Population transcriptomic characterization of the genetic and expression variation of a candidate progenitor of Miscanthus energy crops

Abstract

The use of transcriptome data in the study of the population genetics of a species can capture faint signals of both genetic variation and expression variation and can provide a broad picture of a species' genomic response to environmental conditions. In this study, we characterized the genetic and expression diversity of Miscanthus lutarioriparius by comparing more than 16,225 transcripts obtained from 78 individuals, belonging to 10 populations distributed across the species' entire geographic range. We only observed a low level of nucleotide diversity (π = 0.000434) among the transcriptome data of these populations, which is consistent with highly conserved sequences of functional elements and protein-coding genes captured with this method. Tests of population divergence using the transcriptome data were consistent with previous microsatellite data but proved to be more sensitive, particularly if gene expression variation was considered as well. For example, the analysis of expression data showed that genes involved in photosynthetic processes and responses to temperature or reactive oxygen species stimuli were significantly enriched in certain populations. This differential gene expression was primarily observed among populations and not within populations. Interestingly, nucleotide diversity was significantly negatively correlated with expression diversity within populations, while this correlation was positive among populations. This suggests that genetic and expression variation play separate roles in adaptation and population persistence. Combining analyses of genetic and gene expression variation represents a promising approach for studying the population genetics of wild species and may uncover both adaptive and nonadaptive processes.

Population transcriptomic sequencing reveals allopatric divergence and local adaptation in Pseudotaxus chienii (Taxaceae)

“…Transcriptome sequencing is a powerful tool that represents a cost-effective approach for examining genetic and expression patterns and investigating adaptive divergence at the levels of sequences, genes or biological metabolic pathways among natural populations in nonmodel organisms [14]. For example, Yan et al (2017) [15] sequenced the transcriptomes of 78 Miscanthus lutarioriparius individuals from 10 populations and found genes related to photosynthetic processes and responses to environmental stimuli such as temperature and reactive oxygen species. Sun et al (2020) [16] compared the transcriptomes of Pinus yunnanensis from high-and low-elevation sites and identified 103,608 high-quality SNPs and 321 outlier SNPs based on RNA-Seq to investigate adaptive genetic variation.…”

Population genetics and evolutionary history of Miscanthus species in China

“…During recent years, we have made extensive field collections of Chinese Miscanthus species throughout their distribution ranges in China. We have undertaken in‐depth investigations on the phylogeny and taxonomy of Miscanthus and its relatives as well as genetic diversity and adaptation of Miscanthus species (Yan et al, , , ; Ma, ; Ma et al, ; Xu et al, ; Song et al, ; Zhu et al, ). In this study we used 24 nuclear DNA microsatellites to genotype 100 populations of four Chinese Miscanthus species.…”

Utilization of Tissue Ploidy Level Variation in de Novo Transcriptome Assembly of Pinus sylvestris

“…The use of transcriptomes as a reference for obtaining SNPs and estimating genetic diversity is becoming a common strategy for non-model species that lack a reference genome (Gayral et al 2013; Romiguier et al 2014; Xu et al 2016; Yan et al 2017). However, several factors can introduce errors, and careful assessment of the assembled transcriptome is required before employing this downstream application.…”