RNA sequencing and weighted gene co-expression network analysis uncover the hub genes controlling cold tolerance in Helictotrichon virescens seedlings

Tissue-specific transcriptomic analysis reveals the molecular mechanisms responsive to cold stress in Poa crymophila, and development of EST-SSR markers linked to cold tolerance candidate genes

BACKGROUND

Poa crymophila is a perennial, cold-tolerant, native grass species, widely distributed in the Qinghai-Tibet Plateau. However, the tissue-specific regulatory mechanisms and key regulatory genes underlying its cold tolerance remain poorly characterized. Therefore, in this study, based on the screening and evaluation of cold tolerance of four Poa species, the cold tolerance mechanism of P. crymophila's roots, stems, and leaves and its cold tolerance candidate genes were investigated through physiological and transcriptomic analyses.

RESULTS

Results of the present study suggested that the cold tolerance of the four Poa species was in the following order: P. crymophila > P. botryoides > P. pratensis var. anceps > P. pratensis. Cold stress significantly changed the physiological characteristics of roots, stems, and leaves of P. crymophila in this study. In addition, the transcriptome results showed that 4434, 8793, and 14,942 differentially expressed genes (DEGs) were identified in roots, stems, and leaves, respectively; however, 464 DEGs were commonly identified in these three tissues. KEGG enrichment analysis showed that these DEGs were mainly enriched in the phenylpropanoid biosynthesis pathway (roots), photosynthesis pathway (stems and leaves), circadian rhythm-plant pathway (stems and leaves), starch and sucrose metabolism pathway (roots, stems, and leaves), and galactose metabolism pathway (roots, stems, and leaves). A total of 392 candidate genes involved in Ca2+ signaling, ROS scavenging system, hormones, circadian clock, photosynthesis, and transcription factors (TFs) were identified in P. crymophila. Weighted gene co-expression network analysis (WGCNA) identified nine hub genes that may be involved in P. crymophila cold response. A total of 200 candidate gene-based EST-SSRs were developed and characterized. Twenty-nine polymorphic EST-SSRs primers were finally used to study genetic diversity of 40 individuals from four Poa species with different cold tolerance characteristics. UPGMA cluster and STRUCTURE analysis showed that the 40 Poa individuals were clustered into three major groups, individual plant with similar cold tolerance tended to group together. Notably, markers P37 (PcGA2ox3) and P148 (PcERF013) could distinguish P. crymophila from P. pratensis var. anceps, P. pratensis, and P. botryoides.

CONCLUSIONS

This study provides new insights into the molecular mechanisms underlying the cold tolerance of P. crymophila, and also lays a foundation for molecular marker-assisted selection for cold tolerance improvement in Poa species.

Time-course transcriptome analysis reveals gene co-expression networks and transposable element responses to cold stress in cotton

BACKGROUND

Cold stress significantly challenges cotton growth and productivity, yet the genetic and molecular mechanisms underlying cold tolerance remain poorly understood.

RESULTS

We employed RNA-seq and iterative weighted gene co-expression network analysis (WGCNA) to investigate gene and transposable element (TE) expression changes at six cold stress time points (0 h, 2 h, 4 h, 6 h, 12 h, 24 h). Thousands of differentially expressed genes (DEGs) were identified, exhibiting time-specific patterns that highlight a phase-dependent transcriptional response. While the A and D subgenomes contributed comparably to DEG numbers, numerous homeologous gene pairs showed differential expression, indicating regulatory divergence. Iterative WGCNA uncovered 125 gene co-expression modules, with some enriched in specific chromosomes or chromosomal regions, suggesting localized regulatory hotspots for cold stress response. Notably, transcription factors, including MYB73, ERF017, MYB30, and OBP1, emerged as central regulators within these modules. Analysis of 11 plant hormone-related genes revealed dynamic expression, with ethylene (ETH) and cytokinins (CK) playing significant roles in stress-responsive pathways. Furthermore, we documented over 15,000 expressed TEs, with differentially expressed TEs forming five distinct clusters. TE families, such as LTR/Copia, demonstrated significant enrichment in these expression clusters, suggesting their potential role as modulators of gene expression under cold stress.

CONCLUSIONS

These findings provide valuable insights into the complex regulatory networks underlying cold stress response in cotton, highlighting key molecular components involved in cold stress regulation. This study provides potential genetic targets for breeding strategies aimed at enhancing cold tolerance in cotton.

A Multi-Omics View of Maize's (Zea mays L.) Response to Low Temperatures During the Seedling Stage

Maize (Zea mays L.) is highly sensitive to temperature during its growth and development stage. A 1 °C drop in temperature can delay maturity by 10 days, resulting in a yield reduction of over 10%. Low-temperature tolerance in maize is a complex quantitative trait, and different germplasms exhibit significant differences in their responses to low-temperature stress. To explore the differences in gene expression and metabolites between B144 (tolerant) and Q319 (susceptible) during germination under low-temperature stress and to identify key genes and metabolites that respond to this stress, high-throughput transcriptome sequencing was performed on the leaves of B144 and Q319 subjected to low-temperature stress for 24 h and their respective controls using Illumina HiSeqTM 4000 high-throughput sequencing technology. Additionally, high-throughput metabolite sequencing was conducted on the samples using widely targeted metabolome sequencing technology. The results indicated that low-temperature stress triggered the accumulation of stress-related metabolites such as amino acids and their derivatives, lipids, phenolic acids, organic acids, flavonoids, lignin, coumarins, and alkaloids, suggesting their significant roles in the response to low temperature. This stress also promoted gene expression and metabolite accumulation involved in the flavonoid biosynthesis pathway. Notably, there were marked differences in gene expression and metabolites related to the glyoxylate and dicarboxylate metabolism pathways between B144 and Q319. This study, through multi-omics integrated analysis, provides valuable insights into the identification of metabolites, elucidation of metabolic pathways, and the biochemical and genetic basis of plant responses to stress, particularly under low-temperature conditions.

