Mapping patterns of abiotic and biotic stress resilience uncovers conservation gaps and breeding potential of Vigna wild relatives

Chromosome-Level Genome Assembly and Population Genomic Analyses Reveal Geographic Variation and Population Genetic Structure of Prunus tenella

Prunus tenella is a rare and precious relict plant in China. It is an important genetic resource for almond improvement and an indispensable material in ecological protection and landscaping. However, the research into molecular breeding and genetic evolution has been severely restricted due to the lack of genome information. In this investigation, we created a chromosome-level genomic pattern of P. tenella, 231 Mb in length with a contig N50 of 18.1 Mb by Hi-C techniques and high-accuracy PacBio HiFi sequencing. The present assembly predicted 32,088 protein-coding genes, and an examination of the genome assembly indicated that 94.7% among all assembled transcripts were alignable to the genome assembly; most (97.24%) were functionally annotated. By phylogenomic genome comparison, we found that P. tenella is an ancient group that diverged approximately 13.4 million years ago (mya) from 13 additional closely related species and about 6.5 Mya from the cultivated almond. Collinearity analysis revealed that P. tenella is highly syntenic and has high sequence conservation with almond and peach. However, this species also exhibits many presence/absence variants. Moreover, a large inversion at the 7588 kb position of chromosome 5 was observed, which may have a significant association with phenotypic traits. Lastly, population genetic structure analysis in eight different populations indicated a high genetic differentiation among the natural distribution of P. tenella. This high-quality genome assembly provides critical clues and comprehensive information for the systematic evolution, genetic characteristics, and functional gene research of P. tenella. Moreover, it provides a valuable genomic resource for in-depth study in protection, developing, and utilizing P. tenella germplasm resources.

Advances in Cereal Crop Genomics for Resilience under Climate Change

Adapting to climate change, providing sufficient human food and nutritional needs, and securing sufficient energy supplies will call for a radical transformation from the current conventional adaptation approaches to more broad-based and transformative alternatives. This entails diversifying the agricultural system and boosting productivity of major cereal crops through development of climate-resilient cultivars that can sustainably maintain higher yields under climate change conditions, expanding our focus to crop wild relatives, and better exploitation of underutilized crop species. This is facilitated by the recent developments in plant genomics, such as advances in genome sequencing, assembly, and annotation, as well as gene editing technologies, which have increased the availability of high-quality reference genomes for various model and non-model plant species. This has necessitated genomics-assisted breeding of crops, including underutilized species, consequently broadening genetic variation of the available germplasm; improving the discovery of novel alleles controlling important agronomic traits; and enhancing creation of new crop cultivars with improved tolerance to biotic and abiotic stresses and superior nutritive quality. Here, therefore, we summarize these recent developments in plant genomics and their application, with particular reference to cereal crops (including underutilized species). Particularly, we discuss genome sequencing approaches, quantitative trait loci (QTL) mapping and genome-wide association (GWAS) studies, directed mutagenesis, plant non-coding RNAs, precise gene editing technologies such as CRISPR-Cas9, and complementation of crop genotyping by crop phenotyping. We then conclude by providing an outlook that, as we step into the future, high-throughput phenotyping, pan-genomics, transposable elements analysis, and machine learning hold much promise for crop improvements related to climate resilience and nutritional superiority.

Implementing Sustainable Irrigation in Water-Scarce Regions under the Impact of Climate Change

The sustainability of irrigated agriculture is threatening due to adverse climate change, given future projections that every one in four people on Earth might be suffering from extreme water scarcity by the year 2025. Pressurized irrigation systems and appropriate irrigation schedules can increase water productivity (i.e., product yield per unit volume of water consumed by the crop) and reduce the evaporative or system loss of water as opposed to traditional surface irrigation methods. However, in water-scarce countries, irrigation management frequently becomes a complex task. Deficit irrigation and the use of non-conventional water resources (e.g., wastewater, brackish groundwater) has been adopted in many cases as part of a climate change mitigation measures to tackle the water poverty issue. Protected cultivation systems such as greenhouses or screenhouses equipped with artificial intelligence systems present another sustainable option for improving water productivity and may help to alleviate water scarcity in these countries. This article presents a comprehensive review of the literature, which deals with sustainable irrigation for open-field and protected cultivation systems under the impact of climatic change in vulnerable areas, including the Mediterranean region.

