Capturing crop adaptation to abiotic stress using image-based technologies

Farmers and breeders aim to improve crop responses to abiotic stresses and secure yield under adverse environmental conditions. To achieve this goal and select the most resilient genotypes, plant breeders and researchers rely on phenotyping to quantify crop responses to abiotic stress. Recent advances in imaging technologies allow researchers to collect physiological data non-destructively and throughout time, making it possible to dissect complex plant responses into quantifiable traits. The use of image-based technologies enables the quantification of crop responses to stress in both controlled environmental conditions and field trials. This paper summarizes phenotyping imaging technologies (RGB, multispectral and hyperspectral sensors, among others) that have been used to assess different abiotic stresses including salinity, drought and nitrogen deficiency, while discussing their advantages and drawbacks. We present a detailed review of traits involved in abiotic tolerance, which have been quantified by a range of imaging sensors under high-throughput phenotyping facilities or using unmanned aerial vehicles in the field. We also provide an up-to-date compilation of spectral tolerance indices and discuss the progress and challenges in machine learning, including supervised and unsupervised models as well as deep learning.     

High-throughput Phenotyping and Genomic Selection:The Frontiers of Crop Breeding Converge

Genomic selection (GS) and high-throughput phenotyping have recently been captivating the interest of the crop breeding com-munity from both the public and private sectors world-wide.Both approaches promise to revolutionize the prediction of complex traits,including growth,yield and adaptation to stress.Whereas high-throughput phenotyping may help to improve understanding of crop physiology,most powerful techniques for high-throughput field phenotyping are empirical rather than analytical and compa-rable to genomic selection.Despite the fact that the two method-ological approaches represent the extremes of what is understood as the breeding process (phenotype versus genome),they both consider the targeted traits (e.g.grain yield,growth,phenology,plant adaptation to stress) as a black box instead of dissecting them as a set of secondary traits (i.e.physiological) putatively related to the target trait.Both GS and high-throughput phenotyping have in common their empirical approach enabling breeders to use genome profile or phenotype without understanding the underlying biology.This short review discusses the main aspects of both approaches and focuses on the case of genomic selection of maize flowering traits and near-infrared spectroscopy (NIRS) and plant spectral reflectance as high-throughput field phenotyping methods for complex traits such as crop growth and yield.     

Expression of the Arabidopsis vacuolar H+‐pyrophosphatase gene (AVP1) improves the shoot biomass of transgenic barley and increases grain yield in a saline field

Cereal varieties with improved salinity tolerance are needed to achieve profitable grain yields in saline soils. The expression of AVP1, an Arabidopsis gene encoding a vacuolar proton pumping pyrophosphatase (H⁺‐PPase), has been shown to improve the salinity tolerance of transgenic plants in greenhouse conditions. However, the potential for this gene to improve the grain yield of cereal crops in a saline field has yet to be evaluated. Recent advances in high‐throughput nondestructive phenotyping technologies also offer an opportunity to quantitatively evaluate the growth of transgenic plants under abiotic stress through time. In this study, the growth of transgenic barley expressing AVP1 was evaluated under saline conditions in a pot experiment using nondestructive plant imaging and in a saline field trial. Greenhouse‐grown transgenic barley expressing AVP1 produced a larger shoot biomass compared to null segregants, as determined by an increase in projected shoot area, when grown in soil with 150 mm NaCl. This increase in shoot biomass of transgenic AVP1 barley occurred from an early growth stage and also in nonsaline conditions. In a saline field, the transgenic barley expressing AVP1 also showed an increase in shoot biomass and, importantly, produced a greater grain yield per plant compared to wild‐type plants. Interestingly, the expression of AVP1 did not alter barley leaf sodium concentrations in either greenhouse‐ or field‐grown plants. This study validates our greenhouse‐based experiments and indicates that transgenic barley expressing AVP1 is a promising option for increasing cereal crop productivity in saline fields.     

