Quantitative trait loci and crop performance under abiotic stress: where do we stand?

Drought tolerance in wheat

Drought is one of the most important phenomena which limit crops' production and yield. Crops demonstrate various morphological, physiological, biochemical, and molecular responses to tackle drought stress. Plants' vegetative and reproductive stages are intensively influenced by drought stress. Drought tolerance is a complicated trait which is controlled by polygenes and their expressions are influenced by various environmental elements. This means that breeding for this trait is so difficult and new molecular methods such as molecular markers, quantitative trait loci (QTL) mapping strategies, and expression patterns of genes should be applied to produce drought tolerant genotypes. In wheat, there are several genes which are responsible for drought stress tolerance and produce different types of enzymes and proteins for instance, late embryogenesis abundant (lea), responsive to abscisic acid (Rab), rubisco, helicase, proline, glutathione-S-transferase (GST), and carbohydrates during drought stress. This review paper has concentrated on the study of water limitation and its effects on morphological, physiological, biochemical, and molecular responses of wheat with the possible losses caused by drought stress.

Root traits contributing to plant productivity under drought

Geneticists and breeders are positioned to breed plants with root traits that improve productivity under drought. However, a better understanding of root functional traits and how traits are related to whole plant strategies to increase crop productivity under different drought conditions is needed. Root traits associated with maintaining plant productivity under drought include small fine root diameters, long specific root length, and considerable root length density, especially at depths in soil with available water. In environments with late season water deficits, small xylem diameters in targeted seminal roots save soil water deep in the soil profile for use during crop maturation and result in improved yields. Capacity for deep root growth and large xylem diameters in deep roots may also improve root acquisition of water when ample water at depth is available. Xylem pit anatomy that makes xylem less "leaky" and prone to cavitation warrants further exploration holding promise that such traits may improve plant productivity in water-limited environments without negatively impacting yield under adequate water conditions. Rapid resumption of root growth following soil rewetting may improve plant productivity under episodic drought. Genetic control of many of these traits through breeding appears feasible. Several recent reviews have covered methods for screening root traits but an appreciation for the complexity of root systems (e.g., functional differences between fine and coarse roots) needs to be paired with these methods to successfully identify relevant traits for crop improvement. Screening of root traits at early stages in plant development can proxy traits at mature stages but verification is needed on a case by case basis that traits are linked to increased crop productivity under drought. Examples in lesquerella (Physaria) and rice (Oryza) show approaches to phenotyping of root traits and current understanding of root trait genetics for breeding.

Root traits contributing to plant productivity under drought

Geneticists and breeders are positioned to breed plants with root traits that improve productivity under drought. However, a better understanding of root functional traits and how traits are related to whole plant strategies to increase crop productivity under different drought conditions is needed. Root traits associated with maintaining plant productivity under drought include small fine root diameters, long specific root length, and considerable root length density, especially at depths in soil with available water. In environments with late season water deficits, small xylem diameters in targeted seminal roots save soil water deep in the soil profile for use during crop maturation and result in improved yields. Capacity for deep root growth and large xylem diameters in deep roots may also improve root acquisition of water when ample water at depth is available. Xylem pit anatomy that makes xylem less "leaky" and prone to cavitation warrants further exploration holding promise that such traits may improve plant productivity in water-limited environments without negatively impacting yield under adequate water conditions. Rapid resumption of root growth following soil rewetting may improve plant productivity under episodic drought. Genetic control of many of these traits through breeding appears feasible. Several recent reviews have covered methods for screening root traits but an appreciation for the complexity of root systems (e.g., functional differences between fine and coarse roots) needs to be paired with these methods to successfully identify relevant traits for crop improvement. Screening of root traits at early stages in plant development can proxy traits at mature stages but verification is needed on a case by case basis that traits are linked to increased crop productivity under drought. Examples in lesquerella (Physaria) and rice (Oryza) show approaches to phenotyping of root traits and current understanding of root trait genetics for breeding.

Physiological and biotechnological implications of transcript-level variation under abiotic stress

The discovery of genes that can be used to increase plant tolerance to environmental stress has practical implications for agriculture, since knowledge at the molecular level can potentially be translated from model plants to crops or from tolerant to sensitive cultivars. For more than a decade, researchers have attempted to identify transcriptional and metabolic pathways involved in stress tolerance using functional genomics tools. In some cases, promising results were obtained when a clear causal link was found between transcripts and tolerance/sensitivity to stress. However, recent reports question the global translational power of functional genomics for biotechnological applications, as one of the main limitations seems to be the large variability in gene expression. Transcript-level variability under stress has not been considered of interest in the scientific literature because it is intuitively obvious, but most reports seem to naively overlook the consequences. Here, three case situations are reviewed (variability between genotypes, variability due to environmental interactions and variability between stressors) in support of the concept that inherent transcript-level variation in biological systems may limit our knowledge of environmental plant tolerance and of functional genomics in molecular stress physiology.

SNP marker discovery, linkage map construction and identification of QTLs for enhanced salinity tolerance in field pea (Pisum sativum L.)

BACKGROUND

Field pea (Pisum sativum L.) is a self-pollinating, diploid, cool-season food legume. Crop production is constrained by multiple biotic and abiotic stress factors, including salinity, that cause reduced growth and yield. Recent advances in genomics have permitted the development of low-cost high-throughput genotyping systems, allowing the construction of saturated genetic linkage maps for identification of quantitative trait loci (QTLs) associated with traits of interest. Genetic markers in close linkage with the relevant genomic regions may then be implemented in varietal improvement programs.

RESULTS

In this study, single nucleotide polymorphism (SNP) markers associated with expressed sequence tags (ESTs) were developed and used to generate comprehensive linkage maps for field pea. From a set of 36,188 variant nucleotide positions detected through in silico analysis, 768 were selected for genotyping of a recombinant inbred line (RIL) population. A total of 705 SNPs (91.7%) successfully detected segregating polymorphisms. In addition to SNPs, genomic and EST-derived simple sequence repeats (SSRs) were assigned to the genetic map in order to obtain an evenly distributed genome-wide coverage. Sequences associated with the mapped molecular markers were used for comparative genomic analysis with other legume species. Higher levels of conserved synteny were observed with the genomes of Medicago truncatula Gaertn. and chickpea (Cicer arietinum L.) than with soybean (Glycine max [L.] Merr.), Lotus japonicus L. and pigeon pea (Cajanus cajan [L.] Millsp.). Parents and RIL progeny were screened at the seedling growth stage for responses to salinity stress, imposed by addition of NaCl in the watering solution at a concentration of 18 dS m-1. Salinity-induced symptoms showed normal distribution, and the severity of the symptoms increased over time. QTLs for salinity tolerance were identified on linkage groups Ps III and VII, with flanking SNP markers suitable for selection of resistant cultivars. Comparison of sequences underpinning these SNP markers to the M. truncatula genome defined genomic regions containing candidate genes associated with saline stress tolerance.

CONCLUSION

The SNP assays and associated genetic linkage maps developed in this study permitted identification of salinity tolerance QTLs and candidate genes. This constitutes an important set of tools for marker-assisted selection (MAS) programs aimed at performance enhancement of field pea cultivars.

Advanced genetic tools for plant biotechnology

Basic research has provided a much better understanding of the genetic networks and regulatory hierarchies in plants. To meet the challenges of agriculture, we must be able to rapidly translate this knowledge into generating improved plants. Therefore, in this Review, we discuss advanced tools that are currently available for use in plant biotechnology to produce new products in plants and to generate plants with new functions. These tools include synthetic promoters, 'tunable' transcription factors, genome-editing tools and site-specific recombinases. We also review some tools with the potential to enable crop improvement, such as methods for the assembly and synthesis of large DNA molecules, plant transformation with linked multigenes and plant artificial chromosomes. These genetic technologies should be integrated to realize their potential for applications to pressing agricultural and environmental problems.

