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Schwabenlander MD, Bartz JC, Carstensen M, Fameli A, Glaser L, Larsen RJ, Li M, Shoemaker RL, Rowden G, Stone S, Walter WD, Wolf TM, Larsen PA. Prion forensics: a multidisciplinary approach to investigate CWD at an illegal deer carcass disposal site. Prion 2024; 18:72-86. [PMID: 38676289 PMCID: PMC11057675 DOI: 10.1080/19336896.2024.2343298] [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: 01/15/2024] [Accepted: 04/10/2024] [Indexed: 04/28/2024] Open
Abstract
Infectious prions are resistant to degradation and remain infectious in the environment for several years. Chronic wasting disease (CWD) has been detected in cervids inhabiting North America, the Nordic countries, and South Korea. CWD-prion spread is partially attributed to carcass transport and disposal. We employed a forensic approach to investigate an illegal carcass dump site connected with a CWD-positive herd. We integrated anatomic, genetic, and prion amplification methods to discover CWD-positive remains from six white-tailed deer (Odocoileus virginianus) and, using microsatellite markers, confirmed a portion originated from the CWD-infected herd. This approach provides a foundation for future studies of carcass prion transmission risk.
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Affiliation(s)
- Marc D. Schwabenlander
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Jason C. Bartz
- Minnesota Center for Prion Research and Outreach, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Michelle Carstensen
- Department of Medical Microbiology and Immunology, School of Medicine, Creighton University, Omaha, NE, USA
| | - Alberto Fameli
- Minnesota Department of Natural Resources, Wildlife Health Program, Forest Lake, MN, USA
| | - Linda Glaser
- Pennsylvania Cooperative Fish & Wildlife Research Unit, The Pennsylvania State University, University Park, PA, USA
| | - Roxanne J. Larsen
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Manci Li
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Rachel L. Shoemaker
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Gage Rowden
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Suzanne Stone
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - W. David Walter
- Minnesota Board of Animal Health, Farmed Cervidae Program, St. Paul, MN, USA
| | - Tiffany M. Wolf
- U.S. Geological Survey, Pennsylvania Cooperative Fish and Wildlife Research Unit, The Pennsylvania State University, University Park, PA, USA
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
| | - Peter A. Larsen
- Department of Veterinary and Biomedical Sciences, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
- Department of Veterinary Population Medicine, College of Veterinary Medicine, University of Minnesota, St. Paul, MN, USA
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Wu Y, Yang K, Wen X, Sun Y. Genetic Differentiation and Relationship among Castanopsis chinensis, C. qiongbeiensis, and C. glabrifolia (Fagaceae) as Revealed by Nuclear SSR Markers. PLANTS (BASEL, SWITZERLAND) 2024; 13:1486. [PMID: 38891296 PMCID: PMC11175008 DOI: 10.3390/plants13111486] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/19/2024] [Revised: 05/17/2024] [Accepted: 05/22/2024] [Indexed: 06/21/2024]
Abstract
Castanopsis chinensis (Spreng.) Hance is widespread in the subtropical forests of China. Castanopsis qiongbeiensis G.A. Fu and Castanopsis glabrifolia J. Q. Li & Li Chen are limited to the coastal beaches of Wenchang county in the northeast of Hainan Island, and have similar morphological characteristics to C. chinensis. It is supposed that C. qiongbeiensis and C. glabrifolia are closely related to C. chinensis. In the present study, the genetic differentiation, gene flow, and genetic relationship of C. chinensis, C. qiongbeiensis, and C. glabrifolia were investigated by using 15 nuclear microsatellite markers; a total of 308 individuals from 17 populations were sampled in the three species. The allelic variation of nuclear microsatellites revealed moderate but significant genetic differentiation (FCT = 0.076) among C. chinensis, C. qiongbeiensis, and C. glabrifolia, and genetic differentiation between C. chinensis and C. glabrifolia was larger than that between C. chinensis and C. qiongbeiensis. Demographic simulations revealed unidirectional gene flow from C. chinensis to C. glabrifolia and C. qiongbeiensis, which highlight dispersal from mainland to island. The isolation effect of Qiongzhou Strait increased the genetic differentiation of species on both sides of the strait; however, the differentiation was diminished by gene flow that occurred during the historical period when Hainan Island was connected to mainland China. Our results supported the argument that C. glabrifolia should be considered an independent species and argued that C. qiongbeiensis should be regarded as an incipient species and independent conservation unit.
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Affiliation(s)
- Yang Wu
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Y.W.); (K.Y.)
| | - Kai Yang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Y.W.); (K.Y.)
| | - Xiangying Wen
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Ye Sun
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (Y.W.); (K.Y.)
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Ma Y, Liu P, Li Z, Yue Y, Zhao Y, He J, Zhao J, Song X, Wang J, Liu Q, Lu L. High genetic diversity of the himalayan marmot relative to plague outbreaks in the Qinghai-Tibet Plateau, China. BMC Genomics 2024; 25:262. [PMID: 38459433 PMCID: PMC10921737 DOI: 10.1186/s12864-024-10171-y] [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: 09/17/2023] [Accepted: 02/28/2024] [Indexed: 03/10/2024] Open
Abstract
Plague, as an ancient zoonotic disease caused by Yersinia pestis, has brought great disasters. The natural plague focus of Marmota himalayana in the Qinghai-Tibet Plateau is the largest, which has been constantly active and the leading source of human plague in China for decades. Understanding the population genetics of M. himalayana and relating that information to the biogeographic distribution of Yersinia pestis and plague outbreaks are greatly beneficial for the knowledge of plague spillover and arecrucial for pandemic prevention. In the present research, we assessed the population genetics of M. himalayana. We carried out a comparative study of plague outbreaks and the population genetics of M. himalayana on the Qinghai-Tibet Plateau. We found that M. himalayana populations are divided into two main clusters located in the south and north of the Qinghai-Tibet Plateau. Fourteen DFR genomovars of Y. pestis were found and exhibited a significant region-specific distribution. Additionally, the increased genetic diversity of plague hosts is positively associated with human plague outbreaks. This insight gained can improve our understanding of biodiversity for pathogen spillover and provide municipally directed targets for One Health surveillance development, which will be an informative next step toward increased monitoring of M. himalayana dynamics.
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Affiliation(s)
- Ying Ma
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, 811602, China
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
| | - Pengbo Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
| | - Ziyan Li
- College of Life Sciences, WuHan University, Wuhan, 430072, China
| | - Yujuan Yue
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
| | - Yanmei Zhao
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, 811602, China
| | - Jian He
- Qinghai Institute for Endemic Disease Prevention and Control, Xining, 811602, China
| | - Jiaxin Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
- Center for Disease Control and Prevention of Chaoyang District, Beijing, 100021, China
| | - Xiuping Song
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
| | - Jun Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
| | - Qiyong Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China
| | - Liang Lu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, Chinese Center for Disease Control and Prevention, National Institute for Communicable Disease Control and Prevention, Beijing, 102206, China.
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Zhou K, Zhang J, Yang L, Li G, Wu M. Genetic Diversity and Population Structure of Leptosphaeria biglobosa from the Winter Oilseed Rape Region in China. J Fungi (Basel) 2023; 9:1092. [PMID: 37998897 PMCID: PMC10672222 DOI: 10.3390/jof9111092] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/27/2023] [Revised: 10/31/2023] [Accepted: 11/01/2023] [Indexed: 11/25/2023] Open
Abstract
Phoma stem canker (blackleg), caused by the fungi Leptosphaeria maculans (anamorph Phoma lingam) and L. biglobosa, is one of the most devastating diseases in oilseed rape (Brassica napus L.) production worldwide. However, the population structure and genetic variation of L. biglobosa populations in China have rarely been investigated. Here, a collection of 214 fungal strains of blackleg from China (including Shaanxi, Jiangxi, Hubei, Jiangsu, Chongqing, Sichuan, Guangxi, Guizhou, Hunan, and Henan) and Europe (France and Ukraine) was identified as L. biglobosa. Three simple sequence repeat (SSR) markers were developed to characterize their population structure. The results showed that the Nei's average gene diversity ranged from 0.6771 for the population from Jiangsu to 0.3009 for the population from Hunan. In addition, most of the genetic variability (96%) occurred within groups and there were only relatively small amounts among groups (4.0%) (FST = 0.043, p = 0.042 < 0.05). Pairwise population differentiation (FST) suggested that significant genetic differentiation was observed between different L. biglobosa populations. Bayesian and unweighted average method analysis revealed that these L. biglobosa strains were clustered into three branches, and three European strains were similar to those from eastern China. The pathogenicity assay showed that those in Group III were significantly more virulent than those in Group I (t = 2.69, p = 0.016). The study also showed that Group III was dominant in Chinese L. biglobosa populations, which provides new insights for the further study of population evolution and the management of this pathogen.
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Affiliation(s)
- Kang Zhou
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (K.Z.); (J.Z.); (L.Y.); (G.L.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Jing Zhang
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (K.Z.); (J.Z.); (L.Y.); (G.L.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Long Yang
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (K.Z.); (J.Z.); (L.Y.); (G.L.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Guoqing Li
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (K.Z.); (J.Z.); (L.Y.); (G.L.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
| | - Mingde Wu
- The State Key Laboratory of Agricultural Microbiology, Huazhong Agricultural University, Wuhan 430070, China; (K.Z.); (J.Z.); (L.Y.); (G.L.)
- Hubei Key Laboratory of Plant Pathology, Huazhong Agricultural University, Wuhan 430070, China
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Liu S, He G, Xie G, Gong Y, Zhu N, Xiao C. De novo assembly of Iron-Heart Cunninghamia lanceolata transcriptome and EST-SSR marker development for genetic diversity analysis. PLoS One 2023; 18:e0293245. [PMID: 37917740 PMCID: PMC10621985 DOI: 10.1371/journal.pone.0293245] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/23/2022] [Accepted: 10/09/2023] [Indexed: 11/04/2023] Open
Abstract
Iron-Heart Cunninghamia lanceolata, a wild relative of Chinese fir with valuable genetic and breeding traits, has been limited in genetic studies due to a lack of genomic resources and markers. In this study, we conducted transcriptome sequencing of Iron-Heart C. lanceolata leaves using Illumina NovaSeq 6000 and performed assembly and analysis. We obtained 45,326,576 clean reads and 115,501 unigenes. Comparative analysis in five functional databases resulted in successful annotation of 26,278 unigenes, with 6,693 unigenes annotated in all databases (5.79% of the total). UniProt and Pfam databases provided annotations for 22,673 and 18,315 unigenes, respectively. Gene Ontology analysis categorized 23,962 unigenes into three categories. KEGG database alignment annotated 10,195 unigenes, classifying them into five categories: metabolism, genetic information, biological systems, cellular processes, and environmental information processing. From the unigenes, we identified 5,645 SSRs, with dinucleotides repeats being the most common (41.47%). We observed variations in repeat numbers and base compositions, with the majority of markers ranging from 12 to 29 bp in length. We randomly selected 200 primer pairs and successfully amplified 15 pairs of polymorphic SSR primers, which effectively distinguished Chinese fir plants of different origins. This study provides insights into the genetic characteristics of Iron-Heart C. lanceolata and offers a foundation for future molecular marker development, breeding programs, genetic diversity analysis, and conservation strategies.
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Affiliation(s)
- Sen Liu
- Faculty of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Gongxiu He
- Faculty of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Gongliang Xie
- Faculty of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Yamei Gong
- Faculty of Forestry, Central South University of Forestry and Technology, Changsha, China
| | - Ninghua Zhu
- Faculty of Forestry, Central South University of Forestry and Technology, Changsha, China
- National Long-Term Scientific Research Base for Forestry in Mid-Subtropics China, Central South University of Forestry and Technology, Changsha, China
| | - Can Xiao
- Jiangxi Environmental Engineering Vocational College, Ganzhou, China
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Sun M, Cheng Y, Gao C, Peng H, Wang N, Gu W, Lu D. Construction and characterization of microsatellite markers for the Schistosoma japonicum isolate from a hilly area of China based on whole genome sequencing. Parasitol Res 2023; 122:2737-2748. [PMID: 37710024 DOI: 10.1007/s00436-023-07976-3] [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: 07/10/2023] [Accepted: 09/10/2023] [Indexed: 09/16/2023]
Abstract
Schistosoma japonicum had once caused the greatest disease burden in China and has still been transmitted in some hilly areas, for example, in Shitai of Anhui province, where rodents are projected to be the main reservoir. This may lead to a critical need of molecular tools with high efficiency in monitoring the dynamic of the rodent-associated S. japonicum, as an appropriate amount of schistosome input can re-establish its life cycle in a place with snails and then result in the re-emergence of schistosomiasis. Therefore, the goal of this study was to develop high polymorphic microsatellites from the whole genome of rodent-associated S. japonicum strain to monitor its transmission dynamic. We sampled the hilly schistosome isolate from Shitai of Anhui in China and sequenced the parasite with the next-generation sequencing technology. The whole genome was assembled with four different approaches. We then developed 71 microsatellite markers at a genome-wide scale throughout two best assembled genomes. Based on their chromosome mapping and the expected length of targeted sequences, we selected 24 markers for the development of multiplex reactions. Two multiplexes composed of 10 loci were finally developed, and their potential was revealed by their successful application on and capturing the genetic diversity of three schistosome populations. The selected 10 markers, each with clear chromosome location and characteristics, will be greatly useful in tracing the dispersal pathways or/and dynamics of the rodent-associated S. japonicum or others in the hilly area of China or elsewhere.
