Ottawa Research and Development Centre

ABSTRACT The use of genotype main effect (G) plus genotype‐by‐environment (GE) interaction (G+GE) biplot analysis by plant breeders and other agricultural researchers has increased dramatically during the past 5 yr for analyzing multi‐environment trial (MET) data. Recently, however, its legitimacy was questioned by a proponent of Additive Main Effect and Multiplicative Interaction (AMMI) analysis. The objectives of this review are: (i) to compare GGE biplot analysis and AMMI analysis on three aspects of genotype‐by‐environment data (GED) analysis, namely mega‐environment analysis, genotype evaluation, and test‐environment evaluation; (ii) to discuss whether G and GE should be combined or separated in these three aspects of GED analysis; and (iii) to discuss the role and importance of model diagnosis in biplot analysis of GED. Our main conclusions are: (i) both GGE biplot analysis and AMMI analysis combine rather than separate G and GE in mega‐environment analysis and genotype evaluation, (ii) the GGE biplot is superior to the AMMI1 graph in mega‐environment analysis and genotype evaluation because it explains more G+GE and has the inner‐product property of the biplot, (iii) the discriminating power vs. representativeness view of the GGE biplot is effective in evaluating test environments, which is not possible in AMMI analysis, and (iv) model diagnosis for each dataset is useful, but accuracy gain from model diagnosis should not be overstated.

The molecular mechanisms underlying the initiation and maintenance of the embryonic pathway in plants are largely unknown. To obtain more insight into these processes, we used subtractive hybridization to identify genes that are upregulated during the in vitro induction of embryo development from immature pollen grains of Brassica napus (microspore embryogenesis). One of the genes identified, BABY BOOM (BBM), shows similarity to the AP2/ERF family of transcription factors and is expressed preferentially in developing embryos and seeds. Ectopic expression of BBM in Arabidopsis and Brassica led to the spontaneous formation of somatic embryos and cotyledon-like structures on seedlings. Ectopic BBM expression induced additional pleiotropic phenotypes, including neoplastic growth, hormone-free regeneration of explants, and alterations in leaf and flower morphology. The expression pattern of BBM in developing seeds combined with the BBM overexpression phenotype suggests a role for this gene in promoting cell proliferation and morphogenesis during embryogenesis.

Abstract Advances in genomics have expedited the improvement of several agriculturally important crops but similar efforts in wheat ( Triticum spp.) have been more challenging. This is largely owing to the size and complexity of the wheat genome 1 , and the lack of genome-assembly data for multiple wheat lines 2,3 . Here we generated ten chromosome pseudomolecule and five scaffold assemblies of hexaploid wheat to explore the genomic diversity among wheat lines from global breeding programs. Comparative analysis revealed extensive structural rearrangements, introgressions from wild relatives and differences in gene content resulting from complex breeding histories aimed at improving adaptation to diverse environments, grain yield and quality, and resistance to stresses 4,5 . We provide examples outlining the utility of these genomes, including a detailed multi-genome-derived nucleotide-binding leucine-rich repeat protein repertoire involved in disease resistance and the characterization of Sm1 6 , a gene associated with insect resistance. These genome assemblies will provide a basis for functional gene discovery and breeding to deliver the next generation of modern wheat cultivars.

Soy consumption has been associated with many potential health benefits in reducing chronic diseases such as obesity, cardiovascular disease, insulin-resistance/type II diabetes, certain type of cancers, and immune disorders. These physiological functions have been attributed to soy proteins either as intact soy protein or more commonly as functional or bioactive peptides derived from soybean processing. These findings have led to the approval of a health claim in the USA regarding the ability of soy proteins in reducing the risk for coronary heart disease and the acceptance of a health claim in Canada that soy protein can help lower cholesterol levels. Using different approaches, many soy bioactive peptides that have a variety of physiological functions such as hypolipidemic, anti-hypertensive, and anti-cancer properties, and anti-inflammatory, antioxidant, and immunomodulatory effects have been identified. Some soy peptides like lunasin and soymorphins possess more than one of these properties and play a role in the prevention of multiple chronic diseases. Overall, progress has been made in understanding the functional and bioactive components of soy. However, more studies are required to further identify their target organs, and elucidate their biological mechanisms of action in order to be potentially used as functional foods or even therapeutics for the prevention or treatment of chronic diseases.

