Molecular Phylogeography and Intraspecific Divergences in Siberian Wildrye (Elymus sibiricus L.) Wild Populations in China, Inferred From Chloroplast DNA Sequence and cpSSR Markers

Abstract

A detailed understanding of the distribution and degree of genetic variation within a species is important for determining their evolutionary potential, which in return facilitates the development of efficient conservation strategies aimed at preserving adaptive genetic variation. As an important perennial, cool-season grass in temperate Eurasia, increasing attention has been paid to Siberian wildrye (Elymus sibiricus) due to its excellent ecological utilization value and forage production potential in China, particularly in the Qinghai–Tibet Plateau (QTP) regions. In this study, we applied two chloroplast (cp) genes (matK and rbcL), three cp spacer regions (trnY-GUA∼trnD-GUC, atpH∼atpF, and rps4∼trnT-UGU), and six cpSSR markers to the genetic and phylogenetic analysis of 137 wild E. sibiricus accessions from 23 natural populations that represent the main distribution regions in China. The results show the highest genetic diversity (h = 0.913) and haplotype richness (10 haplotypes) for the QTP population, which indicates QTP as the probable diversity center and geographic origin of E. sibiricus in China. Population divergence was high, indicating a significant phylogeographic structure together with a significantly higher Nst value (Nst > Gst, P < 0.05) at the species level, QTP+XJ (combined populations from QTP and Xinjiang), QTP+NC (combined populations from QTP and North China), and XJ+NC (combined populations from Xinjiang and North China) group levels, respectively. An expansion was revealed in the distributional range of E. sibiricus in China from paleo times up to the recent past, while a dramatic range of contraction was predicted for the near future. The predicted main limiting factor for the further spread of E. sibiricus is an increasing global mean temperature. We recommend that the combination of Es-cpDNA1 and Es-cpDNA3+4+5 can be used as effective markers for phylogenetic analysis and phylogeographical history analysis of E. sibiricus. These findings shed new light on the historical population dynamics of cold-season herbs in the QTP region and the north of China and are of great significance for the future establishment of protection and collection strategies for wild E. sibiricus germplasm.

Effects of Climatic Change on Phylogeography and Ecological Niche of the Endemic Herb Elymus breviaristatus on the Qinghai-Tibet Plateau

“…Since E. breviaristatus is endemic to the QTP and has a narrow distribution, it was initially expected to have lower genetic diversity compared with other Elymus species. However, the present study revealed a high Hd (0.825) and π (0.00114), which was comparable to the genetic diversity of the widespread species of Elymus sibiricus in the QTP region detected based on cpDNA ( Hd = 0.834, π = 0.00108) and even higher than the genetic diversity of E. sibiricus in Xinjiang and northern China ( Hd = 0.527 and 0.543, π = 0.00042 and 0.00053, respectively) [ 32 ]. The high level of genetic diversity observed in E. breviaristatus could be due in part to the large number of samples in the study.…”

The Complete Chloroplast Genomes of Two Physalis Species, Physalis macrophysa and P. ixocarpa: Comparative Genomics, Evolutionary Dynamics and Phylogenetic Relationships

“…As more and more cp genomes have been sequenced and published, the development and application of cpSSRs have been widely adopted. In recent years, cpSSR markers have been widely used in plant germplasm identification, genetic diversity assessment, and phylogenetic analysis [59][60][61][62]. In our study, 61 SSR loci in PMA were identified, containing 67.2% located in IGS region, 26.2% in PCG region, and 6.6% among tRNA genes.…”

Phylogeographic analysis reveals extensive genetic variation of native grass Elymus nutans (Poaceae) on the Qinghai-Tibetan plateau

“…A high H d (0.805) and π (0.67×10 -3 ) were revealed in our study, indicating values lower than those observed in the related and widespread species of Elymus sibiricus in the QTP region detected based on cpDNA ( H d = 0.834, π = 1.08×10 -3 ). Conversely, these values surpassed those documented for E. sibiricus populations in Xinjiang and northern China, which exhibit respective H d values of 0.527 and 0.543, and π values of 0.042×10 -3 and 0.53×10 -3 , respectively ( Xiong et al., 2022 ). Similarly, this high degree of genetic diversity has also been confirmed in other plants on the Tibetan Plateau, such as Stellera chamaejasme ( H d = 0.834) ( Zhang et al., 2010 ), Iris lozyi ( H d = 0.820) ( Zhang et al., 2021 ).…”

“…Four cpDNA fragments ( trn H- psb A, trn L-F, mat K, and rbc L) were amplified and sequenced across all E. nutans samples. These fragments were amplified using primers previously reported in the literature, known for showcasing polymorphisms in other Elymus species ( Xiong et al., 2022 ). Amplification was conducted in a 30 μL reaction volume, comprising of 30 ng of genomic DNA, 1.5 μL of each primer, and 15 μL of 2× Es Taq MasterMix (CoWin Biosciences, Beijing, China), using a C1000 Touch Thermal Cycler (BIO-RAD, Foster City, CA, USA).…”