1
|
Kang S, Kim S, Park KC, Petrašiūnas A, Shin HC, Jo E, Cho SM, Kim JH. Molecular evidence for multiple origins and high genetic differentiation of non-native winter crane fly, Trichocera maculipennis (Diptera: Trichoceridae), in the maritime Antarctic. ENVIRONMENTAL RESEARCH 2024; 242:117636. [PMID: 37952853 DOI: 10.1016/j.envres.2023.117636] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/15/2023] [Revised: 11/07/2023] [Accepted: 11/08/2023] [Indexed: 11/14/2023]
Abstract
Native biodiversity and ecosystems of Antarctica safeguarded from biological invasion face recent threats from non-native species, accelerated by increasing human activities and climate changes. Over two decades ago, the winter crane fly, Trichocera maculipennis, was first detected on King George Island. It has now successfully colonized several research stations across King George Island. To understand the origin, genetic diversity, and population structure of this Holarctic species, we conducted mitochondrial DNA cytochrome c oxidase subunit I (COI) sequence analysis across both its native and invasive ranges. In parallel, we performed microsatellite loci analysis within the invasive ranges, utilizing 12 polymorphic microsatellite markers. Furthermore, we compared body sizes among adult males and females collected from three different locations of King George Island. Our COI sequence analysis exhibited two different lineages present on King George Island. Lineage I was linked to Arctic Svalbard and Polish cave populations and Lineage II was related to Canadian Terra Nova National Park populations, implying multiple origins. Microsatellite analysis further exhibited high levels of genetic diversity and significant levels of genetic differentiation among invasive populations. Body sizes of adult T. maculipennis were significantly different among invasive populations but were not attributed to genetics. This significant genetic diversity likely facilitated the rapid colonization and establishment of T. maculipennis on King George Island, contributing to their successful invasion. Molecular analysis results revealed a substantial amount of genetic variation within invasive populations, which can serve as management units for invasive species control. Furthermore, the genetic markers we developed in the study will be invaluable tools for tracking impending invasion events and the travel routes of new individuals. Taken together, these findings illustrate the highly invasive and adaptable characteristics of T. maculipennis. Therefore, immediate action is necessary to mitigate their ongoing invasion and facilitate their eradication.
Collapse
Affiliation(s)
- Seunghyun Kang
- Korea Polar Research Institute, Incheon, 21990, South Korea
| | - Sanghee Kim
- Korea Polar Research Institute, Incheon, 21990, South Korea
| | - Kye Chung Park
- The New Zealand Institute for Plant and Food Research Ltd., Christchurch, 8140, New Zealand
| | - Andrius Petrašiūnas
- Department of Zoology, Institute of Biosciences, Vilnius University Life Sciences Center, LT 1022, Vilnius, Lithuania
| | | | - Euna Jo
- Korea Polar Research Institute, Incheon, 21990, South Korea
| | - Sung Mi Cho
- Korea Polar Research Institute, Incheon, 21990, South Korea
| | - Ji Hee Kim
- Korea Polar Research Institute, Incheon, 21990, South Korea.
| |
Collapse
|
2
|
Mugula BB, Omondi SF, Curto M, Kiboi SK, Kanya JI, Egeru A, Okullo P, Meimberg H. Microsatellites reveal divergence in population genetic diversity, and structure of osyris lanceolata (santalaceae) in Uganda and Kenya. BMC Ecol Evol 2023; 23:73. [PMID: 38062381 PMCID: PMC10704637 DOI: 10.1186/s12862-023-02182-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/13/2023] [Accepted: 11/27/2023] [Indexed: 12/18/2023] Open
Abstract
BACKGROUND Osyris lanceolata (Hochst. & Steud.) (Santalaceae) is a multipurpose plant highly valued culturally and economically in Africa. However, O. lanceolata populations have rapidly dwindled in East Africa due to overexploitation and this is believed to cause further consequences on the species' genetic diversity and structure within the region. Information regarding a species' genetic diversity and structure is necessary for conservation but this is currently lacking for O. lanceolata in Uganda and Kenya. Lack of adequate scientific data hinders conservation efforts hence threatening the species survival and livelihoods. This study investigated patterns in genetic diversity and structure of O. lanceolata in Uganda and Kenya. Ten polymorphic microsatellite loci were used to genotype 210 individuals: 96 from Ugandan and 114 from Kenyan populations. RESULTS All populations were highly polymorphic (80-100% polymorphism). A genetic differentiation was found between Kenyan and Ugandan populations. The highest genetic differentiation was among individuals and the least among populations. The Kenyan populations showed higher genetic diversity than Ugandan populations. The Ugandan populations showed more marker deviations from Hardy-Weinberg equilibrium and inbreeding coefficient. Two populations showed evidence of going through a recent bottleneck. There was significant genetic differentiation and structuring at higher K values into larger clusters and observed admixture between populations. The populations were significantly isolated by altitude as opposed to distance and climatic variables. Main barriers were associated with altitude differences. The data supports the idea of long-distance gene-flow between high altitude populations in both countries. CONCLUSION The divergence in genetic structure suggests unrecognised taxonomic units within O. lanceolata which are characteristic to lower altitudes and higher altitudes including most Kenyan populations with divergent evolutionary patterns. Geographical barriers and environmental gradients could have influenced this genetic divergence, and such patterns may escalate the species microevolutionary processes into full allopatric speciation. Further investigations into the species' genetic admixture and emerging taxonomic units are necessary to guide conservation strategies in the region.
Collapse
Affiliation(s)
- Ben Belden Mugula
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya.
- Department of Agriculture and Environmental Sciences, Bugema University, Kampala, Uganda.