Novel species of microfungi described in the present study include the following from South Africa: Cercosporella dolichandrae from Dolichandra unguiscati, Seiridium podocarpi from Podocarpus latifolius, Pseudocercospora parapseudarthriae from Pseudarthria hookeri, Neodevriesia coryneliae from Corynelia uberata on leaves of Afrocarpus falcatus, Ramichloridium eucleae from Euclea undulata and Stachybotrys aloeticola from Aloe sp. (South Africa), as novel member of the Stachybotriaceae fam. nov. Several species were also described from Zambia, and these include Chaetomella zambiensis on unknown Fabaceae, Schizoparme pseudogranati from Terminalia stuhlmannii, Diaporthe isoberliniae from Isoberlinia angolensis, Peyronellaea combreti from Combretum mossambiciensis, Zasmidium rothmanniae and Phaeococcomyces rothmanniae from Rothmannia engleriana, Diaporthe vangueriae from Vangueria infausta and Diaporthe parapterocarpi from Pterocarpus brenanii. Novel species from the Netherlands include: Stagonospora trichophoricola, Keissleriella trichophoricola and Dinemasporium trichophoricola from Trichophorum cespitosum, Phaeosphaeria poae, Keissleriella poagena, Phaeosphaeria poagena, Parastagonospora poagena and Pyrenochaetopsis poae from Poa sp., Septoriella oudemansii from Phragmites australis and Dendryphion europaeum from Hedera helix (Germany) and Heracleum sphondylium (the Netherlands). Novel species from Australia include: Anungitea eucalyptorum from Eucalyptus leaf litter, Beltraniopsis neolitseae and Acrodontium neolitseae from Neolitsea australiensis, Beltraniella endiandrae from Endiandra introrsa, Phaeophleospora parsoniae from Parsonia straminea, Penicillifer martinii from Cynodon dactylon, Ochroconis macrozamiae from Macrozamia leaf litter, Triposporium cycadicola, Circinotrichum cycadis, Cladosporium cycadicola and Acrocalymma cycadis from Cycas spp. Furthermore, Vermiculariopsiella dichapetali is described from Dichapetalum rhodesicum (Botswana), Ophiognomonia acadiensis from Picea rubens (Canada), Setophoma vernoniae from Vernonia polyanthes and Penicillium restingae from soil (Brazil), Pseudolachnella guaviyunis from Myrcianthes pungens (Uruguay) and Pseudocercospora neriicola from Nerium oleander (Italy). Novelties from Spain include: Dendryphiella eucalyptorum from Eucalyptus globulus, Conioscypha minutispora from dead wood, Diplogelasinospora moalensis and Pseudoneurospora canariensis from soil and Inocybe lanatopurpurea from reforested woodland of Pinus spp. Novelties from France include: Kellermania triseptata from Agave angustifolia, Zetiasplozna acaciae from Acacia melanoxylon, Pyrenochaeta pinicola from Pinus sp. and Pseudonectria rusci from Ruscus aculeatus. New species from China include: Dematiocladium celtidicola from Celtis bungeana, Beltrania pseudorhombica, Chaetopsina beijingensis and Toxicocladosporium pini from Pinus spp. and Setophaeosphaeria badalingensis from Hemerocallis fulva. Novel genera of Ascomycetes include Alfaria from Cyperus esculentus (Spain), Rinaldiella from a contaminated human lesion (Georgia), Hyalocladosporiella from Tectona grandis (Brazil), Pseudoacremonium from Saccharum spontaneum and Melnikomyces from leaf litter (Vietnam), Annellosympodiella from Juniperus procera (Ethiopia), Neoceratosperma from Eucalyptus leaves (Thailand), Ramopenidiella from Cycas calcicola (Australia), Cephalotrichiella from air in the Netherlands, Neocamarosporium from Mesembryanthemum sp. and Acervuloseptoria from Ziziphus mucronata (South Africa) and Setophaeosphaeria from Hemerocallis fulva (China). Several novel combinations are also introduced, namely for Phaeosphaeria setosa as Setophaeosphaeria setosa, Phoma heteroderae as Peyronellaea heteroderae and Phyllosticta maydis as Peyronellaea maydis. Morphological and culture characteristics along with ITS DNA barcodes are provided for all taxa.

