[Show abstract][Hide abstract] ABSTRACT: Background
In flowering plants it has been shown that de novo genome assemblies of different species and genera show a significant drop in the proportion of alignable sequence. Within a plant species, however, it is assumed that different haplotypes of the same chromosome align well. In this paper we have compared three de novo assemblies of potato chromosome 5 and report on the sequence variation and the proportion of sequence that can be aligned.
For the diploid potato clone RH89-039-16 (RH) we produced two linkage phase controlled and haplotype-specific assemblies of chromosome 5 based on BAC-by-BAC sequencing, which were aligned to each other and compared to the 52 Mb chromosome 5 reference sequence of the doubled monoploid clone DM 1–3 516 R44 (DM). We identified 17.0 Mb of non-redundant sequence scaffolds derived from euchromatic regions of RH and 38.4 Mb from the pericentromeric heterochromatin. For 32.7 Mb of the RH sequences the correct position and order on chromosome 5 was determined, using genetic markers, fluorescence in situ hybridisation and alignment to the DM reference genome. This ordered fraction of the RH sequences is situated in the euchromatic arms and in the heterochromatin borders. In the euchromatic regions, the sequence collinearity between the three chromosomal homologs is good, but interruption of collinearity occurs at nine gene clusters. Towards and into the heterochromatin borders, absence of collinearity due to structural variation was more extensive and was caused by hemizygous and poorly aligning regions of up to 450 kb in length. In the most central heterochromatin, a total of 22.7 Mb sequence from both RH haplotypes remained unordered. These RH sequences have very few syntenic regions and represent a non-alignable region between the RH and DM heterochromatin haplotypes of chromosome 5.
Our results show that among homologous potato chromosomes large regions are present with dramatic loss of sequence collinearity. This stresses the need for more de novo reference assemblies in order to capture genome diversity in this crop. The discovery of three highly diverged pericentric heterochromatin haplotypes within one species is a novelty in plant genome analysis. The possible origin and cytogenetic implication of this heterochromatin haplotype diversity are discussed.
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The online version of this article (doi:10.1186/s12864-015-1578-1) contains supplementary material, which is available to authorized users.
[Show abstract][Hide abstract] ABSTRACT: One
of the most powerful technologies in unraveling the organization of a eukaryotic plant genome is high-resolution Fluorescent in situ hybridization of repeats and single copy DNA sequences on pachytene chromosomes. This technology allows the integration of physical mapping information with chromosomal positions, including centromeres, telomeres, nucleolar-organizing region, and euchromatin and heterochromatin. In this report, we established chromosomal positions of different repeat fractions of the potato genomic DNA (Cot100, Cot500 and Cot1000) on the chromosomes. We also analysed various repeat elements that are unique to potato including the moderately repetitive P5 and REP2 elements, where the REP2 is part of a larger Gypsy-type LTR retrotransposon and cover most chromosome regions, with some brighter fluorescing spots in the heterochromatin. The most abundant tandem repeat is the potato genomic repeat 1 that covers subtelomeric regions of most chromosome arms. Extensive multiple alignments of these repetitive sequences in the assembled RH89-039-16 potato BACs and the draft assembly of the DM1-3 516 R44 genome shed light on the conservation of these repeats within the potato genome. The consensus sequences thus obtained revealed the native complete transposable elements from which they were derived.
[Show abstract][Hide abstract] ABSTRACT: Nineteen tuber quality traits in potato were phenotyped in 205 cultivars and 299 breeder clones. Association analysis using 3364 AFLP loci and 653 SSR-alleles identified QTL for these traits. Two association mapping panels were analysed for marker-trait associations to identify quantitative trait loci (QTL). The first panel comprised 205 historical and contemporary tetraploid potato cultivars that were phenotyped in field trials at two locations with two replicates (the academic panel). The second panel consisted of 299 potato cultivars and included recent breeds obtained from five Dutch potato breeding companies and reference cultivars (the industrial panel). Phenotypic data for the second panel were collected during subsequent clonal selection generations at the individual breeding companies. QTL were identified for 19 agro-morphological and quality traits. Two association mapping models were used: a baseline model without, and a more advanced model with correction for population structure and genetic relatedness. Correction for population structure and genetic relatedness was performed with a kinship matrix estimated from marker information. The detected QTL partly not only confirmed previous studies, e.g. for tuber shape and frying colour, but also new QTL were found like for after baking darkening and enzymatic browning. Pleiotropic effects could be discerned for several QTL.
