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Johnson JP, Piche L, Worral H, Atanda SA, Coyne CJ, McGee RJ, McPhee K, Bandillo N. Effective population size in field pea. BMC Genomics 2024; 25:695. [PMID: 39009980 PMCID: PMC11251210 DOI: 10.1186/s12864-024-10587-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/02/2024] [Accepted: 07/02/2024] [Indexed: 07/17/2024] Open
Abstract
BACKGROUND Effective population size (Ne) is a pivotal parameter in population genetics as it can provide information on the rate of inbreeding and the contemporary status of genetic diversity in breeding populations. The population with smaller Ne can lead to faster inbreeding, with little potential for genetic gain making selections ineffective. The importance of Ne has become increasingly recognized in plant breeding, which can help breeders monitor and enhance the genetic variability or redesign their selection protocols. Here, we present the first Ne estimates based on linkage disequilibrium (LD) in the pea genome. RESULTS We calculated and compared Ne using SNP markers from North Dakota State University (NDSU) modern breeding lines and United States Department of Agriculture (USDA) diversity panel. The extent of LD was highly variable not only between populations but also among different regions and chromosomes of the genome. Overall, NDSU had a higher and longer-range LD than the USDA that could extend up to 500 Kb, with a genome-wide average r2 of 0.57 (vs 0.34), likely due to its lower recombination rates and the selection background. The estimated Ne for the USDA was nearly three-fold higher (Ne = 174) than NDSU (Ne = 64), which can be confounded by a high degree of population structure due to the selfing nature of pea. CONCLUSIONS Our results provided insights into the genetic diversity of the germplasm studied, which can guide plant breeders to actively monitor Ne in successive cycles of breeding to sustain viability of the breeding efforts in the long term.
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Affiliation(s)
| | - Lisa Piche
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Hannah Worral
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Sikiru Adeniyi Atanda
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA
| | - Clarice J Coyne
- USDA-ARS Plant Germplasm Introduction and Testing, Washington State University, Pullman, WA, 99164, USA
| | - Rebecca J McGee
- USDA-ARS Grain Legume Genetics and Physiology Research, Pullman, WA, 99164, USA
- Department of Horticulture, Washington State University, Pullman, WA, 99164, USA
| | - Kevin McPhee
- Department of Plant Science and Plant Pathology, Montana State University, 119 Plant Bioscience Building, Bozeman, MT, 59717-3150, USA
| | - Nonoy Bandillo
- Department of Plant Sciences, North Dakota State University, Fargo, ND, 58108-6050, USA.
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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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3
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Wagutu GK, Fan X, Fu W, Tengwer MC, Li W, Chen Y. Genetic structure of wild rice Zizania latifolia in an expansive heterogeneous landscape along a latitudinal gradient. Front Ecol Evol 2022. [DOI: 10.3389/fevo.2022.929944] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Global aquatic habitats are undergoing rapid degradation and fragmentation as a result of climate change and changes in land use. Understanding the genetic variability and adaptive potential of aquatic plant species is thus important for conservation purposes. In this study, we investigated the genetic diversity and structure of the extant natural populations of Zizania latifolia from five river basins in China based on 46 microsatellite markers. We tested isolation by environment (IBE), isolation by resistance (IBR), and isolation by distance (IBD) patterns using a reciprocal causal model (RCM). Furthermore, we elucidated the impact of the environment on Z. latifolia genetic diversity using generalized linear models (GLMs) and spatially explicit mixed models. Low genetic diversity (HE = 0.125–0.433) and high genetic differentiation (FST = 0.641, Øpt = 0.654) were found. Higher historical gene flow (MH = 0.212–2.354) than contemporary gene flow (MC = 0.0112–0.0247) and significant bottlenecks in almost all populations were identified, highlighting the negative impact of wetland fragmentation. The IBE model was exclusively supported for all populations and in three river basins. The IBD and IBR models were supported in one river basin each. The maximum temperature of the warmest month and precipitation seasonality were the plausible environmental parameters responsible for the observed pattern of genetic diversity. Local adaptation signatures were found, with nine loci identified as outliers, four of which were gene-linked and associated with environmental variables. Based on these findings, IBE is more important than IBD and IBR in shaping the genetic structure of Z. latifolia.
