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Chen T, Xu J, Wang L, Wang H, You E, Deng C, Bian H, Shen Y. Landscape genomics reveals adaptive genetic differentiation driven by multiple environmental variables in naked barley on the Qinghai-Tibetan Plateau. Heredity (Edinb) 2023; 131:316-326. [PMID: 37935814 PMCID: PMC10673939 DOI: 10.1038/s41437-023-00647-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Revised: 08/21/2023] [Accepted: 08/23/2023] [Indexed: 11/09/2023] Open
Abstract
Understanding the local adaptation of crops has long been a concern of evolutionary biologists and molecular ecologists. Identifying the adaptive genetic variability in the genome is crucial not only to provide insights into the genetic mechanism of local adaptation but also to explore the adaptation potential of crops. This study aimed to identify the climatic drivers of naked barley landraces and putative adaptive loci driving local adaptation on the Qinghai-Tibetan Plateau (QTP). To this end, a total of 157 diverse naked barley accessions were genotyped using the genotyping-by-sequencing approach, which yielded 3123 high-quality SNPs for population structure analysis and partial redundancy analysis, and 37,636 SNPs for outlier analysis. The population structure analysis indicated that naked barley landraces could be divided into four groups. We found that the genomic diversity of naked barley landraces could be partly traced back to the geographical and environmental diversity of the landscape. In total, 136 signatures associated with temperature, precipitation, and ultraviolet radiation were identified, of which 13 had pleiotropic effects. We mapped 447 genes, including a known gene HvSs1. Some genes involved in cold stress and regulation of flowering time were detected near eight signatures. Taken together, these results highlight the existence of putative adaptive loci in naked barley on QTP and thus improve our current understanding of the genetic basis of local adaptation.
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Affiliation(s)
- Tongrui Chen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jinqing Xu
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, 810000, China
| | - Lei Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, 810000, China
| | - Handong Wang
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, 810000, China
| | - En You
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Chao Deng
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Haiyan Bian
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yuhu Shen
- Key Laboratory of Adaptation and Evolution of Plateau Biota, Laboratory for Research and Utilization of Qinghai Tibetan Plateau Germplasm Resources, Qinghai Provincial Key Laboratory of Crop Molecular Breeding, Northwest Institute of Plateau Biology, Chinese Academy of Sciences, Xining, 810000, China.
- Innovation Academy for Seed Design, Chinese Academy of Sciences, Xining, 810000, China.
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Yang YL, Cushman SA, Wang SC, Wang F, Li Q, Liu HL, Li Y. Genome-wide investigation of the WRKY transcription factor gene family in weeping forsythia: expression profile and cold and drought stress responses. Genetica 2023; 151:153-165. [PMID: 36853516 PMCID: PMC9973247 DOI: 10.1007/s10709-023-00184-y] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/12/2023] [Accepted: 02/21/2023] [Indexed: 03/01/2023]
Abstract
Weeping forsythia is a wide-spread shrub in China with important ornamental, medicinal and ecological values. It is widely distributed in China's warm temperate zone. In plants, WRKY transcription factors play important regulatory roles in seed germination, flower development, fruit ripening and coloring, and biotic and abiotic stress response. To date, WRKY transcription factors have not been systematically studied in weeping forsythia. In this study, we identified 79 WRKY genes in weeping forsythia and classified them according to their naming rules in Arabidopsis thaliana. Phylogenetic tree analysis showed that, except for IIe subfamily, whose clustering was inconsistent with A. thaliana clustering, other subfamily clustering groups were consistent. Cis-element analysis showed that WRKY genes related to pathogen resistance in weeping forsythia might be related to methyl jasmonate and salicylic acid-mediated signaling pathways. Combining cis-element and expression pattern analyses of WRKY genes showed that more than half of WRKY genes were involved in light-dependent development and morphogenesis in different tissues. The gene expression results showed that 13 WRKY genes were involved in drought response, most of which might be related to the abscisic acid signaling pathway, and a few of which might be regulated by MYB transcription factors. The gene expression results under cold stress showed that 17 WRKY genes were involved in low temperature response, and 9 of them had low temperature responsiveness cis-elements. Our study of WRKY family in weeping forsythia provided useful resources for molecular breeding and important clues for their functional verification.
