Transcriptome and DNA methylome divergence of inflorescence development between 2 ecotypes in Panicum hallii

Weng, Xiaoyu; Song, Haili; Sreedasyam, Avinash; Haque, Taslima; Zhang, Li; Chen, Cindy; Yoshinaga, Yuko; Williams, Melissa; O’Malley, Ronan C.; Grimwood, Jane; Schmutz, Jeremy; Juenger, Thomas E.

doi:10.1093/plphys/kiad209

Title: Transcriptome and DNA methylome divergence of inflorescence development between 2 ecotypes in Panicum hallii

Journal Article · Wed Apr 05 00:00:00 EDT 2023 · Plant Physiology (Bethesda)

DOI:https://doi.org/10.1093/plphys/kiad209· OSTI ID:2228595

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Univ. of Texas, Austin, TX (United States)
HudsonAlpha Institute for Biotechnology, Huntsville, AL (United States)
USDOE Joint Genome Institute (JGI), Berkeley, CA (United States); Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States)

The morphological diversity of the inflorescence determines flower and seed production, which is critical for plant adaptation. Hall's panicgrass (Panicum hallii, P. hallii) is a wild perennial grass that has been developed as a model to study perennial grass biology and adaptive evolution. Highly divergent inflorescences have evolved between the 2 major ecotypes in P. hallii, the upland ecotype (P. hallii var hallii, HAL2 genotype) with compact inflorescence and large seed and the lowland ecotype (P. hallii var filipes, FIL2 genotype) with an open inflorescence and small seed. Here we conducted a comparative analysis of the transcriptome and DNA methylome, an epigenetic mark that influences gene expression regulation, across different stages of inflorescence development using genomic references for each ecotype. Global transcriptome analysis of differentially expressed genes (DEGs) and co-expression modules underlying the inflorescence divergence revealed the potential role of cytokinin signaling in heterochronic changes. Comparing DNA methylome profiles revealed a remarkable level of differential DNA methylation associated with the evolution of P. hallii inflorescence. We found that a large proportion of differentially methylated regions (DMRs) were located in the flanking regulatory regions of genes. Intriguingly, we observed a substantial bias of CHH hypermethylation in the promoters of FIL2 genes. The integration of DEGs, DMRs, and $$K_a$$/$$K_s$$ ratio results characterized the evolutionary features of DMR-associated DEGs that contribute to the divergence of the P. hallii inflorescence. This study provides insights into the transcriptome and epigenetic landscape of inflorescence divergence in P. hallii and a genomic resource for perennial grass biology.

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Research Organization:: Lawrence Berkeley National Laboratory (LBNL), Berkeley, CA (United States); USDOE Joint Genome Institute (JGI), Berkeley, CA (United States)

Sponsoring Organization:: USDOE Office of Science (SC), Basic Energy Sciences (BES). Scientific User Facilities (SUF)

Grant/Contract Number:: AC02-05CH11231

OSTI ID:: 2228595

Journal Information:: Plant Physiology (Bethesda), Vol. 192, Issue 3; ISSN 0032-0889

Publisher:: American Society of Plant BiologistsCopyright Statement

Country of Publication:: United States

Language:: English

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