Mycorrhizal Inoculation of Big Sacaton: Implications for Grassland Restoration of Abandoned Agricultural Fields

Grasslands dominated by Sporobolus wrightii (big sacaton) once covered riparian floodplains in southwestern United States and northern Sonora, Mexico but now occupy less than 5% of their historic range, mostly due to clearing for agriculture. Many agricultural fields have been abandoned because of changing land uses, and efforts are under way to restore native grassland habitat. Arbuscular mycorrhizal (AM) fungi are known to form associations with S. wrightii and can be a potential factor in grassland restoration efforts. The goal of this study was to determine the effects of mycorrhizal inoculation on S. wrightii during transplant production and in a restoration trial. Sporobolus wrightii was grown with and without AM fungi in 2.8‐L tall pots and 150‐mL nursery containers under greenhouse conditions for 8 weeks and then transplanted into an abandoned agricultural field. Plants were monitored for growth, survival, and mycorrhizal infection. Seedling emergence in the greenhouse was higher in pots with mycorrhizal inoculation, but inoculation had little effect on growth except more tillers were produced by pre‐inoculated plants grown in the smaller containers. In the abandoned field, pre‐inoculated plants had greater survival, basal diameter, and tiller and panicle production through the first two growing seasons. Plants started in smaller containers also had greater survival, height, basal diameter, and tiller production than those started in tall pots. Root colonization was detected in all plants by 2 months after transplanting but was not consistent throughout the experiment except for pre‐inoculated plants started in the smaller containers. These results indicate that mycorrhizal inoculation can benefit restoration efforts in abandoned agriculture fields in semiarid regions.     

Inducing drought tolerance in plants: Recent advances

Undoubtedly, drought is one of the prime abiotic stresses in the world. Crop yield losses due to drought stress are considerable. Although a variety of approaches have been used to alleviate the problem of drought, plant breeding, either conventional breeding or genetic engineering, seems to be an efficient and economic means of tailoring crops to enable them to grow successfully in drought-prone environments. During the last century, although plant breeders have made ample progress through conventional breeding in developing drought tolerant lines/cultivars of some selected crops, the approach is, in fact, highly time-consuming and labor- and cost-intensive. Alternatively, marker-assisted breeding (MAB) is a more efficient approach, which identifies the usefulness of thousands of genomic regions of a crop under stress conditions, which was, in reality, previously not possible. Quantitative trait loci (QTL) for drought tolerance have been identified for a variety of traits in different crops. With the development of comprehensive molecular linkage maps, marker-assisted selection procedures have led to pyramiding desirable traits to achieve improvements in crop drought tolerance. However, the accuracy and preciseness in QTL identification are problematic. Furthermore, significant genetic × environment interaction, large number of genes encoding yield, and use of wrong mapping populations, have all harmed programs involved in mapping of QTL for high growth and yield under water limited conditions. Under such circumstances, a transgenic approach to the problem seems more convincing and practicable, and it is being pursued vigorously to improve qualitative and quantitative traits including tolerance to biotic and abiotic stresses in different crops. Rapid advance in knowledge on genomics and proteomics will certainly be beneficial to fine-tune the molecular breeding and transformation approaches so as to achieve a significant progress in crop improvement in future. Knowledge of gene regulation and signal transduction to generate drought tolerant crop cultivars/lines has been discussed in the present review. In addition, the advantages and disadvantages as well as future prospects of each breeding approach have also been discussed.     

Bee visitation rates to cultivated sunflowers increase with the amount and accessibility of nectar sugars

Pollinators make foraging decisions based on numerous floral traits, including nectar and pollen rewards, and associated visual and olfactory cues. For insect‐pollinated crops, identifying and breeding for attractive floral traits may increase yields. In this study, we examined floral trait variation within cultivated sunflowers and its effects on bee foraging behaviours. Over 2 years, we planted different sunflower inbred lines, including male‐fertile and male‐sterile lines, and measured nectar volume, nectar sugar concentration and composition, and corolla length. During bloom, we recorded visits by both managed honey bees and wild bees. We then examined consistency in relative nectar production by comparing field results to those from a greenhouse experiment. Sunflower inbred lines varied significantly in all floral traits, including the amount and composition of nectar sugars, and in corolla length. Both wild bee and honey bee visits significantly increased with nectar sugar amount and decreased with corolla length, but appeared unaffected by nectar sugar composition. While wild bees made more visits to sunflowers providing pollen (male‐fertile), honey bees preferred plants without pollen (male‐sterile). Differences in nectar quantity among greenhouse‐grown sunflower lines were similar to those measured in the field, and bumble bees preferentially visited lines with more nectar in greenhouse observations. Our results show that sunflowers with greater quantities of nectar sugar and shorter corollas receive greater pollination services from both managed and wild bees. Selecting for these traits could thus increase sunflower crop yields and provide greater floral resources for bees.     