[Show abstract][Hide abstract] ABSTRACT: The objective of this paper is to evaluate the performance of the
conventional system of classifying maturity type in potato and to provide a
concept of maturity type based on crop physiology. We present an approach in
which physiological traits are used to quantify and assess maturity type unam-
biguously for a set of varieties covering a wide range of maturity classes and a
diploid F1 population separating for maturity and well-adapted to Dutch grow-
ing conditions, both grown in six environments. We defined physiological
maturity based on four traits: the duration of maximum green canopy, the area
under the green canopy cover progress curve, and the rate and duration of tuber
bulking. The results indicated that physiological maturity type criteria tended to
define maturity classes less ambiguously than the conventional criterion.
Moreover, the conventional criterion was subject to more random noise and
lacked stability and/or repeatability compared with the physiological traits. The
physiological maturity criteria also illustrated the physiological trade-offs that
existed between the selected traits and underlined the subtle complexities in
classifying maturity type. This study highlighted the capabilities of different
maturity type criteria in discriminating between different maturity classes
among the large set of genotypes. Our new approach involving key physiological
traits could be beneficial in offering physiology-based criteria to re-define
maturity type. An improved criterion based on important physiological traits would allow relating the maturity to crop phenology and physiology. These new
criteria may be amenable to further genetic analysis and could help in designing
strategies for potato ideotype breeding for genotypes with specific maturity
European Potato Journal 06/2013; 56(2):127-146. DOI:10.1007/s11540-013-9235-z · 0.84 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Assessment of genomic DNA sequence variation and genotype calling in autotetraploids implies the ability to distinguish among five possible alternative allele copy number states. This study demonstrates the accuracy of genotyping-by-sequencing (GBS) of a large collection of autotetraploid potato cultivars using next-generation sequencing. It is still costly to reach sufficient read depths on a genome wide scale, across the cultivated gene pool. Therefore, we enriched cultivar-specific DNA sequencing libraries using an in-solution hybridisation method (SureSelect). This complexity reduction allowed to confine our study to 807 target genes distributed across the genomes of 83 tetraploid cultivars and one reference (DM 1-3 511). Indexed sequencing libraries were paired-end sequenced in 7 pools of 12 samples using Illumina HiSeq2000. After filtering and processing the raw sequence data, 12.4 Gigabases of high-quality sequence data was obtained, which mapped to 2.1 Mb of the potato reference genome, with a median average read depth of 63× per cultivar. We detected 129,156 sequence variants and genotyped the allele copy number of each variant for every cultivar. In this cultivar panel a variant density of 1 SNP/24 bp in exons and 1 SNP/15 bp in introns was obtained. The average minor allele frequency (MAF) of a variant was 0.14. Potato germplasm displayed a large number of relatively rare variants and/or haplotypes, with 61% of the variants having a MAF below 0.05. A very high average nucleotide diversity (π = 0.0107) was observed. Nucleotide diversity varied among potato chromosomes. Several genes under selection were identified. Genotyping-by-sequencing results, with allele copy number estimates, were validated with a KASP genotyping assay. This validation showed that read depths of ∼60-80× can be used as a lower boundary for reliable assessment of allele copy number of sequence variants in autotetraploids. Genotypic data were associated with traits, and alleles strongly influencing maturity and flesh colour were identified.
