Abiotic and Biotic Stress Responses in Solanum tuberosum Group Phureja DM1-3 516 R44 as Measured through Whole Transcriptome Sequencing

This study conducted an in-depth analysis of the potato (Solanum tuberosum L.) transcriptome in response to abiotic (salinity, drought, and heat) and biotic (Phytophthora infestans, DL-b amino-n-butyric acid, and acibenzolar-s-methyl) stresses and plant hormone treatment (abscisic acid, 6-benzylaminopurine, gibberellic acid, and indole-3-acetic acid) using ribonucleic acid sequencing (RNA-seq) of the doubled monoploid S. tuberosum Group Phureja DM1-3 516 R44 clone. Extensive changes in gene expression were observed with 37% of the expressed genes being differentially expressed in at least one comparison of stress to control tissue. Stress-inducible genes known to function in stress tolerance or to be involved in the regulation of gene expression were among the highest differentially expressed. Members of the MYB, APETALA2 (AP2)/ethylene-responsive element binding factor (ERF), and NAM, ATAF1/2, and CUC2 (NAC) transcription factor families were the most represented regulatory genes. A weighted gene co-expression network analysis yielded 37 co-expression modules containing 9198 genes. Fifty percent of the genes within these co-expression modules were specific to a stress condition indicating conditionspecific responses. Cross-species comparison between potato and Arabidopsis thaliana (L.) Heynh. uncovered differentially expressed orthologs and defined evolutionary conserved genes. Collectively, the transcriptional profiling of RNA-seq data presented here provide a valuable reference for potato stress responses to environmental factors that is supported by statistically significant differences in expression changes, highly interconnected genes in co-expression networks, and evidence of evolutionary conservation. Plants growing in natural habitats are exposed to multiple environmental stresses resulting from abiotic and biotic factors. Adaptation and response to these stresses is highly complex and involve changes at the molecular, cellular, and physiological levels. Abiotic stress factors such as heat, drought, and salinity have a significant impact on cultivated potato, affecting yield, tuber quality, and market value (Wang-Pruski and Schofield, 2012). Water availability is by far the most important limiting factor in crop production. Potato plants use water relatively efficiently; however, due in part to its sparse and shallow root system, potato is considered a drought-sensitive crop (Yuan et al., 2003). Salinity is another serious threat to crop production that may increase under anticipated climate change scenarios (Yeo, 1998). Although potatoes are considered moderately salt sensitive (Katerji et al., 2000), significant variations in salt tolerance exist among Solanum tuberosum cultivars and wild Solanum species (Khrais et al., 1998). Furthermore, potato responses to salt stress are related to the responses of other abiotic stresses, as revealed by microarray analysis of leaf responses to cold and salt Published in The Plant Genome 6 doi: 10.3835/plantgenome2013.05.0014 © Crop Science Society of America 5585 Guilford Rd., Madison, WI 53711 USA An open-access publication All rights reserved. No part of this periodical may be reproduced or transmitted in any form or by any means, electronic or mechanical, including photocopying, recording, or any information storage and retrieval system, without permission in writing from the publisher. Permission for printing and for reprinting the material contained herein has been obtained by the publisher. Dep. of Plant Biology, Michigan State Univ., East Lansing, MI 48824. Received 17 May 2013. *Corresponding author (buell@