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Affiliation(s)
- Ya-Lin Yang
- Innovation Platform of Molecular Biology, College of Landscape and Art, Henan Agricultural University, Zhengzhou, China
| | - Samuel A Cushman
- School of Forestry, Northern Arizona University, Flagstaff, AZ, USA
| | - Shu-Chen Wang
- Innovation Platform of Molecular Biology, College of Landscape and Art, Henan Agricultural University, Zhengzhou, China
| | - Fan Wang
- Innovation Platform of Molecular Biology, College of Landscape and Art, Henan Agricultural University, Zhengzhou, China
| | - Qian Li
- Innovation Platform of Molecular Biology, College of Landscape and Art, Henan Agricultural University, Zhengzhou, China
| | - Hong-Li Liu
- Innovation Platform of Molecular Biology, College of Landscape and Art, Henan Agricultural University, Zhengzhou, China
| | - Yong Li
- College of Life Science and Technology, Inner Mongolia Normal University, Huhehaote, China. .,State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, China.
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Li Z, Yun L, Gao Z, Wang T, Ren X, Zhao Y. EST-SSR Primer Development and Genetic Structure Analysis of Psathyrostachys juncea Nevski. FRONTIERS IN PLANT SCIENCE 2022; 13:837787. [PMID: 35295628 PMCID: PMC8919075 DOI: 10.3389/fpls.2022.837787] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/17/2021] [Accepted: 02/07/2022] [Indexed: 05/14/2023]
Abstract
Psathyrostachys juncea is a perennial forage grass which plays an important role in soil and water conservation and ecological maintenance in cold and dry areas of temperate regions. In P. juncea, a variety of biotic and abiotic stress related genes have been used in crop improvement, indicating its agronomic, economic, forage, and breeding value. To date, there have been few studies on the genetic structure of P. juncea. Here, the genetic diversity and population structure of P. juncea were analyzed by EST-SSR molecular markers to evaluate the genetic differentiation related to tillering traits in P. juncea germplasm resources. The results showed that 400 simple sequence repeat (SSR) loci were detected in 2,020 differentially expressed tillering related genes. A total of 344 scored bands were amplified using 103 primer pairs, out of which 308 (89.53%) were polymorphic. The Nei's gene diversity of 480 individuals was between 0.092 and 0.449, and the genetic similarity coefficient was between 0.5008 and 0.9111, with an average of 0.6618. Analysis of molecular variance analysis showed that 93% of the variance was due to differences within the population, and the remaining 7% was due to differences among populations. Psathyrostachys juncea materials were clustered into five groups based on population genetic structure, principal coordinate analysis and unweighted pair-group method with arithmetic means (UPGMA) analysis. The results were similar between clustering methods, but a few individual plants were distributed differently by the three models. The clustering results, gene diversity and genetic similarity coefficients showed that the overall genetic relationship of P. juncea individuals was relatively close. A Mantel test, UPGMA and structural analysis also showed a significant correlation between genetic relationship and geographical distribution. These results provide references for future breeding programs, genetic improvement and core germplasm collection of P. juncea.
