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SNP Alleles Associated With Low Bolting Tendency in Sugar Beet.

ABSTRACT: The identification of efficient molecular markers related to low bolting tendency is a priority in sugar beet (Beta vulgaris L.) breeding. This study aimed to identify SNP markers associated with low bolting tendency by establishing a genome-wide association study. An elaborate 3-year field trial comprising 13 sugar beet lines identified L14 as the one exhibiting the lowest bolting tendency along with an increased survival rate after autumnal sowing. For SNP discovery following phenotyping, contrasting phenotypes of 24 non-bolting and 15 bolting plants of the L14 line were sequenced by restriction site-associated DNA sequencing (RAD-seq). An association model was established with a set of 10,924 RAD-based single nucleotide polymorphism (SNP) markers. The allelic status of the most significantly associated SNPs ranked based on their differential allelic status between contrasting phenotypes (p < 0.01) was confirmed on three different validation datasets comprising diverse sugar beet lines and varieties adopting a range of SNP detection technologies. This study has led to the identification of SNP_36780842 and SNP_48607347 linked to low bolting tendency and can be used for marker-assisted breeding and selection in sugar beet.

SUBMITTER: Ravi S

PROVIDER: S-EPMC8311237 | biostudies-literature |

REPOSITORIES: biostudies-literature

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SNP alleles associated with low bolting tendency in sugar beet

Project description:Release of SNP_36780842 and SNP_48607347 linked to low bolting tendency for marker-assisted breeding and selection in sugar beet.

| PRJEB42403 | ENA

Epigenomics and bolting tolerance in sugar beet genotypes.

Project description:In sugar beet (Beta vulgaris altissima), bolting tolerance is an essential agronomic trait reflecting the bolting response of genotypes after vernalization. Genes involved in induction of sugar beet bolting have now been identified, and evidence suggests that epigenetic factors are involved in their control. Indeed, the time course and amplitude of DNA methylation variations in the shoot apical meristem have been shown to be critical in inducing sugar beet bolting, and a few functional targets of DNA methylation during vernalization have been identified. However, molecular mechanisms controlling bolting tolerance levels among genotypes are still poorly understood. Here, gene expression and DNA methylation profiles were compared in shoot apical meristems of three bolting-resistant and three bolting-sensitive genotypes after vernalization. Using Cot fractionation followed by 454 sequencing of the isolated low-copy DNA, 6231 contigs were obtained that were used along with public sugar beet DNA sequences to design custom Agilent microarrays for expression (56k) and methylation (244k) analyses. A total of 169 differentially expressed genes and 111 differentially methylated regions were identified between resistant and sensitive vernalized genotypes. Fourteen sequences were both differentially expressed and differentially methylated, with a negative correlation between their methylation and expression levels. Genes involved in cold perception, phytohormone signalling, and flowering induction were over-represented and collectively represent an integrative gene network from environmental perception to bolting induction. Altogether, the data suggest that the genotype-dependent control of DNA methylation and expression of an integrative gene network participate in bolting tolerance in sugar beet, opening up perspectives for crop improvement.

| S-EPMC4682430 | biostudies-literature

Transcriptomic analysis of bolting tolerance in six sugar beet genotypes

Project description:The aim of this study was to identify genes that could be involved in sugar beet bolting tolerance. We focused on shoot apical meristem, the site of floral transition, from six sugar beet genotypes that were submitted to 9 weeks of vernalization treatment. This duration of cold exposure allowed bolting in the 3 sensitive genotypes but not in the 3 resistant ones. Single-copy sequences of DNA, potentially enriched in coding sequences, were isolated by Cot analysis and sequenced using Roche's GS-FLX sequencing technology in order to complete public sugar beet databases. Oligonucleotide arrays based on our single-copy sequences (about 42 000 predicted Open Reading Frames (ORFs)) and public database sequences (30 235 ESTs) were designed and used for transcriptomic and methylation analyses. We identified 1580 differentially expressed sequences (DES) and 1526 differentially methylated sequences (DMS) between bolting resistant and bolting sensitive genotypes. Using higher stringency criteria, we focused on 169 DES (with 87 up-regulated in R genotypes and 82 up-regulated in S ones) and 111 DMS (all hyper-methylated in S genotypes). In addition, 14 sequences were found to be both differentially methylated and differentially expressed, exhibiting negative correlation between their methylation and expression. We showed that bolting tolerance involved an integrated network of genes from environment perception, phytohormone signaling to flowering induction.

