Exploiting genetic diversity from landraces in wheat breeding for adaptation to climate change

Identification of Quantitative Trait Loci Associated with Plant Adaptation Traits Using Nested Association Mapping Population

This study evaluated 290 recombinant inbred lines (RILs) of the nested association mapping (NAM) population from the UK. The population derived from 24 families, where a common parent was "Paragon," one of the UK's spring wheat cultivar standards. All genotypes were tested in two regions of Kazakhstan at the Kazakh Research Institute of Agriculture and Plant Industry (KRIAPI, Almaty region, Southeast Kazakhstan, 2019-2022 years) and Alexandr Barayev Scientific-Production Center for Grain Farming (SPCGF, Shortandy, Akmola region, Northern Kazakhstan, 2019-2022 years). The studied traits consisted of plant adaptation-related traits, including heading date (HD, days), seed maturation date (SMD, days), plant height (PH, cm), and peduncle length (PL, cm). In addition, the yield per m2 was analyzed in both regions. Based on a field evaluation of the population in northern and southeastern Kazakhstan and using 10,448 polymorphic SNP (single-nucleotide polymorphism) markers, the genome-wide association study (GWAS) allowed for detecting 74 QTLs in four studied agronomic traits (HD, SMD, PH, and PL). The literature survey suggested that 16 of the 74 QTLs identified in our study had also been detected in previous QTL mapping studies and GWASs for all studied traits. The results will be used for further studies related to the adaptation and productivity of wheat in breeding projects for higher grain productivity.

Halophytes and heavy metals: A multi-omics approach to understand the role of gene and genome duplication in the abiotic stress tolerance of Cakile maritima

PREMISE

The origin of diversity is a fundamental biological question. Gene duplications are one mechanism that provides raw material for the emergence of novel traits, but evolutionary outcomes depend on which genes are retained and how they become functionalized. Yet, following different duplication types (polyploidy and tandem duplication), the events driving gene retention and functionalization remain poorly understood. Here we used Cakile maritima, a species that is tolerant to salt and heavy metals and shares an ancient whole-genome triplication with closely related salt-sensitive mustard crops (Brassica), as a model to explore the evolution of abiotic stress tolerance following polyploidy.

METHODS

Using a combination of ionomics, free amino acid profiling, and comparative genomics, we characterize aspects of salt stress response in C. maritima and identify retained duplicate genes that have likely enabled adaptation to salt and mild levels of cadmium.

RESULTS

Cakile maritima is tolerant to both cadmium and salt treatments through uptake of cadmium in the roots. Proline constitutes greater than 30% of the free amino acid pool in C. maritima and likely contributes to abiotic stress tolerance. We find duplicated gene families are enriched in metabolic and transport processes and identify key transport genes that may be involved in C. maritima abiotic stress tolerance.

CONCLUSIONS

These findings identify pathways and genes that could be used to enhance plant resilience and provide a putative understanding of the roles of duplication types and retention on the evolution of abiotic stress response.

Genetic diversity and population structure of wheat landraces in Southern Winter Wheat Region of China

BACKGROUND

Wheat landraces are considered a valuable source of genetic diversity for breeding programs. It is useful to evaluate the genetic diversity in breeding studies such as marker-assisted selection (MAS), genome-wide association studies (GWAS), and genomic selection. In addition, constructing a core germplasm set that represents the genetic diversity of the entire variety set is of great significance for the efficient conservation and utilization of wheat landrace germplasms.

RESULTS

To understand the genetic diversity in wheat landrace, 2,023 accessions in the Jiangsu Provincial Crop Germplasm Resource Bank were used to explore the molecular diversity and population structure using the Illumina 15 K single nucleotide polymorphism (SNP) chip. These accessions were divided into five subpopulations based on population structure, principal coordinate and kinship analysis. A significant variation was found within and among the subpopulations based on the molecular variance analysis (AMOVA). Subpopulation 3 showed more genetic variability based on the different allelic patterns (Na, Ne and I). The M strategy as implemented in MStratv 4.1 software was used to construct the representative core collection. A core collection with a total of 311 accessions (15.37%) was selected from the entire landrace germplasm based on genotype and 12 different phenotypic traits. Compared to the initial landrace collections, the core collection displayed higher gene diversity (0.31) and polymorphism information content (PIC) (0.25), and represented almost all phenotypic variation.

CONCLUSIONS

A core collection comprising 311 accessions containing 100% of the genetic variation in the initial population was developed. This collection provides a germplasm base for effective management, conservation, and utilization of the variation in the original set.

Floods and droughts research progress and its contributions toward sustainability

In 2015, the United Nations General Assembly launched seventeen Sustainable Development Goals (SDGs), aimed at being achieved by 2030. The SDGs 6 (clean water & sanitation) and 13 (climate actions) are two critically important goals concerning water resources that need to be addressed. This study used the Scopus database to explore climate extremes, specifically droughts and floods, in East Asia and highlight the region's efforts and contributions towards achieving SDGs 6 and 13. We found that even before the implementation of SDGs, the topics related to solving the problems of water resources, water quality, and treatment of wastewater using different conceptual models and methodologies were the main concerns in the region. The adoption of SDGs has led to a heightened focus on water and climate sustainability in East Asia, with the considerable surge in climate-related studies after 2019. Under SDG 13, all countries have contributed substantially to climate action research. Keyword analysis indicates that climate change, water management, water treatment, water quality, and adsorption remain prominent. SDGs 6 and 13 have emerged as crucial areas of focus for research and initiatives as the global community grapples with escalating water resources and climate challenges. Under specific keywords search, China has 2nd place in the search with climate and water during the SDGs period, accounting for 21 % of the entire publication from 2015 to 2023. Japan and South Korea account for of 4 % and 3 %, respectively. The research on floods and droughts has garnered significant attention, with half of the ten highly co-cited literature examining the changing pattern of drought, the influence of extreme events on crop yield, and other related topics. Despite the positive contribution of the East Asia region towards SDGs 6 and 13, there is still an urgent need for a more robust framework to improve the complex interconnections between climate actions, clean water, and sanitation for a sustainable soil-water-plant-atmosphere ecosystem.

Transcriptome variations in hybrids of wild emmer wheat (Triticum turgidum ssp. dicoccoides)

BACKGROUND

Wild emmer wheat is a great candidate to revitalize domesticated wheat genetic diversity. Recent years have seen intensive investigation into the evolution and domestication of wild emmer wheat, including whole-genome DNA and transcriptome sequencing. However, the impact of intraspecific hybridization on the transcriptome of wild emmer wheat has been poorly studied. In this study, we assessed changes in methylation patterns and transcriptomic variations in two accessions of wild emmer wheat collected from two marginal populations, Mt. Hermon and Mt. Amasa, and in their stable F4 hybrid.

RESULTS

Methylation-Sensitive Amplified Polymorphism (MSAP) detected significant cytosine demethylation in F4 hybrids vs. parental lines, suggesting potential transcriptome variation. After a detailed analysis, we examined nine RNA-Seq samples, which included three biological replicates from the F4 hybrid and its parental lines. RNA-Seq databases contained approximately 200 million reads, with each library consisting of 15 to 25 million reads. There are a total of 62,490 well-annotated genes in these databases, with 6,602 genes showing differential expression between F4 hybrid and parental lines Mt. Hermon and Mt. Amasa. The differentially expressed genes were classified into four main categories based on their expression patterns. Gene ontology (GO) analysis revealed that differentially expressed genes are associated with DNA/RNA metabolism, photosynthesis, stress response, phosphorylation and developmental processes.

CONCLUSION

This study highlights the significant transcriptomic changes resulting from intraspecific hybridization within natural plant populations, which might aid the nascent hybrid in adapting to various environmental conditions.

Future of durum wheat research and breeding: Insights from early career researchers

Durum wheat (Triticum turgidum ssp. durum) is globally cultivated for pasta, couscous, and bulgur production. With the changing climate and growing world population, the need to significantly increase durum production to meet the anticipated demand is paramount. This review summarizes recent advancements in durum research, encompassing the exploitation of existing and novel genetic diversity, exploration of potential new diversity sources, breeding for climate-resilient varieties, enhancements in production and management practices, and the utilization of modern technologies in breeding and cultivar development. In comparison to bread wheat (T. aestivum), the durum wheat community and production area are considerably smaller, often comprising many small-family farmers, notably in African and Asian countries. Public breeding programs such as the International Maize and Wheat Improvement Center (CIMMYT) and the International Center for Agricultural Research in the Dry Areas (ICARDA) play a pivotal role in providing new and adapted cultivars for these small-scale growers. We spotlight the contributions of these and others in this review. Additionally, we offer our recommendations on key areas for the durum research community to explore in addressing the challenges posed by climate change while striving to enhance durum production and sustainability. As part of the Wheat Initiative, the Expert Working Group on Durum Wheat Genomics and Breeding recognizes the significance of collaborative efforts in advancing toward a shared objective. We hope the insights presented in this review stimulate future research and deliberations on the trajectory for durum wheat genomics and breeding.

