Stay-green in spring wheat can be determined by spectral reflectance measurements (normalized difference vegetation index) independently from phenology

The green area displayed by a crop is a good indicator of its photosynthetic capacity, while chlorophyll retention or 'stay-green' is regarded as a key indicator of stress adaptation. Remote-sensing methods were tested to estimate these parameters in diverse wheat genotypes under different growing conditions. Two wheat populations (a diverse set of 294 advanced lines and a recombinant inbred line population of 169 sister lines derived from the cross between Seri and Babax) were grown in Mexico under three environments: drought, heat, and heat combined with drought. In the two populations studied here, a moderate heritable expression of stay-green was found-when the normalized difference vegetation index (NDVI) at physiological maturity was estimated using the regression of NDVI over time from the mid-stages of grain-filling to physiological maturity-and for the rate of senescence during the same period. Under heat and heat combined with drought environments, stay-green calculated as NDVI at physiological maturity and the rate of senescence, showed positive and negative correlations with yield, respectively. Moreover, stay-green calculated as an estimation of NDVI at physiological maturity and the rate of senescence regressed on degree days give an independent measurement of stay-green without the confounding effect of phenology. On average, in both populations under heat and heat combined with drought environments CTgf and stay-green variables accounted for around 30% of yield variability in multiple regression analysis. It is concluded that stay-green traits may provide cumulative effects, together with other traits, to improve adaptation under stress further.     

Review of prospects for germplasm improvement for waterlogging tolerance in wheat,barley and oats

A review is presented for prospects of germplasm improvement for waterlogging tolerance in wheat, barley and oats using a mechanistic approach based on adaptive physiological traits. In `The waterlogged environments for crop production' section, the extent of waterlogging is reviewed commencing with determination of environmental factors which may limit plant growth and development in waterlogging prone regions. This highlights that different types of waterlogging may exist, there may be large spatial and temporal variation in waterlogging, and that waterlogging may be confounded in field experiments with additional environmental factors. Environmental characterisation is therefore a key step to using mechanistic approaches for germplasm improvement for target environments, for extrapolation to other environments, and for development of screening protocols under controlled conditions that accurately reflect the field environment. In the `Information on key components required for germplasm improvement' section, the genetic diversity in wheat, barley and oats for waterlogging tolerance is confirmed. Physiological mechanisms for waterlogging tolerance are diverse and can be grouped into adaptive traits relating to (1) phenology, (2) morphology and anatomy, (3) nutrition, (4) metabolism including anaerobic catabolism and anoxia tolerance, and (5) post anoxic damage and recovery. For wheat and barley, there is some genetic diversity for waterlogging tolerance at the germination stage, however the full potential seems yet to be exploited. Varietal differences in tolerance at the germination stage often differ from tolerance at later stages of development, and this supports the view that different mechanisms of tolerance exist at the whole plant and tissue level. Limited work from genetic studies indicates a high heritability for waterlogging tolerance. It is concluded that the best opportunities for germplasm improvement are for further exploration and utilisation of genetic diversity by improving selection criteria including the use of marker assisted selection. Additional opportunities are described for increasing genetic diversity using wide hybridisations and development of transgenic plants.     

Genetic and physiological bases for phenological responses to current and predicted climates

We are now reaching the stage at which specific genetic factors with known physiological effects can be tied directly and quantitatively to variation in phenology. With such a mechanistic understanding, scientists can better predict phenological responses to novel seasonal climates. Using the widespread model species Arabidopsis thaliana, we explore how variation in different genetic pathways can be linked to phenology and life-history variation across geographical regions and seasons. We show that the expression of phenological traits including flowering depends critically on the growth season, and we outline an integrated life-history approach to phenology in which the timing of later life-history events can be contingent on the environmental cues regulating earlier life stages. As flowering time in many plants is determined by the integration of multiple environmentally sensitive gene pathways, the novel combinations of important seasonal cues in projected future climates will alter how phenology responds to variation in the flowering time gene network with important consequences for plant life history. We discuss how phenology models in other systems—both natural and agricultural—could employ a similar framework to explore the potential contribution of genetic variation to the physiological integration of cues determining phenology.     