The existence of transgenic hybrids resulting from transgene escape from genetically modified (GM) crops to wild or weedy relatives is well documented but the fate of the transgene over time in recipient wild species populations is still relatively unknown. This is the first report of the persistence and apparent introgression, i.e. stable incorporation of genes from one differentiated gene pool into another, of an herbicide resistance transgene from Brassica napus into the gene pool of its weedy relative, Brassica rapa, monitored under natural commercial field conditions. Hybridization between glyphosate-resistant [herbicide resistance (HR)]B. napus and B. rapa was first observed at two Québec sites, Ste Agathe and St Henri, in 2001. B. rapa populations at these two locations were monitored in 2002, 2003 and 2005 for the presence of hybrids and transgene persistence. Hybrid numbers decreased over the 3-year period, from 85 out of approximately 200 plants surveyed in 2002 to only five out of 200 plants in 2005 (St Henri site). Most hybrids had the HR trait, reduced male fertility, intermediate genome structure, and presence of both species-specific amplified fragment length polymorphism markers. Both F(1) and backcross hybrid generations were detected. One introgressed individual, i.e. with the HR trait and diploid ploidy level of B. rapa, was observed in 2005. The latter had reduced pollen viability but produced approximately 480 seeds. Forty-eight of the 50 progeny grown from this plant were diploid with high pollen viability and 22 had the transgene (1:1 segregation). These observations confirm the persistence of the HR trait over time. Persistence occurred over a 6-year period, in the absence of herbicide selection pressure (with the exception of possible exposure to glyphosate in 2002), and in spite of the fitness cost associated with hybridization.

A comprehensive phylogenetic reassessment of the ascomycete genus Cosmospora (Hypocreales, Nectriaceae) is undertaken using fresh isolates and historical strains, sequences of two protein encoding genes, the second largest subunit of RNA polymerase II (rpb2), and a new phylogenetic marker, the larger subunit of ATP citrate lyase (acl1). The result is an extensive revision of taxonomic concepts, typification, and nomenclatural details of many anamorph- and teleomorph-typified genera of the Nectriaceae, most notably Cosmospora and Fusarium. The combined phylogenetic analysis shows that the present concept of Fusarium is not monophyletic and that the genus divides into two large groups, one basal in the family, the other terminal, separated by a large group of species classified in genera such as Calonectria, Neonectria, and Volutella. All accepted genera received high statistical support in the phylogenetic analyses. Preliminary polythetic morphological descriptions are presented for each genus, providing details of perithecia, micro- and/or macro-conidial synanamorphs, cultural characters, and ecological traits. Eight species are included in our restricted concept of Cosmospora, two of which have previously documented teleomorphs and all of which have Acremonium-like microconidial anamorphs. A key is provided to the three anamorphic species recognised in Atractium, which is removed from synonymy with Fusarium and epitypified for two macroconidial synnematous species and one sporodochial species associated with waterlogged wood. Dialonectria is recognised as distinct from Cosmospora and two species with teleomorph, macroconidia and microconidia are accepted, including the new species D. ullevolea. Seven species, one with a known teleomorph, are classified in Fusicolla, formerly considered a synonym of Fusarium including members of the F. aquaeductuum and F. merismoides species complex, with several former varieties raised to species rank. Originally a section of Nectria, Macroconia is raised to generic rank for five species, all producing a teleomorph and macroconidial anamorph. A new species of the Verticillium-like anamorphic genus Mariannaea is described as M. samuelsii. Microcera is recognised as distinct from Fusarium and a key is included for four macroconidial species, that are usually parasites of scale insects, two of them with teleomorphs. The four accepted species of Stylonectria each produce a teleomorph and micro- and macroconidial synanamorphs. The Volutella species sampled fall into three clades. Pseudonectria is accepted for a perithecial and sporodochial species that occurs on Buxus. Volutella s. str. also includes perithecial and/or sporodochial species and is revised to include a synnematous species formerly included in Stilbella. The third Volutella-like clade remains unnamed. All fungi in this paper are named using a single name system that gives priority to the oldest generic names and species epithets, irrespective of whether they are originally based on anamorph or teleomorph structures. The rationale behind this is discussed.