Plant responses to co-occurring heat and water deficit stress: A comparative study of tolerance mechanisms in old and modern wheat genotypes

Global climate change increases the likelihood of co-occurrence of hot and dry spells with increased intensity, frequency, and duration. Studying the impact of the two stresses provide a better understanding of tolerance mechanisms in wheat, and our study was focused on revealing plant stress responses to different severities of combined stress at two phenophases in old and modern wheat genotypes. During the stem elongation and anthesis stages, plants were exposed to four treatments: control, deficit irrigation, combined heat, and deficit irrigation at 31 °C (HD31) and 37 °C (HD37). The modern genotypes were less affected by deficit irrigation at stem elongation as they maintained higher photosynthesis, stomatal conductance, and leaf cooling than old genotypes. When the HD37 stress was imposed during anthesis, the modern genotypes exhibited superior performance compared to the old, which was due to their higher photosynthetic rates resulting from improved biochemical regulation and a higher chlorophyll content. The plant responses varied during two phenophases under the combined stress exposure. Genotypes subjected to HD37 stress during stem elongation, photosynthesis was mainly controlled by stomatal regulation, whereas at anthesis it was predominated by biochemical regulation. These findings contribute to a deeper comprehension of plant tolerance mechanisms in response to different intensities of co-occurring hot and dry weather conditions.

A diverse panel of 755 bread wheat accessions harbors untapped genetic diversity in landraces and reveals novel genetic regions conferring powdery mildew resistance

KEY MESSAGE

A bread wheat panel reveals rich genetic diversity in Turkish, Pakistani and Iranian landraces and novel resistance loci to diverse powdery mildew isolates via subsetting approaches in association studies. Wheat breeding for disease resistance relies on the availability and use of diverse genetic resources. More than 800,000 wheat accessions are globally conserved in gene banks, but they are mostly uncharacterized for the presence of resistance genes and their potential for agriculture. Based on the selective reduction of previously assembled collections for allele mining for disease resistance, we assembled a trait-customized panel of 755 geographically diverse bread wheat accessions with a focus on landraces, called the LandracePLUS panel. Population structure analysis of this panel based on the TaBW35K SNP array revealed an increased genetic diversity compared to 632 landraces genotyped in an earlier study and 17 high-quality sequenced wheat accessions. The additional genetic diversity found here mostly originated from Turkish, Iranian and Pakistani landraces. We characterized the LandracePLUS panel for resistance to ten diverse isolates of the fungal pathogen powdery mildew. Performing genome-wide association studies and dividing the panel further by a targeted subsetting approach for accessions of distinct geographical origin, we detected several known and already cloned genes, including the Pm2a gene. In addition, we identified 22 putatively novel powdery mildew resistance loci that represent useful sources for resistance breeding and for research on the mildew-wheat pathosystem. Our study shows the value of assembling trait-customized collections and utilizing a diverse range of pathogen races to detect novel loci. It further highlights the importance of integrating landraces of different geographical origins into future diversity studies.

Exploitation of the Genetic Variability of Diverse Metric Traits of Durum Wheat (Triticum turgidum L. ssp. durum Desf.) Cultivars for Local Adaptation to Semi-Arid Regions of Algeria

Abiotic stresses pose significant challenges to wheat farming, yet exploiting the genetic variability within germplasm collections offers an opportunity to effectively address these challenges. In this study, we investigated the genetic diversity of key agronomic traits among twenty durum wheat cultivars, with the intention to pinpoint those better suited to semi-arid conditions. Field trials were conducted at the ITGC-FDPS Institute, Setif, Algeria, during the winter season of 2021/22. A completely randomized design was used with three replicates. Statistical analyses revealed significant variation among the genotypes for most of the studied traits, with some cultivars exhibiting a superior performance in a stressful environment. Notably, traits like the number of grains per spike (NGS) and the grain yield (GY) displayed high genotypic coefficients of variation (CVg). Except for membrane thermostability (MT) and biological yield (BY), the majority of the assessed traits exhibited moderate-to-high heritability estimates. Genotypic and phenotypic correlation studies have confirmed the importance of many yield-related traits in the expression of GY. The harvest index (HI) underscored the highest genotypic direct effect on GY, followed closely by spike number (SN), serving as consistent pathways through which most of the measured traits indirectly influenced GY. The cluster analysis categorized the durum wheat cultivars into seven distinct clusters. The largest inter-cluster distance was observed between clusters G3 and G4 (D2 = 6145.86), reflecting maximum dissimilarity between the individuals of these clusters. Hybridizing divergent clusters may benefit future breeding programs aiming to develop potential durum wheat varieties through cross combinations. This study's findings contribute to sustainable agriculture efforts by facilitating the selection of genotypes with enhanced resilience and productivity, particularly for cultivation in challenging semi-arid regions.

Characterization among and within Sicilian Tetraploid Wheat Landraces by Gluten Protein Analysis for Traceability Purposes

The criteria of "Distinctness, Uniformity and Stability" as well as a high "overall quality index" are used to register the Italian modern varieties to the national register. Differently, local conservation varieties can be certified under different EU Directives that facilitate, as an overall objective, the preservation of biodiversity and the containment of genetic erosion. In recent years, products derived from ancient grains are perceived to be healthier and more sustainable by consumers, especially in Italy, with consequent higher market prices. The ancient tetraploid wheat varieties registered in the national register of conservation varieties amount to 28, 24 of which are Sicilian. They are supposed to have wide genetic variability compared to modern ones, making them vulnerable to fraud because they are difficult to trace. It is therefore important to have tools able to discriminate between autochthonous Sicilian varieties. This can be completed by gluten proteins composition, which also provides information on the technological properties of derived products. Fifty-one accessions belonging to twenty-two ancient varieties of Sicilian tetraploid (mostly durum) wheat were analyzed. Although wide intra-accession and intra-varietal variability measurements were assessed, the gliadin pattern of bulks of seeds belonging to each variety was discriminatory. Moreover, differences in technological attitudes were found between landraces. This paves the way to use gluten protein patterns for traceability, allowing local farmers and producers to valorize their products and assure consumers regarding the transparency of the entire supply chain.

Heat and Wheat: Adaptation strategies with respect to heat shock proteins and antioxidant potential; an era of climate change

Extreme changes in weather including heat-wave and high-temperature fluctuations are predicted to increase in intensity and duration due to climate change. Wheat being a major staple crop is under severe threat of heat stress especially during the grain-filling stage. Widespread food insecurity underscores the critical need to comprehend crop responses to forthcoming climatic shifts, pivotal for devising adaptive strategies ensuring sustainable crop productivity. This review addresses insights concerning antioxidant, physiological, molecular impacts, tolerance mechanisms, and nanotechnology-based strategies and how wheat copes with heat stress at the reproductive stage. In this study stress resilience strategies were documented for sustainable grain production under heat stress at reproductive stage. Additionally, the mechanisms of heat resilience including gene expression, nanomaterials that trigger transcription factors, (HSPs) during stress, and physiological and antioxidant traits were explored. The most reliable method to improve plant resilience to heat stress must include nano-biotechnology-based strategies, such as the adoption of nano-fertilizers in climate-smart practices and the use of advanced molecular approaches. Notably, the novel resistance genes through advanced molecular approach and nanomaterials exhibit promise for incorporation into wheat cultivars, conferring resilience against imminent adverse environmental conditions. This review will help scientific communities in thermo-tolerance wheat cultivars and new emerging strategies to mitigate the deleterious impact of heat stress.

Whole-genome sequencing of diverse wheat accessions uncovers genetic changes during modern breeding in China and the United States

Breeding has dramatically changed the plant architecture of wheat (Triticum aestivum), resulting in the development of high-yielding varieties adapted to modern farming systems. However, how wheat breeding shaped the genomic architecture of this crop remains poorly understood. Here, we performed a comprehensive comparative analysis of a whole-genome resequencing panel of 355 common wheat accessions (representing diverse landraces and modern cultivars from China and the United States) at the phenotypic and genomic levels. The genetic diversity of modern wheat cultivars was clearly reduced compared to landraces. Consistent with these genetic changes, most phenotypes of cultivars from China and the United States were significantly altered. Of the 21 agronomic traits investigated, 8 showed convergent changes between the 2 countries. Moreover, of the 207 loci associated with these 21 traits, more than half overlapped with genomic regions that showed evidence of selection. The distribution of selected loci between the Chinese and American cultivars suggests that breeding for increased productivity in these 2 regions was accomplished by pyramiding both shared and region-specific variants. This work provides a framework to understand the genetic architecture of the adaptation of wheat to diverse agricultural production environments, as well as guidelines for optimizing breeding strategies to design better wheat varieties.

