Pangenome of cultivated beet and crop wild relatives reveals parental relationships of a tetraploid wild beet

Abstract

Most crop plants, including sugar beet (Beta vulgaris subsp. vulgaris), suffer from domestication bottlenecks and low genetic diversity caused by extensive selection for few traits. However, crop wild relatives (CWRs) harbour useful traits relevant for crop improvement, including enhanced adaptation to biotic and abiotic stresses. Especially polyploids are interesting from an evolutionary perspective as genes undergo reorganisation after the polyploidisation event. Through neo- and subfunctionalisation, novel functions emerge, which enable plants to cope with changing environments and extreme/harsh conditions. Particularly in the face of climate change, specific stress and pathogen resistances or tolerances gain importance. To introduce such traits into breeding material, CWRs have already been identified as an important source for sustainable breeding. The identification of genes underlying traits of interest is crucial for crop improvement. For beets, the section Corollinae contains the tetraploid species Beta corolliflora (2n=4x=36) that harbours salt and frost tolerances as well as a wealth of pathogen resistances. The number of beneficial traits of B. corolliflora is increased compared to those of the known diploids in this section (all 2n=2x=18). Nevertheless, neither the parental relationships of B. corolliflora have been resolved, nor are genomic resources available to steer sustainable, genomics-informed breeding. To benefit from the resources offered by polyploid beet wild relatives, we generated a comprehensive pangenome dataset including B. corolliflora, Beta lomatogona, and Beta macrorhiza, as well as a more distant wild beet Patellifolia procumbens (2n=2x=18). Joined analyses with publicly available genome sequences of two additional wild beets allowed the identification of genomic regions absent from cultivated beet, providing a sequence database harbouring traits relevant for future breeding endeavours. In addition, we present strong evidence for the parental relationship of the B. corolliflora wild beet as an autotetraploid emerging from B. macrorhiza.

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

“…We explored and visualized sequences with the multipurpose software Geneious 6.1.8 (Kearse et al ., 2012). Dotplots were generated with FlexiDot (Seibt et al ., 2018) with a word size of 20 bp using long reads of B. vulgaris (PacBio; accession number SRX3402137; Funk et al ., 2018), B. corolliflora (ONT; accession number ERS13530775; Sielemann et al ., 2023a), and P. procumbens (ONT; accession number ERS13530778; Sielemann et al ., 2023a).…”

“…We target all major species across all sections, including higher polyploids. Building onto the plastome-based phylogenetics framework (Sielemann et al, 2022(Sielemann et al, , 2023a, our 17-beet-speciespanel represents a well-characterized sugar beet and CWR panel with regard to tracing genome evolution, chromosome stability, pangenomics, and taxonomy.…”

“…To understand the impact of repeats on crossing barriers, beet genomic resources are needed. So far there are three published reference genome sequence assemblies for sugar beet at our disposal (consecutive RefBeet versions: Dohm et al ., 2014; consecutive EL10 versions: Funk et al ., 2018 and McGrath et al ., 2020; KWS2320ONT_v1.0: Sielemann et al ., 2023b) and the number of studies comparing the wild beet germplasm to cultivated varieties is continuously increasing (Sielemann et al ., 2022, 2023a; Wascher et al ., 2022). Hence, sugar beet and its CWRs are well-suited to serve as a reference for maintaining stable karyotypes despite global changes across the repetitive genome.…”

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

“…Given the fact that di-and polyploid species are present in all of these gene pools (Frese & Ford-Lloyd, 2020) and due to the chromosome uniformity across all beet clades, polyploidization and restructuring of chromosomes seem to play a rather subordinate role in the emergence of genomic variety in Beta and Patellifolia species. Instead, differences at the DNA sequence level (Sielemann, Schmidt, et al, 2023) may be the cause of flawed chromosome pairing, thus resulting in the observed crossing barriers.…”

“…To add a (pan-)genomic layer, we generated low-pass whole genome shotgun data for all accessions as well as long reads for selected beet genomes. After assessing the phylogenetic placements of these accessions (Sielemann et al, 2022;Sielemann, Schmidt, et al, 2023), we estimated their repetitive DNA content and finely classified their repetitive DNA sequences in the respective TE and TR hierarchies. This not only allows following repetitive DNA evolution comprehensively across the beet genera, determining repeat gains, losses, and replacements, but also linking it back to chromosomal location and karyotypic stability.…”