Genome sequence and analysis of the tuber crop potato

Xu, X.; Pan, P.; Cheng, S.; Zhang, B.; Mu, D.; Ni, P.; Zhang, G.; Yang, S.; Li, R.; Wang, J.; Orjeda, G.; Guzman, F.; Torres, M.; Lozano, R.; Ponce, O.; Martinez, D.; Cruz, G. de la.; Chakrabarti, S.K.; Patil, V.U.; Skryabin, K.G.; Kuznetsov, B.B.; Ravin, N.V.; Kolganova, T.V.; Beletsky, A.V.; Mardanov, A.V.; Genova, A.D.; Bolser, D.M.; Martin, D.M.A.; Li, G.; Yang, Y.; Kuang, H.; Hu, Q.; Xiong, X.; Bishop, G.J.; Sagredo, B.; Mejia, N.; Zagorski, W.; Gromadka, R.; Gawor, J.; Szczesny, P.; Huang, S.; Zhang, Z.; Liang, C.; He, J.; Li, Y.; He, Y.; Xu, J.; Zhang, Y.; Xie, B.; Du, Y.; Qu, D.; Bonierbale, M.; Ghislain, M.; Herrera, M.R.; Giuliano, G.; Pietrella, M.; Perrotta, G.; Facella, P.; OﾒBrien, K; Feingold, S.E.; Barreiro, L.E.; Massa, G.A.; Diambra, L.; Whitty, B.R.; Vaillancourt, B.; Lin, H.; Massa, A.N.; Geoffroy, M.; Lundback, S.; DellaPenna, D.; Buell, R.; Sharma, S.K.; Marshall, D.F.; Waugh, R.; Bryan, G.J.; Destefanis, M.; Nagy, I.; Milbourne, D.; Thomson, S.J.; Fiers, M.; Jacobs, J.M.E.; Nielsen, K.L.; Sonderkaer, M.; Iovene, M.; Torres, G.A.; Jiang, J.; Veilleux, R.E.; Bachem, C.W.B.; Boer, J. de.; Borm, T.; Kloosterman, B.; Eck, H. van.; Datema, E.; Lintel Hekkert, B. te.; Goverse, A.; Ham, R.C.H.J. van.; Visser, R.G.F. 2011. Genome sequence and analysis of the tuber crop potato. Nature. (USA). ISSN 0028-0836. 475(7355):189-195.

Abstract/Description

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. The genome of the potato (Solanum tuberosum L.), a staple crop vital to food security, has been sequenced. The Potato Genome Sequencing Consortium sequenced a homozygous doubled-monoploid potato clone as well as a heterozygous diploid clone. Genome analysis reveals traces of at least two genome duplication events and genes specific to Asterids, a large clade of flowering plants of which the potato is the first to be sequenced. Gene presence/absence variants and other potentially deleterious mutations are frequent and may be the cause of inbreeding depression. The genome sequence will facilitate genetic improvements in the potato with a view to improving yield and to increasing disease and stress resistance of this crop, which is a now a significant component of worldwide food production and is becoming increasingly important in the developing world.