Defining selection criteria to improve yield under drought

The many selection criteria that have been proposed to increase drought resistance of our crops have had little, if any, impact on improving crop yields in dry environments. There are several likely reasons for this lack of success. Some of these are: (i) criteria proposed have been related more to survival mechanisms under drought than to productivity, (ii) criteria are inappropriate to the target environment, and (iii) criteria are temporal and are therefore likely to have minimal impact on growth and yield over the entire lifecycle. Another important reason is that breeders have not been convinced the proposed criteria will be successful as they are too difficult to measure. On the other hand, empirical breeding programmes to improve yield under drought have been successful. Surprisingly, some of the greatest successes have been achieved by breeding in environments where water is non-limiting. This paper reviews breeding approaches to improve yield under drought. It focuses on critical factors that must be considered to identify likely plant attributes that can be targeted. These factors, their link with yield, the nature of the target environment, the level of organisation where the trait is expressed are discussed. Three quite different examples are given to emphasize the above considerations and which show substantial promise in targeting traits to improve yield under drought. They are drought at flowering, improving transpiration efficiency and improving early leaf area development.     

Abiotic stress QTL in lettuce crop–wild hybrids: comparing greenhouse and field experiments

The development of stress‐tolerant crops is an increasingly important goal of current crop breeding. A higher abiotic stress tolerance could increase the probability of introgression of genes from crops to wild relatives. This is particularly relevant to the discussion on the risks of new GM crops that may be engineered to increase abiotic stress resistance. We investigated abiotic stress QTL in greenhouse and field experiments in which we subjected recombinant inbred lines from a cross between cultivated Lactuca sativa cv. Salinas and its wild relative L. serriola to drought, low nutrients, salt stress, and aboveground competition. Aboveground biomass at the end of the rosette stage was used as a proxy for the performance of plants under a particular stress. We detected a mosaic of abiotic stress QTL over the entire genome with little overlap between QTL from different stresses. The two QTL clusters that were identified reflected general growth rather than specific stress responses and colocated with clusters found in earlier studies for leaf shape and flowering time. Genetic correlations across treatments were often higher among different stress treatments within the same experiment (greenhouse or field), than among the same type of stress applied in different experiments. Moreover, the effects of the field stress treatments were more correlated with those of the greenhouse competition treatments than to those of the other greenhouse stress experiments, suggesting that competition rather than abiotic stress is a major factor in the field. In conclusion, the introgression risk of stress tolerance (trans‐)genes under field conditions cannot easily be predicted based on genomic background selection patterns from controlled QTL experiments in greenhouses, especially field data will be needed to assess potential (negative) ecological effects of introgression of these transgenes into wild relatives.     

Cell Wall Composition and Bioenergy Potential of Rice Straw Tissues Are Influenced by Environment,Tissue Type,and Genotype

Breeding has transformed wild plant species into modern crops, increasing the allocation of their photosynthetic assimilate into grain, fiber, and other products for human use. Despite progress in increasing the harvest index, much of the biomass of crop plants is not utilized. Potential uses for the large amounts of agricultural residues that accumulate are animal fodder or bioenergy, though these may not be economically viable without additional efforts such as targeted breeding or improved processing. We characterized leaf and stem tissue from a diverse set of rice genotypes (varieties) grown in two environments (greenhouse and field) and report bioenergy-related traits across these variables. Among the 16 traits measured, cellulose, hemicelluloses, lignin, ash, total glucose, and glucose yield changed across environments, irrespective of the genotypes. Stem and leaf tissue composition differed for most traits, consistent with their unique functional contributions and suggesting that they are under separate genetic control. Plant variety had the least influence on the measured traits. High glucose yield was associated with high total glucose and hemicelluloses, but low lignin and ash content. Bioenergy yield of greenhouse-grown biomass was higher than field-grown biomass, suggesting that greenhouse studies overestimate bioenergy potential. Nevertheless, glucose yield in the greenhouse predicts glucose yield in the field (ρ?=?0.85, p?<?0.01) and could be used to optimize greenhouse (GH) and field breeding trials. Overall, efforts to improve cell wall composition for bioenergy require consideration of production environment, tissue type, and variety.     