Data from clinical studies established that there was an inverse linear relationship between measures of postprandial blood glucose and insulin responses to an oral glucose load, consumed in a drink, and the logarithm of viscosity of the drink. These data have been re-analysed using concentration and molecular weight as the dependent variables. Molecular weight (M) of the beta-glucans used was determined using high-performance size exclusion chromatography equipped with a triple detector system of right angle light scattering, viscometry and refractive index. A significant relationship between changes in peak blood glucose and a combination of logarithm of the concentration and logarithm of M was found.

The underlying waveform has always been a shaping factor for each generation of the cellular networks, such as orthogonal frequency division multiplexing (OFDM) for the 4th generation cellular networks (4G). To meet the diversified and pronounced expectations upon the upcoming 5G cellular networks, here we present an enabler for flexible waveform configuration, named as filtered-OFDM (f-OFDM). With the conventional OFDM, a unified numerology is applied across the bandwidth provided, balancing among the channel characteristics and the service requirements, and the spectrum efficiency is limited by the compromise we made. In contrast, with f-OFDM, the assigned bandwidth is split up into several subbands, and different types of services are accommodated in different subbands with the most suitable waveform and numerology, leading to an improved spectrum utilization. After outlining the general framework of f-OFDM, several important design aspects are also discussed, including filter design and guard tone arrangement. In addition, an extensive comparison among the existing 5G waveform candidates is also included to illustrate the advantages of f-OFDM. Our simulations indicate that, in a specific scenario with four distinct types of services, f-OFDM provides up to 46% of throughput gains over the conventional OFDM scheme.

BACKGROUND: Resistance gene analogs (RGAs), such as NBS-encoding proteins, receptor-like protein kinases (RLKs) and receptor-like proteins (RLPs), are potential R-genes that contain specific conserved domains and motifs. Thus, RGAs can be predicted based on their conserved structural features using bioinformatics tools. Computer programs have been developed for the identification of individual domains and motifs from the protein sequences of RGAs but none offer a systematic assessment of the different types of RGAs. A user-friendly and efficient pipeline is needed for large-scale genome-wide RGA predictions of the growing number of sequenced plant genomes. RESULTS: An integrative pipeline, named RGAugury, was developed to automate RGA prediction. The pipeline first identifies RGA-related protein domains and motifs, namely nucleotide binding site (NB-ARC), leucine rich repeat (LRR), transmembrane (TM), serine/threonine and tyrosine kinase (STTK), lysin motif (LysM), coiled-coil (CC) and Toll/Interleukin-1 receptor (TIR). RGA candidates are identified and classified into four major families based on the presence of combinations of these RGA domains and motifs: NBS-encoding, TM-CC, and membrane associated RLP and RLK. All time-consuming analyses of the pipeline are paralleled to improve performance. The pipeline was evaluated using the well-annotated Arabidopsis genome. A total of 98.5, 85.2, and 100 % of the reported NBS-encoding genes, membrane associated RLPs and RLKs were validated, respectively. The pipeline was also successfully applied to predict RGAs for 50 sequenced plant genomes. A user-friendly web interface was implemented to ease command line operations, facilitate visualization and simplify result management for multiple datasets. CONCLUSIONS: RGAugury is an efficiently integrative bioinformatics tool for large scale genome-wide identification of RGAs. It is freely available at Bitbucket: https://bitbucket.org/yaanlpc/rgaugury .