Plant science and agricultural productivity: why are we hitting the yield ceiling?

Trends in conventional plant breeding and in biotechnology research are analyzed with a focus on production and productivity of individual organisms. Our growing understanding of the productive/adaptive potential of (crop) plants is a prerequisite to increasing this potential and also its expression under environmental constraints. This review concentrates on growth rate, ribosome activity, and photosynthetic rate to link these key cellular processes to plant productivity. Examples of how they may be integrated in heterosis, organ growth control, and responses to abiotic stresses are presented. The yield components in rice are presented as a model. The ultimate goal of research programs, that concentrate on yield and productivity and integrating the panoply of systems biology tools, is to achieve "low input, high output" agriculture, i.e. shifting from a conventional "productivist" agriculture to an efficient sustainable agriculture. This is of critical, strategic importance, because the extent to which we, both locally and globally, secure and manage the long-term productive potential of plant resources will determine the future of humanity.

Plant tolerance to high temperature in a changing environment: scientific fundamentals and production of heat stress-tolerant crops

Global warming is predicted to have a general negative effect on plant growth due to the damaging effect of high temperatures on plant development. The increasing threat of climatological extremes including very high temperatures might lead to catastrophic loss of crop productivity and result in wide spread famine. In this review, we assess the impact of global climate change on the agricultural crop production. There is a differential effect of climate change both in terms of geographic location and the crops that will likely show the most extreme reductions in yield as a result of expected extreme fluctuations in temperature and global warming in general. High temperature stress has a wide range of effects on plants in terms of physiology, biochemistry and gene regulation pathways. However, strategies exist to crop improvement for heat stress tolerance. In this review, we present recent advances of research on all these levels of investigation and focus on potential leads that may help to understand more fully the mechanisms that make plants tolerant or susceptible to heat stress. Finally, we review possible procedures and methods which could lead to the generation of new varieties with sustainable yield production, in a world likely to be challenged both by increasing population, higher average temperatures and larger temperature fluctuations.

Natural variation and genetic constraints on drought tolerance

Drought is a central abiotic stress for both natural plant populations and agricultural crops. Substantial natural genetic variation in drought resistance traits has been identified in plant populations, crop species, and laboratory model systems. In particular, studies in Arabidopsis thaliana have discovered variation in a number of key physiological traits involved in plant-water relations that may underlie evolved drought stress responses among accessions. Despite this abundant variation, we still know little about the complex genetic architecture of drought tolerance or its role in constraining evolution. Unfortunately, few natural allelic variants have been cloned for drought related traits--progress cloning QTL, the use of RNA-sequencing methods for evaluating gene expression responses to soil drying, and improved methodology for exploring complex multivariate data all hold promise for moving the field forward. In particular, a better understanding of the molecular nature of pleiotropic gene action and the genetics of phenotypic plasticity will give insight into local adaptation in plants and provide new avenues for improving crops.

Large-scale characterization of drought pattern: a continent-wide modelling approach applied to the Australian wheatbelt--spatial and temporal trends

Plant response to drought is complex, so that traits adapted to a specific drought type can confer disadvantage in another drought type. Understanding which type(s) of drought to target is of prime importance for crop improvement. Modelling was used to quantify seasonal drought patterns for a check variety across the Australian wheatbelt, using 123 yr of weather data for representative locations and managements. Two other genotypes were used to simulate the impact of maturity on drought pattern. Four major environment types summarized the variability in drought pattern over time and space. Severe stress beginning before flowering was common (44% of occurrences), with (24%) or without (20%) relief during grain filling. High variability occurred from year to year, differing with geographical region. With few exceptions, all four environment types occurred in most seasons, for each location, management system and genotype. Applications of such environment characterization are proposed to assist breeding and research to focus on germplasm, traits and genes of interest for target environments. The method was applied at a continental scale to highly variable environments and could be extended to other crops, to other drought-prone regions around the world, and to quantify potential changes in drought patterns under future climates.

QTL mapping in three tropical maize populations reveals a set of constitutive and adaptive genomic regions for drought tolerance

Despite numerous published reports of quantitative trait loci (QTL) for drought-related traits, practical applications of such QTL in maize improvement are scarce. Identifying QTL of sizeable effects that express more or less uniformly in diverse genetic backgrounds across contrasting water regimes could significantly complement conventional breeding efforts to improve drought tolerance. We evaluated three tropical bi-parental populations under water-stress (WS) and well-watered (WW) regimes in Mexico, Kenya and Zimbabwe to identify genomic regions responsible for grain yield (GY) and anthesis-silking interval (ASI) across multiple environments and diverse genetic backgrounds. Across the three populations, on average, drought stress reduced GY by more than 50 % and increased ASI by 3.2 days. We identified a total of 83 and 62 QTL through individual environment analyses for GY and ASI, respectively. In each population, most QTL consistently showed up in each water regime. Across the three populations, the phenotypic variance explained by various individual QTL ranged from 2.6 to 17.8 % for GY and 1.7 to 17.8 % for ASI under WS environments and from 5 to 19.5 % for GY under WW environments. Meta-QTL (mQTL) analysis across the three populations and multiple environments identified seven genomic regions for GY and one for ASI, of which six mQTL on chr.1, 4, 5 and 10 for GY were constitutively expressed across WS and WW environments. One mQTL on chr.7 for GY and one on chr.3 for ASI were found to be 'adaptive' to WS conditions. High throughput assays were developed for SNPs that delimit the physical intervals of these mQTL. At most of the QTL, almost equal number of favorable alleles was donated by either of the parents within each cross, thereby demonstrating the potential of drought tolerant × drought tolerant crosses to identify QTL under contrasting water regimes.

Metabolomics of forage plants: a review

BACKGROUND

Forage plant breeding is under increasing pressure to deliver new cultivars with improved yield, quality and persistence to the pastoral industry. New innovations in DNA sequencing technologies mean that quantitative trait loci analysis and marker-assisted selection approaches are becoming faster and cheaper, and are increasingly used in the breeding process with the aim to speed it up and improve its precision. High-throughput phenotyping is currently a major bottle neck and emerging technologies such as metabolomics are being developed to bridge the gap between genotype and phenotype; metabolomics studies on forages are reviewed in this article.

SCOPE

Major challenges for pasture production arise from the reduced availability of resources, mainly water, nitrogen and phosphorus, and metabolomics studies on metabolic responses to these abiotic stresses in Lolium perenne and Lotus species will be discussed here. Many forage plants can be associated with symbiotic microorganisms such as legumes with nitrogen fixing rhizobia, grasses and legumes with phosphorus-solubilizing arbuscular mycorrhizal fungi, and cool temperate grasses with fungal anti-herbivorous alkaloid-producing Neotyphodium endophytes and metabolomics studies have shown that these associations can significantly affect the metabolic composition of forage plants. The combination of genetics and metabolomics, also known as genetical metabolomics can be a powerful tool to identify genetic regions related to specific metabolites or metabolic profiles, but this approach has not been widely adopted for forages yet, and we argue here that more studies are needed to improve our chances of success in forage breeding.