Assessment of Genotype Ranking in Long-term Biomass Production of Salix Based on Juvenile Plant Traits: Breeding Implications

Willow (Salix spp.) is among the most promising energy crops to be grown on agricultural land and breeding research to increase biomass yield of this perennial crop is performed in Europe and North America. Biomass willows are grown in short rotation and harvests are performed every 3 to 5 years (i.e., at 3- to 5-year cutting cycles) for a period of up to 25 years. However, breeding programs to improve long-term biomass yield are often relying on the results of short-term screening studies performed on juvenile plants. A pre-requisite for successful breeding of perennial energy crops is thus the identification of relevant juvenile plant traits indicative of long-term plant performance under field conditions. In this study a number of juvenile plant traits, measured at various Salix genotypes grown in a short-term experiment were evaluated in terms of their capacity to predict the long-term performance in biomass production after the first and second cutting cycle. The objective was to develop a simple model linking juvenile plant traits such as shoot biomass, total leaf area and leaf nitrogen (N) concentration to the long-term biomass productivity of field-grown plants. A two-component regression model combining juvenile shoot biomass and leaf N concentration provided the highest prediction accuracy (coefficients of determination around 0.8). The model based on two easy-to-measure juvenile plant traits clearly has implications for willow breeding programs. The implications for breeding are discussed in the light of the possibilities and limitations associated with the chosen approach.     

Plant domestication disrupts biodiversity effects across major crop types

Plant diversity fosters productivity in natural ecosystems. Biodiversity effects might increase agricultural yields at no cost in additional inputs. However, the effects of diversity on crop assemblages are inconsistent, probably because crops and wild plants differ in a range of traits relevant to plant–plant interactions. We tested whether domestication has changed the potential of crop mixtures to over‐yield by comparing the performance and traits of major crop species and those of their wild progenitors under varying levels of diversity. We found stronger biodiversity effects in mixtures of wild progenitors, due to larger selection effects. Variation in selection effects was partly explained by within‐mixture differences in leaf size. Our results indicate that domestication might disrupt the ability of crops to benefit from diverse neighbourhoods via reduced trait variance. These results highlight potential limitations of current crop mixtures to over‐yield and the potential of breeding to re‐establish variance and increase mixture performance.     

Molecular approaches for genetic improvement of seed quality and characterization of genetic diversity in soybean: a critical review

Soybean is an economically important leguminous crop. Genetic improvements of soybeans have focused on enhancement of seed and oil yield, development of varieties suited to different cropping systems, and breeding resistant/tolerant varieties for various biotic and abiotic stresses. Plant breeders have used conventional breeding techniques for the improvement of these traits in soybean. The conventional breeding process can be greatly accelerated through the application of molecular and genomic approaches. Molecular markers have proved to be a new tool in soybean breeding by enhancing selection efficiency in a rapid and time-bound manner. An overview of molecular approaches for the genetic improvement of soybean seed quality parameters, considering recent applications of marker-assisted selection and ‘omics’ research, is provided in this article.     

Striga infestation of cereal crops - an unsolved problem in resource limited agriculture

The parasitic weed Striga causes devastating losses in cereal yields in sub-Saharan Africa. The parasite lifecycle is intimately linked with its host via a complex interchange of signals. Understanding the molecular basis of these interactions and of host resistance to Striga is essential for the identification of genes for improving crop yield via biotechnological or marker assisted breeding strategies. Cloning and sequencing of ESTs from the 'model' parasite Triphysaria versicolor is facilitating the identification of parasitism genes. The identification of resistance to Striga in sorghum and rice germplasm is allowing molecular dissection of these traits using genomic platforms and quantitative trait loci (QTL) analysis. QTL underlying different resistance phenotypes have been identified and the use of advanced backcross populations is allowing the exploitation of sources of resistance in wild relatives of cereals.     

Effect of chemical forms of cadmium,zinc, and lead in polluted soils on their uptake by cabbage plants

Sorghum (Sorhum bicolor L. Moench) is an important cereal crop of the world. Performance of sorghum in acid infertile soils that are common to the tropics is rather poor. Research was undertaken in greenhouse and field conditions to evaluate the differences in growth, grain yield, and nutrient efficiency ratio (NER) of sorghum genotypes grown at three levels of Al saturation. The growth of shoots and roots and the grain yields showed significant differences with respect to Al-saturation, genotypes and their interactions. The shoot weights, root weights, and visual scores of the greenhouse study were highly related to grain yields obtained in field. The greenhouse technique adapted in this study appears to be a reliable method for separation of genotypes into Al-tolerant and intolerant types. The NER values helped differentiate genotypes into efficient and inefficient utilizers of the absorbed nutrients. The sorghum entries showed intraspecific genetic diversity in growth and NER values for the essential elements in the presence or absence of toxic levels of Al. We concluded that selection of acid soil tolerant genotypes and further breeding of acid soil (Al) tolerant cultivars is feasible in sorghum.IICA/EMBRAPA/World Bank     