Genome wide association in Spanish bread wheat landraces identifies six key genomic regions that constitute potential targets for improving grain yield related traits

KEY MESSAGE

Association mapping conducted in 189 Spanish bread wheat landraces revealed six key genomic regions that constitute stable QTLs for yield and include 15 candidate genes. Genetically diverse landraces provide an ideal population to conduct association analysis. In this study, association mapping was conducted in a collection of 189 Spanish bread wheat landraces whose genomic diversity had been previously assessed. These genomic data were combined with characterization for yield-related traits, including grain size and shape, and phenological traits screened across five seasons. The association analysis revealed a total of 881 significant marker trait associations, involving 434 markers across the genome, that could be grouped in 366 QTLs based on linkage disequilibrium. After accounting for days to heading, we defined 33 high density QTL genomic regions associated to at least four traits. Considering the importance of detecting stable QTLs, 6 regions associated to several grain traits and thousand kernel weight in at least three environments were selected as the most promising ones to harbour targets for breeding. To dissect the genetic cause of the observed associations, we studied the function and in silico expression of the 413 genes located inside these six regions. This identified 15 candidate genes that provide a starting point for future analysis aimed at the identification and validation of wheat yield related genes.

Acceleration of wheat breeding: enhancing efficiency and practical application of the speed breeding system

BACKGROUND

Crop breeding should be accelerated to address global warming and climate change. Wheat (Triticum aestivum L.) is a major food crop. Speed breeding (SB) and speed vernalization (SV) techniques for spring and winter wheat have recently been established. However, there are few practical examples of these strategies being used economically and efficiently in breeding programs. We aimed to establish and evaluate the performance of a breeder-friendly and energy-saving generation acceleration system by modifying the SV + SB system.

RESULTS

In this study, a four-generation advancement system for wheat (regardless of its growth habits) was established and evaluated using an energy-efficient extended photoperiod treatment. A glasshouse with a 22-hour photoperiod that used 10 h of natural sunlight and 12 h of LED lights, and minimized temperature control during the winter season, was successful in accelerating generation. Even with one or two field tests, modified speed breeding (mSB) combined with a speed vernalization system (SV + mSB) reduced breeding time by more than half compared to traditional field-based methods. When compared to the existing SV + SB system, the SV + mSB system reduced energy use by 80% to maintain a 22-hour photoperiod. Significant correlations were found between the SV + mSB and field conditions in the number of days to heading (DTH) and culm length (CL). Genetic resources, recombinant inbred lines, and breeding materials that exhibited shorter DTH and CL values under SV + mSB conditions showed the same pattern in the field.

CONCLUSIONS

The results of our SV + mSB model, as well as its practical application in wheat breeding programs, are expected to help breeders worldwide incorporate generation acceleration systems into their conventional breeding programs.

Do diverse wheat genotypes unleash their biochemical arsenal differentially to conquer cold stress? A comprehensive study in the Western Himalayas

Wheat is one of the most important cereal crops in the world. Cold stress is a major constraint in production of wheat grown in cold climate regions. In this study, we conducted a comprehensive assessment of cold stress tolerance in wheat genotypes through field screening, cell membrane stability through electrolyte leakage assay and biochemical profiling. A core set comprising 4560 genotypes was evaluated for two years (2021-2022), revealing substantial genetic variation for cold stress tolerance. Most genotypes exhibited moderate tolerance, while a smaller proportion showed susceptibility to cold stress. Based on the cold screening data in the field, a mini-core set of 350 genotypes was selected for membrane stability analysis using electrical conductivity assays. Significant differences were observed in membrane stability among the genotypes, indicating the presence of genetic variation for this trait. Furthermore, a mini-core set was narrowed down to 50 diverse candidate genotypes that were subsequently profiled for various biochemicals, including reactive oxygen species (ROS) like lipid peroxidation (MDA) and hydrogen peroxide (H2 02 ), osmoprotectant (proline) and enzymatic antioxidants including ascorbate peroxidase (APX), superoxide dismutase (SOD), guaiacol peroxidase (GPX), and catalase (CAT). Correlation analysis of the biochemicals revealed negative associations between antioxidants and reactive oxygen species (ROS), highlighting their role in mitigating oxidative damage under cold stress. This study enhances our understanding of the physiological and biochemical mechanisms underlying cold stress tolerance in wheat. The identified genotypes with superior cold stress tolerance can serve as valuable genetic resources for wheat breeding.

Genome-wide association analysis of tan spot disease resistance in durum wheat accessions from Tunisia

Background: Tunisia harbors a rich collection of unexploited durum wheat landraces (Triticum durum ssp. durum) that have been gradually replaced by elite cultivars since the 1970s. These landraces represent an important potential source for broadening the genetic background of elite durum wheat cultivars and for the introgression of novel genes for key traits, including disease resistance, into these cultivars. Methods: In this study, single nucleotide polymorphism (SNP) markers were used to investigate the genetic diversity and population structure of a core collection of 235 durum wheat accessions consisting mainly of landraces. The high phenotypic and genetic diversity of the fungal pathogen Pyrenophora tritici-repentis (cause of tan spot disease of wheat) in Tunisia allowed the assessment of the accessions for tan spot resistance at the adult plant stage under field conditions over three cropping seasons. A genome-wide association study (GWAS) was performed using a 90k SNP array. Results: Bayesian population structure analysis with 9191 polymorphic SNP markers classified the accessions into two groups, where groups 1 and 2 included 49.79% and 31.49% of the accessions, respectively, while the remaining 18.72% were admixtures. Principal coordinate analysis, the unweighted pair group method with arithmetic mean and the neighbor-joining method clustered the accessions into three to five groups. Analysis of molecular variance indicated that 76% of the genetic variation was among individuals and 23% was between individuals. Genome-wide association analyses identified 26 SNPs associated with tan spot resistance and explained between 8.1% to 20.2% of the phenotypic variation. The SNPs were located on chromosomes 1B (1 SNP), 2B (4 SNPs), 3A (2 SNPs), 3B (2 SNPs), 4A (2 SNPs), 4B (1 SNP), 5A (2 SNPs), 5B (4 SNPs), 6A (5 SNPs), 6B (2 SNPs), and 7B (1 SNP). Four markers, one on each of chromosomes 1B, and 5A, and two on 5B, coincided with previously reported SNPs for tan spot resistance, while the remaining SNPs were either novel markers or closely related to previously reported SNPs. Eight durum wheat accessions were identified as possible novel sources of tan spot resistance that could be introgressed into elite cultivars. Conclusion: The results highlighted the significance of chromosomes 2B, 5B, and 6A as genomic regions associated with tan spot resistance.

Genomic characterization and gene bank curation of Aegilops: the wild relatives of wheat

Genetic diversity found in crop wild relatives is critical to preserve and utilize for crop improvement to achieve sustainable food production amid climate change and increased demand. We genetically characterized a large collection of 1,041 Aegilops accessions distributed among 23 different species using more than 45K single nucleotide polymorphisms identified by genotyping-by-sequencing. The Wheat Genetics Resource Center (WGRC) Aegilops germplasm collection was curated through the identification of misclassified and redundant accessions. There were 49 misclassified and 28 sets of redundant accessions within the four diploid species. The curated germplasm sets now have improved utility for genetic studies and wheat improvement. We constructed a phylogenetic tree and principal component analysis cluster for all Aegilops species together, giving one of the most comprehensive views of Aegilops. The Sitopsis section and the U genome Aegilops clade were further scrutinized with in-depth population analysis. The genetic relatedness among the pair of Aegilops species provided strong evidence for the species evolution, speciation, and diversification. We inferred genome symbols for two species Ae. neglecta and Ae. columnaris based on the sequence read mapping and the presence of segregating loci on the pertinent genomes as well as genetic clustering. The high genetic diversity observed among Aegilops species indicated that the genus could play an even greater role in providing the critical need for untapped genetic diversity for future wheat breeding and improvement. To fully characterize these Aegilops species, there is an urgent need to generate reference assemblies for these wild wheats, especially for the polyploid Aegilops.

Differences in mucilage properties and stomatal sensitivity of locally adapted Zea mays in relation with precipitation seasonality and vapour pressure deficit regime of their native environment

With ongoing climate change and the increase in extreme weather events, especially droughts, the challenge of maintaining food security is becoming ever greater. Locally adapted landraces of crops represent a valuable source of adaptation to stressful environments. In the light of future droughts-both by altered soil water supply and increasing atmospheric water demand (vapor pressure deficit [VPD])-plants need to improve their water efficiency. To do so, plants can enhance their access to soil water by improving rhizosphere hydraulic conductivity via the exudation of mucilage. Furthermore, plants can reduce transpirational water loss via stomatal regulation. Although the role of mucilage and stomata regulation on plant water management have been extensively studied, little is known about a possible coordination between root mucilage properties and stomatal sensitivity as well as abiotic drivers shaping the development of drought resistant trait suits within landraces. Mucilage properties and stomatal sensitivity of eight Mexican landraces of Zea mays in contrast with one inbred line were first quantified under controlled conditions and second related to water demand and supply at their respective site of origin. Mucilage physical properties-namely, viscosity, contact angle, and surface tension-differed between the investigated maize varieties. We found strong influences of precipitation seasonality, thus plant water availability, on mucilage production (R 2 = .88, p < .01) and mucilage viscosity (R 2 = .93, p < .01). Further, stomatal sensitivity to increased atmospheric water demand was related to mucilage viscosity and contact angle, both of which are crucial in determining mucilage's water repellent, thus maladaptive, behavior upon soil drying. The identification of landraces with pre-adapted suitable trait sets with regard to drought resistance is of utmost importance, for example, trait combinations such as exhibited in one of the here investigated landraces. Our results suggest a strong environmental selective force of seasonality in plant water availability on mucilage properties as well as regulatory stomatal effects to avoid mucilage's maladaptive potential upon drying and likely delay critical levels of hydraulic dysfunction. By this, landraces from highly seasonal climates may exhibit beneficial mucilage and stomatal traits to prolong plant functioning under edaphic drought. These findings may help breeders to efficiently screen for local landraces with pre-adaptations to drought to ultimately increase crop yield resistance under future climatic variability.

