfully breed blue cod for the first time, which could support the development of a new aquaculture industry for the country, reports Stuff. Researchers at Plant & Food Research in Nelson, NZ, managed to breed and grow blue cod to fingerlings. Around 2,000 hatchlings have been raised, most of which are now around 5 to 7 centimeters long. Their parents were wild blue cod from the Marlborough Sounds in NZ's south island. “Having our first population of blue cod juveniles is an exciting development and shows proof-of-concept for raising blue cod for aquaculture or perhaps re-stocking," said Plant & Food Research’s science group leader Alistair Jerrett. "The next step is figuring out the best way to scale-up the hatchery to one of commercial potential." Joseph Thomas, CEO of Ngai Tahu Seafood, a company supporting the program, said the outcomes of this program could have real commercial and kaitiakitanga (guardianship) benefit for the seafood industry. “By enhancing our understanding of blue cod breeding we may be able to identify ways to replenish and strengthen our fishing stocks, which will have a positive impact on customary, recreational and commercial availability,” said Thomas. Around 2,000 metric tons of blue cod are caught each year, according NZ's quota management system. Most of this is consumed in-market, although NZ also exports 29t of blue cod each year with a value of NZD 650,000, mainly as frozen fish or fillets for the Asian market. Click here for the full story.

PubMed | University of Auckland, New Zealand Institute for Plant and Food Research and Plant & Food Research
Type: | Journal: Horticulture research | Year: 2015

For any given genotype, the environment in which an apple is grown can influence the properties of the fruit considerably. While there has been extensive research on the mechanism of the genetic control of fruit quality traits, less effort has been made to investigate the way that these genetic mechanisms interact with the environment. To address this issue, we employed a large Royal Gala Braeburn population of 572 seedlings replicated over sites in three climatically diverse apple-growing regions in New Zealand. Phenotyping for traits including fruit maturation timing, firmness and dry matter content was performed at each of these three sites for a single growing season (2011), and at two sites (Motueka and Hawkes Bay) for two seasons (2009 and 2010). The phenotype data collected over 2 years at two sites enabled the detection of 190 quantitative trait loci (QTL) that controlled these traits regardless of year or growing location, as well as some chromosomal loci that influenced the traits in a single given environment or year. For those loci that were environmentally stable over three sites, there was an interdependency of fruit maturation date, dry matter content and storage potential within this population, with two regions on Linkage Groups (LGs) 10 and 16 strongly contributing. If these loci were used in a marker-assisted selection programme to select for progeny bearing firmer fruit, this would have the unintentional consequence of selecting, high dry matter content, later maturing apples. In addition, a further 113 new QTLs with a smaller effect were identified, some of which were exhibited only in a single growing environment, demonstrating the underlying complexity of control of traits determining fruit quality, in addition to the need for being aware of environmental effects when developing new apple varieties.

PubMed | University of Florida, La Trobe University, New Zealand Institute for Plant and Food Research and Plant & Food Research
Type: Journal Article | Journal: G3 (Bethesda, Md.) | Year: 2015

The nonadditive genetic effects may have an important contribution to total genetic variation of phenotypes, so estimates of both the additive and nonadditive effects are desirable for breeding and selection purposes. Our main objectives were to: estimate additive, dominance and epistatic variances of apple (Malus domestica Borkh.) phenotypes using relationship matrices constructed from genome-wide dense single nucleotide polymorphism (SNP) markers; and compare the accuracy of genomic predictions using genomic best linear unbiased prediction models with or without including nonadditive genetic effects. A set of 247 clonally replicated individuals was assessed for six fruit quality traits at two sites, and also genotyped using an Illumina 8K SNP array. Across several fruit quality traits, the additive, dominance, and epistatic effects contributed about 30%, 16%, and 19%, respectively, to the total phenotypic variance. Models ignoring nonadditive components yielded upwardly biased estimates of additive variance (heritability) for all traits in this study. The accuracy of genomic predicted genetic values (GEGV) varied from about 0.15 to 0.35 for various traits, and these were almost identical for models with or without including nonadditive effects. However, models including nonadditive genetic effects further reduced the bias of GEGV. Between-site genotypic correlations were high (>0.85) for all traits, and genotype-site interaction accounted for <10% of the phenotypic variability. The accuracy of prediction, when the validation set was present only at one site, was generally similar for both sites, and varied from about 0.50 to 0.85. The prediction accuracies were strongly influenced by trait heritability, and genetic relatedness between the training and validation families.

