Comparative transcriptome study of switchgrass (Panicum virgatum L.) homologous autopolyploid and its parental amphidiploid responding to consistent drought stress

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.

Transcriptome analysis revealed the regulation of gibberellin and the establishment of photosynthetic system promote rapid seed germination and early growth of seedling in pearl millet

“…A total of 3 μg RNA from each sample as a sequencing input material, and the detailed method refers to our previous research [ 70 , 71 ]. First strand cDNA synthesis was implemented by using random hexamer primer and M-MuLV Reverse Transcriptase (RNase H-), and second strand cDNA synthesis was implemented by using mixture containing DNA Polymerase I and RNase H. Total 24 sequencing libraries were generated using NEBNext ® Ultra™ RNA Library Prep Kit for Illumina ® (NEB, USA) [ 72 ].…”

Molecular Mechanisms of Nitric Oxide (NO) Signaling and Reactive Oxygen Species (ROS) Homeostasis during Abiotic Stresses in Plants

“…Plants respond to drought stress through various adaptations, such as increased cuticle thickness due to deposition of wax crystals to reduce cuticular transpiration [69], development of an extensive root system to improve water supply, changes in leaf size, sunken stomata, and development of spongy tissue to reduce water loss [70]. These drought-tolerance mechanisms, generally classified as drought escape, drought avoidance, and drought recovery, usually involve NO and sometimes symbiotic rhizobacteria to modify the root system [22,71].…”

Secondary Metabolism and Hormone Response Reveal the Molecular Mechanism of Triploid Mulberry (Morus Alba L.) Trees Against Drought

“…Moreover, many polyploidy studies have focused on allopolyploidy, which interferes with heterogeneous genome alongside its ploidy effects, meaning far less attention is paid to autopolyploid. Based on an admittedly limited number of examined species, autopolyploid may confer better stress tolerance to water deficit, such as in autopolyploid Panicum virgatum L., Dianthus broteri, and tetraploidy Arabidopsis (Del Pozo and Ramirez-Parra, 2014;Lopez-Jurado et al, 2019;Chen et al, 2020). However, there are relatively few such studies on woody plants, despite their unique and well-known physiological mechanisms for maintaining water balance, such as perennation, woody stem tissue formations, and long-distance transportation of water.…”