Structural degradation of silt clay loam soils in Delta, British Columbia, has resulted from intensive cultivation of vegetable crops. A field experiment and a laboratory incubation study were conducted to assess the ability of nonleguminous winter cover crops, spring barley ( Hordeum vulgare L.), fall rye ( Secale cereale L.), and annual ryegrass ( Lolium multiflorum Lam.), to affect soil organic C, total and dilute acid extractable polysaccharides, and aggregate stability, expressed as mean weight diameter (MWD). The field experiment included four treatments: three cover crops (spring barley, fall rye, and annual ryegrass) and control (bare soil) arranged in a randomized complete block design. Annual ryegrass and fall rye increased MWD, and all of the cover crops increased soil dilute acid extractable polysaccharides. In the incubation experiment, starch (2.68 g C kg −1 soil) or chopped shoots and coarse roots of fall rye (single‐ [4.14 g C kg −1 soil] and double‐dose [8.28 g C kg −1 soil]) and annual ryegrass (4.62 g C kg −1 soil) were added to a soil from the cover‐crop site and incubated for 2, 4, and 8 wk. Cover crop and starch amendments increased soil organic C, dilute acid–extractable polysaccharides, and soil MWD. After 2‐wk incubation, the starch amendment had the greatest MWD in all the treatments, increasing by 25, 44, and 45%, compared with the annual ryegrass, double‐dose fall rye, and fall rye amendments, respectively ( P < 0.05). After 8‐wk incubation, however, the MWD in the starch amendment containers decreased by 18% compared with that in the double‐dose fall rye amendment treatments ( P < 0.05). All the cover crop amendments increased MWD and percentages of water stable 2‐ to 6‐mm aggregates at all incubation periods ( P < 0.05). Soil aggregate stability highly correlated with dilute acid‐extractable polysaccharides in the field and in incubation experiments. This study suggests that the dilute acid‐extractable polysaccharide fraction represents active binding agents under short‐term cover crops. It has been shown that soil aggregate stability can be increased under 8‐mo nonleguminous cover crops in the intensively cultivated soils.

Because crop management has a strong influence on soil C, we analyzed results of a 30-yr crop rotation experiment, initiated in 1967 on a medium textured Orthic Brown Chernozem at Swift Current, Saskatchewan, to determine the influence of cropping frequency, fertilizers and crop types on soil organic C (SOC) changes in the 0- to 15-cm depth. Soil organic C in the 0- to 15-cm and 15- to 30-cm depths were measured in 1976, 1981, 1984, 1990, 1993, and 1996, but results are only presented for the 0- to 15-cm depth since changes in the 15- to 30-cm depth were not significant. We developed an empirical equation to estimate SOC dynamics in the rotations. This equation uses two first order kinetic expressions, one to estimate crop residue decomposition and the other to estimate soil humus C mineralization. Crop residues (including roots) were estimated from straw yields, either measured or calculated from grain yields. The parameter values in our equation were obtained from the scientific literature or were based on various assumptions. Carbon lost by wind and water erosion was estimated using the EPIC model. We found that (i) SOC was increased most by annual cropping with application of adequate fertilizer N and P; (ii) that frequent fallowing resulted in lowest SOC except when fall-seeded crops, such as fall rye (Secale cereale L.), that reduce erosion were included in the rotation, and (iii) the fallow effects are exacerbated when low residue yielding flax (Linum usitatissimum L.) was included in the rotation. Some of the imprecision in SOC values we speculated to be related to variations in soil texture at the test site. In the first 10 yr of the experiment, SOC was low and constant for fallow-spring wheat (Triticum aestivum L.) (F-W) and F-W-W rotations because this land was managed in this manner for the previous 50 yr. However, in rotations that received N + P fertilizer and were cropped annually [continuous wheat (Cont W) and wheat-lentil (Lens culinaris L.)], or that included fall-seeded crops (e.g., F-Rye-W), SOC appeared to increase sharply in this period. In the drought period (1984–1988) SOC was generally constant, but large increases occurred in the wet period (1990 to 1996) in response to high residue inputs. The efficiency of conversion of residue C to SOC for the 30-yr experimental period was about 10–12% for F-W, F-W-W and Cont W (+P) systems, and it was about 17–18% for the well fertilized F-Rye-W, Cont W, and W-Lent systems. The average annual SOC gains (Mg ha −1 yr −1 ) between 1967 and 1996 were 0.11 for F-W (N + P), 0.09 for the mean of the three F-W-W rotations (N + P, + N, + P), 0.23 for F-Rye-W (N + P), 0.32 for Cont W (N + P), 0.12 for Cont W (+P), and 0.28 for W-Lent (N + P). The corresponding mean estimated (by our equation) annual SOC gains for these rotations, were 0.06, 0.10, 0.16, 0.22, 0.14, and 0.22 Mg ha −1 yr −1 , respectively. Because soil C measurements are usually so variable, we recommend that calculations such as ours may be employed to assist in the interpretation of measured C trends and to test if they seem reasonable. Key words: Carbon sequestration, carbon conversion efficiency, eroded carbon, crop residue carbon, cropping frequency, wheat, fall rye, flax

