In pursuit of a better world: crop improvement and the CGIAR.

The CGIAR crop improvement (CI) programs, unlike commercial CI programs, which are mainly geared to profit though meeting farmers' needs, are charged with meeting multiple objectives with target populations that include both farmers and the community at large. We compiled the opinions from >30 experts in the private and public sector on key strategies, methodologies, and activities that could the help CGIAR meet the challenges of providing farmers with improved varieties while simultaneously meeting the goals of: (i) nutrition, health, and food security; (ii) poverty reduction, livelihoods, and jobs; (iii) gender equality, youth, and inclusion; (iv) climate adaptation and mitigation; and (v) environmental health and biodiversity. We review the crop improvement processes starting with crop choice, moving through to breeding objectives, production of potential new varieties, selection, and finally adoption by farmers. The importance of multidisciplinary teams working towards common objectives is stressed as a key factor to success. The role of the distinct disciplines, actors, and their interactions throughout the process from crop choice through to adoption by farmers is discussed and illustrated.

Evolutionary Plant Breeding as a Response to the Complexity of Climate Change.

Climate change is one of the processes that have already overstepped the safe planetary boundaries, together with the rate of biodiversity loss and human interference with the nitrogen and phosphorus cycles. The three processes are related to agriculture and, as such, to both food safety and food security, and ultimately to human health. Adaptation to climate change is a difficult breeding objective because of its complexity, its unpredictability, and its location specificity. However, one strategy exists, which is based on a more dynamic use of agrobiodiversity in agriculture through the cultivation of evolutionary populations. In this review, we show how the translation into agricultural practice of nearly 100 years of research on evolutionary populations and mixtures is able to address the complexity of climate change while stabilizing yield, decreasing the use of most agrochemicals, thus reducing emissions and producing healthy food.

The increased use of diversity in cereal cropping requires more descriptive precision.

BACKGROUND: Until 100 years ago, cereals were grown only as populations with varying amounts of genetic diversity both within and among different crops. However, since the nineteenth century, methods for isolating and reproducing monocultural varieties have become universal, particularly among larger producers, leading to widespread within-field genetic monotony. A range of approaches is now being used to increase genetic diversity within and among crops including bringing back into cultivation a range of populations using a variety of different names, such as old varieties, landraces, ancient grains, heritage varieties, heirloom varieties, and mixtures. The objective of this paper, which is the result of the First International Conference on Landraces (Bologna, July 2018), is to contribute to the more precise definition of the names that are used more frequently. RESULTS: One early approach to increasing diversity among such monocultures was the use of variety mixtures, initially using static mixtures, meaning mixtures that were re-constituted from their original component varieties for each growing season. Some farmers, however, preferred to re-grow static mixtures from the harvested, and therefore selected, seed, thus converting them to what can be termed dynamic mixtures. Consequent natural inter-crossing within such dynamic mixtures means that, within a few seasons, following natural segregation, recombination and selection, they become populations. There is a wide body of literature on both static and dynamic mixtures, the discussion of which is beyond the scope of this paper. More recently, interest has been increasing in modern forms of evolutionary breeding of populations through direct hybridization of monocultural varieties followed by segregation and, commonly, natural selection, often in target production areas. As expected from evolutionary theory, such populations exhibit considerable resilience under variable environmental conditions, which is increasingly important in relation to the complexity of climate change. CONCLUSION: To help identify different approaches, and communicate information, definitions can be based on the approximate known historical age of the plant material in question and its genetic structure. © 2019 Society of Chemical Industry.

Diversifying Food Systems in the Pursuit of Sustainable Food Production and Healthy Diets.

Increasing demand for nutritious, safe, and healthy food because of a growing population, and the pledge to maintain biodiversity and other resources, pose a major challenge to agriculture that is already threatened by a changing climate. Diverse and healthy diets, largely based on plant-derived food, may reduce diet-related illnesses. Investments in plant sciences will be necessary to design diverse cropping systems balancing productivity, sustainability, and nutritional quality. Cultivar diversity and nutritional quality are crucial. We call for better cooperation between food and medical scientists, food sector industries, breeders, and farmers to develop diversified and nutritious cultivars that reduce soil degradation and dependence on external inputs, such as fertilizers and pesticides, and to increase adaptation to climate change and resistance to emerging pests.

Landrace Germplasm for Improving Yield and Abiotic Stress Adaptation.

Plant landraces represent heterogeneous, local adaptations of domesticated species, and thereby provide genetic resources that meet current and new challenges for farming in stressful environments. These local ecotypes can show variable phenology and low-to-moderate edible yield, but are often highly nutritious. The main contributions of landraces to plant breeding have been traits for more efficient nutrient uptake and utilization, as well as useful genes for adaptation to stressful environments such as water stress, salinity, and high temperatures. We propose that a systematic landrace evaluation may define patterns of diversity, which will facilitate identifying alleles for enhancing yield and abiotic stress adaptation, thus raising the productivity and stability of staple crops in vulnerable environments.

Analysis of >1000 single nucleotide polymorphisms in geographically matched samples of landrace and wild barley indicates secondary contact and chromosome-level differences in diversity around domestication genes.