- Department of Integrative Biology and Biodiversity Research, Institute of Integrative Nature Conservation Research, University of Natural Resources and Life Sciences, Vienna, Austria.
| | - S F Omondi
- Kenya Forestry Research Institute (KEFRI), Nairobi, Kenya.
| | - Manuel Curto
- CIBIO-Research Center in Biodiversity and Genetic Resources, University of Porto, Vairão, 4485-661, Portugal
- BIOPOLIS Program in Genomics, Biodiversity and Land Planning, CIBIO, Campus de Vairão, Vairão, 4485-661, Portugal
| | - Samuel Kuria Kiboi
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya
| | - James Ireri Kanya
- Department of Biology, Faculty of Science and Technology, University of Nairobi, Nairobi, Kenya
| | - Anthony Egeru
- College of Environmental and Agricultural Sciences, Makerere University, P.O. Box 7062, Kampala, Uganda
| | - Paul Okullo
- Nabuin Zonal Agricultural Research & Development Institute, National Agricultural Research Organisation (NARO), P.O. Box 132, Moroto, Uganda
| | - Harald Meimberg
- Department of Integrative Biology and Biodiversity Research, Institute of Integrative Nature Conservation Research, University of Natural Resources and Life Sciences, Vienna, Austria
| |
Collapse
|
3
|
Xu L, Yu R, Lin X, Zhang B, Li N, Lin K, Zhang D, Bai W. Different rates of pollen and seed gene flow cause branch-length and geographic cytonuclear discordance within Asian butternuts. THE NEW PHYTOLOGIST 2021; 232:388-403. [PMID: 34143496 PMCID: PMC8519134 DOI: 10.1111/nph.17564] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/22/2020] [Accepted: 06/13/2021] [Indexed: 05/03/2023]
Abstract
Topological cytonuclear discordance is commonly observed in plant phylogenetic and phylogeographic studies, yet few studies have attempted to detect two other forms of cytonuclear discordance (branch length and geographical) and to uncover the causes of the discordance. We used the whole nuclear and chloroplast genome data from 80 individual Asian butternuts to reveal the pattern and processes of cytonuclear discordance. Our findings indicate that the chloroplast genome had substantially deeper divergence (branch-length discordance) and a steeper cline in the contact zone (geographic discordance) compared with the nuclear genome. After various hypothesis have been tested, the results suggest that incomplete lineage sorting, positive selection and cytonuclear incompatibility are probably insufficient to explain this pattern. However, isolation-by-distance analysis and gene flow estimation point to a much higher level of gene flow by pollen compared with by seeds, which may have slowed down lineage divergence and mediated wider contact for nuclear genome compared with the chloroplast genome. Altogether, this study highlights a critical role of sex-biased dispersal in causing discordance between the nuclear and plastid genome of Asian butternuts. Given its ubiquity among plants, asymmetric gene flow should be given a high priority in future studies of cytonuclear discordance.
Collapse
Affiliation(s)
- Lin‐Lin Xu
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijing100875China
| | - Rui‐Min Yu
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijing100875China
| | - Xin‐Rui Lin
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijing100875China
| | - Bo‐Wen Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijing100875China
- Centre for Individualised Infection Medicine (CiiM) & TWINCOREJoint ventures between the Helmholtz‐Centre for Infection Research (HZI) and the Hannover Medical School (MHH)Hannover30625Germany
| | - Nan Li
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijing100875China
| | - Kui Lin
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijing100875China
| | - Da‐Yong Zhang
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijing100875China
| | - Wei‐Ning Bai
- State Key Laboratory of Earth Surface Processes and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijing100875China
| |
Collapse
|
4
|
Lu Z, Sun Y, Li Y, Yang Y, Wang G, Liu J. Species delimitation and hybridization history of a hazel species complex. ANNALS OF BOTANY 2021; 127:875-886. [PMID: 33564860 PMCID: PMC8225278 DOI: 10.1093/aob/mcab015] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Accepted: 02/03/2021] [Indexed: 06/01/2023]
Abstract
BACKGROUND AND AIMS Hybridization increases species adaptation and biodiversity but also obscures species boundaries. In this study, species delimitation and hybridization history were examined within one Chinese hazel species complex (Corylus chinensis-Corylus fargesii). Two species including four varieties have already been described for this complex, with overlapping distributions. METHODS A total of 322 trees from 44 populations of these four varieties across their ranges were sampled for morphological and molecular analyses. Climatic datasets based on 108 geographical locations were used to evaluate their niche differentiations. Flowering phenology was also observed for two co-occurring species or varieties. KEY RESULTS Four statistically different phenotypic clusters were revealed, but these clusters were highly inconsistent with the traditional taxonomic groups. All the clusters showed statistically distinct niches, with complete or partial geographical isolation. Only two clusters displayed a distributional overlap, but they had distinct flowering phenologies at the site where they co-occurred. Population-level evidence based on the genotypes of ten simple sequence repeat loci supported four phenotypic clusters. In addition, one cluster was shown to have an admixed genetic composition derived from the other three clusters through repeated historical hybridizations. CONCLUSIONS Based on our new evidence, it is better to treat the four clusters identified here as four independent species. One of them was shown to have an admixed genetic composition derived from the other three through repeated historical hybridizations. This study highlights the importance of applying integrative and statistical methods to infer species delimitations and hybridization history. Such a protocol should be adopted widely for future taxonomic studies.
