Sugar Beet Genome Research Articles

Genome-wide identification of shaker K+ channel gene family in sugar beet (Beta vulgaris L.) and function of BvSKOR in response to salt and drought stresses

Potassium (K+) is the most abundant cation in plants, which is absorbed by roots and distributed throughout the plants and within plant cells, and is involved in various cellular processes. Shaker K+ channel plays crucial roles in the absorption and distribution of K+ and in the response to abiotic stress in plants. Herein, a total of six shaker K+ channel genes, BvKAT1, BvKAT3, BvAKT1, BvAKT2, BvAKT5, and BvSKOR, were identified in the genome of sugar beet (Beta vulgaris L.). The coding domain sequences (CDS) of these genes ranged from 2232 to 2739bp, and protein lengths were varied from 743 to 912 aa. The shaker K+ channel genes contained hormone-related and light responsiveness cis-acting regulatory elements. The phylogenetic analysis showed that BvSKOR was highly conserved and contained six transmembrane structures. The expression patterns of BvSKOR under salt and osmotic stress were analyzed by qRT-PCR, and found that the expression level of BvSKOR under low concentration salt and osmotic stress at short period of treatment were significantly higher than that of the control group. The function of BvSKOR was further verified in tobacco (Nicotiana tabacum), and the results showed that under salt and osmotic stress, the roots of transgenic plants were significantly stronger than those of wild type (WT) plants, and the relative water content (RWC), chlorophyll, proline, soluble sugar, soluble proteins contents and antioxidant enzyme activity were significantly higher than those of WT plants. These results indicated that overexpression of BvSKOR can significantly enhance the salt and drought tolerance in transgenic tobacco plants. This study could provide theoretical support and genetic resources for genetic improvement of crops stress resistance.

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.

In silico analysis of sirtuin-type histone deacetylase genes in sugar beet (Beta vulgaris L.)

Histone deacetylase (HDAC) enzymes catalyze the removal of an acetyl group from the lysine residues of histone N-terminal tails, and they repress gene transcription through condensation of chromatin. In plants, the sirtuins/silent information regulator 2 (SIR2) proteins which are NAD+-dependent deacetylases, have been identified in distinct plant species such as Arabidopsis, rice, tomato, soybean, maize, etc., but little is known about their functions in plants. They are mainly investigated in Arabidopsis and rice and found to be involved in H3K9 acetylation, metabolic pathways, repression of genes associated with stress response, and energy metabolism. A total of eight RPD3/HDA1 family HDAC genes have been recently identified in the sugar beet (Beta vulgaris L.) genome. However, B. vulgaris SIR2-type HDACs have not yet been identified and characterized. In this work, an in silico analysis of SIR2 family members was performed in sugar beet. Three SIR2 family HDACs were identified from the sugar beet genome, named BvSRT1, BvSRT2, and BvSRT3. The beet SIR2 gene family is found to be located on chromosomes 4, and 9. The phylogenetic tree building with B. vulgaris, Arabidopsis, tomato, soybean, Vitis vinifera, pepper, rice, maize, and Sorghum bicolor showed that 3 sugar beet SRTs were divided into two classes: Class II (BvSRT2) and IV (BvSRT1 and BvSRT3). SIR2 family proteins consisted of SIR2 domain (PF02146). The conserved motifs ranged from 6 to 50 amino acids, while the intron-exon numbers of genes ranged from 10 to 14. BvSRT1 and BvSRT3 exhibited similar motif distributions and exon/intron structures. Moreover, nuclear, and cytoplasmic localization of BvSRT1 and BvSRT3 has been predicted. BvSRT2 protein was located on the mitochondrion. Analysis of cis-elements revealed the involvement of BvSRT genes in hormone regulation, light response, abiotic stress response, and meristem expression. This study may shed light on the potential role of SIR2-type HDACs in beets.

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

Main conclusionThis 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.

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.

Investigation of the expansin gene family in sugar beet (Beta vulgaris) by the genome-wide level and their expression responses under abiotic stresses.

