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Boscari E, Palle SD, Vitulo N, Scapolatiello A, Schiavon L, Cariani A, Papetti C, Zane L, Marino IAM, Congiu L. MIPs: multi-locus intron polymorphisms in species identification and population genomics. Sci Rep 2024; 14:17870. [PMID: 39090215 PMCID: PMC11294542 DOI: 10.1038/s41598-024-68065-8] [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: 10/30/2023] [Accepted: 07/19/2024] [Indexed: 08/04/2024] Open
Abstract
The study of species groups in which the presence of interspecific hybridization or introgression phenomena is known or suspected involves analysing shared bi-parentally inherited molecular markers. Current methods are based on different categories of markers among which the classical microsatellites or the more recent genome wide approaches for the analyses of thousands of SNPs or hundreds of microhaplotypes through high throughput sequencing. Our approach utilizes intron-targeted amplicon sequencing to characterise multi-locus intron polymorphisms (MIPs) and assess genetic diversity. These highly variable intron regions, combined with inter-specific transferable loci, serve as powerful multiple-SNP markers potentially suitable for various applications, from species and hybrid identification to population comparisons, without prior species knowledge. We developed the first panel of MIPs highly transferable across fish genomes, effectively distinguishing between species, even those closely related, and populations with different structures. MIPs offer versatile, hypervariable nuclear markers and promise to be especially useful when multiple nuclear loci must be genotyped across different species, such as for the monitoring of interspecific hybridization. Moreover, the relatively long sequences obtained ease the development of single-locus PCR-based diagnostic markers. This method, here demonstrated in teleost fishes, can be readily applied to other taxa, unlocking a new source of genetic variation.
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Affiliation(s)
- Elisa Boscari
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35121, Padova, Italy.
| | - Stefano Dalle Palle
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35121, Padova, Italy
| | - Nicola Vitulo
- Department of Biotechnology, University of Verona, Strada le Grazie, 15, 37134, Verona, Italy
| | | | - Luca Schiavon
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35121, Padova, Italy
| | - Alessia Cariani
- Department Biological, Geological and Environmental Sciences, University of Bologna, Campus of Ravenna, Via Sant'Alberto 163, 48123, Ravenna, Italy
- Consorzio Nazionale Interuniversitario Per le Scienze del Mare (CoNISMa), Piazzale Flaminio 9, 00196, Roma, Italy
- National Biodiversity Future Center, Palermo, Italy
| | - Chiara Papetti
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35121, Padova, Italy
- Consorzio Nazionale Interuniversitario Per le Scienze del Mare (CoNISMa), Piazzale Flaminio 9, 00196, Roma, Italy
- Zoological Station Anton Dohrn, Villa Comunale, 80121, Naples, Italy
| | - Lorenzo Zane
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35121, Padova, Italy
- Consorzio Nazionale Interuniversitario Per le Scienze del Mare (CoNISMa), Piazzale Flaminio 9, 00196, Roma, Italy
- National Biodiversity Future Center, Palermo, Italy
| | | | - Leonardo Congiu
- Department of Biology, University of Padova, Via Ugo Bassi 58B, 35121, Padova, Italy
- Consorzio Nazionale Interuniversitario Per le Scienze del Mare (CoNISMa), Piazzale Flaminio 9, 00196, Roma, Italy
- National Biodiversity Future Center, Palermo, Italy
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Taraveau F, Bru D, Quembo CJ, Jourdan-Pineau H. Development of microsatellite markers for the soft tick Ornithodoros phacochoerus. Parasit Vectors 2024; 17:301. [PMID: 38992704 PMCID: PMC11238500 DOI: 10.1186/s13071-024-06382-7] [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: 01/23/2024] [Accepted: 06/28/2024] [Indexed: 07/13/2024] Open
Abstract
BACKGROUND Soft ticks of the genus Ornithodoros are responsible for the maintenance and transmission of the African swine fever (ASF) virus in the sylvatic and domestic viral cycles in Southern Africa. They are also the main vectors of the Borrelia species causing relapsing fevers. Currently, no genetic markers are available for Afrotropical Ornithodoros ticks. As ASF spreads globally, such markers are needed to assess the role of ticks in the emergence of new outbreaks. The aim of this study is to design microsatellite markers that could be used for ticks of the Ornithodoros moubata complex, particularly Ornithodoros phacochoerus, to assess population structure and tick movements in ASF endemic areas. METHODS A total of 151 markers were designed using the O. moubata and O. porcinus genomes after elimination of repeated sequences in the genomes. All designed markers were tested on O. phacochoerus and O. porcinus DNA to select the best markers. RESULTS A total of 24 microsatellite markers were genotyped on two populations of O. phacochoerus and on individuals from four other Ornithodoros species. Nineteen markers were selected to be as robust as possible for population genetic studies on O. phacochoerus. CONCLUSIONS The microsatellite markers developed here represent the first genetic tool to study nidicolous populations of O. phacochoerus.
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Affiliation(s)
- Florian Taraveau
- UMR ASTRE, CIRAD, INRAE, Campus de Baillarguet, 34398, Montpellier, France.
| | - David Bru
- UMR ASTRE, CIRAD, INRAE, Campus de Baillarguet, 34398, Montpellier, France
| | - Carlos João Quembo
- Central Region Office-Regional Veterinary Laboratory, Agricultural Research Institute of Mozambique, Chimoio, EN6.CP42, Mozambique
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Koontz AC, Schumacher EK, Spence ES, Hoban SM. Ex situ conservation of two rare oak species using microsatellite and SNP markers. Evol Appl 2024; 17:e13650. [PMID: 38524684 PMCID: PMC10960078 DOI: 10.1111/eva.13650] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/03/2023] [Revised: 12/27/2023] [Accepted: 01/14/2024] [Indexed: 03/26/2024] Open
Abstract
Plant collections held by botanic gardens and arboreta are key components of ex situ conservation. Maintaining genetic diversity in such collections allows them to be used as resources for supplementing wild populations. However, most recommended minimum sample sizes for sufficient ex situ genetic diversity are based on microsatellite markers, and it remains unknown whether these sample sizes remain valid in light of more recently developed next-generation sequencing (NGS) approaches. To address this knowledge gap, we examine how ex situ conservation status and sampling recommendations differ when derived from microsatellites and single nucleotide polymorphisms (SNPs) in garden and wild samples of two threatened oak species. For Quercus acerifolia, SNPs show lower ex situ representation of wild allelic diversity and slightly lower minimum sample size estimates than microsatellites, while results for each marker are largely similar for Q. boyntonii. The application of missing data filters tends to lead to higher ex situ representation, while the impact of different SNP calling approaches is dependent on the species being analyzed. Measures of population differentiation within species are broadly similar between markers, but larger numbers of SNP loci allow for greater resolution of population structure and clearer assignment of ex situ individuals to wild source populations. Our results offer guidance for future ex situ conservation assessments utilizing SNP data, such as the application of missing data filters and the usage of a reference genome, and illustrate that both microsatellites and SNPs remain viable options for botanic gardens and arboreta seeking to ensure the genetic diversity of their collections.
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Affiliation(s)
| | | | - Emma S. Spence
- Morton ArboretumCenter for Tree ScienceLisleIllinoisUSA
- Cornell UniversityDepartment of Public and Ecosystem HealthIthacaNew YorkUSA
| | - Sean M. Hoban
- Morton ArboretumCenter for Tree ScienceLisleIllinoisUSA
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Kim KR, Sung MS, Hwang Y, Jeong JH, Yu JN. Assessment of the Genetic Diversity and Structure of the Korean Endemic Freshwater Fish Microphysogobio longidorsalis (Gobioninae) Using Microsatellite Markers: A First Glance from Population Genetics. Genes (Basel) 2024; 15:69. [PMID: 38254959 PMCID: PMC10815670 DOI: 10.3390/genes15010069] [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: 11/16/2023] [Revised: 12/30/2023] [Accepted: 01/02/2024] [Indexed: 01/24/2024] Open
Abstract
Microphysogobio longidorsalis is endemic to South Korea and inhabits small areas of the Namhangang, Bukhangang, and Imjingang Rivers in the Hangang River water system. Endemic species usually are more vulnerable than species with a wide distribution. Notably, there is a lack of basic conservation data for M. longidorsalis. We analyzed 19 microsatellite loci in six populations of M. longidorsalis in South Korea to characterize their population structure and genetic diversity. The genetic diversity of the microsatellites was 0.741-0.779, which is lower than that of other freshwater fishes. The pairwise genetic differentiation of microsatellite (FST) values ranged from 0.007 to 0.041, suggesting low genetic differentiation between the populations. The Jojongicheon stream population (CP) had an effective population size of <100. Therefore, conservation efforts are required to prevent inbreeding depression in M. longidorsalis. Discriminant analysis of principal components showed that the Hangang River water system would be a single management unit (MU). Our findings provide fundamental genetic insights for the formulation of conservation strategies for M. longidorsalis.
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Affiliation(s)
- Kang-Rae Kim
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea; (K.-R.K.); (Y.H.); (J.H.J.)
| | - Mu-Sung Sung
- Muldeuli Research, Icheon 12607, Republic of Korea;
| | - Yujin Hwang
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea; (K.-R.K.); (Y.H.); (J.H.J.)
| | - Ju Hui Jeong
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea; (K.-R.K.); (Y.H.); (J.H.J.)
| | - Jeong-Nam Yu
- Animal & Plant Research Department, Nakdonggang National Institute of Biological Resources, Sangju 37242, Republic of Korea; (K.-R.K.); (Y.H.); (J.H.J.)
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Boris KV, Trifonova AA, Dubrovsky ML, Shamshin IN, Kudryavtsev AM. Genetic Diversity of Apple Clonal Rootstocks from the Collection of the Michurinsk State Agrarian University Based on SSR Markers. PLANTS (BASEL, SWITZERLAND) 2023; 12:2991. [PMID: 37631205 PMCID: PMC10458785 DOI: 10.3390/plants12162991] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/27/2023] [Revised: 08/07/2023] [Accepted: 08/17/2023] [Indexed: 08/27/2023]
Abstract
The Michurinsk State Agrarian University (Michurinsk SAU) is one of the leading centers for breeding apple clonal rootstocks. A diverse collection of apple rootstocks, founded in 1930s by V.I. Budagovsky, is maintained at the Michurinsk SAU. In the present study, 87 rootstocks from this collection were analyzed using 18 SSR markers to assess their genetic diversity and relatedness. The detected polymorphism level was rather high compared to the previous estimates of apple rootstock genetic variability. A total of 199 alleles were detected with an average of 11.1 alleles per locus. Among the detected alleles, 67 (33.67%) were rare and 43 (21.61%) were unique. The average PIC value was 0.73, and the expected and observed heterozygosity averaged 0.76 and 0.69, respectively. All the studied accessions except two could be identified with the used marker set. Cluster analysis revealed several groups according to the rootstocks' pedigrees and genetic origin. Furthermore, Structure analysis revealed two main groups of the studied rootstock accessions. No significant differentiation of the studied sample according to dwarfing ability was detected, while weak differentiation was detected according to leaf color. SSR genotyping data can be used for rootstock fingerprinting and pedigree verification and will facilitate collection management. In addition, data on the genetic diversity and structure of the studied collection may be useful for further development of the Michurinsk SAU rootstock breeding program.
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Affiliation(s)
- Ksenia V. Boris
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119333 Moscow, Russia; (K.V.B.); (M.L.D.); (I.N.S.); (A.M.K.)
| | - Aya A. Trifonova
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119333 Moscow, Russia; (K.V.B.); (M.L.D.); (I.N.S.); (A.M.K.)
| | - Maksim L. Dubrovsky
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119333 Moscow, Russia; (K.V.B.); (M.L.D.); (I.N.S.); (A.M.K.)
- Michurinsk State Agrarian University, Research Center of Biotechnologies and Breeding, 393760 Michurinsk, Russia
| | - Ivan N. Shamshin
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119333 Moscow, Russia; (K.V.B.); (M.L.D.); (I.N.S.); (A.M.K.)
- Michurinsk State Agrarian University, Research Center of Biotechnologies and Breeding, 393760 Michurinsk, Russia
| | - Aleksander M. Kudryavtsev
- Vavilov Institute of General Genetics Russian Academy of Sciences, 119333 Moscow, Russia; (K.V.B.); (M.L.D.); (I.N.S.); (A.M.K.)
