QTL discovery for agronomic and quality traits in diploid potato clones using PotatoMASH amplicon sequencing.

We genotyped a population of 618 diploid potato clones derived from six independent potato-breeding programmes from NW-Europe. The diploids were phenotyped for 23 traits, using standardized protocols and common check varieties, enabling us to derive whole population estimators for most traits. We subsequently performed a genome-wide association study (GWAS) to identify quantitative trait loci (QTL) for all traits with SNPs and short-read haplotypes derived from read-backed phasing.

Identification of two mutant JASON-RELATED genes associated with unreduced pollen production in potato.

Multiple QTLs control unreduced pollen production in potato. Two major-effect QTLs co-locate with mutant alleles of genes with homology to AtJAS, a known regulator of meiotic spindle orientation. In diploid potato the production of unreduced gametes with a diploid (2n) rather than a haploid (n) number of chromosomes has been widely reported.

Crossover shortage in potato is caused by StMSH4 mutant alleles and leads to either highly uniform unreduced pollen or sterility.

The balanced segregation of homologous chromosomes during meiosis is essential for fertility and is mediated by crossovers (COs). A strong reduction of CO number leads to the unpairing of homologous chromosomes after the withdrawal of the synaptonemal complex. This results in the random segregation of univalents during meiosis I and ultimately to the production of unbalanced and sterile gametes.

GWAS in tetraploid potato: identification and validation of SNP markers associated with glycoalkaloid content.

Unlabelled: Genome-wide association studies (GWAS) are a useful tool to unravel the genetic architecture of complex traits, but the results can be difficult to interpret. Population structure, genetic heterogeneity, and rare alleles easily result in false positive or false negative associations. This paper describes the analysis of a GWAS panel combined with three bi-parental mapping populations to validate GWAS results, using phenotypic data for steroidal glycoalkaloid (SGA) accumulation and the ratio (SGR) between the two major glycoalkaloids α-solanine and α-chaconine in potato tubers.

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

Cultivated potato is a clonally propagated autotetraploid species with a highly heterogeneous genome. Phased assemblies of six cultivars including two chromosome-scale phased genome assemblies revealed extensive allelic diversity, including altered coding and transcript sequences, preferential allele expression, and structural variation that collectively result in a highly complex transcriptome and predicted proteome, which are distributed across the homologous chromosomes. Wild species contribute to the extensive allelic diversity in tetraploid cultivars, demonstrating ancestral introgressions predating modern breeding efforts.

A Hitchhiker's guide to the potato wart disease resistance galaxy.

Two novel major effect loci (Sen4 and Sen5) and several minor effect QTLs for potato wart disease resistance have been mapped. The importance of minor effect loci to bring full resistance to wart disease was investigated. Using the newly identified and known wart disease resistances, a panel of potato breeding germplasm and Solanum wild species was screened.

The origin and widespread occurrence of Sli-based self-compatibility in potato.

Self-compatible (SC) diploid potatoes allow innovative potato breeding. Therefore, the Sli gene, originally described in S. chacoense, has received much attention.

Distribution of P1(D1) wart disease resistance in potato germplasm and GWAS identification of haplotype-specific SNP markers.

A Genome-Wide Association Study using 330 commercial potato varieties identified haplotype specific SNP markers associated with pathotype 1(D1) wart disease resistance. Synchytrium endobioticum is a soilborne obligate biotrophic fungus responsible for wart disease. Growing resistant varieties is the most effective way to manage the disease.

Comparative Subsequence Sets Analysis (CoSSA) is a robust approach to identify haplotype specific SNPs; mapping and pedigree analysis of a potato wart disease resistance gene .

Background: Standard strategies to identify genomic regions involved in a specific trait variation are often limited by time and resource consuming genotyping methods. Other limiting pre-requisites are the phenotyping of large segregating populations or of diversity panels and the availability and quality of a closely related reference genome. To overcome these limitations, we designed efficient Comparative Subsequence Sets Analysis (CoSSA) workflows to identify haplotype specific SNPs linked to a trait of interest from Whole Genome Sequencing data.

A common genetic mechanism underlies morphological diversity in fruits and other plant organs.

Shapes of edible plant organs vary dramatically among and within crop plants. To explain and ultimately employ this variation towards crop improvement, we determined the genetic, molecular and cellular bases of fruit shape diversity in tomato. Through positional cloning, protein interaction studies, and genome editing, we report that OVATE Family Proteins and TONNEAU1 Recruiting Motif proteins regulate cell division patterns in ovary development to alter final fruit shape.

Graphical genotyping as a method to map Ny and Gpa5 using a reference panel of tetraploid potato cultivars.

The method of graphical genotyping is applied to a panel of tetraploid potato cultivars to visualize haplotype sharing. The method allowed to map genes involved in virus and nematode resistance. The physical coordinates of the amount of linkage drag surrounding these genes are easily interpretable.

Evaluation of LD decay and various LD-decay estimators in simulated and SNP-array data of tetraploid potato.

The number of SNPs required for QTL discovery is justified by the distance at which linkage disequilibrium has decayed. Simulations and real potato SNP data showed how to estimate and interpret LD decay. The magnitude of linkage disequilibrium (LD) and its decay with genetic distance determine the resolution of association mapping, and are useful for assessing the desired numbers of SNPs on arrays.

Development and analysis of a 20K SNP array for potato (Solanum tuberosum): an insight into the breeding history.

A 20K SNP array was developed and a comprehensive set of tetraploid cultivar was genotyped. This allowed us to identify footprints of the breeding history in contemporary breeding material such as identification of introgression segments, selection and founder signatures. A non-redundant subset of 15,138 previously identified SNPs and 4454 SNPs originating from the SolCAP project were combined into a 20k Infinium SNP array for genotyping a total of 569 potato genotypes.

Homologues of potato chromosome 5 show variable collinearity in the euchromatin, but dramatic absence of sequence similarity in the pericentromeric heterochromatin.

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.

Chromosomal organizations of major repeat families on potato (Solanum tuberosum) and further exploring in its sequenced genome.

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.

Identification of agronomically important QTL in tetraploid potato cultivars using a marker-trait association analysis.

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).

Naturally occurring allele diversity allows potato cultivation in northern latitudes.

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.

A hybrid BAC physical map of potato: a framework for sequencing a heterozygous genome.

Background: 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).

Genome sequence and analysis of the tuber crop potato.

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.

A genome-wide genetic map of NB-LRR disease resistance loci in potato.

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.

Population structure and linkage disequilibrium unravelled in tetraploid potato.

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.

A pipeline for high throughput detection and mapping of SNPs from EST databases.

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.