Performance and Stability Analysis of Selected Durum Wheat Genotypes Differing in Their Kernel Characteristics

Breeding of high-yielding and stable durum wheat varieties with improved kernel characteristics is needed for dry regions around the globe. The aim of this study was to investigate the performance and stability of eight durum wheat genotypes varying in their kernel characteristics across 15 contrasting environments. The tested material included three recombinant inbred lines (NUR-072, NUR-106 and NUR-238) derived from a cross between Norsi, a Jordanian landrace with special kernel characteristics and UC1113 Yr36+Gpc-B1, an elite line from USA. Field trials were carried out for three constitutive growing seasons under rainfed conditions, except for three environments where supplementary irrigation was provided. After the harvest, grain yield (GY), total yield (TW), and harvest index (HI) were recorded. Additionally, several kernel-related traits, including thousand kernel weight (TKW), kernel area (KA), kernel width (KW), kernel length (KL), kernel circularity (KC), and kernel length-width ratio (KL:KW) were evaluated. Analysis of variance for all tested traits revealed high significant variations (p ≤ 0.01) between the genotype (except for TW) and the genotype × environment (G × E) interaction. Genotype effect contributed to substantial percentage of variation (>75%) for KA, KL, KC and KL:KW, whereas KW showed a lower percentage similar to GY. Regarding the G × E effect, explained variation was highest for the TW (67.79%), and lowest for KL (6.47%). For GY, Norsi produced significantly the lowest mean value (249.99 g.m^-2) while, Bolenga produced the highest mean value (377.85 g.m^-2) although no significant differences were observed with the remaining genotypes. On the other hand, Norsi, NUR-072 and NUR-106 showed best performance for TKW and kernel-related traits with NUR-106 producing the highest mean value for KL (9.07 mm). The GGE biplot and AMMI analysis of GY identified Bolenga, Um Qais and NUR-106 as good performers across several environments, while Norsi exhibited the poorest performance. For TKW, Norsi was the best performer across different environments followed by NUR-106, which showed excellent performance under irrigated and saline conditions. For stability analysis, NUR-106 emerged as the most stable genotype in this study for GY and several kernel-related traits, particularly for KL and KC. In conclusion, the results of this study offer valuable insights for durum wheat breeders seeking to develop high-yielding and stable varieties with special kernel characteristics suitable for cultivation in dry areas.

Sicilian Rivet Wheat Landraces: Grain Characteristics and Technological Quality of Flour and Bread

In recent years, the growth of tetraploid Sicilian wheat landraces has been arousing increasing interest. In this study, eighteen local genotypes of Triticum turgidum subsp. turgidum, belonging to the groups 'Bufala', 'Ciciredda', 'Bivona' and 'Paola', and two cultivars of Triticum turgidum subsp. durum (the old variety 'Bidì', and a more recent variety 'Simeto') were assessed for the characteristics of the grain and bread-making performance of their flours and doughs, as well as the quality of the loaves. The grain of the twenty genotypes came from a field trial conducted during 2018-2019 in south-eastern Sicily. The main commercial features of the grain (thousand kernel weight and hectolitre weight), including the defects (starchy, black pointed and shrunken kernels), were determined. The wholemeal flours and doughs obtained from the grain of each genotype were evaluated for the main technological quality (physico-chemical and rheological characteristics), and processed into loaves, whose main quality indices (volume, height, weight, moisture and porosity) were assessed. The results from such analyses allowed the authors to evaluate the genotypes' bread-making suitability. In particular, for the grain characteristics, hectolitre weight varied from 68.23 ('Bufala Rossa Lunga 01') to 77.43 ('Bidì 03') kg/hL, passing through the typical values for common and durum wheat. Among the grain defects, the black point defect was absent in all the grain samples, except for that of 'Bufala Nera Corta 01' (2%). Dry gluten content varied from 6.22 to 10.23 g/100 g, and sedimentation test values were low or medium-low, with values ranging from 22 to 35 mL. Amylase activity was low and highly variable among the genotypes, with the maximum value observed for 'Bufala Rossa Corta b01' (509 s). The doughs evidenced a poor quality for bread making with alveograph values of W ranging from 12 to 145 (10^-4 × Joule) and thus the volume of the loaves varied from 346.25 cm³ of 'Bivona' and 'Ciciredda' to 415.00 cm³ of 'Bufala Rossa Lunga'. A Tandem Cluster Analysis was conducted on a set of all the response variables. The Hierarchical Cluster Analysis was initially run. A five-cluster solution identified three clusters further segmented and two single branches. Overall, the study highlighted the possibility of using some of these landraces alone for the production of traditional breads locally appreciated or together with other ingredients for the production of crumbly baked goods such as substitutes for bread and biscuits.

Bread Wheat Landraces Adaptability to Low-Input Agriculture

Bread wheat landraces were an important source of biodiversity used in agriculture before the widespread adoption of high-yielding commercial cultivars adapted to high inputs. Could future agriculture exploit these landraces in different cropping systems in organic or lower-input environments? A two-year field trial was conducted to evaluate grain yield, agronomic performance, and grain quality of bread wheat landraces under different cropping systems, including low-input/organic/conventional environments. Significant variability was found for almost all characteristics among landraces, which makes landraces valuable sources of genetic variation for breeding programs aimed at achieving high and consistent production as well as high-quality products in low-input/organic environments. Additionally, landraces play a crucial role in expanding the genetic diversity of cultivated bread wheat and mitigating biodiversity erosion, thereby enabling crops to better withstand the challenges of low-input/organic agriculture. The landrace "Xilokastro Lamias" had the highest yield among the landraces evaluated in the first growing season (2.65 t·ha^-1) and one of the highest yields (2.52 t·ha^-1) of all genotypes in the second growing season, which shows promising potential as a starting material in breeding programs targeting high and stable yields. GGE biplot analysis identified the landrace "Xilokastro Lamias", along with commercial cultivars "Yecora E" and "Panifor", as suitable candidates for direct use in low-input/organic wheat farming systems to achieve enhanced productivity. In the conventional environment (C2-IPGRB), commercial cultivars showed the highest values (3.09 to 3.41 ton·ha^-1). Of the landraces, only the X4 showed a high GY (3.10 ton·ha^-1) while the other landraces had ~33-85% lower yield. In the organic environment (O2-IPGRB), the highest productivity was found in the commercial cultivar X5 and the landrace X4. Commercial cultivars X8 and X7 showed ~68% reduction in GY in the organic environment compared to the conventional, while this reduction was half for the landraces. Finally, the reduction in grain yield between conventional and organic environments was observed to be 45% for commercial cultivars, while it was only half for landraces. This finding confirms the adaptability of landraces to organic agriculture.

Potential for surprising heat and drought events in wheat-producing regions of USA and China

Previous analyses of the possibility of global breadbasket failures have extrapolated risks based on historical relationships between climate and yields. However, climate change is causing unprecedented events globally, which could exceed critical thresholds and reduce yields, even if there is no historical precedent. This means that we are likely underestimating climate risks to our food system. In the case of wheat, parts of the USA and China show little historical relationship between yields and temperature, but extreme temperatures are now possible that exceed critical physiological thresholds in wheat plants. UNprecedented Simulated Extreme ENsemble (UNSEEN) approaches use large ensembles to generate plausible unprecedented events, which can inform our assessment of the risk to crops. We use the UNSEEN approach with a large ensemble of archived seasonal forecasts to generate thousands of plausible events over the last 40 years and compare the results with historically observed extreme temperature and precipitation. In the US midwest, extreme temperatures that would have happened approximately 1-in-100-years in 1981 now have a return period of 1-in-6 years, while in China, the current return period is on the order of 1-in-16 years. This means that in the US midwest, extreme temperatures that used to have a 1% chance to occur in 1981 now have a 17% chance to occur in any given year, while in China, the chance increased from 1% to 6%. Record-breaking years exceeding critical thresholds for enzymes in the wheat plant are now more likely than in the past, and these record-breaking hot years are associated with extremely dry conditions in both locations. Using geopotential height and wind anomalies from the UNSEEN ensemble, we demonstrate that strong winds over land pull dry air towards the regions these during extremely hot and dry unseen events. We characterize plausible extremes from the UNSEEN ensemble that can be used to help imagine otherwise unforeseen events, including a compound event in which high impacts co-occur in both regions, informing adaptation planning in these regions. Recent temperature extremes, especially in the US midwest, are unlikely to be a good proxy for what to expect in the next few years of today's climate, and local stakeholders might perceive their risk to be lower than it really is. We find that there is a high potential for surprise in these regions if people base risk analyses solely on historical datasets.

