Genomics-based approaches to improve drought tolerance of crops

The genetic bases of the molecular, cellular and developmental responses to drought involve many gene functions regulated by water availability. Genomics-based approaches provide access to agronomically desirable alleles present at quantitative trait loci (QTLs) that affect such responses, thus enabling us to improve the drought tolerance and yield of crops under water-limited conditions more effectively. Marker-assisted selection is already helping breeders improve drought-related traits. Analysis of sequence data and gene products should facilitate the identification and cloning of genes at target QTLs. Based on such premises, we envision a quick broadening of our understanding of the genetic and functional basis of drought tolerance. Novel opportunities will be generated for tailoring new genotypes "by design". Harnessing the full potential of genomics-assisted breeding will require a multidisciplinary approach and an integrated knowledge of the molecular and physiological processes influencing tolerance to drought.     

Genomics-based precision breeding approaches to improve drought tolerance in rice

Rice (Oryza sativa L.), the major staple food crop of the world, faces a severe threat from widespread drought. The development of drought-tolerant rice varieties is considered a feasible option to counteract drought stress. The screening of rice germplasm under drought and its characterization at the morphological, genetic, and molecular levels revealed the existence of genetic variation for drought tolerance within the rice gene pool. The improvements made in managed drought screening and selection for grain yield under drought have significantly contributed to progress in drought breeding programs. The availability of rice genome sequence information, genome-wide molecular markers, and low-cost genotyping platforms now makes it possible to routinely apply marker-assisted breeding approaches to improve grain yield under drought. Grain yield QTLs with a large and consistent effect under drought have been indentified and successfully pyramided in popular rice mega-varieties. Various rice functional genomics resources, databases, tools, and recent advances in “-omics” are facilitating the characterization of genes and pathways involved in drought tolerance, providing the basis for candidate gene identification and allele mining. The transgenic approach is successful in generating drought tolerance in rice under controlled conditions, but field-level testing is necessary. Genomics-assisted drought breeding approaches hold great promise, but a well-planned integration with standardized phenotyping is highly essential to exploit their full potential.     

Regulating transgenic crops sensibly: lessons from plant breeding, biotechnology and genomics

The costs of meeting regulatory requirements and market restrictions guided by regulatory criteria are substantial impediments to the commercialization of transgenic crops. Although a cautious approach may have been prudent initially, we argue that some regulatory requirements can now be modified to reduce costs and uncertainty without compromising safety. Long-accepted plant breeding methods for incorporating new diversity into crop varieties, experience from two decades of research on and commercialization of transgenic crops, and expanding knowledge of plant genome structure and dynamics all indicate that if a gene or trait is safe, the genetic engineering process itself presents little potential for unexpected consequences that would not be identified or eliminated in the variety development process before commercialization. We propose that as in conventional breeding, regulatory emphasis should be on phenotypic rather than genomic characteristics once a gene or trait has been shown to be safe.     

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.     

Challenges in pea breeding for tolerance to drought: Status and prospects

Drought is increasingly frequent in the context of climate change and is considered a major constraint for crop yield. Water scarcity can impair growth, disturb plant water relations and reduce water use efficiency. Pea (Pisum sativum) is a temperate grain legume rich in protein, fibre, micronutrients and bioactive compounds that can benefit human health. In reducing pea yield because of drought, the intensity and duration of stress are critical. This review describes several drought resistance mechanisms in pea based on morphology, physiology and biochemical changes during/after the water deficit period. Drought tolerance of pea can be managed by adopting strategies such as screening, breeding and marker-assisted selection. Therefore, various biotechnological approaches have led to the development of drought-tolerant pea cultivars. Finally, the main objective of the current research is to point out some useful traits for drought tolerance in peas and also, mention the methods that can be useful for future studies and breeding programmes.     

Molecular and physiological approaches to maize improvement for drought tolerance.

Average maize yields have increased steadily over the years in the USA and yet the variations in harvestable yield have also markedly increased. Much of the increase in yield variability can be attributed to (1) varying environmental stress conditions; (2) improved nitrogen inputs and better weed control; and (3) continuing sensitivity of different maize lines to the variation in input supply, especially rainfall. Drought stress alone can account for a significant percentage of average yield losses. Yet despite variable environments, new commercially available maize hybrids continue to be produced each year with ever-increasing harvestable yield. Since many factors contribute to high plant performance under water deficits, efforts are being made to elucidate the nature of water-stress tolerance in an attempt to improve maize hybrids further. Such factors include better partitioning of biomass to the developing ear resulting in faster spikelet growth and improved reproductive success. An emphasis on faster spikelet growth rate may result in a reduction in the number of spikelets formed on the ear that facilitates overall seed set by reducing water and carbon constraints per spikelet. To understand the molecular mechanisms for drought tolerance in improved maize lines better, a variety of genomic tools are being used. Newer molecular markers and comprehensive gene expression profiling methods provide opportunities to direct the continued breeding of genotypes that provide stable grain yield under widely varied environmental conditions.     

