Comparative transcriptome study of switchgrass ( Panicum virgatum L.) homologous autopolyploid and its parental amphidip
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Biotechnology for Biofuels Open Access
RESEARCH
Comparative transcriptome study of switchgrass (Panicum virgatum L.) homologous autopolyploid and its parental amphidiploid responding to consistent drought stress Peilin Chen1,2, Jing Chen1, Min Sun1, Haidong Yan1,3, Guangyan Feng1, Bingchao Wu1, Xinquan Zhang1, Xiaoshan Wang1 and Linkai Huang1*
Abstract Background: Newly formed polyploids may experience short-term adaptative changes in their genome that may enhance the resistance of plants to stress. Considering the increasingly serious effects of drought on biofuel plants, whole genome duplication (WGD) may be an efficient way to proceed with drought resistant breeding. However, the molecular mechanism of drought response before/after WGD remains largely unclear. Result: We found that autoploid switchgrass (Panicum virgatum L.) 8X Alamo had higher drought tolerance than its parent amphidiploid 4X Alamo using physiological tests. RNA and microRNA sequencing at different time points during drought were then conducted on 8X Alamo and 4X Alamo switchgrass. The specific differentially expressed transcripts (DETs) that related to drought stress (DS) in 8X Alamo were enriched in ribonucleoside and ribonucleotide binding, while the drought-related DETs in 4X Alamo were enriched in structural molecule activity. Ploidy-related DETs were primarily associated with signal transduction mechanisms. Weighted gene co-expression network analysis (WGCNA) detected three significant DS-related modules, and their DETs were primarily enriched in biosynthesis process and photosynthesis. A total of 26 differentially expressed microRNAs (DEmiRs) were detected, and among them, sbi-microRNA 399b was only expressed in 8X Alamo. The targets of microRNAs that were responded to polyploidization and drought stress all contained cytochrome P450 and superoxide dismutase genes. Conclusions: This study explored the drought response of 8X and 4X Alamo switchgrass on both physiological and transcriptional levels, and provided experimental and sequencing data basis for a short-term adaptability study and drought-resistant biofuel plant breeding. Keywords: Panicum virgatum L., Whole genome duplication, Drought response, MicroRNA, Transcriptome, WGCNA
*Correspondence: [email protected] 1 Department of Grassland Science, Animal Science and Technology College, Sichuan Agricultural University, Chengdu 611130, China Full list of author information is available at the end of the article
Background Switchgrass (Panicum virgatum L.), as a well-known bioenergy crop found on marginal lands [1], has a substantial potential to help relieve the world energy shortage [2]. It does not just have the dual purposes as a forage and energy crop [3], but it is even able to improve
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