Population Transcriptomic Landscape of Miscanthus Energy Crop Domestication

Background: Second-generation energy crops, such as Miscanthus, hold a great potential to provide renewable energy and material and mitigate climate change.  However, it is unknown whether the dedicated energy crops can be domesticated in a reasonably short term to meet these needs.  This study aimed at unlocking genomic potentials for the rapid domestication of Miscanthus lutarioriparius through the development of a population transcriptomic approach that characterized gene expression variation critical to crop adaptation and production.  

Results: RNA-seq were conducted for 90 individuals of three Miscanthus species, including 80 individuals of M. lutarioriparius collected across its distribution range and planted in two field sites.  A reference transcriptome consisting of 18,503 high-quality transcripts were obtained using a pipeline developed for de novo assembling of population RNA-seq data.  The population structure and level of genetic variation of M. lutarioriparius were estimated based on 30,609 detected SNPs.  Gene expression variation was evaluated with newly defined parameters, population expression (E_p), expression diversity (E_d), and expression hill (E_h), which depicted a domestication landscape.  It was found that expression diversity increased while genetic diversity decreased following the transplanting of the species from its native habitats to the domestication site, especially for genes involved in abiotic stress resistance, histone methylation, and biomass synthesis under water limitation.

Conclusions: The adaptation of M. lutarioriparius to the domestication site with harsh growing conditions was coupled by marked increase in gene expression diversity, which provides a new source of variation that can be targeted by artificial selection to speed up crop domestication.