Selection on QTL and complex traits in complex environments

Understanding genetic variation for complex traits in heterogeneous environments is a fundamental problem in biology. In this issue of Molecular Ecology, Fournier‐Level et al. ( 2013 ) analyse quantitative trait loci (QTL) influencing ecologically important phenotypes in mapping populations of Arabidopsis thaliana grown in four habitats across its native European range. They used causal modelling to quantify the selective consequences of life history and morphological traits and QTL on components of fitness. They found phenology QTL colocalizing with known flowering time genes as well as novel loci. Most QTL influenced fitness via life history and size traits, rather than QTL having direct effects on fitness. Comparison of phenotypes among environments found no evidence for genetic trade‐offs for phenology or growth traits, but genetic trade‐offs for fitness resulted because flowering time had opposite fitness effects in different environments. These changes in QTL effects and selective consequences may maintain genetic variation among populations.     

Assortative mating by flowering time and its effect on correlated traits in variable environments

Reproductive timing is a key life‐history trait that impacts the pool of available mates, the environment experienced during flowering, and the expression of other traits through genetic covariation. Selection on phenology, and its consequences on other life‐history traits, has considerable implications in the context of ongoing climate change and shifting growing seasons. To test this, we grew field‐collected seed from the wildflower Mimulus guttatus in a greenhouse to assess the standing genetic variation for flowering time and covariation with other traits. We then created full‐sib families through phenological assortative mating and grew offspring in three photoperiod treatments representing seasonal variation in daylength. We find substantial quantitative genetic variation for the onset of flowering time, which covaried with vegetative traits. The assortatively‐mated offspring varied in their critical photoperiod by over two hours, so that families differed in their probability of flowering across treatments Allocation to flowering and vegetative growth changed across the daylength treatments, with consistent direction and magnitude of covariation among flowering time and other traits. Our results suggest that future studies of flowering time evolution should consider the joint evolution of correlated traits and shifting seasonal selection to understand how environmental variation influences life histories.     

Next-generation sequencing applications for wheat crop improvement

? Bread wheat (Triticum aestivum; Poaceae) is a crop plant of great importance. It provides nearly 20% of the world's daily food supply measured by calorie intake, similar to that provided by rice. The yield of wheat has doubled over the last 40 years due to a combination of advanced agronomic practice and improved germplasm through selective breeding. More recently, yield growth has been less dramatic, and a significant improvement in wheat production will be required if demand from the growing human population is to be met. ? Next-generation sequencing (NGS) technologies are revolutionizing biology and can be applied to address critical issues in plant biology. Technologies can produce draft sequences of genomes with a significant reduction to the cost and timeframe of traditional technologies. In addition, NGS technologies can be used to assess gene structure and expression, and importantly, to identify heritable genome variation underlying important agronomic traits. ? This review provides an overview of the wheat genome and NGS technologies, details some of the problems in applying NGS technology to wheat, and describes how NGS technologies are starting to impact wheat crop improvement.     

Water stress resilient cereal crops: Lessons from wild relatives

Cereal crops are significant contributors to global diets. As climate change disrupts weather patterns and wreaks havoc on crops, the need for generating stress-resilient, high-yielding varieties is more urgent than ever. One extremely promising avenue in this regard is to exploit the tremendous genetic diversity expressed by the wild ancestors of current day crop species. These crop wild relatives thrive in a range of environments and accordingly often harbor an array of traits that allow them to do so. The identification and introgression of these traits into our staple cereal crops can lessen yield losses in stressful environments. In the last decades, a surge in extreme drought and flooding events have severely impacted cereal crop production. Climate models predict a persistence of this trend, thus reinforcing the need for research on water stress resilience. Here we review: (i) how water stress (drought and flooding) impacts crop performance; and (ii) how identification of tolerance traits and mechanisms from wild relatives of the main cereal crops, that is, rice, maize, wheat, and barley, can lead to improved survival and sustained yields in these crops under water stress conditions.     

