The Harbinger transposon‐derived gene PANDA epigenetically coordinates panicle number and grain size in rice

Abstract

Summary Transposons significantly contribute to genome fractions in many plants. Although numerous transposon‐related mutations have been identified, the evidence regarding transposon‐derived genes regulating crop yield and other agronomic 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 the deposition of H3K27me3 in the target genes, thereby epigenetically repressing their expression. Among the target genes, both OsMADS55 and OsEMF1 were 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.

Transposons repressed by H3K27me3 were co-opted as cis-regulatory elements of H3K27me3 controlled protein coding genes during evolution of plants

“…Interestingly, a recent report showed that a transposon-derived gene controlled by PRC2 was selected as regulator of a reproductive trait in rice 48 suggesting that TE-derived cis-elements and proteins coding genes controlled by PRC2 contributed to developmental regulation in plants. These were likely the source of Polycomb gene networks that control multiple aspects of development in land plants and response to environmental cues 15,21,49 .…”

“…In Arabidopsis TEs are bound by transcription factors that recruit PRC2 depositing H3K27me3 on the contiguous PCGs and these transcription factors control expression of genes regulating flower development also controlled by PRC2 47 . Interestingly, a recent report showed that a transposon-derived gene controlled by PRC2 was selected as regulator of a reproductive trait in rice 48 suggesting that TE-derived cis-elements and proteins coding genes controlled by PRC2 contributed to developmental regulation in plants. These were likely the source of Polycomb gene networks that control multiple aspects of development in land plants and response to environmental cues 15,21,49 .…”

Co-Overexpression of Two Key Source Genes, OsBMY4 and OsISA3, Improves Multiple Key Traits of Rice Seeds

“…Thanks to the ‘Green Revolution’ and the development of hybrid rice, great achievements have been realized in grain yield and quality using modern breeding practices. In addition, a series of other efforts have also been made to further enhance crop yield, including promoting photosynthetic efficiency, , increasing panicle number and size, , and modulating grain size. , However, improving one or several of these traits usually results in unexpected negative effects on other traits or on the overall performance of the plants, generating rice varieties with high yield but low grain quality, or even decreased yield in certain situations. In general, the grain quality of most high yielding rice varieties is poor, making them unpopular with consumers and reducing their competitive advantage in the rice market.…”

“…For example, scientists usually seek to clone novel target genes involved in controlling the panicle number, grain number, and grain weight and size, using them to generate rice varieties with more panicles and grains, larger and heavier grains, and finally increased rice yield. − In general, the majority of these cloned genes in rice are related to sink organs. It is impressive that more than 80 grain size-related genes have been cloned, , including GS3 , DEP1 , GW2 , and qGL3 / OsPPKL1 . , In addition, the number of genes controlling the panicle number and size that have been cloned is also increasing, and examples are IPA1 , PANDA , and OsSAUR27 . Studies on rice quality improvement, especially ECQ and appearance quality, have been focused on the enzymes involved in the biosynthesis of amylose and amylopectin, the constituent starch polymers in seeds.…”

“…It is impressive that more than 80 grain size-related genes have been cloned, 5,6 including GS3, 7 DEP1, 8 GW2, 9 and qGL3/OsPPKL1. 10,11 In addition, the number of genes controlling the panicle number and size that have been cloned is also increasing, and examples are IPA1, 12 PANDA, 13 and OsSAUR27. 14 Studies on rice quality improvement, especially ECQ and appearance quality, have been focused on the enzymes involved in the biosynthesis of amylose and amylopectin, the constituent starch polymers in seeds.…”