CONCLUSIONS

Metabolomics combined with other '-omics' technologies and genome sequencing can be invaluable tools for large-scale geno- and phenotyping of breeding populations, although the implementation of these approaches in forage breeding programmes still lags behind. The majority of studies using metabolomics approaches have been performed with model species or cereals and findings from these studies are not easily translated to forage species. To be most effective these approaches should be accompanied by whole-plant physiology and proof of concept (modelling) studies. Wider considerations of possible consequences of novel traits on the fitness of new cultivars and symbiotic associations need also to be taken into account.

Quantitative trait loci associated with androgenic responsiveness in triticale (×Triticosecale Wittm.) anther culture

Quantitative trait loci (QTLs) associated with androgenic responsiveness in triticale were analyzed using a population of 90 DH lines derived from the F1 cross between inbred line 'Saka 3006' and cv. 'Modus', which was used in a number of earlier studies on molecular mapping in this crop. Using Windows QTL Cartographer and MapQTL 5.0, composite interval mapping (CIM) and association studies (Kruskal-Wallis test; K-W) for five androgenesis parameters (androgenic embryo induction, total regeneration and green plant regeneration ability, and two characteristics describing final androgenesis efficiency) were conducted. For the studied components of androgenic response, CIM detected in total 28 QTLs which were localized on 5 chromosomes from A and R genomes. Effects of all QTLs that were identified at 2.0 or above of the LOD score explained 5.1-21.7 % of the phenotypic variation. Androgenesis induction was associated with seven QTLs (LOD between 2.0 and 5.8) detected on chromosomes 5A, 4R, 5R and 7R, all of them confirmed by K-W test as regions containing the markers significantly linked to the studied trait. What is more, K-W test revealed additional markers on chromosomes: 5A, 2BL, 7B and 5R. Both total and green regeneration ability were controlled by genes localized on chromosome 4A. Some of the QTLs that affected final androgenesis efficiency were identical with those associated with androgenic embryo induction efficiency, suggesting that the observed correlation may be either due to tight linkage or to pleiotropy. Key message Five regions of the triticale genome were indicated as revealing significant marker/trait association. Markers located in these regions are potentially useful for triticale breeding through marker-assisted selection.

Detection of two major grain yield QTL in bread wheat (Triticum aestivum L.) under heat, drought and high yield potential environments

A large proportion of the worlds' wheat growing regions suffers water and/or heat stress at some stage during the crop growth cycle. With few exceptions, there has been no utilisation of managed environments to screen mapping populations under repeatable abiotic stress conditions, such as the facilities developed by the International Wheat and Maize Improvement Centre (CIMMYT). Through careful management of irrigation and sowing date over three consecutive seasons, repeatable heat, drought and high yield potential conditions were imposed on the RAC875/Kukri doubled haploid population to identify genetic loci for grain yield, yield components and key morpho-physiological traits under these conditions. Two of the detected quantitative trait loci (QTL) were located on chromosome 3B and had a large effect on canopy temperature and grain yield, accounting for up to 22 % of the variance for these traits. The locus on chromosome arm 3BL was detected under all three treatments but had its largest effect under the heat stress conditions, with the RAC875 allele increasing grain yield by 131 kg ha(-1) (or phenotypically, 7 % of treatment average). Only two of the eight yield QTL detected in the current study (including linkage groups 3A, 3D, 4D 5B and 7A) were previously detected in the RAC875/Kukri doubled haploid population; and there were also different yield components driving grain yield. A number of discussion points are raised to understand differences between the Mexican and southern Australian production environments and explain the lack of correlation between the datasets. The two key QTL detected on chromosome 3B in the present study are candidates for further genetic dissection and development of molecular markers.

Phenotyping for drought tolerance of crops in the genomics era

Improving crops yield under water-limited conditions is the most daunting challenge faced by breeders. To this end, accurate, relevant phenotyping plays an increasingly pivotal role for the selection of drought-resilient genotypes and, more in general, for a meaningful dissection of the quantitative genetic landscape that underscores the adaptive response of crops to drought. A major and universally recognized obstacle to a more effective translation of the results produced by drought-related studies into improved cultivars is the difficulty in properly phenotyping in a high-throughput fashion in order to identify the quantitative trait loci that govern yield and related traits across different water regimes. This review provides basic principles and a broad set of references useful for the management of phenotyping practices for the study and genetic dissection of drought tolerance and, ultimately, for the release of drought-tolerant cultivars.

Integrated genomics, physiology and breeding approaches for improving drought tolerance in crops

Drought is one of the most serious production constraint for world agriculture and is projected to worsen with anticipated climate change. Inter-disciplinary scientists have been trying to understand and dissect the mechanisms of plant tolerance to drought stress using a variety of approaches; however, success has been limited. Modern genomics and genetic approaches coupled with advances in precise phenotyping and breeding methodologies are expected to more effectively unravel the genes and metabolic pathways that confer drought tolerance in crops. This article discusses the most recent advances in plant physiology for precision phenotyping of drought response, a vital step before implementing the genetic and molecular-physiological strategies to unravel the complex multilayered drought tolerance mechanism and further exploration using molecular breeding approaches for crop improvement. Emphasis has been given to molecular dissection of drought tolerance by QTL or gene discovery through linkage and association mapping, QTL cloning, candidate gene identification, transcriptomics and functional genomics. Molecular breeding approaches such as marker-assisted backcrossing, marker-assisted recurrent selection and genome-wide selection have been suggested to be integrated in crop improvement strategies to develop drought-tolerant cultivars that will enhance food security in the context of a changing and more variable climate.

Quantitative trait locus analysis and construction of consensus genetic map for drought tolerance traits based on three recombinant inbred line populations in cultivated groundnut (Arachis hypogaea L.)

Groundnut (Arachis hypogaea L.) is an important food and cash crop grown mainly in semi-arid tropics (SAT) regions of the world where drought is the major constraint on productivity. With the aim of understanding the genetic basis and identification of quantitative trait loci (QTL) for drought tolerance, two new recombinant inbred line (RIL) mapping populations, namely ICGS 76 × CSMG 84-1 (RIL-2) and ICGS 44 × ICGS 76 (RIL-3), were used. After screening of 3,215 simple sequence repeat (SSR) markers on the parental genotypes of these populations, two new genetic maps were developed with 119 (RIL-2) and 82 (RIL-3) SSR loci. Together with these maps and the reference map with 191 SSR loci based on TAG 24 × ICGV 86031 (RIL-1), a consensus map was constructed with 293 SSR loci distributed over 20 linkage groups, spanning 2,840.8 cM. As all these three populations segregate for drought-tolerance-related traits, a comprehensive QTL analysis identified 153 main effect QTL (M-QTL) and 25 epistatic QTL (E-QTL) for drought-tolerance-related traits. Localization of these QTL on the consensus map provided 16 genomic regions that contained 125 QTL. A few key genomic regions were selected on the basis of the QTL identified in each region, and their expected role in drought adaptation is also discussed. Given that no major QTL for drought adaptation were identified, novel breeding approaches such as marker-assisted recurrent selection (MARS) and genomic selection (GS) approaches are likely to be the preferred approaches for introgression of a larger number of QTL in order to breed drought-tolerant groundnut genotypes. ELECTRONIC SUPPLEMENTARY MATERIAL: The online version of this article (doi:10.1007/s11032-011-9660-0) contains supplementary material, which is available to authorized users.

