Taxonomic, spatial and adaptive genetic variation of Beta section Beta

Genetic diversity of the table beet (<I>Beta</I> L.) collection at VIR as a potential source for breeding (a review)

This review presents brief information about the history of the table beet (Beta vulgaris L. subsp. vulgaris var. conditiva Alef.) collection at the N.I. Vavilov All-Russian Institute of Plant Genetic Resources (VIR), its composition, research trends, and significance for domestic breeding. The collection started in 1924 with Vavilov’s collecting activities. Currently, the collection consists of 2512 accessions; the table beet variety is represented by 461 accessions from 45 countries, collected in numerous expeditions, obtained from foreign genebanks through germplasm exchange and seed requests, received from domestic and foreign breeders, plus materials developed by VIR researchers. Table beet is an economically important, high-yielding, ubiquitous crop that has a wide cultivation area and is a valuable biochemical food product with beneficial effects on human health.

The information is provided on the genetic diversity of VIR’s table beet collection, including current trends of its study and use in breeding. Characteristics of table beet accessions available in the collection, their morphological features and value, and the names of accessions from different trait groups and genetic sources are described. Presently, 125 cultivars and 38 F1 hybrids of table beet are listed in the State Register of Breeding Achievements of the Russian Federation, 70% of which are products of domestic breeding. 

Similar Responses of Relatively Salt-Tolerant Plants to Na and K during Chloride Salinity: Comparison of Growth, Water Content and Ion Accumulation

The aim of the present study was to compare changes in growth, ion accumulation and tissue water content in relatively salt-tolerant plant taxa—Beta vulgaris subsp. maritima, Beta vulgaris subsp. vulgaris var. cicla, Cochlearia officinalis, Mentha aquatica and Plantago maritima—as a result of NaCl and KCl salinity in controlled conditions. Similar growth responses to Na⁺ and K⁺ salinity in a form of chloride salts were found for all model plants, including growth stimulation at low concentrations, an increase in water content in leaves, and growth inhibition at high salinity for less salt-resistant taxa. All plant taxa were cultivated in soil except M. aquatica, which was cultivated in hydroponics. While the morphological responses of B. vulgaris subsp. vulgaris var. cicla, B. vulgaris subsp. maritima and P. maritima plants to NaCl and KCl were rather similar, C. officinalis plants tended to perform worse when treated with KCl, but the opposite was evident for M. aquatica. Plants treated with KCl accumulated higher concentrations of K⁺ in comparison to the accumulation of Na⁺ in plants treated with equimolar concentrations of NaCl. KCl-treated plants also had higher tissue levels of electrical conductivity than NaCl-treated plants. Based on the results of the present study, it seems that both positive and negative effects of Na⁺ and K⁺ on plant growth were due to unspecific ionic effects of monovalent cations or/and the specific effect of Cl⁻.

A contiguous de novo genome assembly of sugar beet EL10 (Beta vulgaris L.)

A contiguous assembly of the inbred 'EL10' sugar beet (Beta vulgaris ssp. vulgaris) genome was constructed using PacBio long-read sequencing, BioNano optical mapping, Hi-C scaffolding, and Illumina short-read error correction. The EL10.1 assembly was 540 Mb, of which 96.2% was contained in nine chromosome-sized pseudomolecules with lengths from 52 to 65 Mb, and 31 contigs with a median size of 282 kb that remained unassembled. Gene annotation incorporating RNA-seq data and curated sequences via the MAKER annotation pipeline generated 24,255 gene models. Results indicated that the EL10.1 genome assembly is a contiguous genome assembly highly congruent with the published sugar beet reference genome. Gross duplicate gene analyses of EL10.1 revealed little large-scale intra-genome duplication. Reduced gene copy number for well-annotated gene families relative to other core eudicots was observed, especially for transcription factors. Variation in genome size in B. vulgaris was investigated by flow cytometry among 50 individuals producing estimates from 633 to 875 Mb/1C. Read-depth mapping with short-read whole-genome sequences from other sugar beet germplasm suggested that relatively few regions of the sugar beet genome appeared associated with high-copy number variation.