Multi-parent populations in crops: a toolbox integrating genomics and genetic mapping with breeding

Crop populations derived from experimental crosses enable the genetic dissection of complex traits and support modern plant breeding. Among these, multi-parent populations now play a central role. By mixing and recombining the genomes of multiple founders, multi-parent populations combine many commonly sought beneficial properties of genetic mapping populations. For example, they have high power and resolution for mapping quantitative trait loci, high genetic diversity and minimal population structure. Many multi-parent populations have been constructed in crop species, and their inbred germplasm and associated phenotypic and genotypic data serve as enduring resources. Their utility has grown from being a tool for mapping quantitative trait loci to a means of providing germplasm for breeding programmes. Genomics approaches, including de novo genome assemblies and gene annotations for the population founders, have allowed the imputation of rich sequence information into the descendent population, expanding the breadth of research and breeding applications of multi-parent populations. Here, we report recent successes from crop multi-parent populations in crops. We also propose an ideal genotypic, phenotypic and germplasm ‘package’ that multi-parent populations should feature to optimise their use as powerful community resources for crop research, development and breeding.Subject terms: Plant genetics, Plant breeding, Agricultural genetics, Quantitative trait

Over recent years, numerous multi-parent populations (MPPs) have been successfully developed in crops (Huang et al. 2015; Cockram and Mackay 2018). MPPs bring together key genomic, phenotypic and germplasm resources to form a platform for research and development. In this review, we examine three themes covering new developments in crop MPP research: (1) we survey the rapidly expanding variety of crop MPPs, explaining how differences in their design and construction affect their power and precision in mapping quantitative trait loci (QTL), on which we provide a brief primer. (2) We review the use of genomic technologies in MPPs, which have proven particularly suitable for gathering dense genomic information across large populations. We make general recommendations for collecting genotypic resources in MPPs. (3) We discuss successful applications of MPPs, particularly where they have been used for breeding and pre-breeding. This includes the identification of QTL, the application of genomic prediction to MPPs, and the direct use of MPP lines as germplasm for varietal release or pre-breeding. These recent developments have shown the potential of MPPs for crop improvement.     

Efficiency of physiological trait-based and empirical selection approaches for drought tolerance in groundnut

Drought is the major abiotic constraint affecting groundnut productivity and quality worldwide. Most breeding programmes in groundnut follow an empirical approach to drought resistance breeding, largely based on kernel yield and traits of local adaptation, resulting in slow progress. Recent advances in the use of easily measurable surrogates for complex physiological traits associated with drought tolerance encouraged breeders to integrate these in their selection schemes. However, there has been no direct comparison of the relative efficiency of a physiological trait‐based selection approach (Tr) vis‐à‐vis an empirical approach (E) to ascertain the benefits of the former. The genetic material used in the present study originated from three common crosses and one institute‐specific cross from four collaborating institutes in India (total seven crosses). Each institute contributed six genotypes and each followed both the Tr and E selection approaches in each cross. The field trial of all selections, consisting of 192 genotypes (96 each Tr and E selections), was grown in 2000/2001 in a 4 × 48 alpha design in 12 season × location environments in India. The selection efficiency of Tr relative to E, RE_Tr, was estimated using the genetic concept of response to selection. Based on all the 12 environments, the two selection methods performed more or less similarly (RE_Tr= 1.045). When the 12 environments were grouped into rainy season and post‐rainy season, the relative response to selection in Tr method was higher in the rainy than in the post‐rainy season (RE_Tr= 1.220 vs 0.657) due to a higher genetic variance, lower G × E, and high h². When the 12 environments were classified into four clusters based on plant extractable soil‐water availability, the selection method Tr was superior to E in three of the four clusters (RE_Tr= 1.495, 0.612, 1.308, and 1.144) due to an increase in genetic variance and h² under Tr in clustered environments. Although the crosses exhibited significant differences for kernel yield, the two methods of selection did not interact significantly with crosses. Both methods contributed more or less equally to the 10 highest‐yielding selections (six for E and four for Tr). The six E selections had a higher kernel yield, higher transpiration (T), and nearly equal transpiration efficiency (TE) and harvest index (HI) relative to four Tr selections. The yield advantage in E selections came largely from greater T, which would likely not be an advantage in water‐deficient environments. From the results of these multi‐environment studies, it is evident that Tr method did not show a consistent superiority over E method of drought resistance breeding in producing a higher kernel yield in groundnut. Nonetheless, the integration of physiological traits (or their surrogates) in the selection scheme would be advantageous in selecting genotypes which are more efficient water utilisers or partitioners of photosynthates into economic yield. New biotechnological tools are being explored to increase efficiency of physiological trait‐based drought resistance breeding in groundnut.     