Sugar beet (Beta vulgaris ssp. vulgaris) is primarily used in sugar production worldwide. Expansins are a gene family of cell wall proteins effective in regulating cell wall structure. They also participate in developmental stages, including cell and leaf growth, root development, and fruit ripening. This study comprehensively characterizes the expansin gene family members found in the sugar beet genome. In addition, in silico expression analysis of sugar beet expansin genes under variable abiotic stress conditions and expression profiles of expansin genes under combined drought and heat stresses by the qRT-PCR method were evaluated in the study. A total of 31 sugar beet expansin genes were identified. BvuEXLA-02 and BvuEXLB-02 genes can have abiotic stress tolerance roles besides their roles in normal development. Determining the properties of sugar beet expansin, family members can help enable the cellulose hydrolysis mechanism and raise plant biomass. Elucidating expression profiles of the sugar beet expansin genes under variable stress conditions can support improving plant productivity. The results of the current study may also contribute to the deep understanding of sugar beet expansin genes in the future.

Genome-Wide Identification of B-Box Gene Family and Expression Analysis Suggest Its Roles in Responses to Cercospora Leaf Spot in Sugar Beet (Beta Vulgaris L.).

The B-box (BBX) protein, which is a zinc-finger protein containing one or two B-box domains, plays a crucial role in the growth and development of plants. Plant B-box genes are generally involved in morphogenesis, the growth of floral organs, and various life activities in response to stress. In this study, the sugar beet B-box genes (hereafter referred to as BvBBXs) were identified by searching the homologous sequences of the Arabidopsis thaliana B-box gene family. The gene structure, protein physicochemical properties, and phylogenetic analysis of these genes were systematically analyzed. In this study, 17 B-box gene family members were identified from the sugar beet genome. A B-box domain can be found in all sugar beet BBX proteins. BvBBXs encode 135 to 517 amino acids with a theoretical isoelectric point of 4.12 to 6.70. Chromosome localization studies revealed that BvBBXs were dispersed across nine sugar beet chromosomes except chromosomes 5 and 7. The sugar beet BBX gene family was divided into five subfamilies using phylogenetic analysis. The gene architectures of subfamily members on the same evolutionary tree branch are quite similar. Light, hormonal, and stress-related cis-acting elements can be found in the promoter region of BvBBXs. The BvBBX gene family was differently expressed in sugar beet following Cercospora leaf spot infection, according to RT-qPCR data. It is shown that the BvBBX gene family may influence how the plant reacts to a pathogen infection.

Genome-wide analysis of WD40 protein family and functional characterization of BvWD40-82 in sugar beet.

Sugar beet is one of the most important sugar crops in the world. It contributes greatly to the global sugar production, but salt stress negatively affects the crop yield. WD40 proteins play important roles in plant growth and response to abiotic stresses through their involvement in a variety of biological processes, such as signal transduction, histone modification, ubiquitination, and RNA processing. The WD40 protein family has been well-studied in Arabidopsis thaliana, rice and other plants, but the systematic analysis of the sugar beet WD40 proteins has not been reported. In this study, a total of 177 BvWD40 proteins were identified from the sugar beet genome, and their evolutionary characteristics, protein structure, gene structure, protein interaction network and gene ontology were systematically analyzed to understand their evolution and function. Meanwhile, the expression patterns of BvWD40s under salt stress were characterized, and a BvWD40-82 gene was hypothesized as a salt-tolerant candidate gene. Its function was further characterized using molecular and genetic methods. The result showed that BvWD40-82 enhanced salt stress tolerance in transgenic Arabidopsis seedlings by increasing the contents of osmolytes and antioxidant enzyme activities, maintaining intracellular ion homeostasis and increasing the expression of genes related to SOS and ABA pathways. The result has laid a foundation for further mechanistic study of the BvWD40 genes in sugar beet tolerance to salt stress, and it may inform biotechnological applications in improving crop stress resilience.

Genomic variation in the genus Beta based on 656 sequenced beet genomes

Cultivated beets (Beta vulgaris ssp. vulgaris) constitute important crop plants, in particular sugar beet as an indispensable source of sucrose. Several species of wild beets of the genus Beta with distribution along the European Atlantic coast, Macaronesia, and throughout the Mediterranean area exist. Thorough characterization of beet genomes is required for straightforward access to genes promoting genetic resistance against biotic and abiotic stress. Analysing short-read data of 656 sequenced beet genomes, we identified 10 million variant positions in comparison to the sugar beet reference genome RefBeet-1.2. The main groups of species and subspecies were distinguishable based on shared variation, and the separation of sea beets (Beta vulgaris ssp. maritima) into a Mediterranean and an Atlantic subgroup as suggested by previous studies could be confirmed. Complementary approaches of variant-based clustering were employed based on PCA, genotype likelihoods, tree calculations, and admixture analysis. Outliers suggested the occurrence of inter(sub)specific hybridisation, independently confirmed by different analyses. Screens for regions under artificial selection in the sugar beet genome identified 15 Mbp of the genome as variation-poor, enriched for genes involved in shoot system development, stress response, and carbohydrate metabolism. The resources presented herein will be valuable for crop improvement and wild species monitoring and conservation efforts, and for studies on beet genealogy, population structure and population dynamics. Our study provides a wealth of data for in-depth analyses of further aspects of the beet genome towards a thorough understanding of the biology of this important complex of a crop species and its wild relatives.