Isolation and characterization of two ABRE-binding proteins: EABF and EABF1 from the oil palm

Abscisic acid (ABA) is an important phytohormone involved in the abiotic stress resistance in plants. The ABA-responsive element (ABRE) binding factors play significant roles in the plant development and response to abiotic stresses, but none so far have been isolated and characterized from the oil palm. Two ABA-responsive cDNA clones, named EABF and EABF1, were isolated from the oil palm fruits using yeast one-hybrid system. The EABF had a conserved AP2/EREBP DNA-binding domain (DNA-BD) and a potential nuclear localization sequence (NLS). No previously known DNA-BD was identified from the EABF1 sequence. The EABF and EABF1 proteins were classified as DREB/CBF and bZIP family members based on the multiple sequence alignment and phylogenetic analysis. Both proteins showed ABRE-binding and transcriptional activation properties in yeast. Furthermore, both proteins were able to trans-activate the down-stream expression of the LacZ reporter gene in yeast. An electrophoretic mobility shift assay revealed that in addition to the ABRE sequence, both proteins could bind to the DRE sequence as well. Transcriptional analysis revealed that the expression of EABF was induced in response to the ABA in the oil palm fruits and leaves, but not in roots, while the EABF1 was constitutively induced in all tissues. The expressions of both genes were strongly induced in fruits in response to the ABA, ethylene, methyl jasmonate, drought, cold and high-salinity treatments, indicating that the EABF and EABF1 might act as connectors among different stress signal transduction pathways. Our results indicate that the EABF and EABF1 are novel stress-responsive transcription factors, which are involved in the abiotic stress response and ABA signaling in the oil palm and could be used for production of stress-tolerant transgenic crops.

High-throughput imaging and analysis of root system architecture in Brachypodium distachyon under differential nutrient availability

Nitrogen (N) and phosphorus (P) deficiency are primary constraints for plant productivity, and root system architecture (RSA) plays a vital role in the acquisition of these nutrients. The genetic determinants of RSA are poorly understood, primarily owing to the complexity of crop genomes and the lack of sufficient RSA phenotyping methods. The objective of this study was to characterize the RSA of two Brachypodium distachyon accessions under different nutrient availability. To do so, we used a high-throughput plant growth and imaging platform, and developed software that quantified 19 different RSA traits. We found significant differences in RSA between two Brachypodium accessions grown on nutrient-rich, low-N and low-P conditions. More specifically, one accession maintained axile root growth under low N, while the other accession maintained lateral root growth under low P. These traits resemble the RSA of crops adapted to low-N and -P conditions, respectively. Furthermore, we found that a number of these traits were highly heritable. This work lays the foundation for future identification of important genetic components of RSA traits under nutrient limitation using a mapping population derived from these two accessions.

The interaction of plant biotic and abiotic stresses: from genes to the field

Plant responses to different stresses are highly complex and involve changes at the transcriptome, cellular, and physiological levels. Recent evidence shows that plants respond to multiple stresses differently from how they do to individual stresses, activating a specific programme of gene expression relating to the exact environmental conditions encountered. Rather than being additive, the presence of an abiotic stress can have the effect of reducing or enhancing susceptibility to a biotic pest or pathogen, and vice versa. This interaction between biotic and abiotic stresses is orchestrated by hormone signalling pathways that may induce or antagonize one another, in particular that of abscisic acid. Specificity in multiple stress responses is further controlled by a range of molecular mechanisms that act together in a complex regulatory network. Transcription factors, kinase cascades, and reactive oxygen species are key components of this cross-talk, as are heat shock factors and small RNAs. This review aims to characterize the interaction between biotic and abiotic stress responses at a molecular level, focusing on regulatory mechanisms important to both pathways. Identifying master regulators that connect both biotic and abiotic stress response pathways is fundamental in providing opportunities for developing broad-spectrum stress-tolerant crop plants.

Plant hormone interactions: innovative targets for crop breeding and management

Here we highlight how both the root and shoot environment impact on whole plant hormone balance, particularly under stresses such as soil drying, and relate hormone ratios and relative abundances to processes influencing plant performance and yield under both mild and more severe stress. We discuss evidence (i) that abscisic acid (ABA) and ethylene act antagonistically on grain-filling rate amongst other yield-impacting processes; (ii) that ABA's effectiveness as an agent of stomatal closure can be modulated by coincident ethylene or cytokinin accumulation; and (iii) that enhanced cytokinin production can increase growth and yield by improving foliar stay-green indices under stress, and by improving processes that impact grain-filling and number, and that this can be the result of altered relative abundances of cytokinin and ABA (and other hormones). We describe evidence and novel processes whereby these phenomena are/could be amenable to manipulation through genetic and management routes, such that plant performance and yield can be improved. We explore the possibility that a range of ABA-ethylene and ABA-cytokinin relative abundances could represent targets for breeding/managing for yield resilience under a spectrum of stress levels between severe and mild, and could circumvent some of the pitfalls so far encountered in the massive research effort towards breeding for increases in the complex trait of yield.

Complex genetics controls natural variation among seed quality phenotypes in a recombinant inbred population of an interspecific cross between Solanum lycopersicum × Solanum pimpinellifolium

Seed quality in tomato is associated with many complex physiological and genetic traits. While plant processes are frequently controlled by the action of small- to large-effect genes that follow classic Mendelian inheritance, our study suggests that seed quality is primarily quantitative and genetically complex. Using a recombinant inbred line population of Solanum lycopersicum × Solanum pimpinellifolium, we identified quantitative trait loci (QTLs) influencing seed quality phenotypes under non-stress, as well as salt, osmotic, cold, high-temperature and oxidative stress conditions. In total, 42 seed quality traits were analysed and 120 QTLs were identified for germination traits under different conditions. Significant phenotypic correlations were observed between germination traits under optimal conditions, as well as under different stress conditions. In conclusion, one or more QTLs were identified for each trait with some of these QTLs co-locating. Co-location of QTLs for different traits can be an indication that a locus has pleiotropic effects on multiple traits due to a common mechanistic basis. However, several QTLs also dissected seed quality in its separate components, suggesting different physiological mechanisms and signalling pathways for different seed quality attributes.

Multienvironment quantitative trait Loci analysis for photosynthate acquisition, accumulation, and remobilization traits in common bean under drought stress

Many of the world’s common bean (Phaseolus vulgaris L.) growing regions are prone to either intermittent or terminal drought stress, making drought the primary cause of yield loss under farmers’ field conditions. Improved photosynthate acquisition, accumulation, and then remobilization have been observed as important mechanisms for adaptation to drought stress. The objective of this study was to tag quantitative trait loci (QTL) for photosynthate acquisition, accumulation, and remobilization to grain by using a recombinant inbred line population developed from the Mesoamerican intragenepool cross of drought-susceptible DOR364 and drought-tolerant BAT477 grown under eight environments differing in drought stress across two continents: Africa and South America. The recombinant inbred line population expressed quantitative variation and transgressive segregation for 11 traits associated with drought tolerance. QTL were detected by both a mixed multienvironment model and by composite interval mapping for each environment using a linkage map constructed with 165 genetic markers that covered 11 linkage groups of the common bean genome. In the multienvironment, mixed model, nine QTL were detected for 10 drought stress tolerance mechanism traits found on six of the 11 linkage groups. Significant QTL × environment interaction was observed for six of the nine QTL. QTL × environment interaction was of the cross-over type for three of the six significant QTL with contrasting effect of the parental alleles across different environments. In the composite interval mapping, we found 69 QTL in total. The majority of these were found for Palmira (47) or Awassa (18), with fewer in Malawi (4). Phenotypic variation explained by QTL in single environments ranged up to 37%, and the most consistent QTL were for Soil Plant Analysis Development (SPAD) leaf chlorophyll reading and pod partitioning traits. QTL alignment between the two detection methods showed that yield QTL on b08 and stem carbohydrate QTL on b05 were most consistent between the multilocation model and the single environment detection. Our results indicate the relevance of QTL detection in the sites in which bean breeding will be undertaken and the importance of photosynthate accumulation as a trait for common bean drought tolerance.

