Epigenetic and Genetic Contribution for Expression Bias of Homologous Alleles in Polyploid Sugarcane
Yajie Xue,
Yan Shi,
Yuchuan Qi,
Hang Yu,
Chengwu Zou,
Xueying Cao,
Cuimin Sun,
Baoshan Chen,
Haifeng Wang
Affiliations
Yajie Xue
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab for Sugarcane Biology, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
Yan Shi
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab for Sugarcane Biology, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
Yuchuan Qi
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab for Sugarcane Biology, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
Hang Yu
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab for Sugarcane Biology, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
Chengwu Zou
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab for Sugarcane Biology, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
Xueying Cao
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab for Sugarcane Biology, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
Cuimin Sun
School of Computer, Electronics and Information, Guangxi University, Nanning 530004, China
Baoshan Chen
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab for Sugarcane Biology, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
Haifeng Wang
State Key Laboratory for Conservation and Utilization of Subtropical Agro-Bioresources, Guangxi Key Lab for Sugarcane Biology, National Demonstration Center for Experimental Plant Science Education, College of Agriculture, Guangxi University, Nanning 530004, China
DNA methylation regulates gene expression in eukaryotes, but their roles in gene expression changes in polyploids are poorly understood. Here, we comparatively analyzed the DNA methylation profiles and transcriptome maps of four tissues (leaf, rind, pith, and root) in autopolyploid sugarcane (Saccharum spontaneum). The overall DNA methylation levels were relatively equal and were consistent with the similar genome-wide expression levels of homologous alleles among different homologous chromosomes. However, tetrad alleles showed a large proportion of non-balanced alleles (85–89%) compared with balanced alleles (11–15%). For tetrad alleles, highly-expressed alleles showed lower Ka/Ks values than those in lowly-expressed alleles, indicating that dominant (and non-suppressed) alleles were under strong purifying selection pressure compared to non-dominant (and suppressed) alleles. Specifically, higher DNA methylation levels were found in non-balanced alleles compared to balanced alleles, as well as a higher CG to TG substitution rate, suggesting epigenetic and genetic variation associated with transcription divergence. Moreover, among non-balanced alleles, which were associated with DNA methylation changes, many were involved in several processes relevant to agronomic traits, such as responses to stress and carbohydrate transport. Taken together, our results provide unique epigenetic insights into the transcriptional regulation of homologous alleles, which contribute to the key agronomic traits in sugarcane and facilitate epigenetic studies in other polyploid crops.
