International Center for Agricultural Research in the Dry Areas

Abstract Food security concerns and the scarcity of new productive land have put productivity enhancement of degraded lands back on the political agenda. In such a context, salt‐affected lands are a valuable resource that cannot be neglected nor easily abandoned even with their lower crop yields, especially in areas where significant investments have already been made in irrigation and drainage infrastructure. A review of previous studies shows a very limited number of highly variable estimates of the costs of salt‐induced land degradation combined with methodological and contextual differences. Simple extrapolation suggests that the global annual cost of salt‐induced land degradation in irrigated areas could be US $ 27.3 billion because of lost crop production. We present selected case studies that highlight the potential for economic and environmental benefits of taking action to remediate salt‐affected lands. The findings indicate that it can be cost‐effective to invest in sustainable land management in countries confronting salt‐induced land degradation. Such investments in effective remediation of salt‐affected lands should form part of a broader strategy for food security and be defined in national action plans. This broader strategy is required to ensure the identification and effective removal of barriers to the adoption of sustainable land management, such as perverse subsidies. Whereas reversing salt‐induced land degradation would require several years, interim salinity management strategies could provide a pathway for effective remediation and further showcase the importance of reversing land degradation and the rewards of investing in sustainable land management.

Drought tolerance is a key trait for increasing and stabilizing barley productivity in dry areas worldwide. Identification of the genes responsible for drought tolerance in barley (Hordeum vulgare L.) will facilitate understanding of the molecular mechanisms of drought tolerance, and also facilitate the genetic improvement of barley through marker-assisted selection or gene transformation. To monitor the changes in gene expression at the transcriptional level in barley leaves during the reproductive stage under drought conditions, the 22K Affymetrix Barley 1 microarray was used to screen two drought-tolerant barley genotypes, Martin and Hordeum spontaneum 41-1 (HS41-1), and one drought-sensitive genotype Moroc9-75. Seventeen genes were expressed exclusively in the two drought-tolerant genotypes under drought stress, and their encoded proteins may play significant roles in enhancing drought tolerance through controlling stomatal closure via carbon metabolism (NADP malic enzyme, NADP-ME, and pyruvate dehydrogenase, PDH), synthesizing the osmoprotectant glycine-betaine (C-4 sterol methyl oxidase, CSMO), generating protectants against reactive-oxygen-species scavenging (aldehyde dehydrogenase,ALDH, ascorbate-dependent oxidoreductase, ADOR), and stabilizing membranes and proteins (heat-shock protein 17.8, HSP17.8, and dehydrin 3, DHN3). Moreover, 17 genes were abundantly expressed in Martin and HS41-1 compared with Moroc9-75 under both drought and control conditions. These genes were possibly constitutively expressed in drought-tolerant genotypes. Among them, seven known annotated genes might enhance drought tolerance through signalling [such as calcium-dependent protein kinase (CDPK) and membrane steroid binding protein (MSBP)], anti-senescence (G2 pea dark accumulated protein, GDA2), and detoxification (glutathione S-transferase, GST) pathways. In addition, 18 genes, including those encoding Delta(l)-pyrroline-5-carboxylate synthetase (P5CS), protein phosphatase 2C-like protein (PP2C), and several chaperones, were differentially expressed in all genotypes under drought; thus they were more likely to be general drought-responsive genes in barley. These results could provide new insights into further understanding of drought-tolerance mechanisms in barley.

SUMMARY Climate change is now unequivocal, particularly in terms of increasing temperature, increasing CO 2 concentration, widespread melting of snow and ice and rising global average sea level, while the increase in the frequency of drought is very probable but not as certain. However, climate changes are not new and some of them have had dramatic impacts, such as the appearance of leaves about 400 million years ago as a response to a drastic decrease in CO 2 concentration, the birth of agriculture due to the end of the last ice age about 11 000 years ago and the collapse of civilizations due to the late Holocene droughts between 5000 and 1000 years ago. The climate changes that are occurring at present will have – and are already having – an adverse effect on food production and food quality with the poorest farmers and the poorest countries most at risk. The adverse effect is a consequence of the expected or probable increased frequency of some abiotic stresses such as heat and drought, and of the increased frequency of biotic stresses (pests and diseases). In addition, climate change is also expected to cause losses of biodiversity, mainly in more marginal environments. Plant breeding has addressed both abiotic and biotic stresses. Strategies of adaptation to climate changes may include a more accurate matching of phenology to moisture availability using photoperiod-temperature response, increased access to a suite of varieties with different duration to escape or avoid predictable occurrences of stress at critical periods in crop life cycles, improved water use efficiency and a re-emphasis on population breeding in the form of evolutionary participatory plant breeding to provide a buffer against increasing unpredictability. ICARDA, in collaboration with scientists in Iran, Algeria, Jordan, Eritrea and Morocco, has recently started evolutionary participatory programmes for barley and durum wheat. These measures will go hand in hand with breeding for resistance to biotic stresses and with an efficient system of variety delivery to farmers.

