The harbinger transposon-derived gene PANDA epigenetically coordinates panicle number and grain size in rice

Authors: MAO, DONGHAI - Chinese Academy Of Sciences; TAO, SHENTONG - Nanjing Agricultural University; LI, XIN - Chinese Academy Of Sciences; Gao, Dongying; TANG, MINGFENG - Chinese Academy Of Sciences; LIU, CHENGBING - Three Gorges University; WANG, XIAODONG - Chinese Academy Of Sciences; BAI, LIANGLI - Chinese Academy Of Sciences; WU, DAM - Chinese Academy Of Sciences; MENG, LU - Chinese Academy Of Sciences; ZHU, YUXING - Chinese Academy Of Sciences; ZHANG, DECHUN - Three Gorges University; ZHANG, WENLI - Nanjing Agricultural University; CHEN, CAIYAN - Chinese Academy Of Sciences

Submitted to: Plant Biotechnology Journal
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 2/17/2022
Publication Date: 5/25/2022
Citation: Mao, D., Tao, S., Li, X., Gao, D., Tang, M., Liu, C., Wang, X., Bai, L., Wu, D., Meng, L., Zhu, Y., Zhang, D., Zhang, W., Chen, C. 2022. The harbinger transposon-derived gene PANDA epigenetically coordinates panicle number and grain size in rice. Plant Biotechnology Journal. 20:1154-1166. https://doi.org/10.1111/pbi.13799.
DOI: https://doi.org/10.1111/pbi.13799

Interpretive Summary: The genomes of many important crops including barley, wheat, and maize consist of abundant repetitive sequences. In most cases, their impacts on host genomes were neutral and caused no visible morphological changes. In this study, we identified a rice mutant which showed less tiller number, but larger seed size than the wild type. Molecular cloning and functional characterization revealed that the phenotypic variation was caused by a point mutation in a rice regulator gene PANDA. Further investigation indicated that the gene was likely domesticated from an ancient transposon. Impressively, the homologous sequences of PANDA were identified in barley, wheat, maize, soybean, rapeseed, and other crops. Transgenic experiment indicated that overexpression of PANDA can increase the grain yield. Our results suggest that plant transposons can be "domesticated" for modification of agronomic traits in rice. The gene identified in rice may also have a potential for yield improvement in barley, wheat, and other crops.

Technical Abstract: Transposons significantly contribute to genome fractions in many plants. Despite numerous transposon-related mutations have been identified, the evidences regarding transposon-derived genes regulate crop yield and other agronomically important traits is very limited. In this study we characterized a rice Harbinger transposon-derived gene called PANICLE NUMBER AND GRAIN SIZE (PANDA) which epigenetically coordinates panicle number and grain size. Mutation of PANDA caused reduced panicle number but increased grain size in rice, while transgenic plants overexpressing this gene showed the opposite phenotypic change. The PANDA-encoding protein can bind to the core polycomb repressive complex 2 (PRC2) components OsMSI1 and OsFIE2, and regulates deposition of H3K27me3 in the target genes, thereby epigenetically repressing their expression. Among the target genes, both OsMADS55 and OsEMF1 are negative regulators of panicle number but positive regulators of grain size, partly explaining the involvement of PANDA in balancing panicle number and grain size. Moreover, moderate overexpression of PANDA driven by its own promoter in the indica rice cultivar can increase grain yield. Thus, our findings present a novel insight into the epigenetic control of rice yield traits by a Harbinger transposon-derived gene and provide its potential application for rice yield improvement.