PubMed | University of Auckland, New Zealand Institute for Plant and Food Research and Plant & Food Research
Type: | Journal: BMC plant biology | Year: 2015

The vigour and precocity of trees highly influences their efficiency in commercial production. In apple, dwarfing rootstocks allow high-density plantings while their precocious flowering enables earlier fruit production. Currently, there is a lack of pear (Pyrus communis L.) rootstocks that are equivalent to the high yielding apple rootstock M9. For the efficient breeding of new Pyrus rootstocks it is crucial to understand the genetic determinants of vigour control and precocity. In this study we used quantitative trait loci (QTLs) analysis to identify genetic loci associated with the desired traits, using a segregating population of 405F1 P. communis seedlings from a cross between Old Home and Louise Bonne de Jersey (OHxLBJ). The seedlings were grafted as rootstocks with Doyenne du Comice scions and comprehensively phenotyped over four growing seasons for traits related to tree architecture and flowering, in order to describe the growth of the scions.A high density single nucleotide polymorphism (SNP)-based genetic map comprising 597 polymorphic pear and 113 apple markers enabled the detection of QTLs influencing expression of scion vigour and precocity located on linkage groups (LG)5 and LG6 of Old Home. The LG5 QTL maps to a position that is syntenic to the apple Malling 9 (M9) Dw1 locus at the upper end of LG5. An allele of a simple sequence repeat (SSR) associated with apple Dw1 segregated with dwarfing and precocity in pear and was identified in other pear germplasm accessions. The orthology of the vigour-controlling LG5 QTL between apple and pear raises the possibility that the dwarfing locus Dw1 arose before the divergence of apple and pear, and might therefore be present in other Rosaceae species.We report the first QTLs associated with vigour control and flowering traits in pear rootstocks. Orthologous loci were found to control scion growth and precocity in apple and pear rootstocks. The application of our results may assist in the breeding process of a pear rootstock that confers both vigour control and precocity to the grafted scion cultivar.

PubMed | Wageningen University, New Zealand Institute for Plant and Food Research, Plant & Food Research and University of Liège
Type: Journal Article | Journal: Molecular plant pathology | Year: 2016

Apple scab, caused by the fungal pathogen Venturia inaequalis, is one of the most severe diseases of apple worldwide. It is the most studied plant-pathogen interaction involving a woody species using modern genetic, genomic, proteomic and bioinformatic approaches in both species. Although Geneva apple was recognized long ago as a potential source of resistance to scab, this resistance has not been characterized previously. Differential interactions between various monoconidial isolates of V.inaequalis and six segregating F1 and F2 populations indicate the presence of at least five loci governing the resistance in Geneva. The 17 chromosomes of apple were screened using genotyping-by-sequencing, as well as single marker mapping, to position loci controlling the V.inaequalis resistance on linkage group 4. Next, we fine mapped a 5-cM region containing five loci conferring both dominant and recessive scab resistance to the distal end of the linkage group. This region corresponds to 2.2Mbp (from 20.3 to 22.5Mbp) on the physical map of Golden Delicious containing nine candidate nucleotide-binding site leucine-rich repeat (NBS-LRR) resistance genes. This study increases our understanding of the complex genetic basis of apple scab resistance conferred by Geneva, as well as the gene-for-gene (GfG) relationships between the effector genes in the pathogen and resistance genes in the host.

PubMed | Lincoln University at Christchurch, Massey University, Agresearch Ltd. and Plant & Food Research
Type: Journal Article | Journal: The New phytologist | Year: 2015

The transcriptional regulation of four phylogenetically distinct members of a family of Kunitz proteinase inhibitor (KPI) genes isolated from white clover (Trifolium repens; designated Tr-KPI1, Tr-KPI2, Tr-KPI4 and Tr-KPI5) has been investigated to determine their wider functional role. The four genes displayed differential transcription during seed germination, and in different tissues of the mature plant, and transcription was also ontogenetically regulated. Heterologous over-expression of Tr-KPI1, Tr-KPI2, Tr-KPI4 and Tr-KPI5 in Nicotiana tabacum retarded larval growth of the herbivore Spodoptera litura, and an increase in the transcription of the pathogenesis-related genes PR1 and PR4 was observed in the Tr-KPI1 and Tr-KPI4 over-expressing lines. RNA interference (RNAi) knock-down lines in white clover displayed significantly altered vegetative growth phenotypes with inhibition of shoot growth and a stimulation of root growth, while knock-down of Tr-KPI1, Tr-KPI2 and Tr-KPI5 transcript abundance also retarded larval growth of S.litura. Examination of these RNAi lines revealed constitutive stress-associated phenotypes as well as altered transcription of cellular signalling genes. These results reveal a functional redundancy across members of the KPI gene family. Further, the regulation of transcription of at least one member of the family, Tr-KPI2, may occupy a central role in the maintenance of a cellular homeostasis.

