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ARS Home » Midwest Area » Madison, Wisconsin » Vegetable Crops Research » Research » Publications at this Location » Publication #343721
Title: Genomic analyses yield markers for identifying agronomically important genes in potato

Author
item LI, YANGPING - Sichuan University
item COLLEONI, CHRISTOPHE - Universite De Lille
item ZHANG, JUNJIE - Sichuan Agricultural University
item LIANG, QIQI - Novogene Bioinformatics Institue
item HU, YUFENG - Sichuan University
item Ruess, Holly
item SIMON, REINHARD - International Potato Center
item LIU, YINGHONG - Sichuan Agricultural University
item LIU, HANMEI - Sichuan Agricultural University
item YU, GUOWU - Sichuan University
item SCHMITT, ERIC - Universite De Lille
item PONITZKI, CHLOE - Universite De Lille
item LIU, GUANGJIAN - Novogene Bioinformatics Institue
item HUANG, HUANHUAN - Sichuan University
item ZHAN, FEILONG - Sichuan University
item CHEN, LIN - Sichuan University
item HUANG, YUBI - Sichuan University
item Spooner, David
item HUANG, BINQUAN - Sichuan Agricultural University

Submitted to: Molecular Plant
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 1/22/2018
Publication Date: 3/5/2018
Citation: Li, Y., Colleoni, C., Zhang, J., Liang, Q., Hu, Y., Ruess, H.M., Simon, R., Liu, Y., Liu, H., Yu, G., Schmitt, E., Ponitzki, C., Liu, G., Huang, H., Zhan, F., Chen, L., Huang, Y., Spooner, D.M., Huang, B. 2018. Genomic analyses yield markers for identifying agronomically important genes in potato. Molecular Plant. 11(3):473-484. https://doi.org/10.1016/j.molp.2018.01.009.

Interpretive Summary: Next generation sequencing is a set of advanced new techniques that generates hundreds of thousands of DNA sequences quickly and accurately. This study uses next generation sequencing to investigate the genetics of potato taxonomy and evolution using 201 samples of wild and cultivated potatoes. We identified 450 genes likely responsible for the change of wild potato to cultivated potato including genes responsible for the production of large tubers (the edible part of potatoes). We also identified the wild species S. candolleanum to be the progenitor of cultivated potato and determined the main evolutionary lineages of wild potatoes and confirmed cultivated potato to have evolved in southern Peru. We identified thousands of genes which may have been responsible for potato to be adapted to different environments. This study provides strategies to address questions of potato domestication, tuberization, disease resistance, and breeding.

Technical Abstract: This study explores the genetic architecture underling the potato evolution through a comprehensive assessment of wild and cultivated potato species based on the re-sequencing of 201 accessions of Solanum section Petota with >12 × genome coverage. We identified 450 domesticated genes, which showed evidence of selection on tuberization of potato. A phylogenetic analysis confirmed the wild species S. candolleanum to be the progenitor of cultivated potato, confirmed the cladistic structure of wild and cultivated potatoes (Solanum section Petota) into major clades, and supported the monophyletic origin in southern Peru. We found thousands of high differentiation genes between phylogenetic subgroups, which represent candidate genes for environmental adaption. Through GWAS, we identified a number of strong association candidate genes for two maturity traits. To determine the ancestral state of genes in wild species, we re-sequenced the progenitor of cultivated potato, S. candolleanum, to depth with 68 × genome coverage, from which 2901 novel genes were annotated. This study provides strategies to address questions of potato domestication, tuberization, disease resistance, and breeding.