Collapse
Affiliation(s)
- Zhiqiang Lu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China
| | - Yongshuai Sun
- CAS Key Laboratory of Tropical Forest Ecology, Xishuangbanna Tropical Botanical Garden, Chinese Academy of Sciences, Mengla, Yunnan, China
| | - Ying Li
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Yongzhi Yang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Gaini Wang
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
| | - Jianquan Liu
- State Key Laboratory of Grassland Agro-Ecosystem, Institute of Innovation Ecology & School of Life Sciences, Lanzhou University, Lanzhou, Gansu, China
- Key Laboratory for Bio-resources and Eco-environment of Ministry of Education, College of Life Sciences, Sichuan University, Chengdu, Sichuan, China
| |
Collapse
|
5
|
Zhao T, Ma W, Yang Z, Liang L, Chen X, Wang G, Ma Q, Wang L. A chromosome-level reference genome of the hazelnut, Corylus heterophylla Fisch. Gigascience 2021; 10:6237163. [PMID: 33871007 PMCID: PMC8054262 DOI: 10.1093/gigascience/giab027] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/28/2020] [Revised: 02/19/2021] [Accepted: 03/22/2021] [Indexed: 12/31/2022] Open
Abstract
BACKGROUND Corylus heterophylla Fisch. is a species of the Betulaceae family native to China. As an economically and ecologically important nut tree, C. heterophylla can survive in extremely low temperatures (-30 to -40 °C). To deepen our knowledge of the Betulaceae species and facilitate the use of C. heterophylla for breeding and its genetic improvement, we have sequenced the whole genome of C. heterophylla. FINDINGS Based on >64.99 Gb (∼175.30×) of Nanopore long reads, we assembled a 370.75-Mb C. heterophylla genome with contig N50 and scaffold N50 sizes of 2.07 and 31.33 Mb, respectively, accounting for 99.23% of the estimated genome size (373.61 Mb). Furthermore, 361.90 Mb contigs were anchored to 11 chromosomes using Hi-C link data, representing 97.61% of the assembled genome sequences. Transcriptomes representing 4 different tissues were sequenced to assist protein-coding gene prediction. A total of 27,591 protein-coding genes were identified, of which 92.02% (25,389) were functionally annotated. The phylogenetic analysis showed that C. heterophylla is close to Ostrya japonica, and they diverged from their common ancestor ∼52.79 million years ago. CONCLUSIONS We generated a high-quality chromosome-level genome of C. heterophylla. This genome resource will promote research on the molecular mechanisms of how the hazelnut responds to environmental stresses and serves as an important resource for genome-assisted improvement in cold and drought resistance of the Corylus genus.
Collapse
Affiliation(s)
- Tiantian Zhao
- Research Institute of Forestry, Chinese Academy of Forestry/Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, No.1 Dongxiaofu, Xiangshan Road, Haidian District, Beijing 100091, China.,National Hazelnut Industry Innovation Alliance/Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Xiangshan Road, Haidian District, Beijing 100091, China
| | - Wenxu Ma
- Research Institute of Forestry, Chinese Academy of Forestry/Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, No.1 Dongxiaofu, Xiangshan Road, Haidian District, Beijing 100091, China.,National Hazelnut Industry Innovation Alliance/Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Xiangshan Road, Haidian District, Beijing 100091, China
| | - Zhen Yang
- Research Institute of Forestry, Chinese Academy of Forestry/Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, No.1 Dongxiaofu, Xiangshan Road, Haidian District, Beijing 100091, China.,National Hazelnut Industry Innovation Alliance/Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Xiangshan Road, Haidian District, Beijing 100091, China
| | - Lisong Liang
- Research Institute of Forestry, Chinese Academy of Forestry/Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, No.1 Dongxiaofu, Xiangshan Road, Haidian District, Beijing 100091, China.,National Hazelnut Industry Innovation Alliance/Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Xiangshan Road, Haidian District, Beijing 100091, China
| | - Xin Chen
- National Hazelnut Industry Innovation Alliance/Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Xiangshan Road, Haidian District, Beijing 100091, China.,Shandong Institute of Pomology, Shandong Academy of Agricultural Sciences, No. 66 Longtan Road, Taishan District, Taian 271000, China
| | - Guixi Wang
- Research Institute of Forestry, Chinese Academy of Forestry/Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, No.1 Dongxiaofu, Xiangshan Road, Haidian District, Beijing 100091, China.,National Hazelnut Industry Innovation Alliance/Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Xiangshan Road, Haidian District, Beijing 100091, China
| | - Qinghua Ma
- Research Institute of Forestry, Chinese Academy of Forestry/Key Laboratory of Tree Breeding and Cultivation of the State Forestry and Grassland Administration, No.1 Dongxiaofu, Xiangshan Road, Haidian District, Beijing 100091, China.,National Hazelnut Industry Innovation Alliance/Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Xiangshan Road, Haidian District, Beijing 100091, China
| | - Lujun Wang
- National Hazelnut Industry Innovation Alliance/Hazelnut Engineering and Technical Research Center of the State Forestry and Grassland Administration, Xiangshan Road, Haidian District, Beijing 100091, China.,Anhui Academy of Forestry, No. 820 Changjiangxi Road, Shushan District, Hefei 230031, China
| |
Collapse
|
6
|
Development of SSR markers based on transcriptome data and association mapping analysis for fruit shell thickness associated traits in oil palm ( Elaeis guineensis Jacq.). 3 Biotech 2020; 10:280. [PMID: 32537380 DOI: 10.1007/s13205-020-02269-3] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/23/2020] [Accepted: 05/20/2020] [Indexed: 10/24/2022] Open
Abstract
Present study mainly aimed to ascertain the distribution characteristics of gene-based microsatellite loci and to develop polymorphic SSR markers from the already available transcriptome data of Elaeis guineensis Jacq, an important oil crop. From this study, we identified the sum of 5791 SSRs across 51,425 unigenes from the transcripts of oil palm. We were able to evaluate 331primer pairs and characterized 183 polymorphic gene-based SSR markers. We identified a total of 506 alleles from the 183 polymorphic SSR loci, with an average of 2.77 alleles per locus. The characterized gene-based SSR markers from the transcriptome data of oil palm exhibited moderate levels of polymorphism with a significant level of heterozygosity ranges from 0.096 to 0.594 (mean = 0.336 ± 0.11). Among the identified SSR markers, sixty polymorphic markers were used to analyze genotypes of 55 oil palm accessions selected from three different provinces of China. Association mapping analysis provided the information of four markers that are associated with fruit shell thickness trait of oil palm. Among the four markers identified from association analysis, one SSR marker obtained from Unigene17150 is strictly associated with the oil palm fruit shell thickness trait.