2014-12-31 | GSE55951 | GEO

DNA methylation variations between six sugar beet genotypes with distinct bolting tolerance levels

Project description:The aim of this study was to explore epigenetic variations between sugar beet genotypes with distinct bolting tolerance levels and to identify genes that could be involved in sugar beet bolting tolerance. We focused on shoot apical meristem, the site of floral transition, from six sugar beet genotypes that were submitted to 9 weeks of vernalization treatment. This duration of cold exposure allowed bolting in the 3 sensitive genotypes but not in the 3 resistant ones. Single-copy sequences of DNA, potentially enriched in coding sequences, were isolated by Cot analysis and sequenced using Roche's GS-FLX sequencing technology in order to complete public sugar beet databases. Oligonucleotide arrays based on our single-copy sequences (about 42 000 predicted Open Reading Frames (ORFs)) and public database sequences (30 235 ESTs) were designed and used for transcriptomic and methylation analyses. We identified 1580 differentially expressed sequences (DES) and 1526 differentially methylated sequences (DMS) between bolting resistant and bolting sensitive genotypes. Using higher stringency criteria, we focused on 169 DES (with 87 up-regulated in R genotypes and 82 up-regulated in S ones) and 111 DMS (all hyper-methylated in S genotypes). In addition, 14 sequences were found to be both differentially methylated and differentially expressed, exhibiting negative correlation between their methylation and expression. We showed that bolting tolerance involved an integrated network of genes from environment perception, phytohormone signaling to flowering induction.

2014-12-31 | GSE56413 | GEO

Transcriptome and DNA methylation variations between six sugar beet genotypes with distinct bolting tolerance levels

Project description:This SuperSeries is composed of the SubSeries listed below.

2014-12-31 | GSE56415 | GEO

A Detailed Analysis of the BR1 Locus Suggests a New Mechanism for Bolting after Winter in Sugar Beet (Beta vulgaris L.).

Project description:Sugar beet (Beta vulgaris ssp. vulgaris) is a biennial, sucrose-storing plant, which is mainly cultivated as a spring crop and harvested in the vegetative stage before winter. For increasing beet yield, over-winter cultivation would be advantageous. However, bolting is induced after winter and drastically reduces yield. Thus, post-winter bolting control is essential for winter beet cultivation. To identify genetic factors controlling bolting after winter, a F2 population was previously developed by crossing the sugar beet accessions BETA 1773 with reduced bolting tendency and 93161P with complete bolting after winter. For a mapping-by-sequencing analysis, pools of 26 bolting-resistant and 297 bolting F2 plants were used. Thereby, a single continuous homozygous region of 103 kb was co-localized to the previously published BR1 QTL for post-winter bolting resistance (Pfeiffer et al., 2014). The BR1 locus was narrowed down to 11 candidate genes from which a homolog of the Arabidopsis CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR 73-I (CPSF73-I) was identified as the most promising candidate. A 2 bp deletion within the BETA 1773 allele of BvCPSF73-Ia results in a truncated protein. However, the null allele of BvCPSF73-Ia might partially be compensated by a second BvCPSF73-Ib gene. This gene is located 954 bp upstream of BvCPSF73-Ia and could be responsible for the incomplete penetrance of the post-winter bolting resistance allele of BETA 1773. This result is an important milestone for breeding winter beets with complete bolting resistance after winter.

| S-EPMC5107561 | biostudies-literature

Sugar beet contains a large CONSTANS-LIKE gene family including a CO homologue that is independent of the early-bolting (B) gene locus.

Project description:Floral transition in the obligate long-day (LD) plant sugar beet (Beta vulgaris ssp. vulgaris) is tightly linked to the B gene, a dominant early-bolting quantitative trait locus, the expression of which is positively regulated by LD photoperiod. Thus, photoperiod regulators like CONSTANS (CO) and CONSTANS-LIKE (COL) genes identified in many LD and short-day (SD)-responsive plants have long been considered constituents and/or candidates for the B gene. Until now, the photoperiod response pathway of sugar beet (a Caryophyllid), diverged from the Rosids and Asterids has not been identified. Here, evidence supporting the existence of a COL gene family is provided and the presence of Group I, II, and III COL genes in sugar beet, as characterized by different zinc-finger (B-box) and CCT (CO, CO-like, TOC) domains is demonstrated. BvCOL1 is identified as a close-homologue of Group 1a (AtCO, AtCOL1, AtCOL2) COL genes, hence a good candidate for flowering time control and it is shown that it maps to chromosome II but distant from the B gene locus. The late-flowering phenotype of A. thaliana co-2 mutants was rescued by over-expression of BvCOL1 thereby suggesting functional equivalence with AtCO, and it is shown that BvCOL1 interacts appropriately with the endogenous downstream genes, AtFT and AtSOC1 in the transgenic plants. Curiously, BvCOL1 has a dawn-phased diurnal pattern of transcription, mimicking that of AtCOL1 and AtCOL2 while contrasting with AtCO. Taken together, these data suggest that BvCOL1 plays an important role in the photoperiod response of sugar beet.

| S-EPMC2486466 | biostudies-literature

Metagenomic analysis of the bacterial community associated with the taproot of sugar beet.