Water stress effects on stay green and chlorophyll fluorescence with focus on yield characteristics of diverse bread wheats

MAIN CONCLUSION

The study provided an insight toward better understanding of stay-green mechanisms for drought tolerance improvement and identified that synthetic-derived wheats proved as a promising germplasm for improved tolerance against water stress. Stay-green (SG) trait is considered to be related with the ability of wheat plants to maintain photosynthesis and CO₂ assimilation. The present study explored the interaction of water stress with SG expression through physio-biochemical, agronomic and phenotypic responses among diverse wheat germplasm comprising of 200 synthetic hexaploids, 12 synthetic derivatives, 97 landraces and 16 conventional bread wheat varieties, for 2 years. The study established that variation of SG trait existed in the studied wheat germplasm and there was positive association between SG trait and tolerance to water stress. The relationship of SG trait with chlorophyll content (r = 0.97), ETR (r = 0.28), GNS (r = 0.44), BMP (r = 0.34) and GYP (r = 0.44) was particularly promising under water stress environment. Regarding chlorophyll fluorescence, the positive correlation of фPSII (r = 0.21), qP (r = 0.27) and ETR (r = 0.44) with grain yield per plant was noted. The improved ΦPSII and Fv/Fm of PSII photochemistry resulted in the high photosynthesis activity in SG wheat genotypes. Regarding relative water content and photochemical quenching coefficient, synthetic-derived wheats were better by maintaining 20.9, 9.8 and 16.1% more RWC and exhibiting 30.2, 13.5 and 17.9% more qP when compared with landraces, varieties and synthetic hexaploids, respectively, under water stress environment. Synthetic derived wheats also exhibited relatively more SG character with good yield and were more tolerant to water stress in terms of grain yield, grain weight per plant, better photosynthetic performance through chlorophyll fluorescence measurement, high leaf chlorophyll and proline content, and hence, may be used as novel sources for breeding drought tolerant materials. The study will further facilitate research on wheat leaf senescence and will add to better understanding of SG mechanisms for drought tolerance improvement.

Evaluation of antioxidant and antimicrobial activities of whole flours obtained from different species of Triticum genus

Whole wheat is an exceptional source of phenolic compounds representing a promising phytochemical class to prevent diet-related chronic diseases thanks to its antioxidant activities. The present work reports the phenolic profile, the antioxidant capacity, the antimicrobial activity and the effect on Lactobacillus brevis growth of eight whole flours obtained from four ancient and modern wheat genotypes of Italian Triticum genus. Total phenolic content (TPC) and total flavonoid content (TFC) were quantified, and antioxidant activities were assessed using oxygen radical absorbance capacity (ORAC) and 2,2-diphenyl-1-picrylhydrazyl (DPPH) in vitro tests. HPLC-DAD/FLD was used to detect the presence of phenolic compounds. Moreover, antimicrobial activity of whole flour extracts against some potentially pathogenic Gram negative and Gram positive bacteria and the effect of extracts on Lactobacillus brevis growth were assessed. Results showed quantitative differences (p < 0.05) in antioxidant activities, total phenolic content and concentrations of five phenolic acids (resorcinol, tyrosol, caffeic acid, syringic acid and ferulic acid) among the wheat genotypes. Pathogenic bacteria were significantly negatively affected by wheat extracts while the growth of L. brevis was stimulated. The principal component analysis (PCA) confirmed that the phenolic profile and the antioxidant activities were influenced by the genotypic characteristics of studied varieties, suggesting that the ancient Saragolla stand out for the most interesting phenolic profile. Overall, this research emphasizes how ancient and modern Italian Triticum spp. grains must be investigated to select the grains richer in bioactive compounds.

Graphical abstract

SNP Diversity and Genetic Structure of "Rogosija", an Old Western Balkan Durum Wheat Collection

Durum wheat landraces represent a genetic resource for the identification and isolation of new valuable genes and alleles, useful to increase the crop adaptability to climate change. Several durum wheat landraces, all denominated "Rogosija", were extensively cultivated in the Western Balkan Peninsula until the first half of the 20th century. Within the conservation program of the Montenegro Plant Gene Bank, these landraces were collected, but without being characterized. The main goal of this study was to estimate the genetic diversity of the "Rogosija collection" consisting of 89 durum accessions, using 17 morphological descriptors and the 25K Illumina single nucleotide polymorphism (SNP) array. The genetic structure analysis of the Rogosija collection showed two distinguished clusters localized in two different Montenegro eco-geographic micro-areas, characterized by continental Mediterranean climate and maritime Mediterranean climate. Data suggest that these clusters could be composed of two different Balkan durum landrace collections evolved in two different eco-geographic micro-areas. Moreover, the origin of Balkan durum landraces is discussed.

Leaf wettability and leaf angle affect air-moisture deposition in wheat for self-irrigation

BACKGROUND

Climate change and depleting water sources demand scarce natural water supplies like air moisture to be used as an irrigation water source. Wheat production is threatened by the climate variability and extremes climate events especially heat waves and drought. The present study focused to develop the wheat plant for self-irrigation through optimizing leaf architecture and surface properties for precise irrigation.

METHODS

Thirty-four genotypes were selected from 1796 genotypes with all combinations of leaf angle and leaf rolling. These genotypes were characterized for morpho-physiological traits and soil moisture content at stem-elongation and booting stages. Further, a core set of ten genotypes was evaluated for stem flow efficiency and leaf wettability.

RESULTS

Biplot, heat map, and correlation analysis indicated wide diversity and traits association. The environmental parameters indicated substantial amount of air moisture (> 60% relative humidity) at the critical wheat growth stages. Leaf angle showed negative association with leaf rolling, physiological and yield traits, adaxial and abaxial contact angle while leaf angle showed positive association with the stem flow water. The wettability and air moisture harvesting indicated that the genotypes (coded as 1, 7, and 18) having semi-erect to erect leaf angle, spiral rolling, and hydrophilic leaf surface (<90^o) with contact angle hysteresis less than 10^o had higher soil moisture content (6-8%) and moisture harvesting efficiency (3.5 ml).

CONCLUSIONS

These findings can provide the basis to develop self-irrigating, drought-tolerant wheat cultivars as an adaptation to climate change.

Uncovering the genetic basis for quality traits in the Mediterranean old wheat germplasm and phenotypic and genomic prediction assessment by cross-validation test

The release of new wheat varieties is based on two main characteristics, grain yield and quality, to meet the consumer's demand. Identifying the genetic architecture for yield and key quality traits has wide attention for genetic improvement to meet the global requirement. In this sense, the use of landraces represents an impressive source of natural allelic variation. In this study, a genome-wide association analysis (GWAS) with PCA and kinship matrix was performed to detect QTLs in bread wheat for fifteen quality and agronomic traits using 170 diverse landraces from 24 Mediterranean countries in two years of field trials. A total of 53 QTL hotspots containing 165 significant marker-trait associations (MTAs) were located across the genome for quality and agronomical traits except for chromosome 2D. The major specific QTL hotspots for quality traits were QTL_3B.3 (13 MTAs with a mean PVE of 8.2%) and QTL_4A.3 (15 MTAs, mean PVE of 11.0%), and for yield-related traits were QTL_2B.1 (8 MTAs, mean PVE of 7.4%) and QTL_4B.2 (5 MTAs, mean PVE of 10.0%). A search for candidate genes (CG) identified 807 gene models within the QTL hotspots. Ten of these CGs were expressed specifically in grain supporting the role of identified QTLs in Landraces, associated to bread wheat quality traits and grain formation. A cross-validation approach within the collection was performed to calculate the accuracies of genomic prediction for quality and agronomical traits, ranging from -0.03 to 0.64 for quality and 0.46 to 0.65 for agronomic traits. In addition, five prediction equations using the phenotypic data were developed to predict bread loaf volume in landraces. The prediction ability varied from 0.67 to 0.82 depending on the complexity of the traits considered to predict loaf volume.

Genetic approaches to exploit landraces for improvement of Triticum turgidum ssp. durum in the age of climate change

Addressing the challenges of climate change and durum wheat production is becoming an important driver for food and nutrition security in the Mediterranean area, where are located the major producing countries (Italy, Spain, France, Greece, Morocco, Algeria, Tunisia, Turkey, and Syria). One of the emergent strategies, to cope with durum wheat adaptation, is the exploration and exploitation of the existing genetic variability in landrace populations. In this context, this review aims to highlight the important role of durum wheat landraces as a useful genetic resource to improve the sustainability of Mediterranean agroecosystems, with a focus on adaptation to environmental stresses. We described the most recent molecular techniques and statistical approaches suitable for the identification of beneficial genes/alleles related to the most important traits in landraces and the development of molecular markers for marker-assisted selection. Finally, we outline the state of the art about landraces genetic diversity and signature of selection, already identified from these accessions, for adaptability to the environment.

