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

Abstract

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, Am. J. Pot Res (2009) 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 BACends 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 AFLP TM markers. From this integrated geneticphysical 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 potato.Resumen La papa es un miembro de las Solanaceae, una familia de plantas que incluye varias otras especies económicamente importantes, tales como tomate, berenjena, petunia, tabaco y ají o chili. El consorcio de secuenciación del genoma de la papa (PGSC) tiene por objeto dilucidar la secuencia completa del genoma de la papa, el tercer cultivo alimentario más importante del mundo. El PGSC es una colaboración entre 13 grupos de investigación procedentes de China, India, Polonia, Rusia, los Países Bajos, Irlanda, Argentina, Brasil, Chile, Perú, EE.UU., Nueva Zelanda y el Reino Unido. El genoma de la papa consiste de 12 cromosomas y tiene una longitud (haploide) de aproximadamente 840 millones de pares de bases, por lo que es una planta con un genoma de tamaño mediano. El proyecto de secuenciación se basa en una biblioteca de 78000 clones de cromosoma artificial bacteriano genomico de papa diploide (BAC), del que se ha obtenido la huella genética y alineado en 7000~contigs de mapa físico. Además, los extremos terminales BAC se han secuenciado y están a disposición del público. Aproximadamente 30000 BACS están anclados al mapa genético de ultra alta densidad de la papa, compuesto de 10000 marcadores AFLP TM únicos. De esta ...

Genome sequence and analysis of the tuber crop potato

“…The indirect mapping approach exploited in silico anchoring using the RH genetic and physical map 28,40 , as well as tomato genetic map data from SGN (http://solgenomics.net/). Amplified fragment length polymorphism markers from the RH genetic map were linked to DM sequence scaffolds via BLAST alignment 36 of whole-genome-profiling sequence tags 41 obtained from anchored seed BACs in the RH physical map, or by direct alignment of fully sequenced RH seed BACs to the DM sequence.…”

Using SSR to Evaluate the Genetic Diversity of Potato Cultivars from Yunnan Province (SW China)

“…Among these methods, database searching is the most direct and accurate way of developing primers. Visser et al (2009) stated that "the potato genome sequence will provide a major boost to gaining a better understanding of potato trait biology, underpinning future breeding efforts." The Potato Genome Sequence Consortium (PGSC), bringing together scientists from many nations including China (Potato Genome Sequencing Consortium, 2011) has worked on potato genome sequencing and annotation, providing information for primer design through database searching; the organization provides a platform for genetic improvement of the disease resistance, stress resistance, cultivar quality and yield of potato.…”

Suppression of the Vacuolar Invertase Gene Prevents Cold-Induced Sweetening in Potato

“…The RNA was converted to cDNA using the mRNA-Seq Kit from Illumina and sequenced on an Illumina GA2 sequencer, generating 41-bp fragments. Purity-filtered reads were aligned to the Potato Genome Sequencing Consortium version 3 draft assembly of Solanum phureja DM1-3 516R44 (http://www.potatogenome.net/index.php/; Visser et al, 2009) using the TopHat short-read alignment program (Trapnell et al, 2009). Expression levels were determined from 33,655 gene models constructed from the FGENESH (Salamov and Solovyev, 2000) ab initio gene finder (dicot matrix) using Cufflinks (0.8.2; http://cufflinks.cbcb.umd.edu/), which generates expression levels in the form of reads/FPKM.…”