Genotype by environment interaction and stability analysis for harvest date in sugar beet cultivars.

This research assessed the quantitative and qualitative reactions of commercially grown sugar beets to four different harvest dates and their yield stability. The study followed a split-plot design within a randomized complete block design over 3 years. The main plot involved 10 sugar beet cultivars, while the subplot involved four harvest dates: August 13 (HD1), September 7 (HD2), October 3 (HD3), and November 12 (HD4). The study found that environmental conditions, genotypes, and harvest dates significantly affected various traits of sugar beet. Yearly environmental variations and their interactions with genotypes and harvest dates had substantial impacts on all measured traits at the 1% probability level. Additive main effect and multiplicative interaction analysis based on white sugar yield indicated that genotype and environment's additive effects, as well as the genotype-environment interaction, were significant at 1% probability level. Shokoufa and Arya, which exhibit high white sugar yield (WSY) and low first interaction principal component (IPC1) values, are identified as desirable due to their stability across different environments. Among the harvest dates in different years, the fourth and third dates showed a higher yield than the total average. Perfekta and Ekbatan exhibited high specific adaptability. According to the multi-trait stability index, Arta, Arya and Sina were recognized as stable and superior across all measured traits.

Genome-Wide Identification of GRAS Transcription Factors and Their Functional Analysis in Salt Stress Response in Sugar Beet.

GAI-RGA-and-SCR (GRAS) transcription factors can regulate many biological processes such as plant growth and development and stress defense, but there are few related studies in sugar beet. Salt stress can seriously affect the yield and quality of sugar beet (Beta vulgaris). Therefore, this study used bioinformatics methods to identify GRAS transcription factors in sugar beet and analyzed their structural characteristics, evolutionary relationships, regulatory networks and salt stress response patterns. A total of 28 BvGRAS genes were identified in the whole genome of sugar beet, and the sequence composition was relatively conservative. According to the topology of the phylogenetic tree, BvGRAS can be divided into nine subfamilies: LISCL, SHR, PAT1, SCR, SCL3, LAS, SCL4/7, HAM and DELLA. Synteny analysis showed that there were two pairs of fragment replication genes in the BvGRAS gene, indicating that gene replication was not the main source of BvGRAS family members. Regulatory network analysis showed that BvGRAS could participate in the regulation of protein interaction, material transport, redox balance, ion homeostasis, osmotic substance accumulation and plant morphological structure to affect the tolerance of sugar beet to salt stress. Under salt stress, BvGRAS and its target genes showed an up-regulated expression trend. Among them, BvGRAS-15, BvGRAS-19, BvGRAS-20, BvGRAS-21, LOC104892636 and LOC104893770 may be the key genes for sugar beet's salt stress response. In this study, the structural characteristics and biological functions of BvGRAS transcription factors were analyzed, which provided data for the further study of the molecular mechanisms of salt stress and molecular breeding of sugar beet.

A 3D printed plant model for accurate and reliable 3D plant phenotyping.

BACKGROUND: This study addresses the importance of precise referencing in 3-dimensional (3D) plant phenotyping, which is crucial for advancing plant breeding and improving crop production. Traditionally, reference data in plant phenotyping rely on invasive methods. Recent advancements in 3D sensing technologies offer the possibility to collect parameters that cannot be referenced by manual measurements. This work focuses on evaluating a 3D printed sugar beet plant model as a referencing tool. RESULTS: Fused deposition modeling has turned out to be a suitable 3D printing technique for creating reference objects in 3D plant phenotyping. Production deviations of the created reference model were in a low and acceptable range. We were able to achieve deviations ranging from -10 mm to +5 mm. In parallel, we demonstrated a high-dimensional stability of the reference model, reaching only ±4 mm deformation over the course of 1 year. Detailed print files, assembly descriptions, and benchmark parameters are provided, facilitating replication and benefiting the research community. CONCLUSION: Consumer-grade 3D printing was utilized to create a stable and reproducible 3D reference model of a sugar beet plant, addressing challenges in referencing morphological parameters in 3D plant phenotyping. The reference model is applicable in 3 demonstrated use cases: evaluating and comparing 3D sensor systems, investigating the potential accuracy of parameter extraction algorithms, and continuously monitoring these algorithms in practical experiments in greenhouse and field experiments. Using this approach, it is possible to monitor the extraction of a nonverifiable parameter and create reference data. The process serves as a model for developing reference models for other agricultural crops.