PubMed | Queen's University of Belfast, University of Chicago, Hannover Medical School, Plant & Food Research and 3 more.
Type: | Journal: Physiological genomics | Year: 2017

Muscle fiber cross-sectional area (CSA) and proportion of different fiber types are important determinants of muscle function and overall metabolism. Genetic variation plays a substantial role in phenotypic variation of these traits, however, the underlying genes remain poorly understood.This study aimed to map quantitative trait loci (QTL) affecting differences in soleus muscle fiber traits between the LG/J and SM/J mouse strains.Fiber number, CSA, and proportion of oxidative type I fibers were assessed in the soleus of 334 genotyped male and female mice of the F34 generation of advanced intercross lines (AIL) derived from the LG/J and SM/J strains. To increase the QTL detection power, these data were combined with 94 soleus samples from the F2 intercross of the same strains. Transcriptome of the soleus muscle of LG/J and SM/J females was analysed using microarray.Genome-wide association analysis mapped 4 QTL (genome-wide p<0.05) affecting the properties of muscle fibers to Chromosome 2, 3, 4 and 11. A 1.5-LOD QTL support interval ranged between 2.36 Mb and 4.67 Mb. Based on the genomic sequence information, functional and transcriptome data, candidate genes were identified for each of these QTL.Combination of analyses in F2 and F34 AIL populations with transcriptome and genomic sequence data in the parental strains is an effective strategy for refining QTL and nomination of the candidate genes.

PubMed | Scion Research, Landcare Research, NIWA - National Institute of Water and Atmospheric Research, Agresearch Ltd. and Plant & Food Research
Type: Journal Article | Journal: Global change biology | Year: 2015

Future human well-being under climate change depends on the ongoing delivery of food, fibre and wood from the land-based primary sector. The ability to deliver these provisioning services depends on soil-based ecosystem services (e.g. carbon, nutrient and water cycling and storage), yet we lack an in-depth understanding of the likely response of soil-based ecosystem services to climate change. We review the current knowledge on this topic for temperate ecosystems, focusing on mechanisms that are likely to underpin differences in climate change responses between four primary sector systems: cropping, intensive grazing, extensive grazing and plantation forestry. We then illustrate how our findings can be applied to assess service delivery under climate change in a specific region, using New Zealand as an example system. Differences in the climate change responses of carbon and nutrient-related services between systems will largely be driven by whether they are reliant on externally added or internally cycled nutrients, the extent to which plant communities could influence responses, and variation in vulnerability to erosion. The ability of soils to regulate water under climate change will mostly be driven by changes in rainfall, but can be influenced by different primary sector systems vulnerability to soil water repellency and differences in evapotranspiration rates. These changes in regulating services resulted in different potentials for increased biomass production across systems, with intensively managed systems being the most likely to benefit from climate change. Quantitative prediction of net effects of climate change on soil ecosystem services remains a challenge, in part due to knowledge gaps, but also due to the complex interactions between different aspects of climate change. Despite this challenge, it is critical to gain the information required to make such predictions as robust as possible given the fundamental role of soils in supporting human well-being.

Andersen M.T.,Plant & Food Research
Methods in molecular biology (Clifton, N.J.) | Year: 2013

Phytoplasma plasmids have generally been detected from DNA extracted from plants and insects using methods designed for the purification of total phytoplasma DNA. Methods include extraction from tissues that are high in phytoplasma titre, such as the phloem of plants, with the use of CsCl-bisbenzimide gradients that exploit the low G+C content of phytoplasma DNA. Many of the methods employed for phytoplasma purification have been described elsewhere in this book. Here we describe in detail two methods that are specifically aimed at isolating plasmid DNA.

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