Differences in functional traits among distinct populations of the plant invader Bunias orientalis

入侵植物疣果匙荠不同种群间的功能性状差异 特定环境下植物扩大领域入侵到其他区域时,其功能性状会发生改变。原产地环境已形成植物原有功能性状,当植物居住环境发生改变时,其功能性状亦会随之改变。本文旨在探讨居于常见条件与原产地气候条件的原状态、入侵状态、归化状态下不同疣果匙荠(Bunias orientalis)种群间的性状变异。自8个国家收集了12种疣果匙荠种子(每种状态各4种),将其种植于标准条件下的同质园中,并比较不同状态不同种类的物候、生长、繁殖等功能性状变化。 研究结果表明, 物候不因植物状态而异,但某些原产于常年低温地区的原状态植物并未开花。相比原状态植物,入侵状态植物的叶子更多,这表明了其在积累植被生物量上的活力。短角果的数量和质量,以及其他的生长性状在不同的状态间没有差异,但在不同种群间存在差异。一些功能性状的变异可能是由于原生地对当地条件的长期适应和遗传多样性所致,而其他环境因素在新环境下的差异可能导致了较高的性状变异。     

Genetic and molecular bases of yield-associated traits: a translational biology approach between rice and wheat

Transferring the knowledge bases between related species may assist in enlarging the yield potential of crop plants. Being cereals, rice and wheat share a high level of gene conservation; however, they differ at metabolic levels as a part of the environmental adaptation resulting in different yield capacities. This review focuses on the current understanding of genetic and molecular regulation of yield-associated traits in both crop species, highlights the similarities and differences and presents the putative knowledge gaps. We focus on the traits associated with phenology, photosynthesis, and assimilate partitioning and lodging resistance; the most important drivers of yield potential. Currently, there are large knowledge gaps in the genetic and molecular control of such major biological processes that can be filled in a translational biology approach in transferring genomics and genetics informations between rice and wheat.     

Ecological and methodological drivers of species’ distribution and phenology responses to climate change

Climate change is shifting species’ distribution and phenology. Ecological traits, such as mobility or reproductive mode, explain variation in observed rates of shift for some taxa. However, estimates of relationships between traits and climate responses could be influenced by how responses are measured. We compiled a global data set of 651 published marine species’ responses to climate change, from 47 papers on distribution shifts and 32 papers on phenology change. We assessed the relative importance of two classes of predictors of the rate of change, ecological traits of the responding taxa and methodological approaches for quantifying biological responses. Methodological differences explained 22% of the variation in range shifts, more than the 7.8% of the variation explained by ecological traits. For phenology change, methodological approaches accounted for 4% of the variation in measurements, whereas 8% of the variation was explained by ecological traits. Our ability to predict responses from traits was hindered by poor representation of species from the tropics, where temperature isotherms are moving most rapidly. Thus, the mean rate of distribution change may be underestimated by this and other global syntheses. Our analyses indicate that methodological approaches should be explicitly considered when designing, analysing and comparing results among studies. To improve climate impact studies, we recommend that (1) reanalyses of existing time series state how the existing data sets may limit the inferences about possible climate responses; (2) qualitative comparisons of species’ responses across different studies be limited to studies with similar methodological approaches; (3) meta‐analyses of climate responses include methodological attributes as covariates; and (4) that new time series be designed to include the detection of early warnings of change or ecologically relevant change. Greater consideration of methodological attributes will improve the accuracy of analyses that seek to quantify the role of climate change in species’ distribution and phenology changes.     

QTL analysis and QTL-based prediction of flowering phenology in recombinant inbred lines of barley

Combining ecophysiological modelling and genetic mapping has increasingly received attention from researchers who wish to predict complex plant or crop traits under diverse environmental conditions. The potential for using this combined approach to predict flowering time of individual genotypes in a recombinant inbred line (RIL) population of spring barley (Hordeum vulgare L.) was examined. An ecophysiological phenology model predicts preflowering duration as affected by temperature and photoperiod, based on the following four input traits: f(o) (the minimum number of days to flowering at the optimum temperature and photoperiod), theta1 and theta2 (the development stages for the start and the end of the photoperiod-sensitive phase, respectively), and delta (the photoperiod sensitivity). The model-input trait values were obtained from a photoperiod-controlled greenhouse experiment. Assuming additivity of QTL effects, a multiple QTL model was fitted for the model-input traits using composite interval mapping. Four to seven QTL were identified for each trait. Each trait had at least one QTL specific to that trait alone. Other QTL were shared by two or all traits. Values of the model-input traits predicted for the RILs from the QTL model were fed back into the ecophysiological model. This QTL-based ecophysiological model was subsequently used to predict preflowering duration (d) for eight field trial environments. The model accounted for 72% of the observed variation among 94 RILs and 94% of the variation among the two parents across the eight environments, when observations in different environments were pooled. However, due to the low percentage (34-41%) of phenotypic variation accounted for by the identified QTL for three model-input traits (theta1, theta2 and delta), the QTL-based model accounted for somewhat less variation among the RILs than the model using original phenotypic input trait values. Nevertheless, days to flowering as predicted from the QTL-based ecophysiological model were highly correlated with days to flowering as predicted from QTL-models per environment for days to flowering per se. The ecophysiological phenology model was thus capable of extrapolating (QTL) information from one environment to another.     

