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Many present crop plants are in danger of failing due to extreme conditions induced by climate change. This along with a rapidly growing world population threatens global food security. In this paper, I provide an overview of different plant genetic resources, of possibilities to broaden their base by including crop wild relative species and other underutilized sources, and of conservation and characterization needs and tools. The increased environmental variability implies that we will need access to an even wider range of plant genetic resources than used today for breeding new crop varieties, which contain useful traits, such as pest and disease resistances and ability to withstand drought or extreme temperatures.

Supplementary file for a publication

Selenium (Se) acquirement from daily diet can help reduce the risk of many diseases. The edible parts of crop plants are the main source of dietary Se, while the Se content in crops is determined by Se bioavailability in soil. We summarize recent research on the biogeochemical cycle of Se driven by specific microorganisms and emphasize the oxidizing process in the Se cycle. Moreover, we discuss how plant root exudates and rhizosphere microorganisms affect soil Se availability. Finally, we cover beneficial microorganisms, including endophytes, that promote crop quality and improve crop tolerance to environmental stresses. Se availability to plants depends on the balance between adsorption and desorption, reduction, methylation and oxidation, which are determined by interactions among soil properties, microbial communities and plants. Reduction and methylation processes governed by bacteria or fungi lead to declined Se availability, while Se oxidation regulated by Se-oxidizing microorganisms increases Se availability to plants. Despite a much lower rate of Se oxidization compared to reduction and methylation, the potential roles of microbial communities in increasing Se bioavailability are probably largely underestimated. Enhancing Se oxidation and Se desorption are crucial for the promotion of Se bioavailability and uptake, particularly in Se-deficient soils. Beneficial roles of Se are reported in terms of improved crop growth and quality, and enhanced protection against fungal diseases and abiotic stress through improved photosynthetic traits, increased sugar and amino acid contents, and promoted defense systems. Understanding Se transformation along the plant-soil continuum is crucial for agricultural production and even for human health.

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Additional file 1: Supplementary methods. Table S1. Bacterial and fungal co-occurrence network characteristics in each niche. Table S2. The physiological traits and microbial functions of rhizosphere soil affected by sex and nitrogen treatment. Table S3. The growth characteristics of P. cathayana males and females under different N treatments. Figure S1. The composition and relative abundance of bacterial (a) and fungal (b) communities in the rhizosphere soil, roots, old leaves and young leaves of P. cathayana males and females in different N treatments. Figure S2. The Shannon diversity of bacterial and fungal communities in different N treatments. From left to right: rhizosphere soil, roots, old leaves and young leaves. Figure S3. The volcano plot illustrating the enrichment and depletion patterns of bacterial and fungal microbiomes in each niche (male vs female). Figure S4. Different niche effects on the networks of bacterial (a) and fungal (b) communities. Figure S5. Phylogenetic tree, taxonomic composition, and distribution patterns of dominant fungal taxa living in roots, old leaves and young leaves. (a) Dominant fungal taxa in P. cathayana females and males, respectively. (b) The distribution pattern of dominant fungal taxa in P. cathayana females. (c) The number of dominant fungal taxa, the shared and specific bacterial OTUs in P. cathayana females and males. (d) The distribution pattern of dominant fungal taxa in P. cathayana males. Figure S6. Heatmaps of the expression profiles (a), differential expression analysis (DEGs) (b) and functional-enrichment analysis (KEGG) (c). MC, young male leaves in control-nitrogen treatment; MN, young male leaves in limited-nitrogen treatment; FC, young female leaves in control-nitrogen treatment; FN, young female leaves in limited-nitrogen treatment.

Medemia argun is a wild, dioecious palm, adapted to the harsh arid environment of the Nubian Desert in Sudan and southern Egypt. There is a concern about its conservation status, since little is known about its distribution, abundance, and genetic variation. M. argun grows on the floodplains of seasonal rivers (wadis). The continuing loss of suitable habitats in the Nubian Desert is threatening the survival of this species. We analyzed the genetic diversity, population genetic structure, and occurrence of M. argun populations to foster the development of conservation strategies for M. argun. Genotyping-by-sequencing (GBS) analyses were performed using a whole-genome profiling service. We found an overall low genetic diversity and moderate genetic structuring based on 40 single-nucleotide polymorphisms (SNPs) and 9,866 SilicoDArT markers. The expected heterozygosity of the total population (H-T) equaled 0.036 and 0.127, and genetic differentiation among populations/groups (F-ST) was 0.052 and 0.092, based on SNP and SilicoDArT markers, respectively. Bayesian clustering analyses defined five genetic clusters that did not display any ancestral gene flow among each other. Based on SilicoDArT markers, the results of the analysis of molecular variance (AMOVA) confirmed the previously observed genetic differentiation among generation groups (23%; p < 0.01). Pairwise F-ST values indicated a genetic gap between old and young individuals. The observed low genetic diversity and its loss among generation groups, even under the detected high gene flow, show genetically vulnerable M. argun populations in the Nubian Desert in Sudan. To enrich and maintain genetic variability in these populations, conservation plans are required, including collection of seed material from genetically diverse populations and development of ex situ gene banks.

We conducted a large-scale population genetic survey of genetic diversity of the host grass Festuca rubra s.l., which fitness can be highly dependent on its symbiotic fungus Epichloe festucae, to evaluate genetic variation and population structure across the European range. The 27 studied populations have previously been found to differ in frequencies of occurrence of the symbiotic fungus E. festucae and ploidy levels. As predicted, we found decreased genetic diversity in previously glaciated areas in comparison with nonglaciated regions and discovered three major maternal genetic groups: southern, northeastern, and northwestern Europe. Interestingly, host populations from Greenland were genetically similar to those from the Faroe Islands and Iceland, suggesting gene flow also between those areas. The level of variation among populations within regions is evidently highly dependent on the postglacial colonization history, in particular on the number of independent long-distance seed colonization events. Yet, also anthropogenic effects may have affected the population structure in F. rubra. We did not observe higher fungal infection rates in grass populations with lower levels of genetic variability. In fact, the fungal infection rates of E. festucae in relation to genetic variability of the host populations varied widely among geographical areas, which indicate differences in population histories due to colonization events and possible costs of systemic fungi in harsh environmental conditions. We found that the plants of different ploidy levels are genetically closely related within geographic areas indicating independent formation of polyploids in different maternal lineages.