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Karbstein K, Römermann C, Hellwig F, Prinz K. Population size affected by environmental variability impacts genetics, traits, and plant performance in Trifolium montanum L. Ecol Evol 2023; 13:e10376. [PMID: 37560178 PMCID: PMC10406824 DOI: 10.1002/ece3.10376] [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: 02/22/2023] [Revised: 07/07/2023] [Accepted: 07/12/2023] [Indexed: 08/11/2023] Open
Abstract
Population size, genetic diversity, and performance have fundamental importance for ecology, evolution, and nature conservation of plant species. Despite well-studied relationships among environmental, genetic, and intraspecific trait variation (ITV), the influence of population size on these aspects is less understood. To assess the sources of population size variation, but also its impact on genetic, functional trait, and performance aspects, we conducted detailed population size estimations, assessed 23 abiotic and biotic environmental habitat factors, performed population genetic analyses using nine microsatellite markers, and recorded nine functional traits based on 260 Trifolium montanum individuals from 13 semi-dry grassland locations of Central Europe. Modern statistical analyses based on a multivariate framework (path analysis) with preselected linear regression models revealed that the variation of abiotic factors (in contrast to factors per se) almost completely, significantly explained fluctuations in population size (R 2 = .93). In general, abiotic habitat variation (heterogeneity) was not affected by habitat area. Population size significantly explained genetic diversity (N A: R 2 = .42, H o: R 2 = .67, H e: R 2 = .43, and I: R 2 = .59), inbreeding (F IS: R 2 = .35), and differentiation (G ST: R 2 = .20). We also found that iFDCV (ITV) was significantly explained by abiotic habitat heterogeneity, and to a lesser extent by genetic diversity H e (R 2 = .81). Nevertheless, habitat heterogeneity did not statistically affect genetic diversity. This may be due to the use of selectively neutral microsatellite markers, and possibly by insufficient abiotic selective pressures on habitats examined. Small T. montanum populations in nonoptimal habitats were characterized by reduced genetic and functional trait diversity, and elevated genetic inbreeding and differentiation. This indicates reduced adaptability to current and future environmental changes. The long-term survival of small populations with reduced genetic diversity and beginning inbreeding will be highly dependent on habitat protection and adequate land-use actions.
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Affiliation(s)
- Kevin Karbstein
- Institute of Ecology and EvolutionFriedrich Schiller UniversityJenaGermany
- Department of Systematics, Biodiversity and Evolution of Plants (with Herbarium)Albrecht‐von‐Haller Institute for Plant SciencesUniversity of GöttingenGöttingenGermany
- Department of Biogeochemical IntegrationMax Planck Institute for BiogeochemistryJenaGermany
| | - Christine Römermann
- Institute of Ecology and EvolutionFriedrich Schiller UniversityJenaGermany
- German Centre for Integrative Biodiversity Research (iDiv) Halle‐Jena‐LeipzigLeipzigGermany
| | - Frank Hellwig
- Institute of Ecology and EvolutionFriedrich Schiller UniversityJenaGermany
| | - Kathleen Prinz
- Institute of Ecology and EvolutionFriedrich Schiller UniversityJenaGermany
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7
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Hulke JM, Criscione CD. Characterization of 21 microsatellite loci for the precocious, grass-shrimp trematode Alloglossidium renale. Mol Biochem Parasitol 2023; 254:111563. [PMID: 37086899 DOI: 10.1016/j.molbiopara.2023.111563] [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: 01/31/2023] [Revised: 04/04/2023] [Accepted: 04/19/2023] [Indexed: 04/24/2023]
Abstract
We developed microsatellite markers to use in studying the population genetics of the trematode Alloglossidium renale, a fluke with a precocious life cycle where sexual maturation occurs in a grass shrimp. Among 21 tested loci in a Mississippi population sample, 14 were polymorphic, 12 of which significantly deviated from Hardy-Weinberg Equilibrium (HWE). We estimated identity disequilibrium (ID) to confirm whether the deviations from HWE were due to significant amounts of selfing or due to technical factors. The selfing rate derived from FIS was 86.6%, whereas the selfing rate obtained by ID was 83.9%, indicating that the deviation in HWE was due to a high amount of selfing within the population. These markers will be useful for ecological and evolutionary studies of A. renale especially in relation to the interplay of hermaphroditic mating systems, inbreeding depression, and transmission dynamics.
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Affiliation(s)
- Jenna M Hulke
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, Texas 77843.
| | - Charles D Criscione
- Department of Biology, Texas A&M University, 3258 TAMU, College Station, Texas 77843
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Shahi Shavvon R, Qi HL, Mafakheri M, Fan PZ, Wu HY, Bazdid Vahdati F, Al-Shmgani HS, Wang YH, Liu J. Unravelling the genetic diversity and population structure of common walnut in the Iranian Plateau. BMC PLANT BIOLOGY 2023; 23:201. [PMID: 37072719 PMCID: PMC10111805 DOI: 10.1186/s12870-023-04190-2] [Citation(s) in RCA: 4] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/03/2022] [Accepted: 03/24/2023] [Indexed: 05/03/2023]
Abstract
BACKGROUND Common walnut (Juglans regia L.) has a long cultivation history, given its highly valuable wood and rich nutritious nuts. The Iranian Plateau has been considered as one of the last glaciation refugia and a centre of origin and domestication for the common walnut. However, a prerequisite to conserve or utilize the genetic resources of J. regia in the plateau is a comprehensive evaluation of the genetic diversity that is conspicuously lacking. In this regard, we used 31 polymorphic simple sequence repeat (SSR) markers to delineate the genetic variation and population structure of 508 J. regia individuals among 27 populations from the Iranian Plateau. RESULTS The SSR markers expressed a high level of genetic diversity (HO = 0.438, and HE = 0.437). Genetic differentiation among the populations was moderate (FST = 0.124), and genetic variation within the populations (79%) significantly surpassed among populations (21%). The gene flow (Nm = 1.840) may have remarkably influenced the population genetic structure of J. regia, which can be attributed to anthropological activities and wind dispersal of pollen. The STRUCTURE analysis divided the 27 populations into two main clusters. Comparing the neighbor-joining and principal coordinate analysis dendrograms and the Bayesian STRUCTURE analysis revealed the general agreement between the population subdivisions and the genetic relationships among the populations. However, a few geographically close populations dispersed into different clusters. Further, the low genetic diversity of the Sulaymaniyah (SMR) population of Iraq necessitates urgent conservation by propagation and seedling management or tissue culture methods; additionally, we recommend the indispensable preservation of the Gonabad (RGR) and Arak (AKR) populations in Iran. CONCLUSIONS These results reflected consistent high geographical affinity of the accession across the plateau. Our findings suggest that gene flow is a driving factor influencing the genetic structure of J. regia populations, whereas ecological and geological variables did not act as strong barriers. Moreover, the data reported herein provide new insights into the population structure of J. regia germplasm, which will help conserve genetic resources for the future, hence improving walnut breeding programs' efficiency.
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Affiliation(s)
| | - Hai-Ling Qi
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- Germplasm of Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
| | - Mohammad Mafakheri
- Department of Plant Sciences, University of California - Davis, Davis, CA, 95616, USA
| | - Pen-Zheng Fan
- Germplasm of Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | - Hong-Yu Wu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China
- University of Chinese Academy of Sciences, Beijing, 100049, China
| | | | - Hanady S Al-Shmgani
- Department of Biology, College of Education for Pure Sciences (Ibn Al-Haitham), University of Baghdad, Baghdad, Iraq
| | - Yue-Hua Wang
- School of Ecology and Environmental Science, Yunnan University, Kunming, 650091, China
| | - Jie Liu
- CAS Key Laboratory for Plant Diversity and Biogeography of East Asia, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
- Germplasm of Bank of Wild Species, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, 650201, Yunnan, China.
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Grosser MR, Sites SK, Murata MM, Lopez Y, Chamusco KC, Love Harriage K, Grosser JW, Graham JH, Gmitter FG, Chase CD. Plant mitochondrial introns as genetic markers - conservation and variation. FRONTIERS IN PLANT SCIENCE 2023; 14:1116851. [PMID: 37021319 PMCID: PMC10067590 DOI: 10.3389/fpls.2023.1116851] [Citation(s) in RCA: 2] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/05/2022] [Accepted: 03/02/2023] [Indexed: 06/19/2023]
Abstract
Plant genomes are comprised of nuclear, plastid and mitochondrial components characterized by different patterns of inheritance and evolution. Genetic markers from the three genomes provide complementary tools for investigations of inheritance, genetic relationships and phenotypic contributions. Plant mitochondrial genomes are challenging for universal marker development because they are highly variable in terms of size, gene order and intergenic sequences and highly conserved with respect to protein-coding sequences. PCR amplification of introns with primers that anneal to conserved, flanking exons is effective for the development of polymorphic nuclear genome markers. The potential for plant mitochondrial intron polymorphisms to distinguish between congeneric species or intraspecific varieties has not been systematically investigated and is possibly constrained by requirements for intron secondary structure and interactions with co-evolved organelle intron splicing factors. To explore the potential for broadly applicable plant mitochondrial intron markers, PCR primer sets based upon conserved sequences flanking 11 introns common to seven angiosperm species were tested across a range of plant orders. PCR-amplified introns were screened for indel polymorphisms among a group of cross-compatible Citrus species and relatives; two Raphanus sativus mitotypes; representatives of the two Phaseolus vulgaris gene pools; and congeneric pairs of Cynodon, Cenchrus, Solanum, and Vaccinium species. All introns were successfully amplified from each plant entry. Length polymorphisms distinguishable by gel electrophoresis were common among genera but infrequent within genera. Sequencing of three introns amplified from 16 entries identified additional short indel polymorphisms and nucleotide substitutions that separated Citrus, Cynodon, Cenchrus and Vaccinium congeners, but failed to distinguish Solanum congeners or representatives of the Phaseolus vulgaris major gene pools. The ability of primer sets to amplify a wider range of plant species' introns and the presence of intron polymorphisms that distinguish congeners was confirmed by in silico analysis. While mitochondrial intron variation is limited in comparison to nuclear introns, these exon-based primer sets provide robust tools for the amplification of mitochondrial introns across a wide range of plant species wherein useful polymorphisms can be identified.
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Affiliation(s)
- Melinda R. Grosser
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Samantha K. Sites
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Mayara M. Murata
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Yolanda Lopez
- Agronomy Department, University of Florida, Gainesville, FL, United States
| | - Karen C. Chamusco
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Kyra Love Harriage
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
| | - Jude W. Grosser
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - James H. Graham
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Fred G. Gmitter
- Citrus Research and Education Center, University of Florida, Lake Alfred, FL, United States
| | - Christine D. Chase
- Horticultural Sciences Department, University of Florida, Gainesville, FL, United States
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Dufresnes C, Dutoit L, Brelsford A, Goldstein-Witsenburg F, Clément L, López-Baucells A, Palmeirim J, Pavlinić I, Scaravelli D, Ševčík M, Christe P, Goudet J. Inferring genetic structure when there is little: population genetics versus genomics of the threatened bat Miniopterus schreibersii across Europe. Sci Rep 2023; 13:1523. [PMID: 36707640 PMCID: PMC9883447 DOI: 10.1038/s41598-023-27988-4] [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: 07/10/2022] [Accepted: 01/11/2023] [Indexed: 01/28/2023] Open
Abstract
Despite their paramount importance in molecular ecology and conservation, genetic diversity and structure remain challenging to quantify with traditional genotyping methods. Next-generation sequencing holds great promises, but this has not been properly tested in highly mobile species. In this article, we compared microsatellite and RAD-sequencing (RAD-seq) analyses to investigate population structure in the declining bent-winged bat (Miniopterus schreibersii) across Europe. Both markers retrieved general patterns of weak range-wide differentiation, little sex-biased dispersal, and strong isolation by distance that associated with significant genetic structure between the three Mediterranean Peninsulas, which could have acted as glacial refugia. Microsatellites proved uninformative in individual-based analyses, but the resolution offered by genomic SNPs illuminated on regional substructures within several countries, with colonies sharing migrators of distinct ancestry without admixture. This finding is consistent with a marked philopatry and spatial partitioning between mating and rearing grounds in the species, which was suspected from marked-recaptured data. Our study advocates that genomic data are necessary to properly unveil the genetic footprints left by biogeographic processes and social organization in long-distant flyers, which are otherwise rapidly blurred by their high levels of gene flow.
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Affiliation(s)
- Christophe Dufresnes
- Laboratory for Amphibian Systematic and Evolutionary Research, College of Biology and the Environment, Nanjing Forestry University, Nanjing, People's Republic of China.
| | - Ludovic Dutoit
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.,Department of Zoology, University of Otago, Dunedin, New Zealand
| | - Alan Brelsford
- Department of Evolution, Ecology, and Organismal Biology, University of California Riverside, Riverside, CA, USA
| | | | - Laura Clément
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland
| | - Adria López-Baucells
- Bat Research Area, Granollers Museum of Natural Sciences, Carrer Palaudaries 102, 08402, Granollers, Spain
| | - Jorge Palmeirim
- Department of Animal Biology, Centre for Ecology, Evolution and Environmental Change - cE3c, University of Lisbon, 1749-016, Lisbon, Portugal
| | - Igor Pavlinić
- Department of Zoology, Croatian Natural History Museum, Demetrova 1, 10000, Zagreb, Croatia
| | - Dino Scaravelli
- Department of Biological, Geological, and Environmental Sciences, University of Bologna, Via Selmi 3, 40126, Bologna, Italy
| | - Martin Ševčík
- Department of Zoology, Faculty of Science, Charles University in Prague, Viničná 7, 128 44, Prague 2, Czech Republic
| | - Philippe Christe
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.
| | - Jérôme Goudet
- Department of Ecology and Evolution, University of Lausanne, 1015, Lausanne, Switzerland.