园艺植物水分胁迫生理及耐旱机制研究进展

概述了园艺植物在水分胁迫下的生理生化,分子反应及耐旱机制研究进展,并指出尚需进一步研究的问题。     

Arguments for the use of physiological criteria for improving the salt tolerance in crops

Efforts to develop new crop varieties with improved salt tolerance have been intensified over the past 15–20 years. Despite the existence of genetic variation for salt tolerance within species, and many methods available for expanding the source of genetic variation, there is only a limited number of varieties that have been developed with improved tolerance. These new varieties have all been based upon selection for agronomic characters such as yield or survival in saline conditions. That is, based upon characters that integrate the various physiological mechanisms responsible for tolerance. Yet over the same time period, knowledge of physiological salt responses has increased substantially.Selection and breeding to increase salt tolerance might be more successful if selection is based directly on the physiological mechanisms or characters conferring tolerance. Basic questions associated with using physiological selection criteria are discussed in the paper. These are centred around the need for genetic variation, the importance of the targeted mechanism, the ease of detection of the physiological mechanism (including the analytical requirements) and the breeding strategy. Many mechanisms, including ion exclusion, ion accumulation, compatible solute production and osmotic adjustment have been associated with genetic variation in salt tolerance. Yet their successful use in improving salt tolerance, via physiological selection criteria, is largely non-existent. Consideration is given to the role of physiological criteria in the short and long term in improving salt tolerance. In several glycophytic species, particularly legumes, physiological selection based on ion exclusion from the shoots shows promise. Recent results for white clover indicate the potential for using a broad physiological selection criterion of restricted Cl accumulation in the shoots, with scope for future refinement based upon the specific physiological characters that combined result in ion exclusion.     

Advances in rice breeding,genetics and genomics

Molecular Breeding -     

Yield-trait performance landscapes: from theory to application in breeding maize for drought tolerance

The effectiveness of breeding strategies to increase drought resistance in crops could be increased further if some of the complexities in gene-to-phenotype (G → P) relations associated with epistasis, pleiotropy, and genotype-by-environment interactions could be captured in realistic G → P models, and represented in a quantitative manner useful for selection. This paper outlines a promising methodology. First, the concept of landscapes was extended from the study of fitness landscapes used in evolutionary genetics to the characterization of yield-trait-performance landscapes for agricultural environments and applications in plant breeding. Second, the E(NK) model of trait genetic architecture was extended to incorporate biophysical, physiological, and statistical components. Third, a graphical representation is proposed to visualize the yield-trait performance landscape concept for use in selection decisions. The methodology was demonstrated at a particular stage of a maize breeding programme with the objective of improving the drought tolerance of maize hybrids for the US Western Corn-Belt. The application of the framework to the genetic improvement of drought tolerance in maize supported selection of Doubled Haploid (DH) lines with improved levels of drought tolerance based on physiological genetic knowledge, prediction of test-cross yield within the target population of environments, and their predicted potential to sustain further genetic progress with additional cycles of selection. The existence of rugged yield-performance landscapes with multiple peaks and intervening valleys of lower performance, as shown in this study, supports the proposition that phenotyping strategies, and the directions emphasized in genomic selection can be improved by creating knowledge of the topology of yield-trait performance landscapes.     

Metabolite database for root,tuber, and banana crops to facilitate modern breeding in understudied crops

Roots, tubers, and bananas (RTB) are vital staples for food security in the world's poorest nations. A major constraint to current RTB breeding programmes is limited knowledge on the available diversity due to lack of efficient germplasm characterization and structure. In recent years large‐scale efforts have begun to elucidate the genetic and phenotypic diversity of germplasm collections and populations and, yet, biochemical measurements have often been overlooked despite metabolite composition being directly associated with agronomic and consumer traits. Here we present a compound database and concentration range for metabolites detected in the major RTB crops: banana (Musa spp.), cassava (Manihot esculenta), potato (Solanum tuberosum), sweet potato (Ipomoea batatas), and yam (Dioscorea spp.), following metabolomics‐based diversity screening of global collections held within the CGIAR institutes. The dataset including 711 chemical features provides a valuable resource regarding the comparative biochemical composition of each RTB crop and highlights the potential diversity available for incorporation into crop improvement programmes. Particularly, the tropical crops cassava, sweet potato and banana displayed more complex compositional metabolite profiles with representations of up to 22 chemical classes (unknowns excluded) than that of potato, for which only metabolites from 10 chemical classes were detected. Additionally, over 20% of biochemical signatures remained unidentified for every crop analyzed. Integration of metabolomics with the on‐going genomic and phenotypic studies will enhance ’omics‐wide associations of molecular signatures with agronomic and consumer traits via easily quantifiable biochemical markers to aid gene discovery and functional characterization.     

Dose-dependent response of Trichoderma harzianum in improving drought tolerance in rice genotypes

Planta - This study demonstrates a dose-dependent response of Trichoderma harzianum Th-56 in improving drought tolerance in rice by modulating proline, SOD, lipid peroxidation product and DHN / AQU...