Vernalization promotes bolting in sugar beet by inhibiting the transcriptional repressors of BvGI.

Sugar beet (Beta vulgaris L.), a biennial sugar crop, contributes about 16% of the world's sugar production. The transition from vegetative growth, during which sugar accumulated in beet, to reproductive growth, during which sugar exhausted in beet, is determined by vernalization and photoperiod. GIGANTEA (GI) is a key photoperiodic flowering gene that is induced by vernalization in sugar beet. To identify the upstream regulatory factors of BvGI, candidate transcription factors (TF) that were co-expressed with BvGI and could bind to the BvGI promoter were screened based on weighted gene co-expression network analysis (WGCNA) and TF binding site prediction. Subsequently, their transcriptional regulatory role on the BvGI was validated through subcellular localization, dual-luciferase assays and yeast transformation tests. A total of 7,586 differentially expressed genes were identified after vernalization and divided into 18 co-expression modules by WGCNA, of which one (MEcyan) and two (MEdarkorange2 and MEmidnightblue) modules were positively and negatively correlated with the expression of BvGI, respectively. TF binding site predictions using PlantTFDB enabled the screening of BvLHY, BvTCP4 and BvCRF4 as candidate TFs that negatively regulated the expression of BvGI by affecting its transcription. Subcellular localization showed that BvLHY, BvTCP4 and BvCRF4 were localized to the nucleus. The results of dual-luciferase assays and yeast transformation tests showed that the relative luciferase activity and expression of HIS3 was reduced in the BvLHY, BvTCP4 and BvCRF4 transformants, which suggested that the three TFs inhibited the BvGI promoter. In addition, real-time quantitative reverse transcription PCR showed that BvLHY and BvTCP4 exhibited rhythmic expression characteristics similar to that of BvGI, while BvCRF4 did not. Our results revealed that vernalization crosstalked with the photoperiod pathway to initiate bolting in sugar beet by inhibiting the transcriptional repressors of BvGI.

Effect of BvAgNP on growth, development, and glyoxalase gene expression analysis in Mammillaria bombycina and Selenicereus undatus.

BACKGROUND: Silver nanoparticles (AgNPs) have been used in plant tissue culture as growth stimulants, promoting bud initiation, germination, and rooting. In prior studies, AgNPs were synthesized and characterized by green synthesis using extracts from Beta vulgaris var. cicla (BvAgNP), and their functionality as seed disinfectant and antimicrobial was verified. In this study, we evaluated the effect of BvAgNP on the growth and development of Mammillaria bombycina and Selenicereus undatus in vitro, as well as the expression of glyoxalase genes. METHODS: Explants from M. bombycina and S. undatus in vitro were treated with 25, 50, and 100 mg/L of BvAgNP. After 90 days, morphological characteristics were evaluated, and the expression of glyoxalase genes was analyzed by qPCR. RESULTS: All treatments inhibited rooting for M. bombycina and no bud initiation was observed. S. undatus, showed a maximum response in rooting and bud generation at 25 mg/L of BvAgNP. Scanning electron microscopy (SEM) results exhibited a higher number of vacuoles in stem cells treated with BvAgNP compared to the control for both species. Expression of glyoxalase genes in M. bombycina increased in all treatments, whereas it decreased for S. undatus, however, increasing in roots. CONCLUSIONS: This study presents the effects of BvAgNP on the growth and development of M. bombycina and S. undatus, with the aim of proposing treatments that promote in vitro rooting and bud initiation.

Sugar beet PMT5a and STP13 carriers suitable for proton-driven plasma membrane sucrose and glucose import in taproots.