Discovering Loci for Breeding Prospective and Phenology in Wheat Mediterranean Landraces by Environmental and eigenGWAS

Knowledge of the genetic basis of traits controlling phenology, differentiation patterns, and environmental adaptation is essential to develop new cultivars under climate change conditions. Landrace collections are an appropriate platform to study the hidden variation caused by crop breeding. The use of genome-wide association analysis for phenology, climatic data and differentiation among Mediterranean landraces led to the identification of 651 marker-trait associations that could be grouped in 46 QTL hotspots. A candidate gene analysis using the annotation of the genome sequence of the wheat cultivar 'Chinese Spring' detected 1097 gene models within 33 selected QTL hotspots. From all the gene models, 42 were shown to be differentially expressed (upregulated) under abiotic stress conditions, and 9 were selected based on their levels of expression. Different gene families previously reported for their involvement in different stress responses were found (protein kinases, ras-like GTP binding proteins and ethylene-responsive transcription factors). Finally, the synteny analysis in the QTL hotspots regions among the genomes of wheat and other cereal species identified 23, 21 and 7 ortho-QTLs for Brachypodium, rice and maize, respectively, confirming the importance of these loci.

Potential abiotic stress targets for modern genetic manipulation

Research into crop yield and resilience has underpinned global food security, evident in yields tripling in the past 5 decades. The challenges that global agriculture now faces are not just to feed 10+ billion people within a generation, but to do so under a harsher, more variable, and less predictable climate, and in many cases with less water, more expensive inputs, and declining soil quality. The challenges of climate change are not simply to breed for a "hotter drier climate," but to enable resilience to floods and droughts and frosts and heat waves, possibly even within a single growing season. How well we prepare for the coming decades of climate variability will depend on our ability to modify current practices, innovate with novel breeding methods, and communicate and work with farming communities to ensure viability and profitability. Here we define how future climates will impact farming systems and growing seasons, thereby identifying the traits and practices needed and including exemplars being implemented and developed. Critically, this review will also consider societal perspectives and public engagement about emerging technologies for climate resilience, with participatory approaches presented as the best approach.

Preliminary Dissection of Grain Yield and Related Traits at Differential Nitrogen Levels in Diverse Pre-Breeding Wheat Germplasm Through Association Mapping

Development of nutrient efficient cultivars depends on effective identification and utilization of genetic variation. We characterized a set of 276 pre-breeding lines (PBLs) for several traits at different levels of nitrogen application. These PBLs originate from synthetic wheats and landraces. We witnessed significant variation in various traits among PBLs to different nitrogen doses. There was ~ 4-18% variation range in different agronomic traits in response to nitrogen application, with the highest variation for the biological yield (BY) and the harvest index. Among various agronomic traits measured, plant height, tiller number, and BY showed a positive correlation with nitrogen applications. GWAS analysis detected 182 marker-trait associations (MTAs) (at p-value < 0.001), out of which 8 MTAs on chromosomes 5D, 4A, 6A, 1B, and 5B explained more than 10% phenotypic variance. Out of all, 40 MTAs observed for differential nitrogen application response were contributed by the synthetic derivatives. Moreover, 20 PBLs exhibited significantly higher grain yield than checks and can be selected as potential donors for improved plant nitrogen use efficiency (pNUE).

Improving in-season wheat yield prediction using remote sensing and additional agronomic traits as predictors

The development of accurate grain yield (GY) multivariate models using normalized difference vegetation index (NDVI) assessments obtained from aerial vehicles and additional agronomic traits is a promising option to assist, or even substitute, laborious agronomic in-field evaluations for wheat variety trials. This study proposed improved GY prediction models for wheat experimental trials. Calibration models were developed using all possible combinations of aerial NDVI, plant height, phenology, and ear density from experimental trials of three crop seasons. First, models were developed using 20, 50 and 100 plots in training sets and GY predictions were only moderately improved by increasing the size of the training set. Then, the best models predicting GY were defined in terms of the lowest Bayesian information criterion (BIC) and the inclusion of days to heading, ear density or plant height together with NDVI in most cases were better (lower BIC) than NDVI alone. This was particularly evident when NDVI saturates (with yields above 8 t ha^-1) with models including NDVI and days to heading providing a 50% increase in the prediction accuracy and a 10% decrease in the root mean square error. These results showed an improvement of NDVI prediction models by the addition of other agronomic traits. Moreover, NDVI and additional agronomic traits were unreliable predictors of grain yield in wheat landraces and conventional yield quantification methods must be used in this case. Saturation and underestimation of productivity may be explained by differences in other yield components that NDVI alone cannot detect (e.g. differences in grain size and number).

Environment-oriented selection criteria to overcome controversies in breeding for drought resistance in wheat

Wheat is one of the most important cereal crops, representing a fundamental source of calories and protein for the global human population. Drought stress (DS) is a widespread phenomenon, already affecting large wheat-growing areas worldwide, and a major threat for cereal productivity, resulting in consistent losses in average grain yield (GY). Climate change is projected to exacerbate DS incidence and severity by increasing temperatures and changing rainfall patterns. Estimating that wheat production has to substantially increase to guarantee food security to a demographically expanding human population, the need for breeding programs focused on improving wheat drought resistance is manifest. Drought occurrence, in terms of time of appearance, duration, frequency, and severity, along the plant's life cycle varies significantly among different environments and different agricultural years, making it difficult to identify reliable phenological, morphological, and functional traits to be used as effective breeding tools. The situation is further complicated by the presence of confounding factors, e.g., other concomitant abiotic stresses, in an open-field context. Consequently, the relationship between morpho-functional traits and GY under water deficit is often contradictory; moreover, controversies have emerged not only on which traits are to be preferred, but also on how one specific trait should be desired. In this review, we attempt to identify the possible causes of these disputes and propose the most suitable selection criteria in different target environments and, thus, the best trait combinations for breeders in different drought contexts. In fact, an environment-oriented approach could be a valuable solution to overcome controversies in identifying the proper selection criteria for improving wheat drought resistance.

Validation of Novel spot blotch disease resistance alleles identified in unexplored wheat (Triticum aestivum L.) germplasm lines through KASP markers

BACKGROUND

During the last few decades, the diverse sources of resistance, several genes and QTLs for spot blotch resistance have been identified. However, a large set of germplasm lines are still unexplored that have the potential to develop highly resistant wheat cultivars for the target environments. Therefore, the identification of new sources of resistance to spot blotch is essential for breeding programmes to develop spot blotch resistant cultivars and sustain wheat production. The association mapping panel of 294 diverse bread wheat accessions was used to explore new sources of spot blotch disease resistance and to identify genomic regions using genome wide association analysis (GWAS). The genotypes were tested in replicated trials for spot blotch disease at three major hot spots in India (Varanasi in UP, Pusa in Bihar, and Cooch Behar in West Bengal). The area under the disease progress curve (AUDPC) was calculated to assess the level of resistance in each genotype.

RESULTS

A total of 19 highly and 76 moderately resistant lines were identified. Three accessions (EC664204, IC534306 and IC535188) were nearly immune to spot blotch disease. The genotyping of all accessions resulted in a total of 16,787 high-quality polymorphic SNPs. The GWAS was performed using a Compressed Mixed Linear Model (CMLM) and a Mixed Linear Model (MLM). A total of seven significant MTAs, common in both the models and consistent across the environment, were further validated to develop KASP markers. Four MTAs (AX-94710084, AX-94865722, AX-95135556, and AX-94529408) on three chromosomes (2AL, 2BL, and 3BL) have been successfully validated through the KASP marker.

CONCLUSIONS

The new source of resistance was identified from unexplored germplasm lines. The genomic regions identified through GWAS were validated through KASP markers. The marker information and the highly resistant sources are valuable resources to rapidly develop immune or near immune wheat varieties.

Mining Sources of Resistance to Durum Leaf Rust among Tetraploid Wheat Accessions from CIMMYT's Germplasm Bank

A collection of 482 tetraploid wheat accessions from the CIMMYT Germplasm Bank was screened in the greenhouse for resistance to leaf rust disease caused by the fungus Puccinia triticina E. The accessions were screened against two races CBG/BP and BBG/BP in the field at two locations: against race CBG/BP at the Norman E. Borlaug Experimental Station (CENEB) located in the Yaqui Valley in the northern state of Sonora in Mexico during the 2014-2015 growing season; and against race BBG/BP at CIMMYT headquarters in El Batan, Texcoco, in the state of Mexico in the summer of 2015. Among the accessions, 79 durum genotypes were identified, of which 68 continued demonstrating their resistance in the field (past the seedling stage) against the two leaf rust races. An additional set of 41 genotypes was susceptible at the seedling stage, but adult plant race-specific resistance was identified in the field. The 79 seedling-resistant genotypes were tested against 15 different leaf rust races at the seedling stage to measure the usefulness of their resistance in a breeding program. Among the 79 accessions tested, 35 were resistant to all races used in the tests. Two sample sources, CIMMYT (18/35) pre-breeding germplasm and Ethiopian landraces (17/35), showed seedling resistance to all races tested except for seven landraces from Ethiopia, which became susceptible to the Cirno race identified in 2017.