Genomic associations for drought tolerance on the short arm of wheat chromosome 4B

Drought is a major constraint to maintaining yield stability of wheat in rain fed and limited irrigation agro-ecosystems. Genetic improvement for drought tolerance in wheat has been difficult due to quantitative nature of the trait involving multiple genes with variable effects and lack of effective selection strategies employing molecular markers. Here, a framework molecular linkage map was constructed using 173 DNA markers randomly distributed over the 21 wheat chromosomes. Grain yield and other drought-responsive shoot and root traits were phenotyped for 2 years under drought stress and well-watered conditions on a mapping population of recombinant inbred lines (RILs) derived from a cross between drought-sensitive semidwarf variety "WL711" and drought-tolerant traditional variety "C306". Thirty-seven genomics region were identified for 10 drought-related traits at 18 different chromosomal locations but most of these showed small inconsistent effects. A consistent genomic region associated with drought susceptibility index (qDSI.4B.1) was mapped on the short arm of chromosome 4B, which also controlled grain yield per plant, harvest index, and root biomass under drought. Transcriptome profiling of the parents and two RIL bulks with extreme phenotypes revealed five genes underlying this genomic region that were differentially expressed between the parents as well as the two RIL bulks, suggesting that they are likely candidates for drought tolerance. Syntenic genomic regions of barley, rice, sorghum, and maize genomes were identified that also harbor genes for drought tolerance. Markers tightly linked to this genomic region in combination with other important regions on group 7 chromosomes may be used in marker-assisted breeding for drought tolerance in wheat.

A sequential quantitative trait locus fine-mapping strategy using recombinant-derived progeny

A thorough understanding of the quantitative trait loci (QTLs) that underlie agronomically important traits in crops would greatly increase agricultural productivity. Although advances have been made in QTL cloning, the majority of QTLs remain unknown because of their low heritability and minor contributions to phenotypic performance. Here we summarize the key advantages and disadvantages of current QTL fine-mapping methodologies, and then introduce a sequential QTL fine-mapping strategy based on both genotypes and phenotypes of progeny derived from recombinants. With this mapping strategy, experimental errors could be dramatically diminished so as to reveal the authentic genetic effect of target QTLs. The number of progeny required to detect QTLs at various R2 values was calculated, and the backcross generation suitable to start QTL fine-mapping was also estimated. This mapping strategy has proved to be very powerful in narrowing down QTL regions, particularly minor-effect QTLs, as revealed by fine-mapping of various resistance QTLs in maize. Application of this sequential QTL mapping strategy should accelerate cloning of agronomically important QTLs, which is currently a substantial challenge in crops.

Rootstock control of scion transpiration and its acclimation to water deficit are controlled by different genes

The stomatal control of transpiration is one of the major strategies by which plants cope with water stress. Here, we investigated the genetic architecture of the rootstock control of scion transpiration-related traits over a period of 3 yr. The rootstocks studied were full sibs from a controlled interspecific cross (Vitis vinifera cv. Cabernet Sauvignon × Vitis riparia cv. Gloire de Montpellier), onto which we grafted a single scion genotype. After 10 d without stress, the water supply was progressively limited over a period of 10 d, and a stable water deficit was then applied for 15 d. Transpiration rate was estimated daily and a mathematical curve was fitted to its response to water deficit intensity. We also determined δ(13) C values in leaves, transpiration efficiency and water extraction capacity. These traits were then analysed in a multienvironment (year and water status) quantitative trait locus (QTL) analysis. Quantitative trait loci, independent of year and water status, were detected for each trait. One genomic region was specifically implicated in the acclimation of scion transpiration induced by the rootstock. The QTLs identified colocalized with genes involved in water deficit responses, such as those relating to ABA and hydraulic regulation. Scion transpiration rate and its acclimation to water deficit are thus controlled genetically by the rootstock, through different genetic architectures.

Aluminum tolerance association mapping in triticale

Background

Crop production practices and industrialization processes result in increasing acidification of arable soils. At lower pH levels (below 5.0), aluminum (Al) remains in a cationic form that is toxic to plants, reducing growth and yield. The effect of aluminum on agronomic performance is particularly important in cereals like wheat, which has promoted the development of programs directed towards selection of tolerant forms. Even in intermediately tolerant cereals (i.e., triticale), the decrease in yield may be significant. In triticale, Al tolerance seems to be influenced by both wheat and rye genomes. However, little is known about the precise chromosomal location of tolerance-related genes, and whether wheat or rye genomes are crucial for the expression of that trait in the hybrid.

Results

A mapping population consisting of 232 advanced breeding triticale forms was developed and phenotyped for Al tolerance using physiological tests. AFLP, SSR and DArT marker platforms were applied to obtain a sufficiently large set of molecular markers (over 3000). Associations between the markers and the trait were tested using General (GLM) and Multiple (MLM) Linear Models, as well as the Statistical Machine Learning (SML) approach. The chromosomal locations of candidate markers were verified based on known assignments of SSRs and DArTs or by using genetic maps of rye and triticale.

Two candidate markers on chromosome 3R and 9, 15 and 11 on chromosomes 4R, 6R and 7R, respectively, were identified. The r² values were between 0.066 and 0.220 in most cases, indicating a good fit of the data, with better results obtained with the GML than the MLM approach. Several QTLs on rye chromosomes appeared to be involved in the phenotypic expression of the trait, suggesting that rye genome factors are predominantly responsible for Al tolerance in triticale.

Conclusions

The Diversity Arrays Technology was applied successfully to association mapping studies performed on triticale breeding forms. Statistical approaches allowed the identification of numerous markers associated with Al tolerance. Available rye and triticale genetic maps suggested the putative location of the markers and demonstrated that they formed several linked groups assigned to distinct chromosomes (3R, 4R, 6R and 7R). Markers associated with genomic regions under positive selection were identified and indirectly mapped in the vicinity of the Al-tolerant markers. The present findings were in agreement with prior reports.

Comparative metabolomics of drought acclimation in model and forage legumes

Water limitation has become a major concern for agriculture. Such constraints reinforce the urgent need to understand mechanisms by which plants cope with water deprivation. We used a non-targeted metabolomic approach to explore plastic systems responses to non-lethal drought in model and forage legume species of the Lotus genus. In the model legume Lotus. japonicus, increased water stress caused gradual increases of most of the soluble small molecules profiled, reflecting a global and progressive reprogramming of metabolic pathways. The comparative metabolomic approach between Lotus species revealed conserved and unique metabolic responses to drought stress. Importantly, only few drought-responsive metabolites were conserved among all species. Thus we highlight a potential impediment to translational approaches that aim to engineer traits linked to the accumulation of compatible solutes. Finally, a broad comparison of the metabolic changes elicited by drought and salt acclimation revealed partial conservation of these metabolic stress responses within each of the Lotus species, but only few salt- and drought-responsive metabolites were shared between all. The implications of these results are discussed with regard to the current insights into legume water stress physiology.

