# Transposable element‐mediated DNA methylation of the NAC20 and NAC26 promoters led to a maternal effect on grain filling

## TL;DR

This study shows that transposable elements cause DNA methylation in rice genes NAC20 and NAC26, leading to a maternal effect on grain filling in high-latitude Japonica rice.

## Contribution

The novel finding is that TE insertions and DNA methylation mediate maternal expression of NAC20/26, affecting grain filling in specific rice varieties.

## Key findings

- NAC20/26 show allele-specific maternal expression linked to transposable element insertions in Japonica rice.
- TE deletions reduce DNA methylation and restore biallelic expression of NAC20/26.
- High-latitude Japonica varieties carry TEs associated with the maternal effect on grain filling.

## Abstract

Parent‐of‐origin effects are usually caused by selective expression of maternal or paternal alleles. Although genome‐wide studies suggest that imprinted gene expression occurs primarily in the endosperm in plants, detailed studies of allele‐specific gene expression and its associations with parent‐of‐origin phenotypes are scarce. NAC20 and NAC26 (NAC20/26 hereafter), a pair of tightly linked NAC‐family transcription factors, redundantly regulate grain filling and albumin accumulation in rice endosperm. Here, we show that NAC20/26 exhibited allele‐specific maternal expression, and the floury endosperm phenotype of the nac20/26 double mutant was inherited with a maternal effect. Further studies showed that the imprinted NAC20/26 expression and floury endosperm phenotype with a maternal effect are associated with insertions of two TEs in NAC20/26 of two Japonica rice varieties, but not in two Indica ones examined. The maternal NAC20/26 expression was associated with elevated DNA methylation in their paternal DMRs, and deletions of those TEs by gene editing led to decreased methylation in these DMRs, and biallelic NAC20/26 expression. Geographical analyses showed that Japonica varieties with high‐latitude origins examined carried these TEs. These results establish that TE‐mediated DNA methylation lead to grain filling with a maternal effect in high‐latitude Japonica rice varieties, which may associate with northward expansion of rice during domestication.

The rice transcription factor genes NAC20 and NAC26 regulate grain filling and show allele‐specific maternal expression due to transposable element insertions and paternal hypermethylation in their 5' upstream regions. Geographical analyses showed that japonica varieties that originated at high latitudes carried these transposable elements.