Barley is a model species for the investigation of the evolution, adaptation and spread of the world's important crops. In this article, we describe the first application of an oligonucleotide pool assay single nucleotide polymorphism (SNP) platform to assess the evolution of barley in a portion of the Fertile Crescent, a key region in the development of farming. A large collection of >1000 genetically mapped, genome-wide SNPs was assayed in geographically matched landrace and wild barley accessions (N=448) from Jordan and Syria. Landrace and wild barley categories were clearly genetically differentiated, but a limited degree of secondary contact was evident. Significant chromosome-level differences in diversity between barley types were observed around genes known to be involved in the evolution of cultivars. The region of Jordan and southern Syria, compared with the north of Syria, was supported by SNP data as a more likely domestication origin. Our data provide evidence for hybridization as a possible mechanism for the continued adaptation of landrace barley under cultivation, indicate regions of the genome that may be subject to selection processes and suggest limited origins for the development of the cultivated crop.

Differentially expressed genes between drought-tolerant and drought-sensitive barley genotypes in response to drought stress during the reproductive stage.

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.

Asymmetric allele-specific expression in relation to developmental variation and drought stress in barley hybrids.

In the present study, we analysed allele-specific expression (ASE) in the selfing species barley to assess the frequency of cis-acting regulatory variation and the effects of genetic background, developmental differences and drought stress on allelic expression levels. We measured ASE ratios in 30 genes putatively involved in stress responses in five hybrids and their reciprocals, namely Hordeum spontaneum 41-1/Alexis (HAl), Hordeum spontaneum 41-1/Arta (HAr), Sloop/WI3408 (SW), Tadmor/Sloop (TS) and Tadmor/WI3408 (TW). In order to detect cis-acting variation related to drought and developmental changes, the barley hybrids were grown under control and water-limited conditions, and leaf tissue was harvested at two developmental stages. The analysis demonstrated that more than half of the genes measured (63%) showed allelic differences in expression of up to 19-fold due to cis-regulatory variation in at least one cross by treatment/stage combination. Drought stress induced changes in allelic expression ratios, indicating differences between drought responsive cis-elements. In addition, ASE differences between developmental stages suggested the presence of cis-acting elements interacting with developmental cues. We were also able to demonstrate that the levels and frequency of allelic imbalance and hence differences in cis-regulatory elements are correlated with the genetic divergence between the parental lines, but may also arise as an adaptation to diverse habitats. Our findings suggest that cis-regulatory variation is a common phenomenon in barley, and may provide a molecular basis of transgression. Differential expression of near-isogenic members of the same gene family could potentially result in hybrid lines out performing their parents in terms of expression level, timing and response to developmental and environmental cues. Identification and targeted manipulation of cis-regulatory elements will assist in breeding improved crops with a better adaptation to changing environments.

Genetic diversity and association analysis for salinity tolerance, heading date and plant height of barley germplasm using simple sequence repeat markers.

The objective of this study was to investigate the genetic diversity of barley accessions. Additionally, association trait analysis was conducted for grain yield under salinity, heading date and plant height. For this purpose, 48 barley genotypes were analyzed with 22 microsatellite simple sequence repeat (SSR) markers. Four of the 22 markers (Bmac316, scssr03907, HVM67 and Bmag770) were able to differentiate all barley genotypes. Cluster and principal coordinate analysis allowed a clear grouping between countries from the same region. The genotypes used in this study have been evaluated for agronomic performance in different environments. Conducting association analysis for grain yield under salinity conditions using TASSEL software revealed a close association of the marker Bmag749 (2H, bin 13) in two different environments with common significant alleles (175, 177), whereas the HVHOTR1 marker (2H, bin 3) was only significant in Sakhar_Egypt with alleles size being 158 and 161. Heading date also showed an association with scssr03907 through the common significant specific allele 111 and EBmac0415 markers in three different agro climatic locations, whereas HVCMA, scssr00103 and HVM67 were linked to heading date in the Egyptian environment only. The plant height association analysis revealed significant markers Bmag770 via the significant allele 152 and scssr09398.

Differential Selection on Rhynchosporium secalis During Parasitic and Saprophytic Phases in the Barley Scald Disease Cycle.

ABSTRACT Competition among eight Rhynchosporium secalis isolates was assessed during parasitic and saprophytic phases of the disease cycle in field experiments conducted at two locations and over two growing seasons. The eight isolates were inoculated onto six barley populations exhibiting varying degrees of resistance. Microsatellite analysis of 2,866 isolates recovered from the field experiments showed significant, and sometimes opposite, changes in the frequencies of R. secalis genotypes during the growing season (parasitic phase) and between growing seasons (saprophytic phase). Isolates that showed the most complex virulence in greenhouse seedling assays had the lowest fitness in the field experiment. Significant differences in isolate fitness were found on different host populations and in different environments. Selection coefficients were large, indicating that evolution can occur rapidly in field populations. Although inoculated isolates had the lowest overall fitness on the moderately resistant landrace cv. Arabi Aswad, some isolates were more virulent and consistently increased in frequency on this landrace, suggesting a risk of directional selection and possible erosion of the resistance following its widespread deployment in monoculture. These results provide the first direct evidence that R. secalis pathogen genotypes differ in their saprophytic ability and parasitic fitness under field conditions.