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

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.

Genomic insights into genetic diversity and local adaptation of a dominant desert steppe feather grass, Stipa breviflora Griseb.

“…We detected a low level of genetic diversity in S. breviflora ( He = 0.1284) using RAD sequencing data ( Table 1 ). This is in sharp contrast to previous studies by Yan et al. (2020) ( He = 0.34) and Ren et al.…”

“…Compared with other grassland types, the desert steppe has far less vegetation, which is susceptible to climate change and anthropogenic disturbances ( Zhao et al., 2002 ; Angerer et al., 2008 ). Stipa breviflora Griseb., as one of the dominant species in the desert steppe, is an important foraging resource because of its palatability, rich nutrient content, early greening, and resistance to grazing and drought ( Ren et al., 2017 ; Yan et al., 2020 ). Moreover, S. breviflora has attracted attention for its potential use for water and soil conservation and for desertification control ( Wang et al., 2018 ; Chen et al., 2020 ).…”

Transcriptome-Wide Gene Expression Plasticity in Stipa grandis in Response to Grazing Intensity Differences

“…This number of DEGs was much higher than previously reported in a comparison of grazed and non-grazed pastures of S. grandis , wherein 13,221 DEGs were identified among 94,674 transcripts [ 37 ]. A lower number of DEGs were found in a comparison of over-grazed and non-grazed pastures of L. chinensis : 3341 DEGs identified in 116,356 unigenes [ 38 ], and an even lower number of DEGs were found in a comparison of ungrazed and grazed populations of Stipa breviflora : 686 DEGs obtained from 111,018 unigenes [ 44 ]. While the number of DEGs identified will be influenced by the analysis pipelines and filtering parameters used (please see comment below on DEGseq), the difference in the relative number of DEGs may also be explained by the greater environmental gradient across our four grazing conditions ( Figure 5 ).…”

Growth of Stipa breviflora does not respond to nitrogen addition because of its conservative nitrogen utilization

“…(needlegrass) is a common species that is mainly found in the dry regions of China, especially in Inner Mongolia, Xinjiang, and Ningxia as the dominant species of desert steppe grassland. S. breviflora is an excellent pasture grass in the desert steppe that produces early green shoots with fine palatability and other advantages (Yan et al, 2020). A long-term experiment in the desert steppe showed that S. breviflora biomass production do not respond to N deposition (Wu et al, 2020).…”