A Unique Cytoplasmic-Nuclear Interaction in Sunflower (Helianthus annuus L.) Causing Reduced-Vigor Plants and the Genetics of Vigor Restoration

Wild Helianthus species are an important genetic resource for sunflower improvement, but sometimes there are adverse interactions between the wild and cultivated sunflowers. This study reports the inheritance of reduced vigor and its restoration resulting from an interaction of perennial Helianthus cytoplasms with nuclear genes of cultivated sunflower lines. The large number of vigor restoration (V) genes identified in cultivated lines are all located at the same locus, designated V₁ , suggesting a common origin of these genes. Additional V genes derived from the wild perennial species H. giganteus L. and H. hirsutus Raf. are located at a different locus than V₁ , designated V₂ . A major difference between the wild annual Helianthus cytoplasms and perennial cytoplasms is the lack of the vigor-reducing cytoplasms, but surprisingly V genes were observed in wild annual H. annuus L. and H. petiolaris Nutt. which were at the same locus as V₁ . A common vigor-reducing cytoplasmic effect of the perennial Helianthus species and the existence of a common vigor restoration V gene in most perennial Helianthus species could be explained as a result of vigor selection during Helianthus speciation. V₁ was mapped on linkage group (LG) 7 of the sunflower genome, using an F₂ population derived from MOL-RV/HA 821. V₁ co-segregated with an InDel marker ZVG31, with three single-nucleotide polymorphism (SNP) markers, SFW01024, SFW07230, and SFW00604, located above it on the map at a genetic distance of 0.8 cM, and another SNP marker, SFW08671, below it at a distance of 0.4 cM. The physical distance between the two closest flanking SNP markers corresponds to 0.56 and 1.37 Mb on the HA 412-HO and XRQ assemblies, respectively. The tightly linked markers will help select normal vigor progenies when using perennial Helianthus cytoplasms in a breeding program, which will also provide a basis for studying the mechanism of the cytonuclear interaction, and the speciation of annual and perennial Helianthus species.

Irrigation Groundwater Quality Characteristics: A Case Study of Cyprus

This study was conducted in order to investigate possible quality changes in Cyprus’ groundwater resources over a 10-year period of pumping and to check the suitability of primary irrigation water. Water samples (n = 890) from private wells in agricultural areas were analyzed from 2009 to 2018 to determine various physicochemical properties. The sodium adsorption ratio (SAR) and residual sodium carbonate (RSC) were also calculated to evaluate potential soil degradation issues. Sodium, chloride and sulphate were found to be the predominant ions in groundwater. Quality evaluation showed possible restrictions in groundwater use for irrigation in relation to its salt content and the toxicity of specific ions having adverse effects on sensitive and several moderately sensitive crops. In particular, an increasing trend was observed in pumped groundwater for boron ion concentrations. Nevertheless, all samples evaluated were suitable for irrigation in terms of soil sodicitation and soil infiltration rate. This study indicates that in order to maintain long-term agricultural sustainability it is imperative to develop strategic plants to mitigate the adverse effects of water-pumped quality deterioration on soils and crops. Precision agriculture techniques may be adapted for better water and nutrient input/output management, thus protecting groundwater from salinization in agricultural areas. These results, among others, may be a useful tool to enhance the ability of Cyprus’s agricultural water sector to adapt to observed and anticipated climate impacts.