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Affiliation(s)
- Zhen Li
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Lan Yun
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
- Key Laboratory of Grassland Resources Ministry of Education, Hohhot, China
| | - Zhiqi Gao
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Tian Wang
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Xiaomin Ren
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
| | - Yan Zhao
- College of Grassland, Resources and Environment, Inner Mongolia Agricultural University, Hohhot, China
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Trense D, Hoffmann AA, Fischer K. Large- and small-scale geographic structures affecting genetic patterns across populations of an Alpine butterfly. Ecol Evol 2021; 11:14697-14714. [PMID: 34765135 PMCID: PMC8571576 DOI: 10.1002/ece3.8157] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/29/2021] [Revised: 09/04/2021] [Accepted: 09/08/2021] [Indexed: 11/09/2022] Open
Abstract
Understanding factors influencing patterns of genetic diversity and the population genetic structure of species is of particular importance in the current era of global climate change and habitat loss. These factors include the evolutionary history of a species as well as heterogeneity in the environment it occupies, which in turn can change across time. Most studies investigating spatio-temporal genetic patterns have focused on patterns across wide geographic areas rather than local variation, but the latter can nevertheless be important particularly in topographically complex areas. Here, we consider these issues in the Sooty Copper butterfly (Lycaena tityrus) from the European Alps, using genome-wide SNPs identified through RADseq. We found strong genetic differentiation within the Alps with four genetic clusters, indicating western, central, and eastern refuges, and a strong reduction of genetic diversity from west to east. This reduction in diversity may suggest that the southwestern refuge was the largest one in comparison to other refuges. Also, the high genetic diversity in the west may result from (a) admixture of different western refuges, (b) more recent demographic changes, or (c) introgression of lowland L. tityrus populations. At small spatial scales, populations were structured by several landscape features and especially by high mountain ridges and large river valleys. We detected 36 outlier loci likely under altitudinal selection, including several loci related to membranes and cellular processes. We suggest that efforts to preserve alpine L. tityrus should focus on the genetically diverse populations in the western Alps, and that the dolomite populations should be treated as genetically distinct management units, since they appear to be currently more threatened than others. This study demonstrates the usefulness of SNP-based approaches for understanding patterns of genetic diversity, gene flow, and selection in a region that is expected to be particularly vulnerable to climate change.
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Affiliation(s)
- Daronja Trense
- Institute for Integrated Natural Sciences, ZoologyUniversity Koblenz‐LandauKoblenzGermany
| | - Ary A. Hoffmann
- Pest & Environmental Adaptation Research GroupSchool of BiosciencesBio21 InstituteParkvilleVic.Australia
| | - Klaus Fischer
- Institute for Integrated Natural Sciences, ZoologyUniversity Koblenz‐LandauKoblenzGermany
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Zhang JX, Wang M, Fan J, Guo ZP, Guan Y, Qu G, Zhang CJ, Guo YX, Yan X. Non-linear genetic diversity and notable population differentiation caused by low gene flow of bermudagrass [ Cynodon dactylon (L.) Pers.] along longitude gradients. PeerJ 2021; 9:e11953. [PMID: 34458022 PMCID: PMC8378333 DOI: 10.7717/peerj.11953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 07/21/2021] [Indexed: 11/20/2022] Open
Abstract
Background Environmental variation related to ecological habitat is the main driver of plant adaptive divergence. Longitude plays an important role in the formation of plant population structure, indicating that environmental differentiation can significantly shape population structure. Methods Genetic diversity and population genetic structure were estimated using 105 expressed sequence tag-derived simple sequence repeat (EST-SSR) loci. A total of 249 C. dactylon (L.) Pers. (common bermudagrass) individuals were sampled from 13 geographic sites along the longitude (105°57′34″–119°27′06″E). Results There was no obvious linear trend of intra-population genetic diversity along longitude and the intra-population genetic diversity was not related to climate in this study. Low gene flow (Nm = 0.7701) meant a rich genetic differentiation among populations of C. dactylon along longitude gradients. Significantly positive Mantel correlation (r = 0.438, P = 0.001) was found between genetic distance and geographical interval while no significant partial Mantel correlation after controlling the effect of mean annual precipitation, which indicated geographic distance correlated with mean annual precipitation affect genetic distance. The genetic diversity of C. dactylon with higher ploidy level was higher than that with lower ploidy level and groups of individuals with higher ploidy level were separated further away by genetic distance from the lower ploidy levels. Understanding the different genetic bases of local adaptation comparatively between latitude and longitude is one of the core findings in the adaptive evolution of plants.
