A Transcriptomic Analysis Reveals Diverse Regulatory Networks That Respond to Cold Stress in Strawberry (Fragaria×ananassa)

Abstract

Strawberry is often subjected to cold stress in temperate regions when insulation measures are not strictly applied in protected cultivation. Cold stress adversely influences plant growth and development by triggering a massive change to the transcriptome. To provide the potential strategies in improving strawberry cold tolerance and give a glimpse into the understanding of the complex cold signaling pathways in plants, this study identified attractive candidate genes and revealed diverse regulatory networks that responded to cold stress in strawberry (Fragaria×ananassa) by a transcriptomic analysis. Totally, there were 2397 differentially expressed genes (DEGs) under cold stress treatment (T1) vs. normal treatment (CK). Of these, 1180 DEGs were upregulated, while 1217 DEGs were downregulated. Functional enrichment analysis showed that DEGs were significantly (adjusted P value < 0.05) overrepresented in six pathways including plant hormone signal transduction, flavonoid biosynthesis, mitogen-activated protein kinase (MAPK) signaling, starch and sucrose metabolism, circadian rhythm, and alpha-linolenic acid metabolism. The cold signaling initiated expression of downstream cold-responsive (COR) genes with cis-acting element ABRE or CRT/DRE in the ABA-independent or ABA-dependent pathway to impel plant defense against the stress. Strikingly, GIGANTEA (gene id 101308922), two-component response regulator-like PRR95 (gene id 101295449), and ethylene-responsive transcription factor ERF105-like (gene id 101295082) were dramatically induced under low-temperature treatment, indicating that they played an important role in response to cold stress in strawberry.

Population Transcriptomes Reveal the Interspecific Adaptive Genetic Differentiation of Liriodendron by Landscape Genetics

“…The ubiquitin-mediated proteolysis pathway is involved in the immune response in Arabidopsis [76], and the carotenoid biosynthesis pathway plays important roles in fruit development, petal coloration and photosynthesis [77][78][79]. The alpha-linolenic acid metabolism pathway relates to salt tolerance and cold stress [80,81], and the phagosome pathway is involved in environmental stress [82]. These results suggested that most of the variation loci obtained from environmental correlation analysis are indeed closely related to the adaptation of species.…”

Integrating transcriptome and metabolome analyses of the response to cold stress in pumpkin (Cucurbita maxima)

“…Many genes indeed displayed altered expression levels in several hormone-mediated branches, such as ABA, IAA, CK, GA, ET, BR, JA, and SA. Obviously, most of the genes in auxin signaling pathway in C. maxima leaves exposed to cold stress were inhibited, which generally are obligated to cell elongation, division, cycle, and growth [13,73]. Auxin is an endogenous small molecule with an incredibly large impact on plant growth and and response to stress in concert with other hormonal pathways [74][75][76].…”

“…Phenylalanine and tyrosine have different functions in stress resistance and are central to plant metabolism [88]. The increase in amino acids in A. thaliana, tomato, and other plants under during stress acclimation indicate that the accumulation of amino acids is related to the degradation of proteins [13,89,90]. It has been reported that the exogenous application of phenylalanine can promote chilling tolerance in tomato by activating ROS-scavenging systems; an increase in the abundance of the phenylalanine is also induced by low temperature [91].…”

“…The study of global gene expression using RNA-Seq can help researchers to unveil the regulatory genes and key pathways that may induce cold resistance. Hence, an increasing number of cold sensitive genes and transcription factors have been identified and analyzed in plants under cold stress [9,[11][12][13][14]. WRKY, NAC, MYB, AP2/ERF, and bZIP were the most abundant transcription factor families under cold stress.…”

“…Recently, the best approach has been to integrate transcriptomics and metabolomics methods to reveal the complex reaction process that occurs under low temperature stress and provide more information about this response. In recent years, this integrative method has become a useful tool for producing a large amount of molecular information about global cellular events and has been used to study peach, tobacco, seaweed, tomato, and grape, etc [11,13,[16][17][18]. Although several molecular mechanisms related to cold stress have been revealed in these plants, little is known about the response of pumpkin, Cucurbita maxita, to cold stress.…”