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11
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Tibihika PD, Meimberg H, Curto M. Understanding the translocation dynamics of Nile tilapia ( Oreochromis niloticus) and its ecological consequences in East Africa. AFRICAN ZOOLOGY 2022. [DOI: 10.1080/15627020.2022.2154169] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 12/14/2022]
Affiliation(s)
- Papius Dias Tibihika
- National Fisheries Resources Research Institute, National Agricultural Research Organization, Kampala, Uganda
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Wien, Austria
| | - Harald Meimberg
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Wien, Austria
| | - Manuel Curto
- Institute for Integrative Nature Conservation Research, University of Natural Resources and Life Sciences Vienna (BOKU), Wien, Austria
- MARE−Marine and Environmental Sciences Centre, University of Lisbon, Lisbon, Portugal
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12
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Phylogeographic structure of common sage (Salvia officinalis L.) reveals microrefugia throughout the Balkans and colonizations of the Apennines. Sci Rep 2022; 12:15726. [PMID: 36130954 PMCID: PMC9492721 DOI: 10.1038/s41598-022-20055-4] [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: 06/07/2022] [Accepted: 09/08/2022] [Indexed: 11/24/2022] Open
Abstract
Studying the population-genetic and phylogeographic structures of a representative species of a particular geographical region can not only provide us with information regarding its evolutionary history, but also improve our understanding of the evolutionary processes underlying the patterns of species diversity in that area. By analysing eight highly polymorphic microsatellite loci and two chloroplast DNA regions, we have investigated the influence of Pleistocene climate fluctuations on the evolutionary history of Salvia officinalis L. (common sage). The populations with the highest genetic diversity were located in the central parts of the Balkan distribution range. A large group of closely related haplotypes was distributed throughout the Balkans and the central Apennines, while the private lineage occupied the southern Apennines. In addition, two highly differentiated lineages were scattered only over the Balkans. The results suggest that a single refugium of the studied species from the last glacial period was located in the central part of the range in the Balkans. Numerous microrefugia, probably spanning several glaciation cycles, were scattered across the Balkans, while colonisation of the Apennines from the Balkans occurred at least on two occasions.
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13
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Rosche C, Baasch A, Runge K, Brade P, Träger S, Parisod C, Hensen I. Tracking population genetic signatures of local extinction with herbarium specimens. ANNALS OF BOTANY 2022; 129:857-868. [PMID: 35670810 PMCID: PMC9292615 DOI: 10.1093/aob/mcac061] [Citation(s) in RCA: 6] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/13/2022] [Indexed: 05/29/2023]
Abstract
BACKGROUND AND AIMS Habitat degradation and landscape fragmentation dramatically lower population sizes of rare plant species. Decreasing population sizes may, in turn, negatively affect genetic diversity and reproductive fitness, which can ultimately lead to local extinction of populations. Although such extinction vortex dynamics have been postulated in theory and modelling for decades, empirical evidence from local extinctions of plant populations is scarce. In particular, comparisons between current vs. historical genetic diversity and differentiation are lacking despite their potential to guide conservation management. METHODS We studied the population genetic signatures of the local extinction of Biscutella laevigata subsp. gracilis populations in Central Germany. We used microsatellites to genotype individuals from 15 current populations, one ex situ population, and 81 herbarium samples from five extant and 22 extinct populations. In the current populations, we recorded population size and fitness proxies, collected seeds for a germination trial and conducted a vegetation survey. The latter served as a surrogate for habitat conditions to study how habitat dissimilarity affects functional connectivity among the current populations. KEY RESULTS Bayesian clustering revealed similar gene pool distribution in current and historical samples but also indicated that a distinct genetic cluster was significantly associated with extinction probability. Gene flow was affected by both the spatial distance and floristic composition of population sites, highlighting the potential of floristic composition as a powerful predictor of functional connectivity which may promote decision-making for reintroduction measures. For an extinct population, we found a negative relationship between sampling year and heterozygosity. Inbreeding negatively affected germination. CONCLUSIONS Our study illustrates the usefulness of historical DNA to study extinction vortices in threatened species. Our novel combination of classical population genetics together with data from herbarium specimens, an ex situ population and a germination trial underlines the need for genetic rescue measures to prevent extinction of B. laevigata in Central Germany.
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Affiliation(s)
- Christoph Rosche
- Martin Luther University Halle-Wittenberg, Institute of Biology/Geobotany and Botanical Garden, Große Steinstraße 79/80, 06108 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Annett Baasch
- Anhalt University of Applied Sciences, Department of Agriculture, Ecotrophology and Landscape Development, Strenzfelder Allee 28, 06406 Bernburg (Saale), Germany
| | - Karen Runge
- Anhalt University of Applied Sciences, Department of Agriculture, Ecotrophology and Landscape Development, Strenzfelder Allee 28, 06406 Bernburg (Saale), Germany
| | - Philipp Brade
- Anhalt University of Applied Sciences, Department of Agriculture, Ecotrophology and Landscape Development, Strenzfelder Allee 28, 06406 Bernburg (Saale), Germany
| | - Sabrina Träger
- Martin Luther University Halle-Wittenberg, Institute of Biology/Geobotany and Botanical Garden, Große Steinstraße 79/80, 06108 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
| | - Christian Parisod
- University of Fribourg, Department of Biology, Chemin du Musée 10, 1700 Fribourg, Switzerland
| | - Isabell Hensen
- Martin Luther University Halle-Wittenberg, Institute of Biology/Geobotany and Botanical Garden, Große Steinstraße 79/80, 06108 Halle (Saale), Germany
- German Centre for Integrative Biodiversity Research (iDiv) Halle-Jena-Leipzig, Puschstraße 4, 04103 Leipzig, Germany
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14
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Nishida S, Mimura K, Mori H, Chiba S. Characterization of polymorphic microsatellite markers for the Japanese endangered land snail Mandarina. BMC Res Notes 2022; 15:255. [PMID: 35842672 PMCID: PMC9288687 DOI: 10.1186/s13104-022-06147-4] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/27/2022] [Accepted: 07/05/2022] [Indexed: 11/10/2022] Open
Abstract
Objective Mandarina is an endangered land snail genus of the oceanic Ogasawara archipelago. On Chichijima Island, the largest inhabited island in Ogasawara, this genus is almost extinct in the wild due to predation by invasive species. Although ex situ conservation programs started in 2010, genetic diversity and population structure remain unclear due to a lack of genetic markers with sufficient genetic variation. In this study, we designed polymorphic microsatellite markers of Mandarina to enable genetic analysis and to develop appropriate conservation plans. Results Twenty-three polymorphic microsatellite markers were identified from the genomic DNA of wild samples of Mandarina mandarina. We assessed the genetic diversity of each marker. In 16 markers, neither linkage disequilibrium nor deviation from Hardy–Weinberg equilibrium was detected. These 16 markers were tested for multiplex PCR using low-density DNA extracted non-lethally from captive samples of M. mandarina, M. chichijimana and M. suenoae. Of the 16 markers, 15, 12 and 9 were usable for multiplex PCR, respectively. Genetic analysis using these microsatellite loci will be an important resource for the conservation of Mandarina. Supplementary Information The online version contains supplementary material available at 10.1186/s13104-022-06147-4.
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Affiliation(s)
- Shu Nishida
- Graduate School of Life Sciences, Tohoku University, 6-3 Aramaki aza aoba, Aoba-ku, Sendai, Miyagi, 980-8578, Japan.
| | - Kotaro Mimura
- Graduate School of Life Sciences, Tohoku University, 6-3 Aramaki aza aoba, Aoba-ku, Sendai, Miyagi, 980-8578, Japan
| | - Hideaki Mori
- Japan Wildlife Research Center, Kotobashi 3-3-7 Sumida-ku Tokyo, Tokyo, 130-8606, Japan
| | - Satoshi Chiba
- Graduate School of Life Sciences, Tohoku University, 6-3 Aramaki aza aoba, Aoba-ku, Sendai, Miyagi, 980-8578, Japan.,Center for Northeast Asian Studies, Tohoku University, 12-2, Kawauchi, Aoba-ku, Sendai, Miyagi, 980-8578, Japan
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15
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Ranathunge C, Chimahusky ME, Welch ME. A comparative study of population genetic structure reveals patterns consistent with selection at functional microsatellites in common sunflower. Mol Genet Genomics 2022; 297:1329-1342. [PMID: 35786764 DOI: 10.1007/s00438-022-01920-3] [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: 12/25/2021] [Accepted: 06/16/2022] [Indexed: 10/17/2022]
Abstract
Microsatellites, also known as short tandem repeats (STRs), have long been considered non-functional, neutrally evolving regions of the genome. Recent findings suggest that they can function as drivers of rapid adaptive evolution. Previous work on the common sunflower identified 479 transcribed microsatellites where allele length significantly correlates with gene expression (eSTRs) in a stepwise manner. Here, a population genetic approach is used to test whether eSTR allele length variation is under selection. Genotypic variation among and within populations at 13 eSTRs was compared with that at 19 anonymous microsatellites in 672 individuals from 17 natural populations of sunflower from across a cline running from Saskatchewan to Oklahoma (distance of approximately 1600 km). Expected heterozygosity, allelic richness, and allelic diversity were significantly lower at eSTRs, a pattern consistent with higher relative rates of purifying selection. Further, an analysis of variation in microsatellite allele lengths (lnRV), and heterozygosities (lnRH), indicate recent selective sweeps at the eSTRs. Mean microsatellite allele lengths at four eSTRs within populations are significantly correlated with latitude consistent with the predictions of the tuning-knob model which predicts stepwise relationships between microsatellite allele length and phenotypes. This finding suggests that shorter or longer alleles at eSTRs may be favored in climatic extremes. Collectively, our results imply that eSTRs are likely under selection and that they may be playing a role in facilitating local adaptation across a well-defined cline in the common sunflower.
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Affiliation(s)
- Chathurani Ranathunge
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39762, USA.
- School of Health Professions, Eastern Virginia Medical School, Norfolk, VA, 23507, USA.
| | - Melody E Chimahusky
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39762, USA
| | - Mark E Welch
- Department of Biological Sciences, Mississippi State University, Starkville, MS, 39762, USA
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16
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Lyman RA, Edwards CE. Revisiting the comparative phylogeography of unglaciated eastern North America: 15 years of patterns and progress. Ecol Evol 2022; 12:e8827. [PMID: 35475178 PMCID: PMC9019306 DOI: 10.1002/ece3.8827] [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: 12/13/2021] [Revised: 03/17/2022] [Accepted: 03/18/2022] [Indexed: 11/28/2022] Open
Abstract
In a landmark comparative phylogeographic study, “Comparative phylogeography of unglaciated eastern North America,” Soltis et al. (Molecular Ecology, 2006, 15, 4261) identified geographic discontinuities in genetic variation shared across taxa occupying unglaciated eastern North America and proposed several common biogeographical discontinuities related to past climate fluctuations and geographic barriers. Since 2006, researchers have published many phylogeographical studies and achieved many advances in genotyping and analytical techniques; however, it is unknown how this work has changed our understanding of the factors shaping the phylogeography of eastern North American taxa. We analyzed 184 phylogeographical studies of eastern North American taxa published between 2007 and 2019 to evaluate: (1) the taxonomic focus of studies and whether a previously detected taxonomic bias towards studies focused on vertebrates has changed over time, (2) the extent to which studies have adopted genotyping technologies that improve the resolution of genetic groups (i.e., NGS DNA sequencing) and analytical approaches that facilitate hypothesis‐testing (i.e., divergence time estimation and niche modeling), and (3) whether new studies support the hypothesized biogeographic discontinuities proposed by Soltis et al. (Molecular Ecology, 2006, 15, 4261) or instead support new, previously undetected discontinuities. We observed little change in taxonomic focus over time, with studies still biased toward vertebrates. Although many technological and analytical advances became available during the period, uptake was slow and they were employed in only a small proportion of studies. We found variable support for previously identified discontinuities and identified one new recurrent discontinuity. However, the limited resolution and taxonomic breadth of many studies hindered our ability to clarify the most important climatological or geographical factors affecting taxa in the region. Broadening the taxonomic focus to include more non‐vertebrate taxa, employing technologies that improve genetic resolution, and using analytical approaches that improve hypothesis testing are necessary to strengthen our inference of the forces shaping the phylogeography of eastern North America.
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Affiliation(s)
- Rachel Ann Lyman
- Ecology, Evolution, and Population Biology Program Washington University in St. Louis St. Louis Missouri USA
- Center for Conservation and Sustainable Development Missouri Botanical Garden St. Louis Missouri USA
| | - Christine E. Edwards
- Center for Conservation and Sustainable Development Missouri Botanical Garden St. Louis Missouri USA
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17
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Yu M, Liu Q, Wu Y, Guo P, Yang K. Genetic diversity and sex‐biased dispersal in the brown spotted pitviper (
Protobothrops mucrosquamatus
): Evidence from microsatellite markers. Ecol Evol 2022; 12:e8652. [PMID: 35261743 PMCID: PMC8888261 DOI: 10.1002/ece3.8652] [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: 10/23/2021] [Revised: 01/20/2022] [Accepted: 01/28/2022] [Indexed: 11/18/2022] Open
Abstract
Dispersal plays a vital role in the geographical distribution, population genetic structure, quantity dynamics, and evolution of a species. Sex‐biased dispersal is common among vertebrates and many studies have documented a tendency toward male‐biased dispersal in mammals and female‐biased dispersal in birds. However, dispersal patterns in reptiles remain poorly understood. In this study, we explored the genetic diversity and dispersal patterns of the widely distributed Asian pitviper Protobothrops mucrosquamatus. In total, 16 polymorphic microsatellite loci were screened in 150 snakes (48 males, 44 females, 58 samples without sex information) covering most of their distribution. Microsatellite analysis revealed high genetic diversity in P. mucrosquamatus. Bayesian clustering of population assignment identified two major clusters for all populations, somewhat inconsistent with the mitochondrial DNA phylogeny of P. mucrosquamatus reported in previous research. Analyses based on 92 sex‐determined and 37 samples of P. mucrosquamatus from three small sites in Sichuan, China (Mingshan, Yibin, and Zizhong) consistently suggested female‐biased dispersal in P. mucrosquamatus, which is the first example of this pattern in snakes. The female‐biased dispersal patterns in P. mucrosquamatus may be explained by local resource competition.