Sugar beet (Beta vulgaris) is the major sugar-producing crop in Europe and Northern America, as the taproot stores sucrose at a concentration of around 20%. Genome sequence analysis together with biochemical and electrophysiological approaches led to the identification and characterization of the TST sucrose transporter driving vacuolar sugar accumulation in the taproot. However, the sugar transporters mediating sucrose uptake across the plasma membrane of taproot parenchyma cells remained unknown. As with glucose, sucrose stimulation of taproot parenchyma cells caused inward proton fluxes and plasma membrane depolarization, indicating a sugar/proton symport mechanism. To decipher the nature of the corresponding proton-driven sugar transporters, we performed taproot transcriptomic profiling and identified the cold-induced PMT5a and STP13 transporters. When expressed in Xenopus laevis oocytes, BvPMT5a was characterized as a voltage- and H+-driven low-affinity glucose transporter, which does not transport sucrose. In contrast, BvSTP13 operated as a high-affinity H+/sugar symporter, transporting glucose better than sucrose, and being more cold-tolerant than BvPMT5a. Modeling of the BvSTP13 structure with bound mono- and disaccharides suggests plasticity of the binding cleft to accommodate the different saccharides. The identification of BvPMT5a and BvSTP13 as taproot sugar transporters could improve breeding of sugar beet to provide a sustainable energy crop.

Applicability of SCoT markers in unraveling genetic variation and population structure among sugar beet (Beta vulgaris L.) germplasm.

BACKGROUND: Sugar beet (Beta vulgaris L.) holds significant importance as a crop globally cultivated for sugar production. The genetic diversity present in sugar beet accessions plays a crucial role in crop improvement programs. METHODS AND RESULTS: During the present study, we collected 96 sugar beet accessions from different regions and extracted DNA from their leaves. Genomic DNA was amplified using SCoT primers, and the resulting fragments were separated by gel electrophoresis. The data were analyzed using various genetic diversity indices, and constructed a population STRUCTURE, applied the unweighted pair-group method with arithmetic mean (UPGMA), and conducted Principle Coordinate Analysis (PCoA). The results revealed a high level of genetic diversity among the sugar beet accessions, with 265 bands produced by the 10 SCoT primers used. The percentage of polymorphic bands was 97.60%, indicating substantial genetic variation. The study uncovered significant genetic variation, leading to higher values for overall gene diversity (0.21), genetic distance (0.517), number of effective alleles (1.36), Shannon's information index (0.33), and polymorphism information contents (0.239). The analysis of molecular variance suggested a considerable amount of genetic variation, with 89% existing within the population. Using STRUCTURE and UPGMA analysis, the sugar beet germplasm was divided into two major populations. Structure analysis partitioned the germplasm based on the origin and domestication history of sugar beet, resulting in neighboring countries clustering together. CONCLUSION: The utilization of SCoT markers unveiled a noteworthy degree of genetic variation within the sugar beet germplasm in this study. These findings can be used in future breeding programs with the objective of enhancing both sugar beet yield and quality.

Regulation of photosynthetic function and reactive oxygen species metabolism in sugar beet (Beta vulgaris L.) cultivars under waterlogging stress and associated tolerance mechanisms.

Sugar beet (Beta vulgaris L.) is an economically important sugar crop worldwide that is susceptible to sudden waterlogging stress during seedling cultivation, which poses a major threat to sugar beet development and production. Our understanding of the physiological basis of waterlogging tolerance in sugar beet is limited. To investigate the photosynthetic adaptation strategies of sugar beet to waterlogging stress conditions, the tolerant cultivar KUHN1260 (KU) and sensitive cultivar SV1433 (SV) were grown under waterlogging stress, and their photosynthetic function and reactive oxygen species (ROS) metabolism were assessed. Our results showed that waterlogging stress significantly reduced the photosynthetic pigment content, rubisco activity, and expression level of the photosynthetic enzyme genes SvRuBP, SvGAPDH, and SvPRK, gas exchange parameters, and chlorophyll fluorescence parameters, induced damage to the ultrastructure of the chloroplast of the two sugar beet cultivars, inhibited the photosynthetic carbon assimilation capacity of sugar beet leaves, damaged the structural stability of photosystem II (PSII), and disturbed the equilibrium between electrons at the acceptor and donor sides of PSII, which was the result of stomatal and non-stomatal limiting factors. Moreover, the level of ROS, H2O2, and O2▪-, antioxidant enzyme activity, and gene expression levels in the leaves of the two sugar beet cultivars increased over time under waterlogging stress; ROS accumulation was lower and antioxidant enzyme activities and gene expression levels were higher in the waterlogging-tolerant cultivar (KU) than the waterlogging-sensitive cultivar (SV). In sum, these responses in the more tolerant cultivars are associated with their resistance to waterlogging stress. Our findings will aid the breeding of waterlogging-tolerant sugar beet cultivars.