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Liang S, Zhang X, Wei R. Ecological adaptation shaped the genetic structure of homoploid ferns against strong dispersal capacity. Mol Ecol 2022; 31:2679-2697. [DOI: 10.1111/mec.16420] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/04/2021] [Revised: 02/26/2022] [Accepted: 02/28/2022] [Indexed: 11/26/2022]
Affiliation(s)
- Si‐Qi Liang
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany The Chinese Academy of Sciences Beijing 100093 China
- University of Chinese Academy of Sciences College of Life Sciences Beijing 100049 China
| | - Xian‐Chun Zhang
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany The Chinese Academy of Sciences Beijing 100093 China
| | - Ran Wei
- State Key Laboratory of Systematic and Evolutionary Botany Institute of Botany The Chinese Academy of Sciences Beijing 100093 China
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Cui X, Li C, Qin S, Huang Z, Gan B, Jiang Z, Huang X, Yang X, Li Q, Xiang X, Chen J, Zhao Y, Rong J. High-throughput sequencing-based microsatellite genotyping for polyploids to resolve allele dosage uncertainty and improve analyses of genetic diversity, structure and differentiation: A case study of the hexaploid Camellia oleifera. Mol Ecol Resour 2021; 22:199-211. [PMID: 34260828 DOI: 10.1111/1755-0998.13469] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 11/30/2022]
Abstract
Conventional microsatellite (simple sequence repeat, SSR) genotyping methods cannot accurately identify polyploid genotypes leading to allele dosage uncertainty, introducing biases in population genetic analysis. Here, a new SSR genotyping method was developed to directly infer accurate polyploid genotypes. The frequency distribution of SSR sequences was obtained based on deep-coverage high-throughput sequencing data. Corrections were performed accounting for the "stutter peak" and amplification efficiency of SSR sequences. Perl scripts and an online SSR genotyping tool "SSRSeq" were provided to process the sequencing data and output genotypes with corrected allele dosages. Hexaploid Camellia oleifera is the dominant woody oilseed crop in China. Understanding the geographical pattern of genetic variation in wild C. oleifera is essential for the conservation and utilization of genetic resources. Six wild C. oleifera populations were sampled across geographical ranges in subtropical evergreen broadleaf forests of China. Using 35 SSR markers, the high-throughput sequencing-based SSRSeq method was applied to obtain accurate hexaploid genotypes of wild C. oleifera. The results demonstrated that the new method could resolve allele dosage uncertainty and considerably improve genetic diversity, structure and differentiation analyses for polyploids. The genetic variation patterns of wild C. oleifera across geographical ranges agree with the "central-marginal hypothesis", stating that genetic diversity is high in the central population and declines from the central to the peripheral populations, and genetic differentiation increases from the centre to the periphery. This method and findings can facilitate the utilization of wild C. oleifera genetic resources for the breeding of cultivated C. oleifera.
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Affiliation(s)
- Xiangyan Cui
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Caihua Li
- Center for Genetic & Genomic Analysis, Genesky Biotechnologies Inc, Shanghai, China
| | - Shengyuan Qin
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Zebin Huang
- Center for Genetic & Genomic Analysis, Genesky Biotechnologies Inc, Shanghai, China
| | - Bin Gan
- Center for Genetic & Genomic Analysis, Genesky Biotechnologies Inc, Shanghai, China
| | | | - Xiaomao Huang
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Xiaoqiang Yang
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Qin Li
- Fudan Development Institute, Fudan University, Shanghai, China
| | - Xiaoguo Xiang
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Jiakuan Chen
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China.,Fudan Development Institute, Fudan University, Shanghai, China
| | - Yao Zhao
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China.,Lushan Botanical Garden, Chinese Academy of Sciences, Lushan, China
| | - Jun Rong
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China.,Lushan Botanical Garden, Chinese Academy of Sciences, Lushan, China
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6
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Peng X, Tun W, Dai SF, Li JY, Zhang QJ, Yin GY, Yoon J, Cho LH, An G, Gao LZ. Genome-Wide Analysis of CCT Transcript Factors to Identify Genes Contributing to Photoperiodic Flowering in Oryza rufipogon. FRONTIERS IN PLANT SCIENCE 2021; 12:736419. [PMID: 34819938 PMCID: PMC8606741 DOI: 10.3389/fpls.2021.736419] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 07/05/2021] [Accepted: 10/08/2021] [Indexed: 05/03/2023]
Abstract
Photoperiod sensitivity is a dominant determinant for the phase transition in cereal crops. CCT (CONSTANS, CO-like, and TOC1) transcription factors (TFs) are involved in many physiological functions including the regulation of the photoperiodic flowering. However, the functional roles of CCT TFs have not been elucidated in the wild progenitors of crops. In this study, we identified 41 CCT TFs, including 19 CMF, 17 COL, and five PRR TFs in Oryza rufipogon, the presumed wild ancestor of Asian cultivated rice. There are thirty-eight orthologous CCT genes in Oryza sativa, of which ten pairs of duplicated CCT TFs are shared with O. rufipogon. We investigated daily expression patterns, showing that 36 OrCCT genes exhibited circadian rhythmic expression. A total of thirteen OrCCT genes were identified as putative flowering suppressors in O. rufipogon based on rhythmic and developmental expression patterns and transgenic phenotypes. We propose that OrCCT08, OrCCT24, and OrCCT26 are the strong functional alleles of rice DTH2, Ghd7, and OsPRR37, respectively. The SD treatment at 80 DAG stimulated flowering of the LD-grown O. rufipogon plants. Our results further showed that the nine OrCCT genes were significantly downregulated under the treatment. Our findings would provide valuable information for the construction of photoperiodic flowering regulatory network and functional characterization of the CCT TFs in both O. rufipogon and O. sativa.