Grain yield is a major goal for the improvement of durum wheat, particularly in drought-prone areas. In this study, the genetic basis of grain yield (GY), heading date (HD), and plant height (PH) was investigated in a durum wheat population of 249 recombinant inbred lines evaluated in 16 environments (10 rainfed and 6 irrigated) characterized by a broad range of water availability and GY (from 5.6 to 58.8 q ha(-1)). Among the 16 quantitative trait loci (QTL) that affected GY, two major QTL on chromosomes 2BL and 3BS showed significant effects in 8 and 7 environments, with R2 values of 21.5 and 13.8% (mean data of all 16 environments), respectively. In both cases, extensive overlap was observed between the LOD profiles of GY and PH, but not with those for HD. QTL specific for PH were identified on chromosomes 1BS, 3AL, and 7AS. Additionally, three major QTL for HD on chromosomes 2AS, 2BL, and 7BS showed limited or no effects on GY. For both PH and GY, notable epistasis between the chromosome 2BL and 3BS QTL was detected across several environments.

Summary Farming systems in west Asia and north Africa have evolved to cope with the problems of highly variable and, frequently, chronically deficient rainfall. Cereals (mainly wheat and barley) are the dominant arable crops with food legumes (chickpea, lentil and faba bean) occupying only 5 to 10% of the area planted to cereals. Livestock is closely integrated into the farming system and crop production practices often reflect the importance of animals as a major source of income, particularly on the smaller farms. Soils of the region are predominantly calcareous, frequently phosphate deficient, and their depth and texture are important in determining the maximum amount of water that can be stored which, in turn, may determine the effective length of the growing season. Rain falls mainly during the winter months so that crops must often rely on stored soil moisture when they are growing most rapidly. Analysis of equations relating crop growth and water use shows that there are three ways in which the ‘water use efficiency’ of dry matter production can be increased. First, the amount of dry matter produced per unit of water transpired might be increased; second, if the water supply is limited, the amount of water transpired might be increased relative to evaporation from the soil surface; and third, the total amount of water used might be increased to produce extra growth provided that this results in increased transpiration rather than simply increasing evaporation from the soil surface. These three possible routes to increased crop growth are reviewed in relation to possible improvements in water management and crop genotypes in the Mediterranean environment. Scope for improving transpiration efficiency is limited although genotypic differences exist and may be useful in the future. More immediately, changes in crop management, such as applications of fertilizer, improved tillage and better weed control, will all increase the amount of water transpired. Application of mulches will also reduce evaporation from the soil surface but crop residues are usually eaten by livestock and are, therefore, often unavailable. The barley/livestock farming system of west Asia is used as a case study to illustrate how the Fanning Systems Programme of ICARDA has developed on-farm research programmes of direct relevance to current farming systems. Research on experimental sites directed at improving water use efficiency has been developed into on-farm trials and into collaborative trials with the Syrian Soils Directorate.

