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Lv T, Harris AJ, Liu Y, Liu T, Liang R, Ma Z, Su X. Population genetic structure and evolutionary history of Psammochloa villosa (Trin.) Bor (Poaceae) revealed by AFLP marker. Ecol Evol 2021; 11:10258-10276. [PMID: 34367573 PMCID: PMC8328423 DOI: 10.1002/ece3.7831] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2021] [Revised: 05/17/2021] [Accepted: 06/09/2021] [Indexed: 01/26/2023] Open
Abstract
Psammochloa villosa is an ecologically important desert grass that occurs in the Inner Mongolian Plateau where it is frequently the dominant species and is involved in sand stabilization and wind breaking. We sought to generate a preliminary demographic framework for P. villosa to support the future studies of this species, its conservation, and sustainable utilization. To accomplish this, we characterized the genetic diversity and structure of 210 individuals from 43 natural populations of P. villosa using amplified fragment length polymorphism (AFLP) markers. We obtained 1,728 well-defined amplified bands from eight pairs of primers, of which 1,654 bands (95.7%) were polymorphic. Results obtained from the AFLPs suggested effective alleles among populations of 1.32, a Nei's standard genetic distance value of 0.206, a Shannon index of 0.332, a coefficient of gene differentiation (G ST) of 0.469, and a gene flow parameter (Nm) of 0.576. All these values indicate that there is abundant genetic diversity in P. villosa, but limited gene flow. An analysis of molecular variance (AMOVA) showed that genetic variation mainly exists within populations (64.2%), and we found that the most genetically similar populations were often not geographically adjacent. Thus, this suggests that the mechanisms of gene flow are surprisingly complex in this species and may occur over long distances. In addition, we predicted the distribution dynamics of P. villosa based on the spatial distribution modeling and found that its range has contracted continuously since the last interglacial period. We speculate that dry, cold climates have been critical in determining the geographic distribution of P. villosa during the Quaternary period. Our study provides new insights into the population genetics and evolutionary history of P. villosa in the Inner Mongolian Plateau and provides a resource that can be used to design in situ conservation actions and prioritize sustainable utilization.
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Affiliation(s)
- Ting Lv
- School of GeosciencesQinghai Normal UniversityXiningChina
- Academy of Plateau Science and SustainabilityXiningChina
| | - AJ Harris
- Key Laboratory of Plant Resources Conservation and Sustainable UtilizationSouth China Botanical GardenChinese Academy of SciencesGuangzhouChina
| | - Yuping Liu
- Academy of Plateau Science and SustainabilityXiningChina
- Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai‐Tibet Plateau in Qinghai ProvinceSchool of Life ScienceQinghai Normal UniversityXiningChina
| | - Tao Liu
- School of GeosciencesQinghai Normal UniversityXiningChina
| | - Ruifang Liang
- Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai‐Tibet Plateau in Qinghai ProvinceSchool of Life ScienceQinghai Normal UniversityXiningChina
| | - Zilan Ma
- Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai‐Tibet Plateau in Qinghai ProvinceSchool of Life ScienceQinghai Normal UniversityXiningChina
| | - Xu Su
- School of GeosciencesQinghai Normal UniversityXiningChina
- Academy of Plateau Science and SustainabilityXiningChina
- Key Laboratory of Medicinal Animal and Plant Resources of the Qinghai‐Tibet Plateau in Qinghai ProvinceSchool of Life ScienceQinghai Normal UniversityXiningChina
- Key Laboratory of Education Ministry of Earth Surface Processes and Ecological Conservation of the Qinghai‐Tibet PlateauQinghai Normal UniversityXiningChina
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Ma K, Song Y, Yang X, Zhang Z, Zhang D. Variation in genomic methylation in natural populations of chinese white poplar. PLoS One 2013; 8:e63977. [PMID: 23704963 PMCID: PMC3660595 DOI: 10.1371/journal.pone.0063977] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2013] [Accepted: 04/07/2013] [Indexed: 11/29/2022] Open
Abstract
Background It is thought that methylcytosine can be inherited through meiosis and mitosis, and that epigenetic variation may be under genetic control or correlation may be caused by neutral drift. However, DNA methylation also varies with tissue, developmental stage, and environmental factors. Eliminating these factors, we analyzed the levels and patterns, diversity and structure of genomic methylcytosine in the xylem of nine natural populations of Chinese white poplar. Principal Findings On average, the relative total methylation and non-methylation levels were approximately 26.567% and 42.708% (P<0.001), respectively. Also, the relative CNG methylation level was higher than the relative CG methylation level. The relative methylation/non-methylation levels were significantly different among the nine natural populations. Epigenetic diversity ranged from 0.811 (Gansu) to 1.211 (Shaanxi), and the coefficients of epigenetic differentiation (GST = 0.159) were assessed by Shannon’s diversity index. Co-inertia analysis indicated that methylation-sensitive polymorphism (MSP) and genomic methylation pattern (CG-CNG) profiles gave similar distributions. Using a between-group eigen analysis, we found that the Hebei and Shanxi populations were independent of each other, but the Henan population intersected with the other populations, to some degree. Conclusions Genome methylation in Populus tomentosa presented tissue-specific characteristics and the relative 5′-CCGG methylation level was higher in xylem than in leaves. Meanwhile, the genome methylation in the xylem shows great epigenetic variation and could be fixed and inherited though mitosis. Compared to genetic structure, data suggest that epigenetic and genetic variation do not completely match.
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Affiliation(s)
- Kaifeng Ma
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Yuepeng Song
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Xiaohui Yang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Zhiyi Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
| | - Deqiang Zhang
- National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, P.R. China
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