Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes

Schneider, Katharina; Kulosa, Dagmar; Soerensen, Thomas Rosleff; Möhring, Silke; Heine, Martin; Durstewitz, Gregor; Polley, Andreas; Weber, Eberhard; Jamsari, Jamsari; Lein, Jens Christoph LeinJ.C.; Hohmann, U.; Tahiro, Emma; Weißhaar, Bernd; Schulz, Britta; Koch, Georg; Jung, Christian; Ganal, Martin W.

doi:10.1007/s00122-007-0591-4

Cited by 59 publications

(75 citation statements)

References 46 publications

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“…Correspondence and requests for materials should be addressed to H.H. (Heinz.himmelbauer@crg.es) 2,14 were sequenced at low coverage (Supplementary Methods).…”

Section: Methods Summarymentioning

confidence: 99%

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

Dohm

Minoche

Holtgräwe

et al. 2013

Nature

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Sugar beet (Beta vulgaris ssp. vulgaris) is an important crop of temperate climates which provides nearly 30% of the world's annual sugar production and is a source for bioethanol and animal feed. The species belongs to the order of Caryophylalles, is diploid with 2n 5 18 chromosomes, has an estimated genome size of 714-758 megabases 1 and shares an ancient genome triplication with other eudicot plants 2 . Leafy beets have been cultivated since Roman times, but sugar beet is one of the most recently domesticated crops. It arose in the late eighteenth century when lines accumulating sugar in the storage root were selected from crosses made with chard and fodder beet 3 . Here we present a reference genome sequence for sugar beet as the first non-rosid, non-asterid eudicot genome, advancing comparative genomics and phylogenetic reconstructions. The genome sequence comprises 567 megabases, of which 85% could be assigned to chromosomes. The assembly covers a large proportion of the repetitive sequence content that was estimated 4 to be 63%. We predicted 27,421 protein-coding genes supported by transcript data and annotated them on the basis of sequence homology. Phylogenetic analyses provided evidence for the separation of Caryophyllales before the split of asterids and rosids, and revealed lineage-specific gene family expansions and losses. We sequenced spinach (Spinacia oleracea), another Caryophyllales species, and validated features that separate this clade from rosids and asterids. Intraspecific genomic variation was analysed based on the genome sequences of sea beet (Beta vulgaris ssp. maritima; progenitor of all beet crops) and four additional sugar beet accessions. We identified seven million variant positions in the reference genome, and also large regions of low variability, indicating artificial selection. The sugar beet genome sequence enables the identification of genes affecting agronomically relevant traits, supports molecular breeding and maximizes the plant's potential in energy biotechnology.During the last 200 years of sugar beet breeding, the sugar content has increased from 8% to 18% in today's cultivars. Breeding has also actively selected for traits like resistance to viral and fungal diseases, improved taproot yield, monogermy of the seed and bolting resistance.

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“…Correspondence and requests for materials should be addressed to H.H. (Heinz.himmelbauer@crg.es) 2,14 were sequenced at low coverage (Supplementary Methods).…”

Section: Methods Summarymentioning

confidence: 99%

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

Dohm

Minoche

Holtgräwe

et al. 2013

Nature

Self Cite

544

586

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“…We used the physical map (27) and different versions of the sugar beet draft genome (http://bvseq.molgen.mpg.de) and a collection of preliminary predicted gene models (RefBeet-0.3geneModels) for which the latest version is now available (13). Published sequences like expressed sequence tags (ESTs) (28) and BvFT1 (12) were used to find scaffolds which are located on chromosome 9. BLAST analyses (29) were performed to map known sequences to the reference sequence using the BLASTN function of the CLC Main Workbench 5.5 (CLC Bio).…”

Section: Methodsmentioning

confidence: 99%

The B2 flowering time locus of beet encodes a zinc finger transcription factor

Dally

Xiao

Holtgräwe

et al. 2014

Proc. Natl. Acad. Sci. U.S.A.

