Genetic interaction network of quantitative trait genes for heading date in rice

Mengjiao Chen; Yifeng Hong; Jiongjiong Fan; Dengyi Cao; Chong Yin; Anjie Yu; Jie Qiu; Xuehui Huang; Xin Wei

doi:10.1016/j.jgg.2024.12.019

Volume 52 Issue 6

Jun. 2025

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Article Navigation > Journal of Genetics and Genomics > 2025 > 52(6): 747-760

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Genetic interaction network of quantitative trait genes for heading date in rice

doi: 10.1016/j.jgg.2024.12.019

a. Shanghai Key Laboratory of Plant Molecular Sciences, Shanghai Engineering Research Center of Plant Germplasm Resources, College of Life Sciences, Shanghai Normal University, Shanghai 200234, China;
b. State Key Laboratory of Tree Genetics and Breeding, Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, Research Institute of Forestry, Chinese Academy of Forestry, Beijing 100091, China;
c. State Key Laboratory of Rice Biology and Breeding, China National Rice Research Institute, Hangzhou, Zhejiang 311401, China

Funds:

This work was supported by the National Natural Science Foundation of China (32222064 and 32341030), the Natural Science Foundation of Shanghai (22ZR1445800), and Zhejiang Provincial Natural Science Foundation of China (LQ24C130008).

Received Date: 2024-09-30
Accepted Date: 2024-12-30
Rev Recd Date: 2024-12-30

Available Online: 2025-07-11

Publish Date: 2025-01-06

Abstract

Abstract

Several quantitative trait genes (QTGs) related to rice heading date, a key factor for crop development and yield, have been identified, along with complex interactions among genes. However, a comprehensive genetic interaction network for these QTGs has not yet been established. In this study, we use 18K-rice lines to identify QTGs and their epistatic interactions affecting rice heading date. We identify 264 pairs of interacting quantitative trait loci (QTL) and construct a comprehensive genetic network of these QTL. On average, the epistatic effects of QTL pairs are estimated to be approximately 12.5% of additive effects of identified QTL. Importantly, epistasis varies among different alleles of several heading date genes. Additionally, 57 pairs of interacting QTGs are also significant in their epistatic effects on 12 other agronomic traits. The identified QTL genetic interactions are further validated using near-isogenic lines, yeast two-hybrid, and split-luciferase complementation assays. Overall, this study provides a genetic network of rice heading date genes, which plays a crucial role in regulating rice heading date and influencing multiple related agronomic traits. This network serves as a foundation for understanding the genetic mechanisms of rice quantitative traits and for advancing rice molecular breeding.
- Genetic network,
- Epistasis,
- Epistatic effect,
- Quantitative trait gene,
- Rice,
- Heading date

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References

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