Stem rust, caused by Puccinia graminis f. sp. tritici, historically was one of the most destructive diseases of wheat and barley. The disease has been under effective control worldwide through the widespread use of host resistance. A number of stem rust resistance genes in wheat have been characterized for their reactions to specific races of P. graminis f. sp. tritici. Adult plant responses to race TTKS (also known as Ug99) of monogenic lines for Sr genes, a direct measurement of the effectiveness for a given gene, have not been investigated to any extent. This report summarizes adult plant infection responses and seedling infection types for monogenic lines of designated Sr genes challenged with race TTKS. High infection types at the seedling stage and susceptible infection responses in adult plants were observed on monogenic lines carrying Sr5, 6, 7a, 7b, 8a, 8b, 9a, 9b, 9d, 9g, 10, 11, 12, 15, 16, 17, 18, 19, 20, 23, 30, 31, 34, 38, and Wld-1. Monogenic lines of resistance genes Sr13, 22, 24, 25, 26, 27, 28, 32, 33, 35, 36, 37, 39, 40, 44, Tmp, and Tt-3 were effective against TTKS both at the seedling and adult plant stages. The low infection types to race TTKS observed for these resistance genes corresponded to the expected low infections of these genes to other incompatible races of P. graminis f. sp. tritici. The level of resistance conferred by these genes at the adult plant stage varied between highly resistant to moderately susceptible. The results from this study were inconclusive for determining the effectiveness of resistance genes Sr9e, 14, 21, and 29 against race TTKS. The understanding of the effectiveness of individual Sr genes against race TTKS will facilitate the utilization of these genes in breeding for stem rust resistance in wheat.

Abstract Recent trends and future demographic projections suggest that the need to produce more food and fibre will necessitate effective utilization of salt‐affected land and saline water resources. Currently at least 20 per cent of the world's irrigated land is salt affected and/or irrigated with waters containing elevated levels of salts. Several major irrigation schemes have suffered from the problems of salinity and sodicity, reducing their agricultural productivity and sustainability. Productivity enhancement of salt‐affected land and saline water resources through crop‐based management has the potential to transform them from environmental burdens into economic opportunities. Research efforts have led to the identification of a number of field crops, forage grasses and shrubs, aromatic and medicinal species, bio‐fuel crops, and fruit tree and agroforestry systems, which are profitable and suit a variety of salt‐affected environments. Several of these species have agricultural significance in terms of their local utilization on the farm. Therefore, crop diversification systems based on salt‐tolerant plant species are likely to be the key to future agricultural and economic growth in regions where salt‐affected soils exist, saline drainage waters are generated, and/or saline aquifers are pumped for irrigation. However, such systems will need to consider three issues: improving the productivity per unit of salt‐affected land and saline water resources, protecting the environment and involving farmers in the most suitable and sustainable crop diversifying systems to mitigate any perceived risks. This review covers different aspects of salt‐affected land and saline water resources, synthesizes research knowledge on salinity/sodicity tolerances in different plant species, and highlights promising examples of crop diversification and management to improve and maximize benefits from these resources. Copyright © 2008 John Wiley & Sons, Ltd.

Abstract Mediterranean-type soils generally have free CaCO3, high pH, and low organic matter. Consequently, nutrient disorders in these soils are the most important limiting factor to crop production, second only to moisture stress. Major problems are deficiencies of nitrogen and phosphorus; however, recent research has revealed that micronutrient problems are also hampering crop production. Unlike major nutrient deficiencies, micronutrient problems are highly genotype-specific and location-specific. Zinc (Zn) deficiency is the most widespread problem, because of factors like alkaline soil pH, calcareousness, low organic matter, exposed subsoils, Zn-free fertilizers, and/or flooding-induced electro-chemical changes. Now zinc sulfate is commonly used in rice, wheat, barley, potato, citrus, deciduous fruits, and many other crops. Soil-applied Zn has a relatively long residual effect. Efforts are also underway to develop crop varieties for higher Zn efficiency. Iron (Fe) chlorosis, the second most important micronutrient disorder, is induced by high soil in calcareous soils; high moisture and cold temperature accentuate it. Legumes, citrus, and deciduous fruits are more susceptible. Soil fertilization for iron is problematic; therefore, foliar feeding or breeding for tolerance remains the practical solutions. Boron (B) is a nonmetal micronutrient. While B deficiency has not been observed widely, research in the recent past has revealed this to be a widespread problem in crops like cotton, rapeseed, wheat, peanut, sorghum, and rice. The deficiency can be corrected by its soil application or by foliar feeding. As the concentration range between B deficiency and toxicity is exceptionally narrow, both are field-scale problems in the Mediterranean-type soils. Unlike B deficiency, B toxicity diagnosis is not simple, because of its accumulation in sub soils and resemblance of the symptoms with leaf fungal diseases. Also, B toxicity cannot be ameliorated for all practical purposes. Thus, breeding for B tolerance remains the only option. Luckily, many landraces of barley and wheat are quite tolerant to B toxicity. Deficiencies of manganese (Mn) and copper (Cu) are not a perceived problem, and availability of molybdenum (Mo) and chloride (Cl) is high in Mediterranean-type soils. Soil micronutrient deficiencies not only reduce crop productivity, but low Zn and Fe plant food is also adversely affecting human health and well-being. Though fertilizer use for micronutrients is highly cost-effective, actual use remains rather limited to a few specific crops in various countries. Thus, micronutrient problems are likely to be accentuated because of increased pressure on soil resources.