Distribution of Biodiversity of Wild Beet Species (Genus Beta L.) in Armenia under Ongoing Climate Change Conditions

The reported annual temperature increase and significant precipitation drop in Armenia impact the country’s ecosystems and biodiversity. The present study surveyed the geographical distribution of the local wild beet species under the ongoing climate change conditions. We showed that B. lomatogona, B. corolliflora and B. macrorhiza are sensitive to climate change and were affected to various degrees, depending on their location. The most affected species was B. lomatogona, which is at the verge of extinction. Migration for ca. 90 and 200–300 m up the mountain belt was recorded for B. lomatogona and B. macrorhiza, respectively. B. corolliflora was found at 100–150 m lower altitudes than in the 1980s. A general reduction in the beet’s population size in the native habitats was observed, with an increased number of plants within the populations, recorded for B. corolliflora and B. macrorhiza. A new natural hybrid Beta x intermedium Aloyan between B. corolliflora and B. macrorhiza was described and confirmed using chloroplast DNA trnL-trnF intergenic spacer (LF) and partially sequenced alcohol dehydrogenase (adh) of nuclear DNA. An overview of the wild beets reported in Armenia with the taxonomic background, morphological features, and distribution is provided. Conservation measures for preservation of these genetic resources are presented.

Effects of cadmium stress on the morphology, physiology, cellular ultrastructure, and BvHIPP24 gene expression of sugar beet (Beta vulgaris L.)

To clarify the mechanism of the response of sugar beet (Beta vulgaris L.) to cadmium (Cd) stress, this study investigated changes in the phenotype, physiological indexes, and subcellular structure of B. vulgaris under Cd treatment and the transcriptional pattern of the BvHIPP24 gene (a heavy metal-associated isoprenylated plant protein involved in heavy metal detoxification). The plant height and shoot and root growth of B. vulgaris seedlings were inhibited to some extent under 0.5 and 1 mM Cd, with gradually wilting and yellowing of leaves and dark brown roots. When the Cd concentration was increased, malondialdehyde content and the activities of peroxidase, superoxide dismutase, and glutathione S-transferase increased differentially. qPCR indicated that the expression of BvHIPP24 was induced by different concentrations of Cd. Although transmission electron microscopy revealed damage to nuclei, mitochondria, and chloroplasts, B. vulgaris exhibited strong adaptability to 0.5 mM Cd according to a comprehensive analysis using the membership function. The results showed that B. vulgaris may reduce cell damage and improve its Cd tolerance by regulating functional gene expression and antioxidant enzymes. This study increases our understanding of the Cd-tolerance mechanism of B. vulgaris and provides insights into the use of B. vulgaris in Cd bioremediation.

Genomic distances reveal relationships of wild and cultivated beets

Cultivated beets (Beta vulgaris ssp. vulgaris), including sugar beet, rank among the most important crops. The wild ancestor of beet crops is the sea beet Beta vulgaris ssp. maritima. Species and subspecies of wild beets are readily crossable with cultivated beets and are thus available for crop improvement. To study genomic relationships in the genus Beta, we sequence and analyse 606 beet genomes, encompassing sugar beet, sea beet, B. v. adanensis, B. macrocarpa, and B. patula. We observe two genetically distinct groups of sea beets, one from the Atlantic coast and the other from the Mediterranean area. Genomic comparisons based on k-mers identify sea beets from Greece as the closest wild relatives of sugar beet, suggesting that domestication of the ancestors of sugar beet may be traced to this area. Our work provides comprehensive insight into the phylogeny of wild and cultivated beets and establishes a framework for classification of further accessions of unknown (sub-)species assignment.

Assembly and characterization of the genome of chard (Beta vulgaris ssp. vulgaris var. cicla)

Chard (Beta vulgaris ssp. vulgaris var. cicla) is a member of one of four different cultigroups of beets. While the genome of sugar beet, the most prominent beet crop, has been studied extensively, molecular data on other beet cultivars is scant. Here, we present a genome assembly of chard, a vegetable crop grown for its fleshy leaves. We report a de novo genome assembly of 604 Mbp, slightly larger than sugar beet assemblies presented so far. About 57 % of the assembly was annotated as repetitive sequence, of which LTR retrotransposons were the most abundant. Based on the presence of conserved genes, the chard assembly was estimated to be at least 96 % complete regarding its gene space. We predicted 34,521 genes of which 27,582 genes were supported by evidence from transcriptomic sequencing reads, and 5503 of the evidence-supported genes had multiple isoforms. We compared the chard gene set with gene sets from sugar beet and two wild beets (i.e. Beta vulgaris ssp. maritima and Beta patula) to find orthology relationships and identified genome-wide syntenic regions between chard and sugar beet. Lastly, we determined genomic variants that distinguish sugar beet and chard. Assessing the variation distribution along the chard chromosomes, we found extensive haplotype sharing between the two cultivars. In summary, our work provides a foundation for the molecular analysis of Beta vulgaris cultigroups as a basis for chard genomics and to unravel the domestication history of beet crops.