Response Mechanism of Extracellular Polymeric Substances Synthesized by Alternaria sp. on Drought Stress in Alfalfa (Medicago sativa L.)

This study investigates how extracellular polymeric substances (EPS) synthesized by dark septate endophytic (DSE) improve alfalfa's drought resistance. Drought stress was simulated in hydroponic culture, and roots were treated with different EPS concentrations to determine their effects on drought tolerance and applicable concentrations. Hydroponic solutions with 0.25 and 0.50% EPS concentrations alleviated leaf wilting and increased total plant fresh weight by 35.8 and 57.7%, respectively. SEM shows that EPS attached to the roots and may have served to protect the root system. EPS treatment significantly depressed the MDA contents of the roots, stems, and leaves. Roots responded to drought stress by increasing soluble sugar contents and antioxidant enzyme activities, while mitigating stem and leaf stress by synthesizing lipid compounds, amino acids, and organic acid metabolites. Five metabolites in the stem have been reported to be associated with plant stress tolerance and growth, namely 3-O-methyl 5-O-(2-methyl propyl) (4S)-2,6-dimethyl-4-(2-nitrophenyl)-3,4-dihydropyridine-3,5-dicarboxylate, malic acid, PA (20:1(11Z)/15:0), N-methyl-4,6,7-trihydroxy-1,2,3,4-tetrahydroisoquinoline, and 2-(S-glutathionyl) acetyl glutathione. In summary, EPS treatment induced oxidative stress and altered plant metabolism, and this in turn increased plant antioxidant capacity. The results provide a theoretical basis for the application of EPS in commercial products that increase plant resistance and ecological restoration.

Transcriptomics integrated with metabolomics provides a new strategy for mining key genes in response to low temperature stress in Helictotrichon virescens

H. virescens is a perennial herbaceous plant with highly tolerant to cold weather, but the key genes that respond to low temperature stress still remain unclear. Hence, RNA-seq was performed using leaves of H. virescens treated at 0 °C and 25 °C for 12 h, 36 h, and 60 h, respectively, and a total of 9416 DEGs were significantly enriched into seven KEGG pathways. The LC-QTRAP platform was performed using leaves of H. virescens leaves at 0 °C and 25 °C for 12 h, 36 h, and 60 h, respectively, and a total of 1075 metabolites were detected, which were divided into 10 categories. Additionally, 18 major metabolites, two key pathways, and six key genes were mined using a multi-omics analytical strategy. The RT-PCR results showed that with the extension of treatment time, the expression levels of key genes in the treatment group gradually increased, and the difference between the treatment group and the control group was extremely significant. Notably, the functional verification results showed that the key genes positively regulated cold tolerance of H. virescens. These results can lay a foundation for the in-depth analysis of the mechanism of response of perennial herbs to low temperature stress.

QTL-seq and transcriptomic integrative analyses reveal two positively regulated genes that control the low-temperature germination ability of MTP-maize introgression lines

KEY MESSAGE

Two candidate genes (ZmbZIP113 and ZmTSAH1) controlling low-temperature germination ability were identified by QTL-seq and integrative transcriptomic analyses. The functional verification results showed that two candidate genes positively regulated the low-temperature germination ability of IB030. Low-temperature conditions cause slow maize (Zea mays L.) seed metabolism, resulting in slow seedling emergence and irregular seedling emergence, which can cause serious yield loss. Thus, improving a maize cultivar's low-temperature germination ability (LTGA) is vital for increasing yield production. Wild relatives of maize, such as Z. perennis and Tripsacum dactyloides, are strongly tolerant of cold stress and can thus be used to improve the LTGA of maize. In a previous study, the genetic bridge MTP was constructed (from maize, T. dactyloides, and Z. perennis) and used to obtain a highly LTGA maize introgression line (IB030) by backcross breeding. In this study, IB030 (Strong-LTGA) and Mo17 (Weak-LTGA) were selected as parents to construct an F₂ offspring. Additionally, two major QTLs (qCS1-1 and qCS10-1) were mapped. Then, RNA-seq was performed using seeds of IB030 and the recurrent parent B73 treated at 10 °C for 27 days and 25 °C for 7 days, respectively, and two candidate genes (ZmbZIP113 and ZmTSAH1) controlling LTGA were located using QTL-seq and integrative transcriptomic analyses. The functional verification results showed that the two candidate genes positively regulated LTGA of IB030. Notably, homologous cloning showed that the source of variation in both candidate genes was the stable inheritance of introgressed alleles from Z. perennis. This study was thus able to analyze the LTGA mechanism of IB030 and identify resistance genes for genetic improvement in maize, and it proved that using MTP genetic bridge confers desirable traits or phenotypes of Z. perennis and tripsacum essential to maize breeding systems.