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Affiliation(s)
- Xin Peng
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
- Crop Biotech Institute, Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Win Tun
- Crop Biotech Institute, Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Shuang-feng Dai
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Jia-yue Li
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Qun-jie Zhang
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Guo-ying Yin
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
| | - Jinmi Yoon
- Crop Biotech Institute, Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
| | - Lae-hyeon Cho
- Crop Biotech Institute, Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
- Department of Plant Bioscience, Pusan National University, Miryang, South Korea
| | - Gynheung An
- Crop Biotech Institute, Graduate School of Biotechnology, Kyung Hee University, Yongin, South Korea
- *Correspondence: Gynheung An,
| | - Li-zhi Gao
- Institution of Genomics and Bioinformatics, South China Agricultural University, Guangzhou, China
- Li-zhi Gao,
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7
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Wang J, Shi J, Liu S, Sun X, Huang J, Qiao W, Cheng Y, Zhang L, Zheng X, Yang Q. Conservation recommendations for Oryza rufipogon Griff. in China based on genetic diversity analysis. Sci Rep 2020; 10:14375. [PMID: 32873826 PMCID: PMC7462988 DOI: 10.1038/s41598-020-70989-w] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/04/2020] [Accepted: 08/06/2020] [Indexed: 11/26/2022] Open
Abstract
Over the past 30 years, human disturbance and habitat fragmentation have severely endangered the survival of common wild rice (Oryza rufipogon Griff.) in China. A better understanding of the genetic structure of O. rufipogon populations will therefore be useful for the development of conservation strategies. We examined the diversity and genetic structure of natural O. rufipogon populations at the national, provincial, and local levels using simple sequence repeat (SSR) markers. Twenty representative populations from sites across China showed high levels of genetic variability, and approximately 44% of the total genetic variation was among populations. At the local level, we studied fourteen populations in Guangxi Province and four populations in Jiangxi Province. Populations from similar ecosystems showed less genetic differentiation, and local environmental conditions rather than geographic distance appeared to have influenced gene flow during population genetic evolution. We identified a triangular area, including northern Hainan, southern Guangdong, and southwestern Guangxi, as the genetic diversity center of O. rufipogon in China, and we proposed that this area should be given priority during the development of ex situ and in situ conservation strategies. Populations from less common ecosystem types should also be given priority for in situ conservation.
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Affiliation(s)
- Junrui Wang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Jinxia Shi
- Shanghai Normal University, Shanghai, China
| | - Sha Liu
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiping Sun
- Shanxi Agricultural University, Jinzhong, China
| | - Juan Huang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Institute of Rice Research, Guangxi Academy of Agricultural Sciences, Nanning, China
| | - Weihua Qiao
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
- Agricultural Science and Technology Innovation Program/Crop Germplasm Resources Preservation and Sharing Innovation Team, Beijing, China
| | - Yunlian Cheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Lifang Zhang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China
| | - Xiaoming Zheng
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
- Agricultural Science and Technology Innovation Program/Crop Germplasm Resources Preservation and Sharing Innovation Team, Beijing, China.
| | - Qingwen Yang
- Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China.
- Agricultural Science and Technology Innovation Program/Crop Germplasm Resources Preservation and Sharing Innovation Team, Beijing, China.