Recessive resistance against beet chlorosis virus is conferred by the eukaryotic translation initiation factor (iso)4E in Beta vulgaris.

Eukaryotic translation initiation factors (eIFs) are important for mRNA translation but also pivotal for plant-virus interaction. Most of these plant-virus interactions were found between plant eIFs and the viral protein genome-linked (VPg) of potyviruses. In case of lost interaction due to mutation or deletion of eIFs, the viral translation and subsequent replication within its host is negatively affected, resulting in a recessive resistance. Here we report the identification of the Beta vulgaris Bv-eIF(iso)4E as a susceptibility factor towards the VPg-carrying beet chlorosis virus (genus Polerovirus). Using yeast two-hybrid and bimolecular fluorescence complementation assays, the physical interaction between Bv-eIF(iso)4E and the putative BChV-VPg was detected, while the VPg of the closely related beet mild yellowing virus (BMYV) was found to interact with the two isoforms Bv-eIF4E and Bv-eIF(iso)4E. These VPg-eIF interactions within the polerovirus-beet pathosystem were demonstrated to be highly specific, as single mutations within the predicted cap-binding pocket of Bv-eIF(iso)4E resulted in a loss of interaction. To investigate the suitability of eIFs as a resistance resource against beet infecting poleroviruses, B. vulgaris plants were genome edited by CRISPR/Cas9 resulting in knockouts of different eIFs. A simultaneous knockout of the identified BMYV-interaction partners Bv-eIF4E and Bv-eIF(iso)4E was not achieved, but Bv-eIF(iso)4EKO plants showed a significantly lowered BChV accumulation and decrease in infection rate from 100% to 28.86%, while no influence on BMYV accumulation was observed. Still, these observations support that eIFs are promising candidate genes for polerovirus resistance breeding in sugar beet.

Debottlenecking the L-DOPA 4,5-dioxygenase step with enhanced tyrosine supply boosts betalain production in Nicotiana benthamiana.

Synthetic biology provides emerging tools to produce valuable compounds in plant hosts as sustainable chemical production platforms. However, little is known about how supply and utilization of precursors is coordinated at the interface of plant primary and specialized metabolism, limiting our ability to efficiently produce high levels of target specialized metabolites in plants. L-Tyrosine is an aromatic amino acid precursor of diverse plant natural products including betalain pigments, which are used as the major natural food red colorants and more recently a visual marker for plant transformation. Here, we studied the impact of enhanced L-tyrosine supply on the production of betalain pigments by expressing arogenate dehydrogenase (TyrA) from table beet (Beta vulgaris, BvTyrAα), which has relaxed feedback inhibition by L-tyrosine. Unexpectedly, betalain levels were reduced when BvTyrAα was coexpressed with the betalain pathway genes in Nicotiana benthamiana leaves; L-tyrosine and 3,4-dihydroxy-L-phenylalanine (L-DOPA) levels were drastically elevated but not efficiently converted to betalains. An additional expression of L-DOPA 4,5-dioxygenase (DODA), but not CYP76AD1 or cyclo-DOPA 5-O-glucosyltransferase, together with BvTyrAα and the betalain pathway, drastically enhanced betalain production, indicating that DODA is a major rate-limiting step of betalain biosynthesis in this system. Learning from this initial test and further debottlenecking the DODA step maximized betalain yield to an equivalent or higher level than that in table beet. Our data suggest that balancing between enhanced supply ("push") and effective utilization ("pull") of precursor by alleviating a bottleneck step is critical in successful plant synthetic biology to produce high levels of target compounds.

Genome-wide identification, phylogenetic classification of histone acetyltransferase genes, and their expression analysis in sugar beet (Beta vulgaris L.) under salt stress.