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Sugar beet (Beta vulgaris) is a biennial root crop that grows vegetatively in the first year and starts shoot elongation (bolting) and flowering after exposure to cold temperatures over winter. Early bolting before winter is controlled by the dominant allele of the B locus. Recently, the BOLTING TIME CONTROL 1 (BTC1) gene has been cloned from this locus. BTC1 promotes early bolting through repression of the downstream bolting repressor B. vulgaris FLOWERING LOCUS T1 (BvFT1) and activation of the downstream floral activator BvFT2. We have identified a new bolting locus B2 acting epistatically to B. B2 houses a transcription factor which is diurnally regulated and acts like BTC1 upstream of BvFT1 and BvFT2. It was termed BvBBX19 according to its closest homolog from Arabidopsis thaliana. The encoded protein has two conserved domains with homology to zinc finger B-boxes. Ethyl methanesulfonate-induced mutations within the second B-box caused up-regulation of BvFT1 and complete down-regulation of BvFT2. In Arabidopsis, the expression of FT is promoted by the B-box containing protein CONSTANS (CO). We performed a phylogenetic analysis with B-box genes from beet and A. thaliana but only BvCOL1 clustered with CO. However, BvCOL1 had been excluded as a CO ortholog by previous studies. Therefore, a new model for flowering induction in beet is proposed in which BTC1 and BvBBX19 complement each other and thus acquire a CO function to regulate their downstream targets BvFT1 and BvFT2.winter beet | sucrose | map-based cloning

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“…A two-fold increase of haplotype diversity over individual SNPs was found in maize (Ching et al 2002). Higher haplotype diversities were also observed in sugar beet (Schneider et al 2007), soybean (Zhu et al 2003), and barley (Russell et al 2004). As shown in humans, haplotype analysis offers the advantage of capturing most of the genetic variation across a region, and a minimal set of SNPs can be selected and used to distinguish common haplotypes in a block (Cardon and Abecasis 2003).…”

Section: Comparison Between Snp and Ssr Diversity Valuesmentioning

confidence: 95%

“…In out-crossing species, some average SNP densities include: 1 SNP/ 47 bp in non-coding regions of 36 inbred lines of maize (Ching et al 2002); 1 SNP/73 bp in regions corresponding to 592 unigenes of 12 inbred maize lines (Vroh Bi et al 2006); and 1 SNP/72 bp in 315 EST-derived loci of a panel of 13 lines of sugar beet (Beta vulgaris L.) (Schneider et al 2007). The average SNP densities among self-pollinated species, however, tend to be lower: an estimated 1 SNP/ 270 bp in non-coding and random genomic regions of 25 soybean cultivars (Zhu et al 2003) and 1 SNP/ 200 bp in 870 unigene-derived genomic regions of eight diverse accessions of barley (Rostoks et al 2005).…”

Section: Introductionmentioning

confidence: 99%

Analysis of gene-derived SNP marker polymorphism in US wheat (Triticum aestivum L.) cultivars

et al. 2008

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In this study, we developed 359 detection primers for single nucleotide polymorphisms (SNPs) previously discovered within intron sequences of wheat genes and used them to evaluate SNP polymorphism in common wheat (Triticum aestivum L.). These SNPs showed an average polymorphism information content (PIC) of 0.18 among 20 US elite wheat cultivars, representing seven market classes. This value increased to 0.23 when SNPs were preselected for polymorphisms among a diverse set of 13 hexaploid wheat accessions (excluding synthetic wheats) used in the wheat SNP discovery project (http://wheat.pw.usda.gov/SNP). PIC values for SNP markers in the D genome were approximately half of those for the A and B genomes. D genome SNPs also showed a larger PIC reduction relative to the other genomes (P \ 0.05) when US cultivars were compared with the more diverse set of 13 wheat accessions. Within those accessions, D genome SNPs show a higher proportion of alleles with low minor allele frequencies (\0.125) than found in the other two genomes. These data suggest that the reduction of PIC values in the D genome was caused by differential loss of low frequency alleles during the population size bottleneck that accompanied the development of modern commercial cultivars. Additional SNP discovery efforts targeted to the D genome in elite wheat germplasm will likely be required to offset the lower diversity of this genome. With increasing SNP discovery projects and the development of highthroughput SNP assay technologies, it is anticipated that SNP markers will play an increasingly important role in wheat genetics and breeding applications.

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Analysis of DNA polymorphisms in sugar beet (Beta vulgaris L.) and development of an SNP-based map of expressed genes

Cited by 59 publications

References 46 publications

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

The genome of the recently domesticated crop plant sugar beet (Beta vulgaris)

The B2 flowering time locus of beet encodes a zinc finger transcription factor

Analysis of gene-derived SNP marker polymorphism in US wheat (Triticum aestivum L.) cultivars

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