Palaeohexaploid ancestry for Caryophyllales inferred from extensive gene‐based physical and genetic mapping of the sugar beet genome (Beta vulgaris)

Abstract

Sugar beet (Beta vulgaris) is an important crop plant that accounts for 30% of the world's sugar production annually. The genus Beta is a distant relative of currently sequenced taxa within the core eudicotyledons; the genomic characterization of sugar beet is essential to make its genome accessible to molecular dissection. Here, we present comprehensive genomic information in genetic and physical maps that cover all nine chromosomes. Based on this information we identified the proposed ancestral linkage groups of rosids and asterids within the sugar beet genome. We generated an extended genetic map that comprises 1127 single nucleotide polymorphism markers prepared from expressed sequence tags and bacterial artificial chromosome (BAC) end sequences. To construct a genome-wide physical map, we hybridized gene-derived oligomer probes against two BAC libraries with 9.5-fold cumulative coverage of the 758 Mbp genome. More than 2500 probes and clones were integrated both in genetic maps and the physical data. The final physical map encompasses 535 chromosomally anchored contigs that contains 8361 probes and 22 815 BAC clones. By using the gene order established with the physical map, we detected regions of synteny between sugar beet (order Caryophyllales) and rosid species that involves 1400-2700 genes in the sequenced genomes of Arabidopsis, poplar, grapevine, and cacao. The data suggest that Caryophyllales share the palaeohexaploid ancestor proposed for rosids and asterids. Taken together, we here provide extensive molecular resources for sugar beet and enable future high-resolution trait mapping, gene identification, and cross-referencing to regions sequenced in other plant species.

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

“…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 1 shows the positions of genetic markes in the genetic map 2 and RefBeet. Section 2 shows the distribution (stacked area graph) of predicted coding sequence (CDS) and repetitive sequence of the Gypsy type (LTR retrotransposon), the SINE type (non-LTR retrotransposon), the En/Spm type (DNA transposon), and three classes of satellite DNA (intercalary, centromeric, subtelomeric).…”

“…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.…”

“…The initial assembly was integrated with genome-wide genetic and physical map information 2 , resulting in 225 genetically anchored scaffolds (394.6 Mb), assigned to nine chromosomes (Table 1, Fig. 1, Extended Data Figs 1 and 2).…”

A Sequence-Ready Physical Map of Barley Anchored Genetically by Two Million Single-Nucleotide Polymorphisms

“…The high number of informative markers obtained by highthroughput sequencing enabled genetic anchoring at a clone-by-clone scale and thereby provided an independent method of validating the physical map. This method could also complement other genome projects following a hierarchical shotgun strategy (Paux et al, 2008;Lin et al, 2010;Dohm et al, 2012). At present, POPSEQ anchoring of the barley physical map is limited by the paucity of high-quality sequence information from each individual BAC contig.…”