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ORIGINAL RESEARCH article

Front. Plant Sci.
Sec. Plant Systematics and Evolution
Volume 15 - 2024 | doi: 10.3389/fpls.2024.1457980

Extensive transcriptome data providing great efficacy in genetic research and adaptive gene discovery: a case study of Elymus sibiricus L. (Poaceae, Triticeae)

Provisionally accepted
Yanli Xiong Yanli Xiong 1Daxu Li Daxu Li 2Liu Tianqi Liu Tianqi 1Yi Xiong Yi Xiong 1Qingqing Yu Qingqing Yu 2Xiong LEI Xiong LEI 2Junming Zhao Junming Zhao 1Lijun Yan Lijun Yan 2Xiao Ma Xiao Ma 1*
  • 1 College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China
  • 2 Sichuan Academy of Grassland Sciences, Chengdu, Sichuan Province, China

The final, formatted version of the article will be published soon.

    Genetic markers play a central role in understanding genetic diversity, speciation, evolutionary processes, and how species respond to environmental stresses. However, conventional molecular markers are less effective when studying polyploid species with large genomes. In this study, we compared gene expression levels in 101 accessions of Elymus sibiricus, a widely distributed allotetraploid forage species across the Eurasian continent. A total of 20,273 high quality transcriptomic SNPs were identified. In addition, 72,344 evolutionary information loci of these accessions of E. sibiricus were identified using genome skimming data in conjunction with the assembled composite genome. The population structure results suggest that transcriptome SNPs were more effective than SNPs derived from genome skimming data in revealing the population structure of E. sibiricus from different locations, and also outperformed gene expression levels. Compared with transcriptome SNPs, the investigation of population-specifically-expressed genes (PSEGs) using expression levels revealed a larger number of locally adapted genes mainly involved in the ion response process in the Sichuan, Inner Mongolia, and Xizang geographical groups. Furthermore, we performed the weighted gene co-expression network analysis (WGCNA) and successfully identified potential regulators of PSEGs.Therefore, for species lacking genomic information, the use of transcriptome SNPs is an efficient approach to perform population structure analysis. In addition, analyzing genes under selection through nucleotide diversity and genetic differentiation index analysis based on transcriptome SNPs, and exploring PSEG through expression levels is an effective method for analyzing locally adaptive genes.

    Keywords: Adaptability, Transcriptome, Genome skimming, snps, WGCNA, Elymus sibiricus

    Received: 01 Jul 2024; Accepted: 02 Sep 2024.

    Copyright: © 2024 Xiong, Li, Tianqi, Xiong, Yu, LEI, Zhao, Yan and Ma. This is an open-access article distributed under the terms of the Creative Commons Attribution License (CC BY). The use, distribution or reproduction in other forums is permitted, provided the original author(s) or licensor are credited and that the original publication in this journal is cited, in accordance with accepted academic practice. No use, distribution or reproduction is permitted which does not comply with these terms.

    * Correspondence: Xiao Ma, College of Grassland Science and Technology, Sichuan Agricultural University, Chengdu, China

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