Current Perspectives on Introgression Breeding in Food Legumes

Food legumes are important for defeating malnutrition and sustaining agri-food systems globally. Breeding efforts in legume crops have been largely confined to the exploitation of genetic variation available within the primary genepool, resulting in narrow genetic base. Introgression as a breeding scheme has been remarkably successful for an array of inheritance and molecular studies in food legumes. Crop wild relatives (CWRs), landraces, and exotic germplasm offer great potential for introgression of novel variation not only to widen the genetic base of the elite genepool for continuous incremental gains over breeding cycles but also to discover the cryptic genetic variation hitherto unexpressed. CWRs also harbor positive quantitative trait loci (QTLs) for improving agronomic traits. However, for transferring polygenic traits, "specialized population concept" has been advocated for transferring QTLs from CWR into elite backgrounds. Recently, introgression breeding has been successful in developing improved cultivars in chickpea (Cicer arietinum), pigeonpea (Cajanus cajan), peanut (Arachis hypogaea), lentil (Lens culinaris), mungbean (Vigna radiata), urdbean (Vigna mungo), and common bean (Phaseolus vulgaris). Successful examples indicated that the usable genetic variation could be exploited by unleashing new gene recombination and hidden variability even in late filial generations. In mungbean alone, distant hybridization has been deployed to develop seven improved commercial cultivars, whereas in urdbean, three such cultivars have been reported. Similarly, in chickpea, three superior cultivars have been developed from crosses between C. arietinum and Cicer reticulatum. Pigeonpea has benefited the most where different cytoplasmic male sterility genes have been transferred from CWRs, whereas a number of disease-resistant germplasm have also been developed in Phaseolus. As vertical gene transfer has resulted in most of the useful gene introgressions of practical importance in food legumes, the horizontal gene transfer through transgenic technology, somatic hybridization, and, more recently, intragenesis also offer promise. The gains through introgression breeding are significant and underline the need of bringing it in the purview of mainstream breeding while deploying tools and techniques to increase the recombination rate in wide crosses and reduce the linkage drag. The resurgence of interest in introgression breeding needs to be capitalized for development of commercial food legume cultivars.

Wild Relatives of Maize, Rice, Cotton, and Soybean: Treasure Troves for Tolerance to Biotic and Abiotic Stresses

Global food demand is expected to nearly double by 2050 due to an increase in the world's population. The Green Revolution has played a key role in the past century by increasing agricultural productivity worldwide, however, limited availability and continued depletion of natural resources such as arable land and water will continue to pose a serious challenge for global food security in the coming decades. High yielding varieties with proven tolerance to biotic and abiotic stresses, superior nutritional profiles, and the ability to adapt to the changing environment are needed for continued agricultural sustainability. The narrow genetic base of modern cultivars is becoming a major bottleneck for crop improvement efforts and, therefore, the use of crop wild relatives (CWRs) is a promising approach to enhance genetic diversity of cultivated crops. This article provides a review of the efforts to date on the exploration of CWRs as a source of tolerance to multiple biotic and abiotic stresses in four global crops of importance; maize, rice, cotton, and soybean. In addition to the overview of the repertoire and geographical spread of CWRs in each of the respective crops, we have provided a comprehensive discussion on the morphological and/or genetic basis of the traits along with some examples, when available, of the research in the transfer of traits from CWRs to cultivated varieties. The emergence of modern molecular and genomic technologies has not only accelerated the pace of dissecting the genetics underlying the traits found in CWRs, but also enabled rapid and efficient trait transfer and genome manipulation. The potential and promise of these technologies has also been highlighted in this review.

Genetic Transformation of Hordeum vulgare ssp. spontaneum for the Development of a Transposon-Based Insertional Mutagenesis System

Domestication and intensive selective breeding of plants has triggered erosion of genetic diversity of important stress-related alleles. Researchers highlight the potential of using wild accessions as a gene source for improvement of cereals such as barley, which has major economic and social importance worldwide. Previously, we have successfully introduced the maize Ac/Ds transposon system for gene identification in cultivated barley. The objective of current research was to investigate the response of Hordeum vulgare ssp. spontaneum wild barley accessions in tissue culture to standardize parameters for introduction of Ac/Ds transposons through genetic transformation. We investigated the response of ten wild barley genotypes for callus induction, regenerative green callus induction and regeneration of fertile plants. The activity of exogenous Ac/Ds elements was observed through a transient assay on immature wild barley embryos/callus whereby transformed embryos/calli were identified by the expression of GUS. Transient Ds expression bombardment experiments were performed on 352 pieces of callus (3-5 mm each) or immature embryos in 4 genotypes of wild barley. The transformation frequency of putative transgenic callus lines based on transient GUS expression ranged between 72 and100 % in wild barley genotypes. This is the first report of a transformation system in H. vulgare ssp. spontaneum.