De novo assembly, annotation, marker discovery, and genetic diversity of the Stipa breviflora Griseb. (Poaceae) response to grazing.

Dongqing Yan,Jiamei Liu,Jing Ren,Jianming Niu,Yu Ding,Branislav T Šiler

doi:10.1371/journal.pone.0244222

Abstract

Grassland is one of the most widely-distributed ecosystems on Earth and provides a variety of ecosystem services. Grasslands, however, currently suffer from severe degradation induced by human activities, overgrazing pressure and climate change. In the present study, we explored the transcriptome response of Stipa breviflora, a dominant species in the desert steppe, to grazing through transcriptome sequencing, the development of simple sequence repeat (SSR) markers, and analysis of genetic diversity. De novo assembly produced 111,018 unigenes, of which 88,164 (79.41%) unigenes were annotated. A total of 686 unigenes showed significantly different expression under grazing, including 304 and 382 that were upregulated and downregulated, respectively. These differentially expressed genes (DEGs) were significantly enriched in the "alpha-linolenic acid metabolism" and "plant-pathogen interaction" pathways. Based on transcriptome sequencing data, we developed eight SSR molecular markers and investigated the genetic diversity of S. breviflora in grazed and ungrazed sites. We found that a relatively high level of S. breviflora genetic diversity occurred under grazing. The findings of genes that improve resistance to grazing are helpful for the restoration, conservation, and management of desert steppe.

Highlights

Chinese grasslands are diverse and constitute the third largest grassland area worldwide, covering 41.7% of the country’s territory and stretching from northern China to the QinghaiTibetan Plateau [1,2,3]
1130 1852 49.38 a Mean length of the assembled sequences. b The length of the content or unigene corresponding to the sequence, which is added to 50% of the total assembled bases when the assembled sequences are sorted from short to long. c GC content
The results showed that 46.02% of unigene sequences matched Brachypodium distachyon, followed by other species (28.93%), Hordeum vulgare subsp

Summary

Introduction

Chinese grasslands are diverse and constitute the third largest grassland area worldwide, covering 41.7% of the country’s territory and stretching from northern China to the QinghaiTibetan Plateau [1,2,3]. These grasslands are currently in danger of degradation owing to climate change and anthropogenic activities, and over 33% of the degradation is due to overgrazing [4, 5]. Plants can adapt to grazing pressure by developing certain characteristics, such as small sizes, fast growth, short life-spans, and low palatability, to avoid livestock. Transcriptome response and genetic diversity of S. breviflora to grazing.

Methods

Results

Discussion

Conclusion