Collapse
|
7
|
Yao YX, Shang XP, Yang J, Lin RZ, Huai WX, Zhao WX. Genetic Variation May Have Promoted the Successful Colonization of the Invasive Gall Midge, Obolodiplosis robiniae, in China. Front Genet 2020; 11:387. [PMID: 32362914 PMCID: PMC7180195 DOI: 10.3389/fgene.2020.00387] [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: 01/10/2020] [Accepted: 03/27/2020] [Indexed: 11/13/2022] Open
Abstract
Invasive species often cause serious economic and ecological damage. Despite decades of extensive impacts of invasives on bio-diversity and agroforestry, the mechanisms underlying the genetic adaptation and rapid evolution of invading populations remain poorly understood. The black locust gall midge, Obolodiplosis robiniae, a highly invasive species that originated in North America, spread widely throughout Asia and Europe in the past decade. Here, we used 11 microsatellite DNA markers to analyze the genetic variation of 22 O. robiniae populations in China (the introduced region) and two additional US populations (the native region). A relatively high level of genetic diversity was detected among the introduced populations, even though they exhibited lower diversity than the native US populations. Evidence for genetic differentiation among the introduced Chinese populations was also found based on the high Fst value compared to the relatively low among the native US populations. Phylogenetic trees, structure graphical output, and principal coordinate analysis plots suggested that the Chinese O. robiniae populations (separated by up to 2,540 km) cluster into two main groups independent of geographical distance. Genetic variation has been observed to increase rapidly during adaptation to a new environment, possibly contributing to population establishment and spread. Our results provide insights into the genetic mechanisms underlying successful invasion, and identify factors that have contributed to colonization by an economically important pest species in China. In addition, the findings improve our understanding of the role that genetic structure plays during invasion by O. robiniae.
Collapse
Affiliation(s)
| | | | | | | | | | - Wen-Xia Zhao
- Key Laboratory of Forest Protection of National Forestry and Grassland Administration/Research Institute of Forest Ecology, Environment and Protection, Chinese Academy of Forestry, Beijing, China
| |
Collapse
|
8
|
Kahraman K, Lucas SJ. Comparison of different annotation tools for characterization of the complete chloroplast genome of Corylus avellana cv Tombul. BMC Genomics 2019; 20:874. [PMID: 31747873 PMCID: PMC6865063 DOI: 10.1186/s12864-019-6253-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2019] [Accepted: 10/31/2019] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Several bioinformatics tools have been designed for assembly and annotation of chloroplast (cp) genomes, making it difficult to decide which is most useful and applicable to a specific case. The increasing number of plant genomes provide an opportunity to accurately obtain cp genomes from whole genome shotgun (WGS) sequences. Due to the limited genetic information available for European hazelnut (Corylus avellana L.) and as part of a genome sequencing project, we analyzed the complete chloroplast genome of the cultivar 'Tombul' with multiple annotation tools. RESULTS Three different annotation strategies were tested, and the complete cp genome of C. avellana cv Tombul was constructed, which was 161,667 bp in length, and had a typical quadripartite structure. A large single copy (LSC) region of 90,198 bp and a small single copy (SSC) region of 18,733 bp were separated by a pair of inverted repeat (IR) regions of 26,368 bp. In total, 125 predicted functional genes were annotated, including 76 protein-coding, 25 tRNA, and 4 rRNA unique genes. Comparative genomics indicated that the cp genome sequences were relatively highly conserved in species belonging to the same order. However, there were still some variations, especially in intergenic regions, that could be used as molecular markers for analyses of phylogeny and plant identification. Simple sequence repeat (SSR) analysis showed that there were 83 SSRs in the cp genome of cv Tombul. Phylogenetic analysis suggested that C. avellana cv Tombul had a close affinity to the sister group of C. fargesii and C. chinensis, and then a closer evolutionary relationship with Betulaceae family than other species of Fagales. CONCLUSION In this study, the complete cp genome of Corylus avellana cv Tombul, the most widely cultivated variety in Turkey, was obtained and annotated, and additionally phylogenetic relationships were predicted among Fagales species. Our results suggest a very accurate assembly of chloroplast genome from next generation whole genome shotgun (WGS) sequences. Enhancement of taxon sampling in Corylus species provide genomic insights into phylogenetic analyses. The nucleotide sequences of cv Tombul cp genomes can provide comprehensive genetic insight into the evolution of genus Corylus.