MAIN CONCLUSION: This study identified seven histone acetyltransferase-encoding genes (HATs) from Beta vulgaris L. (sugar beet) genome through bioinformatics tools and analyzed their expression profiles under salt stress. Sugar beet HATs are phylogenetically divided into four families: GNAT, MYST, CBP, and TAFII250. The BvHAT genes were differentially transcribed in leaves, stems, and roots of B. vulgaris salt-resistant (Casino) and -sensitive (Bravo) cultivars under salt stress. Histone acetylation is regulated by histone acetyltransferases (HATs), which catalyze ɛ-amino bond formation between lysine residues and acetyl groups with a cofactor, acetyl-CoA. Even though the HATs are known to participate in stress response and development in model plants, little is known about the functions of HATs in crops. In sugar beet (Beta vulgaris L.), they have not yet been identified and characterized. Here, an in silico analysis of the HAT gene family in sugar beet was performed, and their expression patterns in leaves, stems, and roots of B. vulgaris were analyzed under salt stress. Salt-resistant (Casino) and -sensitive (Bravo) beet cultivars were used for gene expression assays. Seven HATs were identified from sugar beet genome, and named BvHAG1, BvHAG2, BvHAG3, BvHAG4, BvHAC1, BvHAC2, and BvHAF1. The HAT proteins were divided into 4 groups including MYST, GNAT (GCN5, HAT1, ELP3), CBP and TAFII250. Analysis of cis-acting elements indicated that the BvHAT genes might be involved in hormonal regulation, light response, plant development, and abiotic stress response. The BvHAT genes were differentially expressed in leaves, stems, and roots under control and 300 mM NaCl. In roots of B. vulgaris cv. Bravo, the BvHAG1, BvHAG2, BvHAG4, BvHAF1, and BvHAC1 genes were dramatically expressed after 7 and 14 days of salt stress. Interestingly, the BvHAC2 gene was not expressed under both control and stress conditions. However, the expression of BvHAG2, BvHAG3, BvHAG4, BvHAC1, BvHAC2 genes showed a significant increase in response to salt stress in the roots of cv. Casino. This study provides new insights into the potential roles of histone acetyltransferases in sugar beet.

AMMI and GGE biplot analysis for genotype × environment interactions affecting the yield and quality characteristics of sugar beet.

Sugar beet, an important sugar crop, contributes significantly to the world's sugar production. However, genotype-environment interactions (GEI) often affect the quality characteristics of sugar beet. Hence, understanding the effects of GEI on sugar beet quality can aid in identifying high-quality genotypes that can adapt to different environments. Traditional variance analysis can only be used to examine the yield of a variety and not its specific adaptability to specific conditions. Therefore, more comprehensive analytical methods are required to evaluate the characteristics of the variety under specific environments. Additive main effects and multiplicative interaction (AMMI) and genotype main effect and genotype × environment interaction (GGE) biplot models can be employed to comprehensively evaluate different varieties and address the drawbacks associated with a single evaluation method. Moreover, these models also allow us to explore new varieties more objectively and comprehensively. In this study, the adaptability and stability of 16 sugar beet varieties, in terms of yield and sugar content, were evaluated using AMMI and GGE biplot analysis in seven pilot projects undertaken in 2022. In the assessment of a small but significant proportion of the total GEI variance for the two qualitative traits (yield and sugar content), 80.58% of the variance was explained by the cumulative contribution of IPC1, IPC2, and IPC3. AMMI and GGE biplots clearly highlighted that KWS4207 (G3) exhibited high and stable quality. They also demonstrated that the experiments in Jalaid Banner (Inner Mongolia) (E7) were the most representative. Together, the results suggested that the comprehensive application of AMMI and GGE biplot analysis allowed for a more comprehensive, scientific, and effective evaluation of sugar beet varieties across different regions. The findings offer a theoretical basis for sugar beet breeding and could guide the rational design of experiments for testing new varieties of sugar beet.

The Effects of DNA Methylation on Cytoplasmic Male Sterility in Sugar Beet.

