Researchers from the College of Horticulture at South China Agricultural University, led by Jian-Guo Li, have made significant progress in understanding how DNA methylation regulates the development of litchi seeds. The research, supported by the Lingnan Modern Agriculture Science and Technology Guangdong Provincial Laboratory and the National Modern Litchi Longan Industry Technology System, was published in the Journal of Experimental Botany.
Seed size is a critical factor determining the commercial value of litchi. Depending on their development, litchi varieties are categorized into three types: normal (large-seed), fully abortive (shrunken-seed), and partially abortive. Varieties with a higher rate of shrunken seeds are more economically valuable. Although the formation of shrunken litchi seeds is influenced by genetics and environmental factors, the underlying regulatory mechanisms are not well understood.
To address this, Li's team first conducted whole-genome bisulfite sequencing and discovered that the CHH methylation level significantly increases during the development of large-seed litchi. They then combined differential methylation region analysis with weighted gene co-expression network analysis to identify 46 candidate genes involved in DNA methylation-mediated seed development. Further investigations using transient gene silencing and genetic transformation confirmed that the RNA splicing regulator LcSR45 negatively regulates litchi seed development; silencing LcSR45 in shrunken-seed varieties significantly increases the formation of large seeds. This study not only elucidates the dynamic characteristics of DNA methylation modifications during litchi seed development but also clarifies the relationship between seed development and DNA methylation, providing vital genetic resources for breeding litchi varieties with high shrunken-seed rates.
Additionally, Li's team explored the DNA methylation levels in the early stages of seed development in the large-seed variety 'Huai Zhi' and the shrunken-seed variety 'Nuomi Ci'. Their findings, published in Molecular Horticulture, suggest that DNA methylation-mediated regulation of reactive oxygen species (ROS) homeostasis plays a crucial role in litchi seed development.
The study found that DNA methylation levels during the early development stages of 'Huai Zhi' seeds are significantly higher than those in 'Nuomi Ci'. Differential methylation in both varieties enriches genes in the ROS metabolic pathways, highlighting the key gene LcGPX6, which is responsible for clearing ROS and shows higher methylation and lower expression in 'Nuomi Ci' compared to 'Huai Zhi'. Quantitative and qualitative analyses of ROS further confirmed that 'Nuomi Ci' seeds accumulate more ROS than those of 'Huai Zhi'. The analysis established that LcGPX6 plays a role in clearing ROS and regulating seed development.
This research reveals the critical function of DNA methylation-mediated ROS homeostasis in regulating the development of litchi seeds. High levels of DNA methylation may inhibit the transcription of genes like LcGPX6, leading to the accumulation of ROS in seeds, disrupting ROS balance, and consequently resulting in the formation of shrunken seeds.
For more information on the papers: https://doi.org/10.1093/jxb/erad427
