Genome-wide identification and expression analysis of the CCT gene family reveals its function in regulating heading date in proso millet (Panicum miliaceum L.)

TL;DR

This study identifies and analyzes CCT genes in proso millet, revealing their role in controlling heading date based on day length.

Contribution

The study systematically identifies 74 CCT genes in proso millet and identifies ten marker genes linked to photoperiod-dependent heading date regulation.

Findings

74 CCT genes were identified and classified into four subfamilies in proso millet.

17 PmCCT genes showed differential expression under long-day and short-day conditions.

Ten marker PmCCT genes were strongly induced during heading transition in photoperiod-sensitive accessions.

Abstract

Proso millet (Panicum miliaceum L.) is an important short-day cereal crop whose heading date is highly sensitive to photoperiod, a key factor influencing its yield and geographical adaptation. The CCT (CONSTANS, CONSTANS-LIKE and TOC1) gene family plays a crucial role in regulating plant photoperiod pathway and flowering time.

In this study, a comprehensive genome-wide identification, characterization and expression analysis were performed of the CCT gene family in proso millet. CCT family members were identified, and their phylogenetic relationships, gene structures, conserved motifs, and duplication events were analyzed. Expression patterns were examined using RNA-seq data from leaves and shoot apical meristems under different photoperiod conditions, and further analyzed by qRT‑PCR across proso millet germplasms with varying heading dates.

A total of 74 CCT genes (PmCCT1–PmCCT74) were identified and found to be unevenly distributed across the 18 chromosomes. Phylogenetic analysis classified them into four major subfamilies: CONSTANS (COL)-like, CCT MOTIF FAMILY (CMF)-like, pseudo-response regulator (PRR)-like, and TIFY-like. Expression profiling revealed that 17 PmCCT genes exhibited differential expression under long-day (LD) and short-day (SD) conditions, with elevated transcript levels in both leaves and spikelets. Subsequent qRT-PCR analysis across proso millet germplasms with varying heading dates further identified ten marker PmCCT genes that were strongly induced during the heading transition under SD treatment, specifically in the photoperiod-sensitive accession. Their dynamic expression patterns closely correlated with heading time variation.

This study provides a systematic understanding of the potential functions of PmCCT genes in photoperiod-mediated regulation of heading date in proso millet. The identified ten candidate marker genes highlight their role in photoperiod-dependent regulation, offering valuable molecular targets and a theoretical foundation for molecular breeding aimed at improving geographical adaptations of proso millet accessions.

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