DNA methylation is widely found in higher plants and can control gene expression by regulation without changing the DNA sequence. In this study, the whole-genome methylation map of sugar beet was constructed by WGBS (whole-genome bisulfite sequencing) technology, and the results of WGBS were verified by bisulfite transformation, indicating that the results of WGBS technology were reliable. In addition, 12 differential methylation genes (DMGs) were identified, which were related to carbohydrate and energy metabolism, pollen wall development, and endogenous hormone regulation. Quantitative real-time PCR (qRT-PCR) showed that 75% of DMG expression levels showed negative feedback with methylation level, indicating that DNA methylation can affect gene expression to a certain extent. In addition, we found hypermethylation inhibited gene expression, which laid a foundation for further study on the molecular mechanism of DNA methylation at the epigenetic level in sugar beet male sterility.

Genotype by environment and genotype by yield*trait interactions in sugar beet: analyzing yield stability and determining key traits association.

The genotype by environment interaction significantly influences plant yield, making it imperative to understand its nature for the creation of breeding programs to enhance crop production. However, this is not the only obstacle in the yield improvement process. Breeders also face the significant challenge of unfavorable and negative correlations among key traits. In this study, the stability of root yield and white sugar yield, and the association between the key traits of root yield, sugar content, nitrogen, sodium, and potassium were examined in 20 sugar beet genotypes. The study was conducted using a randomized complete block design with four replications over two consecutive years across five locations. The combined analysis of variance results revealed significant main effects of year, location, and genotype on both root yield and white sugar yield. Notably, two-way and three-way interactions between these main effects on root yield and white sugar yield resulted in a significant difference. The additive main effect and multiplicative interaction analysis revealed that the first five interaction principal components significantly impacted both the root yield and white sugar yield. The linear mixed model results for root yield and white sugar yield indicated that the genotype effect and the genotype by environment interaction were significant. The weighted average absolute scores of the best linear unbiased predictions biplot demonstrated that genotypes 20, 4, 7, 2, 16, 3, 6, 1, 14, and 15 were superior in terms of root yield. For white sugar yield, genotypes 4, 16, 3, 7, 5, 1, 10, 20, 2, and 6 stood out. These genotypes were not only stable but also had a yield value higher than the total average. All key traits, which include sugar content, sodium, potassium, and alpha amino nitrogen, demonstrated a negative correlation with root yield. Based on the genotype by yield*trait analysis results, genotypes 20, 19, and 16 demonstrated optimal performance when considering the combination of root yield with sugar content, sodium, alpha amino nitrogen, and potassium. The multi-trait stability study, genotype 13 ranked first, and genotypes 10, 8, and 9 were identified as the most ideal stable genotypes across all traits. According to the multi-trait stability index, genotype 13 emerged as the top-ranking genotype. Additionally, genotypes 10, 8, and 9 were recognized as the most stable genotypes.

Temporal and species-specific resistance of sugar beet to green peach aphid and black bean aphid: mechanisms and implications for breeding.

BACKGROUND: Sugar beet (Beta vulgaris ssp. vulgaris), a key crop for sugar production, faces significant yield losses caused by the black bean aphid Aphis fabae (Scop.) and the green peach aphid Myzus persicae (Sulzer), which also transmits viruses. The restriction on neonicotinoid usage in Europe has intensified this problem, emphasizing the urgent need for breeding resistant crop varieties. This study evaluated 26 sugar beet germplasms for resistance against both aphid species by using performance and feeding behavior assays. Additionally, whole plant bioassays and semi-field experiments were carried out with Myzus persicae. RESULTS: Our findings demonstrate the presence of temporal resistance against both aphid species in the primary sugar beet gene pool. Beet yellows virus (BYV) carrying aphids showed enhanced performance. Different levels of plant defense mechanisms were involved including resistance against Myzus persicae before reaching the phloem, particularly in sugar beet line G3. In contrast, resistance against Aphis fabae turned out to be predominately phloem-located. Furthermore, a high incidence of black inclusion bodies inside the stomach of Myzus persicae was observed for approximately 85% of the plant genotypes tested, indicating a general and strong incompatibility between sugar beet and Myzus persicae in an initial phase of interaction. CONCLUSION: Sugar beet resistance against aphids involved different mechanisms and is species-specific. The identification of these mechanisms and interactions represents a crucial milestone in advancing the breeding of sugar beet varieties with improved resistance. © 2023 Julius Kühn-Institut and The Authors. Pest Management Science published by John Wiley & Sons Ltd on behalf of Society of Chemical Industry.