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Affiliation(s)
- Jing-Xue Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China.,College of Animal and Veterinary Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Miaoli Wang
- College of Animal and Veterinary Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Jibiao Fan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhi-Peng Guo
- College of Animal and Veterinary Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yongzhuo Guan
- College of Animal and Veterinary Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Gen Qu
- College of Animal and Veterinary Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Chuan-Jie Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yu-Xia Guo
- College of Animal and Veterinary Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xuebing Yan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
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Li Y, Shi LC, Pei NC, Cushman SA, Si YT. Transcriptomic responses to drought stress among natural populations provide insights into local adaptation of weeping forsythia. BMC PLANT BIOLOGY 2021; 21:273. [PMID: 34130656 PMCID: PMC8204298 DOI: 10.1186/s12870-021-03075-6] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/25/2021] [Accepted: 05/26/2021] [Indexed: 05/04/2023]
Abstract
BACKGROUND Understanding the genetic mechanisms of local adaptation is an important emerging topic in molecular ecology and evolutionary biology. RESULTS Here, we identify the physiological changes and differential expression of genes among different weeping forsythia populations under drought stress in common garden experiments. Physiological results showed that HBWZ might have higher drought tolerance among four populations. RNA-seq results showed that significant differential expression in the genes responding to the synthesis of flavonoids, aromatic substances, aromatic amino acids, oxidation-reduction process, and transmembrane transport occured among four populations. By further reanalysis of results of previous studies, sequence differentiation was found in the genes related to the synthesis of aromatic substances among different weeping forsythia populations. CONCLUSIONS Overall, our study supports the hypothesis that the dual differentiation in gene efficiency and expression increases among populations in response to heterogeneous environments and is an important evolutionary process of local adaptation. Here, we proposed a new working model of local adaptation of weeping forsythia populations under different intensities of drought stress, which provides new insights for understanding the genetic mechanisms of local adaptation for non-model species.
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Affiliation(s)
- Yong Li
- Innovation Platform of Molecular Biology, College of Landscape and Art, Henan Agricultural University, Zhengzhou, China
| | - Long-Chen Shi
- Innovation Platform of Molecular Biology, College of Landscape and Art, Henan Agricultural University, Zhengzhou, China
| | - Nan-Cai Pei
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou, China
| | - Samuel A. Cushman
- U.S. Forest Service, Rocky Mountain Research Station, 2500 S. Pine Knoll Dr., Flagstaff, AZ USA
| | - Yu-Tao Si
- Innovation Platform of Molecular Biology, College of Landscape and Art, Henan Agricultural University, Zhengzhou, China
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Li LF, Cushman SA, He YX, Li Y. Genome sequencing and population genomics modeling provide insights into the local adaptation of weeping forsythia. HORTICULTURE RESEARCH 2020; 7:130. [PMID: 32821413 PMCID: PMC7395120 DOI: 10.1038/s41438-020-00352-7] [Citation(s) in RCA: 25] [Impact Index Per Article: 6.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/26/2020] [Revised: 05/24/2020] [Accepted: 05/24/2020] [Indexed: 05/06/2023]
Abstract
Understanding the genetic basis underlying the local adaptation of nonmodel species is a fundamental goal in evolutionary biology. In this study, we explored the genetic mechanisms of the local adaptation of Forsythia suspensa using genome sequence and population genomics data obtained from specific-locus amplified fragment sequencing. We assembled a high-quality reference genome of weeping forsythia (Scaffold N50 = 7.3 Mb) using ultralong Nanopore reads. Then, genome-wide comparative analysis was performed for 15 natural populations of weeping forsythia across its current distribution range. Our results revealed that candidate genes associated with local adaptation are functionally correlated with solar radiation, temperature and water variables across heterogeneous environmental scenarios. In particular, solar radiation during the period of fruit development and seed drying after ripening, cold, and drought significantly contributed to the adaptive differentiation of F. suspensa. Natural selection exerted by environmental factors contributed substantially to the population genetic structure of F. suspensa. Our results supported the hypothesis that adaptive differentiation should be highly pronounced in the genes involved in signal crosstalk between different environmental variables. Our population genomics study of F. suspensa provides insights into the fundamental genetic mechanisms of the local adaptation of plant species to climatic gradients.