Morphological and genetic diversity of maize landraces along an altitudinal gradient in the Southern Andes

Maize (Zea mays ssp. mays) is a major cereal crop worldwide and is traditionally or commercially cultivated almost all over the Americas. The North-Western Argentina (NWA) region constitutes one of the main diversity hotspots of the Southern Andes, with contrasting landscapes and a large number of landraces. Despite the extensive collections performed by the "Banco Activo de Germoplasma INTA Pergamino, Argentina" (BAP), most of them have not been characterized yet. Here we report the morphological and molecular evaluation of 30 accessions collected from NWA, along an altitudinal gradient between 1120 and 2950 meters above sea level (masl). Assessment of morphological variation in a common garden allowed the discrimination of two groups, which differed mainly in endosperm type and overall plant size. Although the groups retrieved by the molecular analyses were not consistent with morphological clusters, they showed a clear pattern of altitudinal structuring. Affinities among accessions were not in accordance with racial assignments. Overall, our results revealed that there are two maize gene pools co-existing in NWA, probably resulting from various waves of maize introduction in pre-Columbian times as well as from the adoption of modern varieties by local farmers. In conclusion, the NWA maize landraces preserved at the BAP possess high morphological and molecular variability. Our results highlight their potential as a source of diversity for increasing the genetic basis of breeding programs and provide useful information to guide future sampling and conservation efforts.

Prospects of Feral Crop De Novo Redomestication

Modern agriculture depends on a narrow variety of crop species, leaving global food and nutritional security highly vulnerable to the adverse effects of climate change and population expansion. Crop improvement using conventional and molecular breeding approaches leveraging plant genetic diversity using crop wild relatives (CWRs) has been one approach to address these issues. However, the rapid pace of the global change requires additional innovative solutions to adapt agriculture to meet global needs. Neodomestication-the rapid and targeted introduction of domestication traits using introgression or genome editing of CWRs-is being explored as a supplementary approach. These methods show promise; however, they have so far been limited in efficiency and applicability. We propose expanding the scope of neodomestication beyond truly wild CWRs to include feral crops as a source of genetic diversity for novel crop development, in this case 'redomestication'. Feral crops are plants that have escaped cultivation and evolved independently, typically adapting to their local environments. Thus, feral crops potentially contain valuable adaptive features while retaining some domestication traits. Due to their genetic proximity to crop species, feral crops may be easier targets for de novo domestication (i.e. neodomestication via genome editing techniques). In this review, we explore the potential of de novo redomestication as an application for novel crop development by genome editing of feral crops. This approach to efficiently exploit plant genetic diversity would access an underutilized reservoir of genetic diversity that could prove important in support of global food insecurity in the face of the climate change.

Multi-trait selection for mean performance and stability of maize hybrids in mega-environments delineated using envirotyping techniques

Under global climate changes, understanding climate variables that are most associated with environmental kinships can contribute to improving the success of hybrid selection, mainly in environments with high climate variations. The main goal of this study is to integrate envirotyping techniques and multi-trait selection for mean performance and the stability of maize genotypes growing in the Huanghuaihai plain in China. A panel of 26 maize hybrids growing in 10 locations in two crop seasons was evaluated for 9 traits. Considering 20 years of climate information and 19 environmental covariables, we identified four mega-environments (ME) in the Huanghuaihai plain which grouped locations that share similar long-term weather patterns. All the studied traits were significantly affected by the genotype × mega-environment × year interaction, suggesting that evaluating maize stability using single-year, multi-environment trials may provide misleading recommendations. Counterintuitively, the highest yields were not observed in the locations with higher accumulated rainfall, leading to the hypothesis that lower vapor pressure deficit, minimum temperatures, and high relative humidity are climate variables that -under no water restriction- reduce plant transpiration and consequently the yield. Utilizing the multi-trait mean performance and stability index (MTMPS) prominent hybrids with satisfactory mean performance and stability across cultivation years were identified. G23 and G25 were selected within three out of the four mega-environments, being considered the most stable and widely adapted hybrids from the panel. The G5 showed satisfactory yield and stability across contrasting years in the drier, warmer, and with higher vapor pressure deficit mega-environment, which included locations in the Hubei province. Overall, this study opens the door to a more systematic and dynamic characterization of the environment to better understand the genotype-by-environment interaction in multi-environment trials.

Elucidating the Genetic Relationships on the Original Old Sicilian Triticum Spp. Collection by SNP Genotyping

Several Triticum species spread in cultivation in Sicily and neighboring regions over the centuries, which led to the establishment of a large genetic diversity. Many ancient varieties were widely cultivated until the beginning of the last century before being replaced by modern varieties. Recently, they have been reintroduced in cultivation in Sicily. Here, the genetic diversity of 115 and 11 accessions from Sicily and Calabria, respectively, belonging to Triticum species was evaluated using a high-density SNP array. Einkorn, emmer, and spelta wheat genotypes were used as outgroups for species and subspecies; five modern varieties of durum and bread wheat were used as references. A principal coordinates analysis (PCoA) and an unweighted pair group method with arithmetic mean (UPGMA) showed four distinct groups among Triticum species and T. turgidum subspecies. The population structure analysis distinguished five gene pools, among which three appeared private to the T. aestivum, T. turgidum subsp. Turgidum, and 'Timilia' group. The principal component analysis (PCA) displayed a bio-morphological trait relationship of a subset (110) of ancient wheat varieties and their wide variability within the T. turgidum subsp. durum subgroups. A discriminant analysis of principal components (DAPC) and phylogenetic analyses applied to the four durum wheat subgroups revealed that the improved varieties harbored a different gene pool compared to the most ancient varieties. The 'Russello' and 'Russello Ibleo' groups were distinguished; both displayed higher genetic variability compared to the 'Timilia' group accessions. This research represents a comprehensive approach to fingerprinting the old wheat Sicilian germplasm, which is useful in avoiding commercial fraud and sustaining the cultivation of landraces and ancient varieties.

Insights into breeding history, hotspot regions of selection, and untapped allelic diversity for bread wheat breeding

Breeding has increasingly altered the genetics of crop plants since the domestication of their wild progenitors. It is postulated that the genetic diversity of elite wheat breeding pools is too narrow to cope with future challenges. In contrast, plant genetic resources (PGRs) of wheat stored in genebanks are valuable sources of unexploited genetic diversity. Therefore, to ensure breeding progress in the future, it is of prime importance to identify the useful allelic diversity available in PGRs and to transfer it into elite breeding pools. Here, a diverse collection consisting of modern winter wheat cultivars and genebank accessions was investigated based on reduced-representation genomic sequencing and an iSelect single nucleotide polymorphism (SNP) chip array. Analyses of these datasets provided detailed insights into population structure, levels of genetic diversity, sources of new allelic diversity, and genomic regions affected by breeding activities. We identified 57 regions representing genomic signatures of selection and 827 regions representing private alleles associated exclusively with genebank accessions. The presence of known functional wheat genes, quantitative trait loci, and large chromosomal modifications, i.e., introgressions from wheat wild relatives, provided initial evidence for putative traits associated within these identified regions. These findings were supported by the results of ontology enrichment analyses. The results reported here will stimulate further research and promote breeding in the future by allowing for the targeted introduction of novel allelic diversity into elite wheat breeding pools.

Genomic analyses of rice bean landraces reveal adaptation and yield related loci to accelerate breeding

Rice bean (Vigna umbellata) is an underexploited domesticated legume crop consumed for dietary protein in Asia, yet little is known about the genetic diversity of this species. Here, we present a high-quality reference genome for a rice bean landrace (FF25) built using PacBio long-read data and a Hi-C chromatin interaction map, and assess the phylogenetic position and speciation time of rice bean within the Vigna genus. We sequence 440 landraces (two core collections), and GWAS based on data for growth sites at three widely divergent latitudes reveal loci associated with flowering and yield. Loci harboring orthologs of FUL (FRUITFULL), FT (FLOWERING LOCUS T), and PRR3 (PSEUDO-RESPONSE REGULATOR 3) contribute to the adaptation of rice bean from its low latitude center of origin towards higher latitudes, and the landraces which pyramid early-flowering alleles for these loci display maximally short flowering times. We also demonstrate that copy-number-variation for VumCYP78A6 can regulate seed-yield traits. Intriguingly, 32 landraces collected from a mountainous region in South-Central China harbor a recently acquired InDel in TFL1 (TERMINAL FLOWER1) affecting stem determinacy; these materials also have exceptionally high values for multiple human-desired traits and could therefore substantially advance breeding efforts to improve rice bean.

Rice bean is an underexploited legume crop that has many desirable properties against bio and abiotic stresses. Here, the authors report the genome assembly of this species, conduct population genetics studies and reveal the genetic variations associated with adaptation and yield traits.

Worldwide Selection Footprints for Drought and Heat in Bread Wheat (Triticum aestivum L.)