Collapse
Affiliation(s)
- Kadriye Kahraman
- Faculty of Engineering and Natural Sciences, Sabanci University, 34956, Istanbul, Turkey
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Sabanci University, 34956, Istanbul, Turkey
| | - Stuart James Lucas
- Sabanci University Nanotechnology Research and Application Centre (SUNUM), Sabanci University, 34956, Istanbul, Turkey.
| |
Collapse
|
9
|
Narrow gene pool can threaten the survival of Calamus nagbettai R. R. Fernald & Dey: a highly, endemic dioecious rattan species in the Western Ghats of India. J Genet 2019. [DOI: 10.1007/s12041-019-1147-5] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/25/2022]
|
10
|
Dev SA, Balakrishnan S, Kurian A, Sreekumar VB. Narrow gene pool can threaten the survival of Calamus nagbettai R. R. Fernald & Dey: a highly, endemic dioecious rattan species in the Western Ghats of India. J Genet 2019; 98:100. [PMID: 31767820] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 06/10/2023]
Abstract
Rattans, the spiny climbing palms of Arecaceae (Palmae) family exhibit high endemism to the biodiversity hot spots in India. Of the five rattan genera, Calamus is the only genus found in peninsular India with 15 of 21 species, endemic to the Western Ghats. The extensive utilization of rattans owing to their strength, durability and huge demand has resulted in depletion of their natural resources. Of the 15 endemic species, C. nagbettai is the most affected species on account of endemism, low population size and restricted distribution with fragmented populations. The present study revealed high amount of genetic diversity in the surviving scattered populations of the species using microsatellite markers. High gene flow (Nm = 1.498) observed across the populations resulted in low genetic differentiation (14%). A clear genetic admixture could be seen in Kerala as well as one of the Karnataka's populations while the remaining two populations were genetically distinct. UPGMA, PCoA and STRUCTURE analyses showed significantly different genetic composition in Kerala population compared to other populations. Kerala and Karnataka populations of C. nagbettai were also unique in their genetic structure and allelic composition. Therefore, effective management and conservation strategies have to be implemented to preserve the rarealleles with adaptive potential to protect this economically valuable Calamus species from endangerment. Over exploitation, low seed set and poor regeneration, as well as habitat fragmentation can further threaten the survival of this endemic, narrowly distributed dioecious rattan species in the Western Ghats region.
Collapse
Affiliation(s)
- Suma Arun Dev
- Forest Genetics and Biotechnology Division, Kerala Forest Research Institute, Peechi, Thrissur 680 653, India.
| | | | | | | |
Collapse
|
11
|
Genetic Diversity and Population Structure of Bermudagrass [Cynodon dactylon (L.) Pers.] along Latitudinal Gradients and the Relationship with Polyploidy Level. DIVERSITY 2019. [DOI: 10.3390/d11080135] [Citation(s) in RCA: 8] [Impact Index Per Article: 1.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
Abstract
Understanding the population genetic pattern and process of gene flow requires a detailed knowledge of how landscape characteristics structure populations. Although Cynodon dactylon (L.) Pers. (common bermudagrass) is widely distributed in the world, information on its genetic pattern and population structure along latitudinal gradients is limited. We tried to estimate the genetic diversity and genetic structure of C. dactylon along a latitudinal gradient across China. Genetic diversity among different ploidy levels was also compared in the study. The material used consisted of 296 C. dactylon individuals sampled from 16 geographic sites from 22°35′ N to 36°18′ N. Genetic diversity was estimated using 153 expressed sequence tag-derived simple sequence repeat (EST-SSR) loci. Higher within-population genetic diversity appeared at low-latitude, as well as having positive correlation with temperature and precipitation. The genetic diversity increased with the ploidy level of C. dactylon, suggesting polyploidy creates higher genetic diversity. No isolation by distance and notable admixture structure existed among populations along latitudes. Both seed dispersal (or vegetative organs) and extrinsic pollen played important roles for gene flow in shaping the spatial admixture population structure of C. dactylon along latitudes. In addition, populations were separated into three clusters according to ploidy levels. C. dactylon has many such biological characters of perennial growth, wind-pollination, polyploidy, low genetic differentiation among populations, sexual and asexual reproduction leading to higher genetic diversity, which gives it strong adaptability with its genetic patterns being very complex across all the sampled latitudes. The findings of this study are related to landscape population evolution, polyploidy speciation, preservation, and use of bermudagrass breeding.
Collapse
|
12
|
Thongkumkoon P, Chomdej S, Kampuansai J, Pradit W, Waikham P, Elliott S, Chairuangsri S, Shannon DP, Wangpakapattanawong P, Liu A. Genetic assessment of three Fagaceae species in forest restoration trials. PeerJ 2019; 7:e6958. [PMID: 31179177 PMCID: PMC6544010 DOI: 10.7717/peerj.6958] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 04/14/2019] [Indexed: 11/20/2022] Open
Abstract
Restoring isolated patches of forest ecosystems in degraded landscapes could potentially lead to genetic loss and inbreeding. Therefore, this study determined the occurrence of genetic diversity among the tree species Castanopsis tribuloides, C. calathiformis, and Lithocarpus polystachyus all of which were proven previously to be effective native tree species in the restoration of upland evergreen forests in northern Thailand when using the seed sample collection method. We tested our hypothesis as to whether the genetic diversity of a plant population that had been planted from the seeds of 4–6 adult trees would be lower and whether incidences of fixation index (Fis) would be higher among the second generation seedlings of these three Fagaceae species in isolated forest restoration trial plots. Microsatellite primers were selected from the entire genome sequence of C. tribuloides and the genetic sequences of C. tribuloides, L. polystachyus, and C. calathiformis were analyzed. Our results indicated a high degree of genetic diversity (He) in C. tribuloides (0.736) and C. calathiformis (0.481); however, a low level of genetic diversity was observed in L. polystachyus (0.281) within the restored forest. The fixation index for the second generation of L. polystachyus and C. calathiformis in the restored forest showed evidence of inbreeding. These results imply the efficiency of the seed sample collection method and verify that it does not reduce the level of genetic diversity in C. tribuloides and C. calathiformis. However, it may result in incidences of an inbreeding phenomena, suggesting the need to increase the number of adult trees used at the seed collection stage.