PLoS ONE 05/2013; 8(5):e62355. DOI:10.1371/journal.pone.0062355 · 3.23 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Potato (Solanum tuberosum L.) originates from the Andes and evolved short-day-dependent tuber formation as a vegetative propagation strategy. Here we describe the identification of a central regulator underlying a major-effect quantitative trait locus for plant maturity and initiation of tuber development. We show that this gene belongs to the family of DOF (DNA-binding with one finger) transcription factors and regulates tuberization and plant life cycle length, by acting as a mediator between the circadian clock and the StSP6A mobile tuberization signal. We also show that natural allelic variants evade post-translational light regulation, allowing cultivation outside the geographical centre of origin of potato. Potato is a member of the Solanaceae family and is one of the world's most important food crops. This annual plant originates from the Andean regions of South America. Potato develops tubers from underground stems called stolons. Its equatorial origin makes potato essentially short-day dependent for tuberization and potato will not make tubers in the long-day conditions of spring and summer in the northern latitudes. When introduced in temperate zones, wild material will form tubers in the course of the autumnal shortening of day-length. Thus, one of the first selected traits in potato leading to a European potato type is likely to have been long-day acclimation for tuberization. Potato breeders can exploit the naturally occurring variation in tuberization onset and life cycle length, allowing varietal breeding for different latitudes, harvest times and markets.
[Show abstract][Hide abstract] ABSTRACT: After the publication of the article 'A hybrid BAC physical map of potato: a framework forsequencing a heterozygous genome [BMC Genomics 2011, 12:594]' the submitting authorwas notified that the contributions of LWP and LdL were quite substantial. To properly showtheir contribution to the manuscript, they have been taken out of the acknowlegdementssection and are now added to the authors list. LWP performed the BAC AFLP fingerprinting.LdL performed BAC pool AFLP reactions and BAC pool AFLP fingerprinting. Also, thesubmitting author was notified that patents and patent applications for technologies used inthis publication should have been included in the acknowledgements section. Therefore, thisarticle presents corrections to authors list, to the authors' contributions section, and to theacknowledgements section. Also, we declare the existence competing interests. We apologizefor any inconveniences these omissions may have caused.
[Show abstract][Hide abstract] ABSTRACT: Potato is the world's third most important food crop, yet cultivar improvement and genomic research in general remain difficult because of the heterozygous and tetraploid nature of its genome. The development of physical map resources that can facilitate genomic analyses in potato has so far been very limited. Here we present the methods of construction and the general statistics of the first two genome-wide BAC physical maps of potato, which were made from the heterozygous diploid clone RH89-039-16 (RH).
First, a gel electrophoresis-based physical map was made by AFLP fingerprinting of 64478 BAC clones, which were aligned into 4150 contigs with an estimated total length of 1361 Mb. Screening of BAC pools, followed by the KeyMaps in silico anchoring procedure, identified 1725 AFLP markers in the physical map, and 1252 BAC contigs were anchored the ultradense potato genetic map. A second, sequence-tag-based physical map was constructed from 65919 whole genome profiling (WGP) BAC fingerprints and these were aligned into 3601 BAC contigs spanning 1396 Mb. The 39733 BAC clones that overlap between both physical maps provided anchors to 1127 contigs in the WGP physical map, and reduced the number of contigs to around 2800 in each map separately. Both physical maps were 1.64 times longer than the 850 Mb potato genome. Genome heterozygosity and incomplete merging of BAC contigs are two factors that can explain this map inflation. The contig information of both physical maps was united in a single table that describes hybrid potato physical map.
The AFLP physical map has already been used by the Potato Genome Sequencing Consortium for sequencing 10% of the heterozygous genome of clone RH on a BAC-by-BAC basis. By layering a new WGP physical map on top of the AFLP physical map, a genetically anchored genome-wide framework of 322434 sequence tags has been created. This reference framework can be used for anchoring and ordering of genomic sequences of clone RH (and other potato genotypes), and opens the possibility to finish sequencing of the RH genome in a more efficient way via high throughput next generation approaches.
[Show abstract][Hide abstract] ABSTRACT: Background / Purpose:
Polyploid species, such as the autotetraploid crop potato, can have four highly diverse genomes, and a large number of highly diverse haplotypes can be found across the gene pool.