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8
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Cheng J, Kao H, Dong S. Population genetic structure and gene flow of rare and endangered Tetraena mongolica Maxim. revealed by reduced representation sequencing. BMC PLANT BIOLOGY 2020; 20:391. [PMID: 32842966 PMCID: PMC7448513 DOI: 10.1186/s12870-020-02594-y] [Citation(s) in RCA: 16] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/01/2020] [Accepted: 08/12/2020] [Indexed: 05/28/2023]
Abstract
BACKGROUND Studying population genetic structure and gene flow of plant populations and their influencing factors is of particular significance in the field of conservation biology, especially important for species such as rare and endangered plants. Tetraena mongolica Maxim. (TM), belongs to Zygophyllaceae family, a rare and endangered plant with narrow distribution. However, for the last decade, due to excessive logging, urban expansion, industrial and tourism development, habitat fragmentation and loss of natural habitats have become major threats to the population of endangered plants. RESULTS In this study, genetic diversity, population genetic structure and gene flow of TM populations were evaluated by reduced representation sequencing technology, and a total of more than 133.45 GB high-quality clean reads and 38,097 high-quality SNPs were generated. Analysis based on multiple methods, we found that the existing TM populations have moderate levels of genetic diversity, and very low genetic differentiation as well as high levels of gene flow between populations. Population structure and principal coordinates analysis showed that 8 TM populations can be divided into two groups. The Mantel test detected no significant correlation between geographical distances and genetic distance for the whole sampling. Moreover, the migration model indicated that the gene flow is more of a north to south migration pattern in history. CONCLUSIONS This study demonstrates that the present genetic structure is mainly due to habitat fragmentation caused by urban sprawl, industrial development and coal mining. Our recommendation with respect to conservation management is that, all 8 populations should be preserved as a whole population, rather than just those in the core area of TM nature reserve. In particular, the populations near the edge of TM distribution in cities and industrial areas deserve our special protection.
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Affiliation(s)
- Jin Cheng
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Huixia Kao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
| | - Shubin Dong
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China.
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Zhao Y, Song Z, Zhong L, Li Q, Chen J, Rong J. Inferring the Origin of Cultivated Zizania latifolia, an Aquatic Vegetable of a Plant-Fungus Complex in the Yangtze River Basin. FRONTIERS IN PLANT SCIENCE 2019; 10:1406. [PMID: 31787995 PMCID: PMC6856052 DOI: 10.3389/fpls.2019.01406] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/24/2019] [Accepted: 10/10/2019] [Indexed: 05/10/2023]
Abstract
Crop domestication is one of the essential topics in evolutionary biology. Cultivated Zizania latifolia, domesticated as the special form of a plant-fungus (the host Zizania latifolia and the endophyte Ustilago esculenta) complex, is a popular aquatic vegetable endemic in East Asia. The rapid domestication of cultivated Z. latifolia can be traced in the historical literature but still need more evidence. This study focused on deciphering the genetic relationship between wild and cultivated Z. latifolia, as well as the corresponding parasitic U. esculenta. Twelve microsatellites markers were used to study the genetic variations of 32 wild populations and 135 landraces of Z. latifolia. Model simulations based on approximate Bayesian computation (ABC) were then performed to hierarchically infer the population history. We also analyzed the ITS sequences of the smut fungus U. esculenta to reveal its genetic structure. Our results indicated a significant genetic divergence between cultivated Z. latifolia and its wild ancestors. The wild Z. latifolia populations showed significant hierarchical genetic subdivisions, which may be attributed to the joint effect of isolation by distance and hydrological unconnectedness between watersheds. Cultivated Z. latifolia was supposedly domesticated once in the low reaches of the Yangtze River. The genetic structure of U. esculenta also indicated a single domestication event, and the genetic variations in this fungus might be associated with the diversification of cultivars. These findings provided molecular evidence in accordance with the historical literature that addressed the domestication of cultivated Z. latifolia involved adaptive evolution driven by artificial selection in both the plant and fungus.
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Affiliation(s)
- Yao Zhao
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Zhiping Song
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Lan Zhong
- Institute of Vegetable, Wuhan Academy of Agriculture Science and Technology, Wuhan, China
| | - Qin Li
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Jiakuan Chen
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Jun Rong
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
- *Correspondence: Jun Rong,
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10
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Zhao Y, Zhong L, Zhou K, Song Z, Chen J, Rong J. Seed characteristic variations and genetic structure of wild Zizania latifolia along a latitudinal gradient in China: implications for neo-domestication as a grain crop. AOB PLANTS 2018; 10:ply072. [PMID: 30595833 PMCID: PMC6304442 DOI: 10.1093/aobpla/ply072] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 08/24/2018] [Accepted: 11/29/2018] [Indexed: 06/09/2023]
Abstract
Crop wild relatives are not only important genetic resources for crop improvement, but also domestication candidates for selecting new crops. As a close relative of American wild rice Zizania palustris, Z. latifolia is a perennial aquatic grass widely distributed in China. Although Z. latifolia has been domesticated and cultivated as an aquatic vegetable for >1000 years, a neo-domestication for grain production needs to be soundly evaluated. In this study, we investigated the seed characteristic variations and genetic structure of 15 Z. latifolia wild populations along a latitudinal gradient in China. Our results showed that Z. latifolia tended to produce relatively larger seeds with lower moisture content and lower investments in seed pericarp at lower latitudes. The width, size, shape, seed-pericarp ratio and relative water content of seeds were significantly associated with climatic variables. The seeds of Z. latifolia showed a relatively low germination percentage and strong dormancy, which might hinder the neo-domestication. In addition, high genetic differentiation had been found among Z. latifolia populations, which could be attributed to isolation by distance. This study offered preliminary information for the utilization and conservation of wild Z. latifolia. It suggested that the wild populations in the middle and lower reaches of the Yangtze River could be good candidates for grain crop domestication due to appropriate seed traits and high genetic diversity. The neo-domestication of wild Z. latifolia requires further researches on the genetic mechanism of the Domestication Syndrome and more works on artificial breeding.