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Affiliation(s)
- Mengtao Sun
- Department of Epidemiology and Statistics, School of Public Health, Soochow University, Suzhou, China
| | - Yuheng Cheng
- Department of Epidemiology and Statistics, School of Public Health, Soochow University, Suzhou, China
| | - Changzhe Gao
- Department of Epidemiology and Statistics, School of Public Health, Soochow University, Suzhou, China
| | - Hanqi Peng
- Department of Epidemiology and Statistics, School of Public Health, Soochow University, Suzhou, China
| | - Ning Wang
- Department of Epidemiology and Statistics, School of Public Health, Soochow University, Suzhou, China
| | - Weiling Gu
- Jiaxing Center for Disease Control and Prevention, Jiaxing, Zhejiang, China.
| | - Dabing Lu
- Department of Epidemiology and Statistics, School of Public Health, Soochow University, Suzhou, China.
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Chen X, Feng Y, Chen S, Yang K, Wen X, Sun Y. Species Delimitation and Genetic Relationship of Castanopsis hainanensis and Castanopsis wenchangensis (Fagaceae). PLANTS (BASEL, SWITZERLAND) 2023; 12:3544. [PMID: 37896008 PMCID: PMC10609670 DOI: 10.3390/plants12203544] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/19/2023] [Revised: 09/30/2023] [Accepted: 10/09/2023] [Indexed: 10/29/2023]
Abstract
Castanopsis is one of the most common genus of trees in subtropical evergreen broad-leaved forests and tropical monsoon rainforests in China. Castanopsis hainanensis and Castanopsis wenchangensis are endemic to Hainan Island, but they were once confused as the same species due to very similar morphologies. In this study, nuclear microsatellite markers and chloroplast genomes were used to delimit C. hainanensis and C. wenchangensis. The allelic variations of nuclear microsatellites revealed that C. hainanensis and C. wenchangensis were highly genetically differentiated with very limited gene admixture. Both showed higher genetic diversity within populations and lower genetic diversity among populations, and neither had further population genetic structure. Furthermore, C. wenchangensis and C. hainanensis had very different chloroplast genomes. The independent genetic units, very limited gene admixture, different distribution ranges, and distinct habitats all suggest that C. wenchangensis and C. hainanensis are independent species, thus they should be treated as distinct conservation units.
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Affiliation(s)
- Xing Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.C.); (Y.F.); (S.C.); (K.Y.)
| | - Yi Feng
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.C.); (Y.F.); (S.C.); (K.Y.)
| | - Shuang Chen
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.C.); (Y.F.); (S.C.); (K.Y.)
| | - Kai Yang
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.C.); (Y.F.); (S.C.); (K.Y.)
| | - Xiangying Wen
- South China Botanical Garden, Chinese Academy of Sciences, Guangzhou 510650, China
| | - Ye Sun
- Guangdong Key Laboratory for Innovative Development and Utilization of Forest Plant Germplasm, College of Forestry and Landscape Architecture, South China Agricultural University, Guangzhou 510642, China; (X.C.); (Y.F.); (S.C.); (K.Y.)
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Morgan EJ, Kaiser-Bunbury CN, Edwards PJ, Fleischer-Dogley F, Kettle CJ. Mate-choice for close kin is associated with improved offspring survival in Lodoicea maldivica, the largest-seeded plant in the world. Sci Rep 2023; 13:15305. [PMID: 37723314 PMCID: PMC10507110 DOI: 10.1038/s41598-023-41419-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/14/2022] [Accepted: 08/26/2023] [Indexed: 09/20/2023] Open
Abstract
We studied spatial patterns of kinship in the offspring of the endangered Lodoicea maldivica, a dioecious palm that produces the largest seed of any plant. Previous research has suggested that restricted seed and pollen dispersal in populations resulted in strong spatial genetic structure. We used microsatellites to genotype young plants and their potential parents at four sites across the species' entire natural range. We determined the most likely parents of each young plant based on the spatial separation of each parent pair, their genetic relatedness, and the level of correlated paternity. We identified both parents (43 female, 54 male) for 139 of 493 young plants. Mean distance between parental pairs was 26.8 m. Correlated paternity was low (0.168), indicating that mother trees were often pollinated by several fathers. Parental pairs were more closely related than expected by chance, suggesting outbreeding depression. Our results highlight the apparent strong mate choice for close kin in parent pairs of surviving offspring. We discuss the alternative biological processes that could lead to this, including the potential for break-up of favourable allelic combinations necessary for the development of the palm's very large seed. Management implications include germinating seeds where they naturally fall, using a diverse range of male plants as pollen donors for hand pollination, and protecting the native community of gecko pollinators.
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Affiliation(s)
- Emma J Morgan
- ITES-Ecosystem Management, ETH Zürich, Universitätstrasse 16, 8092, Zurich, Switzerland.
| | - Christopher N Kaiser-Bunbury
- Centre for Ecology and Conservation, College of Life and Environmental Sciences, University of Exeter, Cornwall Campus, Penryn, UK
| | - Peter J Edwards
- IBZ-Institute of Integrative Biology, ETH Zürich, Universitätstrasse 16, 8092, Zurich, Switzerland
| | | | - Chris J Kettle
- ITES-Ecosystem Management, ETH Zürich, Universitätstrasse 16, 8092, Zurich, Switzerland
- Bioversity International, Via di San Domenico 1, 00153, Rome, Italy
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Liu P, Li G, Zhao N, Song X, Wang J, Shi X, Wang B, Zhang L, Dong L, Li Q, Liu Q, Lu L. Neutral Forces and Balancing Selection Interplay to Shape the Major Histocompatibility Complex Spatial Patterns in the Striped Hamster in Inner Mongolia: Suggestive of Broad-Scale Local Adaptation. Genes (Basel) 2023; 14:1500. [PMID: 37510404 PMCID: PMC10379431 DOI: 10.3390/genes14071500] [Citation(s) in RCA: 1] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/26/2023] [Revised: 07/20/2023] [Accepted: 07/21/2023] [Indexed: 07/30/2023] Open
Abstract
BACKGROUND The major histocompatibility complex (MHC) plays a key role in the adaptive immune response to pathogens due to its extraordinary polymorphism. However, the spatial patterns of MHC variation in the striped hamster remain unclear, particularly regarding the relative contribution of the balancing selection in shaping MHC spatial variation and diversity compared to neutral forces. METHODS In this study, we investigated the immunogenic variation of the striped hamster in four wild populations in Inner Mongolia which experience a heterogeneous parasitic burden. Our goal was to identify local adaptation by comparing the genetic structure at the MHC with that at seven microsatellite loci, taking into account neutral processes. RESULTS We observed significant variation in parasite pressure among sites, with parasite burden showing a correlation with temperature and precipitation. Molecular analysis revealed a similar co-structure between MHC and microsatellite loci. We observed lower genetic differentiation at MHC loci compared to microsatellite loci, and no correlation was found between the two. CONCLUSIONS Overall, these results suggest a complex interplay between neutral evolutionary forces and balancing selection in shaping the spatial patterns of MHC variation. Local adaptation was not detected on a small scale but may be applicable on a larger scale.
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Affiliation(s)
- Pengbo Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Guichang Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Ning Zhao
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xiuping Song
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Jun Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Xinfei Shi
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
- School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Bin Wang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
- Public Health School, Jiamusi University, Jiamusi 154007, China
| | - Lu Zhang
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Li Dong
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
- School of Public Health, Cheeloo College of Medicine, Shandong University, Jinan 250012, China
| | - Qingduo Li
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Qiyong Liu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
| | - Liang Lu
- National Key Laboratory of Intelligent Tracking and Forecasting for Infectious Diseases, National Institute for Communicable Disease Control and Prevention, Chinese Center for Disease Control and Prevention, Beijing 102206, China
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10
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Galante N, Cotroneo R, Furci D, Lodetti G, Casali MB. Applications of artificial intelligence in forensic sciences: Current potential benefits, limitations and perspectives. Int J Legal Med 2023; 137:445-458. [PMID: 36507961 DOI: 10.1007/s00414-022-02928-5] [Citation(s) in RCA: 9] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/28/2022] [Accepted: 12/04/2022] [Indexed: 12/14/2022]
Abstract
In recent years, new studies based on artificial intelligence (AI) have been conducted in the forensic field, posing new challenges and demonstrating the advantages and disadvantages of using AI methodologies to solve forensic well-known problems. Specifically, AI technology has tried to overcome the human subjective bias limitations of the traditional approach of the forensic sciences, which include sex prediction and age estimation from morphometric measurements in forensic anthropology or evaluating the third molar stage of development in forensic odontology. Likewise, AI has been studied as an assisting tool in forensic pathology for a quick and easy identification of the taxonomy of diatoms. The present systematic review follows the PRISMA 2020 statements and aims to explore an emerging topic that has been poorly analyzed in the forensic literature. Benefits, limitations, and forensic implications concerning AI are therefore highlighted, by providing an extensive critical review of its current applications on forensic sciences as well as its future directions. Results are divided into 5 subsections which included forensic anthropology, forensic odontology, forensic pathology, forensic genetics, and other forensic branches. The discussion offers a useful instrument to investigate the potential benefits of AI in the forensic fields as well as to point out the existing open questions and issues concerning its application on real-life scenarios. Procedural notes and technical aspects are also provided to the readers.
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Affiliation(s)
- Nicola Galante
- Healthcare Accountability Lab, Institute of Legal Medicine of Milan, University of Milan, Via Luigi Mangiagalli 37, 20133, Milan, Italy.
- Department of Biomedical Sciences for Health, Institute of Legal Medicine of Milan, University of Milan, Via Luigi Mangiagalli 37, 20133, Milan, Italy.
| | - Rosy Cotroneo
- Healthcare Accountability Lab, Institute of Legal Medicine of Milan, University of Milan, Via Luigi Mangiagalli 37, 20133, Milan, Italy
- Department of Biomedical Sciences for Health, Institute of Legal Medicine of Milan, University of Milan, Via Luigi Mangiagalli 37, 20133, Milan, Italy
| | - Domenico Furci
- Healthcare Accountability Lab, Institute of Legal Medicine of Milan, University of Milan, Via Luigi Mangiagalli 37, 20133, Milan, Italy
- Department of Biomedical Sciences for Health, Institute of Legal Medicine of Milan, University of Milan, Via Luigi Mangiagalli 37, 20133, Milan, Italy
| | - Giorgia Lodetti
- Healthcare Accountability Lab, Institute of Legal Medicine of Milan, University of Milan, Via Luigi Mangiagalli 37, 20133, Milan, Italy
- Department of Biomedical Sciences for Health, Institute of Legal Medicine of Milan, University of Milan, Via Luigi Mangiagalli 37, 20133, Milan, Italy
| | - Michelangelo Bruno Casali
- Healthcare Accountability Lab, Institute of Legal Medicine of Milan, University of Milan, Via Luigi Mangiagalli 37, 20133, Milan, Italy
- Department of Oncology and Hemato-Oncology (DIPO), University of Milan, Via Luigi Mangiagalli 37, 20133, Milan, Italy
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11
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Du Z, Peng Y, Zhang G, Chen L, Jiang S, Kang Z, Zhao J. Direct Evidence Demonstrates that Puccinia striiformis f. sp. tritici Infects Susceptible Barberry to Complete Sexual Cycle in Autumn. PLANT DISEASE 2023; 107:771-783. [PMID: 35939748 DOI: 10.1094/pdis-08-22-1750-re] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 06/15/2023]
Abstract
Wheat stripe rust is an airborne and destructive disease caused by a heteroecious rust fungus Puccinia striiformis f. sp. tritici (Pst). Studies have demonstrated that the rust pathogen accomplishes sexual reproduction on susceptible barberry under natural conditions in spring, whereas Pst infection on barberry is still in blank in other seasons. In late October 2016, aecial production on barberry shrubs were observed in Linzhi, Tibet, China. Therefore, experimental tests were conducted to verify the existence of sexual cycles of Pst in this season. By inoculating 52 aecial clusters from 30 rusted barberry leaves, four Pst samples, T1 to T4, were successfully recovered from the rusted barberry shrubs. Sixty-five single uredinium (SU) isolates were derived from the four Pst samples. Based on virulence tests on the Chinese differential hosts, T1 to T4 samples were unknown races and showed mixed reactions on some differentials. Twenty-one known races and 44 unknown races belonging to five race groups were identified among the 65 SU isolates. Meanwhile, the 65 SU isolates produced 26 various virulence patterns (VPs; called VP1-VP26) on 25 single Yr gene lines and 15 multilocus genotypes (MLGs) at nine simple sequence repeat marker loci. Clustering analysis showed similar lineage among subpopulations and different lineage between subpopulations. Linkage disequilibrium analysis indicated that the SU population was produced sexually. This study first reported that Pst infects susceptible barberry to complete sexual reproduction in autumn. The results update the knowledge of disease cycle and management of wheat stripe rust and contribute to the understanding of rust genetic diversity in Tibet.