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Affiliation(s)
- Min Yu
- Institute of Qinghai‐Tibetan Plateau Southwest Minzu University Chengdu China
- Faculty of Agriculture, Forest and Food Engineering Yibin University Yibin China
| | - Qin Liu
- Faculty of Agriculture, Forest and Food Engineering Yibin University Yibin China
| | - Ya‐Yong Wu
- Faculty of Agriculture, Forest and Food Engineering Yibin University Yibin China
| | - Peng Guo
- Faculty of Agriculture, Forest and Food Engineering Yibin University Yibin China
| | - Kong Yang
- Institute of Qinghai‐Tibetan Plateau Southwest Minzu University Chengdu China
- Faculty of Agriculture, Forest and Food Engineering Yibin University Yibin China
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18
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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] [Key Words] [Grants] [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 EngineeringCollege of Life SciencesBeijing Normal UniversityBeijingChina
| | - Shenghan Gao
- State Key Laboratory of Microbial ResourcesInstitute of MicrobiologyChinese Academy of SciencesBeijingChina
| | - Yu Liu
- MOE Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijingChina
| | - Pengcheng Wang
- Jiangsu Key Laboratory for Biodiversity and BiotechnologyCollege of Life SciencesNanjing Normal UniversityNanjingChina
| | - Zhengwang Zhang
- MOE Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijingChina
| | - De Chen
- MOE Key Laboratory for Biodiversity Science and Ecological EngineeringCollege of Life SciencesBeijing Normal UniversityBeijingChina
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Vasiljevic N, Morf NV, Senn J, Pérez‐Espona S, Mattucci F, Mucci N, Moore‐Jones G, Pisano SRR, Kratzer A, Ogden R. Phylogeography and population genetic structure of the European roe deer in Switzerland following recent recolonization. Ecol Evol 2022; 12:e8626. [PMID: 35222977 PMCID: PMC8858214 DOI: 10.1002/ece3.8626] [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: 09/30/2021] [Revised: 01/03/2022] [Accepted: 01/26/2022] [Indexed: 11/12/2022] Open
Abstract
In the early 1800s, the European roe deer (Capreolus capreolus) was probably extirpated from Switzerland, due to overhunting and deforestation. After a federal law was enacted in 1875 to protect lactating females and young, and limiting the hunting season, the roe deer successfully recovered and recolonized Switzerland. In this study, we use mitochondrial DNA and nuclear DNA markers to investigate the recolonization and assess contemporary genetic structure in relation to broad topographic features, in order to understand underlying ecological processes, inform future roe deer management strategies, and explore the opportunity for development of forensic traceability tools. The results concerning the recolonization origin support natural, multidirectional immigration from neighboring countries. We further demonstrate that there is evidence of weak genetic differentiation within Switzerland among topographic regions. Finally, we conclude that the genetic data support the recognition of a single roe deer management unit within Switzerland, within which there is a potential for broad-scale geographic origin assignment using nuclear markers to support law enforcement.
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Affiliation(s)
- Nina Vasiljevic
- Zurich Institute of Forensic MedicineUniversity of ZurichSwitzerland
| | - Nadja V. Morf
- Zurich Institute of Forensic MedicineUniversity of ZurichSwitzerland
| | - Josef Senn
- Swiss Federal Research Institute WSLBirmensdorfSwitzerland
| | - Sílvia Pérez‐Espona
- Royal (Dick) School of Veterinary Studies and the Roslin InstituteUniversity of EdinburghMidlothianUK
| | - Federica Mattucci
- ISPRA‐Istituto Superiore per la Protezione e la Ricerca AmbientaleArea per la Genetica della Conservazione BIO‐CGEBolognaItaly
| | - Nadia Mucci
- ISPRA‐Istituto Superiore per la Protezione e la Ricerca AmbientaleArea per la Genetica della Conservazione BIO‐CGEBolognaItaly
| | - Gaia Moore‐Jones
- Institute for Fish and Wildlife Health (FIWI), Department of Infectious Diseases and Pathobiology, Vetsuisse‐FacultyUniversity of BernBernSwitzerland
| | - Simone Roberto Rolando Pisano
- Institute for Fish and Wildlife Health (FIWI), Department of Infectious Diseases and Pathobiology, Vetsuisse‐FacultyUniversity of BernBernSwitzerland
| | - Adelgunde Kratzer
- Zurich Institute of Forensic MedicineUniversity of ZurichSwitzerland
| | - Rob Ogden
- Royal (Dick) School of Veterinary Studies and the Roslin InstituteUniversity of EdinburghMidlothianUK
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20
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López-Caamal A, Tovar-Sánchez E. Comparing the population history of Neotropical annual species: The role of climate change and hybridization between Tithonia tubaeformis and T. rotundifolia (Asteraceae). PLANT BIOLOGY (STUTTGART, GERMANY) 2021; 23:962-973. [PMID: 34374194 DOI: 10.1111/plb.13313] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 02/08/2021] [Accepted: 06/14/2021] [Indexed: 06/13/2023]
Abstract
Historical climate changes and interspecific gene flow have played an important role in shaping the distribution and genetic diversity of the biota in the Neotropics. In this study, we explored the role of both the Pleistocene climate changes and hybridization on the contemporary geographic structure of two Neotropical weedy species: Tithonia tubaeformis and T. rotundifolia. Distribution shifts under past and current climate conditions were explored through ecological niche modelling (ENM). We then tested these hypotheses using chloroplast microsatellite (cpSSR) data in T. tubaeformis and compared the patterns deduced with those previously reported for T. rotundifolia using the same cpSSR loci. Lastly, we searched for shared haplotypes between species. Both species exhibited significant downwards altitudinal shifts during the last interglacial (LIG) and the Last Glacial Maximum (LGM). For instance, T. rotundifolia showed large suitable habitat areas since the LIG at xeric conditions in western Mesoamerica. Tithonia tubaeformis showed a ~five-fold range contraction during the LIG compared to current climate conditions, followed by a range expansion in the LGM. Despite the large shared refugial areas predicted through ENM, we found a low number of shared haplotypes, suggesting a minor role of hybridization in shaping the geographic structure of these species. Our results provide additional patterns of the population history of the northern Neotropics during the Quaternary, and we suggest that weedy widespread species are a well-suited group for the study of the effects of historic climatic changes on the biota of this region.
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Affiliation(s)
- A López-Caamal
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
| | - E Tovar-Sánchez
- Centro de Investigación en Biodiversidad y Conservación, Universidad Autónoma del Estado de Morelos, Cuernavaca, Mexico
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21
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Development of a multiplex microsatellite marker set for the study of the solitary red mason bee, Osmia bicornis (Megachilidae). Mol Biol Rep 2021; 49:783-788. [PMID: 34724128 PMCID: PMC8748364 DOI: 10.1007/s11033-021-06796-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/31/2021] [Accepted: 10/01/2021] [Indexed: 11/17/2022]
Abstract
Background Solitary bees, such as the red mason bee (Osmia bicornis), provide important ecosystem services including pollination. In the face of global declines of pollinator abundance, such haplodiploid Hymenopterans have a compounded extinction risk due to the potential for limited genetic diversity. In order to assess the genetic diversity of Osmia bicornis populations, we developed microsatellite markers and characterised them in two populations. Methods and results Microsatellite sequences were mined from the recently published Osmia bicornis genome, which was assembled from DNA extracted from a single male bee originating from the United Kingdom. Sequences were identified that contained dinucleotide, trinucleotide, and tetranucleotide repeat regions. Seventeen polymorphic microsatellite markers were designed and tested, sixteen of which were developed into four multiplex PCR sets to facilitate cheap, fast and efficient genotyping and were characterised in unrelated females from Germany (n = 19) and England (n = 14). Conclusions The microsatellite markers are highly informative, with a combined exclusion probability of 0.997 (first parent), which will enable studies of genetic structure and diversity to inform conservation efforts in this bee. Supplementary Information The online version contains supplementary material available at 10.1007/s11033-021-06796-x.
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22
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Martins FB, Moraes ACL, Aono AH, Ferreira RCU, Chiari L, Simeão RM, Barrios SCL, Santos MF, Jank L, do Valle CB, Vigna BBZ, de Souza AP. A Semi-Automated SNP-Based Approach for Contaminant Identification in Biparental Polyploid Populations of Tropical Forage Grasses. FRONTIERS IN PLANT SCIENCE 2021; 12:737919. [PMID: 34745171 PMCID: PMC8569613 DOI: 10.3389/fpls.2021.737919] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/07/2021] [Accepted: 09/20/2021] [Indexed: 06/13/2023]
Abstract
Artificial hybridization plays a fundamental role in plant breeding programs since it generates new genotypic combinations that can result in desirable phenotypes. Depending on the species and mode of reproduction, controlled crosses may be challenging, and contaminating individuals can be introduced accidentally. In this context, the identification of such contaminants is important to avoid compromising further selection cycles, as well as genetic and genomic studies. The main objective of this work was to propose an automated multivariate methodology for the detection and classification of putative contaminants, including apomictic clones (ACs), self-fertilized individuals, half-siblings (HSs), and full contaminants (FCs), in biparental polyploid progenies of tropical forage grasses. We established a pipeline to identify contaminants in genotyping-by-sequencing (GBS) data encoded as allele dosages of single nucleotide polymorphism (SNP) markers by integrating principal component analysis (PCA), genotypic analysis (GA) measures based on Mendelian segregation, and clustering analysis (CA). The combination of these methods allowed for the correct identification of all contaminants in all simulated progenies and the detection of putative contaminants in three real progenies of tropical forage grasses, providing an easy and promising methodology for the identification of contaminants in biparental progenies of tetraploid and hexaploid species. The proposed pipeline was made available through the polyCID Shiny app and can be easily coupled with traditional genetic approaches, such as linkage map construction, thereby increasing the efficiency of breeding programs.
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Affiliation(s)
- Felipe Bitencourt Martins
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), São Paulo, Brazil
| | - Aline Costa Lima Moraes
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), São Paulo, Brazil
| | - Alexandre Hild Aono
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), São Paulo, Brazil
| | | | - Lucimara Chiari
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | - Rosangela Maria Simeão
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | | | | | - Liana Jank
- Embrapa Gado de Corte, Brazilian Agricultural Research Corporation, Campo Grande, Brazil
| | | | | | - Anete Pereira de Souza
- Center for Molecular Biology and Genetic Engineering (CBMEG), University of Campinas (UNICAMP), São Paulo, Brazil
- Department of Plant Biology, Biology Institute, University of Campinas (UNICAMP), São Paulo, Brazil
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Miller-Crews I, Matz MV, Hofmann HA. A 2b-RAD parentage analysis pipeline for complex and mixed DNA samples. Forensic Sci Int Genet 2021; 55:102590. [PMID: 34509741 DOI: 10.1016/j.fsigen.2021.102590] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/21/2021] [Revised: 08/13/2021] [Accepted: 08/30/2021] [Indexed: 11/24/2022]
Abstract
Next-generation sequencing technology has revolutionized genotyping in many fields of study, yet parentage analysis often still relies on microsatellite markers that are costly to generate and are currently available only for a limited number of species. 2b-RAD sequencing (2b-RAD) is a DNA sequencing technique developed for ecological population genomics that utilizes type IIB restriction enzymes to generate consistent, uniform fragments across samples. This technology is inexpensive, effective with low DNA inputs, and robust to DNA degradation. Here, we developed a probabilistic genotyping-by-sequencing genetic testing pipeline for parentage analysis by using 2b-RAD for inferring familial relationships from mixed DNA samples and populations. Our approach to partial paternity assignment utilizes a novel weighted outlier paternity index (WOPI) adapted for next-generation sequencing data and an identity-by-state (IBS) matrix-based clustering method for pedigree reconstruction. The combination of these two parentage assignment methods overcomes two major obstacles faced by other genetic testing methods: 1) It allows detection of parentage when closely related or inbred individuals are in the alleged parent population (e.g., in laboratory strains); and 2) it resolves mixed DNA samples. We successfully demonstrate this novel approach by correctly inferring paternity for samples pooled from multiple offspring (i.e., entire clutches) in a highly inbred population of an East African cichlid fish. The unique advantages of 2b-RAD in combination with our bioinformatics pipeline enable straightforward and cost-effective parentage analysis in any species regardless of genomic resources available.
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Affiliation(s)
- Isaac Miller-Crews
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Mikhail V Matz
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA
| | - Hans A Hofmann
- Department of Integrative Biology, The University of Texas at Austin, Austin, TX 78712, USA; Institute for Cellular and Molecular Biology, The University of Texas at Austin, Austin, TX 78712, USA; Institue for Neuroscience, The University of Texas at Austin, Austin, TX 78712, USA.