A natural heating experiment: Phenotypic and genotypic responses of plant phenology to geothermal soil warming

Under global warming, the survival of many populations of sedentary organisms in seasonal environments will largely depend on their ability to cope with warming in situ by means of phenotypic plasticity or adaptive evolution. This is particularly true in high‐latitude environments, where current growing seasons are short, and expected temperature increases large. In such short‐growing season environments, the timing of growth and reproduction is critical to survival. Here, we use the unique setting provided by a natural geothermal soil warming gradient (Hengill geothermal area, Iceland) to study the response of Cerastium fontanum flowering phenology to temperature. We hypothesized that trait expression and phenotypic selection on flowering phenology are related to soil temperature, and tested the hypothesis that temperature‐driven differences in selection on phenology have resulted in genetic differentiation using a common garden experiment. In the field, phenology was related to soil temperature, with plants in warmer microsites flowering earlier than plants at colder microsites. In the common garden, plants responded to spring warming in a counter‐gradient fashion; plants originating from warmer microsites flowered relatively later than those originating from colder microsites. A likely explanation for this pattern is that plants from colder microsites have been selected to compensate for the shorter growing season by starting development at lower temperatures. However, in our study we did not find evidence of variation in phenotypic selection on phenology in relation to temperature, but selection consistently favoured early flowering. Our results show that soil temperature influences trait expression and suggest the existence of genetically based variation in flowering phenology leading to counter‐gradient local adaptation along a gradient of soil temperatures. An important implication of our results is that observed phenotypic responses of phenology to global warming might often be a combination of short‐term plastic responses and long‐term evolutionary responses, acting in different directions.     

Model analysis of flowering phenology in recombinant inbred lines of barley

A generic model for flowering phenology as a function of daily temperature and photoperiod was applied to predict differences of flowering times among 96 individuals (including the two parents) of a recombinant inbred line population in barley (Hordeum vulgare L.). Because of the large number of individuals to study, there is a need for simple ways to derive model parameters for each genotype. Therefore the number of genotype-specific parameters was reduced to four, namely f(o) (the minimum number of days to flowering at the optimum temperature and photoperiod), (1) and (2) (the development stages for the start and the end of the photoperiod-sensitive phase, respectively), and delta (the photoperiod sensitivity). Values of these parameters were estimated using a newly described methodological framework based on data from a photoperiod-controlled experiment where plants were mutually transferred between long-day and short-day environments at regular intervals. This modelling approach was tested in eight independent field environments of different sowing dates in two growing seasons. The four-parameter model predicted 37-67% of observed phenotypic variation in an environment, 76% of variation in across-environment mean days to flowering among the genotypes, and 96% of variation in across-genotype mean among the eight environments. When all the observations of the 96 genotypes across the eight environments were pooled, the model explained 81% of the total variation. Sensitivity analysis showed that all four model parameters were important for predicting differences in flowering time among the genotypes; but their relative importance differed and the ranking was in the order of f(o), delta, theta1, and theta2. This study highlighted the potential of using ecophysiological models to assist the genetic analysis of quantitative crop traits whose phenotype is often environment-dependent.     