Biotechnologies for the management of genetic resources for food and agriculture

In recent years, the land area under agriculture has declined as also has the rate of growth in agricultural productivity while the demand for food continues to escalate. The world population now stands at 7 billion and is expected to reach 9 billion in 2045. A broad range of agricultural genetic diversity needs to be available and utilized in order to feed this growing population. Climate change is an added threat to biodiversity that will significantly impact genetic resources for food and agriculture (GRFA) and food production. There is no simple, all-encompassing solution to the challenges of increasing productivity while conserving genetic diversity. Sustainable management of GRFA requires a multipronged approach, and as outlined in the paper, biotechnologies can provide powerful tools for the management of GRFA. These tools vary in complexity from those that are relatively simple to those that are more sophisticated. Further, advances in biotechnologies are occurring at a rapid pace and provide novel opportunities for more effective and efficient management of GRFA. Biotechnology applications must be integrated with ongoing conventional breeding and development programs in order to succeed. Additionally, the generation, adaptation, and adoption of biotechnologies require a consistent level of financial and human resources and appropriate policies need to be in place. These issues were also recognized by Member States at the FAO international technical conference on Agricultural Biotechnologies for Developing Countries (ABDC-10), which took place in March 2010 in Mexico. At the end of the conference, the Member States reached a number of key conclusions, agreeing, inter alia, that developing countries should significantly increase sustained investments in capacity building and the development and use of biotechnologies to maintain the natural resource base; that effective and enabling national biotechnology policies and science-based regulatory frameworks can facilitate the development and appropriate use of biotechnologies in developing countries; and that FAO and other relevant international organizations and donors should significantly increase their efforts to support the strengthening of national capacities in the development and appropriate use of pro-poor agricultural biotechnologies.

Development of a Mesoamerican intra-genepool genetic map for quantitative trait loci detection in a drought tolerant × susceptible common bean (Phaseolus vulgaris L.) cross

Drought is a major constraint to common bean (Phaseolus vulgaris L.) production, especially in developing countries where irrigation for the crop is infrequent. The Mesoamerican genepool is the most widely grown subdivision of common beans that include small red, small cream and black seeded varieties. The objective of this study was to develop a reliable genetic map for a Mesoamerican × Mesoamerican drought tolerant × susceptible cross and to use this map to analyze the inheritance of yield traits under drought and fully irrigated conditions over 3 years of experiments. The source of drought tolerance used in the cross was the cream-seeded advanced line BAT477 crossed with the small red variety DOR364 and the population was made up of recombinant inbred lines in the F5 generation. Quantitative trait loci were detected by composite interval mapping for the traits of overall seed yield, yield per day, 100 seed weight, days to flowering and days to maturity for each field environment consisting of two treatments (irrigated and rainfed) and lattice design experiments with three repetitions for a total of six environments. The genetic map based on amplified fragment length polymorphism and random amplified polymorphic DNA markers was anchored with 60 simple sequence repeat (SSR) markers and had a total map length of 1,087.5 cM across 11 linkage groups covering the whole common bean genome with saturation of one marker every 5.9 cM. Gaps for the genetic map existed on linkage groups b03, b09 and b11 but overall there were only nine gaps larger than 15 cM. All traits were inherited quantitatively, with the greatest number for seed weight followed by yield per day, yield per se, days to flowering and days to maturity. The relevance of these results for breeding common beans is discussed in particular in the light of crop improvement for drought tolerance in the Mesoamerican genepool.

QTL mapping of physiological traits associated with salt tolerance in Medicago truncatula Recombinant Inbred Lines

In this study, QTL mapping of physiological traits in the model Legume (Medicago truncatula) was performed using a set of RILs derived from LR5. Twelve parameters associated with Na+ and K+ content in leaves, stems and roots were measured. Broad-sense heritability of these traits was ranged from 0.15 to 0.83 in control and from 0.14 to 0.61 in salt stress. Variation among RILs was dependent on line, treatment and line by treatment effect. We mapped 6 QTLs in control, 2 in salt stress and 5 for sensitivity index. No major QTL was identified indicating that tolerance to salt stress is governed by several genes with low effects. Detected QTL for leaf, stem and root traits did not share the same map locations, suggesting that genes controlling transport of Na+ and K+ may be different. The maximum of QTL was observed on chromosome 1, no QTL was detected on chromosomes 5 and 6.

qDTY₁.₁, a major QTL for rice grain yield under reproductive-stage drought stress with a consistent effect in multiple elite genetic backgrounds

Background

Drought is one of the most important abiotic stresses causing drastic reductions in yield in rainfed rice environments. The suitability of grain yield (GY) under drought as a selection criterion has been reported in the past few years. Most of the quantitative trait loci (QTLs) for GY under drought in rice reported so far has been in the background of low-yielding susceptible varieties. Such QTLs have not shown a similar effect in multiple high- yielding drought-susceptible varieties, thus limiting their use in marker-assisted selection. Genetic control of GY under reproductive-stage drought stress (RS) in elite genetic backgrounds was studied in three F_3:4 mapping populations derived from crosses of N22, a drought-tolerant aus cultivar, with Swarna, IR64, and MTU1010, three high-yielding popular mega-varieties, with the aim to identify QTLs for GY under RS that show a consistent effect in multiple elite genetic backgrounds. Three populations were phenotyped under RS in the dry seasons (DS) of 2009 and 2010 at IRRI. For genotyping, whole-genome scans for N22/MTU1010 and bulked segregant analysis for N22/Swarna and N22/IR64 were employed using SSR markers.

Results

A major QTL for GY under RS, qDTY_1.1, was identified on rice chromosome 1 flanked by RM11943 and RM431 in all three populations. In combined analysis over two years, qDTY_1.1 showed an additive effect of 29.3%, 24.3%, and 16.1% of mean yield in N22/Swarna, N22/IR64, and N22/MTU1010, respectively, under RS. qDTY_1.1 also showed a positive effect on GY in non-stress (NS) situations in N22/Swarna, N22/IR64 over both years, and N22/MTU1010 in DS2009.

Conclusions

This is the first reported QTL in rice with a major and consistent effect in multiple elite genetic backgrounds under both RS and NS situations. Consistency of the QTL effect across different genetic backgrounds makes it a suitable candidate for use in marker-assisted breeding.

Abiotic stress and control of grain number in cereals

Grain number is the only yield component that is directly associated with increased grain yield in important cereal crops like wheat. Historical yield studies show that increases in grain yield are always accompanied by an increase in grain number. Adverse weather conditions can cause severe fluctuations in grain yield and substantial yield losses in cereal crops. The problem is global and despite its impact on world food production breeding and selection approaches have only met with limited success. A specific period during early reproductive development, the young microspore stage of pollen development, is extremely vulnerable to abiotic stress in self-fertilising cereals (wheat, rice, barley, sorghum). A better understanding of the physiological and molecular processes that lead to stress-induced pollen abortion may provide us with the key to finding solutions for maintaining grain number under abiotic stress conditions. Due to the complexity of the problem, stress-proofing our main cereal crops will be a challenging task and will require joint input from different research disciplines.

Drought resistance - is it really a complex trait?

Drought resistance is being increasingly labelled as being a 'complex trait', especially with the recent expansion of research into its genomics. There is a danger that this label may turn into an axiom that is liable to damage education on the subject as well as research and the delivery of solutions to the farmer. This opinionated review examines whether there is grounds for such an axiom. Drought resistance is labelled as a 'complex trait' mainly when viewed by molecular biologists from the gene discovery platform. This platform is capable of expressing hundreds and thousands of drought-responsive genes, which are up- or down-regulated under dehydration stress according to growth stage, plant organ or even time of day. Sorting out the 'grain out of the chaff' in order to identify the function of the candidate genes towards drought resistance is difficult and, thus, the idea that drought resistance is complex is raised. However, when drought resistance is viewed from the physiological and agronomic whole-plant and crop platform, it appears much simpler; its control, whether constitutive or adaptive, is rather obvious with respect to manipulation in breeding and crop management. The most important and common drought resistance traits function to maintain plant hydration under drought stress due to effective use of water (EUW). The state of our knowledge and the achievements in breeding for drought resistance do not support labelling drought resistance as a complex trait. The genomics road towards drought resistance is complex but we already know that the destination is much simpler.

