Pan-genomic dissection of the CCT gene family in wheat reveals evolutionary dynamics and regulatory divergence
- 1Crop Research Institute, Shandong Academy of Agricultural Sciences/National Engineering Research Center of Wheat and Maize/State Key Laboratory of Wheat Improvement/Key Laboratory of Wheat Biology and Genetic Improvement in North Yellow & Huai River Valley/Shandong Provincial Technology Innovation Center for Wheat
- 2Shandong Luyan Seed Co., Ltd.
Abstract
Introduction: The CCT (CONSTANS, CO-LIKE, and TIMING OF CAB EXPRESSION 1) gene family regulates flowering time, circadian rhythm maintenance, and abiotic stress responses. However, previous investigations in wheat have relied on single-reference genomes, limiting the understanding of inter-varietal structural variation.
Methods: Here, we performed a pan-genomic analysis of the CCT gene family across 16 wheat accessions.
Results and Discussion: Copy numbers varied from 27 in diploid Triticum urartu to 69–103 in modern common wheat cultivars, with subgenomic contributions displaying an A > D > B gradient. Orthogroup classification based on the 12 T. aestivum cultivars identified 22 Core, 9 Softcore, 2 Dispensable, and 2 predicted Private orthogroups, all under strong purifying selection; the Private orthogroups require assembly-level validation because most cultivars used projected gene models. Protein-protein interaction network analysis identified a small set of highly connected nodes, with enrichment in circadian rhythm and photoperiodic flowering pathways, though this is largely expected given the query sequences; DeepGOPlus annotation further supported their roles as transcriptional regulators. Hexaploid wheat possessed longer mRNA lengths than tetraploids and diploids, but this may partly reflect annotation gaps. Promoter cis -elements were conserved across subgenomes, while paired analysis of homoeologous triads revealed significant expression divergence among subgenome copies. Tissue-specific profiling in Chinese Spring identified grain-preferential genes enriched for seed-specific elements, and stress treatments revealed candidate cis-elements, with WUN-motif and CGTCA-motif remaining significant after FDR correction. These findings provide a comprehensive view of CCT gene family evolution and regulatory diversification, offering candidate genes for stress tolerance and yield improvement in wheat.
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BibTeX
@article{zheng2026pangenomic,
title = {{Pan-genomic dissection of the CCT gene family in wheat reveals evolutionary dynamics and regulatory divergence}},
author = {Wenjie Zheng and Peng Li and Baiqiang Yan and Miao Wang and Xin Sun and Ying Liu and Wei Li and Chen Huang and Mingzhu Sun and Zhengyong Cui},
journal = {Frontiers in Plant Science},
year = {2026},
month = oct,
doi = {10.3389/fpls.2026.1978297},
url = {https://www.frontiersin.org/articles/10.3389/fpls.2026.1978297/full},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Pan-genomic dissection of the CCT gene family in wheat reveals evolutionary dynamics and regulatory divergence
AU - Wenjie Zheng
AU - Peng Li
AU - Baiqiang Yan
AU - Miao Wang
AU - Xin Sun
AU - Ying Liu
AU - Wei Li
AU - Chen Huang
AU - Mingzhu Sun
AU - Zhengyong Cui
PY - 2026
DA - 2026/10/26
JO - Frontiers in Plant Science
DO - 10.3389/fpls.2026.1978297
UR - https://www.frontiersin.org/articles/10.3389/fpls.2026.1978297/full
AB - Introduction: The CCT (CONSTANS, CO-LIKE, and TIMING OF CAB EXPRESSION 1) gene family regulates flowering time, circadian rhythm maintenance, and abiotic stress responses. However, previous investigations in wheat have relied on single-reference genomes, limiting the understanding of inter-varietal structural variation. Methods: Here, we performed a pan-genomic analysis of the CCT gene family across 16 wheat accessions. Results and Discussion: Copy numbers varied from 27 in diploid Triticum urartu to 69–103 in modern common wheat cultivars, with subgenomic contributions displaying an A > D > B gradient. Orthogroup classification based on the 12 T. aestivum cultivars identified 22 Core, 9 Softcore, 2 Dispensable, and 2 predicted Private orthogroups, all under strong purifying selection; the Private orthogroups require assembly-level validation because most cultivars used projected gene models. Protein-protein interaction network analysis identified a small set of highly connected nodes, with enrichment in circadian rhythm and photoperiodic flowering pathways, though this is largely expected given the query sequences; DeepGOPlus annotation further supported their roles as transcriptional regulators. Hexaploid wheat possessed longer mRNA lengths than tetraploids and diploids, but this may partly reflect annotation gaps. Promoter cis -elements were conserved across subgenomes, while paired analysis of homoeologous triads revealed significant expression divergence among subgenome copies. Tissue-specific profiling in Chinese Spring identified grain-preferential genes enriched for seed-specific elements, and stress treatments revealed candidate cis-elements, with WUN-motif and CGTCA-motif remaining significant after FDR correction. These findings provide a comprehensive view of CCT gene family evolution and regulatory diversification, offering candidate genes for stress tolerance and yield improvement in wheat.
SN - 1664-462X
ER -