Genetic and phenotypic sources of life history variation along a cline in voltinism in the cricket Allonemobius socius

Clinal variation in life histories can be genetically based, resulting from selection imposed by different environments, or it may be due to the differential expression of phenotypically plastic traits. We examined the cline in voltinism in the egg-diapausing cricket Allonemobius socius, with populations spanning the switch from a univoltine to a bivoltine phenology. A common garden experiment was employed, using environments that mimicked photoperiod and temperature conditions found in the field. There were only small differences in development time among populations, and the difference in phenology observed in the field is likely due to clinal variation in the length of the growing season. We found large genetically-based differences in the reaction norm for egg diapause that were further magnified by environmental cues. The synergism of genetic and environmental effects was an example of cogradient selection. In the zone of transition between phenologies, voltinism appeared to be a conditional strategy, rather than a genetic polymorphism. First-generation females from this area can lay either direct-developing or diapause eggs depending on the likelihood that a second generation will have sufficient time to develop. For this species, the cline in voltinism is the result of a combination of environmental effects on development, and genetic and environmental influences on egg diapause propensity.     

Elucidating the genetic basis of biomass accumulation and radiation use efficiency in spring wheat and its role in yield potential

One of the major challenges for plant scientists is increasing wheat (Triticum aestivum) yield potential (YP). A significant bottleneck for increasing YP is achieving increased biomass through optimization of radiation use efficiency (RUE) along the crop cycle. Exotic material such as landraces and synthetic wheat has been incorporated into breeding programmes in an attempt to alleviate this; however, their contribution to YP is still unclear. To understand the genetic basis of biomass accumulation and RUE, we applied genome‐wide association study (GWAS) to a panel of 150 elite spring wheat genotypes including many landrace and synthetically derived lines. The panel was evaluated for 31 traits over 2 years under optimal growing conditions and genotyped using the 35K wheat breeders array. Marker‐trait association identified 94 SNPs significantly associated with yield, agronomic and phenology‐related traits along with RUE and final biomass (BM_PM) at various growth stages that explained 7%–17% of phenotypic variation. Common SNP markers were identified for grain yield, BM_PM and RUE on chromosomes 5A and 7A. Additionally, landrace and synthetic derivative lines showed higher thousand grain weight (TGW), BM_PM and RUE but lower grain number (GM2) and harvest index (HI). Our work demonstrates the use of exotic material as a valuable resource to increase YP. It also provides markers for use in marker‐assisted breeding to systematically increase BM_PM, RUE and TGW and avoid the TGW/GM2 and BM_PM/HI trade‐off. Thus, achieving greater genetic gains in elite germplasm while also highlighting genomic regions and candidate genes for further study.     

Predicting animal performance through climatic and plant phenology variables: The case of an omnivore hibernating species in Finland

Annual variation in the environment is expected to influence individual performance, e.g. measured as body condition, such as body mass or fat deposition, through its direct or indirect effects on food abundance and availability. Such environmental variation is traditionally measured by climatic observation, but recently, measures of environmental phenology obtained from satellite images have been successfully used. We examined the performance of climatic and plant phenology variables in explaining body condition of an invasive omnivore species: the raccoon dog Nyctereutes procyonoides. We collected data on fat deposition of juveniles in southern Finland from the end of June to the beginning of November. A four-parametric logistic model was fitted separately for each province to the data by non-linear regression procedure and the residuals were compared to the expected average as measure of individual performance. These values were then analysed with respect to the environmental variables. Climatic variables describing spring conditions performed better than plant phenology variables in explaining the variation in fat deposition. Harsh spring conditions negatively affected the amount of fat deposed during the growing season. Plant phenology variables, effective in explaining life history traits in herbivores, might not reflect variation in food abundance and quality for omnivore species. We propose that in Europe raccoon dogs will benefit from climate warming, because of a longer growing season, but increased spring precipitation in the form of snow at higher latitudes might compensate for the effect of greater primary productivity and outline the border of their expansion towards harsher environments.     