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Zhang JX, Wang M, Fan J, Guo ZP, Guan Y, Qu G, Zhang CJ, Guo YX, Yan X. Non-linear genetic diversity and notable population differentiation caused by low gene flow of bermudagrass [ Cynodon dactylon (L.) Pers.] along longitude gradients. PeerJ 2021; 9:e11953. [PMID: 34458022 PMCID: PMC8378333 DOI: 10.7717/peerj.11953] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/27/2020] [Accepted: 07/21/2021] [Indexed: 11/20/2022] Open
Abstract
Background Environmental variation related to ecological habitat is the main driver of plant adaptive divergence. Longitude plays an important role in the formation of plant population structure, indicating that environmental differentiation can significantly shape population structure. Methods Genetic diversity and population genetic structure were estimated using 105 expressed sequence tag-derived simple sequence repeat (EST-SSR) loci. A total of 249 C. dactylon (L.) Pers. (common bermudagrass) individuals were sampled from 13 geographic sites along the longitude (105°57′34″–119°27′06″E). Results There was no obvious linear trend of intra-population genetic diversity along longitude and the intra-population genetic diversity was not related to climate in this study. Low gene flow (Nm = 0.7701) meant a rich genetic differentiation among populations of C. dactylon along longitude gradients. Significantly positive Mantel correlation (r = 0.438, P = 0.001) was found between genetic distance and geographical interval while no significant partial Mantel correlation after controlling the effect of mean annual precipitation, which indicated geographic distance correlated with mean annual precipitation affect genetic distance. The genetic diversity of C. dactylon with higher ploidy level was higher than that with lower ploidy level and groups of individuals with higher ploidy level were separated further away by genetic distance from the lower ploidy levels. Understanding the different genetic bases of local adaptation comparatively between latitude and longitude is one of the core findings in the adaptive evolution of plants.
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Affiliation(s)
- Jing-Xue Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China.,College of Animal and Veterinary Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Miaoli Wang
- College of Animal and Veterinary Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Jibiao Fan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Zhi-Peng Guo
- College of Animal and Veterinary Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Yongzhuo Guan
- College of Animal and Veterinary Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Gen Qu
- College of Animal and Veterinary Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Chuan-Jie Zhang
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
| | - Yu-Xia Guo
- College of Animal and Veterinary Science, Henan Agricultural University, Zhengzhou, Henan, China
| | - Xuebing Yan
- College of Animal Science and Technology, Yangzhou University, Yangzhou, Jiangsu, China
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Fang Y, Chen J, Ruan H, Xu N, Que Z, Liu H. Genetic Diversity and Population Structure of Metaphire vulgaris Based on the Mitochondrial COI Gene and Microsatellites. Front Genet 2021; 12:686246. [PMID: 34168681 PMCID: PMC8217756 DOI: 10.3389/fgene.2021.686246] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/26/2021] [Accepted: 05/18/2021] [Indexed: 11/29/2022] Open
Abstract
The earthworm species Metaphire vulgaris (a member of the Clitellata class) is widely distributed across China, and has important ecological functions and medicinal value. However, investigations into its genetic diversity and differentiation are scarce. Consequently, we evaluated the genetic diversity of five populations of M. vulgaris (GM, HD, NYYZ, QDDY, and QDY) in Yancheng, China via the mitochondrial COI gene and the novel microsatellites developed there. A total of nine haplotypes were obtained by sequencing the mitochondrial COI gene, among which NYYZ and QDDY populations had the greatest number of haplotypes (nh = 5). Further, the nucleotide diversity ranged from 0.00437 to 0.1243. The neighbor-joining trees and the TCS network of haplotypes indicated that earthworm populations within close geographical range were not genetically isolated at these small scale distances. Results of the identification of microsatellite molecular markers revealed that the allele number in 12 microsatellite loci ranged from 4 to 13. The observed heterozygosity ranged from 0.151 to 0.644, whereas the expected heterozygosity ranged from 0.213 to 0.847. The polymorphism data content of most sites was >0.5, which indicated that the designed sites had high polymorphism. Structural analysis results indicated that GM, HD, and NYYZ had similar genetic structures across the five populations. The Nei's genetic distance between HD and NYYZ populations was the smallest (D s = 0.0624), whereas that between HD and QDY populations was the largest (D s = 0.2364). The UPGMA tree showed that HD were initially grouped with NYYZ, followed by GM, and then with QDDY. Furthermore, cross-species amplification tests were conducted for Metaphire guillelmi, which indicated that the presented markers were usable for this species. This study comprised a preliminary study on the genetic diversity of M. vulgaris, which provides basic data for future investigations into this species.
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Affiliation(s)
- Yu Fang
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Jie Chen
- Key Laboratory for Ecology and Pollution Control of Coastal Wetlands (Environmental Protection, Department of Jiangsu), School of Environmental Science and Engineering, Yancheng Institute of Technology, Yancheng, China
| | - Honghua Ruan
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Nan Xu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Ziting Que
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
| | - Hongyi Liu
- College of Biology and the Environment, Nanjing Forestry University, Nanjing, China
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26
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Gharesouran J, Hosseinzadeh H, Ghafouri-Fard S, Taheri M, Rezazadeh M. STRs: Ancient Architectures of the Genome beyond the Sequence. J Mol Neurosci 2021; 71:2441-2455. [PMID: 34056692 DOI: 10.1007/s12031-021-01850-6] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/12/2021] [Accepted: 04/22/2021] [Indexed: 01/24/2023]
Abstract
Short tandem repeats (STRs) are commonly defined as short runs of repetitive nucleotides, consisting of tandemly repeating 2-6- bp motif units, which are ubiquitously distributed throughout genomes. Functional STRs are polymorphic in the population, and their variations influence gene expression, which subsequently may result in pathogenic phenotypes. To understand STR phenotypic effects and their functional roles, we describe four different mutational mechanisms including the unequal crossing-over model, gene conversion, retrotransposition mechanism and replication slippage. Due to the multi-allelic nature, small length, abundance, high variability, codominant inheritance, nearly neutral evolution, extensive genome coverage and simple assaying of STRs, these markers are widely used in various types of biological research, including population genetics studies, genome mapping, molecular epidemiology, paternity analysis and gene flow studies. In this review, we focus on the current knowledge regarding STR genomic distribution, function, mutation and applications.
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Affiliation(s)
- Jalal Gharesouran
- Molecular Genetics Division, GMG center, Tabriz, Iran.,Division of Medical Genetics, Tabriz Childrens Hospital, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Hassan Hosseinzadeh
- Molecular Genetics Division, GMG center, Tabriz, Iran.,Division of Medical Genetics, Tabriz Childrens Hospital, Tabriz University of Medical Sciences, Tabriz, Iran.,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran
| | - Soudeh Ghafouri-Fard
- Department of Medical Genetics, Shahid Beheshti University of Medical Sciences, Tehran, Iran
| | - Mohammad Taheri
- Skull Base Research Center, Loghman Hakim Hospital, Shahid Beheshti University of Medical Sciences, Tehran, Iran.
| | - Maryam Rezazadeh
- Division of Medical Genetics, Tabriz Childrens Hospital, Tabriz University of Medical Sciences, Tabriz, Iran. .,Department of Medical Genetics, Faculty of Medicine, Tabriz University of Medical Sciences, Tabriz, Iran.
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Microsatellites as Agents of Adaptive Change: An RNA-Seq-Based Comparative Study of Transcriptomes from Five Helianthus Species. Symmetry (Basel) 2021. [DOI: 10.3390/sym13060933] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/13/2022] Open
Abstract
Mutations that provide environment-dependent selective advantages drive adaptive divergence among species. Many phenotypic differences among related species are more likely to result from gene expression divergence rather than from non-synonymous mutations. In this regard, cis-regulatory mutations play an important part in generating functionally significant variation. Some proposed mechanisms that explore the role of cis-regulatory mutations in gene expression divergence involve microsatellites. Microsatellites exhibit high mutation rates achieved through symmetric or asymmetric mutation processes and are abundant in both coding and non-coding regions in positions that could influence gene function and products. Here we tested the hypothesis that microsatellites contribute to gene expression divergence among species with 50 individuals from five closely related Helianthus species using an RNA-seq approach. Differential expression analyses of the transcriptomes revealed that genes containing microsatellites in non-coding regions (UTRs and introns) are more likely to be differentially expressed among species when compared to genes with microsatellites in the coding regions and transcripts lacking microsatellites. We detected a greater proportion of shared microsatellites in 5′UTRs and coding regions compared to 3′UTRs and non-coding transcripts among Helianthus spp. Furthermore, allele frequency differences measured by pairwise FST at single nucleotide polymorphisms (SNPs), indicate greater genetic divergence in transcripts containing microsatellites compared to those lacking microsatellites. A gene ontology (GO) analysis revealed that microsatellite-containing differentially expressed genes are significantly enriched for GO terms associated with regulation of transcription and transcription factor activity. Collectively, our study provides compelling evidence to support the role of microsatellites in gene expression divergence.
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Cao Y, Zhang DY, Zeng YF, Bai WN. Recent demographic histories of temperate deciduous trees inferred from microsatellite markers. BMC Ecol Evol 2021; 21:88. [PMID: 34006219 PMCID: PMC8130339 DOI: 10.1186/s12862-021-01805-w] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/06/2020] [Accepted: 04/23/2021] [Indexed: 11/17/2022] Open
Abstract
Background Accurate inference of demographic histories for temperate tree species can aid our understanding of current climate change as a driver of evolution. Microsatellites are more suitable for inferring recent historical events due to their high mutation rates. However, most programs analyzing microsatellite data assume a strict stepwise mutation model (SMM), which could cause false detection of population shrinkage when microsatellite mutation does not follow SMM. Results This study aims to reconstruct the recent demographic histories of five cool-temperate tree species in Eastern Asia, Quercus mongolica, Q. liaotungensis, Juglans cathayensis, J. mandshurica and J. ailantifolia, by using 19 microsatellite markers with two methods considering generalized stepwise mutation model (GSM) (MIGRAINE and VarEff). Both programs revealed that all the five species experienced expansions after the Last Glacial Maximum (LGM). Within butternuts, J. cathayensis experienced a more serious bottleneck than the other species, and within oaks, Q. mongolica showed a moderate increase in population size and remained stable after the expansion. In addition, the point estimates of the multistep mutation proportion in the GSM model (pGSM) for all five species were between 0.50 and 0.65, indicating that when inferring population demographic history of the cool-temperate forest species using microsatellite markers, it is better to assume a GSM rather than a SMM. Conclusions This study provides the first direct evidence that five cool-temperate tree species in East Asia have experienced expansions after the LGM with microsatellite data. Considering the mutation model of microsatellite has a vital influence on demographic inference, combining multiple programs such as MIGRAINE and VarEff can effectively reduce errors caused by inappropriate model selection and prior setting. Supplementary Information The online version contains supplementary material available at 10.1186/s12862-021-01805-w.
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Affiliation(s)
- Yu Cao
- State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Da-Yong Zhang
- State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China
| | - Yan-Fei Zeng
- State Key Laboratory of Tree Genetics and Breeding, Chinese Academy of Forestry, Beijing, 100091, China
| | - Wei-Ning Bai
- State Key Laboratory of Earth Surface Process and Resource Ecology and Ministry of Education Key Laboratory for Biodiversity Science and Ecological Engineering, College of Life Sciences, Beijing Normal University, Beijing, 100875, China.
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29
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Contrasting effects of local environment and grazing pressure on the genetic diversity and structure of Artemisia frigida. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01375-w] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/18/2022]
Abstract
AbstractDrylands count among the most globally extensive biomes, and while many desert and dry rangeland ecosystems are under threat, genetic structures of dryland species are still rarely studied. Artemisia frigida is one of the most widely distributed plant species in the temperate rangelands of Eurasia and North America, and it also dominates in many habitats of Mongolia due to its tolerance to low temperatures, drought and disturbance. Local environmental conditions and grazing pressure can influence species performance and affect spatial patterns of genetic diversity in contrasting ways, and our study set out to evaluate such effects on the genetic diversity and structure of A. frigida. We first developed new species-specific Simple Sequence Repeats (SSRs) markers using whole genome sequencing. We then analysed 11 populations of A. frigida that had been sampled along a large climatic gradient in Mongolia, which were sub-structured according to three levels of grazing intensity. Estimates of genetic diversity at the population level were high (HO = 0.56, HE = 0.73) and tended to increase with higher precipitation and soil nutrient availability. Grazing had no effect on genetic diversity, however, a high number of grazing-specific indicator alleles was found at grazed sites. Genetic differentiation among populations was extremely low (global GST = 0.034). Analysis of Molecular Variance revealed 5% variance between populations along the climatic gradient, with 3% of the variance being partitioned among different grazing intensity levels. We found no relationship between geographic and genetic distances, and thus no isolation by distance in this widely distributed species. The relatively low genetic structuring suggests that considerable gene flow exists among A. frigida populations across the rangelands of Mongolia, in spite of the pervasive grazing in the region.