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Affiliation(s)
- Yao Zhao
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Lan Zhong
- Institute of Vegetable, Wuhan Academy of Agriculture Science and Technology, Wuhan, Hubei Province, China
| | - Kai Zhou
- Institute of Vegetable, Wuhan Academy of Agriculture Science and Technology, Wuhan, Hubei Province, China
| | - Zhiping Song
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Jiakuan Chen
- The Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Shanghai, China
| | - Jun Rong
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
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Spatial genetic structure of an endangered orchid Cypripedium calceolus (Orchidaceae) at a regional scale: limited gene flow in a fragmented landscape. CONSERV GENET 2018. [DOI: 10.1007/s10592-018-1113-4] [Citation(s) in RCA: 14] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
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12
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Gentili R, Solari A, Diekmann M, Duprè C, Monti GS, Armiraglio S, Assini S, Citterio S. Genetic differentiation, local adaptation and phenotypic plasticity in fragmented populations of a rare forest herb. PeerJ 2018; 6:e4929. [PMID: 29915689 PMCID: PMC6004105 DOI: 10.7717/peerj.4929] [Citation(s) in RCA: 12] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Accepted: 05/18/2018] [Indexed: 12/04/2022] Open
Abstract
Background Due to habitat loss and fragmentation, numerous forest species are subject to severe population decline. Investigating variation in genetic diversity, phenotypic plasticity and local adaptation should be a prerequisite for implementing conservation actions. This study aimed to explore these aspects in ten fragmented populations of Physospermum cornubiense in view of translocation measures across its Italian range. Methods For each population we collected environmental data on landscape (habitat size, quality and fragmentation) and local conditions (slope, presence of alien species, incidence of the herbivorous insect Metcalfa pruinosa and soil parameters). We measured vegetative and reproductive traits in the field and analysed the genetic population structure using ISSR markers (STRUCTURE and AMOVA). We then estimated the neutral (FST) and quantitative (PST) genetic differentiation of populations. Results The populations exhibited moderate phenotypic variation. Population size (range: 16–655 individuals), number of flowering adults (range: 3–420 individuals) and inflorescence size (range: 5.0–8.4 cm) were positively related to Mg soil content. Populations’ gene diversity was moderate (Nei-H = 0.071–0.1316); STRUCTURE analysis identified five different clusters and three main geographic groups: upper, lower, and Apennine/Western Po plain. Fragmentation did not have an influence on the local adaptation of populations, which for all measured traits showed PST < FST, indicating convergent selection. Discussion The variation of phenotypic traits across sites was attributed to plastic response rather than local adaptation. Plant translocation from suitable source populations to endangered ones should particularly take into account provenance according to identified genetic clusters and specific soil factors.
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Affiliation(s)
- Rodolfo Gentili
- Department of Earth and Environmental Sciences, University of Milan-Bicocca, Milan, Italy
| | - Aldo Solari
- Department of Economics, Management and Statistics, University of Milan-Bicocca, Milan, Italy
| | | | - Cecilia Duprè
- Institute of Ecology, University of Bremen, Bremen, Germany
| | - Gianna Serafina Monti
- Department of Economics, Management and Statistics, University of Milan-Bicocca, Milan, Italy
| | | | - Silvia Assini
- Department of Earth and Environmental Sciences, University of Pavia, Pavia, Italy
| | - Sandra Citterio
- Department of Earth and Environmental Sciences, University of Milan-Bicocca, Milan, Italy
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13
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The Tanggula Mountains enhance population divergence in Carex moorcroftii: a dominant sedge on the Qinghai-Tibetan Plateau. Sci Rep 2018; 8:2741. [PMID: 29426823 PMCID: PMC5807306 DOI: 10.1038/s41598-018-21129-y] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/05/2017] [Accepted: 01/30/2018] [Indexed: 11/08/2022] Open
Abstract
High-altitude mountains are often geographic barriers to gene flow and play important roles in shaping population divergence. The central Qinghai-Tibetan Plateau (QTP) stands the location of the Tanggula Mountains (TM). We use the TM as a case, using Carex moorcroftii, a dominant species on the QTP to test the effects of geographic barriers on plant population divergence. We sampled 18 C. moorcroftii populations along a north-south transect crossing the TM to investigate the correlations of genetic variation and morphological traits with climate variables. The results showed this species holds high genetic diversity (He = 0.58) and the surveyed populations can be genetically clustered into two groups: populations from the north face of TM, and the other from the south. Gene flow between populations within groups is higher than those between groups. The traits, number and mass of seeds, mass of root and infructescence significantly varied among populations. Mantel-tests detected a weak but significantly positive correlation between genetic and geographic (R2 = 0.107, p = 0.032) and climatic distance (R2 = 0.162, p = 0.005), indicating both isolation by distance and isolation by environment. These findings together suggest high-altitude mountains of TM interrupt habitat continuity, result in distinct climatic conditions on both sides, increasing population divergence of plant species.