Developing rice with high yield under phosphorus deficiency: Pup1 sequence to application

The major quantitative trait locus (QTL) Phosphorus uptake1 (Pup1) confers tolerance of phosphorus deficiency in soil and is currently one of the most promising QTLs for the development of tolerant rice (Oryza sativa) varieties. To facilitate targeted introgression of Pup1 into intolerant varieties, the gene models predicted in the Pup1 region in the donor variety Kasalath were used to develop gene-based molecular markers that are evenly distributed over the fine-mapped 278-kb QTL region. To validate the gene models and optimize the markers, gene expression analyses and partial allelic sequencing were conducted. The markers were tested in more than 80 diverse rice accessions revealing three main groups with different Pup1 allele constitution. Accessions with tolerant (group I) and intolerant (group III) Pup1 alleles were distinguished from genotypes with Kasalath alleles at some of the analyzed loci (partial Pup1; group II). A germplasm survey additionally confirmed earlier data showing that Pup1 is largely absent from irrigated rice varieties but conserved in varieties and breeding lines adapted to drought-prone environments. A core set of Pup1 markers has been defined, and sequence polymorphisms suitable for single-nucleotide polymorphism marker development for high-throughput genotyping were identified. Following a marker-assisted backcrossing approach, Pup1 was introgressed into two irrigated rice varieties and three Indonesian upland varieties. First phenotypic evaluations of the introgression lines suggest that Pup1 is effective in different genetic backgrounds and environments and that it has the potential to significantly enhance grain yield under field conditions.

Meta-analysis of grain yield QTL identified during agricultural drought in grasses showed consensus

BACKGROUND

In the last few years, efforts have been made to identify large effect QTL for grain yield under drought in rice. However, identification of most precise and consistent QTL across the environments and genetics backgrounds is essential for their successful use in Marker-assisted Selection. In this study, an attempt was made to locate consistent QTL regions associated with yield increase under drought by applying a genome-wide QTL meta-analysis approach.

RESULTS

The integration of 15 maps resulted in a consensus map with 531 markers and a total map length of 1821 cM. Fifty-three yield QTL reported in 15 studies were projected on a consensus map and meta-analysis was performed. Fourteen meta-QTL were obtained on seven chromosomes. MQTL1.2, MQTL1.3, MQTL1.4, and MQTL12.1 were around 700 kb and corresponded to a reasonably small genetic distance of 1.8 to 5 cM and they are suitable for use in marker-assisted selection (MAS). The meta-QTL for grain yield under drought coincided with at least one of the meta-QTL identified for root and leaf morphology traits under drought in earlier reports. Validation of major-effect QTL on a panel of random drought-tolerant lines revealed the presence of at least one major QTL in each line. DTY12.1 was present in 85% of the lines, followed by DTY4.1 in 79% and DTY1.1 in 64% of the lines. Comparative genomics of meta-QTL with other cereals revealed that the homologous regions of MQTL1.4 and MQTL3.2 had QTL for grain yield under drought in maize, wheat, and barley respectively. The genes in the meta-QTL regions were analyzed by a comparative genomics approach and candidate genes were deduced for grain yield under drought. Three groups of genes such as stress-inducible genes, growth and development-related genes, and sugar transport-related genes were found in clusters in most of the meta-QTL.

CONCLUSIONS

Meta-QTL with small genetic and physical intervals could be useful in Marker-assisted selection individually and in combinations. Validation and comparative genomics of the major-effect QTL confirmed their consistency within and across the species. The shortlisted candidate genes can be cloned to unravel the molecular mechanism regulating grain yield under drought.

Genetic analysis of abiotic stress tolerance in crops

Abiotic stress tolerance is complex, but as phenotyping technologies improve, components that contribute to abiotic stress tolerance can be quantified with increasing ease. In parallel with these phenomics advances, genetic approaches with more complex genomes are becoming increasingly tractable as genomic information in non-model crops increases and even whole crop genomes can be re-sequenced. Thus, genetic approaches to elucidating the molecular basis to abiotic stress tolerance in crops are becoming more easily achievable.

Enhancing drought tolerance in C(4) crops

Adaptation to abiotic stresses is a quantitative trait controlled by many different genes. Enhancing the tolerance of crop plants to abiotic stresses such as drought has therefore proved to be somewhat elusive in terms of plant breeding. While many C(4) species have significant agronomic importance, most of the research effort on improving drought tolerance has focused on maize. Ideally, drought tolerance has to be achieved without penalties in yield potential. Possibilities for success in this regard are highlighted by studies on maize hybrids performed over the last 70 years that have demonstrated that yield potential and enhanced stress tolerance are associated traits. However, while our understanding of the molecular mechanisms that enable plants to tolerate drought has increased considerably in recent years, there have been relatively few applications of DNA marker technologies in practical C(4) breeding programmes for improved stress tolerance. Moreover, until recently, targeted approaches to drought tolerance have concentrated largely on shoot parameters, particularly those associated with photosynthesis and stay green phenotypes, rather than on root traits such as soil moisture capture for transpiration, root architecture, and improvement of effective use of water. These root traits are now increasingly considered as important targets for yield improvement in C(4) plants under drought stress. Similarly, the molecular mechanisms underpinning heterosis have considerable potential for exploitation in enhancing drought stress tolerance. While current evidence points to the crucial importance of root traits in drought tolerance in C(4) plants, shoot traits may also be important in maintaining high yields during drought.

Identification of several small main-effect QTLs and a large number of epistatic QTLs for drought tolerance related traits in groundnut (Arachis hypogaea L.)

Cultivated groundnut or peanut (Arachis hypogaea L.), an allotetraploid (2n = 4x = 40), is a self pollinated and widely grown crop in the semi-arid regions of the world. Improvement of drought tolerance is an important area of research for groundnut breeding programmes. Therefore, for the identification of candidate QTLs for drought tolerance, a comprehensive and refined genetic map containing 191 SSR loci based on a single mapping population (TAG 24 x ICGV 86031), segregating for drought and surrogate traits was developed. Genotyping data and phenotyping data collected for more than ten drought related traits in 2-3 seasons were analyzed in detail for identification of main effect QTLs (M-QTLs) and epistatic QTLs (E-QTLs) using QTL Cartographer, QTLNetwork and Genotype Matrix Mapping (GMM) programmes. A total of 105 M-QTLs with 3.48-33.36% phenotypic variation explained (PVE) were identified using QTL Cartographer, while only 65 M-QTLs with 1.3-15.01% PVE were identified using QTLNetwork. A total of 53 M-QTLs were such which were identified using both programmes. On the other hand, GMM identified 186 (8.54-44.72% PVE) and 63 (7.11-21.13% PVE), three and two loci interactions, whereas only 8 E-QTL interactions with 1.7-8.34% PVE were identified through QTLNetwork. Interestingly a number of co-localized QTLs controlling 2-9 traits were also identified. The identification of few major, many minor M-QTLs and QTL × QTL interactions during the present study confirmed the complex and quantitative nature of drought tolerance in groundnut. This study suggests deployment of modern approaches like marker-assisted recurrent selection or genomic selection instead of marker-assisted backcrossing approach for breeding for drought tolerance in groundnut.

miRNA expression patterns of Triticum dicoccoides in response to shock drought stress

Drought is a major environmental stress factor that affects plant growth and development worldwide. Wild emmer wheat (Triticum turgidum ssp. dicoccoides), the ancestor of domesticated durum wheat (Triticum turgidum ssp. durum), has great potential for improving the understanding of the wheat drought response. MicroRNAs (miRNAs) are a recently discovered class of gene expression regulators that have also been linked to several plant stress responses; however, this relationship is just beginning to be understood. miRNA expression patterns of drought-resistant wild emmer wheat in response to drought stress were investigated using a plant miRNA microarray platform. Expression was detected to be 205 miRNAs in control and 438 miRNAs in drought-stressed leaf and root tissues. Of these miRNAs, the following 13 were differentially regulated in response to drought: miR1867, miR896, miR398, miR528, miR474, miR1450, miR396, miR1881, miR894, miR156, miR1432, miR166 and miR171. Regulation of miRNAs upon 4 and 8 h drought stress applications observed by qRT-PCR. Target transcripts of differentially regulated miRNAs were computationally predicted. In addition to miRNA microarray study, five new conserved T. turgidum miRNAs were identified through a homology-based approach, and their secondary structures and putative targets were predicted. These findings both computationally and experimentally highlight the presence of miRNAs in T. dicoccoides and further extend the role of miRNAs under shock drought stress conditions.

