The PIN family of proteins in potato and their putative role in tuberisation

The PIN family of trans-membrane proteins mediates auxin efflux throughout the plant and during various phases of plant development. In Arabidopsis thaliana, the PIN family comprised of 8 members, divided into ‘short’ and ‘long’ PINs according to the length of the hydrophilic domain of the protein. Based on sequence homology using the recently published potato genome sequence (Solanum tuberosum group Phureja) we identified ten annotated potato StPIN genes. Mining the publicly available gene expression data, we constructed a catalogue tissue specificity of StPIN gene expression, focusing on the process of tuberization. A total of four StPIN genes exhibited increased expression four days after tuber induction, prior to the onset of stolon swelling. For two PIN genes, StPIN4 and StPIN2, promoter sequences were cloned and fused to the GUS reporter protein to study tissue specificity in more detail. StPIN4 promoter driven GUS staining was detected in the flower stigma, in the flower style, below the ovary and petals, in the root tips, in the vascular tissue of the stolons and in the tuber parenchyma cells. StPIN2 promoter driven GUS staining was detected in flower buds, in the vascular tissue of the swelling stolons and in the storage parenchyma of the growing tubers. Based on our results, we postulate a role for the StPINs in redistributing auxin in the swelling stolon during early events in tuber development

A limited set of starch related genes explain several interrelated traits in potato

To understand the molecular basis of potato starch related traits and the underlying starch biosynthesis and degradation, a Quantitative Trait Locus (QTL) analysis in combination with a candidate gene approach was performed. The diploid mapping population C × E, consisting of 249 individuals, was assayed over two consecutive years, for chipping colour, cold induced sweetening, starch content, starch granule size, starch gelling temperature, starch enthalpy, amylose content and degree of starch phosphorylation. QTLs were observed for all traits, except enthalpy on eight out of the twelve potato chromosomes. Several QTLs were found to be consistent over 2 years. Clustering of co-localizing QTLs was observed on some chromosomes, indicating common genetic factors for the different traits. On chromosome 2, Soluble Starch Synthase 2 mapped on the same position as QTLs for starch phosphorylation, starch gelling temperature and amylose content. a-glucan, water dikinase co-localizes on chromosome 5 together with QTLs for starch phosphorylation and cold induced sweetening. Furthermore, the genes coding for two phosphorylases (StPho1a and StPho2) coincide with QTLs for starch gelling temperature, chipping colour and starch granule size on chromosome 2 and a QTL for starch phosphorylation on chromosome 9, respectively. The results suggest allelic variation acting on the genetics of the different trait

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. 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 cro

The tuberization signal StSP6A represses flower bud development in potato

Potato (Solanum tuberosum L.) can reproduce sexually through flowering and asexually through tuberization. While tuberization has been thoroughly studied, little research has been done on potato flowering. Flower bud development in the strictly short-day tuberizing S. tuberosum group Andigena is impaired under short-day conditions. This impaired development may indicate that tuberization negatively influences flowering. Here, we determine how tuberization affects flower bud development. To find out whether the absence of tubers improves flowering, we prevented tuberization by: (i) grafting potato scions onto wild potato rootstocks, which were unable to form tubers; (ii) removing stolons, the underground structures on which tubers form; and (iii) using plants that were silenced in the tuberization signal StSP6A. Additionally, transgenic plants with increased StSP6A expression were used to determine if flower bud development was impaired. The absence of a tuber sink alone did not accelerate flower bud development, nor did it allow more plants to reach anthesis (open flowering stage) or have more open flowers. Interestingly, reducing StSP6A expression improved flower bud development, and increasing expression impaired it. Our results show that flower bud development in potato is repressed by the tuberization signal StSP6A, and not by competition with the underground tuber sink

Organ specificity and transcriptional control of metabolic routes revealed by expression QTL profiling of source-sink tissues in a segregating potato population