Abstract Low‐input production of barley on the predominantly calcareous soils in most countries of West Asia and North Africa is affected by drought and a low availability of P and Zn. Especially during the early growth stages, P and Zn deficiencies retard seedling growth, rendering the young plantlets particularly sensitive to the frequently encountered dry spells. Seed priming (soaking in water and drying back to storage moisture until use) has been shown to improve crop establishment and, in some instances, to increase crop yields. While increased seedling vigor will improve barley establishment, possible benefits are likely to be limited when P and Zn are deficient. A promising variation of the priming concept is the seed treatment with solutions containing the limiting nutrient. A series of experiments was conducted in a phytotron in 2003 to develop a nutrient‐priming approach to foster the establishment of barley under marginal growing conditions. Seeds of the traditional barley cultivar Arabi aswad were soaked for 0–48 hours in water and for 12 hours in solutions containing 5–500 mM P, Zn, and P+Zn, and dried back to 12% moisture until further use. Seeds were incubated at 10°C, and germination was evaluated over a 6‐ to 8‐day period. Additionally, growth and nutrient uptake of 4‐week‐old seedlings, grown at 25% and 100% field capacity in a typical Xerosol from Syria were evaluated. Water priming for 12 hours with subsequent seed storage of up to 9 weeks increased germination rate from 65% to 95%, and advanced germination by up to 3 days compared to unprimed seeds. Addition of 10 mM Zn and 50 mM P to the priming solution increased the P and Zn content of the seeds without affecting germination. It furthermore significantly stimulated growth and P and Zn uptake by 4‐week‐old seedlings and improved the water use efficiency of drought‐stressed plants by 44% above that of unprimed seeds.

Predicting yield is increasingly important to optimize irrigation under limited available water for enhanced sustainability and profitable production. Food and Agriculture Organization (FAO) of the United Nations addresses this need by providing a yield response to water simulation model (AquaCrop) with limited sophistication. In this study, AquaCrop was parameterized and tested for cotton ( Gossypium hirsutum L.) under full (100%) and deficit (40, 60, and 80% of full) irrigation regimes in the hot, dry, and windy Mediterranean environment of northern Syria. Model parameterization used the 2006 data and was straightforward within the designed user‐interface, owing to the limited number of key parameters. Accurate simulation of canopy cover was central to sound prediction of evapotranspiration and biomass accumulation. Key user‐input parameters for this purpose were identified as the coefficients defining canopy development and the threshold soil water depletion levels for the water stress indices. The parameterized model was tested using data from the 2004 and 2005 seasons, resulting in accurate prediction of evapotranspiration (<13% error). The predicted yield values were within 10% of measurements, except in the 60 and 80% irrigation regimes in 2004, with errors up to 32%. The model closely predicted the trend in total soil water, but deviation existed for individual soil layers. This study provides first estimate values for cotton parameters useful for future model testing and use. Model parameterization is site‐specific, and thus the applicability of key calibrated parameters must to be tested under different climate, soil, variety, irrigation methods, and field management.

Abstract Rust fungi can overcome the effect of host resistance genes rapidly, and spores can disperse long distance by wind. Here we demonstrate a foreign incursion of similar strains of the wheat yellow rust fungus, Puccinia striiformis f. sp. tritici , in North America, Australia and Europe in less than 3 years. One strain defined by identity at 15 virulence loci and 130 amplified fragment length polymorphism (AFLP) fragments was exclusive to North America (present since 2000) and Australia (since 2002). Another strain of the same virulence phenotype, but differing in two AFLP fragments, was exclusive to Europe (present since 2000–2001) as well as Western and Central Asia and the Red Sea Area (first appearance unknown). This may be the most rapid spread of an important crop pathogen on the global scale. The limited divergence between the two strains and their derivatives, and the temporal–spatial occurrence pattern confirmed a recent spread. The data gave evidence for additional intercontinental dispersal events in the past, that is, many isolates sampled before 2000 in Europe, North America and Australia had similar AFLP fingerprints, and isolates from South Africa, which showed no divergence in AFLP, differed by only two fragments from particular isolates from Central Asia, West Asia and South Europe, respectively. Previous research has demonstrated that isolates of the two new strains produced up to two to three times more spores per day than strains found in USA and Europe before 2000, suggesting that increased aggressiveness at this level may accelerate global spread of crop pathogens.