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Genome-wide simple sequence repeats (SSR) markers discovered from whole-genome sequence comparisons of multiple spinach accessions. Sci Rep 2021; 11:9999. [PMID: 33976335 PMCID: PMC8113571 DOI: 10.1038/s41598-021-89473-0] [Citation(s) in RCA: 13] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/13/2020] [Accepted: 04/13/2021] [Indexed: 02/03/2023] Open
Abstract
The availability of well-assembled genome sequences and reduced sequencing costs have enabled the resequencing of many additional accessions in several crops, thus facilitating the rapid discovery and development of simple sequence repeat (SSR) markers. Although the genome sequence of inbred spinach line Sp75 is available, previous efforts have resulted in a limited number of useful SSR markers. Identification of additional polymorphic SSR markers will support genetics and breeding research in spinach. This study aimed to use the available genomic resources to mine and catalog a large number of polymorphic SSR markers. A search for SSR loci on six chromosome sequences of spinach line Sp75 using GMATA identified a total of 42,155 loci with repeat motifs of two to six nucleotides in the Sp75 reference genome. Whole-genome sequences (30x) of additional 21 accessions were aligned against the chromosome sequences of the reference genome and in silico genotyped using the HipSTR program by comparing and counting repeat numbers variation across the SSR loci among the accessions. The HipSTR program generated SSR genotype data were filtered for monomorphic and high missing loci, and a final set of the 5986 polymorphic SSR loci were identified. The polymorphic SSR loci were present at a density of 12.9 SSRs/Mb and were physically mapped. Out of 36 randomly selected SSR loci for validation, two failed to amplify, while the remaining were all polymorphic in a set of 48 spinach accessions from 34 countries. Genetic diversity analysis performed using the SSRs allele score data on the 48 spinach accessions showed three main population groups. This strategy to mine and develop polymorphic SSR markers by a comparative analysis of the genome sequences of multiple accessions and computational genotyping of the candidate SSR loci eliminates the need for laborious experimental screening. Our approach increased the efficiency of discovering a large set of novel polymorphic SSR markers, as demonstrated in this report.
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31
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Bhattarai G, Shi A, Kandel DR, Solís-Gracia N, da Silva JA, Avila CA. Genome-wide simple sequence repeats (SSR) markers discovered from whole-genome sequence comparisons of multiple spinach accessions. Sci Rep 2021. [PMID: 33976335 DOI: 10.1038/s41598-021-89472-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [MESH Headings] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 04/21/2023] Open
Abstract
The availability of well-assembled genome sequences and reduced sequencing costs have enabled the resequencing of many additional accessions in several crops, thus facilitating the rapid discovery and development of simple sequence repeat (SSR) markers. Although the genome sequence of inbred spinach line Sp75 is available, previous efforts have resulted in a limited number of useful SSR markers. Identification of additional polymorphic SSR markers will support genetics and breeding research in spinach. This study aimed to use the available genomic resources to mine and catalog a large number of polymorphic SSR markers. A search for SSR loci on six chromosome sequences of spinach line Sp75 using GMATA identified a total of 42,155 loci with repeat motifs of two to six nucleotides in the Sp75 reference genome. Whole-genome sequences (30x) of additional 21 accessions were aligned against the chromosome sequences of the reference genome and in silico genotyped using the HipSTR program by comparing and counting repeat numbers variation across the SSR loci among the accessions. The HipSTR program generated SSR genotype data were filtered for monomorphic and high missing loci, and a final set of the 5986 polymorphic SSR loci were identified. The polymorphic SSR loci were present at a density of 12.9 SSRs/Mb and were physically mapped. Out of 36 randomly selected SSR loci for validation, two failed to amplify, while the remaining were all polymorphic in a set of 48 spinach accessions from 34 countries. Genetic diversity analysis performed using the SSRs allele score data on the 48 spinach accessions showed three main population groups. This strategy to mine and develop polymorphic SSR markers by a comparative analysis of the genome sequences of multiple accessions and computational genotyping of the candidate SSR loci eliminates the need for laborious experimental screening. Our approach increased the efficiency of discovering a large set of novel polymorphic SSR markers, as demonstrated in this report.
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Affiliation(s)
- Gehendra Bhattarai
- Department of Horticulture, University of Arkansas, Fayetteville, AR, 72701, USA
| | - Ainong Shi
- Department of Horticulture, University of Arkansas, Fayetteville, AR, 72701, USA.
| | - Devi R Kandel
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, 78596, USA
| | - Nora Solís-Gracia
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, 78596, USA
| | - Jorge Alberto da Silva
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, 78596, USA
- Department of Crop and Soil Sciences, Texas A&M University, College Station, TX, 77843, USA
| | - Carlos A Avila
- Texas A&M AgriLife Research and Extension Center, Weslaco, TX, 78596, USA.
- Department of Horticultural Sciences, Texas A&M University, College Station, TX, 77843, USA.
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Abstract
Genetic diversity is a critical resource for species’ survival during times of environmental change. Conserving and sustainably managing genetic diversity requires understanding the distribution and amount of genetic diversity (in situ and ex situ) across multiple species. This paper focuses on three emblematic and IUCN Red List threatened oaks (Quercus, Fagaceae), a highly speciose tree genus that contains numerous rare species and poses challenges for ex situ conservation. We compare the genetic diversity of three rare oak species—Quercus georgiana, Q. oglethorpensis, and Q. boyntonii—to common oaks; investigate the correlation of range size, population size, and the abiotic environment with genetic diversity within and among populations in situ; and test how well genetic diversity preserved in botanic gardens correlates with geographic range size. Our main findings are: (1) these three rare species generally have lower genetic diversity than more abundant oaks; (2) in some cases, small population size and geographic range correlate with genetic diversity and differentiation; and (3) genetic diversity currently protected in botanic gardens is inadequately predicted by geographic range size and number of samples preserved, suggesting non-random sampling of populations for conservation collections. Our results highlight that most populations of these three rare oaks have managed to avoid severe genetic erosion, but their small size will likely necessitate genetic management going forward.
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Wang H, Yang B, Wang H, Xiao H. Impact of different numbers of microsatellite markers on population genetic results using SLAF-seq data for Rhododendron species. Sci Rep 2021; 11:8597. [PMID: 33883608 PMCID: PMC8060317 DOI: 10.1038/s41598-021-87945-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/30/2020] [Accepted: 04/06/2021] [Indexed: 12/30/2022] Open
Abstract
Microsatellites (simple sequence repeats, SSRs) are co-dominant nuclear markers that are widely used in population genetic studies. Population genetic parameters from different studies might be significantly influenced by differences in marker number. In our study, 265 sequences with polymorphic microsatellites were obtained from SLAF-seq data. Then, subpopulations containing different numbers (5, 6, 7,…, 15, 20, 25, 30, 35, 40) of markers were genotyped 10 times to investigate the impact of marker numbers on population genetic diversity results. Our results show that genotyping with less than 11 or 12 microsatellite markers lead to significant deviations in the population genetic diversity or genetic structure results. In order to provide markers for population genetic and conservation studies for Rhododendron, 26 SSR primers were designed and validated in three species.
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Affiliation(s)
- Huaying Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Baiming Yang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Huan Wang
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China
| | - Hongxing Xiao
- Key Laboratory of Molecular Epigenetics of Ministry of Education, Northeast Normal University, Changchun, 130024, China.
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Ribeiro MM, Diamantino T, Domingues J, Montanari Í, Alves MN, Gonçalves JC. Stevia rebaudiana germplasm characterization using microsatellite markers and steviol glycosides quantification by HPLC. Mol Biol Rep 2021; 48:2573-2582. [PMID: 33811576 PMCID: PMC8060219 DOI: 10.1007/s11033-021-06308-x] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/04/2021] [Accepted: 03/19/2021] [Indexed: 11/24/2022]
Abstract
Stevia rebaudiana Bertoni, Asteraceae, is an herbaceous perennial plant native to Paraguay. This species is considered since ancient times a medicinal plant with important bioactive compounds and pharmacologic and food properties, namely diterpenes glycosides. The high natural sweetener potential stevioside and rebaudioside A produced by S. rebaudiana plants are suitable sucrose substitutes, and their obtention is influenced by environmental, phytosociological, and genetic factors. The plants’ genetic profile and sweet potential depiction are needed for suitable plant selection for improvement and deployment. Thirty-one S. rebaudiana accessions grown in the same plot where leaves samples were collected in early 2019, were genotyped using six microsatellite markers, including two steviol glycosides biosynthesis functionally involved markers. Additionally, an aqueous extract of each sample was obtained in a water bath and purified by SPE for stevioside and rebaudioside A quantification by normal phase HPLC. Stevioside and rebaudioside A contents varied between 0.53–7.36% (w w−1) and 0.37–3.60% (w w−1), respectively. Two genotypes displayed interesting ratios of rebaudioside A/stevioside (number 3 and 33). The level of genetic similarity between genotypes was tested through a pairwise similarity coefficient, and two groups of individuals had the same fingerprinting. Strong relatedness was found within genotypes, possibly due to cloning, thus, influx of new germplasm ought to be made to prevent mating between relatives, and for further selection and genetic improvement.
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Affiliation(s)
- Maria Margarida Ribeiro
- Centro de Biotecnologia de Plantas da Beira Interior, Escola Superior Agrária de Castelo Branco, 6001-909, Castelo Branco, Portugal. .,Instituto Politécnico de Castelo BrancoEscola Superior Agrária, 6001-909, Castelo Branco, Portugal. .,Centro de Recursos NaturaisAmbiente e Sociedade (CERNAS) - Instituto Politécnico de Castelo Branco, 6000-084, Castelo Branco, Portugal. .,Forest Research Centre, School of Agriculture, University of Lisbon, Tapada da Ajuda, 1349-017, Lisbon, Portugal.
| | - Tatiana Diamantino
- Centro de Biotecnologia de Plantas da Beira Interior, Escola Superior Agrária de Castelo Branco, 6001-909, Castelo Branco, Portugal
| | - Joana Domingues
- Centro de Biotecnologia de Plantas da Beira Interior, Escola Superior Agrária de Castelo Branco, 6001-909, Castelo Branco, Portugal
| | - Ílio Montanari
- CPQBA/UNICAMP - Centro Pluridisciplinar de Pesquisas Químicas Biológicas e Agrícolas, Universidade Estadual de Campinas, São Paulo, Brazil
| | - Marcos Nopper Alves
- CPQBA/UNICAMP - Centro Pluridisciplinar de Pesquisas Químicas Biológicas e Agrícolas, Universidade Estadual de Campinas, São Paulo, Brazil
| | - José Carlos Gonçalves
- Centro de Biotecnologia de Plantas da Beira Interior, Escola Superior Agrária de Castelo Branco, 6001-909, Castelo Branco, Portugal.,Instituto Politécnico de Castelo BrancoEscola Superior Agrária, 6001-909, Castelo Branco, Portugal.,Centro de Recursos NaturaisAmbiente e Sociedade (CERNAS) - Instituto Politécnico de Castelo Branco, 6000-084, Castelo Branco, Portugal
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35
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The palaeoendemic conifer Pherosphaera hookeriana (Podocarpaceae) exhibits high genetic diversity despite Quaternary range contraction and post glacial bottlenecking. CONSERV GENET 2021. [DOI: 10.1007/s10592-021-01338-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/22/2022]
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Kirschner P, Arthofer W, Pfeifenberger S, Záveská E, Schönswetter P, Steiner FM, Schlick-Steiner BC. Performance comparison of two reduced-representation based genome-wide marker-discovery strategies in a multi-taxon phylogeographic framework. Sci Rep 2021; 11:3978. [PMID: 33597550 PMCID: PMC7889850 DOI: 10.1038/s41598-020-79778-x] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/28/2020] [Accepted: 12/09/2020] [Indexed: 01/31/2023] Open
Abstract
Multi-locus genetic data are pivotal in phylogenetics. Today, high-throughput sequencing (HTS) allows scientists to generate an unprecedented amount of such data from any organism. However, HTS is resource intense and may not be accessible to wide parts of the scientific community. In phylogeography, the use of HTS has concentrated on a few taxonomic groups, and the amount of data used to resolve a phylogeographic pattern often seems arbitrary. We explore the performance of two genetic marker sampling strategies and the effect of marker quantity in a comparative phylogeographic framework focusing on six species (arthropods and plants). The same analyses were applied to data inferred from amplified fragment length polymorphism fingerprinting (AFLP), a cheap, non-HTS based technique that is able to straightforwardly produce several hundred markers, and from restriction site associated DNA sequencing (RADseq), a more expensive, HTS-based technique that produces thousands of single nucleotide polymorphisms. We show that in four of six study species, AFLP leads to results comparable with those of RADseq. While we do not aim to contest the advantages of HTS techniques, we also show that AFLP is a robust technique to delimit evolutionary entities in both plants and animals. The demonstrated similarity of results from the two techniques also strengthens biological conclusions that were based on AFLP data in the past, an important finding given the wide utilization of AFLP over the last decades. We emphasize that whenever the delimitation of evolutionary entities is the central goal, as it is in many fields of biodiversity research, AFLP is still an adequate technique.