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Affiliation(s)
- Zhimin Du
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Yuelin Peng
- Department of Plant Sciences, Agricultural and Animal Husbandry College of Tibet University, Linzhi, Tibet 86000, China
| | - Gensheng Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Li Chen
- Extension Center for Agricultural Technology, Agriculture Department of Tibetan Autonomous Region, Tibet, China
| | - Shuchang Jiang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
| | - Jie Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, China
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12
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Microsatellite Genome-Wide Database Development for the Commercial Blackhead Seabream (Acanthopagrus schlegelii). Genes (Basel) 2023; 14:genes14030620. [PMID: 36980892 PMCID: PMC10048070 DOI: 10.3390/genes14030620] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/08/2023] [Revised: 02/26/2023] [Accepted: 02/27/2023] [Indexed: 03/05/2023] Open
Abstract
Simple sequence repeats (SSRs), the markers with the highest polymorphism and co-dominance degrees, offer a crucial genetic research resource. Limited SSR markers in blackhead seabream have been reported. The availability of the blackhead seabream genome assembly provided the opportunity to carry out genome-wide identification for all microsatellite markers, and bioinformatic analyses open the way for developing a microsatellite genome-wide database in blackhead seabream. In this study, a total of 412,381 SSRs were identified in the 688.08 Mb genome by Krait software. Whole-genome sequences (10×) of 42 samples were aligned against the reference genome and genotyped using the HipSTR tools by comparing and counting repeat number variation across the SSR loci. A total of 156,086 SSRs with a 2–4 bp repeat were genotyped by HipSTR tools, which accounted for 55.78% of the 2–4 bp SSRs in the reference genome. High accuracy of genotyping was observed by comparing HipSTR tools and PCR amplification. A set of 109,131 loci with a number of alleles ≥ 3 and with a number of genotyped individuals ≥ 6 were reserved to constitute the polymorphic SSR database. Fifty-one polymorphic SSR loci were identified through PCR amplification. This strategy to develop polymorphic SSR markers not only obtained a large set of polymorphic SSRs but also eliminated the need for laborious experimental screening. SSR markers developed in this study may facilitate blackhead seabream research, which lays a certain foundation for further gene tagging and genetic linkage analysis, such as marker-assisted selection, genetic mapping, as well as comparative genomic analysis.
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13
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Xie M, Chen C, Wang Y, Li W, Yu L, Hong X, Zhu X. Conservation Genetics of the Asian Giant Soft-Shelled Turtle (Pelochelys cantorii) with Novel Microsatellite Multiplexes. Animals (Basel) 2022; 12:ani12243459. [PMID: 36552380 PMCID: PMC9774628 DOI: 10.3390/ani12243459] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/07/2022] [Revised: 12/03/2022] [Accepted: 12/06/2022] [Indexed: 12/13/2022] Open
Abstract
To understand the genetic structure of the protected turtle species Pelochelys cantorii we used transcriptome data to design more than 30,000 tri- and tetranucleotide repeat microsatellite primer pairs, of which 230 pairs were used for laboratory experiments. After two screenings, only 10 microsatellite markers with good specificity, high amplification efficiency, and polymorphisms were obtained. Using the selected primers, two multiplex PCR systems were established to compare and analyze the genetic diversity of artificially assisted breeding generations from four parents (two females and two males) continuously bred over two years. A total of 25 alleles were detected among the 10 microsatellite loci of the offspring. The polymorphism information content (PIC) was 0.313-0.674, with an average of 0.401, among which two loci were highly polymorphic (PIC ≥ 0.5). The number of alleles was 2-5 and the number of effective alleles was 1.635-3.614. The observed heterozygosity was 0.341-0.813, with an average of 0.582, whereas the average expected heterozygosity was 0.389-0.725, with an average of 0.493. Moreover, on the basis of Nei's genetic distance and the Bayesian clustering algorithm, the 182 offspring were divided into two subgroups, and the results corresponded to the two maternal lines. This is the first study to investigate the molecular markers of P. cantorii, and the results obtained can be used to protect genetic resources and provide a genetic basis for the design of population recovery plans.
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Affiliation(s)
- Minmin Xie
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
- College of Wuxi Fisheries, Nanjing Agricultural University, Wuxi 214081, China
| | - Chen Chen
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Yakun Wang
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Wei Li
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Lingyun Yu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
| | - Xiaoyou Hong
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
- Correspondence: (X.H.); (X.Z.)
| | - Xinping Zhu
- Key Laboratory of Tropical & Subtropical Fishery Resource Application & Cultivation of Ministry of Agriculture, Pearl River Fisheries Research Institute, Chinese Academy of Fishery Sciences, Guangzhou 510380, China
- College of Wuxi Fisheries, Nanjing Agricultural University, Wuxi 214081, China
- Correspondence: (X.H.); (X.Z.)
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14
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Paternal genetic diversity, differentiation and phylogeny of three white yak breeds/populations in China. Sci Rep 2022; 12:19331. [PMID: 36369339 PMCID: PMC9652388 DOI: 10.1038/s41598-022-23453-w] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/15/2022] [Accepted: 10/31/2022] [Indexed: 11/13/2022] Open
Abstract
The white yak, a type of unique and valuable farm animals on the Qinghai-Tibet Plateau, are mainly distributed in Tianzhu (County of Gansu Province), Menyuan, Huzhu and Ledu (three Counties of Qinghai Province) in China. In the present study, the Y-chromosomal genetic diversity, differentiation and phylogeny of three Chinese white yak breeds/populations (Tianzhu, Huzhu and Menyuan) were comprehensively explored using five Y-SNPs (SRY4, USP9Y, UTY19, AMELY3 and OFD1Y10) and one Y-STR (INRA189) markers. The results showed that six Y-haplotypes (H1Y1, H9Y1, H10Y1, H11Y2, H12Y2 and H13Y2) were identified in 97 male yak from three white yak breeds/populations. Among these haplotypes, H1Y1, H10Y1 and H11Y2 were shared by all of breeds/populations and H12Y2 was shared by Tianzhu and Huzhu populations. However, H9Y1 and H13Y2 haplotypes were only detected in Menyuan and Tianzhu white yak populations, respectively. The Y-haplotype diversity was maximum in Huzhu white yak (0.7500 ± 0.0349), the medium in Tianzhu white yak (0.6881 ± 0.0614) and the lowest in Menyuan white yak (0.5720 ± 0.0657). The total Y-haplotype diversity of three white yak breeds/populations was 0.7567 ± 0.0233, indicating rich paternal genetic diversity in white yak. The FST values showed a moderate differentiation between Tianzhu and Menyuan (FST = 0.0763, P < 0.05) populations, but a weak differentiation between Huzhu and Tianzhu white yak breeds/populations (FST = 0.0186, P > 0.05) and Huzhu and Menyuan (FST = - 0.005, P > 0.05) populations. The clustering analysis revealed a close genetic relationship between Huzhu and Menyuan white yak, both were far from Tianzhu white yak breed. The phylogenetic analyses showed that white yak had two Y-haplogroups/lineages (Y1 and Y2) with two potential paternal origins. The findings of present study provide new insight into the basic information for the formulation of molecular breeding programs of white yak. Moreover, it also contributes to the conservation and utilization of this special animal genetic resource.
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15
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Maxombe EL, Vieira LD, Sierens T, Triest L, Collevatti RG. Holocene climate changes explain the spatial pattern in genetic diversity in populations of Cyperus papyrus from Southeast Africa wetlands. Heredity (Edinb) 2022; 129:295-304. [PMID: 36163272 PMCID: PMC9613894 DOI: 10.1038/s41437-022-00563-9] [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: 12/21/2021] [Revised: 09/12/2022] [Accepted: 09/13/2022] [Indexed: 11/08/2022] Open
Abstract
Wetlands are one of the most threatened ecosystems in the world because more than 70% of the area worldwide has been lost since 1900. Wetland plant species rely greatly on water for seeds and propagules, which may lead to a downstream unidirectional dispersal and accumulation of genetic diversity downstream. However, several species show no support for unidirectional genetic diversity, revealing the complexity of population dynamics and gene flow in wetlands. Here, we used microsatellite loci to address how the past demographic dynamics shaped the contemporary spatial pattern in genetic diversity and population structure of Cyperus papyrus in wetlands of Southeast Africa. Using spatially explicit analysis and coalescent modelling, we found no support for unidirectional dispersal. Instead, we found higher genetic diversity in populations upstream than downstream in the river basin. We also found high admixture among populations, most likely due to connections between adjacent river basins during sporadic floods, and ongoing gene flow due to bird-mediated seed dispersal. Our results suggest stepping-stone migration due to strong isolation-by-distance, but not necessarily unidirectional. Moreover, the past demographic dynamics in the Holocene shaped the current pattern of genetic diversity and structure, leading to higher genetic diversity in populations upstream the Zambezi river basin. Our results also point to the very low genetic diversity of C. papyrus populations in Southeast Africa and the need for management and conservation strategies to guarantee the long-term persistence of the species in the region.
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Affiliation(s)
- Elias Luís Maxombe
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74001-970, Brazil
- Faculdade de Geociências, Universidade Rovuma, Avenida Josina Machel, Caixa Postal 544, Nampula, Mozambique
| | - Lucas Donizetti Vieira
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74001-970, Brazil
| | - Tim Sierens
- Plant Biology and Nature Management, Biology Department, Vrije Universiteit Brussel Pleinlaan 2, B-1050, Brussel, Belgium
| | - Ludwig Triest
- Plant Biology and Nature Management, Biology Department, Vrije Universiteit Brussel Pleinlaan 2, B-1050, Brussel, Belgium
| | - Rosane Garcia Collevatti
- Laboratório de Genética & Biodiversidade, Instituto de Ciências Biológicas, Universidade Federal de Goiás, Goiânia, GO, 74001-970, Brazil.
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16
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Zhang S, Lin M, Liu J, Chen J, Liu D, Zhao J, Yao M. A centenary tale: population genetic insights into the introduction history of the oriental fire-bellied toad (Bombina orientalis) in Beijing. BMC Ecol Evol 2022; 22:117. [PMID: 36241967 PMCID: PMC9569074 DOI: 10.1186/s12862-022-02072-z] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/01/2022] [Accepted: 09/02/2022] [Indexed: 11/06/2022] Open
Abstract
Background The successful establishment of a species population following a single introduction of a few individuals to a non-native area has been limited. Nevertheless, the oriental fire-bellied toad (Bombina orientalis) population in Beijing is purportedly descended from a single introduction of about 200 individuals translocated from Yantai, Shandong Province, China, in 1927. Results To resolve the introduction process and to understand the genetic consequences since that introduction approximately 90 years ago, we investigated the population’s genetic diversity and structure using 261 toads from Beijing and two native Shandong populations and inferred the species’ introduction history using simulation-based approaches. Analysis of mitochondrial DNA (mtDNA) sequences showed the two haplotypes found in Beijing nested within Yantai haplotypes, thus corroborating the historical record of the translocation source. The mtDNA and 11 nuclear microsatellite markers revealed both considerably lower genetic diversity in Beijing than in the source population and strong genetic differentiation between them. Although the current census population in Beijing may be in the range of a few thousand, the effective population size was estimated at only 20–57. Simulations also suggest that this population may have descended from 40–60 founders. Conclusions The Beijing population’s genetic patterns were consistent with the consequences of a severe bottleneck during introduction followed by genetic drift. The introduction trajectory constructed for this B. orientalis population reveals the genetic footprints of a small population sustained in isolation for nearly a century. Our results provide an intriguing example of establishment success from limited founders and may inform ex situ conservation efforts as well as the management of biological invasions. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-022-02072-z.
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Affiliation(s)
- Shan Zhang
- grid.11135.370000 0001 2256 9319School of Life Sciences, Peking University, R312, School of Life Sciences Bldg., 100871 Beijing, China ,grid.11135.370000 0001 2256 9319Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871 China
| | - Meixi Lin
- grid.11135.370000 0001 2256 9319School of Life Sciences, Peking University, R312, School of Life Sciences Bldg., 100871 Beijing, China ,grid.19006.3e0000 0000 9632 6718Department of Ecology and Evolutionary Biology, University of California-Los Angeles, Los Angeles, CA 90095 USA
| | - Jiawei Liu
- grid.11135.370000 0001 2256 9319School of Life Sciences, Peking University, R312, School of Life Sciences Bldg., 100871 Beijing, China ,grid.170205.10000 0004 1936 7822Department of Ecology and Evolution, University of Chicago, Chicago, IL 60637 USA
| | - Jiangce Chen
- grid.63054.340000 0001 0860 4915Mechanical Engineering Department, University of Connecticut, Storrs, CT 06269 USA
| | - Dong Liu
- grid.263817.90000 0004 1773 1790Department of Biology, School of Life Sciences, Southern University of Science and Technology, Shenzhen, 518055 China
| | - Jindong Zhao
- grid.11135.370000 0001 2256 9319School of Life Sciences, Peking University, R312, School of Life Sciences Bldg., 100871 Beijing, China ,grid.11135.370000 0001 2256 9319Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871 China
| | - Meng Yao
- grid.11135.370000 0001 2256 9319School of Life Sciences, Peking University, R312, School of Life Sciences Bldg., 100871 Beijing, China ,grid.11135.370000 0001 2256 9319Institute of Ecology, College of Urban and Environmental Sciences, Peking University, Beijing, 100871 China
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17
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Liu K, Xie N. Pipeline for developing polymorphic microsatellites in species without reference genomes. 3 Biotech 2022; 12:248. [PMID: 36039078 PMCID: PMC9418399 DOI: 10.1007/s13205-022-03313-0] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 08/16/2022] [Indexed: 11/01/2022] Open
Abstract
Microsatellites, also known as simple sequence repeats (SSRs), are the preferred type of marker for many genetic applications. In conjunction with the ongoing development of next-generation sequencing, several bioinformatic tools have been developed for identifying SSRs from genomic or transcriptomic sequences. Although these tools are handy for generating polymorphic SSRs, their application almost always depends on an existing reference genome or self-assembly of the reference genome. With this in mind, we propose a pipeline for developing polymorphic SSRs that may be applied to species without reference genomes. Using a species without a reference genome (black Amur bream; Megalobrama terminalis Richardson, 1846) as a model, our pipeline was able to effectively discover polymorphic SSRs. Under different R parameters of a reference-free single nucleotide polymorphisms (SNPs) caller (ebwt2InDel), a total of 258, 208, 102, and 11 polymorphic SSRs were mined. To quantify the accuracy of the polymorphic SSRs detected using our pipeline, we analyzed 25 SSRs with PCR experiments. All primers were successfully amplified, and most SSRs (23 SSRs, 92%) were polymorphic. From the 36 individual black Amur bream, we acquired an average of 3.36 alleles per locus, ranging from one to 11. This demonstrates the effectiveness of our pipeline in identifying polymorphic SSRs and designing primers for SSR genotyping. Ultimately, our pipeline can effectively mine polymorphic SSRs for species without reference genomes, complementing SSR mining approaches based on reference genomes and helping to resolve biological issues that accompany these methods. Supplementary Information The online version contains supplementary material available at 10.1007/s13205-022-03313-0.