Collapse
Affiliation(s)
- Patcharawadee Thongkumkoon
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Environmental Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Siriwadee Chomdej
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Jatupol Kampuansai
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Waranee Pradit
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Pimubon Waikham
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Stephen Elliott
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Forest Restoration Research Unit, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Sutthathorn Chairuangsri
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Forest Restoration Research Unit, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Dia Panitnard Shannon
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Forest Restoration Research Unit, Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Prasit Wangpakapattanawong
- Department of Biology, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand.,Environmental Science Research Center, Faculty of Science, Chiang Mai University, Chiang Mai, Thailand
| | - Aizhong Liu
- Key Laboratory for Forest Resource Conservation and Utilization in the Southwest Mountains of China (Ministry of Education), Southwest Forestry University, Kunming, China
| |
Collapse
|
13
|
Tanhuanpää P, Heinonen M, Bitz L, Rokka VM. Genetic diversity and structure in the northern populations of European hazelnut ( Corylus avellana L.). Genome 2019; 62:537-548. [PMID: 31170350 DOI: 10.1139/gen-2018-0193] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
European hazelnut (Corylus avellana L.) is a strictly cross-pollinated diploid tree species, which has its northernmost populations in Fennoscandia, and it was one of the first species to recolonize northern Europe after the last ice age. Hazelnut produces edible nuts in Finland but nowadays they are underutilized as food, and currently no breeding programmes exist. In the present study, 300 hazelnut specimens were collected from 20 different locations (= populations) in Finland, and they were genetically analyzed using nine simple sequence repeat (SSR) markers. Most of the genetic diversity existed within populations (83%). According to different genetic analyses (STRUCTURE, principal coordinates analysis, and clustering), a general lack of structure was observed, suggesting extensive gene flow among hazelnuts between 17 investigated populations. However, genetic structuring was clearly observed in three populations: Hakavuori, Mustiala, and Pähkinämäki, which might have become isolated due to geographical barriers that kept them separate, diminishing gene flow from other populations. Studying the diversity of European hazelnut is of great interest for understanding population genetics of a species distributed in its marginal areas in the north, and the results are also valuable for further uses in plant conservation, selection, and possible future breeding actions in Finland.
Collapse
Affiliation(s)
- Pirjo Tanhuanpää
- Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland.,Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
| | - Maarit Heinonen
- Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland.,Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
| | - Lidija Bitz
- Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland.,Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
| | - Veli-Matti Rokka
- Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland.,Production Systems, Natural Resources Institute Finland (Luke), FI-31600 Jokioinen, Finland
| |
Collapse
|
14
|
Assessment of Genetic Diversity and Population Genetic Structure of Norway Spruce (Picea abies (L.) Karsten) at Its Southern Lineage in Europe. Implications for Conservation of Forest Genetic Resources. FORESTS 2019. [DOI: 10.3390/f10030258] [Citation(s) in RCA: 23] [Impact Index Per Article: 4.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 01/25/2023]
Abstract
In the present paper we studied the genetic diversity and genetic structure of five Norway spruce (Picea abies (L.) Karsten) natural populations situated in Serbia, belonging to the southern lineage of the species at the southern margin of the species distribution range. Four populations occur as disjunct populations on the outskirts of the Dinaric Alps mountain chain, whereas one is located at the edge of Balkan Mountain range and, therefore, can be considered as ecologically marginal due to drier climatic conditions occurring in this region. Due to the negative effect of biotic and abiotic stress factors, the sustainability of these populations is endangered, making conservation of their genetic resources one of the key measures of Norway spruce persistence in Serbia under climatic changes. The insight on genetic diversity and genetic structure of the studied spruce populations can provide the information required for the initiation of programs aimed at the conservation and utilization of spruce genetic resources at the rear edge of species environmental limits. Norway spruce genetic variation and population genetic structure were estimated using eight EST-SSR markers. The results showed that mean expected heterozygosity was 0.616 and allelic richness 10.22. Genetic differentiation among populations was low (Fst = 0.007). No recent bottleneck effect or isolation by distance were detected. Bayesian clustering, obtained with STRUCTURE, grouped the populations into two genetic clusters, whereas UPGMA analysis distinguished three main groups approximately in line with the geographic area of occurrence. Based on the study results and the EUFORGEN Pan-European strategy for genetic conservation of forest trees, the establishment of additional dynamic gene conservation units must be considered in Serbia in order to protect the adaptive and neutral genetic diversity of the species.
Collapse
|
15
|
Purwoko D, Cartealy IC, Tajuddin T, Dinarti D, Sudarsono S. SSR identification and marker development for sago palm based on NGS genome data. BREEDING SCIENCE 2019; 69:1-10. [PMID: 31086478 PMCID: PMC6507712 DOI: 10.1270/jsbbs.18061] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 05/11/2018] [Accepted: 09/26/2018] [Indexed: 06/09/2023]
Abstract
Sago palm (Metroxylon sagu Rottb.) is one of the most productive carbohydrate-producing crops. Unfortunately, only limited information regarding sago palm genetics is available. This study aimed to develop simple sequence repeat (SSR) markers using sago palm NGS genomic data and use these markers to evaluate the genetic diversity of sago palm from Indonesia. De novo assembly of partial sago palm genomic data and subsequent SSR mining identified 29,953 contigs containing 31,659 perfect SSR loci and 31,578 contigs with 33,576 imperfect SSR loci. The perfect SSR loci density was 132.57/Mb, and AG, AAG and AAAT were the most frequent SSR motifs. Five hundred perfect SSR loci were randomly selected and used for designing SSR primers; 93 SSR primer pairs were identified. After synteny analysis using rice genome sequences, 20 primer pairs were validated using 11 sago palm accessions, and seven primers generated polymorphic alleles. Genetic diversity analysis of 41 sago palm accessions from across Indonesia using polymorphic SSR loci indicated the presence of three clusters. These results demonstrated the success of SSR identification and marker development for sago palm based on NGS genome data, which can be further used for assisting sago palm breeding in the future.
