Potato genome set to revolutionise breeding and ensure food security

An international team of scientists have succeeded in mapping the genome of the potato.  Polish partners included the Institute of Biochemistry and Biophysics (IBB PAS).  The research paper was published on July 14, 2011, in Nature, the world's most cited interdisciplinary science journal.

The achievement holds great promise for speeding up the traditionally time-consuming process of developing new potato variet ies. At the moment it can take 10-12 years to breed a new variety.

fot. LittleMan / sxc.hu

New types of potato could help to ensure future food security because of improved yield, quality, nutritional value, and resistance to pests and diseases.

Potato is a member of the Solanaceae family, which also includes tomato, capsicum (the peppers we all buy in the supermarket), and aubergine. After wheat and rice, potato is the third most important food crop, with a world-wide production of 309 million tonnes in 2007. By  2020 it is estimated that more than two billion people worldwide will depend on potato for  food, feed, or income. Improving potato varieties so that they can better cope with environmental challenges such as drought, and pests or diseases are key objectives of global  potato breeding programmes.  As a food it is becoming more and more popular, and is increasingly important in Africa and many parts of Asia, giving it an important potential role in global food security.

The potato genome

Every organism has a genome, a chemical 'instruction book' or 'blueprint' that describes how all the genes should be put together. This is written down as a DNA sequence, a long sentence made up of the chemical letters A, C, T and G. This sequence contains many tens of thousands of genes which can be thought of as 'words' in the sentence. Each gene controls different aspects of how the organism grows and develops. Slight changes in these instructions give rise to different varieties - each individual has a slightly different version of the DNA sequence for the species.

Understanding the complete genome sequence, the exact spelling of the DNA letters, for potato will help scientists develop a better understanding of how potato grows and develops, leading to improved crops worldwide.

Each copy of the potato genome consists of 12 chromosomes and has a length of approximately 840 million base pairs, making it a medium-sized plant genome. A high quality, well-annotated genome sequence of potato will provide a valuable foundation which can be combined with existing knowledge of potato genetics and the continuing advances in analysing which genes are switched on or off and which chemicals are produced when and where. Observing how these changes are affected by changes in the genome will allow scientists to identify different variants of genes which are responsible for important quantitative traits in potato.

The Potato Genome Sequencing Consortium (PGSC) seeks to provide such a resource to the potato research and breeding community in the near future, allowing the full potential of biotechnology-based improvement of this important crop plant to be realised.

The PGSC released the draft version of the full potato genome towards the end of 2009, and since then it has been refining the ‘assembly’ and performing various types of analysis for publication.

The international Potato Genome Sequencing Consortium (PGSC) is a collaboration between 16 research groups in 14 countries; Argentina, Brazil, China, Chile, India, Ireland, Italy, The Netherlands, New Zealand, Peru, Poland, Russia, the United Kingdom and the United States. The PGSC has its basis in long-standing research on the molecular genetics of potato within the partner organisations, and includes partners with world-leading expertise in genome sequencing and computational analysis.

Each partner raised the funding needed to contribute to the project independently, mostly through grants from government research agencies and industry bodies.

The potato genome assembly and other resources are now available in the public domain at www.potatogenome.net, where a complete listing and contact details for all PGSC members can be found.

Laboratory of DNA Sequencing and Oligonucleotide Synthesis within the IBB PAS (including the following scientists: Beata Babińska, Piotr Dzierzbicki, Małgorzata Filipiuk, Jan Gawor, Ewa Kalińska, Robert Gromadka) participated in sequencing the genomes of the two lines of potato. Initially, the traditional Sanger method using the ABI 3730 apparatus and the ABI 3730/xl (respectively, 48 - and 96 capillary) was used to sequence BACs (Bacterial Artificial Chromosomes) carrying mapped fragments of different chromosomes. After purchasing the GS FLX Titanium (454/Roche) sequencer, it began the direct sequencing of entire genomes. In total, the Laboratory established consensus sequences of 91 BAC fragments of potato chromosomes with a length of 100 to 140 thousand nucleotides reading more than 6 billion base pairs of the potato genome.

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Genome sequence and analysis of the tuber crop potato

Nature 475, 189–195 (14 July 2011), doi:10.1038/nature10158

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.