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Genome-wide analysis of rice dehydrin gene family: Its evolutionary conservedness and expression pattern in response to PEG induced dehydration stress.

ABSTRACT: Abiotic stresses adversely affect cellular homeostasis, impairing overall growth and development of plants. These initial stress signals activate downstream signalling processes, which, subsequently, activate stress-responsive mechanisms to re-establish homeostasis. Dehydrins (DHNs) play an important role in combating dehydration stress. Rice (Oryza sativa L.), which is a paddy crop, is susceptible to drought stress. As drought survival in rice might be viewed as a trait with strong evolutionary selection pressure, we observed DHNs in the light of domestication during the course of evolution. Overall, 65 DHNs were identified by a genome-wide survey of 11 rice species, and 3 DHNs were found to be highly conserved. The correlation of a conserved pattern of DHNs with domestication and diversification of wild to cultivated rice was validated by synonymous substitution rates, indicating that Oryza rufipogon and Oryza sativa ssp. japonica follow an adaptive evolutionary pattern; whereas Oryza nivara and Oryza sativa ssp. indica demonstrate a conserved evolutionary pattern. A comprehensive analysis of tissue-specific expression of DHN genes in japonica and their expression profiles in normal and PEG (poly ethylene glycol)-induced dehydration stress exhibited a spatiotemporal expression pattern. Their interaction network reflects the cross-talk between gene expression and the physiological processes mediating adaptation to dehydration stress. The results obtained strongly indicated the importance of DHNs, as they are conserved during the course of domestication.

SUBMITTER: Verma G

PROVIDER: S-EPMC5411031 | biostudies-literature |

REPOSITORIES: biostudies-literature

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Project description:Jilin ginseng (Panax ginseng C. A. Meyer) has a long history of medicinal use worldwide. The quality of ginseng is governed by a variety of internal and external factors. Nuclear factor Y (NF-Y), an important transcription factor in eukaryotes, plays a crucial role in the plant response to abiotic stresses by binding to a specific promoter, the CCAAT box. However, the NF-Y gene family has not been reported in Panax ginseng. In this study, 115 PgNF-Y transcripts with 40 gene IDs were identified from the Jilin ginseng transcriptome database. These genes were classified into the PgNF-YA (13), PgNF-YB (14), and PgNF-YC (13) subgroups according to their subunit types, and their nucleotide sequence lengths, structural domain information, and amino acid sequence lengths were analyzed. The phylogenetic analysis showed that the 79 PgNF-Y transcripts with complete ORFs were divided into three subfamilies, NF-YA, NF-YB, and NF-YC. PgNF-Y was annotated to eight subclasses under three major functions (BP, MF, and CC) by GO annotation, indicating that these transcripts perform different functions in ginseng growth and development. Expression pattern analysis of the roots of 42 farm cultivars, 14 different tissues of 4-year-old ginseng plants, and the roots of 4 different-ages of ginseng plants showed that PgNF-Y gene expression differed across lineages and had spatiotemporal specificity. Coexpression network analysis showed that PgNF-Ys acted synergistically with each other in Jilin ginseng. In addition, the analysis of the response of PgNF-YB09, PgNF-YC02, and PgNF-YC07-04 genes to salt stress treatment was investigated by fluorescence quantitative PCR. The expression of these genes increased after salt stress treatment, indicating that they may be involved in the regulation of the response to salt stresses in ginseng. These results provide important functional genetic resources for the improvement and gene breeding of ginseng in the future.Conclusions: This study fills a knowledge gap regarding the NF-Y gene family in ginseng, provides systematic theoretical support for subsequent research on PgNF-Y genes, and provides data resources for resistance to salt stress in ginseng.

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Genome-wide analysis of rice dehydrin gene family: Its evolutionary conservedness and expression pattern in response to PEG induced dehydration stress.

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