Integrating Dynamic 3D Chromatin Architecture and Gene Expression Alterations Reveal Heterosis in

Overview

Journal Int J Mol Sci

Publisher MDPI

Specialties Biochemistry
Chemistry
Molecular Biology

Date 2024 Mar 13

PMID 38473815

Authors

Liu E

Shanwu Lyu

Yaolong Wang

Dong Xiao

Tongkun Liu

Xilin Hou

Ying Li

Changwei Zhang

Affiliations

Soon will be listed here.

Abstract

Heterosis plays a significant role in enhancing variety, boosting yield, and raising economic value in crops, but the molecular mechanism is still unclear. We analyzed the transcriptomes and 3D genomes of a hybrid (F) and its parents (w30 and 082). The analysis of the expression revealed a total of 485 specially expressed genes (SEGs), 173 differentially expressed genes (DEGs) above the parental expression level, more actively expressed genes, and up-regulated DEGs in the F. Further study revealed that the DEGs detected in the F and its parents were mainly involved in the response to auxin, plant hormone signal transduction, DNA metabolic process, purine metabolism, starch, and sucrose metabolism, which suggested that these biological processes may play a crucial role in the heterosis of . The analysis of 3D genome data revealed that hybrid F plants tend to contain more transcriptionally active A chromatin compartments after hybridization. Supplementaryly, the F had a smaller TAD (topologically associated domain) genome length, but the number was the highest, and the expression change in activated TAD was higher than that of repressed TAD. More specific TAD boundaries were detected between the parents and F. Subsequently, 140 DEGs with genomic structural variants were selected as potential candidate genes. We found two DEGs with consistent expression changes in A/B compartments and TADs. Our findings suggested that genomic structural variants, such as TADs and A/B chromatin compartments, may affect gene expression and contribute to heterosis in . This study provides further insight into the molecular mechanism of heterosis in .

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