Genetic diversity among cultivated beets (Beta vulgaris) assessed via population-based whole genome sequences

Background

Diversification on the basis of utilization is a hallmark of Beta vulgaris (beet), as well as other crop species. Often, crop improvement and management activities are segregated by crop type, thus preserving unique genome diversity and organization. Full interfertility is typically retained in crosses between these groups and more traits may be accessible if the genetic basis of crop type lineage were known, along with available genetic markers to effect efficient transfer (e.g., via backcrossing). Beta vulgaris L. (2n =18) is a species complex composed of diverged lineages (e.g., crop types), including the familiar table, leaf (chard), fodder, and sugar beet crop types. Using population genetic and statistical methods with whole genome sequence data from pooled samples of 23 beet cultivars and breeding lines, relationships were determined between accessions based on identity-by-state metrics and shared genetic variation among lineages.

Results

Distribution of genetic variation within and between crop types showed extensive shared (e.g. non-unique) genetic variation. Lineage specific variation (e.g. apomorphy) within crop types supported a shared demographic history within each crop type, while principal components analysis revealed strong crop type differentiation. Relative contributions of specific chromosomes to genome wide differentiation were ascertained, with each chromosome revealing a different pattern of differentiation with respect to crop type. Inferred population size history for each crop type helped integrate selection history for each lineage, and highlighted potential genetic bottlenecks in the development of cultivated beet lineages.

Conclusions

A complex evolutionary history of cultigroups in Beta vulgaris was demonstrated, involving lineage divergence as a result of selection and reproductive isolation. Clear delineation of crop types was obfuscated by historical gene flow and common ancestry (e.g. admixture and introgression, and sorting of ancestral polymorphism) which served to share genome variation between crop types and, likely, important phenotypic characters. Table beet was well differentiated as a crop type, and shared more genetic variation within than among crop types. The sugar beet group was not quite as well differentiated as the table beet group. Fodder and chard groups were intermediate between table and sugar groups, perhaps the result of less intensive selection for end use.

Discovery of interesting new polymorphisms in a sugar beet (elite [Formula: see text] exotic) progeny by comparison with an elite panel

KEY MESSAGE

The comparison of QTL detection performed on an elite panel and an (elite [Formula: see text] exotic) progeny shows that introducing exotic germplasm into breeding programs can bring new interesting allelic diversity. Selection of stable varieties producing the highest amount of extractable sugar per hectare (ha), resistant to diseases, and respecting environmental criteria is undoubtedly the main target for sugar beet breeding. As sodium, potassium, and [Formula: see text]-amino nitrogen in sugar beets are the impurities that have the biggest negative impact on white sugar extraction, it is interesting to reduce their concentration in further varieties. However, domestication history and strong selection pressures have affected the genetic diversity needed to achieve this goal. In this study, quantitative trait locus (QTL) detection was performed on two populations, an (elite [Formula: see text] exotic) sugar beet progeny and an elite panel, to find potentially new interesting regions brought by the exotic accession. The three traits linked with impurities content were studied. Some QTLs were detected in both populations, the majority in the elite panel because of most statistical power. Some of the QTLs were colocated and had favorable effect in the progeny since the exotic allele was linked with a decrease in the impurity content. A few number of favorable QTLs were detected in the progeny, only. Consequently, introgressing exotic genetic material into sugar beet breeding programs can allow the incorporation of new interesting alleles.

Genomes of the wild beets Beta patula and Beta vulgaris ssp. maritima

We present draft genome assemblies of Beta patula, a critically endangered wild beet endemic to the Madeira archipelago, and of the closely related Beta vulgaris ssp. maritima (sea beet). Evidence-based reference gene sets for B. patula and sea beet were generated, consisting of 25 127 and 27 662 genes, respectively. The genomes and gene sets of the two wild beets were compared with their cultivated sister taxon B. vulgaris ssp. vulgaris (sugar beet). Large syntenic regions were identified, and a display tool for automatic genome-wide synteny image generation was developed. Phylogenetic analysis based on 9861 genes showing 1:1:1 orthology supported the close relationship of B. patula to sea beet and sugar beet. A comparative analysis of the Rz2 locus, responsible for rhizomania resistance, suggested that the sequenced B. patula accession was rhizomania susceptible. Reference karyotypes for the two wild beets were established, and genomic rearrangements were detected. We consider our data as highly valuable and comprehensive resources for wild beet studies, B. patula conservation management, and sugar beet breeding research.