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14
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Yang X, Li L, Jiang X, Wang W, Cai X, Su J, Wang F, Lu BR. Genetically engineered rice endogenous 5-enolpyruvoylshikimate-3-phosphate synthase (epsps) transgene alters phenology and fitness of crop-wild hybrid offspring. Sci Rep 2017; 7:6834. [PMID: 28754953 PMCID: PMC5533792 DOI: 10.1038/s41598-017-07089-9] [Citation(s) in RCA: 15] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/20/2017] [Accepted: 06/22/2017] [Indexed: 11/15/2022] Open
Abstract
Genetically engineered (GE) rice endogenous epsps (5-enolpyruvoylshikimate-3-phosphate synthase) gene overexpressing EPSPS can increase glyphosate herbicide-resistance of cultivated rice. This type of epsps transgene can enhance the fecundity of rice crop-weed hybrid offspring in the absence of glyphosate, stimulating great concerns over undesired environmental impacts of transgene flow to populations of wild relatives. Here, we report the substantial alteration of phenology and fitness traits in F1-F3 crop-wild hybrid descendants derived from crosses between an epsps GE rice line and two endangered wild rice (Oryza rufipogon) populations, based on the common-garden field experiments. Under the glyphosate-free condition, transgenic hybrid lineages showed significantly earlier tillering and flowering, as well as increased fecundity and overwintering survival/regeneration abilities. In addition, a negative correlation was observed between the contents of endogenous EPSPS of wild, weedy, and cultivated rice parents and fitness differences caused by the incorporation of the epsps transgene. Namely, a lower level of endogenous EPSPS in the transgene-recipient populations displayed a more pronounced enhancement in fitness. The altered phenology and enhanced fitness of crop-wild hybrid offspring by the epsps transgene may cause unwanted environmental consequences when this type of glyphosate-resistance transgene introgressed into wild rice populations through gene flow.
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Affiliation(s)
- Xiao Yang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Songhu Road 2005, Shanghai, 200438, China
| | - Lei Li
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Songhu Road 2005, Shanghai, 200438, China
| | - Xiaoqi Jiang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Songhu Road 2005, Shanghai, 200438, China
| | - Wei Wang
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Songhu Road 2005, Shanghai, 200438, China
| | - Xingxing Cai
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Songhu Road 2005, Shanghai, 200438, China
| | - Jun Su
- Fujian Province Key Laboratory of Genetic Engineering for Agriculture, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Feng Wang
- Fujian Province Key Laboratory of Genetic Engineering for Agriculture, Fujian Academy of Agricultural Sciences, Fuzhou, 350003, China
| | - Bao-Rong Lu
- Ministry of Education Key Laboratory for Biodiversity and Ecological Engineering, Institute of Biodiversity Science, Fudan University, Songhu Road 2005, Shanghai, 200438, China.