In presence of vegetation, the CO 2 –C produced by respiration activity in soils originates from plant C (rhizosphere respiration, R rh ) and from soil C (soil respiration, R s ). Quantitative estimates of the CO 2 produced by each source are required in many studies of C dynamics in the soil–plant system. In this study, we (i) used measurements of the 13 C value of soil CO 2 to separate total soil respiration ( R t ) into subcomponents R rh and R s in a maize ( Zea mays L.) field under undisturbed conditions and (ii) compared these R rh estimates with values obtained using the root‐exclusion approach. The maximum contribution of R rh to total respiration was 45%, observed in August. Estimates of R rh increased from zero 30 d after planting to 2 g CO 2 –C m −2 d −1 70 d after planting, remained relatively constant at that level in August, and then decreased until the end of the growing season. The total C losses as R rh were 17% of the crop net assimilation. Estimates of R s gradually declined from 3.3 g CO 2 –C m −2 d −1 in late June to 1.4 g CO 2 –C m −2 d −1 at the end of the season. Losses of soil C represented ≈6% of total soil C. Variable values of δ 13 C of the soil CO 2 in the control plot after Day 250 made the technique less reliable late in the season. However, several observations indicated that the approach has potential to provide quantitative estimates of R rh and R s First, the seasonal pattern of the R rh estimates coincided with that of the plant growth and physiological activity. Second, the cumulated R rh across the growing season agreed well with published data obtained using 14 C labeling techniques. Third, in the maize plot, variation in the estimated R s was closely correlated with changes in soil temperature with a Q 10 of 1.99 Finally, the estimates of R rh obtained using the isotopic approach agreed well with those obtained using the root exclusion technique.

An association between early maturity and tawny pubescence has been observed in short‐season soybean [ Glycine max (L.) Merr.]. The objectives of this study were to determine if a single locus controls early maturity; and if there is a new locus linked to E1 and T or, alternatively, a third allele at the E1 locus. A cross was made between ‘Harosoy’ isolines OT89‐5 ( e3e3 e4e4 ) and OT94‐47. PI 196529 was the donor of early maturity in the backcrossing program which developed OT94‐47. A total of 229 F 2 plants and the parents were grown under 20‐h photoperiods produced by incandescent lamps. OT94‐47 flowered in 43 ± 1.4 d, OT89‐5 flowered later in 57 ± 4.2 d, and the F 2 population fit a 3 late: 1 early flowering ratio. Early‐flowering F 2 plants produced F 3 families that flowered similarly to OT94‐47. Later‐flowering F 2 plants either segregated for flowering date or flowered similarly to OT89‐5. To test for allelism with E1 and linkage with T , a cross was made between OT93‐26 ( E1E1 e3e3 e4e4 TT ) and OT94‐47. F 2 plants were classified as parental types or intermediate and equivalent to OT89‐5 in maturity. Maturity and pubescence color were recorded in 376 F 3 progeny rows. The data did not fit a single locus model or a two loci dominant epistasis model (12:3:1). The E7 allele was partially, but not completely, dominant over the e7 allele. Therefore, a new locus E7 is proposed. Using the F 3 segregation data, linkage between T and E1 was estimated to be 1.3 ± 0.6 centimorgan (cM). Linkage between E1 and E7 was estimated to be 6.2 cM and linkage between E7 and T was estimated to be 3.9 cM. E7 is a new flowering, maturity, and photoperiod sensitivity locus tightly linked to both E1 and T E7E7 results in later flowering and maturity, and sensitivity to long photoperiods produced by incandescent lamps when compared to e7e7

