Amazing grass: developmental genetics of maize domestication

Wheat2035: Integrating pan-omics and advanced biotechnology for future wheat design

Wheat (Triticum aestivum) production is vital for global food security, providing energy and protein to millions of people worldwide. Recent advancements in wheat research have led to significant increases in production, fueled by technological and scientific innovation. Here, we summarize the major advancements in wheat research, particularly the integration of biotechnologies and a deeper understanding of wheat biology. The shift from multi-omics to pan-omics approaches in wheat research has greatly enhanced our understanding of the complex genome, genomic variations, and regulatory networks to decode complex traits. We also outline key scientific questions, potential research directions, and technological strategies for improving wheat over the next decade. Since global wheat production is expected to increase by 60% in 2050, continued innovation and collaboration are crucial. Integrating biotechnologies and a deeper understanding of wheat biology will be essential for addressing future challenges in wheat production, ensuring sustainable practices and improved productivity.

Biopriming of Maize with their endophyte Aspergillus fumigatus reinforces their resistance to salinity stress and improves their physiological traits

Zea mays L. (Maize) is one of the most crucial world's crops, for their nutritional values, however, the water scarcity and consequent soil salinization are the major challenges that limit the growth and productivity of this plant, particularly in the semi-arid regions in Egypt. Recently, biopriming has been recognized as one of the most efficient natural-ecofriendly approaches to mitigate the abiotic salt stress on plants. The haploid (128) and triploid (368) seeds of maize were selected as model verities for assessing their resistance to salt stress and mitigating their effect by fungal-biopriming. Overall, the haploid and triploid plants viabilities were drastically affected by salt concentration, at 500 mM of NaCl. At 500 mM NaCl, the fresh weights of the triploid and haploid seedlings were reduced by ~ 5 and 6.1 folds, compared to the controls, ensuring slightly higher salt resistance of the triploid than haploid ones. The pattern of the endophytic fugal isolates was plausibly changed with the salt concentration for both plant types, Aspergillus fumigatus isolate was emerged with the higher NaCl concentration (400-500 mM), and their morphological identity was molecularly confirmed and deposited into Genbank with accession # PQ200673. The fungal bioprimed seeds of the haploid and triploid plants were irrigated with 400 mM NaCl. The fungal-bioprimed plants displayed a significant improvement on the shoot density, fibrous roots, root length, shoot length, and leaves numbers and areas of the stressed-plants by ~ 1.7 folds, compared to control, ensures the triggering of different salt resistance machineries in plants upon fungal biopriming. The total antioxidant enzymes activities "catalase, peroxidase, superoxide dismutase" of the salt-stressed bioprimed maize plants were increased by ~ 4.7-5.3%, compared to control, confirming the mitigating effect of the salinity stress on plants upon fungal biopriming. The chlorophyll and carotenoids contents were significantly increased of the salt stressed maize upon biopriming with A. fumigatus. The expression of the sod, apx2, nhx11, hkt1, H + -PPase, nced of the plant salt stressed was strongly increased in response to A. fumigatus biopriming, normalized to β-actin gene. The expression of apx2 was dramatically increased by about 30 and 43 folds, in response to fungal biopriming. The nhx1 was significantly up-regulated by 18.9 fold in response to fungal biopriming, compared to control.

Analysis of gaps in rapeseed (Brassica napus L.) collections in European genebanks

Rapeseed is one of the most important agricultural crops and is used in many ways. Due to the advancing climate crisis, the yield potential of rapeseed is increasingly impaired. In addition to changing environmental conditions, the expansion of cultivated areas also favours the infestation of rapeseed with various pests and pathogens. This results in the need for continuous further development of rapeseed varieties. To this end, the potential of the rapeseed gene pool should be exploited, as the various species included in it contain promising resistance alleles against pests and pathogens. In general, the biodiversity of crops and their wild relatives is increasingly endangered. In order to conserve them and to provide impulses for breeding activities as well, strategies for the conservation of plant genetic resources are necessary. In this study, we investigated to what extent the different species of the rapeseed gene pool are conserved in European genebanks and what gaps exist. In addition, a niche modelling approach was used to investigate how the natural distribution ranges of these species are expected to change by the end of the century, assuming different climate change scenarios. It was found that most species of the rapeseed gene pool are significantly underrepresented in European genebanks, especially regarding representation of the natural distribution areas. The situation is exacerbated by the fact that the natural distributions are expected to change, in some cases significantly, as a result of ongoing climate change. It is therefore necessary to further develop strategies to prevent the loss of wild relatives of rapeseed. Based on the results of the study, as a first step we have proposed a priority list of species that should be targeted for collecting in order to conserve the biodiversity of the rapeseed gene pool in the long term.

