Genetic and phenotypic screening of rice genotypes using a functional marker linked to the SCM2 gene

Document Type : Original Article

Authors

1 Department of Production and Plant Genrtic, Faculty of Agriculture, University of Zanjan, Zanjan, Iran

2 Rice Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Rasht, Iran

3 Rice Research Institute of Iran, Rice Research Institute of Iran, Agricultural Research, Education and Extension Organization (AREEO), Rasht, Iran

10.22034/plant.2026.145069.1185

Abstract

Introduction: With the rapid growth of the global population and the increasing constraints on water and soil resources, achieving sustainable food security-particularly for strategic crops such as rice has emerged as one of the major challenges in agricultural development. Stem lodging is a critical limiting factor affecting grain yield and quality in many local and improved rice cultivars, significantly reducing harvest efficiency and yield loss. Enhancing culm diameter represents one of the most effective genetic strategies for improving lodging resistance, and the identification of genes and alleles influencing this trait can play a pivotal role in enhancing breeding efficiency. In this context, the STRONG CULM2 (SCM2) gene has attracted considerable attention due to its pleiotropic effects on increasing culm diameter, spikelet number, and lodging resistance. The objective of this study was to identify and classify rice genotypes based on the presence or absence of the SCM2 allele and to evaluate the efficiency of a functional molecular marker associated with this gene for screening genotypes for culm diameter.
Materials and Methods: For this purpose, 50 rice genotypes, including local, improved, and imported cultivars from the rice germplasm collection of the Rice Research Institute of Iran, were evaluated in a randomized complete block design with three replications under field conditions in 2021-2022 growing season. Culm diameter was measured 20 days after the onset of flowering at the fourth internode. For molecular evaluation, genomic DNA was extracted from young leaves, and genotypes were screened using a specific functional marker linked to the SCM2 gene. Molecular data were scored based on the presence or absence of the relevant gene allele, and independent t test, cluster analysis, and mean comparison were applied to analyze the association between phenotypic and molecular data.
Results: The results showed that the SCM2 molecular marker effectively segregated the studied genotypes into two distinct groups: Genotypes carrying SCM2 gene allele, which had a larger culm diameter, and genotypes lacking the SCM2 allele, which had a smaller culm diameter. Of the 50 genotypes, 31 possessed the SCM2 allele, while 19 did not. Phenotypic evaluations showed strong consistency with molecular data, and independent t test analysis confirmed a positive and significant relationship between the presence of the SCM2 allele and increased culm diameter, with the statistical model showing over 95%, prediction accuracy, indicating the marker's appropriate precision and efficiency. Additionally, the dendrogram derived from cluster analysis revealed a strong correlation between allele presence and culm diameter, with genotypes clustering logically according to allelic status and phenotypic values.
Conclusion: Overall, the results demonstrate that the SCM2 functional marker is a precise, efficient, and reliable tool for the rapid screening of rice genotypes for culm diameter. Its integration into breeding programs can accelerate the identification of superior genotypes, reduce time and costs associated with breeding, and enhance selection efficiency in early generations, thereby contributing significantly to the development of high-yielding, lodging-resistant cultivars through advanced breeding techniques.
 

Keywords

References

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Plant Production and Genetics
Volume 6, Issue 2 - Serial Number 10
February 2026
Pages 175-188

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