The PREDICTS project-Projecting Responses of Ecological Diversity In Changing Terrestrial Systems (www.predicts.org.uk)-has collated from published studies a large, reasonably representative database of comparable samples of biodiversity from multiple sites that differ in the nature or intensity of human impacts relating to land use. We have used this evidence base to develop global and regional statistical models of how local biodiversity responds to these measures. We describe and make freely available this 2016 release of the database, containing more than 3.2 million records sampled at over 26,000 locations and representing over 47,000 species. We outline how the database can help in answering a range of questions in ecology and conservation biology. To our knowledge, this is the largest and most geographically and taxonomically representative database of spatial comparisons of biodiversity that has been collated to date; it will be useful to researchers and international efforts wishing to model and understand the global status of biodiversity.

Ascochyta blight (AB), caused by Ascochyta rabiei is a major disease of chickpea (Cicer arietinum L.), especially in areas where cool, cloudy, and humid weather persists during the crop season. Several epidemics of AB causing complete yield loss have been reported. The fungus mainly survives between seasons through infected seed and in infected crop debris. Despite extensive pathological and molecular studies, the nature and extent of pathogenic variability in A. rabiei have not been clearly established. Accumulation of phenols, phytoalexins (medicarpin and maackiain), and hydrolytic enzymes has been associated with host-plant resistance (HPR). Seed treatment and foliar application of fungicides are commonly recommended for AB management, but further information on biology and survival of A. rabiei is needed to devise more effective management strategies. Recent studies on inheritance of AB resistance indicate that several quantitative trait loci (QTLs) control resistance. In this paper we review the biology of A. rabiei, HPR, and management options, with an emphasis on future research priorities.

Abstract Currently at least 20 per cent of the world's irrigated land is salt‐affected. However, projections of global population growth, and of an increased demand for food and fibre, suggest that larger areas of salt‐affected soil will need to be cropped in the future. About 60 per cent of salt‐affected soils are sodic, and much of this land is farmed by smallholders. Ameliorating such soils requires the application of a source of calcium (Ca 2+ ), which replaces excess sodium (Na + ) at the cation exchange sites. The displaced Na + is then leached from the root zone through excess irrigation, a process that requires adequate flows of water through the soil. However, it must now be recognized that we can no longer conduct sodic soil amelioration and management solely with the aim of achieving high levels of crop productivity. The economic, social, and environmental impacts of different soil‐amelioration options must also be considered. A holistic approach is therefore needed. This should consider the cost and availability of the inputs needed for amelioration, the soil depth, the level to which sodicity needs to be reduced to allow cropping, the volume and quality of drainage water generated during amelioration, and the options available for drainage‐water disposal or reuse. The quality and cost of water available for post‐amelioration crops, and the economic value of the crops grown during and after amelioration should also be taken into account, as should farmers' livelihoods, the environmental implications of amelioration (such as carbon sequestration), and the long‐term sustainable use of the ameliorated site (in terms of productivity and market value). Consideration of these factors, with the participation of key stakeholders, could sustainably improve sodic soil productivity and help to transform such soils into a useful economic resource. Such an approach would also aid environmental conservation, by minimizing the chances of secondary sodicity developing in soils, particularly under irrigated agriculture. Copyright © 2006 John Wiley & Sons, Ltd.