Genome-wide characterization of the xyloglucan endotransglucosylase/hydrolase family genes and their response to plant hormone in sugar beet.

Xyloglucan endotransglucosylase/hydrolases (XTHs) play a crucial role in plant growth and development. However, their functional response to phytohormone in sugar beet still remains obscure. In this study, we identified 30 putative BvXTH genes in the sugar beet genome. Phylogenetic and evolutionary relationship analysis revealed that they were clustered into three groups and have gone through eight tandem duplication events under purifying selection. Gene structure and motif composition analysis demonstrated that they were highly conserved and all contained one conserved glycoside hydrolase family 16 domain (Glyco_hydro_16) and one xyloglucan endotransglycosylase C-terminus (XET_C) domain. Transcriptional expression analysis exhibited that all BvXTHs were ubiquitously expressed in leaves, root hairs and tuberous roots, and most of them were up-regulated by brassinolide (BR), jasmonic acid (JA), abscisic acid (ABA) and gibberellic acid (GA3). Further mutant complementary experiment demonstrated that expression of BvXTH17 rescued the retarded growth phenotype of xth22, an Arabidopsis knock out mutant of AtXTH22. The findings in our work provide fundamental information on the structure and evolutionary relationship of the XTH family genes in sugar beet, and reveal the potential function of BvXTH17 in plant growth and hormone response.

Repeat turnover meets stable chromosomes: repetitive DNA sequences mark speciation and gene pool boundaries in sugar beet and wild beets.

Sugar beet and its wild relatives share a base chromosome number of nine and similar chromosome morphologies. Yet, interspecific breeding is impeded by chromosome and sequence divergence that is still not fully understood. Since repetitive DNAs are among the fastest evolving parts of the genome, we investigated, if repeatome innovations and losses are linked to chromosomal differentiation and speciation. We traced genome and chromosome-wide evolution across 13 beet species comprising all sections of the genera Beta and Patellifolia. For this, we combined short and long read sequencing, flow cytometry, and cytogenetics to build a comprehensive framework that spans the complete scale from DNA to chromosome to genome. Genome sizes and repeat profiles reflect the separation into three gene pools with contrasting evolutionary patterns. Among all repeats, satellite DNAs harbor most genomic variability, leading to fundamentally different centromere architectures, ranging from chromosomal uniformity in Beta and Patellifolia to the formation of patchwork chromosomes in Corollinae/Nanae. We show that repetitive DNAs are causal for the genome expansions and contractions across the beet genera, providing insights into the genomic underpinnings of beet speciation. Satellite DNAs in particular vary considerably between beet genomes, leading to the evolution of distinct chromosomal setups in the three gene pools, likely contributing to the barriers in beet breeding. Thus, with their isokaryotypic chromosome sets, beet genomes present an ideal system for studying the link between repeats, genomic variability, and chromosomal differentiation and provide a theoretical fundament for understanding barriers in any crop breeding effort.

Transcriptome Dynamics of Brassica juncea Leaves in Response to Omnivorous Beet Armyworm (Spodoptera exigua, Hübner).

Cruciferous plants manufacture glucosinolates (GSLs) as special and important defense compounds against insects. However, how insect feeding induces glucosinolates in Brassica to mediate insect resistance, and how plants regulate the strength of anti-insect defense response during insect feeding, remains unclear. Here, mustard (Brassica juncea), a widely cultivated Brassica plant, and beet armyworm (Spodoptera exigua), an economically important polyphagous pest of many crops, were used to analyze the changes in GSLs and transcriptome of Brassica during insect feeding, thereby revealing the plant-insect interaction in Brassica plants. The results showed that the content of GSLs began to significantly increase after 48 h of herbivory by S. exigua, with sinigrin as the main component. Transcriptome analysis showed that a total of 8940 DEGs were identified in mustard challenged with beet armyworm larvae. The functional enrichment results revealed that the pathways related to the biosynthesis of glucosinolate and jasmonic acid were significantly enriched by upregulated DEGs, suggesting that mustard might provide a defense against herbivory by inducing JA biosynthesis and then promoting GSL accumulation. Surprisingly, genes regulating JA catabolism and inactivation were also activated, and both JA signaling repressors (JAZs and JAMs) and activators (MYCs and NACs) were upregulated during herbivory. Taken together, our results indicate that the accumulation of GSLs regulated by JA signaling, and the regulation of active and inactive JA compound conversion, as well as the activation of JA signaling repressors and activators, collectively control the anti-insect defense response and avoid over-stunted growth in mustard during insect feeding.