Potential of publicly available Beta vulgaris germplasm for sustainable sugarbeet improvement indicated by combining analysis of genetic diversity and historic resistance evaluation

AbstractSugar beet (Beta vulgaris L. ssp. vulgaris Doell.) was originally selected from white fodder beet in the 1780s and was then specifically bred for sucrose production. The relatively recent inception of the crop has led to a narrow genetic base that has bottlenecked sustainable improvement. To evaluate the potential of publicly available germplasm for sugar beet improvement, genetic diversity analysis with SNPs (single‐nucleotide polymorphisms) covering the whole genome of sugar beet was conducted using 1936 publicly available germplasm lines in the United States. The results confirmed the narrow genetic base of sugar beet and identified germplasm accessions with inherently greater diversity that were mostly accessions of wild sea beet (B. vulgaris ssp. maritima (L.) Arcang.), the progenitor species of white fodder beet. These wild accessions displayed a distinct genetic relationship from cultivated sugar beet lines, indicating their high potential for broadening sugar beet genetic diversity. Analysis of historic resistance evaluations also suggested a higher potential of B. vulgaris ssp. maritima accessions to be used as sources of resistance to major diseases and insects of sugar beet. A genome‐wide association study using historic evaluation data identified genomic regions significantly associated with disease and insect resistance. However, genomic regions associated with resistance to nematode, insects, or diseases vectored by insects were of low significance, indicating the need for additional research to allow for a more precise evaluation of germplasm responses to insects. The research confirms that accessions of B. vulgaris ssp. maritima are potentially valuable for improving biotic stress resistance and broadening the genetic base of sugar beet.

Перспективная стратегия применения молекулярных маркеров в селекции Beta vulgaris L. (обзор)

Abstract. Aim of the investigations is to study, summarize and analyze domestic and foreign literature concerning interaction of molecular genetics and classical sugar beet breeding for improvement of resistance to biotic and abiotic stresses. The problems are: 1) to analyze a current state of molecular-genetic investigations in domestic and foreign literature; 2) to study problems of marker-oriented breeding; 3) to estimate development prospects of sugar beet molecular research in Russian Federation. Methods. Analytical methods to inspect and handle information from international databases (PubMed, NCBI, and Academy Google) have been used to study modern strategy of molecular-genetic marking. Results. Use of DNA-technologies is an important part of modern breeding of agricultural crops. There have been discussed the research data permitting to get a more comprehensive idea of current state of sugar beet molecular genetics and breeding that is necessary to work out programs of their further development. There have been presented the results of foreign authors’ experiments and our own investigations on determining DNA-markers to study genetical polymorphism of sugar beet breeding material, select parent pairs for hybridization, identify genes of resistance to bolting, select breeding material with genes of resistance to biotic (Fusarium spp., nematodes, rhizomania) and abiotic stressors (salinization, drought, heavy metals). Now, wide-scale studies on using molecular-genetic markers in sugar beet breeding process have been carried out by Federal State Budgetary Scientific Institution “The A.L. Mazlumov All-Russian Research Institute of Sugar Beet and Sugar”. Use of molecular markers is one of the basic methods in plant breeding because of their general allocation throughout a genome and practical universality of application. In the article, advisability to use actual methods of sugar beet genome analysis employing DNA-markers in breeding process is considered. Scientific novelty involves estimation of the current state of Beta vulgaris L. molecular-genetic investigations in Russian Federation and abroad and their use in the crop breeding process.

Genome-wide Development and Physical Mapping of SSR Markers in Sugar Beet (Beta vulgaris L.)