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Affiliation(s)
- Lin-Feng Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
- Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, School of Life Sciences, Fudan University, Shanghai, 200438 China
| | - Samuel A. Cushman
- U.S. Forest Service, Rocky Mountain Research Station, 2500 S. Pine Knoll Dr., Flagstaff, Arizona USA
| | - Yan-Xia He
- School of Life Sciences, Henan University, Kaifeng, China
| | - Yong Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
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Xiong Y, Xiong Y, Yu Q, Zhao J, Lei X, Dong Z, Yang J, Song S, Peng Y, Liu W, Bai S, Ma X. Genetic variability and structure of an important wild steppe grass Psathyrostachys juncea (Triticeae: Poaceae) germplasm collection from north and central Asia. PeerJ 2020; 8:e9033. [PMID: 32341905 PMCID: PMC7182019 DOI: 10.7717/peerj.9033] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2019] [Accepted: 03/31/2020] [Indexed: 11/20/2022] Open
Abstract
Russian wildrye, Psathyrostachys junceus (Fisch.) Nevski, is an important wild steppe perennial grass, which is characterized by longevity and short robust rhizomes. It also has highly resistance in grazing and abiotic stress. In this study, the genetic diversity of eleven P. juncea wild germplasms from north and central Asia was investigated using AFLP markers. The P. juncea populations were divided into three clades in both UPGMA dendrogram and PCoA clustering corresponding to the three genetic memberships in STRUCTURE analysis. The genetic specificity of Xinjiang (XJ) populations was revealed by the highest Ne (1.5411) and Hj (0.3553) and their dispersion shown in UPGMA. High inbreeding coefficient (Wright’s F statistics, f = 0.496, Fst = 0.128) was observed although a moderate degree of gene flow (Nm = 1.4736) existed, that may ascribe to habitat fragmentation or the low seedling recruitment, which ultimately resulted in decrease of population size and their genetic diversity. The key factors inducing moderate genetic differentiation detected in this study were isolation by distance (IBD), climatic variabilities and geographical barriers. All these results provide insights into the study of genetic status and germplasm collecting of Russian wildrye.
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Affiliation(s)
- Yi Xiong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yanli Xiong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Qingqing Yu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Junming Zhao
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Xiong Lei
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Zhixiao Dong
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Jian Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Sijia Song
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Yan Peng
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
| | - Wenhui Liu
- Key Laboratory of Superior Forage Germplasm in the Qinghai-Tibet Plateau, Qinghai Academy of Animal Science and Veterinary Medicine, Xi-ning, China
| | - Shiqie Bai
- Sichuan Academy of Grassland Sciences, Chengdu, China
| | - Xiao Ma
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, China
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Qian ZH, Li Y, Li MW, He YX, Li JX, Ye XF. Molecular Phylogeography Analysis Reveals Population Dynamics and Genetic Divergence of a Widespread Tree Pterocarya stenoptera in China. Front Genet 2019; 10:1089. [PMID: 31737056 PMCID: PMC6838215 DOI: 10.3389/fgene.2019.01089] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/22/2019] [Accepted: 10/09/2019] [Indexed: 01/19/2023] Open
Abstract
The geological events, past climatic fluctuations, and river systems played key roles in the spatial distribution, population dynamics, and genetic differentiation of species. In this work, we selected Pterocarya stenoptera, a widespread tree species in China, to test the roles of these factors. Four noncoding spacers, eight microsatellite (simple sequence repeat) markers, and species distribution modeling were used to examine the phylogeographical pattern of P. stenoptera. Based on chloroplast DNA data, populations of P. stenoptera were clearly clustered into three groups. The divergence time of these groups fell into the stage of the Qinghai–Tibet Movement, 1.7–2.6 Ma. For simple sequence repeat data, only one western marginal population YNYB could be separated from other populations, whereas other populations were mixed together. Our results indicated that the environmental heterogeneity resulting from the Qinghai–Tibet movement might be response for this genetic divergence. The climatic fluctuations in the Pleistocene did not cause the substantial range shift of P. stenoptera, while the fluctuations affected its population size. Moreover, we also confirmed the river systems did not act as channels or barrier of dispersal for P. stenoptera.
