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Item The effect of defoliation frequency and height on plantain and chicory-based swards(2021) Cranston L; Kenyon P; Morris S; Lopez-Villalobos N; Kemp PItem New targets acquired: Improving locus recovery from the Angiosperms353 probe set(Botanical Society of America, 14/06/2021) McLay T; Birch J; Gunn B; Ning W; Tate J; Nauheimer L; Joyce E; Simpson L; Schmidt-Lebuhn A; Baker W; Forest F; Jackson CPREMISE: Universal target enrichment kits maximize utility across wide evolutionary breadth while minimizing the number of baits required to create a cost-efficient kit. The Angiosperms353 kit has been successfully used to capture loci throughout the angiosperms, but the default target reference file includes sequence information from only 6–18 taxa per locus. Consequently, reads sequenced from on-target DNA molecules may fail to map to references, resulting in fewer on-target reads for assembly, and reducing locus recovery. METHODS: We expanded the Angiosperms353 target file, incorporating sequences from 566 transcriptomes to produce a ‘mega353’ target file, with each locus represented by 17–373 taxa. This mega353 file is a drop-in replacement for the original Angiosperms353 file in HybPiper analyses. We provide tools to subsample the file based on user-selected taxon groups, and to incorporate other transcriptome or protein-coding gene data sets. RESULTS: Compared to the default Angiosperms353 file, the mega353 file increased the percentage of on-target reads by an average of 32%, increased locus recovery at 75% length by 49%, and increased the total length of the concatenated loci by 29%. DISCUSSION: Increasing the phylogenetic density of the target reference file results in improved recovery of target capture loci. The mega353 file and associated scripts are available at: https://github.com/chrisjackson-pellicle/NewTargets.Item Weed Detection by Faster RCNN Model: An Enhanced Anchor Box Approach(MDPI AG, 29/06/2022) Saleem MH; Potgieter J; Arif KMTo apply weed control treatments effectively, the weeds must be accurately detected. Deep learning (DL) has been quite successful in performing the weed identification task. However, various aspects of the DL have not been explored in previous studies. This research aimed to achieve a high average precision (AP) of eight classes of weeds and a negative (non-weed) class, using the DeepWeeds dataset. In this regard, a DL-based two-step methodology has been proposed. This article is the second stage of the research, while the first stage has already been published. The former phase presented a weed detection pipeline and consisted of the evaluation of various neural networks, image resizers, and weight optimization techniques. Although a significant improvement in the mean average precision (mAP) was attained. However, the Chinee apple weed did not reach a high average precision. This result provided a solid ground for the next stage of the study. Hence, this paper presents an in-depth analysis of the Faster Region-based Convolutional Neural Network (RCNN) with ResNet-101, the best-obtained model in the past step. The architectural details of the Faster RCNN model have been thoroughly studied to investigate each class of weeds. It was empirically found that the generation of anchor boxes affects the training and testing performance of the Faster RCNN model. An enhancement to the anchor box scales and aspect ratios has been attempted by various combinations. The final results, with the addition of 64 × 64 scale size, and aspect ratio of 1:3 and 3:1, produced the best classification and localization of all classes of weeds and a negative class. An enhancement of 24.95% AP was obtained in Chinee apple weed. Furthermore, the mAP was improved by 2.58%. The robustness of the approach has been shown by the stratified k-fold cross-validation technique and testing on an external dataset.Item Comparative in situ analyses of cell wall matrix polysaccharide dynamics in developing rice and wheat grain(Springer Verlag, 1/03/2015) Palmer R; Cornuault VRG; Marcus SE; Knox JP; Shewry PR; Tosi PCell wall polysaccharides of wheat and rice endosperm are an important source of dietary fibre. Monoclonal antibodies specific to cell wall polysaccharides were used to determine polysaccharide dynamics during the development of both wheat and rice grain. Wheat and rice grain present near synchronous developmental processes and significantly different endosperm cell wall compositions, allowing the localisation