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

Dongqing Yan; Jiamei Liu; Yanyan Fan; Zhi Lian; Zhenhua Dang; Jianming Niu

doi:10.3389/fpls.2023.1170075

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

Front Plant Sci. 2023 May 17:14:1170075. doi: 10.3389/fpls.2023.1170075. eCollection 2023.

Authors

Dongqing Yan¹, Jiamei Liu¹, Yanyan Fan¹, Zhi Lian¹, Zhenhua Dang^{1

2

3}, Jianming Niu^{1

2

3}

Affiliations

¹ School of Ecology and Environment, Inner Mongolia University, Hohhot, China.
² Ministry of Education Key Laboratory of Ecology and Resource Use of the Mongolian Plateau, Ministry of Science and Technology of China, Hohhot, China.
³ Inner Mongolia Key Laboratory of Grassland Ecology and the Candidate State Key Laboratory of Ministry of Science and Technology, Ministry of Science and Technology of Inner Mongolia Autonomous Region, Hohhot, China.

Abstract

Investigating the genetic mechanisms of local adaptation is critical to understanding how species adapt to heterogeneous environments. In the present study, we analyzed restriction site-associated DNA sequencing (RADseq) data in order to explore genetic diversity, genetic structure, genetic differentiation, and local adaptation of Stipa breviflora. In total, 135 individual plants were sequenced and 25,786 polymorphic loci were obtained. We found low genetic diversity (He = 0.1284) within populations of S. breviflora. Four genetic clusters were identified along its distribution range. The Mantel test, partial Mantel test, and multiple matrix regression with randomization (MMRR) indicate that population differentiation was caused by both geographic distance and environmental factors. Through the F_ST outlier test and environmental association analysis (EAA), 113 candidate loci were identified as putatively adaptive loci. RPK2 and CPRF1, which are associated with meristem maintenance and light responsiveness, respectively, were annotated. To explore the effects of climatic factors on genetic differentiation and local adaptation of S. breviflora, gradient forest (GF) analysis was applied to 25,786 single nucleotide polymorphisms (SNPs) and 113 candidate loci, respectively. The results showed that both temperature and precipitation affected the genetic differentiation of S. breviflora, and precipitation was strongly related to local adaptation. Our study provides a theoretical basis for understanding the local adaptation of S. breviflora.

Keywords: CPRF1; RPK2; Stipa breviflora; climatic factors; population differentiation; steppe.

Grants and funding

This work was supported by the National Natural Science Foundation of China (31860106) and the Major Science and Technology Projects of Inner Mongolia Autonomous Region (2019ZD008).