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Affiliation(s)
- Zhi-Hao Qian
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Yong Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Ming-Wan Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Yan-Xia He
- School of Life Sciences, Henan University, Kaifeng, China
| | - Jia-Xin Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Xiao-Fan Ye
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, Zhengzhou, China
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10
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Zhang XX, Liu BG, Li Y, Liu Y, He YX, Qian ZH, Li JX. Landscape genetics reveals that adaptive genetic divergence in Pinus bungeana (Pinaceae) is driven by environmental variables relating to ecological habitats. BMC Evol Biol 2019; 19:160. [PMID: 31370777 PMCID: PMC6676527 DOI: 10.1186/s12862-019-1489-x] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/04/2018] [Accepted: 07/25/2019] [Indexed: 01/01/2023] Open
Abstract
Background Understanding the genetic basis of local adaptation has long been the concern of biologists. Identifying these adaptive genetic variabilities is crucial not only to improve our knowledge of the genetic mechanism of local adaptation but also to explore the adaptation potential of species. Results Using 10 natural populations and 12 start codon targeted (SCoT) markers, a total of 430 unambiguous loci were yielded. The Bayesian analysis of population structure clearly demonstrated that the 10 populations of P. bungeana could be subdivided into three groups. Redundancy analysis showed that this genetic divergence was caused by divergence selection from environmental variables related to the ecological habitats of “avoidance of flooding” and “avoidance of high temperature and humidity.” LFMM results indicated that Bio1, Bio5, Bio8, Bio12, Bio14, and Bio16, which are related to the ecological habitat of P. bungeana, were correlated with the highest numbers of environment-associated loci (EAL). Conclusions The results of EAL characterization in P. bungeana clearly supported the hypothesis that environmental variations related to the ecological habitat of species are the key drivers of species adaptive divergence. Moreover, a method to calculate the species landscape adaptation index and quantify the adaptation potential of species was proposed and verified using ecological niche modeling. This model could estimate climatically suitable areas of species spatial distribution. Taking the results together, this study improves the current understanding on the genetic basis of local adaptation. Electronic supplementary material The online version of this article (10.1186/s12862-019-1489-x) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Xue-Xia Zhang
- Innovation Platform of Molecular Biology College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002, China
| | - Bao-Guo Liu
- Innovation Platform of Molecular Biology College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002, China
| | - Yong Li
- Innovation Platform of Molecular Biology College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002, China.