Soil environment is a key driver of adaptation in Medicago truncatula: new insights from landscape genomics

Spatial differences in environmental selective pressures interact with the genomes of organisms, ultimately leading to local adaptation. Landscape genomics is an emergent research area that uncovers genome-environment associations, thus allowing researchers to identify candidate loci for adaptation to specific environmental variables. In the present study, we used latent factor mixed models (LFMMs) and Moran spectral outlier detection/randomization (MSOD-MSR) to identify candidate loci for adaptation to 10 environmental variables (climatic, soil and atmospheric) among 43 515 single nucleotide polymorphisms (SNPs) from 202 accessions of the model legume Medicago truncatula. Soil variables were associated with a large number of candidate loci identified through both LFMMs and MSOD-MSR. Genes tagged by candidate loci associated with drought and salinity are involved in the response to biotic and abiotic stresses, while those tagged by candidates associated with soil nitrogen and atmospheric nitrogen, participate in the legume-rhizobia symbiosis. Candidate SNPs identified through both LFMMs and MSOD-MSR explained up to 56% of variance in flowering traits. Our findings highlight the importance of soil in driving adaptation in the system and elucidate the basis of evolutionary potential of M. truncatula to respond to global climate change and anthropogenic disruption of the nitrogen cycle.

Combining six genome scan methods to detect candidate genes to salinity in the Mediterranean striped red mullet (Mullus surmuletus)

Background

Adaptive genomics may help predicting how a species will respond to future environmental changes. Genomic signatures of local adaptation in marine organisms are often driven by environmental selective agents impacting the physiology of organisms. With one of the highest salinity level, the Mediterranean Sea provides an excellent model to investigate adaptive genomic divergence underlying salinity adaptation. In the present study, we combined six genome scan methods to detect potential genomic signal of selection in the striped red mullet (Mullus surmuletus) populations distributed across a wide salinity gradient. We then blasted these outlier sequences on published fish genomic resources in order to identify relevant potential candidate genes for salinity adaptation in this species.

Results

Altogether, the six genome scan methods found 173 outliers out of 1153 SNPs. Using a blast approach, we discovered four candidate SNPs belonging to three genes potentially implicated in adaptation of M. surmuletus to salinity. The allele frequency at one of these SNPs significantly increases with salinity independently from the effect of longitude. The gene associated to this SNP, SOCS2, encodes for an inhibitor of cytokine and has previously been shown to be expressed under osmotic pressure in other marine organisms. Additionally, our results showed that genome scan methods not correcting for spatial structure can still be an efficient strategy to detect potential footprints of selection, when the spatial and environmental variation are confounded, and then, correcting for spatial structure in a second step represents a conservative method.

Conclusion

The present outcomes bring evidences of potential genomic footprint of selection, which suggest an adaptive response of M. surmuletus to salinity conditions in the Mediterranean Sea. Additional genomic data such as sequencing of a full-genome and transcriptome analyses of gene expression would provide new insights regarding the possibility that some striped red mullet populations are locally adapted to their saline environment.

Electronic supplementary material

The online version of this article (10.1186/s12864-018-4579-z) contains supplementary material, which is available to authorized users.

Chloroplastic and nuclear diversity of wild beets at a large geographical scale: Insights into the evolutionary history of the Beta section

Historical demographic processes and mating systems are believed to be major factors in the shaping of the intraspecies genetic diversity of plants. Among Caryophyllales, the Beta section of the genus Beta, within the Amaranthaceae/Chenopodiaceae alliance, is an interesting study model with species and subspecies (Beta macrocarpa, Beta patula, Beta vulgaris maritima and B.v. adanensis) differing in geographical distribution and mating system. In addition, one of the species, B. macrocarpa, mainly diploid, varies in its level of ploidy with a tetraploid cytotype described in the Canary Islands and in Portugal. In this study, we analyzed the nucleotide diversity of chloroplastic and nuclear sequences on a representative sampling of species and subspecies of the Beta section (except B. patula). Our objectives were (1) to assess their genetic relationships through phylogenetic and multivariate analyses, (2) relate their genetic diversity to their mating system, and (3) reconsider the ploidy status and the origin of the Canarian Beta macrocarpa.