Genome–environment Associations (GEA) or Environmental Genome-Wide Association scans (EnvGWAS) have been poorly applied for studying the genomics of adaptive traits in bread wheat landraces (Triticum aestivum L.). We analyzed 990 landraces and seven climatic variables (mean temperature, maximum temperature, precipitation, precipitation seasonality, heat index of mean temperature, heat index of maximum temperature, and drought index) in GEA using the FarmCPU approach with GAPIT. Historical temperature and precipitation values were obtained as monthly averages from 1970 to 2000. Based on 26,064 high-quality SNP loci, landraces were classified into ten subpopulations exhibiting high genetic differentiation. The GEA identified 59 SNPs and nearly 89 protein-encoding genes involved in the response processes to abiotic stress. Genes related to biosynthesis and signaling are mainly mediated by auxins, abscisic acid (ABA), ethylene (ET), salicylic acid (SA), and jasmonates (JA), which are known to operate together in modulation responses to heat stress and drought in plants. In addition, we identified some proteins associated with the response and tolerance to stress by high temperatures, water deficit, and cell wall functions. The results provide candidate regions for selection aimed to improve drought and heat tolerance in bread wheat and provide insights into the genetic mechanisms involved in adaptation to extreme environments.

Transcriptome Analysis Reveals Molecular Mechanisms under Salt Stress in Leaves of Foxtail Millet (Setaria italica L.)

Foxtail millet (Setaria italica L.) is an important cereal for managing future water scarcity and ensuring food security, due to its strong drought and salt stress resistance owing to its developed root system. However, the molecular responses of foxtail millet leaves to salt stress are largely unknown. In this study, seeds of 104 foxtail millet accessions were subjected to 0.17 mol·L^-1 NaCl stress during germination, and various germination-related parameters were analyzed to derive 5 salt-sensitive accessions and 13 salt-tolerant accessions. Hong Gu 2000 and Pu Huang Yu were the most salt-tolerant and salt-sensitive accessions, respectively. To determine the mechanism of the salt stress response, transcriptomic differences between the control and salt-treated groups were investigated. We obtained 2019 and 736 differentially expressed genes under salt stress in the salt-sensitive and salt-tolerant accessions, respectively. The transcription factor families bHLH, WRKY, AP2/ERF, and MYB-MYC were found to play critical roles in foxtail millet's response to salt stress. Additionally, the down-regulation of ribosomal protein-related genes causes stunted growth in the salt-sensitive accessions. The salt-tolerant accession alleviates salt stress by increasing energy production. Our findings provide novel insights into the molecular mechanism of foxtail millet's response to salt stress.

Comparative Genetic Analysis of Durum Wheat Landraces and Cultivars Widespread in Tunisia

The durum wheat (Triticum turgidum L. ssp. durum Desf.) landraces constitute a useful natural germplasm to increase the genetic diversity in the modern durum cultivars. The Tunisian durum germplasm constitutes 28 accessions conserved in Genebank of Tunisia, which are still unexplored. In this study, a comparative genetic analysis was performed to investigate the relationships between the Tunisian durum lines and the modern cultivars and detect divergent loci involved in breeding history. The genetic diversity analyses carried out using nine morphological descriptors and the 25K single-nucleotide polymorphism (SNP) array allowed us to distinguish two groups of Tunisian landraces and one of durum cultivars. The analysis of molecular variance and diversity indices confirmed the genetic variability among the groups. A total of 529 SNP loci were divergent between Tunisian durum landraces and modern cultivars. Candidate genes related to plant and spike architecture, including FLOWERING LOCUS T (FT-B1), zinc finger CONSTANS, and AP2/EREBPs transcription factors, were identified. In addition, divergent genes involved in grain composition and biotic stress nucleotide-binding site and leucine-reach repeats proteins and disease resistance proteins (NBS-LRR and RPM) were found, suggesting that the Tunisian durum germplasm may represent an important source of favorable alleles to be used in future durum breeding programs for developing well-adapted and resilient cultivars.

Leaf rolling dynamics for atmospheric moisture harvesting in wheat plant as an adaptation to arid environments

Plant species surviving in the arid regions have developed novel leaf features to harvest atmospheric water. Before the collected water evaporates, it is absorbed and transported for storage within the tissues and move toward the root zone through the unique chemistry of leaf structures. Deep insights into such features reveal that similarities can be found in the wheat plant. Therefore, this study aimed to evaluate the leaf rolling dynamics among wheat genotypes and their relationships with moisture harvesting and its movement on the leaf surface. For this purpose, genotypes were characterized for leaf rolling at three distinct growth stages (tillering, booting, and spike emergence). The contact angle of leaf surface dynamics (adaxial and abaxial), water budget, and morphophysiological traits of genotypes were measured. The results indicate that leaf rolling varies from inward to twisting type among genotypes and positively affected the water use efficiency and soil moisture difference at all growth stages under normal and drought conditions. Results of wetting property (hydrophilic < 90°) of the leaf surface were positively associated with the atmospheric water collection (4-7 ml). The lower values of contact angle hysteresis (12-19°) also support this mechanism. Thus, genotypes with leaf rolling dynamics (inward rolled and twisted) and surface wettability is an efficient fog harvesting system in wheat for interception and utilization of fog water in drought-prone areas. These results can be exploited to develop self-irrigated and drought-tolerant crops.

Grain Transcriptome Dynamics Induced by Heat in Commercial and Traditional Bread Wheat Genotypes

High temperature (HT) events have negative impact on wheat grains yield and quality. Transcriptome profiles of wheat developing grains of commercial genotypes (Antequera and Bancal) and landraces (Ardito and Magueija) submitted to heatwave-like treatments during grain filling were evaluated. Landraces showed significantly more differentially expressed genes (DEGs) and presented more similar responses than commercial genotypes. DEGs were more associated with transcription and RNA and protein synthesis in Antequera and with metabolism alterations in Bancal and landraces. Landraces upregulated genes encoding proteins already described as HT responsive, like heat shock proteins and cupins. Apart from the genes encoding HSP, two other genes were upregulated in all genotypes, one encoding for Adenylate kinase, essential for the cellular homeostasis, and the other for ferritin, recently related with increased tolerance to several abiotic stress in Arabidopsis. Moreover, a NAC transcription factor involved in plant development, known to be a negative regulator of starch synthesis and grain yield, was found to be upregulated in both commercial varieties and downregulated in Magueija landrace. The detected diversity of molecular processes involved in heat response of commercial and traditional genotypes contribute to understand the importance of genetic diversity and relevant pathways to cope with these extreme events.

Exploring the Genetic Diversity and Population Structure of Wheat Landrace Population Conserved at ICARDA Genebank

Landraces are considered a valuable source of potential genetic diversity that could be used in the selection process in any plant breeding program. Here, we assembled a population of 600 bread wheat landraces collected from eight different countries, conserved at the ICARDA's genebank, and evaluated the genetic diversity and the population structure of the landraces using single nucleotide polymorphism (SNP) markers. A total of 11,830 high-quality SNPs distributed across the genomes A (40.5%), B (45.9%), and D (13.6%) were used for the final analysis. The population structure analysis was evaluated using the model-based method (STRUCTURE) and distance-based methods [discriminant analysis of principal components (DAPC) and principal component analysis (PCA)]. The STRUCTURE method grouped the landraces into two major clusters, with the landraces from Syria and Turkey forming two clusters with high proportions of admixture, whereas the DAPC and PCA analysis grouped the population into three subpopulations mostly according to the geographical information of the landraces, i.e., Syria, Iran, and Turkey with admixture. The analysis of molecular variance revealed that the majority of the variation was due to genetic differences within the populations as compared with between subpopulations, and it was the same for both the cluster-based and distance-based methods. Genetic distance analysis was also studied to estimate the differences between the landraces from different countries, and it was observed that the maximum genetic distance (0.389) was between the landraces from Spain and Palestine, whereas the minimum genetic distance (0.013) was observed between the landraces from Syria and Turkey. It was concluded from the study that the model-based methods (DAPC and PCA) could dissect the population structure more precisely when compared with the STRUCTURE method. The population structure and genetic diversity analysis of the bread wheat landraces presented here highlight the complex genetic architecture of the landraces native to the Fertile Crescent region. The results of this study provide useful information for the genetic improvement of hexaploid wheat and facilitate the use of landraces in wheat breeding programs.

Extraction techniques in food industry: Insights into process parameters and their optimization

This review presents critical evaluation of the key parameters that affect the extraction of targeted components, giving due consideration to safety and environmental aspects. The crucial aspects of the extraction technologies along with protocols and process parameters for designing unit operations have been emphasized. The parameters like solvent usage, substrate type, concentration, particle size, temperature, quality and storage of extract as well as stability of extraction have been elaborately discussed. The process optimization using mathematical and computational modeling highlighting information and communication technologies have been given importance aiming for a green and sustainable industry level scaleup. The findings indicate that the extraction processes vary significantly depending on the category of food and its structure. There is no single extraction method or universal set of process conditions identified for extracting all value-added products from respective sources. A comprehensive understanding of process parameters and their optimization as well as synergistic combination of multiple extraction processes can aid in enhancement of the overall extraction efficiency. Future efforts must be directed toward the design of integrated unit operations that cause minimal harm to the environment along with investigations on economic feasibility to ensure sustainable extraction systems.