Sugar beet (Beta vulgaris L.) is one of the important sugar crops. Thus, development of molecular tools to understand molecular mechanism of agronomic traits such as root yield and sucrose content by using comprehensive genome analysis is important for sugar beet molecular breeding. A prime to such a comprehensive genome analysis is high throughout marker development. In the present study, mining of sugar beet genome for simple sequence repeats (SSRs) revealed 37704 motifs. Dinucleotide repeats were the most abundant accounting for 69.3 %. A total of 22500 SSR primers were developed and these markers were physically mapped in sugar beet genome. The markers distributed over nine chromosomes and the map had a higher resolution (16.73 kb SSR-1). Also 102 SSR markers were found to be putatively associated with carbohydrate synthesis. The present study is the first report of genome-wide development of SSR markers and construction of SSR based physical map in sugar beet. SSR markers increased the number of available sugar beet specific SSR markers by 55-fold. SSR markers developed in the present study are valuable molecular genetic tools for comprehensive genome analysis to facilitate sugar beet molecular breeding

Seed productivity of alloplasmic lines of Beta patula and B. maritima with sterile cytoplasm under the conditions of apozygotic reproduction

Purpose. Revealing the effect of the cytoplasmic genome of replaced lines with the plasma of wild species Beta patula and B. maritima L., and apozygotic lines A4–A8 with the cytoplasm of S vulgaris Owen on the main factors of apozygotic reproduction, seed productivity, germination, monogermity and sterility as affected by the genetic origin of breeding material.
 Methods. The research was carried out in the Cytogenetics Laboratory (IBCSB), the Laboratory for Apomixis and Polyploidy of the Yaltushkiv EBS, and the Laboratory for Adaptive Breeding (Veselyi Podil EBS). Apozygotic seeds were obtained under a pollen-free regime according to the IBCSB’s Methods for Spatial Isolation and Parchment Insulators. Each seed bearer plant phenotype was determined during the flowering period by pollen sterility and partial flowering. Classification of plants was performed according to Owen (1945), with identifying plants of CMS-0, Type CMS-1, and CMS-2 types. The Monogermity of seed plants was assessed visually by the presence of separate fruits on the central shoots. In 2021, the roots of the replaced lines of the Veselyi Podil EBS were planted under the conditions of a pollen-free regime in the experimental field of the IBCSB. Seed production under apozygositic conditions was studied, taking into account the number of set fruits per 10-cm segment with 5 replications for each seed bearer. Germination was determined on the 10th day and germination vigour on the 5th day.
 Results. New sources of cytoplasmic male sterility (CMS) were obtained in the cytogenetics laboratory based on a genetic model of crossbreeding analysis, using differentiation and tools according to the marker-linked genes of hypocotyl color R+r-, and one / two-year development cycle B+b-. The analyzers for the nature of sugar beet sterility were sterility maintainers, dominant homozygotes for recessive genes of anthocyanin color, development cycle, partial fertility and sterility (NBeta vulgaris Sxxzz rr bb). Monogerm pollen-sterile lines with an apomictic way of seed reproduction (Yaltushkiv EBS) (A4–A8 Beta vulgaris Sxxzz rr), selected for the dominant color of the hypocotyl R+r-, stabilized for the trait of monogermity, 100% sterility and 2x gene ploidy, were characterized by low seed productivity. High rates of apozygotic seed development (80 to 96.4% of the number of set flowers) were observed against the background of the sterile cytoplasm of Beta maritima (Turkey). In the CMS BC4S patula line, the number of set apozygotic seeds ranges from 34 ± 0.3 to 39 ± 0.42, and the indicators of degenerated flowers under apozygotic regime varied from 31.2 to 54.3%. Isolated were seed plants with high self-reproduction, such as BC4S maritima Turkey, k.2/1, k.6/2, k.6/3 and k.3/4, k.9/4 on the background of new plasma of wild species of B. patula. The phenomenon of high self-reproduction of seeds (up to 98.5−96.4% of set flowers) was detected in line 21-011 CHS BC5S patula, which was comparable with hybrids and sterility maintainers (97.5−93.1%), which is determined by a special interaction of the beet nuclear genome of sugar beet and new plasma of wild species of the genus Beta L.
 Conclusions. The apomictic way of seed reproduction ensures the shortening of the breeding scheme for sugar beet due to high seed reproduction of mother parent in substituted lines with new plasma and differentiation by gametophytic reduction of parthenogenesis using morphological marker traits.

