Genome assembly of six polyploid potato genomes

Kyriakidou, Maria; Anglin, Noelle L.; Ellis, David; Tai, Helen H.; Strömvik, Martina V.

doi:10.1038/s41597-020-0428-4

Cited by 41 publications

(30 citation statements)

References 30 publications

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“…Long-read assemblies now exist for polyploid crop species such as peanut [ 157 ], wheat [ 60 ], oilseed [ 22 ], and strawberry [ 158 ]. In some instances (e.g., potato [ 159 ]), multiple genome assemblies already exist within species. Nascent polyploid pan-genome studies are uncovering substantial diversity across species.…”

Section: Introductionmentioning

confidence: 99%

How the pan-genome is changing crop genomics and improvement

et al. 2021

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Crop genomics has seen dramatic advances in recent years due to improvements in sequencing technology, assembly methods, and computational resources. These advances have led to the development of new tools to facilitate crop improvement. The study of structural variation within species and the characterization of the pan-genome has revealed extensive genome content variation among individuals within a species that is paradigm shifting to crop genomics and improvement. Here, we review advances in crop genomics and how utilization of these tools is shifting in light of pan-genomes that are becoming available for many crop species.

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Section: Introductionmentioning

confidence: 99%

How the pan-genome is changing crop genomics and improvement

et al. 2021

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“…In this study, the plastomes from a panel of 13 potato accessions were characterized. The nuclear genomes of 12 of these accessions were previously studied for structural variation [14,15], and in the present study we present their complete plastome sequences and from an additional individual wild potato accession. Furthermore, SNPs, InDels, repeat sequences present as well as the type of each plastome are identified based on polymorphisms.…”

Section: Introductionmentioning

confidence: 99%

Complete plastome assemblies from a panel of 13 diverse potato taxa

et al. 2020

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The chloroplasts are a crucial part of photosynthesizing plant cells and are extensively utilized in phylogenetic studies mainly due to their maternal inheritance. Characterization and analysis of complete plastome sequences is necessary to understand their diversity and evolutionary relationships. Here, a panel of thirteen plastomes from various potato taxa are presented. Though they are highly similar with respect to gene order and content, there is also a great extent of SNPs and InDels between them, with one of the Solanum bukasovii plastomes (BUK2) having the highest number of SNPs and InDels. Five different potato plastome types (C, S, A, W, W2) are present in the panel. Interestingly, the S. tuberosum subsp. tuberosum (TBR) accession has a W-type plastome, which is not commonly found in this species. The S-type plastome has a conserved 48 bp deletion not found in other types, which is responsible for the divergence of the S-type from the C-type plastome. Finally, a phylogenetic analysis shows that these plastomes cluster according to their types. Congruence between the nuclear genome and the plastome phylogeny of these accessions was seen, however with considerable differences, supporting the hypothesis of introgression and hybridization between potato species.

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“…The availability of whole‐genome genotyping data and the development of resources and software that deal with these data would make linkage mapping of tetraploid populations generated from already accepted commercial varieties an increasingly useful tool. The availability of whole‐genome genotyping data, improved QTL mapping and GWAS methods and software, and several potato genome sequences (Aversano et al., 2015; Kyriakidou et al., 2020; PGSC, 2011; Sharma et al., 2013) promise to accelerate progress in potato breeding and genetics in the future.…”

Section: Resultsmentioning

confidence: 99%

QTL for pitted scab, hollow heart, and tuber calcium identified in a tetraploid population of potato derived from an Atlantic × Superior cross

et al. 2021

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Common scab, calcium deficiency, and internal tuber defects, such as hollow heart, have severe negative impact on the marketable yield and profitability of potato (Solanum tuberosum L.) farmers. The present study was conducted to detect quantitative trait loci (QTL) controlling these traits. A tetraploid linkage map was constructed using 808 single nucleotide polymorphisms (SNPs) from the SolCAP 8300 Infinium Potato Array using 151 genotypes of an F1 population generated from a cross between cultivars with divergent traits, Atlantic and Superior. Atlantic is susceptible to scab and has high incidence of hollow heart and low tuber calcium. Conversely, Superior has resistance to scab, low incidence of hollow heart, and high tuber calcium. This population was phenotypically evaluated between 2009 and 2012. Seven QTL regions explained pitted scab incidence and severity; two on chromosomes 3 and 11 of Atlantic, and five on chromosomes 1, 2, 5, 6, and 10 of Superior were identified. Also, six QTL regions that explained tuber calcium variation were detected; four QTL were located on chromosomes 1, 4, 5, 7, and 8 of Atlantic; and one QTL on chromosome 3 of Superior. In addition, five QTL were identified for the incidence of hollow heart; two QTL were located on chromosomes 3 and 5 of Atlantic, and three QTL were located on chromosomes 3, 6, and 12 of Superior. These QTL regions can be further studied to develop markers for marker‐assisted selection.

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Genome assembly of six polyploid potato genomes

Cited by 41 publications

References 30 publications

How the pan-genome is changing crop genomics and improvement

How the pan-genome is changing crop genomics and improvement

Complete plastome assemblies from a panel of 13 diverse potato taxa

QTL for pitted scab, hollow heart, and tuber calcium identified in a tetraploid population of potato derived from an Atlantic × Superior cross

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