Structural variations and genetic diversity of rice OsGRF genes and their potential use in rice improvement
Abstract
Background: Growth-Regulating Factors (GRFs) are plant-specific transcription factors that play central regulatory roles in plant growth, development, and stress responses. However, the genetic composition, structural variation (SV), and evolutionary patterns of the OsGRF gene family in rice remain unexplored at the pan-genome level.
Results: In the present study, a pan-genome analysis of the OsGRF gene family was carried out using 150 high-quality rice ( Oryza sativa L.) genomes of Geng ( Japonica ), Xian ( Indica ), Aus , Bas ( Basmati ), and Or ( Oryza rufipogon ) accessions. Under the stated CD-HIT clustering, a total of 22 nonredundant sequence clusters were identified (referred to below as OsGRF-1 to OsGRF-22 ), encompassing three core genes, 18 variable genes, and one private gene, with six of them absent from the Nipponbare reference genome. Phylogenetic analysis classified these genes into five subgroups. Presence-absence variation (PAV) analysis revealed that OsGRF-2 and OsGRF-5 were predominantly found in Or but were almost absent in cultivated ones, consistent with potential domestication-associated loss; OsGRF-1 and OsGRF-19 demonstrated intricate PAV polymorphisms in both cultivated and Or accessions. The majority of OsGRF genes were under purifying selection, whereas OsGRF-13 and OsGRF-15 showed evidence of relaxed selective constraints. A total of 75 SVs overlapping with OsGRF genes were detected. Moreover, in a preliminary accession-level comparison, SVs were associated with altered expression of OsGRF-8 , potentially through the modification of cis -regulatory elements (CREs) within its promoter. Haplotype network analysis of five OsGRF genes revealed nominally significant (uncorrected) associations between major haplotypes and yield-related traits. The frequency changes of predominant haplotypes between landraces (LANs) and modern varieties (MVs) may reflect possible selection in modern rice breeding.
Conclusion: These findings provide a comprehensive description of the genetic constitution and evolutionary patterns of the OsGRF gene family at the pan-genome level. Our results suggest that SV-mediated alterations in the architecture of promoter CREs may represent one of the potential regulatory mechanisms of the expression of OsGRF genes. Moreover, atypical (predicted domain-disrupted) OsGRF gene models were detected in many of the analyzed assemblies; whether these models are expressed, translated, or functional remains an open question. The haplotype-trait associations and breeding frequency dynamics identified in this study are exploratory and uncorrected and should be treated as hypotheses and candidate loci for further validation, rather than as validated markers or causal alleles for marker-assisted selection in rice breeding programs aimed at grain yield and plant architecture.
Clinical trial number: Not applicable.
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BibTeX
@article{yang2026structural,
title = {{Structural variations and genetic diversity of rice OsGRF genes and their potential use in rice improvement}},
author = {Leyuan Yang and Yuanyuan Zhu and Yu Shang and Linjun Yu and Youshuai Shi and Tingting Yu and Kai Xu and Xiaoyu He and Chaopu Zhang and Min Li},
journal = {BMC Genomics},
year = {2026},
month = nov,
doi = {10.1186/s12864-026-13516-x},
url = {https://link.springer.com/article/10.1186/s12864-026-13516-x},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Structural variations and genetic diversity of rice OsGRF genes and their potential use in rice improvement
AU - Leyuan Yang
AU - Yuanyuan Zhu
AU - Yu Shang
AU - Linjun Yu
AU - Youshuai Shi
AU - Tingting Yu
AU - Kai Xu
AU - Xiaoyu He
AU - Chaopu Zhang
AU - Min Li
PY - 2026
DA - 2026/11/03
JO - BMC Genomics
DO - 10.1186/s12864-026-13516-x
UR - https://link.springer.com/article/10.1186/s12864-026-13516-x
AB - Background: Growth-Regulating Factors (GRFs) are plant-specific transcription factors that play central regulatory roles in plant growth, development, and stress responses. However, the genetic composition, structural variation (SV), and evolutionary patterns of the OsGRF gene family in rice remain unexplored at the pan-genome level. Results: In the present study, a pan-genome analysis of the OsGRF gene family was carried out using 150 high-quality rice ( Oryza sativa L.) genomes of Geng ( Japonica ), Xian ( Indica ), Aus , Bas ( Basmati ), and Or ( Oryza rufipogon ) accessions. Under the stated CD-HIT clustering, a total of 22 nonredundant sequence clusters were identified (referred to below as OsGRF-1 to OsGRF-22 ), encompassing three core genes, 18 variable genes, and one private gene, with six of them absent from the Nipponbare reference genome. Phylogenetic analysis classified these genes into five subgroups. Presence-absence variation (PAV) analysis revealed that OsGRF-2 and OsGRF-5 were predominantly found in Or but were almost absent in cultivated ones, consistent with potential domestication-associated loss; OsGRF-1 and OsGRF-19 demonstrated intricate PAV polymorphisms in both cultivated and Or accessions. The majority of OsGRF genes were under purifying selection, whereas OsGRF-13 and OsGRF-15 showed evidence of relaxed selective constraints. A total of 75 SVs overlapping with OsGRF genes were detected. Moreover, in a preliminary accession-level comparison, SVs were associated with altered expression of OsGRF-8 , potentially through the modification of cis -regulatory elements (CREs) within its promoter. Haplotype network analysis of five OsGRF genes revealed nominally significant (uncorrected) associations between major haplotypes and yield-related traits. The frequency changes of predominant haplotypes between landraces (LANs) and modern varieties (MVs) may reflect possible selection in modern rice breeding. Conclusion: These findings provide a comprehensive description of the genetic constitution and evolutionary patterns of the OsGRF gene family at the pan-genome level. Our results suggest that SV-mediated alterations in the architecture of promoter CREs may represent one of the potential regulatory mechanisms of the expression of OsGRF genes. Moreover, atypical (predicted domain-disrupted) OsGRF gene models were detected in many of the analyzed assemblies; whether these models are expressed, translated, or functional remains an open question. The haplotype-trait associations and breeding frequency dynamics identified in this study are exploratory and uncorrected and should be treated as hypotheses and candidate loci for further validation, rather than as validated markers or causal alleles for marker-assisted selection in rice breeding programs aimed at grain yield and plant architecture. Clinical trial number: Not applicable.
SN - 1471-2164
ER -