Collapse
Affiliation(s)
- Devit Purwoko
- Laboratory for Biotechnology, Agroindustrial Technology and Biotechnology, Agency for Assessment and Application of Technology,
Build. 630 Puspiptek Area Setu, South Tangerang 15314, Banten,
Indonesia
| | - Imam Civi Cartealy
- Laboratory for Biotechnology, Agroindustrial Technology and Biotechnology, Agency for Assessment and Application of Technology,
Build. 630 Puspiptek Area Setu, South Tangerang 15314, Banten,
Indonesia
| | - Teuku Tajuddin
- Laboratory for Biotechnology, Agroindustrial Technology and Biotechnology, Agency for Assessment and Application of Technology,
Build. 630 Puspiptek Area Setu, South Tangerang 15314, Banten,
Indonesia
| | - Diny Dinarti
- Plant Molecular Biology Laboratory, Department of Agronomy and Horticulture, Bogor Agricultural University,
Darmaga, Bogor 16680, West Java,
Indonesia
| | - Sudarsono Sudarsono
- Plant Molecular Biology Laboratory, Department of Agronomy and Horticulture, Bogor Agricultural University,
Darmaga, Bogor 16680, West Java,
Indonesia
| |
Collapse
|
16
|
Tan J, Guo JJ, Yin MY, Wang H, Dong WP, Zeng J, Zhou SL. Next Generation Sequencing-Based Molecular Marker Development: A Case Study in Betula Alnoides. Molecules 2018; 23:E2963. [PMID: 30428601 PMCID: PMC6278481 DOI: 10.3390/molecules23112963] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2018] [Revised: 11/09/2018] [Accepted: 11/11/2018] [Indexed: 11/25/2022] Open
Abstract
Betula alnoides is a fast-growing valuable indigenous tree species with multiple uses in the tropical and warm subtropical regions in South-East Asia and southern China. It has been proved to be tetraploid in most parts of its distribution in China. In the present study, next generation sequencing (NGS) technology was applied to develop numerous SSR markers for B. alnoides, and 64,376 contig sequences of 106,452 clean reads containing 164,357 candidate SSR loci were obtained. Among the derived SSR repeats, mono-nucleotide was the main type (77.05%), followed by di- (10.18%), tetra- (6.12%), tri- (3.56%), penta- (2.14%) and hexa-nucleotide (0.95%). The short nucleotide sequence repeats accounted for 90.79%. Among the 291 repeat motifs, AG/CT (46.33%) and AT/AT (44.15%) were the most common di-nucleotide repeats, while AAT/ATT (48.98%) was the most common tri-nucleotide repeats. A total of 2549 primer sets were designed from the identified putative SSR regions of which 900 were randomly selected for evaluation of amplification successfulness and detection of polymorphism if amplified successfully. Three hundred and ten polymorphic markers were obtained through testing with 24 individuals from B. alnoides natural forest in Jingxi County, Guangxi, China. The number of alleles (NA) of each marker ranged from 2 to 19 with a mean of 5.14. The observed (HO) and expected (HE) heterozygosities varied from 0.04 to 1.00 and 0.04 to 0.92 with their means being 0.64 and 0.57, respectively. Shannon-Wiener diversity index (I) ranged from 0.10 to 2.68 with a mean of 1.12. Cross-species transferability was further examined for 96 pairs of SSR primers randomly selected, and it was found that 48.96⁻84.38% of the primer pairs could successfully amplify each of six related Betula species. The obtained SSR markers can be used to study population genetics and molecular marker assisted breeding, particularly genome-wide association study of these species in the future.
Collapse
Affiliation(s)
- Jing Tan
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
| | - Jun-Jie Guo
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
| | - Ming-Yu Yin
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
| | - Huan Wang
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
| | - Wen-Pan Dong
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| | - Jie Zeng
- Research Institute of Tropical Forestry, Chinese Academy of Forestry, Guangzhou 510520, China.
| | - Shi-Liang Zhou
- State Key Laboratory of Systematic and Evolutionary Botany, Institute of Botany, Chinese Academy of Sciences, Beijing 100093, China.
| |
Collapse
|
17
|
Yang Z, Zhao T, Ma Q, Liang L, Wang G. Comparative Genomics and Phylogenetic Analysis Revealed the Chloroplast Genome Variation and Interspecific Relationships of Corylus (Betulaceae) Species. FRONTIERS IN PLANT SCIENCE 2018; 9:927. [PMID: 30038632 PMCID: PMC6046460 DOI: 10.3389/fpls.2018.00927] [Citation(s) in RCA: 37] [Impact Index Per Article: 6.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/20/2018] [Accepted: 06/11/2018] [Indexed: 05/07/2023]
Abstract
Corylus L. is an economically and phylogenetically important genus in the family Betulaceae. Taxonomic and phylogenetic relationships of Corylus species have long been controversial for lack of effective molecular markers. In this study, the complete chloroplast (cp) genomes of six Corylus species were assembled and characterized using next-generation sequencing. We compared the genome features, repeat sequences, sequence divergence, and constructed the phylogenetic relationships of the six Corylus species. The results indicated that Corylus cp genomes were typical of the standard double-stranded DNA molecule, ranging from 160,445 base pairs (bp) (C. ferox var. thibetca) to 161,621 bp (C. yunnanensis) in length. Each genome contained a pair of inverted repeats (IRs), a large single-copy (LSC) region and a small single-copy (SSC) region. Each of the six cp genomes possessed 113 unique genes arranged in the same order, including 80 protein-coding, 29 tRNA, and 4 rRNA genes. C. yunnanensis contained the highest number of repeat sequences, and the richest SSRs in six cp genomes were A/T mononucleotides. Comparative analyses of six Corylus cp genomes revealed four hotspot regions (trnH-psbA, rpoB-trnC, trnF-ndhJ, and rpl32-trnL) that could be used as potential molecular markers. Phylogenetic analyses of the complete chloroplast genomes and 80 protein-coding genes exhibited nearly identical topologies that strongly supported the monophyly of Corylus and simultaneously revealed the generic relationships among Betulaceae. The availability of these genomes can offer valuable genetic information for further taxonomy, phylogeny, and species delimitation in Corylus or even Betulaceae plants.