Innovative management practices are required to increase the efficiency of N fertilizer usage and to reduce nitrous oxide (N 2 O) and carbon dioxide (CO 2 ) emissions from agricultural soils. The objectives of this study were to evaluate the feasibility of using conservation tillage and N fertilizer placement depth to reduce N 2 O and CO 2 emissions associated with corn ( Zea mays L.) production on clay loam soils in Eastern Canada. A 3‐yr field study was established on a wheat ( Triticum aestivum L.)‐corn–soybean [Glycine max (L.) Merr.] rotation with each phase of the rotation present every year. Investigations were focused on the corn phase of the rotation. The tillage treatments following winter wheat included fall moldboard plow tillage (15 cm depth), fall zone‐tillage (21 cm width, 15 cm depth), and no‐tillage. The N placement treatments were “shallow” placement of sidedress N (2‐cm depth) and “deep” placement of sidedress N (10‐cm depth). Nitrous oxide emissions were measured 53 times and CO 2 emissions were measured 43 times over three growing seasons using field‐based sampling chambers. There was a significant tillage and N placement interaction on N 2 O emissions. Averaged over all three tillage systems and site‐years, N 2 O emissions from shallow N placement (2.83 kg N ha −1 yr −1 ) were 26% lower than deep N placement (3.83 kg N ha −1 yr −1 ). The N 2 O emissions were similar among the tillage treatments when N was placed in the soil at a shallow depth. However, when N was placed deeper in the soil (10 cm), the 3‐yr average N 2 O emissions from zone‐tillage (2.98 kg N ha −1 yr −1 ) were 20% lower than from no‐tillage (3.71 kg N ha −1 yr −1 ) and 38% lower than those from moldboard plow tillage (4.81 kg N ha −1 yr −1 ). Tillage type and N placement depth did not affect CO 2 emissions (overall average = 5.80 Mg C ha −1 yr −1 ). Hence, zone‐tillage and shallow N placement depth reduced N 2 O emissions without affecting CO 2 emissions.

Despite a large and multifaceted effort to understand the vast landscape of phenotypic data, their current form inhibits productive data analysis. The lack of a community-wide, consensus-based, human- and machine-interpretable language for describing phenotypes and their genomic and environmental contexts is perhaps the most pressing scientific bottleneck to integration across many key fields in biology, including genomics, systems biology, development, medicine, evolution, ecology, and systematics. Here we survey the current phenomics landscape, including data resources and handling, and the progress that has been made to accurately capture relevant data descriptions for phenotypes. We present an example of the kind of integration across domains that computable phenotypes would enable, and we call upon the broader biology community, publishers, and relevant funding agencies to support efforts to surmount today's data barriers and facilitate analytical reproducibility.

ABSTRACT Understanding of the physiological responses of crop plants to salinity stress is of paramount importance for selection of genotypes with improved tolerance to salt stress. Two naked oat ( Avena sativa L.) genotypes, ‘VAO‐7’ and ‘VAO‐24‘, were subjected to different salt concentrations (0, 50, 100, 150, 200, and 250 m M NaCl) to determine the effects of salt levels and stress duration on seedling growth, ion content, and photosynthetic productivity. Relative growth rate (RGR) and leaf chlorophyll were determined at weekly intervals after salinity was imposed. Total leaf area, plant dry weight, photosynthetic parameters, and plant tissue ion concentrations were determined at 25 d after salinity application. Under salt stress conditions, germination rates varied greatly among the genotypes. The differences between VAO‐7 and VAO‐24 for most parameters measured were significant after 2 wk of stress introduction at 200 and 250 m M NaCl. Salt stress at the lowest level (50 m M ) reduced total leaf area by 35% and plant dry matter by 52%. At 25 d after salt stress, plants treated with the 250 m M NaCl accumulated 36‐fold more Na + , 79% more Ca 2+ , and 2.4‐fold less K + than the control. Salt treatment resulted in the reduction of almost all the growth parameters and coincident increases in plant Na + and Ca 2+ concentrations. Our results indicate that there is great variability for salt tolerance among naked oat germplasms, and greater photosynthesis capacity, higher RGR, and relatively lower tissue Na + accumulation at high salt concentrations appeared to be associated with salt tolerance in naked oats.