Phenotypic plasticity to photon flux density of physiological,anatomical and growth traits in a modern Criollo cocoa clone

Cocoa grows under shade, but some cultivars develop successfully in full sunlight. In order to characterize the response to photosynthetic photon flux density (PPFD) of a Modern Criollo cocoa clone, gas exchange, photochemical activity and leaf traits, and their relation to growth were measured in seedlings growing in a greenhouse at three different values of PPFD, as well as in adults in full sunlight and shade in the field. Plants showed changes in physiological, biochemical, and morpho‐anatomical traits in response to the different light conditions, and in the phenotypic plasticity of these variables. Seedlings subjected to high PPFD in the greenhouse showed decreases in photosynthetic rate, apparent quantum yield of CO₂ fixation and photochemical quenching, and increases in non‐photochemical quenching, suggesting down‐regulation of PSII. In contrast, trees under full sunlight in the field showed a marked reduction in maximum quantum yield of PSII, indicating photoinhibition and supporting that cocoa is a shade tolerant crop. Cocoa showed higher plasticity of physiological and biochemical variables than morpho‐anatomical variables in response to PPFD. Effects of time under treatment in the greenhouse and plant age (greenhouse vs field) on plasticity were observed. The acclimation observed in some of the variables studied after 6 months in high light did not represent a particular advantage to seedlings, since relative growth rate was lower than in low‐ and medium‐light seedlings.     

Dual Δ¹³C/δ¹⁸O response to water and nitrogen availability and its relationship with yield in field-grown durum wheat

The combined use of stable carbon and oxygen isotopes in plant matter is a tool of growing interest in cereal crop management and breeding, owing to its relevance for assessing the photosynthetic and transpirative performance under different growing conditions including water and N regimes. However, this method has not been applied to wheat grown under real field conditions. Here, plant growth, grain yield (GY) and the associated agronomic components, carbon isotope discrimination (Δ¹³C) plus oxygen isotope composition (δ¹⁸O) as well as leaf and canopy gas exchange were measured in field‐grown wheat subjected to different water and N availabilities. Water limitation was the main factor affecting yield, leaf and canopy gas exchange and Δ¹³C and δ¹⁸O, whereas N had a smaller effect on such traits. The combination of Δ¹³C and δ¹⁸O gave a clear advantage compared with gas exchange measurements, as it provides information on the instantaneous and the long‐term plant photosynthetic and transpirative performance and are less labour intensive than gas exchange measurements. In addition, the combination of plant Δ¹³C and δ¹⁸O predicted differences in GY and related agronomical parameters, providing agronomists and breeders with integrative traits for selecting crop management practices and/or genotypes with better performance under water‐limiting and N‐limiting conditions.     

Dispersal and recruitment during population growth in a colonial bird, the great cormorant Phalacrocorax carbo sinensis

While the factors influencing reproduction and survival in colonial populations are relatively well studied, factors involved in dispersal and settlement decisions are not well understood. The present study investigated exchanges of great cormorants Phalacrocorax carbo sinensis among six breeding colonies over a 13‐year period when the breeding population in Denmark increased from 2800 to 36 400 nests. We used a multistate capture‐recapture model that combined multisite resightings and recoveries to examine simultaneously recruitment, natal dispersal, breeding dispersal and annual survival of first‐year, immature and breeding great cormorants. Mean survival of first‐year birds (0.50±0.09, range=0.42–0.66 among colonies) was lower than survival of breeders (0.90±0.06, range=0.81–0.97). Mean survival of immature birds over the study period was 0.87±0.08. Dispersal from a colony increased with decreasing mean brood size in the colony in both first‐time and experienced breeders. The choice of the settlement colony in first‐time breeders was affected by conditions in the natal colony and in the colonies prospected during the pre‐breeding years. In particular, first‐time breeders recruited to colonies where they could expect better breeding success. Experienced breeders relied mainly on cues present early in the season and on their own breeding experience to choose a new breeding colony. Newly established colonies resulted mainly from the immigration of first‐time breeders originating from denser colonies. Dispersal was distance‐dependent and first‐time breeders dispersed longer distances than breeders. We suggest that the prospecting behaviour allows first‐time breeders to recruit in nearby as well as more distant potential breeding colonies. Dispersing breeders preferred to settle in neighbouring colonies likely to benefit from their experience with foraging areas. We discuss the importance of these movements for growth and expansion of the breeding population.