Background With the completion of genome sequences belonging to some of the major crop plants, new challenges arise to utilize this data for crop improvement and increased food security. The field of genetical genomics has the potential to identify genes displaying heritable differential expression associated to important phenotypic traits. Here we describe the identification of expression QTLs (eQTLs) in two different potato tissues of a segregating potato population and query the potato genome sequence to differentiate between cis- and trans-acting eQTLs in relation to gene subfunctionalization. Results Leaf and tuber samples were analysed and screened for the presence of conserved and tissue dependent eQTLs. Expression QTLs present in both tissues are predominantly cis-acting whilst for tissue specific QTLs, the percentage of trans-acting QTLs increases. Tissue dependent eQTLs were assigned to functional classes and visualized in metabolic pathways. We identified a potential regulatory network on chromosome 10 involving genes crucial for maintaining circadian rhythms and controlling clock output genes. In addition, we show that the type of genetic material screened and sampling strategy applied, can have a high impact on the output of genetical genomics studies. Conclusions Identification of tissue dependent regulatory networks based on mapped differential expression not only gives us insight in tissue dependent gene subfunctionalization but brings new insights into key biological processes and delivers targets for future haplotyping and genetic marker development

Sequencing the potato genome: outline and first results to come from the elucidation of the sequence of the world's third most important food crop

Potato is a member of the Solanaceae, a plant family that includes several other economically important species, such as tomato, eggplant, petunia, tobacco and pepper. The Potato Genome Sequencing Consortium (PGSC) aims to elucidate the complete genome sequence of potato, the third most important food crop in the world. The PGSC is a collaboration between 13 research groups from China, India, Poland, Russia, the Netherlands, Ireland, Argentina, Brazil, Chile, Peru, USA, New Zealand and the UK. The potato genome consists of 12 chromosomes and has a (haploid) length of approximately 840 million base pairs, making it a medium-sized plant genome. The sequencing project builds on a diploid potato genomic bacterial artificial chromosome (BAC) clone library of 78000 clones, which has been fingerprinted and aligned into ~7000 physical map contigs. In addition, the BAC-ends have been sequenced and are publicly available. Approximately 30000 BACs are anchored to the Ultra High Density genetic map of potato, composed of 10000 unique AFLPTM markers. From this integrated genetic-physical map, between 50 to 150 seed BACs have currently been identified for every chromosome. Fluorescent in situ hybridization experiments on selected BAC clones confirm these anchor points. The seed clones provide the starting point for a BAC-by-BAC sequencing strategy. This strategy is being complemented by whole genome shotgun sequencing approaches using both 454 GS FLX and Illumina GA2 instruments. Assembly and annotation of the sequence data will be performed using publicly available and tailor-made tools. The availability of the annotated data will help to characterize germplasm collections based on allelic variance and to assist potato breeders to more fully exploit the genetic potential of potat

Possibilities and challenges of the potato genome sequence

This paper describes the progress that has been made since the draft genome sequence of potato has been obtained and the analyses that need to be done to make further progress. Although sequencing has become less expensive and read lengths have increased, making optimal use of the information obtained is still difficult, certainly in the tetraploid potato crop. Major challenges in potato genomics are standardized genome assembly and haplotype analysis. Sequencing methods need to be improved further to achieve precision breeding. With the current new generation sequencing technology, the focus in potato breeding will shift from phenotype improvement to genotype improvement. In this respect, it is essential to realize that different alleles of the same gene can lead to different phenotypes depending on the genetic background and that there is significant epistatic interaction between different alleles. Genome-wide association studies will gain statistical power when binary single nucleotide polymorphism (SNP) data can be replaced with multi-allelic haplotype data. Binary SNP can be distributed across the many different alleles per locus or may be haplotype-specific, and potentially tag specific alleles which clearly differ in their contribution to a certain trait value. Assembling reads from the same linkage phase proved to allow constructing sufficiently long haplotype tracts to ensure their uniqueness. Combining large phenotyping data sets with modern approaches to sequencing and haplotype analysis and proper software will allow the efficiency of potato breeding to increase