Genomic characterization of a nematode tolerance locus in sugar beet.

BACKGROUND: Infection by beet cyst nematodes (BCN, Heterodera schachtii) causes a serious disease of sugar beet, and climatic change is expected to improve the conditions for BCN infection. Yield and yield stability under adverse conditions are among the main breeding objectives. Breeding of BCN tolerant sugar beet cultivars offering high yield in the presence of the pathogen is therefore of high relevance. RESULTS: To identify causal genes providing tolerance against BCN infection, we combined several experimental and bioinformatic approaches. Relevant genomic regions were detected through mapping-by-sequencing using a segregating F2 population. DNA sequencing of contrasting F2 pools and analyses of allele frequencies for variant positions identified a single genomic region which confers nematode tolerance. The genomic interval was confirmed and narrowed down by genotyping with newly developed molecular markers. To pinpoint the causal genes within the potential nematode tolerance locus, we generated long read-based genome sequence assemblies of the tolerant parental breeding line Strube U2Bv and the susceptible reference line 2320Bv. We analyzed continuous sequences of the potential locus with regard to functional gene annotation and differential gene expression upon BCN infection. A cluster of genes with similarity to the Arabidopsis thaliana gene encoding nodule inception protein-like protein 7 (NLP7) was identified. Gene expression analyses confirmed transcriptional activity and revealed clear differences between susceptible and tolerant genotypes. CONCLUSIONS: Our findings provide new insights into the genomic basis of plant-nematode interactions that can be used to design and accelerate novel management strategies against BCN.

Combined Omics Approaches Reveal Distinct Mechanisms of Resistance and/or Susceptibility in Sugar Beet Double Haploid Genotypes at Early Stages of Beet Curly Top Virus Infection.

Sugar beet is susceptible to Beet curly top virus (BCTV), which significantly reduces yield and sugar production in the semi-arid growing regions worldwide. Sources of genetic resistance to BCTV is limited and control depends upon insecticide seed treatments with neonicotinoids. Through double haploid production and genetic selection, BCTV resistant breeding lines have been developed. Using BCTV resistant (R) [KDH13; Line 13 and KDH4-9; Line 4] and susceptible (S) [KDH19-17; Line 19] lines, beet leafhopper mediated natural infection, mRNA/sRNA sequencing, and metabolite analyses, potential mechanisms of resistance against the virus and vector were identified. At early infection stages (2- and 6-days post inoculation), examples of differentially expressed genes highly up-regulated in the 'R' lines (vs. 'S') included EL10Ac5g10437 (inhibitor of trypsin and hageman factor), EL10Ac6g14635 (jasmonate-induced protein), EL10Ac3g06016 (ribosome related), EL10Ac2g02812 (probable prolyl 4-hydroxylase 10), etc. Pathway enrichment analysis showed differentially expressed genes were predominantly involved with peroxisome, amino acids metabolism, fatty acid degradation, amino/nucleotide sugar metabolism, etc. Metabolite analysis revealed significantly higher amounts of specific isoflavonoid O-glycosides, flavonoid 8-C glycosides, triterpenoid, and iridoid-O-glycosides in the leaves of the 'R' lines (vs. 'S'). These data suggest that a combination of transcriptional regulation and production of putative antiviral metabolites might contribute to BCTV resistance. In addition, genome divergence among BCTV strains differentially affects the production of small non-coding RNAs (sncRNAs) and small peptides which may potentially affect pathogenicity and disease symptom development.