Genome-Wide Analysis Elucidates the Role of CONSTANS-like Genes in Stress Responses of Cotton.

Wenqiang Qin,Ya Yu,Chuanjia Chen,Ge Zhao,Xindong Wang,Zhi Li,Yuying Jin,Huiqin Li,Fuguang Li,Ji Liu,Wei Hu,Jianping Xi,Zhaoen Yang

doi:10.3390/ijms19092658

Abstract

The CONSTANS (CO)-like gene family has been well studied for its role in the regulation of plant flowering time. However, their role remains poorly understood in cotton. To better understand the possible roles of CO-like in cotton, we performed a comprehensive genome-wide analysis of CO-like genes in cotton. Phylogenetic tree analysis showed that CO-like genes naturally clustered into three groups. Segmental duplication and whole genome duplication (WGD), which occurred before polyploidy, were important contributors to its expansion within the At (“t” indicates tetraploid) and Dt subgenomes, particularly in Group III. Long-terminal repeat retroelements were identified as the main transposable elements accompanying 18 genes. The genotype of GhCOL12_Dt displayed low diversity; it was a candidate involved in domestication. Selection pressure analyses indicated that relaxed purifying selection might have provided the main impetus during the evolution of CO-like genes in upland cotton. In addition, the high expression in the torus and calycle indicated that CO-like genes might affect flowering. The genes from Group II, and those from Group III involved in segmental duplication or WGD, might play important roles in response to drought and salt stress. Overall, this comprehensive genome-wide study of the CO-like gene family would facilitate further detailed studies in cotton.

Highlights

The CONSTANS (CO) genes encode a small class of transcription factors, characterised by a CCT (CO, CO-like, TOC1 (TIMING OF CAB EXPRESSION1)) domain near the carboxy terminus
21, 18, 38, 11, 16, 15, 13, and 16 genes were confirmed as CO-like family members in G. raimondii, G. arboreum, G. hirsutum, cacao, Populus trichocarpa, rice, sorghum, and maize, respectively (Table S1)
G. hirsutum contained the largest number of CO-like genes, which was close to that of the two diploid cotton species, G. arboreum and G. raimondii (Table S2)

Summary

Introduction

The CONSTANS (CO) genes encode a small class of transcription factors, characterised by a CCT (CO, CO-like, TOC1 (TIMING OF CAB EXPRESSION1)) domain near the carboxy terminus. The CO-like gene family is subdivided into three groups according to the additional B-box domain near the amino terminus. In Arabidopsis, 17 members of the CO-like gene family are divided into three groups. Most studies show that CO-like genes play significant roles in the regulation of flowering time in plants. The Arabidopsis CO gene play important roles in the photoperiod pathway and regulation of flowering time [5,6], and its ortholog, Hd1 (Heading date 1), in rice shows a similar biological function and acts as a pivotal regulator in the photoperiod pathway [7,8]

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