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Affiliation(s)
- Philipp Kirschner
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria ,grid.5771.40000 0001 2151 8122Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Wolfgang Arthofer
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Stefanie Pfeifenberger
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Eliška Záveská
- grid.5771.40000 0001 2151 8122Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | - Peter Schönswetter
- grid.5771.40000 0001 2151 8122Department of Botany, University of Innsbruck, Sternwartestraße 15, 6020 Innsbruck, Austria
| | | | - Florian M. Steiner
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
| | - Birgit C. Schlick-Steiner
- grid.5771.40000 0001 2151 8122Department of Ecology, University of Innsbruck, Technikerstraße 25, 6020 Innsbruck, Austria
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Cmejlova J, Rejlova M, Paprstein F, Cmejla R. A new one-tube reaction kit for the SSR genotyping of apple (Malus × domestica Borkh.). PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 303:110768. [PMID: 33487353 DOI: 10.1016/j.plantsci.2020.110768] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 08/11/2020] [Revised: 11/16/2020] [Accepted: 11/18/2020] [Indexed: 06/12/2023]
Abstract
Though apple genotyping is mainly used for scientific and breeding purposes, it can also be adopted by national authorities to control the authenticity of apple cultivars. To facilitate the introduction of routine apple genotyping into practice, a new apple simple sequence repeat (SSR) genotyping kit was developed (called the Ap17 in. SSR Genotyping Kit). The kit combines 17 SSR markers including those recommended by the Working Group of the European Cooperative Programme for Plant Genetic Resources (ECPGR), covering all apple linkage groups in a one-tube reaction format, using a fragment analysis method to simplify the genotyping procedure. The kit was successfully tested using 880 unique diploid apple germplasm accessions; the kit can also readily discriminate triploid and tetraploid samples. The total probability of identity for the kit and the sample collection used was calculated to be 1.73 × 10-22. Tables for converting results to enable genotype comparisons between currently-used genotyping systems and the Ap17 in. kit are provided. The kit is ideally suited for validation in laboratories genotyping a large number of apple samples, saving time, costs, and labor, while minimizing technical and human errors.
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Affiliation(s)
- Jana Cmejlova
- Research and Breeding Institute of Pomology Holovousy, Ltd., Holovousy 129, 508 01 Horice, Czech Republic
| | - Martina Rejlova
- Research and Breeding Institute of Pomology Holovousy, Ltd., Holovousy 129, 508 01 Horice, Czech Republic
| | - Frantisek Paprstein
- Research and Breeding Institute of Pomology Holovousy, Ltd., Holovousy 129, 508 01 Horice, Czech Republic
| | - Radek Cmejla
- Research and Breeding Institute of Pomology Holovousy, Ltd., Holovousy 129, 508 01 Horice, Czech Republic.
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Klápště J, Kremer A, Burg K, Garnier-Géré P, El-Dien OG, Ratcliffe B, El-Kassaby YA, Porth I. Quercus species divergence is driven by natural selection on evolutionarily less integrated traits. Heredity (Edinb) 2021; 126:366-382. [PMID: 33110229 PMCID: PMC8027598 DOI: 10.1038/s41437-020-00378-6] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/16/2020] [Revised: 10/07/2020] [Accepted: 10/07/2020] [Indexed: 11/09/2022] Open
Abstract
Functional traits are organismal attributes that can respond to environmental cues, thereby providing important ecological functions. In addition, an organism's potential for adaptation is defined by the patterns of covariation among groups of functionally related traits. Whether an organism is evolutionarily constrained or has the potential for adaptation is based on the phenotypic integration or modularity of these traits. Here, we revisited leaf morphology in two European sympatric white oaks (Quercus petraea (Matt.) Liebl. and Quercus robur L.), sampling 2098 individuals, across much of their geographical distribution ranges. At the phenotypic level, leaf morphology traditionally encompasses discriminant attributes among different oak species. Here, we estimated in situ heritability, genetic correlation, and integration across such attributes. Also, we performed Selection Response Decomposition to test these traits for potential differences in oak species' evolutionary responses. Based on the uncovered functional units of traits (modules) in our study, the morphological module "leaf size gradient" was highlighted among functionally integrated traits. Equally, this module was defined in both oaks as being under "global regulation" in vegetative bud establishment and development. Lamina basal shape and intercalary veins' number were not, or, less integrated within the initially defined leaf functional unit, suggesting more than one module within the leaf traits' ensemble. Since these traits generally show the greatest species discriminatory power, they potentially underwent effective differential response to selection among oaks. Indeed, the selection of these traits could have driven the ecological preferences between the two sympatric oaks growing under different microclimates.
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Affiliation(s)
- Jaroslav Klápště
- Department of Genetics and Physiology of Forest Trees, Faculty of Forestry and Wood Sciences, Czech University of Life Sciences in Prague, Kamýcká 129, 165 21, Prague 6, Czechia.
- Scion (New Zealand Forest Research Institute Ltd.), 49 Sala Street, Whakarewarewa, Rotorua, 3010, New Zealand.
| | - Antoine Kremer
- INRA, UMR Biodiversité Gènes et Communautés, 69 route d'Arcachon, 33612, Cestas Cedex, France
- University of Bordeaux, UMR 1202, Biodiversité Gènes et Communautés, F-33400, Talence, France
| | - Kornel Burg
- Department of Health and Environment (Bioresources), AIT Austrian Institute of Technology, Konrad-Lorenz-Straβe 24, 3430, Tulln, Austria
| | - Pauline Garnier-Géré
- INRA, UMR Biodiversité Gènes et Communautés, 69 route d'Arcachon, 33612, Cestas Cedex, France
- University of Bordeaux, UMR 1202, Biodiversité Gènes et Communautés, F-33400, Talence, France
| | - Omnia Gamal El-Dien
- Pharmacognosy Department, Faculty of Pharmacy, Alexandria University, Alexandria, Egypt
| | - Blaise Ratcliffe
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Yousry A El-Kassaby
- Department of Forest and Conservation Sciences, University of British Columbia, 2424 Main Mall, Vancouver, BC, V6T 1Z4, Canada
| | - Ilga Porth
- Département des sciences du bois et de la forêt, Université Laval, 1030, Avenue de la Médecine, Québec, QC, G1V 0A6, Canada
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Lin Z, Wang S, Neumann P, Chen G, Page P, Li L, Hu F, Zheng H, Dietemann V. Population genetics and host specificity of Varroa destructor mites infesting eastern and western honeybees. JOURNAL OF PEST SCIENCE 2021; 94:1487-1504. [PMID: 34720788 PMCID: PMC8549952 DOI: 10.1007/s10340-020-01322-7] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.7] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 07/23/2020] [Revised: 11/20/2020] [Accepted: 12/17/2020] [Indexed: 06/13/2023]
Abstract
In a globalized world, parasites are often brought in contact with new potential hosts. When parasites successfully shift host, severe diseases can emerge at a large cost to society. However, the evolutionary processes leading to successful shifts are rarely understood, hindering risk assessment, prevention, or mitigation of their effects. Here, we screened populations of Varroa destructor, an ectoparasitic mite of the honeybee genus Apis, to investigate their genetic structure and reproductive potential on new and original hosts. From the patterns identified, we deduce the factors that influenced the macro- and microevolutionary processes that led to the structure observed. Among the mite variants identified, we found two genetically similar populations that differed in their reproductive abilities and thus in their host specificity. These lineages could interbreed, which represents a threat due to the possible increased virulence of the parasite on its original host. However, interbreeding was unidirectional from the host-shifted to the nonshifted native mites and could thus lead to speciation of the former. The results improve our understanding of the processes affecting the population structure and evolution of this economically important mite genus and suggest that introgression between shifted and nonshifted lineages may endanger the original host. SUPPLEMENTARY INFORMATION The online version contains supplementary material available at 10.1007/s10340-020-01322-7.
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Affiliation(s)
- Zheguang Lin
- College of Animal Sciences, Zhejiang University, Hangzhou, China
- College of Animal Science and Technology, Yangzhou University, Yangzhou, China
| | - Shuai Wang
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Peter Neumann
- Swiss Bee Research Center, Agroscope, Bern, Switzerland
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Gongwen Chen
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Paul Page
- Swiss Bee Research Center, Agroscope, Bern, Switzerland
- Institute of Bee Health, Vetsuisse Faculty, University of Bern, Bern, Switzerland
| | - Li Li
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Fuliang Hu
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Huoqing Zheng
- College of Animal Sciences, Zhejiang University, Hangzhou, China
| | - Vincent Dietemann
- Swiss Bee Research Center, Agroscope, Bern, Switzerland
- Department of Ecology and Evolution, University of Lausanne, Lausanne, Switzerland
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Manco R, Chiaiese P, Basile B, Corrado G. Comparative analysis of genomic- and EST-SSRs in European plum ( Prunus domestica L.): implications for the diversity analysis of polyploids. 3 Biotech 2020; 10:543. [PMID: 33235823 PMCID: PMC7679426 DOI: 10.1007/s13205-020-02513-w] [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: 04/16/2020] [Accepted: 10/27/2020] [Indexed: 11/23/2022] Open
Abstract
Simple sequence repeats (SSRs) are among the most useful DNA markers in plant science. The aim of this study was to compare the features and usefulness of genomic SSR (gSSR) and EST-SSRs in European plum (Prunus domestica L.), an economically important, hexaploid stone fruit crop globally cultivated to produce fleshy fruits and derived foodstuff. The analysis of an ample set of morphologically diverse varieties indicated that gSSRs and EST-SSRs provide different estimates of some of the locus-based indicators of diversity. Moreover, the two classes of SSRs gave different, weakly correlated, estimations of distance-based parameters with gSSRs being more powerful for discriminating purposes. The two SSR classes provide complementary information in European plum, making the contribution of EST-SSRs useful not only as non-neutral markers. The differences between SSR classes are discussed considering the neutral and non-neutral evolution, and the polyploidy and asexual propagation of the cultivated tree varieties.
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Lewis DH, Jarvis DE, Maughan PJ. SSRgenotyper: A simple sequence repeat genotyping application for whole-genome resequencing and reduced representational sequencing projects. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11402. [PMID: 33344093 PMCID: PMC7742204 DOI: 10.1002/aps3.11402] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/26/2020] [Accepted: 10/13/2020] [Indexed: 05/13/2023]
Abstract
PREMISE Many programs can identify simple sequence repeat (SSR) motifs in genomic data. SSRgenotyper extends SSR identification to en masse genotyping from resequencing data for diversity panels and linkage mapping populations. METHODS AND RESULTS SSRgenotyper will find and genotype SSRs from SAM files and an SSR reference FASTA. Several outputs are possible, including a simple table with the SSR marker name, position, and SSR alleles, defined by the repeat number of the repeat motif. Specific output files include a GENEPOP-formatted file for downstream genetic diversity analyses and a traditional A, H, B mapping file output that is phased to the parents of the population for biparental linkage map construction. Linkage maps produced using SSRgenotyper genotypes were highly collinear with physical maps and correctly inferred known phylogenies. CONCLUSIONS SSRgenotyper provides an easy-to-use, accurate, and scalable SSR genotyping platform for whole-genome resequencing data. SSRgenotyper is freely available at https://github.com/dlewis27/SSRgenotyper.
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Affiliation(s)
- Daniel H. Lewis
- Department of Plant and Wildlife SciencesBrigham Young UniversityProvoUtah84058USA
| | - David E. Jarvis
- Department of Plant and Wildlife SciencesBrigham Young UniversityProvoUtah84058USA
| | - Peter J. Maughan
- Department of Plant and Wildlife SciencesBrigham Young UniversityProvoUtah84058USA
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A reference allelic ladder for Western Capercaillie (Tetrao urogallus) and Black Grouse (Tetrao tetrix) enables linking grouse genetic data across studies. CONSERV GENET RESOUR 2020. [DOI: 10.1007/s12686-020-01180-6] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Abstract
AbstractRapid anthropogenic climate change and progressing habitat degradation are considered top threats to biodiversity. The employment of demanding umbrella species as indicators for ecosystem health is a popular and cost-effective strategy that facilitates continuous monitoring and evaluation within a long-term conservation management scheme. The Western Capercaillie (Tetrao urogallus) and the Black Grouse (Tetrao tetrix) are both considered viable candidates due to their extensive habitat requirements, the possibility for conservative, non-invasive sampling, and their broad popular appeal. Regional population surveys based on genetic data from Short Sequence Repeat (SSR) analysis are being conducted throughout the Palearctic. However, to ensure reliable comparability among laboratories, standardization is required. Here, we report a catalogue of fifty fully characterized reference alleles from twelve SSR loci and the construction of a customizable allelic ladder for genotyping and individualization in Western Capercaillie and Black Grouse. This methodological improvement will help to cost-efficiently generate and collate supraregional data from different grouse surveys and thereby contribute to conservation management. Reference alleles and ladders can be obtained on demand.