Maximizing the crop wild relative resources available to plant breeders for crop improvement

Crop breeders are currently facing the need to continue increasing crop production to feed the growing human population, while mitigating the negative impacts of climate change on agriculture. Taxonomic and genetic diversity, which includes taxa, genes and alleles that offer novel sources of resistance to pests, disease and abiotic factors that affect crop quality and quantity, are a key tool for crop breeders to address these challenges. Lack of access to this diversity is currently limiting crop improvement. This paper focuses on how the breeder's requirement for greater diversity may be met despite the continue challenges of growing human population, and the impacts of climate change. It is argued that gene pool diversity is largely concentrated in crop wild relatives (CWR) and their more active conservation, especially focusing on in situ conservation applications, will enable the breeding challenges to be met. Further, that the science of in situ conservation is only now coming of age but is sufficiently advanced to facilitate the establishment of integrated national, regional, and global in situ CWR conservation networks. For humankind to substantially benefit from the additional adaptive diversity made available through these collaborative networks for CWR in situ conservation for the first time, breeders need to be provided with the critical resources necessary to address the negative impacts of climate changes on food production—therefore promoting greater global food security.

Genomic population structure and local adaptation of the wild strawberry Fragaria nilgerrensis

The crop wild relative, Fragaria nilgerrensis, is adapted to a variety of diverse habitats across its native range in China. Thus, discoveries made in this species could serve useful to guide the development of new superior strawberry cultivars that are resilient to new or variable environments. However, the genetic diversity and genetic architecture of traits in this species underlying important adaptive traits remain poorly understood. Here, we used whole-genome resequencing data from 193 F. nilgerrensis individuals spanning the distribution range in China to investigate the genetic diversity, population structure and the genomic basis of local adaptation. We identified four genetic groups, with the western group located in Hengduan Mountains exhibited the highest genetic diversity. Redundancy analysis suggests that both environment and geographic variables shaped a significant proportion of genomic variation. Our analyses revealed that the environmental difference explains more of the observed genetic variation than geographic distance. This suggests that adaptation to distinct habitats, unique combination of abiotic factors, likely drove genetic differentiation. Lastly, by implementing selective sweeps scans and genome-environment association analysis throughout the genome, we identified the genetic variation associated with local adaptation and investigated the functions of putative candidate genes in F. nilgerrensis.

Design a Database of Italian Vascular Alimurgic Flora (AlimurgITA): Preliminary Results

Despite the large number of data published in Italy on WEPs, there is no database providing a complete knowledge framework. Hence the need to design a database of the Italian alimurgic flora: AlimurgITA. Only strictly alimurgic taxa were chosen, excluding casual alien and cultivated ones. The collected data come from an archive of 358 texts (books and scientific articles) from 1918 to date, chosen with appropriate criteria. For each taxon, the part of the plant used, the method of use, the chorotype, the biological form and the regional distribution in Italy were considered. The 1103 taxa of edible flora already entered in the database equal 13.09% of Italian flora. The most widespread family is that of the Asteraceae (20.22%); the most widely used taxa are Cichorium intybus and Borago officinalis. The not homogeneous regional distribution of WEPs (maximum in the south and minimum in the north) has been interpreted. Texts published reached its peak during the 2001–2010 decade. A database for Italian WEPs is important to have a synthesis and to represent the richness and complexity of this knowledge, also in light of its potential for cultural enhancement, as well as its applications for the agri-food system.

Variation in production of cyanogenic glucosides during early plant development: A comparison of wild and domesticated sorghum

Domestication has narrowed the genetic diversity found in crop wild relatives, potentially reducing plasticity to cope with a changing climate. The tissues of domesticated sorghum (Sorghum bicolor), especially in younger plants, are cyanogenic and potentially toxic. Species of wild sorghum produce lower levels of the cyanogenic glucoside (CNglc) dhurrin than S. bicolor at maturity, but it is not known if this is also the case during germination and early growth. CNglcs play multiple roles in primary and specialised metabolism in domesticated sorghum and other crop plants. In this study, the temporal and spatial distribution of dhurrin in wild and domesticated sorghum at different growth stages was monitored in leaf, sheath and root tissues up to 35 days post germination using S. bicolor and the wild species S. brachypodum and S. macrospermum as the experimental systems. Growth parameters were also measured and allocation of plant total nitrogen (N%) to both dhurrin and nitrate (NO₃^-) was calculated. Negligible amounts of dhurrin were produced in the leaves of the two wild species compared to S. bicolor. The morphology of the two wild sorghums also differed from S. bicolor, with the greatest differences observed for the more distantly related S. brachypodum. S. bicolor had the highest leaf N% whilst the wild species had significantly higher root N%. Allocation of nitrogen to dhurrin in aboveground tissue was significantly higher in S. bicolor compared to the wild species but did not differ in the roots across the three species. The differences in plant morphology, dhurrin content and re-mobilisation, and nitrate/nitrogen allocation suggest that domestication has affected the functional roles of dhurrin in sorghum.