Genome-wide identification of BvHAK gene family in sugar beet (Beta vulgaris) and their expression analysis under salt treatments

High-affinity K+ transporter (HAK) is one of the most important K+ transporter families in plants and plays an important role in plant K+ uptake and transport. To explore the biological functions and gene expression patterns of the HAK gene family members in sugar beet (Beta vulgaris), physicochemical properties, the gene structure, chromosomal location, phylogenetic evolution, conserved motifs, three-dimensional structure, interaction network, cis-acting elements of promoter of BvHAKs were predicted by bioinformatic analysis, and their expression levels in different tissues of sugar beet under salt stress were analyzed by qRT-PCR. A total of 10 BvHAK genes were identified in the sugar beet genome. They contained 8-10 exons and 7-9 introns. The average number of amino acids was 778.30, the average molecular weight was 88.31 kDa, and the isoelectric point was 5.38-9.41. The BvHAK proteins contained 11-14 transmembrane regions. BvHAK4, -5, -7 and -13 were localized on plasma membrane, while others were localized on tonoplast. Phylogenetic analysis showed that HAK in higher plants can be divided into five clusters, namely cluster Ⅰ, Ⅱ, Ⅲ, Ⅳ, and Ⅴ, among which the members of cluster Ⅱ can be divided into three subclusters, including Ⅱa, Ⅱb, and Ⅱc. The BvHAK gene family members were distributed in cluster Ⅰ-Ⅳ with 1, 6, 1, and 2 members, respectively. The promoter of BvHAK gene family mainly contained stress responsive elements, hormone responsive elements, and growth and development responsive elements. The expression pattern of the BvHAK genes were further analyzed in different tissues of sugar beet upon salt treatment, and found that 50 and 100 mmol/L NaCl significantly induced the expression of the BvHAK genes in both shoots and roots. High salt (150 mmol/L) treatment clearly down-regulated their expression levels in shoots, but not in roots. These results suggested that the BvHAK gene family plays important roles in the response of sugar beet to salt stress.

Characteristic of the Ascorbate Oxidase Gene Family in Beta vulgaris and Analysis of the Role of AAO in Response to Salinity and Drought in Beet.

Ascorbate oxidase, which is known to play a key role in regulating the redox state in the apoplast, cell wall metabolism, cell expansion and abiotic stress response in plants, oxidizes apo-plastic ascorbic acid (AA) to dehydroascorbic acid (DHA). However, there is little information about the AAO genes and their functions in beets under abiotic stress. The term salt or drought stress refers to the treatment of plants with slow and gradual salinity/drought. Contrastingly, salt shock consists of exposing plants to high salt levels instantaneously and drought shock occurs under fast drought progression. In the present work, we have subjected plants to salinity or drought treatments to elicit either stress or shock and carried out a genome-wide analysis of ascorbate oxidase (AAO) genes in sugar beet (B. vulgaris cv. Huzar) and its halophytic ancestor (B. maritima). Here, conserved domain analyses showed the existence of twelve BvAAO gene family members in the genome of sugar beet. The BvAAO_1-12 genes are located on chromosomes 4, 5, 6, 8 and 9. The phylogenetic tree exhibited the close relationships between BvAAO_1-12 and AAO genes of Spinacia oleracea and Chenopodium quinoa. In both beet genotypes, downregulation of AAO gene expression with the duration of salt stress or drought treatment was observed. This correlated with a decrease in AAO enzyme activity under defined experimental setup. Under salinity, the key downregulated gene was BvAAO_10 in Beta maritima and under drought the BvAAO_3 gene in both beets. This phenomenon may be involved in determining the high tolerance of beet to salinity and drought.

Genomic and transcriptomic-based analysis of agronomic traits in sugar beet (Beta vulgaris L.) pure line IMA1.

Sugar beet (Beta vulgaris L.) is an important sugar-producing and energy crop worldwide. The sugar beet pure line IMA1 independently bred by Chinese scientists is a standard diploid parent material that is widely used in hybrid-breeding programs. In this study, a high-quality, chromosome-level genome assembly for IMA1was conducted, and 99.1% of genome sequences were assigned to nine chromosomes. A total of 35,003 protein-coding genes were annotated, with 91.56% functionally annotated by public databases. Compared with previously released sugar beet assemblies, the new genome was larger with at least 1.6 times larger N50 size, thereby substantially improving the completeness and continuity of the sugar beet genome. A Genome-Wide Association Studies analysis identified 10 disease-resistance genes associated with three important beet diseases and five genes associated with sugar yield per hectare, which could be key targets to improve sugar productivity. Nine highly expressed genes associated with pollen fertility of sugar beet were also identified. The results of this study provide valuable information to identify and dissect functional genes affecting sugar beet agronomic traits, which can increase sugar beet production and help screen for excellent sugar beet breeding materials. In addition, information is provided that can precisely incorporate biotechnology tools into breeding efforts.