Our results demonstrate that in-solution hybridization enrichment of indexed polyploid DNA samples is a viable and cost-effective approach for performing large-scale resequencing and genotyping studies using high-throughput sequencing technologies. This approach: captured 95% of the 800 target gene sequences identified DNA variants at a high accuracy detected individual zygosity (allele copy-number) for 83 potato cultivars
Current Opinion Conference - Plant Genome Evolution 2011; 10/2011
[Show abstract][Hide abstract] ABSTRACT: Potato (Solanum tuberosum L.) is the world's most important non-grain food crop and is central to global food security. It is clonally propagated, highly heterozygous, autotetraploid, and suffers acute inbreeding depression. Here we use a homozygous doubled-monoploid potato clone to sequence and assemble 86% of the 844-megabase genome. We predict 39,031 protein-coding genes and present evidence for at least two genome duplication events indicative of a palaeopolyploid origin. As the first genome sequence of an asterid, the potato genome reveals 2,642 genes specific to this large angiosperm clade. We also sequenced a heterozygous diploid clone and show that gene presence/absence variants and other potentially deleterious mutations occur frequently and are a likely cause of inbreeding depression. Gene family expansion, tissue-specific expression and recruitment of genes to new pathways contributed to the evolution of tuber development. The potato genome sequence provides a platform for genetic improvement of this vital crop.
[Show abstract][Hide abstract] ABSTRACT: Phenotypic analyses of two different association panels of tetraploid potato cultivars are presented. Association panels are
sets of variously related genotypes assembled for association analysis purposes. The aims of this research were to inspect,
analyse and compare two phenotypic data sets, a first step in association mapping analysis. A first panel of 205 contemporary
and historical cultivars, selected to represent the commercial potato germplasm pool, was evaluated in two trials in 2006,
one on sandy soil and the other on clay soil, both with two replications. It was called the academic panel. Data for the second
panel with 299 genotypes were compiled from contributions from five breeding companies and included 66 locations and 18years.
Each of the participating breeding companies contributed data from their clonal selection programmes for 38 advanced breeding
clones and a series of standard cultivars. It was called the industrial panel. Variance components for genotypic main effects
and genotype-by-environment interactions were calculated, and estimates for the random genotypic main effects were produced.
The genotypic main effects for 19 agro-morphological and quality traits were used to study trait by trait correlations within
each panel. In addition, for the genotypes shared by both panels, the correlation of genetic main effects between the panels
was investigated. The heritability of all traits was high and no large differences were observed between panels. Coefficients
of trait variation were highly correlated (r = 0.9) for both panels and trait by trait correlations in both panels showed highly similar patterns. These results demonstrate
that a single-year balanced field trial as well as using breeders’ records yields robust phenotypic information that can be
used in a genome-wide association study. Issues related to data management and definition of traits are discussed.
KeywordsGenotype-by-environment interaction–Heritabilities–Mixed models–Potato
Potato Research 06/2011; 54(2):157-181. DOI:10.1007/s11540-011-9186-1 · 0.84 Impact Factor
[Show abstract][Hide abstract] ABSTRACT: Like all plants, potato has evolved a surveillance system consisting of a large array of genes encoding for immune receptors that confer resistance to pathogens and pests. The majority of these so-called resistance or R proteins belong to the super-family that harbour a nucleotide binding and a leucine-rich-repeat domain (NB-LRR). Here, sequence information of the conserved NB domain was used to investigate the genome-wide genetic distribution of the NB-LRR resistance gene loci in potato. We analysed the sequences of 288 unique BAC clones selected using filter hybridisation screening of a BAC library of the diploid potato clone RH89-039-16 (S. tuberosum ssp. tuberosum) and a physical map of this BAC library. This resulted in the identification of 738 partial and full-length NB-LRR sequences. Based on homology of these sequences with known resistance genes, 280 and 448 sequences were classified as TIR-NB-LRR (TNL) and CC-NB-LRR (CNL) sequences, respectively. Genetic mapping revealed the presence of 15 TNL and 32 CNL loci. Thirty-six are novel, while three TNL loci and eight CNL loci are syntenic with previously identified functional resistance genes. The genetic map was complemented with 68 universal CAPS markers and 82 disease resistance trait loci described in literature, providing an excellent template for genetic studies and applied research in potato.
