The identification of allelic variation in potato

Abstract

Tuber shape is an intriguing morphological trait, which displays continuous trait variation ranging from flat, round to oval and long. Initially a single locus model was proposed to explain tuber shape, where multiple alleles rather than multiple loci were proposed to explain quantitative variation (van Eck et al. 1994). Besides this major-effect QTL on chromosome 10 another minor effect QTL has been published on chromosome 2, explaining 8% of the variance (Prashar et al. 2014). To obtain a better overview on the loci contributing to variation in tuber shape a comprehensive genome wide association study (GWAS) was performed in a panel of 537 commercial potato cultivars. This confirmed that the Ro locus is the major-effect QTL, but also the minor effect QTL on chromosome 2 was found. In addition, on chromosome 10, colocalization of the major effect QTL for tuber shape and a major QTL for eye depth was observed. For the Ro locus, most significant associations were found to localize on superscaffold PGSC0003DMB000000385 on chromosome 10. To refine this region we performed a recombinant screening in a diploid population (C×E). Recombinant analysis resulted in the identification of 104 recombinants originating from the female meiosis and 27 recombinants from the male meiosis. Recombinant analysis with additional SNPs within the selected region allowed us to confine the Ro locus to a 280 kb region, located on superscaffold DMB546 (323kb). Within this region a cluster of cell wall III peroxidase genes is found. Based on the putative role of peroxidases, this gene family cluster of repeats is likely to be implicated in mediating differences in tuber shape. Keywords Solanum tuberosum, organ morphology, high resolution mapping, GWAS, haplotypes Conclusion: We present a scalable approach that accurately reconstructs haplotypes in polyploid crops. The resulting haplotypes are instrumental for analysing the haplotype composition of the potato gene pool, and haplotype based QTL discovery.

Phased, chromosome-scale genome assemblies of tetraploid potato reveal a complex genome, transcriptome, and predicted proteome landscape underpinning genetic diversity

“…Flow cytometry estimates the tetraploid potato genome at 3.1 Gb (Willemsen, 2018), suggesting that the DeNovoMagic assemblies either under-represent the full assembly and/or that some of the haplotypes are collapsed. Comparisons of read depth across the six DeNovoMagic assemblies revealed that a subset of scaffolds represent collapsed haplotypes (Supplemental Figure 1).…”

“…Genome-scale studies of a heterozygous diploid clone revealed a substantial number of dysfunctional alleles that are fixed in repulsion and contribute to phenotypic diversity (Potato Genome Sequencing Consortium, 2011;Zhou et al, 2020). With an estimated 3.1 alleles per locus within tetraploid cultivars (Willemsen, 2018), coupled with rampant structural variation, the high degree of intra-genome heterogeneity has complicated the generation of a high-quality genome assembly of tetraploid potato.…”

The genetic architectures of vine and skin maturity in tetraploid potato

“…The most significant SNP for vine maturity in our GWAS, PotVar0079081, has been reported in other recent publications (Willemsen 2018; Klaassen et al 2019; Ospina Nieto et al 2021) that used a GWAS panel with mostly European varieties but also some founders of the US red market type, such as Triumph, Katahdin, and Early Rose. From the pedigree analysis of Vos et al (2015), we know the SNP predates modern breeding (“pre-1945”).…”

Paving the way for FAIR data in plant phenotyping

“…This population has frequently been studied in the WUR Plant Breeding department (Acharjee, 2013;Anithakumari, 2011;Carreño-Quintero, 2013;B. C. Celis-Gamboa, 2002;Getahun, 2017;Hurtado-Lopez, 2012;Jongedijk, 1991;Kloosterman, 2006;Park, 2005;Tessema, 2017;Werij, 2011;Willemsen, 2018). She performed multi-environment analyses studying QTL by environment interactions and observed QTLs that were stable across these environments for multiple plant traits.…”

“…The theses mentioned in the illustration are: Acharjee, 2013;Anithakumari, 2011;Carreño-Quintero, 2013;B. C. Celis-Gamboa, 2002;Getahun, 2017;Hurtado-Lopez, 2012;Jongedijk, 1991;Kloosterman, 2006;Park, 2005;Tessema, 2017;Werij, 2011;Willemsen, 2018. Other relevant work includes Hurtado-Lopez et al, 2015;Kloosterman et al, 2013. Findability is achieved with the attribution of unique, persistent identifiers to data. With the same being done to metadata, connections can be drawn between data points and their descriptors.…”