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Affiliation(s)
- Kai Liu
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang China
| | - Nan Xie
- Institute of Fishery Science, Hangzhou Academy of Agricultural Sciences, Hangzhou, Zhejiang China
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18
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Comprehensive Analyses of Simple Sequence Repeat (SSR) in Bamboo Genomes and Development of SSR Markers with Peroxidase Genes. Genes (Basel) 2022; 13:genes13091518. [PMID: 36140687 PMCID: PMC9498332 DOI: 10.3390/genes13091518] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/01/2022] [Revised: 08/17/2022] [Accepted: 08/20/2022] [Indexed: 11/21/2022] Open
Abstract
Simple sequence repeats (SSRs) are one of the most important molecular markers, which are widespread in plants. Bamboos are important forest resources worldwide. Here, the comprehensive identification and comparative analysis of SSRs were performed in three woody and two herbaceous bamboo species. Altogether 567,175 perfect SSRs and 71,141 compound SSRs were identified from 5737.8 Mb genome sequences of five bamboo species. Di-nucleotide SSRs were the most predominant type, with an average of ~50,152.2 per species. Most SSRs were located in intergenic regions, while those located in genic regions were relatively less. Moreover, the results of annotation distribution indicated that terms with P450, peroxidase and ATP-binding cassette transporter related to lignin biosynthesis might play important roles in woody and herbaceous bamboos under the mediation of SSRs. Furthermore, the peroxidase gene family consisted of a large number of genes containing SSRs was selected for the evolutionary relationship analysis and SSR markers development. Fifteen SSR markers derived from peroxidase family genes of Phyllostachys edulis were identified as polymorphic in 34 accessions belonging to seven genera in Bambusoideae. These results provided a comprehensive insight of SSR markers into bamboo genomes, which would facilitate bamboo research related to comparative genomics, evolution and marker-assisted selection.
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19
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Yang R, Deng YW, Liu Y, Zhao J, Bao L, Ge JP, Wang HF. Genetic structure and trait variation within a maple hybrid zone underscore North China as an overlooked diversity hotspot. Sci Rep 2022; 12:13949. [PMID: 35977961 PMCID: PMC9385851 DOI: 10.1038/s41598-022-17538-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/25/2022] [Accepted: 07/27/2022] [Indexed: 11/30/2022] Open
Abstract
Tertiary relict flora in East Asia can be divided into northern and southern regions. North China is a diversity hotspot because it can be the secondary contact zone of ancient lineages from the two regions. To test the extent of ancient lineages hybridization and distinguish between the putative species pair Acer pictum subsp. mono and Acer truncatum, we conducted genetic and ecological studies within a maple hybrid zone in North China. Our results suggest that the two lineages of Acer coexist in the hybrid zone and that adult and offspring populations show typical bimodal genetic patterns. Hybrid individuals are established at intermediate altitudes between the two parental lineages. Flowering phenology is divergent between lineages, whereas the complex sexual system of Acer may ensure pollination among lineages. Leaf and fruit morphologies are different between the northern and southern origin lineages, corresponding to A. pictum subsp. mono and A. truncatum, respectively. Reduced gene flow between lineages suggests that they should be considered as two species. However, large morphological variations within each species and the existence of hybrids offer low reliability of species identification based solely on morphological traits. Our study underscores North China as an overlooked diversity hotspot that requires further study in the future.
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Affiliation(s)
- Rui Yang
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing, 100875, China.,Northeast Tiger and Leopard Biodiversity National Observation and Research Station, Beijing, 100875, China.,College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Ya-Wen Deng
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing, 100875, China.,Northeast Tiger and Leopard Biodiversity National Observation and Research Station, Beijing, 100875, China.,College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yan Liu
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing, 100875, China.,Northeast Tiger and Leopard Biodiversity National Observation and Research Station, Beijing, 100875, China.,College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Jing Zhao
- Daheishan Administrative District, Beipiao City, 122000, Liaoning Province, China
| | - Lei Bao
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing, 100875, China.,Northeast Tiger and Leopard Biodiversity National Observation and Research Station, Beijing, 100875, China.,College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Jian-Ping Ge
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing, 100875, China.,Northeast Tiger and Leopard Biodiversity National Observation and Research Station, Beijing, 100875, China.,College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Hong-Fang Wang
- National Forestry and Grassland Administration Key Laboratory for Conservation Ecology in the Northeast Tiger and Leopard National Park, Beijing, 100875, China. .,Northeast Tiger and Leopard Biodiversity National Observation and Research Station, Beijing, 100875, China. .,College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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20
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Yan Z, Sang L, Ma Y, He Y, Sun J, Ma L, Li S, Miao F, Zhang Z, Huang J, Wang Z, Yang G. A de novo assembled high-quality chromosome-scale Trifolium pratense genome and fine-scale phylogenetic analysis. BMC PLANT BIOLOGY 2022; 22:332. [PMID: 35820796 PMCID: PMC9277957 DOI: 10.1186/s12870-022-03707-5] [Citation(s) in RCA: 2] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/22/2022] [Accepted: 06/20/2022] [Indexed: 05/12/2023]
Abstract
BACKGROUND Red clover (Trifolium pratense L.) is a diploid perennial temperate legume with 14 chromosomes (2n = 14) native to Europe and West Asia, with high nutritional and economic value. It is a very important forage grass and is widely grown in marine climates, such as the United States and Sweden. Genetic research and molecular breeding are limited by the lack of high-quality reference genomes. In this study, we used Illumina, PacBio HiFi, and Hi-C to obtain a high-quality chromosome-scale red clover genome and used genome annotation results to analyze evolutionary relationships among related species. RESULTS The red clover genome obtained by PacBio HiFi assembly sequencing was 423 M. The assembly quality was the highest among legume genome assemblies published to date. The contig N50 was 13 Mb, scaffold N50 was 55 Mb, and BUSCO completeness was 97.9%, accounting for 92.8% of the predicted genome. Genome annotation revealed 44,588 gene models with high confidence and 52.81% repetitive elements in red clover genome. Based on a comparison of genome annotation results, red clover was closely related to Trifolium medium and distantly related to Glycine max, Vigna radiata, Medicago truncatula, and Cicer arietinum among legumes. Analyses of gene family expansions and contractions and forward gene selection revealed gene families and genes related to environmental stress resistance and energy metabolism. CONCLUSIONS We report a high-quality de novo genome assembly for the red clover at the chromosome level, with a substantial improvement in assembly quality over those of previously published red clover genomes. These annotated gene models can provide an important resource for molecular genetic breeding and legume evolution studies. Furthermore, we analyzed the evolutionary relationships among red clover and closely related species, providing a basis for evolutionary studies of clover leaf and legumes, genomics analyses of forage grass, the improvement of agronomic traits.
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Affiliation(s)
- Zhenfei Yan
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Lijun Sang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Yue Ma
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Yong He
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Juan Sun
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Lichao Ma
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Shuo Li
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Fuhong Miao
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China
| | - Zixin Zhang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China
| | | | - Zengyu Wang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China.
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China.
| | - Guofeng Yang
- College of Grassland Science, Qingdao Agricultural University, Qingdao, 266109, China.
- Key Laboratory of National Forestry and Grassland Administration on Grassland Resources and Ecology in the Yellow River Delta, Qingdao, 266109, China.
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Genetic Characterization of Puccinia striiformis f. sp. tritici Populations from Different Wheat Cultivars Using Simple Sequence Repeats. J Fungi (Basel) 2022; 8:jof8070705. [PMID: 35887461 PMCID: PMC9319641 DOI: 10.3390/jof8070705] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2022] [Revised: 06/12/2022] [Accepted: 06/30/2022] [Indexed: 02/01/2023] Open
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most important fungal diseases affecting wheat (Triticum aestivum L.) worldwide. In this study, the genetic diversity and population structure of Pst isolates were analyzed using 15 microsatellite markers. Isolates were collected from five wheat cultivars with different levels of resistance from Yanting county and Fucheng district, Mianyang city, Sichuan province, China. The aim of this study was to investigate whether Pst populations are differentiated by wheat genotype or geographic origin. Seventy-six multilocus genotypes (MLGs) were identified from all 289 single uredinial isolates. In general, the genotypic diversity of Pst populations from five wheat cultivars in Fucheng was higher than that in Yanting. In addition, the genetic diversity was highest in the Pst populations from Mianmai 367, a cultivar considered to be highly resistant. The unweighted pair group method with arithmetic mean (UPGMA) phylogenetic tree, Bayesian clustering analysis, and minimum spanning network for the MLGs revealed two major genetic clusters based on geographical location. Greater differentiation was observed between the populations from the two sampling locations than between the populations from different hosts in the same location. The results suggest that geographic and environmental differences could partially explain the genetic differentiation of Pst more than wheat genotype. This study provides novel insight into the interactions between Pst populations and their hosts. The results could be helpful in designing more effective management strategies for stripe rust in wheat production.
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22
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Zhang C, Jia C, Liu X, Zhao H, Hou L, Li M, Cui B, Li Y. Genetic Diversity Study on Geographical Populations of the Multipurpose Species Elsholtzia stauntonii Using Transferable Microsatellite Markers. FRONTIERS IN PLANT SCIENCE 2022; 13:903674. [PMID: 35646027 PMCID: PMC9134938 DOI: 10.3389/fpls.2022.903674] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 03/24/2022] [Accepted: 04/21/2022] [Indexed: 06/15/2023]
Abstract
Elsholtzia stauntonii Benth. (Lamiaceae) is an economically important ornamental, medicinal and aromatic plant species. To meet the increasing market demand for E. stauntonii, it is necessary to assess genetic diversity within the species to accelerate the process of genetic improvement. Analysis of the transferability of simple sequence repeat (SSR) markers from related species or genera is a fast and economical method to evaluate diversity, and can ensure the availability of molecular markers in crops with limited genomic resources. In this study, the cross-genera transferability of 497 SSR markers selected from other members of the Lamiaceae (Salvia L., Perilla L., Mentha L., Hyptis Jacq., Leonurus L., Pogostemon Desf., Rosmarinus L., and Scutella L.) to E. stauntonii was 9.05% (45 primers). Among the 45 transferable markers, 10 markers revealed relatively high polymorphism in E. stauntonii. The genetic variation among 825 individuals from 18 natural populations of E. stauntonii in Hebei Province of China was analyzed using the 10 polymorphic SSR markers. On the basis of the SSR data, the average number of alleles (N A), expected heterozygosity (H E), and Shannon's information index (I) of the 10 primers pairs were 7.000, 0.478, and 0.688, respectively. Lower gene flow (N m = 1.252) and high genetic differentiation (F st = 0.181) were detected in the populations. Analysis of molecular variance (AMOVA) revealed that most of the variation (81.47%) was within the populations. Integrating the results of STRUCTURE, UPGMA (Unweighted Pair Group Method with Arithmetic Mean) clustering, and principal coordinate analysis, the 825 samples were grouped into two clusters associated with geographical provenance (southwestern and northeastern regions), which was consistent with the results of a Mantel test (r = 0.56, p < 0.001). Overall, SSR markers developed in related genera were effective to study the genetic structure and genetic diversity in geographical populations of E. stauntonii. The results provide a theoretical basis for conservation of genetic resources, genetic improvement, and construction of a core collection for E. stauntonii.
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Affiliation(s)
- Chenxing Zhang
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Chunfeng Jia
- College of Biochemistry and Environmental Engineering, Baoding University, Baoding, China
| | - Xinru Liu
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Hanqing Zhao
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Lu Hou
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Meng Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
| | - Binbin Cui
- College of Biochemistry and Environmental Engineering, Baoding University, Baoding, China
| | - Yingyue Li
- National Engineering Research Center of Tree Breeding and Ecological Restoration, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- Key Laboratory of Genetics and Breeding in Forest Trees and Ornamental Plants, Ministry of Education, College of Biological Sciences and Technology, Beijing Forestry University, Beijing, China
- The Tree and Ornamental Plant Breeding and Biotechnology Laboratory of National Forestry and Grassland Administration, Beijing Forestry University, Beijing, China
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Si SP, Wang CJ, Wan JZ, Qian YL, Zhang CH. Development of novel polymorphic microsatellite markers for Picea brachytyla. Mol Biol Rep 2022; 49:4095-4099. [PMID: 35536498 DOI: 10.1007/s11033-022-07346-9] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2021] [Revised: 03/04/2022] [Accepted: 03/08/2022] [Indexed: 11/29/2022]
Abstract
BACKGROUND Picea brachytyla is a unique tree species in China. Due to being extensively exploited in the past, it is listed as Vulnerable in the IUCN Red List. It is mainly distributed across the Hengduan and Daba-Qinglin mountains and has been found in other areas including Sichuan Province and Qinghai Province, China. Microsatellites, or simple sequence repeats (SSRs), are widely used in correlational studies of genetic protection. Few markers have been developed for P. brachytyla because of the small number of trees and scholarly resources available for study. METHODS AND RESULTS The genomic DNA of P. brachytyla was sequenced using the DNBSEQ platform, and unigenes were obtained after assembly and deredundancy. Of the 100 primer pairs screened, we isolated 10 useful microsatellite loci from P. brachytyla genes. The observed and expected heterozygosity values ranged from 0.173 (P24) to 0.788 (P79; mean 0.469) and 0.199 (P87) to 0.911 (P79; mean 0.700), respectively. Polymorphism-information content (PIC) ranged from 0.190 (P84) to 0.904 (P79; mean 0.666). Only P84 and P72 were in a Hardy-Weinberg equilibrium (P > 0.05) in the different P. brachytyla populations. All the levels of linkage disequilibrium (LD) were high for the 10 SSR loci indicating that there were no autocorrelations among the 10 SSR loci. CONCLUSIONS The novel polymorphic microsatellite markers showed high polymorphism for P. brachytyla. These polymorphic microsatellites can provide a basis for future conservation and genetic research on this rare plant species.
