RNA-sequencing analysis revealed genes associated drought stress responses of different durations in hexaploid sweet potato

Abstract

Purple-fleshed sweet potato (PFSP) is an important food crop, as it is a rich source of nutrients and anthocyanin pigments. Drought has become a major threat to sustainable sweetpotato production, resulting in huge yield losses. Therefore, the present study was conducted to identify drought stressresponsive genes using next-generation (NGS) and third-generation sequencing (TGS) techniques. Five cDNA libraries were constructed from seedling leaf segments treated with a 30% solution of polyethylene glycol (PEG-6000) for 0, 1, 6, 12, and 48 h for second-generation sequencing. Leaf samples taken from upper third of sweet potato seedlings after 1, 6, 12, and 48 h of drought stress were used for the construction of cDNA libraries for third-generation sequencing; however, leaf samples from untreated plants were collected as controls. A total of 184,259,679 clean reads were obtained using second and third-generation sequencing and then assembled into 17,508 unigenes with an average length of 1,783 base pairs. Out of 17,508 unigenes, 642 (3.6%) unigenes failed to hit any homologs in any databases, which might be considered novel genes. A total of 2, 920, 1578, and 2,418 up-regulated unigenes and 3,834, 2,131, and 3,337 down-regulated unigenes from 1 h, 6 h, 12 h, and 48 h library were identified, respectively in drought stress versus control. In addition, after 6, 12, and 48 h of drought stress, 540 up-regulated unigenes, 486 down-regulated unigenes and 414 significantly differentially expressed unigenes were detected. It was found that several gene families including Basic Helix-loop-helix (bHLH), basic leucine zipper (bZIP), Cystein2/Histidine2 (C2H2), C3H, Ethylene-responsive transcription factor (ERF), Homo domain-leucine zipper (HD-ZIP), MYB, NAC (NAM, ATAF1/2, and CUC2), Thiol specific antioxidant and WRKY showed responses to drought stress. In total, 17,472 simple sequence repeats and 510,617 single nucleotide polymorphisms were identified based on transcriptome sequencing of the PFSP. About 96.55% of the obtained sequences are not available online in sweet potato genomics resources. Therefore, it will enrich annotated sweet potato gene sequences and enhance understanding of the mechanisms of drought tolerance through genetic manipulation. Moreover, it represents a sequence resource for genetic and genomic studies of sweet potato. Purple-fleshed sweet potato (PFSP) (Ipomoea batatas (L.) Lam.) is a type of sweet potato, which has purple skin and flesh color of the storage roots due to the large accumulation of anthocyanin pigments 1. It is a root crop widely grown in some Asian and African countries (i.e. China, India, and Kenya). Sweet potato is regarded as the seventh most important food crop. It is among the crops which generate large amounts of food per unit area per unit time 2. Furthermore, it is considered to be a cheap source of energy, carbohydrates, vitamin, potassium, iron, fiber, and protein 3 .

Genome‐wide association analysis of agronomical and physiological traits linked to drought tolerance in a diverse potatoes (Solanum tuberosum) panel

“…The solcap_snp_c1_13430 in chromosome 1 was associated with the β‐amylase gene (ID Soltu.DM.01G022570). Previous authors related the β‐amylase activity with drought tolerance in potatoes (Schafleitner et al., 2007; Watkinson et al., 2008), sweet potatoes (Arisha et al., 2020) and Arabidopsis thaliana (Prasch et al., 2015; Zanella et al., 2016). The β‐amylase activity is involved in the starch catabolic process and the β‐amylase ‐mediated starch breakdown in guard cells can lead to improved plant performance under drought stress (Arisha et al., 2020).…”

Rice aquaporin OsPIP2;2 is a water‐transporting facilitator in relevance to drought‐tolerant responses

“…We further determined the role of OsPIP2;2 in the plant resistance to a physiological drought stress caused by Polyethylene glycol 6,000 (PEG 6000 ). PEG with molecular mass 4,000-8,000 effectively induces physiological drought in a variety of plant species, and PEG 6000 has been mostly used (Arisha et al, 2020;Dong et al, 2005;Hajihashemi & Geuns, 2016;Huang et al, 2019;Ren et al, 2019;Tiwari et al, 2020;Zhang et al, 2017). While PEG induces drought syndromes from leaf wilting to plant collapse, plants in this process may defend themselves by activating the drought tolerance pathway to preserve water relations (Dong et al, 2005;Zhang et al, 2017 PEG 6000 was used as an inducer of physiological drought stress (Dong et al, 2005;Dubois & Inzé, 2020) and applied to 15-day-old rice seedlings.…”

Understanding the Impact of Drought in Coffea Genotypes: Transcriptomic Analysis Supports a Common High Resilience to Moderate Water Deficit but a Genotype Dependent Sensitivity to Severe Water Deficit

“…Integrative approaches for large-scale transcriptomic studies have shown that responses include mainly two sets of genes, one directly involved in protecting cells from stress and the other including regulatory proteins that modulate gene expression. The first group includes water channel proteins and membrane transporters [9], key enzymes for osmolyte biosynthesis (e.g., proline, sugars) [10], detoxification enzymes (e.g., catalase, superoxide dismutase, ascorbate peroxidase) [8], enzymes for fatty acid metabolism, ferritin, and lipid-transfer proteins [11], and proteins for the protection of macromolecules (e.g., late embryogenesis abundant, antifreeze proteins and chaperones) [12]. A second important group of responsive drought-induced genes that are activated by drought include transcription factors (TFs) as the widely known dehydration responsive element binding (DREB) TFs, as well as protein kinases and phosphatases implicated in the regulation of the stress signal transduction to subsequent components in the pathway towards the nucleus [13][14][15].…”