| | - Ying Liu
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-sen University, No.135, Xingang Xi Road, Guangzhou, 510275, China
| | - Yan-Xia He
- School of Life Sciences, Henan University, Kaifeng, 475004, China
| | - Zhi-Hao Qian
- Innovation Platform of Molecular Biology College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002, China
| | - Jia-Xin Li
- Innovation Platform of Molecular Biology College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002, China
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Li JX, Zhu XH, Li Y, Liu Y, Qian ZH, Zhang XX, Sun Y, Ji LY. Adaptive genetic differentiation in Pterocarya stenoptera (Juglandaceae) driven by multiple environmental variables were revealed by landscape genomics. BMC PLANT BIOLOGY 2018; 18:306. [PMID: 30482158 PMCID: PMC6260741 DOI: 10.1186/s12870-018-1524-x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/10/2018] [Accepted: 11/14/2018] [Indexed: 05/06/2023]
Abstract
BACKGROUND The investigation of the genetic basis of local adaptation in non-model species is an interesting focus of evolutionary biologists and molecular ecologists. Identifying these adaptive genetic variabilities on the genome responsible can provide insight into the genetic mechanism of local adaptation. RESULTS We investigated the spatial distribution of genetic variation in 22 natural populations of Pterocarya stenoptera across its distribution area in China to provide insights into the complex interplay between multiple environmental variables and adaptive genetic differentiation. The Bayesian analysis of population structure showed that the 22 populations of P. stenoptera were subdivided into two groups. Redundancy analysis demonstrated that this genetic differentiation was caused by the divergent selection of environmental difference. A total of 44 outlier loci were mutually identified by Arlequin and BayeScan, 43 of which were environment-associated loci (EAL). The results of latent factor mixed model analysis showed that solar radiation in June (Sr6), minimum temperature of the coldest month (Bio6), temperature seasonality (Bio4), and water vapor pressure in January (Wvp1) were associated with the highest numbers of EAL. Sr6 was associated with the ecological habitat of "prefered light", and Bio6 and Wvp1 were associated with the ecological habitat of "warm and humid environment". CONCLUSIONS Our results provided empirical evidence that environmental variables related to the ecological habitats of species play key roles in driving adaptive differentiation of species genome.
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Affiliation(s)
- Jia-Xin Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002 China
| | - Xiu-Hong Zhu
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002 China
| | - Yong Li
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002 China
| | - Ying Liu
- Guangdong Provincial Key Laboratory of Plant Resources, School of Life Sciences, Sun Yat-Sen University, No.135, Xingang Xi Road, Guangzhou, 510275 China
| | - Zhi-Hao Qian
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002 China
| | - Xue-Xia Zhang
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002 China
| | - Yue Sun
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002 China
| | - Liu-Yang Ji
- Innovation Platform of Molecular Biology, College of Forestry, Henan Agricultural University, No.95, Wenhua Road, Zhengzhou, 450002 China
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Li Y, Zhang XX, Mao RL, Yang J, Miao CY, Li Z, Qiu YX. Ten Years of Landscape Genomics: Challenges and Opportunities. FRONTIERS IN PLANT SCIENCE 2017; 8:2136. [PMID: 29312391 PMCID: PMC5733015 DOI: 10.3389/fpls.2017.02136] [Citation(s) in RCA: 46] [Impact Index Per Article: 6.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/14/2017] [Accepted: 12/01/2017] [Indexed: 05/06/2023]
Abstract
Landscape genomics is a relatively new discipline that aims to reveal the relationship between adaptive genetic imprints in genomes and environmental heterogeneity among natural populations. Although the interest in landscape genomics has increased since this term was coined, studies on this topic remain scarce. Landscape genomics has become a powerful method to scan and determine the genes responsible for the complex adaptive evolution of species at population (mostly) and individual (more rarely) level. This review outlines the sampling strategies, molecular marker types and research categories in 37 articles published during the first 10 years of this field (i.e., 2007-2016). We also address major challenges and future directions for landscape genomics. This review aims to promote interest in conducting additional studies in landscape genomics.
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Affiliation(s)
- Yong Li
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Xue-Xia Zhang
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Run-Li Mao
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Jie Yang
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Cai-Yun Miao
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Zhuo Li
- College of Forestry, Henan Agricultural University, Zhengzhou, China
| | - Ying-Xiong Qiu
- Key Laboratory of Conservation Biology for Endangered Wildlife of the Ministry of Education and Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
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