. Oat has a low carbon footprint, substantial health benefits and the potential to replace animal-based food products. However, the lack of a fully annotated reference genome has hampered efforts to deconvolute its complex evolutionary history and functional gene dynamics. Here we present a high-quality reference genome of A. sativa and close relatives of its diploid (Avena longiglumis, AA, 2n = 14) and tetraploid (Avena insularis, CCDD, 2n = 4x = 28) progenitors. We reveal the mosaic structure of the oat genome, trace large-scale genomic reorganizations in the polyploidization history of oat and illustrate a breeding barrier associated with the genome architecture of oat. We showcase detailed analyses of gene families implicated in human health and nutrition, which adds to the evidence supporting oat safety in gluten-free diets, and we perform mapping-by-sequencing of an agronomic trait related to water-use efficiency. This resource for the Avena genus will help to leverage knowledge from other cereal genomes, improve understanding of basic oat biology and accelerate genomics-assisted breeding and reanalysis of quantitative trait studies.

Most studies have the achieved rapid and accurate determination of soil organic carbon (SOC) using laboratory spectroscopy; however, it remains difficult to map the spatial distribution of SOC. To predict and map SOC at a regional scale, we obtained fourteen hyperspectral images from the Gaofen-5 (GF-5) satellite and decomposed and reconstructed the original reflectance (OR) and the first derivative reflectance (FDR) using discrete wavelet transform (DWT) at different scales. At these different scales, as inputs, we selected the 3 optimal bands with the highest weight coefficient using principal component analysis and chose the normalized difference index (NDI), ratio index (RI) and difference index (DI) with the strongest correlation with the SOC content using a contour map method. These inputs were then used to build regional-scale SOC prediction models using random forest (RF), support vector machine (SVM) and back-propagation neural network (BPNN) algorithms. The results indicated that: 1) at a low decomposition scale, DWT can effectively eliminate the noise in satellite hyperspectral data, and the FDR combined with DWT can improve the SOC prediction accuracy significantly; 2) the method of selecting inputs using principal component analysis and a contour map can eliminate the redundancy of hyperspectral data while retaining the physical meaning of the inputs. For the model with the highest prediction accuracy, the inputs were all derived from the wavelength range of SOC variations; 3) the differences in prediction accuracy among the different prediction models are small; and 4) the SOC prediction accuracy using hyperspectral satellite data is greatly improved compared with that of previous SOC prediction studies using multispectral satellite data. This study provides a highly robust and accurate method for predicting and mapping regional SOC contents.

Selected primitive and modern wheat species were evaluated on the basis of their carotenoid composition and effects of the genotype and environment on lutein using spectrometry and liquid chromatography. Carotenoids in the wheat extracts were identified and confirmed on the basis of their UV/vis and mass spectra compared with those of authentic standards. The protonated molecule (M + 1)+ at m/z 569 was the predominant ion for zeaxanthin compared to the fragment ion at m/z 551 for lutein. A similar carotenoid profile was obtained for the wheat species investigated, but significant differences were observed in the concentration of carotenoids. Einkorn (Triticum monococcum) exhibited the highest level of all-trans-lutein, averaging 7.41 microg/g with small amounts of all-trans-zeaxanthin, cis-lutein isomers, and beta-carotene. Durum, Kamut, and Khorasan (Triticum turgidum) had intermediate levels of lutein (5.41-5.77 microg/g), while common bread or pastry wheat (Triticum aestivum) had the lowest content (2.01-2.11 microg/g). Lutein in einkorn appeared to be influenced significantly by environmental growing conditions.