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15
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Pais AL, Whetten RW, Xiang Q(J. Ecological genomics of local adaptation in Cornus florida L. by genotyping by sequencing. Ecol Evol 2017; 7:441-465. [PMID: 28070306 PMCID: PMC5213257 DOI: 10.1002/ece3.2623] [Citation(s) in RCA: 22] [Impact Index Per Article: 3.1] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/10/2016] [Revised: 10/15/2016] [Accepted: 10/20/2016] [Indexed: 12/11/2022] Open
Abstract
Discovering local adaptation, its genetic underpinnings, and environmental drivers is important for conserving forest species. Ecological genomic approaches coupled with next-generation sequencing are useful means to detect local adaptation and uncover its underlying genetic basis in nonmodel species. We report results from a study on flowering dogwood trees (Cornus florida L.) using genotyping by sequencing (GBS). This species is ecologically important to eastern US forests but is severely threatened by fungal diseases. We analyzed subpopulations in divergent ecological habitats within North Carolina to uncover loci under local selection and associated with environmental-functional traits or disease infection. At this scale, we tested the effect of incorporating additional sequencing before scaling for a broader examination of the entire range. To test for biases of GBS, we sequenced two similarly sampled libraries independently from six populations of three ecological habitats. We obtained environmental-functional traits for each subpopulation to identify associations with genotypes via latent factor mixed modeling (LFMM) and gradient forests analysis. To test whether heterogeneity of abiotic pressures resulted in genetic differentiation indicative of local adaptation, we evaluated Fst per locus while accounting for genetic differentiation between coastal subpopulations and Piedmont-Mountain subpopulations. Of the 54 candidate loci with sufficient evidence of being under selection among both libraries, 28-39 were Arlequin-BayeScan Fst outliers. For LFMM, 45 candidates were associated with climate (of 54), 30 were associated with soil properties, and four were associated with plant health. Reanalysis of combined libraries showed that 42 candidate loci still showed evidence of being under selection. We conclude environment-driven selection on specific loci has resulted in local adaptation in response to potassium deficiencies, temperature, precipitation, and (to a marginal extent) disease. High allele turnover along ecological gradients further supports the adaptive significance of loci speculated to be under selection.
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Affiliation(s)
- Andrew L. Pais
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
| | - Ross W. Whetten
- Department of ForestryNorth Carolina State UniversityRaleighNCUSA
| | - Qiu‐Yun (Jenny) Xiang
- Department of Plant and Microbial BiologyNorth Carolina State UniversityRaleighNCUSA
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16
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Yang L, Chen J, Hu W, Yang T, Zhang Y, Yukiyoshi T, Zhou Y, Wang Y. Population Genetic Structure of Glycyrrhiza inflata B. (Fabaceae) Is Shaped by Habitat Fragmentation, Water Resources and Biological Characteristics. PLoS One 2016; 11:e0164129. [PMID: 27711241 PMCID: PMC5053598 DOI: 10.1371/journal.pone.0164129] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/16/2016] [Accepted: 09/20/2016] [Indexed: 11/18/2022] Open
Abstract
BACKGROUND Habitat fragmentation, water resources and biological characteristics are important factors that shape the genetic structure and geographical distribution of desert plants. Analysis of the relationships between these factors and population genetic variation should help to determine the evolutionary potential and conservation strategies for genetic resources for desert plant populations. As a traditional Chinese herb, Glycyrrhiza inflata B. (Fabaceae) is restricted to the fragmented desert habitat in China and has undergone a dramatic decline due to long-term over-excavation. Determining the genetic structure of the G. inflata population and identifying a core collection could help with the development of strategies to conserve this species. RESULTS We investigated the genetic variation of 25 G. inflata populations based on microsatellite markers. A high level of population genetic divergence (FST = 0.257), population bottlenecks, reduced gene flow and moderate genetic variation (HE = 0.383) were detected. The genetic distances between the populations significantly correlated with the geographical distances, and this suggests that habitat fragmentation has driven a special genetic structure of G. inflata in China through isolation by distance. STRUCTURE analysis showed that G. inflata populations were structured into three clusters and that the populations belonged to multiple water systems, which suggests that water resources were related to the genetic structure of G. inflata. In addition, the biological characteristics of the perennial species G. inflata, such as its long-lived seeds, asexual reproduction, and oasis ecology, may be related to its resistance to habitat fragmentation. A core collection of G. inflata, that included 57 accessions was further identified, which captured the main allelic diversity of G. inflata. CONCLUSIONS Recent habitat fragmentation has accelerated genetic divergence. The population genetic structure of G. inflata has been shaped by habitat fragmentation, water resources and biological characteristics. This genetic information and core collection will facilitate the conservation of wild germplasm and breeding of this Chinese medicinal plant.