Electronic supplementary material
The online version of this article (doi:10.1007/s00122-011-1602-z) contains supplementary material, which is available to authorized users.
[Show abstract][Hide abstract] ABSTRACT: Association mapping is considered to be an important alternative strategy for the identification of quantitative trait loci (QTL) as compared to traditional QTL mapping. A necessary prerequisite for association analysis to succeed is detailed information regarding hidden population structure and the extent of linkage disequilibrium. A collection of 430 tetraploid potato cultivars, comprising two association panels, has been analysed with 41 AFLP® and 53 SSR primer combinations yielding 3364 AFLP fragments and 653 microsatellite alleles, respectively. Polymorphism information content values and detected number of alleles for the SSRs studied illustrate that commercial potato germplasm seems to be equally diverse as Latin American landrace material. Genome-wide linkage disequilibrium (LD)—reported for the first time for tetraploid potato—was observed up to approximately 5 cM using r2 higher than 0.1 as a criterion for significant LD. Within-group LD, however, stretched on average twice as far when compared to overall LD. A Bayesian approach, a distance-based hierarchical clustering approach as well as principal coordinate analysis were adopted to enquire into population structure. Groups differing in year of market release and market segment (starch, processing industry and fresh consumption) were repeatedly detected. The observation of LD up to 5 cM is promising because the required marker density is not likely to disable the possibilities for association mapping research in tetraploid potato. Population structure appeared to be weak, but strong enough to demand careful modelling of genetic relationships in subsequent marker-trait association analyses. There seems to be a good chance that linkage-based marker-trait associations can be identified at moderate marker densities.
Electronic supplementary material
The online version of this article (doi:10.1007/s00122-010-1379-5) contains supplementary material, which is available to authorized users.
[Show abstract][Hide abstract] ABSTRACT: We have investigated the genetics and molecular biology of orange flesh colour in potato (Solanum tuberosum L.). To this end the natural diversity in three genes of the carotenoid pathway was assessed by SNP analyses. Association analysis was performed between SNP haplotypes and flesh colour phenotypes in diploid and tetraploid potato genotypes. We observed that among eleven beta-carotene hydroxylase 2 (Chy2) alleles only one dominant allele has a major effect, changing white into yellow flesh colour. In contrast, none of the lycopene epsilon cyclase (Lcye) alleles seemed to have a large effect on flesh colour. Analysis of zeaxanthin epoxidase (Zep) alleles showed that all (diploid) genotypes with orange tuber flesh were homozygous for one specific Zep allele. This Zep allele showed a reduced level of expression. The complete genomic sequence of the recessive Zep allele, including the promoter, was determined, and compared with the sequence of other Zep alleles. The most striking difference was the presence of a non-LTR retrotransposon sequence in intron 1 of the recessive Zep allele, which was absent in all other Zep alleles investigated. We hypothesise that the presence of this large sequence in intron 1 caused the lower expression level, resulting in reduced Zep activity and accumulation of zeaxanthin. Only genotypes combining presence of the dominant Chy2 allele with homozygosity for the recessive Zep allele produced orange-fleshed tubers that accumulated large amounts of zeaxanthin.
Electronic supplementary material
The online version of this article (doi:10.1007/s11103-010-9647-y) contains supplementary material, which is available to authorized users.
