Genome-wide analysis of the CCT gene family in Chinese white pear (Pyrus bretschneideri Rehd.) and characterization of PbPRR2 in response to varying light signals

Zheng Liu,Tao Wu,Li Yang,Yin-Sheng Cheng,Xian-Shuang Nie,Zhong-Qi Qin,Lin An,Jia-Li Liu

doi:10.1186/s12870-022-03476-1

Abstract

BackgroundCanopy architecture is critical in determining the light environment and subsequently the photosynthetic productivity of fruit crops. Numerous CCT domain-containing genes are crucial for plant adaptive responses to diverse environmental cues. Two CCT genes, the orthologues of AtPRR5 in pear, have been reported to be strongly correlated with photosynthetic performance under distinct canopy microclimates. However, knowledge concerning the specific expression patterns and roles of pear CCT family genes (PbCCTs) remains very limited. The key roles played by PbCCTs in the light response led us to examine this large gene family in more detail.ResultsGenome-wide sequence analysis identified 42 putative PbCCTs in the genome of pear (Pyrus bretschneideri Rehd.). Phylogenetic analysis indicated that these genes were divided into five subfamilies, namely, COL (14 members), PRR (8 members), ZIM (6 members), TCR1 (6 members) and ASML2 (8 members). Analysis of exon–intron structures and conserved domains provided support for the classification. Genome duplication analysis indicated that whole-genome duplication/segmental duplication events played a crucial role in the expansion of the CCT family in pear and that the CCT family evolved under the effect of purifying selection. Expression profiles exhibited diverse expression patterns of PbCCTs in various tissues and in response to varying light signals. Additionally, transient overexpression of PbPRR2 in tobacco leaves resulted in inhibition of photosynthetic performance, suggesting its possible involvement in the repression of photosynthesis.ConclusionsThis study provides a comprehensive analysis of the CCT gene family in pear and will facilitate further functional investigations of PbCCTs to uncover their biological roles in the light response.

Highlights

Canopy architecture is critical in determining the light environment and subsequently the photosyn‐ thetic productivity of fruit crops
Our analysis revealed that the CO homlogues (COLs) subfamily consisted of the highest number of CCTgenes in pear, with 33.3% (14 PbCOLs) of the total PbCCTs (Additional file 2)
None of the PbCCTs were from tandem duplication, and all PbCCTgene duplications in pear were caused by whole-genome duplication (WGD)/segmental duplication events (Additional file 4); similar results were observed for other gene families in pear [69,70,71,72]

Summary

Introduction

Canopy architecture is critical in determining the light environment and subsequently the photosyn‐ thetic productivity of fruit crops. The key roles played by PbCCTs in the light response led us to examine this large gene family in more detail. It is well known that CCT family members play diverse and important roles in flowering, circadian rhythms, development and abiotic stress tolerance [12]. Other CO homlogues (COLs) have been associated with abiotic stress tolerance, plant growth, development and metabolic processes, apart from playing a key role in photoperiodic flowering induction [21,22,23,24,25,26]. AtCIA2, AtCIL, and their barley homologues (HvCMF3 and HvCMF7) belong to the TCR1 subfamily and play critical roles in chloroplast development, thylakoid morphology, photosynthetic activity and various abiotic stress responses [36,37,38,39]. Overexpression of AtASML2 results in enhanced expression of a subset of sugar-inducible genes in Arabidopsis [6]

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Discussion

Conclusion