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Affiliation(s)
- Lulu Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P.R. China
- University of the Chinese Academy of Sciences, Beijing, P.R. China
| | - Jianjun Chen
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Weiming Hu
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P.R. China
- University of the Chinese Academy of Sciences, Beijing, P.R. China
| | - Tianshun Yang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P.R. China
| | - Yanjun Zhang
- Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden, Chinese Academy of Sciences, Wuhan, P.R. China
| | | | | | - Ying Wang
- Key Laboratory of South China Agricultural Plant Molecular Analysis and Genetic Improvement, Provincial Key Laboratory of Applied Botany, South China Botanical Garden, Chinese Academy of Sciences, Guangzhou, P.R. China
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17
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Li L, Yang X, Wang L, Yan H, Su J, Wang F, Lu BR. Limited ecological risk of insect-resistance transgene flow from cultivated rice to its wild ancestor based on life-cycle fitness assessment. Sci Bull (Beijing) 2016. [DOI: 10.1007/s11434-016-1152-5] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
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18
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Ortego J, García-Navas V, Noguerales V, Cordero PJ. Discordant patterns of genetic and phenotypic differentiation in five grasshopper species codistributed across a microreserve network. Mol Ecol 2015; 24:5796-812. [DOI: 10.1111/mec.13426] [Citation(s) in RCA: 17] [Impact Index Per Article: 1.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2015] [Revised: 10/11/2015] [Accepted: 10/14/2015] [Indexed: 01/23/2023]
Affiliation(s)
- Joaquín Ortego
- Department of Integrative Ecology; Estación Biológica de Doñana; EBD-CSIC; Avda. Américo Vespucio s/n E-41092 Seville Spain
| | - Vicente García-Navas
- Institute of Evolutionary Biology and Environmental Studies; University of Zurich; Winterthurerstrasse 190 8057 Zurich Switzerland
| | - Víctor Noguerales
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM); Ronda de Toledo s/n E-13005 Ciudad Real Spain
| | - Pedro J. Cordero
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos - IREC (CSIC, UCLM, JCCM); Ronda de Toledo s/n E-13005 Ciudad Real Spain
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19
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Ferrer ES, García-Navas V, Bueno-Enciso J, Barrientos R, Serrano-Davies E, Cáliz-Campal C, Sanz JJ, Ortego J. The influence of landscape configuration and environment on population genetic structure in a sedentary passerine: insights from loci located in different genomic regions. J Evol Biol 2015; 29:205-19. [DOI: 10.1111/jeb.12776] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/20/2015] [Revised: 10/07/2015] [Accepted: 10/12/2015] [Indexed: 11/29/2022]
Affiliation(s)
- E. S. Ferrer
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM); Ciudad Real Spain
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - V. García-Navas
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM); Ciudad Real Spain
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
- Institute of Evolutionary Biology and Environmental Studies; University of Zurich; Zurich Switzerland
| | - J. Bueno-Enciso
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - R. Barrientos
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - E. Serrano-Davies
- Departamento de Ciencias Ambientales; Facultad de Ciencias Ambientales y Bioquímica; Universidad de Castilla-La Mancha; Toledo Spain
| | - C. Cáliz-Campal
- Grupo de Investigación de la Biodiversidad Genética y Cultural; Instituto de Investigación en Recursos Cinegéticos (CSIC-UCLM-JCCM); Ciudad Real Spain
- Department of Integrative Ecology; Estación Biológica de Doñana (EBD-CSIC); Seville Spain
| | - J. J. Sanz
- Departamento de Ecología Evolutiva; Museo Nacional de Ciencias Naturales (CSIC); Madrid Spain
| | - J. Ortego
- Department of Integrative Ecology; Estación Biológica de Doñana (EBD-CSIC); Seville Spain
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Wu Z, Yu D, Wang Z, Li X, Xu X. Great influence of geographic isolation on the genetic differentiation of Myriophyllum spicatum under a steep environmental gradient. Sci Rep 2015; 5:15618. [PMID: 26494202 PMCID: PMC4616052 DOI: 10.1038/srep15618] [Citation(s) in RCA: 14] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/30/2015] [Accepted: 09/28/2015] [Indexed: 11/01/2022] Open
Abstract
Understanding how natural processes affect population genetic structures is an important issue in evolutionary biology. One effective method is to assess the relative importance of environmental and geographical factors in the genetic structure of populations. In this study, we examined the spatial genetic variation of thirteen Myriophyllum spicatum populations from the Qinghai-Tibetan Plateau (QTP) and adjacent highlands (Yunnan-Guizhou Plateau, YGP) by using microsatellite loci and environmental and geographical factors. Bioclim layers, hydrological properties and elevation were considered as environmental variables and reduced by principal component analysis. The genetic isolation by geographic distance (IBD) was tested by Mantel tests and the relative importance of environmental variables on population genetic differentiation was determined by a partial Mantel test and multiple matrix regression with randomization (MMRR). Two genetic clusters corresponding to the QTP and YGP were identified. Both tests and MMRR revealed a significant and strong correlation between genetic divergence and geographic isolation under the influence of environmental heterogeneity at the overall and finer spatial scales. Our findings suggested the dominant role of geography on the evolution of M. spicatum under a steep environmental gradient in the alpine landscape as a result of dispersal limitation and genetic drift.
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Affiliation(s)
- Zhigang Wu
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Dan Yu
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Zhong Wang
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Xing Li
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
| | - Xinwei Xu
- National Field Station of Freshwater Ecosystem of Liangzi Lake, College of Life Sciences, Wuhan University, Wuhan 430072, PR China
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