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Affiliation(s)
- Shuai-Peng Si
- College of Agriculture and Animal Husbandry, Qinghai University, 810016, Xining, China
| | - Chun-Jing Wang
- College of Agriculture and Animal Husbandry, Qinghai University, 810016, Xining, China.
| | - Ji-Zhong Wan
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, 810016, Xining, China.
| | | | - Chun-Hui Zhang
- State Key Laboratory of Plateau Ecology and Agriculture, Qinghai University, 810016, Xining, China
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24
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Morphometric analysis and fluorescent microsatellite markers to evaluate the genetic diversity of five populations of Penaeus japonicus in China. AQUACULTURE AND FISHERIES 2022. [DOI: 10.1016/j.aaf.2020.10.005] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/23/2022]
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25
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Wang H, Gao S, Liu Y, Wang P, Zhang Z, Chen D. A pipeline for effectively developing highly polymorphic simple sequence repeats markers based on multi‐sample genomic data. Ecol Evol 2022; 12:e8705. [PMID: 35342577 PMCID: PMC8928897 DOI: 10.1002/ece3.8705] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/09/2021] [Revised: 01/25/2022] [Accepted: 02/15/2022] [Indexed: 01/24/2023] Open
Abstract
Simple sequence repeats (SSRs) are widely used genetic markers in ecology, evolution, and conservation even in the genomics era, while a general limitation to their application is the difficulty of developing polymorphic SSR markers. Next‐generation sequencing (NGS) offers the opportunity for the rapid development of SSRs; however, previous studies developing SSRs using genomic data from only one individual need redundant experiments to test the polymorphisms of SSRs. In this study, we designed a pipeline for the rapid development of polymorphic SSR markers from multi‐sample genomic data. We used bioinformatic software to genotype multiple individuals using resequencing data, detected highly polymorphic SSRs prior to experimental validation, significantly improved the efficiency and reduced the experimental effort. The pipeline was successfully applied to a globally threatened species, the brown eared‐pheasant (Crossoptilon mantchuricum), which showed very low genomic diversity. The 20 newly developed SSR markers were highly polymorphic, the average number of alleles was much higher than the genomic average. We also evaluated the effect of the number of individuals and sequencing depth on the SSR mining results, and we found that 10 individuals and ~10X sequencing data were enough to obtain a sufficient number of polymorphic SSRs, even for species with low genetic diversity. Furthermore, the genome assembly of NGS data from the optimal number of individuals and sequencing depth can be used as an alternative reference genome if a high‐quality genome is not available. Our pipeline provided a paradigm for the application of NGS technology to mining and developing molecular markers for ecological and evolutionary studies.
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Affiliation(s)
- Hui Wang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University Beijing China
| | - Shenghan Gao
- State Key Laboratory of Microbial Resources Institute of Microbiology Chinese Academy of Sciences Beijing China
| | - Yu Liu
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University Beijing China
| | - Pengcheng Wang
- Jiangsu Key Laboratory for Biodiversity and Biotechnology College of Life Sciences Nanjing Normal University Nanjing China
| | - Zhengwang Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University Beijing China
| | - De Chen
- MOE Key Laboratory for Biodiversity Science and Ecological Engineering College of Life Sciences Beijing Normal University Beijing China
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26
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Holland MM, Tiedge TM, Bender AJ, Gaston-Sanchez SA, McElhoe JA. MaSTR™: an effective probabilistic genotyping tool for interpretation of STR mixtures associated with differentially degraded DNA. Int J Legal Med 2022; 136:433-446. [DOI: 10.1007/s00414-021-02771-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/20/2021] [Accepted: 12/21/2021] [Indexed: 11/30/2022]
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27
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Chong Y, Jiang X, Liu G. An ancient positively selected BMPRIB missense variant increases litter size of Mongolian sheep populations following latitudinal gradient. Mol Genet Genomics 2022; 297:155-167. [PMID: 35013854 DOI: 10.1007/s00438-021-01828-4] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/21/2021] [Accepted: 10/22/2021] [Indexed: 12/11/2022]
Abstract
New gene mutation origination is a driving force for the evolution of organisms. The effect of FecB mutation in BMPRIB gene on the litter size of sheep has been well known for a long time, each copy of the mutant allele increases litter size by 0.4-0.5. However, the origin and adaptive evolution mechanism of FecB mutation are still unclear. Here we carried on the thorough analysis on evolutionary features of BMPRIB gene and found that 150 species as a whole is under purifying selection while sheep lineage shows evidence of positive selection. The results of allele age estimation revealed that the FecB mutation in Mongolian sheep of China originated in Mongolian Plateau at about 5000 years ago. Due the two shape drops in temperature subsequently, Mongolian sheep migrated from north to south following the northern nomadic people. Accordingly, the FecB mutant allele frequency increased, with the lowest in sheep locating at Mongolian plateau (0.01) and the highest in sheep locating at Yangtze River valley (0.96). In conclusion, the FecB mutation in Mongolian sheep of China originated in Mongolian Plateau at about 5000 years ago, and the differentiated litter size of Mongolian sheep might be the result of adaptation to various environments during the migration following latitudinal gradient. This study may well exemplify selection on an ancient variation triggered by drastic ecological shifts, and is also helpful to analyze the adaptive evolution mechanism of economic traits of domestic animals and identify major genes and molecular markers.
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Affiliation(s)
- Yuqing Chong
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Wuhan, 430070, People's Republic of China
| | - Xunping Jiang
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China.,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Wuhan, 430070, People's Republic of China
| | - Guiqiong Liu
- Laboratory of Small Ruminant Genetics, Breeding and Reproduction, College of Animal Science and Technology, Huazhong Agricultural University, Wuhan, 430070, People's Republic of China. .,Key Laboratory of Agricultural Animal Genetics, Breeding and Reproduction of the Ministry of Education, Wuhan, 430070, People's Republic of China.
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28
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Chen W, Zhang Z, Ma X, Zhang G, Yao Q, Kang Z, Zhao J. Phenotyping and Genotyping Analyses Reveal the Spread of Puccinia striiformis f. sp. tritici Aeciospores From Susceptible Barberry to Wheat in Qinghai of China. FRONTIERS IN PLANT SCIENCE 2021; 12:764304. [PMID: 34975948 PMCID: PMC8719489 DOI: 10.3389/fpls.2021.764304] [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: 08/25/2021] [Accepted: 11/22/2021] [Indexed: 05/26/2023]
Abstract
Puccinia striiformis f. sp. tritici Eriks., the cause of wheat yellow or stripe rust on wheat, undergoes sexual reproduction on barberry, but it is unclear if barberry plays any role in stripe rust epidemics under natural conditions. P. striiformis f. sp. tritici was isolated from its alternate host barberry (Berberis spp.) and primary host wheat in the vicinity of barberry by inoculation of aeciospores and urediniospores on Mingxian 169 cultivar in Qinghai province of China in 2018. The P. striiformis f. sp. tritici isolates from barberry and wheat were characterized to virulence patterns by inoculation on 24 differentials bearing Yr gene under control conditions and analyzed using 12 polymorphic simple sequence repeat (SSR) markers. The occurrence frequency of P. striiformis f. sp. tritici on barberry was 1.87% by inoculation aecia, collected from barberry on Mingxian 169 of wheat. A close virulence relationship was presented between P. striiformis f. sp. tritici isolates from both barberry and wheat based on virulence simple matching coefficient and principal coordinates analysis (PCoA). Additionally, the same genetic ancestry, based on structure analysis by STRUCTURE program and genetic relationship analyses using discriminant analysis of principal components and PCoA, was shared between P. striiformis f. sp. tritici isolates from barberry and those from wheat. Together, all the results indicated that the role of barberry in providing aeciospores as an inoculum source causing wheat stripe rust epidemic in Qinghai in spring is of considerable importance.
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Affiliation(s)
- Wen Chen
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
- Guizhou Academy of Agricultural Sciences, Institute of Plant Protection, Guiyang, China
| | - ZeDong Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Xinyao Ma
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Gensheng Zhang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Qiang Yao
- Academy of Agricultural and Forestry Sciences, Qinghai University, Xining, China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
| | - Jie Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling, China
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Fu C, Ai Q, Cai L, Qiu F, Yao L, Wu H. Genetic Diversity and Population Dynamics of Leptobrachium leishanense (Anura: Megophryidae) as Determined by Tetranucleotide Microsatellite Markers Developed from Its Genome. Animals (Basel) 2021; 11:3560. [PMID: 34944336 PMCID: PMC8698065 DOI: 10.3390/ani11123560] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/10/2021] [Revised: 12/06/2021] [Accepted: 12/13/2021] [Indexed: 11/16/2022] Open
Abstract
Persisting declination of amphibians around the world has resulted in the public attaching importance to the conservation of their biodiversity. Genetic data can be greatly helpful in conservation planning and management, especially in species that are small in size and hard to observe. It is essential to perform genetic assessments for the conservation of Leptobrachium leishanense, an endangered toad and receiving secondary protection on the list of state-protected wildlife in China. However, current molecular markers with low reliability and efficiency hinder studies. Here, we sampled 120 adult toes from the population in the Leishan Mountain, 23 of which were used to develop tetranucleotide microsatellite markers based on one reference L. leishanense genome. After primer optimization, stability detection, and polymorphism detection, we obtained 12 satisfactory microsatellite loci. Then, we used these loci to evaluate the genetic diversity and population dynamics of the 120 individuals. Our results show that there is a low degree of inbreeding in the population, and it has a high genetic diversity. Recently, the population has not experienced population bottlenecks, and the estimated effective population size was 424.3. Accordingly, stabilizing genetic diversity will be key to population sustainability. Recovering its habitat and avoiding intentional human use will be useful for conservation of this species.
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Affiliation(s)
| | | | | | | | | | - Hua Wu
- Institute of Evolution and Ecology, School of Life Sciences, Central China Normal University, Wuhan 430079, China; (C.F.); (Q.A.); (L.C.); (F.Q.); (L.Y.)
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Budd K, Sampson C, Leimgruber P, Tonkyn D, Storey K, Garrett M, Eggert LS. Population structure and demography of Myanmar’s conflict elephants. Glob Ecol Conserv 2021. [DOI: 10.1016/j.gecco.2021.e01828] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022] Open
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31
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Triest L, Dierick J, Phan TTH, Luong QD, Huy NQ, Sierens T. Low Genetic Connectivity of Strongly Inbred Ruppia brevipedunculata in Aquaculture Dominated Lagoons (Viet Nam). FRONTIERS IN CONSERVATION SCIENCE 2021. [DOI: 10.3389/fcosc.2021.723376] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
Abstract
Lagoonal environments exhibit high levels of instability depending on hydrological, climatic and ecological factors, thereby influencing the distribution and structure of submerged plant communities. Conditions typically fluctuate widely due to the interaction of freshwater from rivers with saltwater from the sea, as well as from aquaculture activities that together influence submerged hydrophyte community spatial and temporal variability depending on plant survival strategies. Ruppia species feature either underwater pollination mediated by an air bubble or by the release of pollen floating at the water surface, the former promoting self-pollination. Tropical Asian Ruppia brevipedunculata Yu and den Hartog was assumed to pollinate below the water surface and identified as a separate lineage among selfed Ruppia taxa. We used nine nuclear microsatellites to estimate inbreeding levels and connectivity of R. brevipedunculata within a large SE Asian lagoon complex. Ruppia brevipedunculata meadows were strongly inbred as could be derived from the many monomorphic or totally fixed loci for unique alleles in different parts of the lagoon, which appears consistent with selfing behavior. Those from aquaculture ponds were highly inbred (FIS = 0.620), though less than open lagoon sites that showed nearly total inbreeding (FIS = 0.942). Ruppia brevipedunculata from two major lagoon parts were highly differentiated with spatially structured gene pools and a strong barrier between parts of the lagoon over a 30 km distance. Migration-n analysis indicated unidirectional though limited gene flow and following potential hydrological connectivity. Overall, private alleles under homozygote conditions explained a stronger genetic differentiation of populations situated inside aquaculture ponds than of open lagoon populations. Kinship values were only relevant up to 5 km distance in the open lagoon. Within a confined area of aquaculture ponds featuring dense vegetation in stagnant water, there would be opportunity for mixed pollination, thereby explaining the higher diversity of unique multilocus genotypes of aquaculture pond habitats. Low connectivity prevents gene pools to homogenize however promoted sites with private alleles across the lagoon. Complex hydrodynamic systems and human-made habitats enclosed by physical structures impose barriers for propagule dispersal though may create refugia and contribute to conserving regional genetic diversity.