Natural variation of root hydraulics in Arabidopsis grown in normal and salt-stressed conditions

To gain insights into the natural variation of root hydraulics and its molecular components, genotypic differences related to root water transport and plasma membrane intrinsic protein (PIP) aquaporin expression were investigated in 13 natural accessions of Arabidopsis (Arabidopsis thaliana). The hydraulic conductivity of excised root systems (Lpr) showed a 2-fold variation among accessions. The contribution of aquaporins to water uptake was characterized using as inhibitors mercury, propionic acid, and azide. The aquaporin-dependent and -independent paths of water transport made variable contributions to the total hydraulic conductivity in the different accessions. The distinct suberization patterns observed among accessions were not correlated with their root hydraulic properties. Real-time reverse transcription-polymerase chain reaction revealed, by contrast, a positive overall correlation between Lpr and certain highly expressed PIP transcripts. Root hydraulic responses to salt stress were characterized in a subset of five accessions (Bulhary-1, Catania-1, Columbia-0, Dijon-M, and Monte-Tosso-0 [Mr-0]). Lpr was down-regulated in all accessions except Mr-0. In Mr-0 and Catania-1, cortical cell hydraulic conductivity was unresponsive to salt, whereas it was down-regulated in the three other accessions. By contrast, the five accessions showed qualitatively similar aquaporin transcriptional profiles in response to salt. The overall work provides clues on how hydraulic regulation allows plant adaptation to salt stress. It also shows that a wide range of root hydraulic profiles, as previously reported in various species, can be observed in a single model species. This work paves the way for a quantitative genetics analysis of root hydraulics.

Association mapping in durum wheat grown across a broad range of water regimes

Association mapping was used to dissect the genetic basis of drought-adaptive traits and grain yield (GY) in a collection of 189 elite durum wheat accessions evaluated in 15 environments highly different for water availability during the crop cycle (from 146 to 711 mm) and GY (from 9.9 to 67.3 q ha(-1)). For highly heritable traits (e.g. heading date, kernel weight, etc.) several significant experiment-wise marker-trait associations were detected across five or more (up to 13 for kernel weight) environments, with R(2) values ranging from ca. 5 to 10%. As to GY, significant associations (R(2) from 2.5 to 4.2%) were mostly detected in one environment only (56 markers), while decreasing rapidly from two to five environments (from 20 to three markers, respectively) and with only one marker (Xbarc197 on chr. 5A) found significant in six environments (ranging from low- to high-yielding). These results are probably due to the complex genetic basis of GY and its interaction with environmental conditions. The number of markers significantly affecting GY decreased considerably under drought conditions, suggesting a limited effectiveness of association mapping to identify loci for GY under low-moisture conditions, most likely because different genotypes can attain similar phenotypes via different morpho-physiological traits and corresponding gene networks. Our study confirmed the role of major loci for phenology previously described in biparental mapping populations, highlighted a novel set of loci for drought-adaptive traits, and provided information on the agronomic value of the alleles at such loci across a broad range of soil moisture conditions.

Involvement of root ABA and hydraulic conductivity in the control of water relations in wheat plants exposed to increased evaporative demand

We studied the possible involvement of ABA in the control of water relations under conditions of increased evaporative demand. Warming the air by 3°C increased stomatal conductance and raised transpiration rates of hydroponically grown Triticum durum plants while bringing about a temporary loss of relative water content (RWC) and immediate cessation of leaf extension. However, both RWC and extension growth recovered within 30 min although transpiration remained high. The restoration of leaf hydration and growth were enabled by increased root hydraulic conductivity after increasing the air temperature. The use of mercuric chloride (an inhibitor of water channels) to interfere with the rise on root hydraulic conductivity hindered the restoration of extension growth. Air warming increased ABA content in roots and decreased it in shoots. We propose this redistribution of ABA in favour of the roots which increased the root hydraulic conductivity sufficiently to permit rapid recovery of shoot hydration and leaf elongation rates without the involvement of stomatal closure. This proposal is based on known ability of ABA to increase hydraulic conductivity confirmed in these experiments by measuring the effect of exogenous ABA on osmotically driven flow of xylem sap from the roots. Accumulation of root ABA was mainly the outcome of increased export from the shoots. When phloem transport in air-warmed plants was inhibited by cooling the shoot base this prevented ABA enrichment of the roots and favoured an accumulation of ABA in the shoot. As a consequence, stomata closed.

Inside the CBF locus in Poaceae

Several molecular evidences have been gathered in Poaceae that point out a central role of the CBF/DREB1 transcription factors in the signal transduction pathways leading to low-temperature tolerance, although to a quite different extent between crops originating from either temperate or tropical climates. A common feature of the CBF/DREB1 genes in Poaceae is their structural organization at the genome level in clusters of tandemly duplicated genes. In temperate cereals such as barley and wheat, expansion of specific multigene phylogenetic clades of CBFs that map at the Frost Resistance-2 locus has been exclusively observed. In addition, copy number variants of CBF genes between frost resistant and frost sensitive genotypes raise the question if multiple copies of the CBF/DREB1s are required to ensure freezing tolerance. On the other hand, in crops of tropical origin such as rice and maize, a smaller or less-responsive CBF regulon may have evolved, and different mechanisms might determine chilling tolerance. In this review, recent advances on the organization and diversity at the CBF cluster locus in the grasses are provided and discussed.

Testing water-soluble carbohydrate QTL effects in perennial ryegrass (Lolium perenne L.) by marker selection

Water-soluble carbohydrates (WSC) are an important factor determining the nutritional value of grass forage and development of genetic markers for selection of WSC traits in perennial ryegrass would benefit future breeding programmes. Quantitative trait loci (QTLs) for WSC have been published for an F(2) ryegrass mapping family. Markers showing significant associations with these QTLs were used to design narrow-based populations with homozygosity for target QTLs. Founders were selected from within the mapping family. The divergent populations produced were analysed for WSC content in the glasshouse and the field. There was evidence of complex interactions between WSC content and other factors and traits, including the scale of assessment, time/degree of sward establishment and other forage quality parameters. Differences between the divergent pairs of the various populations were small. However, differences observed between the founder selection groups were maintained and the roles of the QTL regions in regulating forage WSC content were confirmed. In general, the individual divergent populations exploited only a limited extent of the large phenotypic variation available within the mapping family. However, this study sets the scene for exploring the opportunities for marker-assisted breeding strategies for complex traits in obligate out-breeding species, and the challenges of doing this are discussed.