Project description:We analyzed a metagenome of the bacterial community associated with the taproot of sugar beet (Beta vulgaris L.) in order to investigate the genes involved in plant growth-promoting traits (PGPTs), namely 1-aminocyclopropane-1-carboxylic acid (ACC) deaminase, indole acetic acid (IAA), N2 fixation, phosphate solubilization, pyrroloquinoline quinone, siderophores, and plant disease suppression as well as methanol, sucrose, and betaine utilization. The most frequently detected gene among the PGPT categories encoded ?-1,3-glucanase (18 per 10(5) reads), which plays a role in the suppression of plant diseases. Genes involved in phosphate solubilization (e.g., for quinoprotein glucose dehydrogenase), methanol utilization (e.g., for methanol dehydrogenase), siderophore production (e.g. isochorismate pyruvate lyase), and ACC deaminase were also abundant. These results suggested that such PGPTs are crucially involved in supporting the growth of sugar beet. In contrast, genes for IAA production (iaaM and ipdC) were less abundant (~1 per 10(5) reads). N2 fixation genes (nifHDK) were not detected; bacterial N2 -fixing activity was not observed in the (15)N2 -feeding experiment. An analysis of nitrogen metabolism suggested that the sugar beet microbiome mainly utilized ammonium and nitroalkane as nitrogen sources. Thus, N2 fixation and IAA production did not appear to contribute to sugar beet growth. Taxonomic assignment of this metagenome revealed the high abundance of Mesorhizobium, Bradyrhizobium, and Streptomyces, suggesting that these genera have ecologically important roles in the taproot of sugar beet. Bradyrhizobium-assigned reads in particular were found in almost all categories of dominant PGPTs with high abundance. The present study revealed the characteristic functional genes in the taproot-associated microbiome of sugar beet, and suggest the opportunity to select sugar beet growth-promoting bacteria.

| S-EPMC4356465 | biostudies-literature

Fungal secretomes enhance sugar beet pulp hydrolysis.

Project description:The recalcitrance of lignocellulose makes enzymatic hydrolysis of plant biomass for the production of second generation biofuels a major challenge. This work investigates an efficient and economic approach for the enzymatic hydrolysis of sugar beet pulp (SBP), which is a difficult to degrade, hemicellulose-rich by-product of the table sugar industry. Three fungal strains were grown on different substrates and the production of various extracellular hydrolytic and oxidative enzymes involved in pectin, hemicellulose, and cellulose breakdown were monitored. In a second step, the ability of the culture supernatants to hydrolyze thermally pretreated SBP was tested in batch experiments. The supernatant of Sclerotium rolfsii, a soil-borne facultative plant pathogen, was found to have the highest hydrolytic activity on SBP and was selected for further hydrolyzation experiments. A low enzyme load of 0.2 mg g(-1) protein from the culture supernatant was sufficient to hydrolyze a large fraction of the pectin and hemicelluloses present in SBP. The addition of Trichoderma reesei cellulase (1-17.5 mg g(-1) SBP) resulted in almost complete hydrolyzation of cellulose. It was found that the combination of pectinolytic, hemicellulolytic, and cellulolytic activities works synergistically on the complex SBP composite, and a combination of these hydrolytic enzymes is required to achieve a high degree of enzymatic SBP hydrolysis with a low enzyme load.

| S-EPMC4162999 | biostudies-literature

Genomic selection in sugar beet breeding populations.

Project description:BackgroundGenomic selection exploits dense genome-wide marker data to predict breeding values. In this study we used a large sugar beet population of 924 lines representing different germplasm types present in breeding populations: unselected segregating families and diverse lines from more advanced stages of selection. All lines have been intensively phenotyped in multi-location field trials for six agronomically important traits and genotyped with 677 SNP markers.ResultsWe used ridge regression best linear unbiased prediction in combination with fivefold cross-validation and obtained high prediction accuracies for all except one trait. In addition, we investigated whether a calibration developed based on a training population composed of diverse lines is suited to predict the phenotypic performance within families. Our results show that the prediction accuracy is lower than that obtained within the diverse set of lines, but comparable to that obtained by cross-validation within the respective families.ConclusionsThe results presented in this study suggest that a training population derived from intensively phenotyped and genotyped diverse lines from a breeding program does hold potential to build up robust calibration models for genomic selection. Taken together, our results indicate that genomic selection is a valuable tool and can thus complement the genomics toolbox in sugar beet breeding.

| S-EPMC3848454 | biostudies-literature

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