BACKGROUND: Drought is the major constraint to increase yield in chickpea (Cicer arietinum). Improving drought tolerance is therefore of outmost importance for breeding. However, the complexity of the trait allowed only marginal progress. A solution to the current stagnation is expected from innovative molecular tools such as transcriptome analyses providing insight into stress-related gene activity, which combined with molecular markers and expression (e)QTL mapping, may accelerate knowledge-based breeding. SuperSAGE, an improved version of the serial analysis of gene expression (SAGE) technique, generating genome-wide, high-quality transcription profiles from any eukaryote, has been employed in the present study. The method produces 26 bp long fragments (26 bp tags) from defined positions in cDNAs, providing sufficient sequence information to unambiguously characterize the mRNAs. Further, SuperSAGE tags may be immediately used to produce microarrays and probes for real-time-PCR, thereby overcoming the lack of genomic tools in non-model organisms. RESULTS: We applied SuperSAGE to the analysis of gene expression in chickpea roots in response to drought. To this end, we sequenced 80,238 26 bp tags representing 17,493 unique transcripts (UniTags) from drought-stressed and non-stressed control roots. A total of 7,532 (43%) UniTags were more than 2.7-fold differentially expressed, and 880 (5.0%) were regulated more than 8-fold upon stress. Their large size enabled the unambiguous annotation of 3,858 (22%) UniTags to genes or proteins in public data bases and thus to stress-response processes. We designed a microarray carrying 3,000 of these 26 bp tags. The chip data confirmed 79% of the tag-based results, whereas RT-PCR confirmed the SuperSAGE data in all cases. CONCLUSION: This study represents the most comprehensive analysis of the drought-response transcriptome of chickpea available to date. It demonstrates that--inter alias--signal transduction, transcription regulation, osmolyte accumulation, and ROS scavenging undergo strong transcriptional remodelling in chickpea roots already 6 h after drought stress. Certain transcript isoforms characterizing these processes are potential targets for breeding for drought tolerance. We demonstrate that these can be easily accessed by micro-arrays and RT-PCR assays readily produced downstream of SuperSAGE. Our study proves that SuperSAGE owns potential for molecular breeding also in non-model crops.

The continuous improvement of crop plants is essential for agriculture in the coming decades and relies on the use of genetic variability through breeding. However, domestication and modern breeding have reduced diversity in the crop germplasm. Global gene banks conserve diversity, but these resources remain underexplored owing to a lack of efficient strategies to isolate important alleles. Here we describe a large-scale allele-mining project at the molecular level. We first selected a set of 1,320 bread wheat landraces from a database of 16,089 accessions, using the focused identification of germplasm strategy. On the basis of a hierarchical selection procedure on this set, we then isolated 7 resistance alleles of the powdery mildew resistance gene Pm3, doubling the known functional allelic diversity at this locus. This targeted approach for molecular utilization of gene bank accessions reveals landraces as a rich resource of new functional alleles. This strategy can be implemented for other studies on the molecular diversity of agriculturally important genes, as well as for molecular breeding.

Soil salinity is an ever-increasing constraint to crop productivity worldwide especially in countries with irrigated agriculture. In contrast to all the soil reclamation strategies to decrease salt concentrations in root zone, the use of sodium (Na+) in plant nutrition may be an interesting tactic. The roles of potassium (K+) and Na+ in plant nutrition suggest that K+ is the only monovalent cation which is essential for most higher plants and is involved in three important functions, i.e., enzyme activation, charge balance and osmoregulation. Plants need a small amount but high concentration of K+ for specific functions in the cytoplasm and a major portion (∼90%) of it is localized in vacuoles, where it acts as an osmoticum. Maintenance of osmotic potential in vacuoles, a nonspecific function of K+, can be achieved by other cations such as Na+. For decades an ample amount of work has been done on the substitution of K+ by Na+ in plant nutrition. In this regard, Na+ has the potential to replace K+ for some of its functions. In some plants, supplementation of Na+ in reduced amounts can eliminate K+ deficiency symptoms under limited K+ supply. Thus, the question of K+ substitution by Na+ in plant physiology is not only of academic interest but has considerable practical implications in relation to fertilizer management and plant growth in salt-affected environments. In this review, we discuss the possibilities of K+ substitution by Na+ under specific soil and environmental conditions.

