Transcriptome Analysis Reveals Potential Roles of Abscisic Acid and Polyphenols in Adaptation of Onobrychis viciifolia to Extreme Environmental Conditions in the Qinghai-Tibetan Plateau

Abstract

A detailed understanding of the molecular mechanisms of plant stress resistance in the face of ever-changing environmental stimuli will be helpful for promoting the growth and production of crop and forage plants. Investigations of plant responses to various single abiotic or biotic factors, or combined stresses, have been extensively reported. However, the molecular mechanisms of plants in responses to environmental stresses under natural conditions are not clearly understood. In this study, we carried out a transcriptome analysis using RNA-sequencing to decipher the underlying molecular mechanisms of Onobrychis viciifolia responding and adapting to the extreme natural environment in the Qinghai-Tibetan Plateau (QTP). The transcriptome data of plant samples collected from two different altitudes revealed a total of 8212 differentially expressed genes (DEGs), including 5387 up-regulated and 2825 down-regulated genes. Detailed analysis of the identified DEGs uncovered that up-regulation of genes potentially leading to changes in hormone homeostasis and signaling, particularly abscisic acid-related ones, and enhanced biosynthesis of polyphenols play vital roles in the adaptive processes of O. viciifolia. Interestingly, several DEGs encoding uridine diphosphate glycosyltransferases, which putatively regulate phytohormone homeostasis to resist environmental stresses, were also discovered. Furthermore, numerous DEGs encoding transcriptional factors, such as members of the myeloblastosis (MYB), homeodomain-leucine zipper (HD-ZIP), WRKY, and nam-ataf1,2-cuc2 (NAC) families, might be involved in the adaptive responses of O. viciifolia to the extreme natural environmental conditions. The DEGs identified in this study represent candidate targets for improving environmental stress resistance of O. viciifolia grown in higher altitudes of the QTP, and can provide deep insights into the molecular mechanisms underlying the responses of this plant species to the extreme natural environmental conditions of the QTP.

Transcriptome Analysis Reveals Roles of Anthocyanin- and Jasmonic Acid-Biosynthetic Pathways in Rapeseed in Response to High Light Stress

“…These data indicate that the up-regulation of both of the PAP genes was closely associated with the increase in anthocyanin biosynthesis and the development of purple pigmentation in rapeseed seedlings exposed to HL conditions. Similar to the color change observed in rapeseed seedlings in our study, PAP1- and PAP2- overexpressing Arabidopsis plants also displayed purple pigmentation in various organs, as well as anthocyanin accumulation [ 65 ]. In addition to the R2R3-MYB s, induction of other TF-encoding genes, such as bHLH and bZIP genes [ 85 ], in rapeseed seedlings under HL conditions, is required for anthocyanin accumulation.…”

“…Alterations in plant color in response to light intensity represents one of the plants’ adaptive responses to light signals [ 64 ]. Rapeseed is an oil crop that is widely planted in the Qinghai-Tibetan plateau, where the solar radiation is generally stronger than that in other low-altitude environments [ 65 ]. The molecular mechanisms underlying the response of rapeseed to light intensity, however, have not been fully elucidated, which has hindered the breeding of high-quality varieties that are tolerant to HL conditions.…”

“…LC-MS analysis of anthocyanins was carried out using a reverse phase Hypersil GOLD™ C18 C18 column (150 mm × 2.1 mm, 2.6 µm, ThermoFisher, Waltham, MA, USA) with 1 mL min −1 flow rate over a 60-min gradient program. Further, 0.5% formic acid and acetonitrile containing 0.1% formic acid were used as solvent A and solvent B, respectively, in a linear step described previously [ 65 ].…”

Transcriptome and metabonomics combined analysis revealed the energy supply mechanism involved in fruiting body initiation in Chinese cordyceps

“…High quality clean reads obtained by filtering raw reads with Trimmomatic software 25 , which was blasted to caterpillar fungus reference gene ( https://ftp.ncbi.nlm.nih.gov/genomes/all/GCA/012/934/285/GCA_0129342 ) using hisat2 software 26 . DESeq was used to analyze the difference of gene expression levels in different samples 27 . We used DIAMOND-BLASTX v0.8.24 to compare the assembled transcript sequences using KEGG ( http://www.kegg.jp/kegg/kegg1.html ), GO, Swiss-Prot, KOG, and NR databases 28 .…”

An insight into sainfoin (Onobrychis viciifolia Scop.) breeding: Challenges and achievements

“…Although a series of genetic markers have been developed for sainfoin (Kempf et al., 2016; Mora‐Ortiz et al., 2016; Shen et al., 2019) and a full chloroplast genome sequence has recently been made available (Jin et al., 2021), no reference nuclear genome sequence exists for this species as of yet. Fortunately, research in this area has been progressing steadily in recent years, with an accumulation of transcriptomic data across various tissues from a small number of genotypes (Jin et al., 2021; Kempf et al., 2016; Mora‐Ortiz et al., 2016; Qiao et al., 2021; Shen et al., 2019; Yin et al., 2020), as well as an assessment of microRNAs (miRNAs) in sainfoin grown at low and high altitudes (Yin et al., 2020). Given the escalating interest in this forage crop, it seems highly likely that advances will continue to be made in this context in coming years, which will facilitate breeding activities going forward.…”