Collapse
Affiliation(s)
| | | | | | | | - Guixi Wang
- *Correspondence: Tiantian Zhao, Guixi Wang,
| |
Collapse
|
18
|
Genetic diversity and population structure of Chinese natural bermudagrass [Cynodon dactylon (L.) Pers.] germplasm based on SRAP markers. PLoS One 2017; 12:e0177508. [PMID: 28493962 PMCID: PMC5426801 DOI: 10.1371/journal.pone.0177508] [Citation(s) in RCA: 25] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/02/2016] [Accepted: 04/30/2017] [Indexed: 01/01/2023] Open
Abstract
Bermudagrass [Cynodon dactylon (L.) Pers.], an important turfgrass used in public parks, home lawns, golf courses and sports fields, is widely distributed in China. In the present study, sequence-related amplified polymorphism (SRAP) markers were used to assess genetic diversity and population structure among 157 indigenous bermudagrass genotypes from 20 provinces in China. The application of 26 SRAP primer pairs produced 340 bands, of which 328 (96.58%) were polymorphic. The polymorphic information content (PIC) ranged from 0.36 to 0.49 with a mean of 0.44. Genetic distance coefficients among accessions ranged from 0.04 to 0.61, with an average of 0.32. The results of STRUCTURE analysis suggested that 157 bermudagrass accessions can be grouped into three subpopulations. Moreover, according to clustering based on the unweighted pair-group method of arithmetic averages (UPGMA), accessions were divided into three major clusters. The UPGMA dendrogram revealed that accessions from identical or adjacent areas were generally, but not entirely, clustered into the same cluster. Comparison of the UPGMA dendrogram and the Bayesian STRUCTURE analysis showed general agreement between the population subdivisions and the genetic relationships among accessions. Principal coordinate analysis (PCoA) with SRAP markers revealed a similar grouping of accessions to the UPGMA dendrogram and STRUCTUE analysis. Analysis of molecular variance (AMOVA) indicated that 18% of total molecular variance was attributed to diversity among subpopulations, while 82% of variance was associated with differences within subpopulations. Our study represents the most comprehensive investigation of the genetic diversity and population structure of bermudagrass in China to date, and provides valuable information for the germplasm collection, genetic improvement, and systematic utilization of bermudagrass.
Collapse
|
19
|
Genetic diversity of SSR markers in wild populations of Tapiscia sinensis, an endangered tree species. BIOCHEM SYST ECOL 2016. [DOI: 10.1016/j.bse.2016.08.004] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/24/2022]
|
20
|
Zhai F, Mao J, Liu J, Peng X, Han L, Sun Z. Male and Female Subpopulations of Salix viminalis Present High Genetic Diversity and High Long-Term Migration Rates between Them. FRONTIERS IN PLANT SCIENCE 2016; 7:330. [PMID: 27047511 PMCID: PMC4796010 DOI: 10.3389/fpls.2016.00330] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/24/2015] [Accepted: 03/04/2016] [Indexed: 05/31/2023]
Abstract
Dioecy distributed in 157 flowering plant families and 959 flowering plant genera. Morphological and physiological differences between male and female plants have been studied extensively, but studies of sex-specific genetic diversity are relatively scarce in dioecious plants. In this study, 20 SSR loci were employed to examine the genetic variance of male subpopulations and female subpopulations in Salix viminalis. The results showed that all of the markers were polymorphic (Na = 14.15, He = 0.7566) and workable to reveal the genetic diversity of S. viminalis. No statistically significant difference was detected between male and female subpopulations, but the average genetic diversity of male subpopulations (Na = 7.12, He = 0.7071) and female subpopulations (Na = 7.31, He = 0.7226) were high. Under unfavorable environments (West Liao basin), the genetic diversity between male and female subpopulations was still not significantly different, but the genetic diversity of sexual subpopulations were lower. The differentiation of the ten subpopulations in S. viminalis was moderate (FST = 0.0858), which was conformed by AMOVA that most of genetic variance (94%) existed within subpopulations. Pairwise FST indicated no differentiation between sexual subpopulations, which was accompanied by high long-term migrate between them (M = 0.73~1.26). However, little recent migration was found between sexual subpopulations. Therefore, artificial crossing or/and transplantation by cutting propagation should be carried out so as to increase the migration during the process of ex situ conservation.
Collapse
Affiliation(s)
- Feifei Zhai
- State Key Laboratory of Tree Genetic and Breeding; Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry AdministrationBeijing, China
| | - Jinmei Mao
- State Key Laboratory of Tree Genetic and Breeding; Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry AdministrationBeijing, China
- Research Institute of Economic Forest, Xinjiang Academy of ForestryXinjiang, China
| | - Junxiang Liu
- State Key Laboratory of Tree Genetic and Breeding; Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry AdministrationBeijing, China
| | - Xiangyong Peng
- State Key Laboratory of Tree Genetic and Breeding; Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry AdministrationBeijing, China
| | - Lei Han
- State Key Laboratory of Tree Genetic and Breeding; Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry AdministrationBeijing, China
| | - Zhenyuan Sun
- State Key Laboratory of Tree Genetic and Breeding; Research Institute of Forestry, Chinese Academy of ForestryBeijing, China
- Key Laboratory of Tree Breeding and Cultivation, State Forestry AdministrationBeijing, China
| |
Collapse
|