Drought is the major constraint to rice production in rainfed areas across Asia and sub-Saharan Africa. In the context of current and predicted water scarcity, increasing irrigation is generally not a viable option for alleviating drought problems in rainfed rice-growing systems. It is therefore critical that genetic management strategies for drought focus on maximum extraction of available soil moisture and its efficient use in crop establishment and growth to maximize biomass and yield. Extensive genetic variation for drought resistance exists in rice germplasm. However, the current challenge is to decipher the complexities of drought resistance in rice and exploit all available genetic resources to produce rice varieties combining drought adaptation with high yield potential, quality, and resistance to biotic stresses. The strategy described here aims at developing a pipeline for elite breeding lines and hybrids that can be integrated with efficient management practices and delivered to rice farmers. This involves the development of high-throughput, high-precision phenotyping systems to allow genes for yield components under stress to be efficiently mapped and their effects assessed on a range of drought-related traits, and then moving the most promising genes into widely grown rice mega-varieties, while scaling up gene detection and delivery for use in marker-aided breeding.

BACKGROUND: Plant genetic resources (PGR) are the basic raw materials for future genetic progress and an insurance against unforeseen threats to agricultural production. An extensive characterization of PGR provides an opportunity to dissect structure, mine allelic variations, and identify diverse accessions for crop improvement. The Generation Challenge Program http://www.generationcp.org conceptualized the development of "composite collections" and extraction of "reference sets" from these for more efficient tapping of global crop-related genetic resources. In this study, we report the genetic structure, diversity and allelic richness in a composite collection of chickpea using SSR markers, and formation of a reference set of 300 accessions. RESULTS: The 48 SSR markers detected 1683 alleles in 2915 accessions, of which, 935 were considered rare, 720 common and 28 most frequent. The alleles per locus ranged from 14 to 67, averaged 35, and the polymorphic information content was from 0.467 to 0.974, averaged 0.854. Marker polymorphism varied between groups of accessions in the composite collection and reference set. A number of group-specific alleles were detected: 104 in Kabuli, 297 in desi, and 69 in wild Cicer; 114 each in Mediterranean and West Asia (WA), 117 in South and South East Asia (SSEA), and 10 in African region accessions. Desi and kabuli shared 436 alleles, while wild Cicer shared 17 and 16 alleles with desi and kabuli, respectively. The accessions from SSEA and WA shared 74 alleles, while those from Mediterranean 38 and 33 alleles with WA and SSEA, respectively. Desi chickpea contained a higher proportion of rare alleles (53%) than kabuli (46%), while wild Cicer accessions were devoid of rare alleles. A genotype-based reference set captured 1315 (78%) of the 1683 composite collection alleles of which 463 were rare, 826 common, and 26 the most frequent alleles. The neighbour-joining tree diagram of this reference set represents diversity from all directions of the tree diagram of the composite collection. CONCLUSION: The genotype-based reference set, reported here, is an ideal set of germplasm for allele mining, association genetics, mapping and cloning gene(s), and in applied breeding for the development of broad-based elite breeding lines/cultivars with superior yield and enhanced adaptation to diverse environments.

A large number of vegetation indices have been developed and widely applied in terrestrial ecosystem research in the recent decades. However, a certain limitation was observed while applying these indices in research in dry areas due to their low sensitivity to low vegetation cover. In this context, the objectives of this study are to develop a new vegetation index, namely, the Generalized Difference Vegetation Index (GDVI), and to examine its applicability to the assessment of dryland environment. Based on the field investigation and crop Leaf Area Index (LAI) measurement, five spring and summer Landsat TM and ETM+ images in the frame with Path/Row number of 174/35, and MODIS (Moderate Resolution Imaging Spectroradiometer) LAI and vegetation indices (VIs) data (MOD15A2 and MOD13Q1), of the same acquisition dates as the Landsat images, were acquired and employed in this study. The results reveal that, despite the same level of correlation with the fractional vegetation cover (FVC) as other VIs, GDVI shows a better correlation with LAI and has higher sensitivity and dynamic range in the low vegetal land cover than other vegetation indices, e.g., the range of GDVI is higher than Normalized Difference Vegetation Index (NDVI),Soil-Adjusted Vegetation Index (SAVI), Enhanced Vegetation Index (EVI), Wide Dynamic Range Vegetation Index (WDRVI), and Soil-Adjusted and Atmospherically Resistant Vegetation Index (SARVI), by 164%–326% in woodland, 185%–720% in olive plantation, and 190%–867% in rangeland. It is, hence, concluded that GDVI is relevant for, and has great potential in, land characterization, as well as land degradation/desertification assessment in dryland environment.