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Development of the first microsatellite markers using high-throughput sequencing for a hexaploid coastal species, Tournefortia argentea L. f. (Boraginaceae). Mol Biol Rep 2021; 48:7049-7055. [PMID: 34462831 DOI: 10.1007/s11033-021-06668-4] [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: 06/16/2021] [Accepted: 08/18/2021] [Indexed: 10/20/2022]
Abstract
BACKGROUD Tournefortia argentea L. f. is a hexaploid shrub or tree species with ecological and evolutionary significances, which forms the fringe of vegetation closest to the sea on tropical coral islands. Previous studies have never addressed on genetic information, and thus genomic resources remain scarce. METHODS AND RESULTS We used nine individuals from different islands to identify polymorphic microsatellites of T. argentea by Illumina high-throughput sequencing. Thirty-five polymorphic microsatellite markers were developed. Characteristics of each locus were tested using 48 individuals collected from three populations of T. argentea. A total of 320 alleles were found across the 35 microsatellite loci. The number of alleles per locus ranged from 5 to 15, with an average of 9.1. Observed and expected heterozygosities in each locus per population varied from 0.000 to 1.000 and from 0.000 to 0.893, respectively. CONCLUSIONS In this study, we report the development of 35 polymorphic microsatellite markers based on Illumina high-throughput sequencing. These markers will facilitate the investigations of genetic diversity, population structures and evolutionary history of T. argentea.
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Verble K, Hallerman EM, Alexander KA. Urban landscapes increase dispersal, gene flow, and pathogen transmission potential in banded mongoose ( Mungos mungo) in northern Botswana. Ecol Evol 2021; 11:9227-9240. [PMID: 34306619 PMCID: PMC8293740 DOI: 10.1002/ece3.7487] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 06/01/2020] [Accepted: 06/04/2020] [Indexed: 11/09/2022] Open
Abstract
Disease transmission can be strongly influenced by the manner in which conspecifics are connected across a landscape and the effects of land use upon these dynamics. In northern Botswana, the territorial and group-living banded mongoose (Mungos mungo) lives across urban and natural landscapes and is infected with a novel Mycobacterium tuberculosis complex pathogen, M. mungi. Using microsatellite markers amplified from DNA derived from banded mongoose fecal and tissue samples (n = 168), we evaluated population genetic structure, individual dispersal, and gene flow for 12 troops. Genetic structure was detectable and moderately strong across groups (F ST = 0.086), with K = 7 being the best-supported number of genetic clusters. Indications of admixture in certain troops suggest formation of new groups through recent fusion events. Differentiation was higher for troops inhabiting natural areas (F ST = 0.102) than for troops in urban landscapes (F ST = 0.081). While this suggests increased levels of gene flow between urban-dwelling troops, the inclusion of a smaller number of study troops from natural land types may have influenced these findings. Of those individuals confirmed infected with M. mungi, the majority (73%, n = 11) were assigned to their natal group which is consistent with previous observations linking lower levels of dispersal with infection. Twenty-one probable dispersing individuals were identified, with all suspected migrants originating from troops within the urban landscape. Findings suggest that urbanized landscapes may increase gene flow and dispersal behavior with a concomitant increase in the risk of pathogen spread. As urban landscapes expand, there is an increasing need to understand how land use and pathogen infection may change wildlife behavior and disease transmission potential.
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Affiliation(s)
- Kelton Verble
- Department of Fish and Wildlife ConservationVirginia TechBlacksburgVAUSA
- Present address:
Department of Biological SciencesUniversity of AlabamaTuscaloosaALUSA
| | - Eric M. Hallerman
- Department of Fish and Wildlife ConservationVirginia TechBlacksburgVAUSA
| | - Kathleen A. Alexander
- Department of Fish and Wildlife ConservationVirginia TechBlacksburgVAUSA
- Chobe Research InstituteCARACALKasaneBotswana
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Dierick J, Phan TTH, Luong QD, Triest L. Persistent Clones and Local Seed Recruitment Contribute to the Resilience of Enhalus acoroides Populations Under Disturbance. FRONTIERS IN PLANT SCIENCE 2021; 12:658213. [PMID: 34220884 PMCID: PMC8248806 DOI: 10.3389/fpls.2021.658213] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 01/25/2021] [Accepted: 05/10/2021] [Indexed: 06/13/2023]
Abstract
Human-induced land use in coastal areas is one of the main threats for seagrass meadows globally causing eutrophication and sedimentation. These environmental stressors induce sudden ecosystem shifts toward new alternative stable states defined by lower seagrass richness and abundance. Enhalus acoroides, a large-sized tropical seagrass species, appears to be more resistant toward environmental change compared to coexisting seagrass species. We hypothesize that reproductive strategy and the extent of seedling recruitment of E. acoroides are altered under disturbance and contribute to the persistence and resilience of E. acoroides meadows. In this research, we studied eight populations of E. acoroides in four lagoons along the South Central Coast of Vietnam using 11 polymorphic microsatellite loci. We classified land use in 6 classes based on Sentinel-2 L2A images and determined the effect of human-induced land use at different spatial scales on clonal richness and structure, fine-scale genetic structure and genetic diversity. No evidence of population size reductions due to disturbance was found, however, lagoons were strongly differentiated and may act as barriers to gene flow. The proportion and size of clones were significantly higher in populations of surrounding catchments with larger areas of agriculture, urbanization and aquaculture. We postulate that large resistant genets contribute to the resilience of E. acoroides meadows under high levels of disturbance. Although the importance of clonal growth increases with disturbance, sexual reproduction and the subsequent recruitment of seedlings remains an essential strategy for the persistence of populations of E. acoroides and should be prioritized in conservation measures to ensure broad-scale and long-term resilience toward future environmental change.
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Affiliation(s)
- Jasper Dierick
- Ecology and Biodiversity Research Group, Biology Department, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Thi Thuy Hang Phan
- Biology Department, University of Sciences, Hue University, Hue, Vietnam
| | - Quang Doc Luong
- Biology Department, University of Sciences, Hue University, Hue, Vietnam
| | - Ludwig Triest
- Ecology and Biodiversity Research Group, Biology Department, Vrije Universiteit Brussel (VUB), Brussels, Belgium
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Chen XD, Yang J, Guo YF, Zhao YM, Zhou T, Zhang X, Ju MM, Li ZH, Zhao GF. Spatial Genetic Structure and Demographic History of the Dominant Forest Oak Quercus fabri Hance in Subtropical China. FRONTIERS IN PLANT SCIENCE 2021; 11:583284. [PMID: 33613578 PMCID: PMC7889815 DOI: 10.3389/fpls.2020.583284] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/14/2020] [Accepted: 12/22/2020] [Indexed: 06/12/2023]
Abstract
Oak trees (Quercus L.) are important models for estimating abiotic impacts on the population structure and demography of long life span tree species. In this study, we generated genetic data for 17 nuclear microsatellite loci in 29 natural populations of Quercus fabri to estimate the population genetic structure. We also integrated approximate Bayesian computation (ABC) and ecological niche analysis to infer the population differentiation processes and demographic history of this oak species. The genetic analyses indicated two genetic clusters across the 29 populations collected, where most approximately corresponded to the intraspecific differentiation among populations from western and eastern China, whereas admixed populations were mainly found in central mountains of China. The best model obtained from hierarchical ABC simulations suggested that the initial intraspecific divergence of Q. fabri potentially occurred during the late Pliocene (ca. 3.99 Ma) to form the two genetic clusters, and the admixed population group might have been generated by genetic admixture of the two differentiated groups at ca. 53.76 ka. Ecological analyses demonstrated clear differentiation among the Q. fabri population structures, and association estimations also indicated significant correlations between geography and climate with the genetic variation in this oak species. Our results suggest abiotic influences, including past climatic changes and ecological factors, might have affected the genetic differentiation and demographic history of Q. fabri in subtropical China.
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Affiliation(s)
- Xiao-Dan Chen
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Jia Yang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Yu-Fan Guo
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Yue-Mei Zhao
- School of Biological Sciences, Guizhou Education University, Guiyang, China
| | - Tao Zhou
- School of Pharmacy, Xi’an Jiaotong University, Xi’an, China
| | - Xiao Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Miao-Miao Ju
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
| | - Gui-Fang Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western China (Ministry of Education), College of Life Sciences, Northwest University, Xi’an, China
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Conservation and Loss of a Putative Iron Utilization Gene Cluster among Genotypes of Aspergillus flavus. Microorganisms 2021; 9:microorganisms9010137. [PMID: 33435439 PMCID: PMC7827000 DOI: 10.3390/microorganisms9010137] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/21/2020] [Revised: 01/04/2021] [Accepted: 01/07/2021] [Indexed: 11/20/2022] Open
Abstract
Iron is an essential component for growth and development. Despite relative abundance in the environment, bioavailability of iron is limited due to oxidation by atmospheric oxygen into insoluble ferric iron. Filamentous fungi have developed diverse pathways to uptake and use iron. In the current study, a putative iron utilization gene cluster (IUC) in Aspergillus flavus was identified and characterized. Gene analyses indicate A. flavus may use reductive as well as siderophore-mediated iron uptake and utilization pathways. The ferroxidation and iron permeation process, in which iron transport depends on the coupling of these two activities, mediates the reductive pathway. The IUC identified in this work includes six genes and is located in a highly polymorphic region of the genome. Diversity among A. flavus genotypes is manifested in the structure of the IUC, which ranged from complete deletion to a region disabled by multiple indels. Molecular profiling of A. flavus populations suggests lineage-specific loss of IUC. The observed variation among A. flavus genotypes in iron utilization and the lineage-specific loss of the iron utilization genes in several A. flavus clonal lineages provide insight on evolution of iron acquisition and utilization within Aspergillus section Flavi. The potential divergence in capacity to acquire iron should be taken into account when selecting A. flavus active ingredients for biocontrol in niches where climate change may alter iron availability.
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Zhao Z, Heideman N, Bester P, Jordaan A, Hofmeyr MD. Climatic and topographic changes since the Miocene influenced the diversification and biogeography of the tent tortoise (Psammobates tentorius) species complex in Southern Africa. BMC Evol Biol 2020; 20:153. [PMID: 33187474 PMCID: PMC7666511 DOI: 10.1186/s12862-020-01717-1] [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: 06/17/2020] [Accepted: 11/02/2020] [Indexed: 11/10/2022] Open
Abstract
BACKGROUND Climatic and topographic changes function as key drivers in shaping genetic structure and cladogenic radiation in many organisms. Southern Africa has an exceptionally diverse tortoise fauna, harbouring one-third of the world's tortoise genera. The distribution of Psammobates tentorius (Kuhl, 1820) covers two of the 25 biodiversity hotspots in the world, the Succulent Karoo and Cape Floristic Region. The highly diverged P. tentorius represents an excellent model species for exploring biogeographic and radiation patterns of reptiles in Southern Africa. RESULTS We investigated genetic structure and radiation patterns against temporal and spatial dimensions since the Miocene in the Psammobates tentorius species complex, using multiple types of DNA markers and niche modelling analyses. Cladogenesis in P. tentorius started in the late Miocene (11.63-5.33 Ma) when populations dispersed from north to south to form two geographically isolated groups. The northern group diverged into a clade north of the Orange River (OR), followed by the splitting of the group south of the OR into a western and an interior clade. The latter divergence corresponded to the intensification of the cold Benguela current, which caused western aridification and rainfall seasonality. In the south, tectonic uplift and subsequent exhumation, together with climatic fluctuations seemed responsible for radiations among the four southern clades since the late Miocene. We found that each clade occurred in a habitat shaped by different climatic parameters, and that the niches differed substantially among the clades of the northern group but were similar among clades of the southern group. CONCLUSION Climatic shifts, and biome and geographic changes were possibly the three major driving forces shaping cladogenesis and genetic structure in Southern African tortoise species. Our results revealed that the cladogenesis of the P. tentorius species complex was probably shaped by environmental cooling, biome shifts and topographic uplift in Southern Africa since the late Miocene. The Last Glacial Maximum (LGM) may have impacted the distribution of P. tentorius substantially. We found the taxonomic diversify of the P. tentorius species complex to be highest in the Greater Cape Floristic Region. All seven clades discovered warrant conservation attention, particularly Ptt-B-Ptr, Ptt-A and Pv-A.
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Affiliation(s)
- Zhongning Zhao
- Department of Zoology and Entomology, University of the Free State, Biology Building B19, 205 Nelson Mandela Dr, Park West, Bloemfontein, South Africa.
| | - Neil Heideman
- Department of Zoology and Entomology, University of the Free State, Biology Building B19, 205 Nelson Mandela Dr, Park West, Bloemfontein, South Africa
| | - Phillip Bester
- Department of Virology, University of the Free State and National Health Laboratory Service (NHLS), Bloemfontein, South Africa
| | - Adriaan Jordaan
- Department of Zoology and Entomology, University of the Free State, Biology Building B19, 205 Nelson Mandela Dr, Park West, Bloemfontein, South Africa
| | - Margaretha D Hofmeyr
- Department of Biodiversity and Conservation Biology, Chelonian Biodiversity and Conservation, University of the Western Cape, Bellville, South Africa
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Shi M, Wang Y, Duan T, Qian X, Zeng T, Zhang D. In situ glacial survival maintains high genetic diversity of Mussaenda kwangtungensis on continental islands in subtropical China. Ecol Evol 2020; 10:11304-11321. [PMID: 33144966 PMCID: PMC7593160 DOI: 10.1002/ece3.6768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/18/2019] [Revised: 07/06/2020] [Accepted: 08/18/2020] [Indexed: 11/23/2022] Open
Abstract
Generally, island populations are predicted to have less genetic variation than their mainland relatives. However, a growing number of studies have nevertheless reported exceptions, indicating that the relationships were impacted by several factors, for example, historical processes. In the present study, we chose a group of subtropical islands located in South China as the study system, which are quite younger and much closer to the mainland than most of the previous studied island systems, to test the hypothesis that in situ glacial survival contributes to high levels of genetic diversity in island populations. We conducted a comparison of genetic variation between 12 island and 11 nearby mainland populations of Mussaenda kwangtungensis using eleven nuclear microsatellite and three chloroplast markers, evaluated effects of the island area and distance to mainland on genetic diversity of island populations, and simulated the potential distribution over the past by ecological niche modeling, together with the genetic data to detect the role of islands during the glacial periods. The island populations displayed comparable levels of genetic diversity and differentiation with mainland populations, overall high levels of unique polymorphisms, and the greatest values of specific within-population genetic diversity. No significant correlation was detected between genetic diversity of island populations and distance to mainland, as well as area of islands, except that allelic richness was significantly positively correlated with the area of islands. Nuclear microsatellites revealed two main clusters, largely corresponding to islands and inland populations, which divergence dated to a time of island formation by ABC analysis. Ecological niche modeling predicted a highly climatic suitability on islands during the last glacial maximum (LGM). Our results suggest that the islands have acted as refugia during the LGM and highlight the role of in situ glacial survival in maintaining high levels of genetic diversity of M. kwangtungensis in continental islands of subtropical China.