of these polysaccharides to be related to developmental changes. Arabinoxylan (AX) and mixed-linkage glucan (MLG) have analogous cellular locations in both species, with deposition of AX and MLG coinciding with the start of grain filling. A glucuronoxylan (GUX) epitope was detected in rice, but not wheat endosperm cell walls. Callose has been reported to be associated with the formation of cell wall outgrowths during endosperm cellularisation and xyloglucan is here shown to be a component of these anticlinal extensions, occurring transiently in both species. Pectic homogalacturonan (HG) was abundant in cell walls of maternal tissues of wheat and rice grain, but only detected in endosperm cell walls of rice in an unesterified HG form. A rhamnogalacturonan-I (RG-I) backbone epitope was observed to be temporally regulated in both species, detected in endosperm cell walls from 12 DAA in rice and 20 DAA in wheat grain. Detection of the LM5 galactan epitope showed a clear distinction between wheat and rice, being detected at the earliest stages of development in rice endosperm cell walls, but not detected in wheat endosperm cell walls, only in maternal tissues. In contrast, the LM6 arabinan epitope was detected in both species around 8 DAA and was transient in wheat grain, but persisted in rice until maturity.Item Influence of water loss on mechanical properties of stored blueberries(Elsevier, 27/02/2021) Rivera S; Kerckhoffs H; Sofkova-Bobcheva S; Hutchins D; East AMoisture loss is considered a main cause of blueberry softening during postharvest storage. However, the causal relationship between softening and water loss has only previously been described by force to 1 mm compression. This study was performed to identify suitable instrumental tests that allow the separation of blueberries with different water loss values during storage. Mechanical properties were measured by double compression (Texture Profile Analysis) and puncture test. Variability on blueberry mechanical properties was created by regulating storage humidity and consequently water loss. As water loss increases during storage, hardness slope (slope of a straight line drawn between the trigger force of 0.06 N and the force at 15 % strain) obtained by the compression test reduces, and the displacement at berry skin break obtained by puncture test, increases. Therefore, these parameters can be potentially used to quantify mechanical changes in stored blueberries.Item Evaluation of sorghum, sudan-grass and pearl millet cultivars in Manawatu(Agronomy Society of New Zealand, 2013-09) Millner JP; Silungwe D; McGill CR; McGill, CR; Hill, GDSorghum, sudan-grass and pearl millet are versatile summer forages able to be grazed or conserved as silage. However, there is little recently published information on the performance these crops in New Zealand. A trial was carried out at Massey University, Palmerston North, to compare forage yields and crop morphology of four sorghum x sudan-grass hybrids (Pac 8421, Pac 8423, Pacific BMR and Bettagraze), two sudan-grass (Superdan 2 and Sprint) and one pearl millet (Nutrifeed) cultivars sown on the 8 and 21 December 2009. At final harvest, 57 and 58 days after sowing for the first and second sowing dates respectively, dry matter yields decreased (P<0.005) with delayed sowing from 12,792 kg ha-1 to 11,356 kg ha-1. There were cultivar differences (P<0.0001) at both sowing dates. Mean yields (across sowing dates) ranged from 9,823 (Nutrifeed) to 13,953 kg DM ha-1 (Pac 8423). There was a significant interaction (P<0.0001) between sowing date and cultivar for yield at the second harvest; cultivar differences for the first sowing date were larger than for the second, which suffered more from cool autumn temperatures. There was a strong, positive, linear relationship between plant height at harvest and DM yield (R2 = 0.69). Mean leaf:stem ratio, for the first sowing (1.9), was significantly (P<0.001) higher than in the second sowing (1.8) and was influenced by cultivar.Item Assessment of manuka provenances for production of high ‘unique manuka factor’ honey(Agronomy Society of New Zealand, 2013) Millner JP; Hamilton G; Robertson A; Stephens J; Hill, GD; McGill, CRManuka (Leptospermum scoparium) honey with high methylglyoxal content, commonly expressed as unique manuka factor (UMF®) content, has strong antibacterial and anti-fungal properties. Consequently, there is a strong demand for high UMF manuka honey in the health food industry both in New Zealand and overseas. Currently manuka