[Show abstract][Hide abstract] ABSTRACT: We investigated the potential of a model-based approach to assist in the genetic analysis of the environment-sensitive, quantitative crop trait canopy cover in potato (Solanum tuberosum L.). We used a model based on beta functions to analyze the genotype×environment interactions related to the dynamics of canopy cover. The model equations describe three phases of canopy growth: build-up phase (P1),
maximum cover phase (P2), and decline phase (P3). The model has five parameters: t m1 indicates the transition from accelerating to diminishing growth during P1, t 1 marks the end of P1 when canopy cover attains its maximum level v max , t 2 marks the end of P2 when canopy cover starts to decline, and t e represents the end of the crop cycle when canopy cover has declined to nil. Values of these parameters were estimated for 100 individuals of an F1 population, their parents, and five standard cultivars differing in maturity type, using data collected in six field experiments. The model successfully described differences in canopy dynamics among individual genotypes across environments. Model parameters were used to
derive several secondary variables: DP2 (duration of P2), DP3 (duration of P3), and A sum (area under the canopy cover curve reflecting the crop ’ s capacity to intercept incoming radiation). The length of P1 (i.e. t1 ) was relatively conservative, but D P2, and DP3 varied greatly. Later genotypes had higher A sum because they had longer DP2, and DP3 . Genotypic and phenotypic variance components of the F1 population were
estimated for all traits across environments and almost all of them proved significant (P<0.01). For most traits, genetic variability and heritability were high. There are opportunities, therefore, for future potato breeding programmes to exploit the genetic variability available in the F1 segregating population and to select for highly heritable traits in order to improve radiation interception efficiency.
[Show abstract][Hide abstract] ABSTRACT: Single nucleotide polymorphisms (SNPs) represent the most abundant type of genetic variation that can be used as molecular markers. The SNPs that are hidden in sequence databases can be unlocked using bioinformatic tools. For efficient application of these SNPs, the sequence set should be error-free as much as possible, targeting single loci and suitable for the SNP scoring platform of choice. We have developed a pipeline to effectively mine SNPs from public EST databases with or without quality information using QualitySNP software, select reliable SNP and prepare the loci for analysis on the Illumina GoldenGate genotyping platform. The applicability of the pipeline was demonstrated using publicly available potato EST data, genotyping individuals from two diploid mapping populations and subsequently mapping the SNP markers (putative genes) in both populations. Over 7000 reliable SNPs were identified that met the criteria for genotyping on the GoldenGate platform. Of the 384 SNPs on the SNP array approximately 12% dropped out. For the two potato mapping populations 165 and 185 SNPs segregating SNP loci could be mapped on the respective genetic maps, illustrating the effectiveness of our pipeline for SNP selection and validation.
Electronic supplementary material
The online version of this article (doi:10.1007/s11032-009-9377-5) contains supplementary material, which is available to authorized users.
[Show abstract][Hide abstract] ABSTRACT: Despite efforts to control late blight in potatoes by introducing R(pi)-genes from wild species into cultivated potato, there are still concerns regarding the durability and level of resistance. Pyramiding R(pi)-genes can be a solution to increase both durability and level of resistance. In this study, two resistance genes, R(Pi-mcd1) and R(Pi-ber), introgressed from the wild tuber-bearing potato species Solanum microdontum and S. berthaultii were combined in a diploid S. tuberosum population. Individual genotypes from this population were classified after four groups, carrying no R(pi)-gene, with only R (Pi-mcd1), with only R(Pi-ber), and a group with the pyramided R(Pi-mcd1) and R (Pi-ber) by means of tightly linked molecular markers. The levels of resistance between the groups were compared in a field experiment in 2007. The group with R(Pi-mcd1) showed a significant delay to reach 50% infection of the leaf area of 3 days. The group with R ( Pi-ber ) showed a delay of 3 weeks. The resistance level in the pyramid group suggested an additive effect of R (Pi-mcd1) with R(Pi-ber). This suggests that potato breeding can benefit from combining individual R(pi)-genes, irrespective of the weak effect of R(Pi-mcd1) or the strong effect of R(Pi-ber).
[Show abstract][Hide abstract] ABSTRACT: Resistance to Globodera pallida Rookmaker (Pa3), originating from wild species Solanum tarijense was identified by QTL analysis and can be largely ascribed to one major QTL. GpaXI
explained 81.3% of the phenotypic variance in the disease test. GpaXI
is mapped to the long arm of chromosome 11. Another minor QTL explained 5.3% of the phenotypic variance and mapped to the long arm of chromosome 9. Clones containing both QTL showed no lower cyst counts than clones with only GpaXI
. After Mendelising the phenotypic data, GpaXI
could be more precisely mapped near markers GP163 and FEN427, thus anchoring GpaXI
to a region with a known R-gene cluster containing virus and nematode resistance genes.