Genome-Wide Identification of the PHD-Finger Family Genes and Their Responses to Environmental Stresses in Oryza sativa L.

Abstract

The PHD-finger family has been demonstrated to be involved in regulating plant growth and development. However, little information is given for its role in environmental stress responses. Here, we identified a total of 59 PHD family genes in the rice genome. These OsPHDs genes were located on eleven chromosomes and synteny analysis only revealed nine duplicated pairs within the rice PHD family. Phylogenetic analysis of all OsPHDs and PHDs from other species revealed that they could be grouped into two major clusters. Furthermore, OsPHDs were clustered into eight groups and members from different groups displayed a great divergence in terms of gene structure, functional domains and conserved motifs. We also found that with the exception of OsPHD6, all OsPHDs were expressed in at least one of the ten tested tissues and OsPHDs from certain groups were expressed in specific tissues. Moreover, our results also uncovered differential responses of OsPHDs expression to environmental stresses, including ABA (abscisic acid), water deficit, cold and high Cd. By using quantitative real-time PCR, we further confirmed the differential expression of OsPHDs under these stresses. OsPHD1/7/8/13/33 were differentially expressed under water deficit and Cd stresses, while OsPHD5/17 showed altered expression under water deficit and cold stresses. Moreover, OsPHD3/44/28 displayed differential expression under ABA and Cd stresses. In conclusion, our results provide valuable information on the rice PHD family in plant responses to environmental stress, which will be helpful for further characterizing their biological roles in responding to environmental stresses.

Genome wide survey, evolution and expression analysis of PHD finger genes reveal their diverse roles during the development and abiotic stress responses in Brassica rapa L.

“…8). This means that some PHD finger genes may play important roles in plant adaption to adverse environmental stresses, an idea that was also supported by other studies [61, 64–66]. These identified PHD finger genes can then serve as a source of candidate genes for genetic engineering and improvement of Brassica crops against abiotic stresses.…”

“…In this study, a total of 145 PHD finger proteins containing 233 PHD domains were identified from the current version of the B. rapa proteome database (Additional file 2: Table S1). This number is considerably higher than those previously identified in maize (67) [64], poplar (73) [65] and rice (59) [66, 96], pear (31) [97] and moso bamboo (60) [67], although it might not yet be exhaustive as other PHD-suspected domain-containing proteins were also detected (Additional file 2: Table S2). This is the consequence of the WGT event occurred ~ 15.9 MYA in Brassica ancestor followed by gene losing [42, 47, 71], while only one tandem duplication event was observed among these PHD finger genes (Fig.…”

“…Interestingly, these PHD finger genes were unevenly distributed on the 10 B. rapa chromosomes (Fig. 2), a phenomenon also observed in A. thaliana [8], maize [64] [65] and rice [66], implying a possible relationship between chromosomal location and their cellular functions.…”

Genome wide association study of 5 agronomic traits in olive (Olea europaea L.)

“…The most significant SNP marker, S1_13767032, was located on 0.497 kb upstream of the Oeu046142.1 gene. This gene is annotated as a PHD finger transcription factor and the family to which this gene belongs, plays a key role in regulating plant growth and development 86 . The analysis of transcriptomes provides genomic resources for functional annotation to discover genes for olive breeding 87 .…”

Ectopic expression of Medicago truncatula homeodomain finger protein, MtPHD6, enhances drought tolerance in Arabidopsis

“…7d). In rice ( O. sativa ), five OsPHD genes were significantly induced while two inhibited by ABA [35]. In soybean, expression of GmPHD 1–6 were induced after ABA and drought treatment, and GmPHD2 transgene upregulated expression of ABA responsive bZIP transcription factor ABI5 [5].…”