honey is produced from natural stands of manuka, but UMF content varies among regions. The active ingredient methylglyoxal is produced by natural chemical transformation of dihydroxyacetone (DHA) present in the nectar. Production of high UMF honey is insufficient to meet market demand; this is due to variation in UMF amongst stands causing unpredictability in quality as well as inaccessibility of many manuka stands. The feasibility of increasing production by establishing manuka plantations using plants known to produce nectar with high DHA content is being investigated. This study compared establishment, growth and nectar DHA content of four manuka provenances; two from Northland, and one each from Waikato and Wairarapa in a replicated, randomised complete block trial (Site A). In addition a manuka plantation of a single provenance was monitored for nectar DHA content (Site B). Both sites are in the Whanganui area. Survival of seedlings in the Site A trial at 12 months was high in all provenances. Nectar DHA content ranged from 3666 to 6902 mg/kg 80° Brix and there were no significant differences amongst the provenances. These DHA levels were considerably higher than levels measured in the local manuka (2565 mg/kg 80° Brix). At Site B nectar DHA content of the plantation manuka (5770 mg/kg 80° Brix) was significantly (P=0.05) higher than the indigenous manuka (2565 mg/kg 80° Brix). Early results suggest that manuka provenances can be utilised on different sites to produce high DHA nectar and ultimately high UMF manuka honey, providing landowners with an additional income and help prevent erosion of marginal hill country.Item The mineral content of some tropical forages commonly used in small ruminant production systems in the Caribbean - Part 2(University of West Indies Press, 2021-01) Cranston LUnderstanding the differences in the mineral concentrations of forages is critical as it informs on which and how species can be used to improve the mineral content of diets. Also, with the constantly changing nutritive value of forages, regulating the mineral composition through on-going forage evaluation is important as deficient minerals can be identified and supplemented. Therefore, the aim of this study was to provide information on the mineral profiles for 12 forage species used in small ruminant production systems in the Caribbean. The forage species included seven grasses (Brachiaria arrecta, Brachiaria ruziziensis x), Cynodon dactylon, Cynodon, nlemfuensis, Digitaria eriantha, Megathyrsus maximus and Pennisetum purpureum); two leguminous multipurpose tree species (LMPTs) (Gliricidia sepium and Leucaena leucocephala) and three non-leguminous multipurpose tree species (NLMPTs) (Moringa oleifera, Morus alba and Trichanthera gigantea). Overall, the calcium, phosphorus, magnesium, cobalt, manganese, and zinc were within the range required for small ruminants. Brachiaria arrecta and Digitaria eriantha were the only two species with Na concentrations that were within the range required for small ruminants (0.9626 and 4.4281 g/kg DM respectively). Brachiaria arrecta, Cynodon dactylon, Cynodon nlemfuensis, Leucaena leucocephala and Trichanthera gigantea were the only species with copper concentrations that were within the range required for small ruminants (11.50, 20.24, 11.95, 8.16 and 16.60 mg/kg DM). The concentration of potassium in Pennisetum purpureum (39.1 g/kg DM), Brachiaria arrecta (32.6 g/kg DM), and Cynodon nlemfuensis (34.0 g/kg DM), the concentration of iron in Cynodon dactylon (3340 g/kg DM) and molybdenum in both Cynodon dactylon (8.615 mg/kg DM) and Cynodon nlemfuensis (7.722 mg/kg DM) were above the maximum tolerable levels for small ruminants. The results of the study suggest that forages varied in mineral concentrations and the toxic and marginal concentrations of specific minerals in various forage species elicit the careful management of inclusion in diets, to ensure that the mineral concentrations are within the range required for small ruminants.Item Genetic susceptibility to Theileria orientalis (Ikeda) in Angus- and Hereford-sired yearling cattle born to dairy cattle on an endemically infected farm in New Zealand(Taylor and Francis Group, 5/03/2023) Lawrence K; Fermin L; Gedye K; Hickson R; lawrence B; coleman L; Pomroy W; Natalia M; Lopez- Villalobos NTheileria orientalis (Ikeda) was first detected in New Zealand in 2012, becoming endemic in most of the North Island, and can cause incidences of anaemia and death. Research has been performed in New Zealand