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Affiliation(s)
- Miaomiao Shi
- Key Laboratory of Plant Resources Conservation and Sustainable UtilizationSouth China Botanical GardenChinese Academy of SciencesGuangzhouChina
- Center of Conservation BiologyCore Botanical GardensChinese Academy of SciencesGuangzhouChina
| | - Yuyuan Wang
- Key Laboratory of Plant Resources Conservation and Sustainable UtilizationSouth China Botanical GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | | | - Xin Qian
- College of Life SciencesFujian Agriculture and Forestry UniversityFuzhouChina
| | - Tong Zeng
- Key Laboratory of Plant Resources Conservation and Sustainable UtilizationSouth China Botanical GardenChinese Academy of SciencesGuangzhouChina
- University of Chinese Academy of SciencesBeijingChina
| | - Dianxiang Zhang
- Key Laboratory of Plant Resources Conservation and Sustainable UtilizationSouth China Botanical GardenChinese Academy of SciencesGuangzhouChina
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Luo W, Wu Q, Yang L, Chen P, Yang S, Wang T, Wang Y, Du Z. SSREnricher: a computational approach for large-scale identification of polymorphic microsatellites based on comparative transcriptome analysis. PeerJ 2020; 8:e9372. [PMID: 32676221 PMCID: PMC7335497 DOI: 10.7717/peerj.9372] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/24/2019] [Accepted: 05/27/2020] [Indexed: 11/20/2022] Open
Abstract
Microsatellite (SSR) markers are the most popular markers for genetic analyses and molecular selective breeding in plants and animals. However, the currently available methods to develop SSRs are relatively time-consuming and expensive. One of the most factors is low frequency of polymorphic SSRs. In this study, we developed a software, SSREnricher, which composes of six core analysis procedures, including SSR mining, sequence clustering, sequence modification, enrichment containing polymorphic SSR sequences, false-positive removal and results output and multiple sequence alignment. After running of transcriptome sequences on this software, a mass of polymorphic SSRs can be identified. The validation experiments showed almost all markers (>90%) that were identified by the SSREnricher as putative polymorphic markers were indeed polymorphic. The frequency of polymorphic SSRs identified by SSREnricher was significantly higher (P < 0.05) than that of traditional and HTS approaches. The software package is publicly accessible on GitHub (https://github.com/byemaxx/SSREnricher).
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Affiliation(s)
- Wei Luo
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Qing Wu
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Lan Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Pengyu Chen
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Siqi Yang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Tianzhu Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Yan Wang
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
| | - Zongjun Du
- College of Animal Science and Technology, Sichuan Agricultural University, Chengdu, Sichuan, China
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40
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Zhao L, Zhang JX, Zhang YH. Genetic boundary and gene flow between 2 parapatric subspecies of brown rats. Curr Zool 2020; 66:677-688. [PMID: 33391367 PMCID: PMC7769575 DOI: 10.1093/cz/zoaa027] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/14/2020] [Accepted: 05/30/2020] [Indexed: 12/30/2022] Open
Abstract
Two parapatric Rattus norvegicus subspecies, R. n. humiliatus (RNH) and R. n. caraco (RNC), are classified according to morphological divergence and are mainly distributed in North and Northeast China. Here, we aimed to explore the population genetic structure, genetic boundary, and gene flow in these rats using 16 microsatellite loci. Structure analysis and principal component analysis revealed 3 ancestral clusters. We found that the intermediate cluster exhibited higher genetic diversity and a lower inbreeding coefficient than the other 2 clusters. The genetic differentiation between the 3 clusters was significant but weak, with a higher FST value being observed between the clusters on both sides. The subspecies boundary inferred from microsatellite markers may indicate the existence of an admixture or hybridization area covering Liaoning, Inner Mongolia, and Jilin Provinces, rather than corresponding to the administrative provincial boundaries between Liaoning and Jilin. The RNH and RNC subspecies presented moderate gene exchange and an asymmetric bidirectional gene flow pattern, with higher gene flow from the RNH subspecies to the RNC subspecies, constraining speciation. Such genetic characteristics might be explained by biological processes such as dispersal ability, mate choice, and dynamic lineage boundaries.
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Affiliation(s)
- Lei Zhao
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Jian-Xu Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing 100101, China.,CAS Center for Excellence in Biotic Interactions, University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Yao-Hua Zhang
- State Key Laboratory of Integrated Management of Pest Insects and Rodents in Agriculture, Institute of Zoology, Chinese Academy of Sciences, Beichen West Road 1-5, Chaoyang District, Beijing 100101, China
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Zhang TT, Zhang NY, Li W, Zhou XJ, Pei XY, Liu YG, Ren ZY, He KL, Zhang WS, Zhou KH, Zhang F, Ma XF, Yang DG, Li ZH. Genetic structure, gene flow pattern, and association analysis of superior germplasm resources in domesticated upland cotton ( Gossypium hirsutum L.). PLANT DIVERSITY 2020; 42:189-197. [PMID: 32695952 PMCID: PMC7361167 DOI: 10.1016/j.pld.2020.03.001] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 07/29/2019] [Revised: 02/28/2020] [Accepted: 03/03/2020] [Indexed: 06/11/2023]
Abstract
Gene flow patterns and the genetic structure of domesticated crops like cotton are not well understood. Furthermore, marker-assisted breeding of cotton has lagged far behind that of other major crops because the loci associated with cotton traits such as fiber yield and quality have scarcely been identified. In this study, we used 19 microsatellites to first determine the population genetic structure and patterns of gene flow of superior germplasm resources in upland cotton. We then used association analysis to identify which markers were associated with 15 agronomic traits (including ten yield and five fiber quality traits). The results showed that the upland cotton accessions have low levels of genetic diversity (polymorphism information content = 0.427), although extensive gene flow occurred among different ecological and geographic regions. Bayesian clustering analysis indicated that the cotton resources used in this study did not belong to obvious geographic populations, which may be the consequence of a single source of domestication followed by frequent genetic introgression mediated by human transference. A total of 82 maker-trait associations were examined in association analysis and the related ratios for phenotypic variations ranged from 3.04% to 47.14%. Interestingly, nine SSR markers were detected in more than one environmental condition. In addition, 14 SSR markers were co-associated with two or more different traits. It was noteworthy that NAU4860 and NAU5077 markers detected at least in two environments were simultaneously associated with three fiber quality traits (uniformity index, specific breaking strength and micronaire value). In conclusion, these findings provide new insights into the population structure and genetic exchange pattern of cultivated cotton accessions. The quantitative trait loci of domesticated cotton identified will also be very useful for improvement of yield and fiber quality of cotton in molecular breeding programs.
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Affiliation(s)
- Ting-Ting Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Na-Yao Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, China
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wei Li
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiao-Jian Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiao-Yu Pei
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Yan-Gai Liu
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhong-Ying Ren
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Kun-Lun He
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Wen-Sheng Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Ke-Hai Zhou
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Fei Zhang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Xiong-Feng Ma
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Dai-Gang Yang
- State Key Laboratory of Cotton Biology, Institute of Cotton Research, Chinese Academy of Agricultural Sciences, Anyang, 455000, China
| | - Zhong-Hu Li
- Key Laboratory of Resource Biology and Biotechnology in Western China, Ministry of Education, College of Life Sciences, Northwest University, Xi'an, 710069, China
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Hina F, Yisilam G, Wang S, Li P, Fu C. De novo Transcriptome Assembly, Gene Annotation and SSR Marker Development in the Moon Seed Genus Menispermum (Menispermaceae). Front Genet 2020; 11:380. [PMID: 32457795 PMCID: PMC7227793 DOI: 10.3389/fgene.2020.00380] [Citation(s) in RCA: 11] [Impact Index Per Article: 2.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/03/2019] [Accepted: 03/27/2020] [Indexed: 12/27/2022] Open
Abstract
The moonseed genus Menispermum L. (Menispermaceae) is disjunctly distributed in East Asia and eastern North America. Although Menispermum has important medicinal value, genetic and genomic information is scarce, with very few available molecular markers. In the current study, we used Illumina transcriptome sequencing and de novo assembly of the two Menispermum species to obtain in-depth genetic knowledge. From de novo assembly, 53,712 and 78,921 unigenes were generated for M. canadense and M. dauricum, with 37,527 (69.87%) and 55,211 (69.96%) showing significant similarities against the six functional databases, respectively. Moreover, 521 polymorphic EST-SSRs were identified. Of them, 23 polymorphic EST-SSR markers were selected to investigate the population genetic diversity within the genus. The newly developed EST-SSR markers also revealed high transferability among the three examined Menispermaceae species. Overall, we provide the very first transcriptomic analyses of this important medicinal genus. In addition, the novel microsatellite markers developed here will aid future studies on the population genetics and phylogeographic patterns of Menispermum at the intercontinental geographical scale.
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Affiliation(s)
- Faiza Hina
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Gulbar Yisilam
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Shenyi Wang
- Department of Botany, University of Wisconsin–Madison, Madison, WI, United States
| | - Pan Li
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
| | - Chengxin Fu
- Laboratory of Systematic and Evolutionary Botany and Biodiversity, College of Life Sciences, Zhejiang University, Hangzhou, China
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Mehmood S, Sajid M, Husnain SK, Zhao J, Huang L, Kang Z. Study of Inheritance and Linkage of Virulence Genes in a Selfing Population of a Pakistani Dominant Race of Puccinia striiformis f. sp. tritici. Int J Mol Sci 2020; 21:ijms21051685. [PMID: 32121459 PMCID: PMC7084513 DOI: 10.3390/ijms21051685] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/10/2019] [Revised: 02/25/2020] [Accepted: 02/26/2020] [Indexed: 11/16/2022] Open
Abstract
Wheat stripe rust is a severe threat of almost all wheat-growing regions in the world. Being an obligate biotrophic fungus, Puccinia striiformis f. sp. tritici (PST) produces new virulent races that break the resistance of wheat varieties. In this study, 115 progeny isolates were generated through sexual reproduction on susceptible Himalayan Berberis pseudumbellata using a dominant Pakistani race (574232) of PST. The parental isolate and progeny isolates were characterized using 24 wheat Yr single-gene lines and ten simple sequence repeat (SSR) markers. From the one-hundred-and-fifteen progeny isolates, 25 virulence phenotypes (VPs) and 60 multilocus genotypes were identified. The parental and all progeny isolates were avirulent to Yr5, Yr10, Yr15, Yr24, Yr32, Yr43, YrSp, YrTr1, YrExp2, Yr26, and YrTye and virulent to Yr1, Yr2, Yr6, Yr7, Yr8, Yr9, Yr17, Yr25, Yr27, Yr28, YrA, Yr44, and Yr3. Based on the avirulence/virulence phenotypes, we found that VPs virulent to Yr1, Yr2, Yr9, Yr17, Yr47, and YrA were controlled by one dominant gene; those to YrSp, YrTr1, and Yr10 by two dominant genes; and those to YrExp2 by two complementary dominant genes. The results are useful in breeding stripe rust-resistant wheat varieties and understanding virulence diversity.
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Affiliation(s)
- Sajid Mehmood
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, China; (S.M.); (Z.K.)
| | - Marina Sajid
- College of Food Science and Engineering, Northwest A&F University, Yangling 712100, China;
| | - Syed Kamil Husnain
- Plant Pathology Section, Barani Agricultural Research Institute, Chakwal 48800, Punjab, Pakistan;
| | - Jie Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, China; (S.M.); (Z.K.)
- Correspondence: (J.Z.); (L.H.); Tel.: +86-29-870-18-1317 (J.Z.); +86-29-8709-1312 (L.H.)
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, China; (S.M.); (Z.K.)
- Correspondence: (J.Z.); (L.H.); Tel.: +86-29-870-18-1317 (J.Z.); +86-29-8709-1312 (L.H.)
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas, College of Plant Protection, Northwest A&F University, Yangling 712100, China; (S.M.); (Z.K.)
