Genome wide identification and functional assignments of C2H2 Zinc-finger family transcription factors in Dichanthelium oligosanthes

Identification of C2H2 zinc finger genes through genome-wide association study and functional analyses of LkZFPs in response to stresses in Larix kaempferi

BACKGROUND

C2H2 zinc finger proteins (C2H2-ZFPs), one of the largest transcription factors, play a variety of roles in plant development and growth as well as stress response. While, the evolutionary history and expression profile of the C2H2-ZFP genes in Larix kaempferi (LkZFPs) have not been reported so far.

RESULTS

In this study, the whole genome of the LkZFPs was identified and characterized, including physicochemical properties, phylogenetic relationships, conservative motifs, the promoter cis-elements and Gene Ontology (GO) annotation. We identified 47 LkZFPs and divided them into four subfamilies based on phylogenetic analysis and conserved motifs. Subcellular localization prediction showed that most of the LkZFPs were located in the nucleus. Promoter cis-element analysis suggested that the LkZFPs may be involved in the regulation of stress responses. Moreover, Real-time quantitative PCR (RT-qPCR) results showed that Q-type LkZFP genes were involved in the response to abiotic stress, such as salt, drought and hormone stresses. Subcellular localization results showed that LkZFP7 and LkZFP37 were located in the nucleus, LkZFP32 was located in both cytoplasm and nucleus.

CONCLUSION

The identification and functional analysis of LkZFPs suggested that some LkZFP genes might play important roles in coping with both biological and abiotic stresses. These results could further increase understanding of the function of the LkZFPs, and provide some research direction and theoretical support.

Genome-Wide Characterization and Analysis of CIPK Gene Family in Two Cultivated Allopolyploid Cotton Species: Sequence Variation, Association with Seed Oil Content, and the Role of GhCIPK6

Calcineurin B-like protein-interacting protein kinases (CIPKs), as key regulators, play an important role in plant growth and development and the response to various stresses. In the present study, we identified 80 and 78 CIPK genes in the Gossypium hirsutum and G. barbadense, respectively. The phylogenetic and gene structure analysis divided the cotton CIPK genes into five groups which were classified into an exon-rich clade and an exon-poor clade. A synteny analysis showed that segmental duplication contributed to the expansion of Gossypium CIPK gene family, and purifying selection played a major role in the evolution of the gene family in cotton. Analyses of expression profiles showed that GhCIPK genes had temporal and spatial specificity and could be induced by various abiotic stresses. Fourteen GhCIPK genes were found to contain 17 non-synonymous single nucleotide polymorphisms (SNPs) and co-localized with oil or protein content quantitative trait loci (QTLs). Additionally, five SNPs from four GhCIPKs were found to be significantly associated with oil content in one of the three field tests. Although most GhCIPK genes were not associated with natural variations in cotton oil content, the overexpression of the GhCIPK6 gene reduced the oil content and increased C18:1 and C18:1+C18:1d6 in transgenic cotton as compared to wild-type plants. In addition, we predicted the potential molecular regulatory mechanisms of the GhCIPK genes. In brief, these results enhance our understanding of the roles of CIPK genes in oil synthesis and stress responses.