Conservation and diversity of seed associated endophytes in Zea across boundaries of evolution, ethnography and ecology

Endophytes are non-pathogenic microbes living inside plants. We asked whether endophytic species were conserved in the agriculturally important plant genus Zea as it became domesticated from its wild ancestors (teosinte) to modern maize (corn) and moved from Mexico to Canada. Kernels from populations of four different teosintes and 10 different maize varieties were screened for endophytic bacteria by culturing, cloning and DNA fingerprinting using terminal restriction fragment length polymorphism (TRFLP) of 16S rDNA. Principle component analysis of TRFLP data showed that seed endophyte community composition varied in relation to plant host phylogeny. However, there was a core microbiota of endophytes that was conserved in Zea seeds across boundaries of evolution, ethnography and ecology. The majority of seed endophytes in the wild ancestor persist today in domesticated maize, though ancient selection against the hard fruitcase surrounding seeds may have altered the abundance of endophytes. Four TRFLP signals including two predicted to represent Clostridium and Paenibacillus species were conserved across all Zea genotypes, while culturing showed that Enterobacter, Methylobacteria, Pantoea and Pseudomonas species were widespread, with γ-proteobacteria being the prevalent class. Twenty-six different genera were cultured, and these were evaluated for their ability to stimulate plant growth, grow on nitrogen-free media, solubilize phosphate, sequester iron, secrete RNAse, antagonize pathogens, catabolize the precursor of ethylene, produce auxin and acetoin/butanediol. Of these traits, phosphate solubilization and production of acetoin/butanediol were the most commonly observed. An isolate from the giant Mexican landrace Mixteco, with 100% identity to Burkholderia phytofirmans, significantly promoted shoot potato biomass. GFP tagging and maize stem injection confirmed that several seed endophytes could spread systemically through the plant. One seed isolate, Enterobacter asburiae, was able to exit the root and colonize the rhizosphere. Conservation and diversity in Zea-microbe relationships are discussed in the context of ecology, crop domestication, selection and migration.

RAPD and internal transcribed spacer sequence analyses reveal Zea nicaraguensis as a section Luxuriantes species close to Zea luxurians

Genetic relationship of a newly discovered teosinte from Nicaragua, Zea nicaraguensis with waterlogging tolerance, was determined based on randomly amplified polymorphic DNA (RAPD) markers and the internal transcribed spacer (ITS) sequences of nuclear ribosomal DNA using 14 accessions from Zea species. RAPD analysis showed that a total of 5,303 fragments were produced by 136 random decamer primers, of which 84.86% bands were polymorphic. RAPD-based UPGMA analysis demonstrated that the genus Zea can be divided into section Luxuriantes including Zea diploperennis, Zea luxurians, Zea perennis and Zea nicaraguensis, and section Zea including Zea mays ssp. mexicana, Zea mays ssp. parviglumis, Zea mays ssp. huehuetenangensis and Zea mays ssp. mays. ITS sequence analysis showed the lengths of the entire ITS region of the 14 taxa in Zea varied from 597 to 605 bp. The average GC content was 67.8%. In addition to the insertion/deletions, 78 variable sites were recorded in the total ITS region with 47 in ITS1, 5 in 5.8S, and 26 in ITS2. Sequences of these taxa were analyzed with neighbor-joining (NJ) and maximum parsimony (MP) methods to construct the phylogenetic trees, selecting Tripsacum dactyloides L. as the outgroup. The phylogenetic relationships of Zea species inferred from the ITS sequences are highly concordant with the RAPD evidence that resolved two major subgenus clades. Both RAPD and ITS sequence analyses indicate that Zea nicaraguensis is more closely related to Zea luxurians than the other teosintes and cultivated maize, which should be regarded as a section Luxuriantes species.

Maize (Zea mays): a model organism for basic and applied research in plant biology

Zea mays ssp. mays is one of the world's most important crop plants, boasting a multibillion dollar annual revenue. In addition to its agronomic importance, maize has been a keystone model organism for basic research for nearly a century. Within the cereals, which include other plant model species such as rice (Oryza sativa), sorghum (Sorghum bicolor), wheat (Triticum spp.), and barley (Hordeum vulgare), maize is the most thoroughly researched genetic system. Several attributes of the maize plant, including a vast collection of mutant stocks, large heterochromatic chromosomes, extensive nucleotide diversity, and genic colinearity within related grasses, have positioned this species as a centerpiece for genetic, cytogenetic, and genomic research. As a model organism, maize is the subject of such far-ranging biological investigations as plant domestication, genome evolution, developmental physiology, epigenetics, pest resistance, heterosis, quantitative inheritance, and comparative genomics. These and other studies will be advanced by the completed sequencing and annotation of the maize gene space, which will be realized during 2009. Here we present an overview of the use of maize as a model system and provide links to several protocols that enable its genetic and genomic analysis.