on the incidence and severity of infection. Through this research anecdotal evidence has been found to suggest a potential genetic susceptibility component in the response of the host to the parasite. To investigate the genetic susceptibility of cattle to T. orientalis (Ikeda), 99 calves born in 2016 as part of a separate experiment and grown in six grazing herds, were examined for their response to the parasite. In addition to measuring live weight, two blood collections were taken in the first four months of life which were used to measure packed cell volume by haematocrit and qPCR to assess parasite load. Heritability was calculated and was low for parasite load, but the result indicates that there is some potential to increase resistance through selective breeding. The mechanisms of the differences in parasite load were not elucidated in this research; however, significant variation was found among herds and sires, indicating that both genetic selection and environmental management could be utilised to reduce parasite load in growing calves.Item Combining ability and heterosis for some canola characteristics sown on recommended and late planting dates using biplot(Biotechnical Faculty of the University of Ljubljana, 2018-09) Millner J; Amiri Oghan H; Shariati F; Sabaghnia N; Alizadeh B; Shirani AH; Gholamhoseini MCanola (Brassica napus L.) is one of the most efficient oilproducing crops in arid and semi-arid regions of the world. In the current study, ten winter canola genotypes [seven genotypes as lines (Zarfam (L1), Talaye (L2), SLM046 (L3), Geronimo (L4), Modena (L5), Opera (L6) and Symbol (L7)] and three genotypes as testers [Okapi (T1), Licord (T2) and Orient (T3)] and their F1 hybrids (21 hybrids) were evaluated to determine the genetic parameters for grain yield, oil content, meal and seed glucosinolate contents under two different planting date [recommended (late September) and late planting (late October)]. According to combined analysis of variance there were significant differences among the genotypes for most studied traits. The genotype main effect and genotype × environment interaction (GGE) biplot method was used for analyzing line × tester design data. Among the lines, L5 showed high negative general combining ability (GCA) effect for meal glucosinolate content in both conditions whereas L1, L5 and L6 revealed high negative GCA effects for seed glucosinolate content in both planting date. From the results, it could be concluded that, hybridization between T1×L1, T1×L6 or T3×L5 is an efficient approach to release genotypes with low seed and meal glucosinolate content. Furthermore, to develop canola cultivars with higher seed and oil yield, hybridization between T1×L7 or T2×L7 is highly recommended. Improved oil content will be achieved if T1×L5, T2×L5 or T3×L6 hybrids are implemented into the breeding programs. SPOSOBNOST KOMBINIRANJA IN HETEROTIČNEGA UČINKA ZA NEKATERE LASTNOSTI OLJNE OGRŠČICE SEJANE OB PRIPOROČENEM IN POZNEM TERMINU Z UPORABO BIPLOTA Oljna ogrščica (Brassica napus L.) je v sušnih in polsušnih območjih sveta ena izmed najbolj učinkovitih poljščin za proizvodnjo olja. V raziskavi je bilo ovrednoteno deset ozimnih genotipov oljne ogrščice [sedem genotipov kot linije (Zarfam (L1), Talaye (L2), SLM046 (L3), Geronimo (L4), Modena (L5), Opera (L6) in Symbol (L7)] in trije genotipi kot testerji [Okapi (T1), Licord (T2) and Orient (T3)] ter njihovi F1 križanci (21 križancev) za določitev genetskih parametrov za pridelek zrnja, vsebnost olja, vsebnost glukozinulatov v pogači in semenu v razmerah priporočene (konec septembra) in pozne setve (konec oktobra). Glede na kombinirano analizo variance so bile med genotipi značilne razlike za večino preučevanih znakov. Za analizo glavnega učinka genotipa in njegove interakcije z okoljem pri križancih linij in testerjev je bila uporablja metoda biplota. Med linijami je L5 pokazala zelo negativno splošno kombinacijsko sposobnost (GCA) za vsebnost glukozinulatov v pogači v obeh terminih setve, v istih razmerah so imele linije L1, L5 in L6 velik negativni GCA učinek na vsebnost glukozinulatov v semenu. Iz rezultatov bi lahko zaključili, da so križanja kot so T1×L1, T1×L6 ali T3×L5 učinkovit pristop za odbor genotipov z majhno vsebnostjo glukozinulatov v semenu in pogači. Še več, za vzgojo sort oljne ogrščice z večjim pridelkom semena in olja so križanja T1×L7 ali T2×L7 zelo priporočena. Izboljšano vsebnost olja bi lahko dosegli,če bi bila križanja T1×L5, T2×L5 ali T3×L6 vključena v žlahniteljske programe.