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Gregório I, Barros T, Pando D, Morante J, Fonseca C, Ferreira E. Paths for colonization or exodus? New insights from the brown bear (Ursus arctos) population of the Cantabrian Mountains. PLoS One 2020; 15:e0227302. [PMID: 32004321 PMCID: PMC6996475 DOI: 10.1371/journal.pone.0227302] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/20/2019] [Accepted: 12/16/2019] [Indexed: 01/30/2023] Open
Abstract
Over the centuries, the geographical distribution of brown bear (Ursus arctos) across the Iberian Peninsula has been decreasing, with the species currently confined to North Iberia. The Cantabrian brown bear population is one of the smallest in Europe and is structured into two subpopulations, positioned along an east-west axis. Given the current critically endangered status of this population, it is essential to have a clear picture of its within-population genetic patterns and processes. We use a set of three molecular markers (mitochondrial DNA, autosomal microsatellites and sex markers) to clarify the genetic origins and assess the migration patterns and gene flow of the Cantabrian brown bear population. Our results reveal the presence of two different mitochondrial (matrilineal) haplotypes in the Cantabrian population, both belonging to European brown bear clade 1a. The two haplotypes are geographically structured between Eastern (haplotype CanE) and Western Cantabrian (haplotype CanW) subpopulations, which is consistent with the genetic structure previously identified using nuclear markers. Additionally, we show that CanE is closer to the historical Pyrenean (Pyr) haplotype than to CanW. Despite strong structuring at the levels of mtDNA and nuclear loci, there is evidence of bidirectional gene flow and admixture among subpopulations. Gene flow is asymmetrical and significantly more intense from the Eastern to the Western Cantabrian subpopulation. In fact, we only detected first generation male migrants from the Eastern to the Western Cantabrian subpopulation. These results suggest more intense migration from the smaller and more vulnerable Eastern Cantabrian subpopulation towards the larger and more stable Western Cantabrian subpopulation. These new insights are relevant for assessments of on-going conservation measures, namely the role of dispersal corridors and enhanced connectivity. We discuss the importance of complementary conservation measures, such as human-wildlife conflict mitigation and habitat improvement, for the conservation of a viable Cantabrian brown bear population.
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Affiliation(s)
- Inês Gregório
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Tânia Barros
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Doriana Pando
- Fondo para la Protección de los Animales Salvajes, Santo Adriano, Asturias, Spain
| | - Joaquín Morante
- Fondo para la Protección de los Animales Salvajes, Santo Adriano, Asturias, Spain
| | - Carlos Fonseca
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
| | - Eduardo Ferreira
- Department of Biology & CESAM, University of Aveiro, Campus Universitário de Santiago, Aveiro, Portugal
- * E-mail:
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Zhou H, Hu Y, Jiang H, Duan G, Ling J, Pan T, Chen X, Wang H, Zhang Y. Population genetics of swamp eel in the Yangtze River: comparative analyses between mitochondrial and microsatellite data provide novel insights. PeerJ 2020; 8:e8415. [PMID: 31998563 PMCID: PMC6979408 DOI: 10.7717/peerj.8415] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/31/2019] [Accepted: 12/16/2019] [Indexed: 11/20/2022] Open
Abstract
The swamp eel (Monopterus albus) is a typical sex reversal fish with high economic value. Several phylogeographic studies have been performed using various markers but comparative research between mitochondrial and nuclear markers is rare. Here, a fine-scale study was performed across six sites along the Yangtze River including three sites on the main stem and three sites from tributaries. A total of 180 swamp eel individuals were collected. Genetic structure and demographic history were explored using data from two mitochondrial genes and eight microsatellite loci. The results revealed the samples from tributary sites formed three separate clades which contained site-specific lineages. Geographic isolation and the habitat patchiness caused by seasonal cutoff were inferred to be the reasons for this differentiation. Strong gene flow was detected among the sites along the main stem. Rapid flow of the river main stem may provide the dynamic for the migration of swamp eel. Interestingly, the comparative analyses between the two marker types was discordant. Mitochondrial results suggested samples from three tributary sites were highly differentiated. However, microsatellite analyses indicated the tributary samples were moderately differentiated. We conclude this discordance is mainly caused by the unique life history of sex reversal fish. Our study provides novel insights regarding the population genetics of sex reversal fish.
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Affiliation(s)
- Huaxing Zhou
- Anhui Key Laboratory of Aquaculture and Stock Enhancement, Fisheries Research Institution, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Yuting Hu
- Anhui Key Laboratory of Aquaculture and Stock Enhancement, Fisheries Research Institution, Anhui Academy of Agricultural Sciences, Hefei, China
| | - He Jiang
- Anhui Key Laboratory of Aquaculture and Stock Enhancement, Fisheries Research Institution, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Guoqing Duan
- Anhui Key Laboratory of Aquaculture and Stock Enhancement, Fisheries Research Institution, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Jun Ling
- Anhui Key Laboratory of Aquaculture and Stock Enhancement, Fisheries Research Institution, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Tingshuang Pan
- Anhui Key Laboratory of Aquaculture and Stock Enhancement, Fisheries Research Institution, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Xiaolei Chen
- Anhui Key Laboratory of Aquaculture and Stock Enhancement, Fisheries Research Institution, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Huan Wang
- Anhui Key Laboratory of Aquaculture and Stock Enhancement, Fisheries Research Institution, Anhui Academy of Agricultural Sciences, Hefei, China
| | - Ye Zhang
- Anhui Key Laboratory of Aquaculture and Stock Enhancement, Fisheries Research Institution, Anhui Academy of Agricultural Sciences, Hefei, China
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Deng JY, van Noort S, Compton SG, Chen Y, Greeff JM. The genetic consequences of habitat specificity for fig trees in southern African fragmented forests. ACTA OECOLOGICA 2020. [DOI: 10.1016/j.actao.2019.103506] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 11/16/2022]
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Sun Y, Hou N, Woeste K, Zhang C, Yue M, Yuan X, Zhao P. Population genetic structure and adaptive differentiation of iron walnut Juglans regia subsp. sigillata in southwestern China. Ecol Evol 2019; 9:14154-14166. [PMID: 31938510 PMCID: PMC6953554 DOI: 10.1002/ece3.5850] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/25/2019] [Revised: 10/29/2019] [Accepted: 10/30/2019] [Indexed: 11/07/2022] Open
Abstract
Southwestern (SW) China is an area of active tectonism and erosion, yielding a dynamic, deeply eroded landscape that influences the genetic structure of the resident populations of plants and animals. Iron walnut (Juglans regia subsp. sigillata) is a deciduous tree species endemic to this region of China and cultivated there for its edible nuts. We sampled 36 iron walnut populations from locations throughout the species' range in SW China and genotyped a total of 765 individuals at five chloroplast DNA regions and 22 nuclear microsatellite loci. Species distribution models were produced to predict the evolution and historical biogeography of iron walnut and to estimate the impacts of climate oscillations and orographic environments on the species' demography. Our results indicated that J. regia subsp. sigillata had relatively low genetic diversity, high interpopulation genetic differentiation, and asymmetric interpopulation gene flow. Based on DIYABC analysis, we identified two lineages of J. sigillata in southwestern China. The lineages (subpopulations) diverge during the last glacial period (~1.34 Ma). Southwestern China was a glacial refuge during the last glacial period, but increasingly colder and arid climates might have fostered the fragmentation of J. regia subsp. sigillata within this refugium. Finally, we found that recent habitat fragmentation has led to a reduction in population connectivity and increased genetic differentiation by genetic drift in isolated populations. Our results support a conclusion that geological and climatic factors since the Miocene triggered the differentiation, evolutionary origin, and range shifts of J. sigillata in the studied region.
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Affiliation(s)
- Yi‐Wei Sun
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
| | - Na Hou
- Guizhou Academy of ForestryGuiyangChina
| | - Keith Woeste
- Department of Forestry and Natural ResourcesUSDA Forest Service Hardwood Tree Improvement and Regeneration Center (HTIRC)Purdue UniversityWest LafayetteINUSA
| | - Chuchu Zhang
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
| | - Ming Yue
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
- Xi'an Botanical Garden of Shaanxi ProvinceXi'anChina
| | - Xiao‐Ying Yuan
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
| | - Peng Zhao
- Key Laboratory of Resource Biology and Biotechnology in Western ChinaMinistry of EducationCollege of Life SciencesNorthwest UniversityXi'anChina
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Ambrose L, Hanson JO, Riginos C, Xu W, Fordyce S, Cooper RD, Beebe NW. Population genetics of Anopheles koliensis through Papua New Guinea: New cryptic species and landscape topography effects on genetic connectivity. Ecol Evol 2019; 9:13375-13388. [PMID: 31871651 PMCID: PMC6912914 DOI: 10.1002/ece3.5792] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/06/2019] [Revised: 07/19/2019] [Accepted: 07/28/2019] [Indexed: 12/01/2022] Open
Abstract
New Guinea is a topographically and biogeographically complex region that supports unique endemic fauna. Studies describing the population connectivity of species through this region are scarce. We present a population and landscape genetic study on the endemic malaria-transmitting mosquito, Anopheles koliensis (Owen). Using mitochondrial and nuclear sequence data, as well as microsatellites, we show the evidence of geographically discrete population structure within Papua New Guinea (PNG). We also confirm the existence of three rDNA ITS2 genotypes within this mosquito and assess reproductive isolation between individuals carrying different genotypes. Microsatellites reveal the clearest population structure and show four clear population units. Microsatellite markers also reveal probable reproductive isolation between sympatric populations in northern PNG with different ITS2 genotypes, suggesting that these populations may represent distinct cryptic species. Excluding individuals belonging to the newly identified putative cryptic species (ITS2 genotype 3), we modeled the genetic differences between A. koliensis populations through PNG as a function of terrain and find that dispersal is most likely along routes with low topographic relief. Overall, these results show that A. koliensis is made up of geographically and genetically discrete populations in Papua New Guinea with landscape topography being important in restricting dispersal.
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Affiliation(s)
- Luke Ambrose
- School of Biological SciencesUniversity of QueenslandBrisbaneQldAustralia
| | - Jeffrey O. Hanson
- School of Biological SciencesUniversity of QueenslandBrisbaneQldAustralia
| | - Cynthia Riginos
- School of Biological SciencesUniversity of QueenslandBrisbaneQldAustralia
| | - Weixin Xu
- School of Biological SciencesUniversity of QueenslandBrisbaneQldAustralia
| | - Sarah Fordyce
- Department of Forensic MedicineUniversity of CopenhagenCopenhagenDenmark
| | - Robert D. Cooper
- ADF Malaria and Infectious Disease InstituteEnoggeraQldAustralia
| | - Nigel W. Beebe
- School of Biological SciencesUniversity of QueenslandBrisbaneQldAustralia
- CSIROSt LuciaQldAustralia
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Siyoum GZ, Zeng Q, Zhao J, Chen X, Badebo A, Tian Y, Huang L, Kang Z, Zhan G. Inheritance of Virulence and Linkages of Virulence Genes in an Ethiopian Isolate of the Wheat Stripe Rust Pathogen ( Puccinia striiformis f. sp. tritici) Determined Through Sexual Recombination on Berberis holstii. PLANT DISEASE 2019; 103:2451-2459. [PMID: 31322491 DOI: 10.1094/pdis-02-19-0269-re] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
Stripe rust, caused by Puccinia striiformis f. sp. tritici, is one of the most devastating wheat diseases in Ethiopia. To study virulence genetics of the pathogen, 117 progeny isolates were produced through sexual reproduction of an Ethiopian isolate of the stripe rust pathogen on Berberis holstii plants under controlled conditions. The parental and progeny isolates were characterized by phenotyping on wheat lines carrying single Yr genes for resistance and genotyped using 10 polymorphic simple sequence repeated (SSR) markers. The progeny isolates were classified into 37 virulence phenotypes and 75 multilocus genotypes. The parental isolate and progeny isolates were all avirulent to resistance genes Yr5, Yr10, Yr15, Yr24, Yr32, YrTr1, YrSP, and Yr76 but virulent to Yr1 and Yr2, indicating that the parental isolate was homozygous avirulent or homozygous virulent at these loci. The progeny isolates segregated for virulence to 12 Yr genes. Virulence phenotypes to Yr6, Yr28, Yr43, and Yr44 were controlled by a single dominant gene; those to Yr7, Yr9, Yr17, Yr27, Yr25, Yr31, and YrExp2 were each controlled by two dominant genes; and the virulence phenotype to Yr8 was controlled by two complementary dominant genes. A linkage map was constructed with seven SSR markers, and 16 virulence loci corresponding to 11 Yr resistance genes were mapped with some loci linked to each other. These results are useful in understanding host-pathogen interactions and selecting resistance genes to develop wheat cultivars with highly effective resistance to stripe rust.
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Affiliation(s)
- Gebreslasie Zeray Siyoum
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Qingdong Zeng
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Jie Zhao
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Xianming Chen
- Wheat Health, Genetics, and Quality Research Unit, U.S. Department of Agriculture Agricultural Research Service, Pullman, WA 99164-6430, U.S.A
| | - Ayele Badebo
- International Maize and Wheat Improvement Center (CIMMYT) Ethiopia, International Livestock Research Institute Gurd Shola Campus, Addis Ababa, Ethiopia
| | - Yuan Tian
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Lili Huang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Zhensheng Kang
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
| | - Gangming Zhan
- State Key Laboratory of Crop Stress Biology for Arid Areas and College of Plant Protection, Northwest A&F University, Yangling, Shaanxi 712100, People's Republic of China
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50
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Pan T, Zhou K, Zhang S, Shu Y, Zhang J, Li E, Wang M, Yan P, Wu H. Effects of dispersal barriers and geographic distance on the genetic structure of a narrowly distributed frog in a spatially structured landscape. J Zool (1987) 2019. [DOI: 10.1111/jzo.12730] [Citation(s) in RCA: 4] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/30/2022]
Affiliation(s)
- T. Pan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - K. Zhou
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - S.‐L. Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - Y.‐L. Shu
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - J.‐H. Zhang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - E. Li
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - M.‐S. Wang
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - P. Yan
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
| | - H.‐L. Wu
- Anhui Provincial Key Laboratory of the Conservation and Exploitation of Biological Resources College of Life Sciences Anhui Normal University Wuhu China
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