The shifting phenological landscape: Within‐ and between‐species variation in leaf emergence in a mixed‐deciduous woodland

Many organisms rely on synchronizing the timing of their life‐history events with those of other trophic levels—known as phenological matching—for survival or successful reproduction. In temperate deciduous forests, the extent of matching with the budburst date of key tree species is of particular relevance for many herbivorous insects and, in turn, insectivorous birds. In order to understand the ecological and evolutionary forces operating in these systems, we require knowledge of the factors influencing leaf emergence of tree communities. However, little is known about how phenology at the level of individual trees varies across landscapes, or how consistent this spatial variation is between different tree species. Here, we use field observations, collected over 2 years, to characterize within‐ and between‐species differences in spring phenology for 825 trees of six species (Quercus robur, Fraxinus excelsior, Fagus sylvatica, Betula pendula, Corylus avellana, and Acer pseudoplatanus) in a 385‐ha woodland. We explore environmental predictors of individual variation in budburst date and bud development rate and establish how these phenological traits vary over space. Trees of all species showed markedly consistent individual differences in their budburst timing. Bud development rate also varied considerably between individuals and was repeatable in oak, beech, and sycamore. We identified multiple predictors of budburst date including altitude, local temperature, and soil type, but none were universal across species. Furthermore, we found no evidence for interspecific covariance of phenology over space within the woodland. These analyses suggest that phenological landscapes are highly complex, varying over small spatial scales both within and between species. Such spatial variation in vegetation phenology is likely to influence patterns of selection on phenology within populations of consumers. Knowledge of the factors shaping the phenological environments experienced by animals is therefore likely to be key in understanding how these evolutionary processes operate.     

High‐density molecular characterization and association mapping in Ethiopian durum wheat landraces reveals high diversity and potential for wheat breeding

Durum wheat (Triticum turgidum subsp. durum) is a key crop worldwide, and yet, its improvement and adaptation to emerging environmental threats is made difficult by the limited amount of allelic variation included in its elite pool. New allelic diversity may provide novel loci to international crop breeding through quantitative trait loci (QTL) mapping in unexplored material. Here, we report the extensive molecular and phenotypic characterization of hundreds of Ethiopian durum wheat landraces and several Ethiopian improved lines. We test 81 587 markers scoring 30 155 single nucleotide polymorphisms and use them to survey the diversity, structure, and genome‐specific variation in the panel. We show the uniqueness of Ethiopian germplasm using a siding collection of Mediterranean durum wheat accessions. We phenotype the Ethiopian panel for ten agronomic traits in two highly diversified Ethiopian environments for two consecutive years and use this information to conduct a genome‐wide association study. We identify several loci underpinning agronomic traits of interest, both confirming loci already reported and describing new promising genomic regions. These loci may be efficiently targeted with molecular markers already available to conduct marker‐assisted selection in Ethiopian and international wheat. We show that Ethiopian durum wheat represents an important and mostly unexplored source of durum wheat diversity. The panel analysed in this study allows the accumulation of QTL mapping experiments, providing the initial step for a quantitative, methodical exploitation of untapped diversity in producing a better wheat.     

Genecology of Douglas fir in western Oregon and Washington

BACKGROUND AND AIMS: Genecological knowledge is important for understanding evolutionary processes and for managing genetic resources. Previous studies of coastal Douglas fir (Pseudotsuga menziesii var. menziesii) have been inconclusive with respect to geographical patterns of variation, due in part to limited sample intensity and geographical and climatic representation. This study describes and maps patterns of genetic variation in adaptive traits in coastal Douglas fir in western Oregon and Washington, USA. METHODS: Traits of growth, phenology and partitioning were measured in seedlings of 1338 parents from 1048 locations grown in common gardens. Relations between traits and environments of seed sources were explored using regressions and canonical correlation analysis. Maps of genetic variation as related to the environment were developed using a geographical information system (GIS). KEY RESULTS: Populations differed considerably for adaptive traits, in particular for bud phenology and emergence. Variation in bud-set, emergence and growth was strongly related to elevation and cool-season temperatures. Variation in bud-burst and partitioning to stem diameter versus height was related to latitude and summer drought. Seedlings from the east side of the Washington Cascades were considerably smaller, set bud later and burst bud earlier than populations from the west side. CONCLUSIONS: Winter temperatures and frost dates are of overriding importance to the adaptation of Douglas fir to Pacific Northwest environments. Summer drought is of less importance. Maps generated using canonical correlation analysis and GIS allow easy visualization of a complex array of traits as related to a complex array of environments. The composite traits derived from canonical correlation analysis show two different patterns of variation associated with different gradients of cool-season temperatures and summer drought. The difference in growth and phenology between the westside and eastside Washington Cascades is hypothesized to be a consequence of the presence of interior variety (P. menziessii var. glauca) on the eastside.