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.

Genome-Wide Identification and Salt Stress Response Analysis of the bZIP Transcription Factor Family in Sugar Beet.

As one of the largest transcription factor families in plants, bZIP transcription factors play important regulatory roles in different biological processes, especially in the process of stress response. Salt stress inhibits the growth and yield of sugar beet. However, bZIP-related studies in sugar beet (Beta vulgaris L.) have not been reported. This study aimed to identify the bZIP transcription factors in sugar beet and analyze their biological functions and response patterns to salt stress. Using bioinformatics, 48 BvbZIP genes were identified in the genome of sugar beet, encoding 77 proteins with large structural differences. Collinearity analysis showed that three pairs of BvbZIP genes were fragment replication genes. The BvbZIP genes were grouped according to the phylogenetic tree topology and conserved structures, and the results are consistent with those reported in Arabidopsis. Under salt stress, the expression levels of most BvbZIP genes were decreased, and only eight genes were up-regulated. GO analysis showed that the BvbZIP genes were mainly negatively regulated in stress response. Protein interaction prediction showed that the BvbZIP genes were mainly involved in light signaling and ABA signal transduction, and also played a certain role in stress responses. In this study, the structures and biological functions of the BvbZIP genes were analyzed to provide foundational data for further mechanistic studies and for facilitating the efforts toward the molecular breeding of stress-resilient sugar beet.

SWEET Gene Family in Sugar Beet (Beta vulgaris): Genome-Wide Survey, Phylogeny and Expression Analysis.

<b>Background and Objective:</b> The SWEET (Sugars Will Eventually be Exported Transporter) proteins play important roles in modulating the growth and development processes in plants. However, little information is available on the SWEET family in sugar beet (<i>Beta vulgaris</i>). The objectives of this present study were to genome-wide identify and characterize the BvSWEET family in sugar beet. <b>Materials and Methods:</b> Based on the available genome, proteome and transcriptome databases of sugar beet, various computational tools have been used to analyze the nucleotide and full-length protein sequences of members of the BvSWEET family. <b>Results:</b> A total of 16 members of the BvSWEET family has been identified in sugar beet at the genome-wide scale. Structural analysis indicated that the BvSWEET family exhibited variable characteristics. Furthermore, the BvSWEET family in sugar beet could be categorized into four distinct groups like in other plant species. Of our interest, we found that some <i>BvSWEET</i> genes exhibited strongly preferential expression in major organs/tissues under adverse environmental stimuli. <b>Conclusion:</b> The results provided a comprehensive foundation for further functional characterization of the <i>BvSWEET </i>gene family.

Genome-Wide Identification and Expression Analysis of the BTB Domain-Containing Protein Gene Family in Sugar Beet

Cercospora leaf spots (CLSs) is a fungal disease of sugar beet caused by C. beticola, which damages leaves and leads to yield cut on sugar beet worldwide. BTB protein genes are critical to plant defense against bacterial infection. Here, 49 members of the BTB protein gene family were identified from the big data of the sugar beet genome, and bioinformatics was used to analyze the BTB protein family. Through molecular techniques, C. beticola of CLS was identified. In addition, the transcriptome data of sugar beet resistant and susceptible materials after C. beticola infection were obtained. Three BTB genes most significantly related to C. beticola stress were screened from the transcriptome data. The three genes are BvBTB1, BvBTB2, and BvBTB3, their full-length cDNA sequences were acquired by RT-PCR. The phenotypes of sugar beet resistant and susceptible materials under different spore concentrations of C. beticola were analyzed. Further, under the stress of C. beticola, qRT-PCR results showed that the expression levels of BvBTB1, BvBTB2, and BvBTB3 in roots and leaves were tissue-specific and expressed differently in various tissues. BvBTB1, BvBTB2, and BvBTB3 were overexpressed in the resistant and susceptible materials within five days after C. beticola infection: the peak appeared on the fifth day, and the highest expression was 25 times that of the control group. However, the lowest was 1.1 times of the control group, moreover, the expression in the resistant material was higher than that in the susceptible material. Overall, these results showed that BvBTB genes were involved in the response in sugar beet to C. beticola infection. Therefore, the study provided a scientific theoretical basis for developing new resistant varieties in sugar beet.