Genetic and Genomic Tools to Asssist Sugar Beet Improvement: The Value of the Crop Wild Relatives

Sugar beet (Beta vulgaris L. ssp. vulgaris) is one of the most important European crops for both food and sugar production. Crop improvement has been developed to enhance productivity, sugar content or other breeder's desirable traits. The introgression of traits from Crop Wild Relatives (CWR) has been done essentially for lessening biotic stresses constraints, namely using Beta and Patellifolia species which exhibit disease resistance characteristics. Several studies have addressed crop-to-wild gene flow, yet, for breeding programs genetic variability associated with agronomically important traits remains unexplored regarding abiotic factors. To accomplish such association from phenotype-to-genotype, screening for wild relatives occurring in habitats where selective pressures are in play (i.e., populations in salt marshes for salinity tolerance; populations subjected to pathogen attacks and likely evolved resistance to pathogens) are the most appropriate streamline to identify causal genetic information. By selecting sugar beet CWR species based on genomic tools, rather than random variations, is a promising but still seldom explored route toward the development of improved crops. In this perspective, a viable streamline for sugar beet improvement is proposed through the use of different genomic tools by recurring to sugar beet CWRs and focusing on agronomic traits associated with abiotic stress tolerance. Overall, identification of genomic and epigenomic landscapes associated to adaptive ecotypes, along with the cytogenetic and habitat characterization of sugar beet CWR, will enable to identify potential hotspots for agrobiodiversity of sugar beet crop improvement toward abiotic stress tolerance.

Insights into the genetic relationships among plants of Beta section Beta using SNP markers

Using a much higher number of SNP markers and larger sample sizes than all the previous studies, we characterized the genetic relationships among wild and cultivated plants of section Beta. We analyzed the genetic variation of Beta section Beta, which includes wild taxa (Beta macrocarpa, B. patula, B. vulgaris subsp. adanensis and B. vulgaris subsp. maritima) and cultivars (fodder beet, sugar beet, garden beet, leaf beet, and swiss chards), using 9724 single nucleotide polymorphism markers. The analyses conducted at the individual level without a priori groups confirmed the strong differentiation of B. macrocarpa and B. vulgaris subsp. adanensis from the other taxa. B. vulgaris subsp. maritima showed a complex genetic structure partly following a geographical pattern, which confounded the differences between this taxon and the cultivated varieties. Cultivated varieties were structured into three main groups: garden beets, fodder and sugar beets, and leaf beets and swiss chards. The genetic structure described here will be helpful to correctly estimate linkage disequilibrium and to test for statistical associations between genetic markers and environmental variables.

Genetic Diversity and Physiological Performance of Portuguese Wild Beet (Beta vulgaris spp. maritima) from Three Contrasting Habitats

The establishment of stress resilient sugar beets (Beta vulgaris spp. vulgaris) is an important breeding goal since this cash crop is susceptible to drought and salinity. The genetic diversity in cultivated sugar beets is low and the beet wild relatives are useful genetic resources for tolerance traits. Three wild beet populations (Beta vulgaris spp. maritima) from contrasting environments, Vaiamonte (VMT, dry inland hill), Comporta (CMP, marsh) and Oeiras (OEI, coastland), and one commercial sugar beet (Isella variety, SB), are compared. At the genetic level, the use of six microsatellite allowed to detect a total of seventy six alleles. It was observed that CMP population has the highest value concerning the effective number of alleles and of expected heterozygosity. By contrast, sugar beet has the lowest values for all the parameters considered. Loci analysis with STRUCTURE allows defining three genetic clusters, the sea beet (OEI and CMP), the inland ruderal beet (VMT) and the sugar beet (SB). A screening test for progressive drought and salinity effects demonstrated that: all populations were able to recover from severe stress; drought impact was higher than that from salinity; the impact on biomass (total, shoot, root) was population specific. The distinct strategies were also visible at physiological level. We evaluated the physiological responses of the populations under drought and salt stress, namely at initial stress stages, late stress stages, and early stress recovery. Multivariate analysis showed that the physiological performance can be used to discriminate between genotypes, with a strong contribution of leaf temperature and leaf osmotic adjustment. However, the separation achieved and the groups formed are dependent on the stress type, stress intensity and duration. Each of the wild beet populations evaluated is very rich in genetic terms (allelic richness) and exhibited physiological plasticity, i.e., the capacity to physiologically adjust to changing environments. These characteristics emphasize the importance of the wild beet ecotypes for beet improvement programs. Two striking ecotypes are VMT, which is the best to cope with drought and salinity, and CMP which has the highest root to shoot ratio. These genotypes can supply breeding programs with distinct goals.