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Machado RM, de Oliveira FA, de Matos Alves F, de Souza AP, Forni-Martins ER. Population Genetics of Polyploid Complex Psidium cattleyanum Sabine (Myrtaceae): Preliminary Analyses Based on New Species-Specific Microsatellite Loci and Extension to Other Species of the Genus. Biochem Genet 2020; 59:219-234. [PMID: 32980958 DOI: 10.1007/s10528-020-10002-1] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/09/2020] [Accepted: 09/18/2020] [Indexed: 11/29/2022]
Abstract
Polyploidy is a phenomenon that alters the genetic diversity of populations and has been reported as one of the most important evolutionary forces for plant diversification. The Psidium cattleyanum complex comprises a group of wild populations with several ploidy levels reported in the literature. The multiple cytotypes, associated with its wide distribution area, make this species a potential key model for understanding evolutionary processes related to polyploidization. In this study, we isolated and characterized nuclear microsatellite markers of P. cattleyanum and tested their transferability to other nine species of the genus. We performed a preliminary analysis of genetic diversity and population structure in three populations of P. cattleyanum. The three populations analyzed had different chromosome numbers, being polyploid cytotypes (2n = 6x = 66, 2n = 7x = 77 and 2n = 8x = 88). We designed 46 primer pairs and successfully amplified 37 markers, from which the 10 best were selected for analysis. Considering both the PIC and DP values, most of markers were highly informative. The new SSR markers were used to assess the levels of genetic diversity of the populations and detected one population with predominance of sexual reproduction. DAPC analysis pointed the formation of three groups, which corresponded to the populations analyzed. The markers were successfully amplified in related species, with some species presenting 80% transferability. By producing this panel of polymorphic microsatellites, we contribute to the understanding evolution in groups of natural polyploids for future studies.
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Affiliation(s)
- Raquel Moura Machado
- Instituto de Biologia, Programa de Pós-graduação em Biologia Vegetal, Universidade Estadual de Campinas, Campinas, Rua Monteiro Lobato 255, Campinas, SP, 13083-862, Brazil.
| | - Fernanda Ancelmo de Oliveira
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato 255, Campinas, SP, 13083-862, Brazil
| | - Fábio de Matos Alves
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato 255, Campinas, SP, 13083-862, Brazil
| | - Anete Pereira de Souza
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato 255, Campinas, SP, 13083-862, Brazil
| | - Eliana Regina Forni-Martins
- Departamento de Biologia Vegetal, Instituto de Biologia, Universidade Estadual de Campinas, Rua Monteiro Lobato 255, Campinas, SP, 13083-862, Brazil
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Camacho-Sanchez M, Velo-Antón G, Hanson JO, Veríssimo A, Martínez-Solano Í, Marques A, Moritz C, Carvalho SB. Comparative assessment of range-wide patterns of genetic diversity and structure with SNPs and microsatellites: A case study with Iberian amphibians. Ecol Evol 2020; 10:10353-10363. [PMID: 33072264 PMCID: PMC7548196 DOI: 10.1002/ece3.6670] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/21/2020] [Accepted: 07/22/2020] [Indexed: 11/11/2022] Open
Abstract
Reduced representation genome sequencing has popularized the application of single nucleotide polymorphisms (SNPs) to address evolutionary and conservation questions in nonmodel organisms. Patterns of genetic structure and diversity based on SNPs often diverge from those obtained with microsatellites to different degrees, but few studies have explicitly compared their performance under similar sampling regimes in a shared analytical framework. We compared range‐wide patterns of genetic structure and diversity in two amphibians endemic to the Iberian Peninsula: Hyla molleri and Pelobates cultripes, based on microsatellite (18 and 14 loci) and SNP (15,412 and 33,140 loci) datasets of comparable sample size and spatial extent. Model‐based clustering analyses with STRUCTURE revealed minor differences in genetic structure between marker types, but inconsistent values of the optimal number of populations (K) inferred. SNPs yielded more repeatable and less admixed ancestries with increasing K compared to microsatellites. Genetic diversity was weakly correlated between marker types, with SNPs providing a better representation of southern refugia and of gradients of genetic diversity congruent with the demographic history of both species. Our results suggest that the larger number of loci in a SNP dataset can provide more reliable inferences of patterns of genetic structure and diversity than a typical microsatellite dataset, at least at the spatial and temporal scales investigated.
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Affiliation(s)
- Miguel Camacho-Sanchez
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
| | - Guillermo Velo-Antón
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
| | - Jeffrey O Hanson
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
| | - Ana Veríssimo
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
| | | | - Adam Marques
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
| | - Craig Moritz
- Centre for Biodiversity Analysis and Research School of Biology The Australian National University Canberra ACT Australia
| | - Sílvia B Carvalho
- CIBIO/InBIO Centro de Investigação em Biodiversidade e Recursos Genéticos da Universidade do Porto Vairão Portugal
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Liu D, Zhang L, Wang J, Ma Y. Conservation Genomics of a Threatened Rhododendron: Contrasting Patterns of Population Structure Revealed From Neutral and Selected SNPs. Front Genet 2020; 11:757. [PMID: 33101354 PMCID: PMC7500208 DOI: 10.3389/fgene.2020.00757] [Citation(s) in RCA: 19] [Impact Index Per Article: 4.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/13/2020] [Accepted: 06/25/2020] [Indexed: 12/13/2022] Open
Abstract
Though it is well-acknowledged that next generation sequencing (NGS) technologies can provide further insights into plant conservation management than traditional molecular markers, studies employing NGS to address conservation genomics and subsequent conservation strategies for threatened plants are still rare. Rhododendron is the largest genus of woody plants in China, and many species are threatened, however, to date there has been no conservation genetic research using NGS in this genus. In the present study, we investigated the conservation genetics of R. cyanocarpum, a threatened species endemic to the Cangshan Mountains in Yunnan, China, using a double digest restriction-site-associated DNA-sequencing (ddRAD-seq) approach. Due to the availability of sufficient SNPs, we were able to distinguish between neutral and putatively selected SNPs and were able to further investigate the genetic diversity, population structure, and differentiation in R. cyanocarpum, as well as make an estimation of its demographic history. A total of 6,584 SNPs were obtained, of which 5,729 were neutral (detected using Tajima’s D). In terms of the 5,729 neutral SNPs, R. cyanocarpum had a higher genetic diversity (π = 0.0702 ± 0.0017, He = 0.0675 ± 0.0016) than other plant species assessed using Rad-seq methods, while population differentiation (Fst from 0.0314 to 0.0452) was weak. Interestingly, contrasting patterns of population structure were revealed from all neutral and selected SNPs, with distinct genetic clusters forming for all SNPs and neutral SNPs, but no distinct subgroups for selected ones. Moreover, we were able to detect changes in effective population size (Ne) of R. cyanocarpum from 150,000 years ago, including a bottleneck event ca. 60,000 years ago, followed by recovery of Ne over a short period, and a subsequent gradual decline in Ne to date. Implications for conserving R. cyanocarpum based on these main results are then discussed.
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Affiliation(s)
- Detuan Liu
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
| | - Lu Zhang
- Flower Research Institute, Yunnan Academy of Agriculture Sciences, Kunming, China
| | - Jihua Wang
- Flower Research Institute, Yunnan Academy of Agriculture Sciences, Kunming, China
| | - Yongpeng Ma
- Yunnan Key Laboratory for Integrative Conservation of Plant Species with Extremely Small Populations, Kunming Institute of Botany, Chinese Academy of Sciences, Kunming, China
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Ab Razak S, Mad Radzuan S, Mohamed N, Nor Azman NHE, Abd Majid AM, Ismail SN, Mohd Yusof MF, Sarip J, Nasir KH. Development of novel microsatellite markers using RAD sequencing technology for diversity assessment of rambutan ( Nephelium lappaceum L.) germplasm. Heliyon 2020; 6:e05077. [PMID: 33024864 PMCID: PMC7527576 DOI: 10.1016/j.heliyon.2020.e05077] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/14/2020] [Revised: 07/18/2020] [Accepted: 09/23/2020] [Indexed: 12/24/2022] Open
Abstract
The trend of microsatellite marker discovery and development revolved as a result of the advancement of next generation sequencing (NGS) technology as it has developed numerous microsatellites within a short period of time at a low cost. This study generated microsatellite markers using RAD sequencing technologies for the understudied Nephelium lappaceum. A total of 1403 microsatellite markers were successfully designed, which consisted of 853 di-, 525 tri-, 17 tetra-, 5 penta-, and 3 hexanucleotide microsatellite markers. Subsequently, selection of 39 microsatellites was made for the evaluation of genetic diversity of the selected 22 rambutan varieties. Twelve microsatellites, which exhibited high call rates across the samples, were used to assess the diversity of the aforementioned rambutan varieties. The analysis of 12 microsatellites revealed the presence of 72 alleles and six alleles per locus in average. Furthermore, the polymorphic information content (PIC) value ranged from 0.326 (NlaSSR20) to 0.832 (NlaSSR32), which included an average of 0.629 per locus, while the generated Neighbour Joining dendrogram showed two major clusters. The pairwise genetic distance of shared alleles exhibited a range of values from 0.046 (R134↔R170) to 0.818 (R5↔R170), which suggested highest dissimilarity detected between R5 and R170. Notably, these research findings would useful for varietal identification, proper management and conservation of the genetic resources, and exploitation and utilization in future breeding programs.
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Affiliation(s)
- Shahril Ab Razak
- Biotechnology & Nanotechnology Research Centre, MARDI Headquarters, 43400, Serdang, Selangor, Malaysia
| | - Salehudin Mad Radzuan
- Horticulture Research Centre, MARDI Sintok, 06050, Bukit Kayu Hitam, Kedah, Malaysia
| | - Norkhairi Mohamed
- Department of Agriculture, Hulu Paka Agricultural Centre, 23300, Dungun, Terengganu, Malaysia
| | - Nor Helwa Ezzah Nor Azman
- Biotechnology & Nanotechnology Research Centre, MARDI Headquarters, 43400, Serdang, Selangor, Malaysia
| | - Alny Marlynni Abd Majid
- Biotechnology & Nanotechnology Research Centre, MARDI Headquarters, 43400, Serdang, Selangor, Malaysia
| | - Siti Norhayati Ismail
- Biotechnology & Nanotechnology Research Centre, MARDI Headquarters, 43400, Serdang, Selangor, Malaysia
| | | | - Johari Sarip
- Horticulture Research Centre, MARDI Headquarters, 43400, Serdang, Selangor, Malaysia
| | - Khairun Hisam Nasir
- Biotechnology & Nanotechnology Research Centre, MARDI Headquarters, 43400, Serdang, Selangor, Malaysia
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Müller B, Mercker M, Brün J. Population size estimates based on the frequency of genetically assigned parent-offspring pairs within a subsample. Ecol Evol 2020; 10:6356-6363. [PMID: 32724517 PMCID: PMC7381586 DOI: 10.1002/ece3.6365] [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: 08/28/2019] [Revised: 03/09/2020] [Accepted: 04/17/2020] [Indexed: 01/28/2023] Open
Abstract
Estimating population density as precise as possible is a key premise for managing wild animal species. This can be a challenging task if the species in question is elusive or, due to high quantities, hard to count. We present a new, mathematically derived estimator for population size, where the estimation is based solely on the frequency of genetically assigned parent-offspring pairs within a subsample of an ungulate population. By use of molecular markers like microsatellites, the number of these parent-offspring pairs can be determined. The study's aim was to clarify whether a classical capture-mark-recapture (CMR) method can be adapted or extended by this genetic element to a genetic-based capture-mark-recapture (g-CMR). We numerically validate the presented estimator (and corresponding variance estimates) and provide the R-code for the computation of estimates of population size including confidence intervals. The presented method provides a new framework to precisely estimate population size based on the genetic analysis of a one-time subsample. This is especially of value where traditional CMR methods or other DNA-based (fecal or hair) capture-recapture methods fail or are too difficult to apply. The DNA source used is basically irrelevant, but in the present case the sampling of an annual hunting bag is to serve as data basis. In addition to the high quality of muscle tissue samples, hunting bags provide additional and essential information for wildlife management practices, such as age, weight, or sex. In cases where a g-CMR method is ecologically and hunting-wise appropriate, it enables a wide applicability, also through its species-independent use.
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Affiliation(s)
- Björn Müller
- Institute for Evolutionary Biology and EcologyUniversity of BonnBonnGermany
| | - Moritz Mercker
- Bionum‐Consultants in Biological, Ecological and Biomedical StatisticsHamburgGermany
| | - Jörg Brün
- Institute for Evolutionary Biology and EcologyUniversity of BonnBonnGermany
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Jiao SQ, Dong AX, Shi TL, Liu H, Porth I, Xin HB, Mao JF. Development of a Large Gene-Associated SSR Marker Set and in-Depth Genetic Characterization in Scarlet Sage. Front Genet 2020; 11:504. [PMID: 32508885 PMCID: PMC7253628 DOI: 10.3389/fgene.2020.00504] [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: 11/15/2019] [Accepted: 04/23/2020] [Indexed: 11/25/2022] Open
Abstract
Salvia splendens, scarlet or tropical sage, is a tender perennial herbaceous flowering plant popularly grown in public and private gardens all over the world. In this study, we developed a set of simple sequence repeats (SSRs) from genome-wide sequences to assess the genetic diversity and population structure among 112 cultivars. We obtained 364,379 SSRs by mining scarlet sage’s recently published whole genome sequence; 14,545 gene-associated SSR loci were identified in 2 kb gene flanking regions. Among the 768 gene-associated SSR primer sets we screened, 576 loci successfully amplified in DNA pools of 3–4 different cultivars, of which 271 remained polymorphic when tested across eight individual plants. We searched for the related gene functions attributable to these gene-associated SSRs using diverse databases, resulting in 259 Non-redundant matching sequences, 205 individual Gene Ontology (GO) terms, 236 assigned to eukaryotic orthologous groups, and 67 KEGG-annotated (Kyoto Encyclopedia of Genes and Genomes) sequences. We finally selected 41 polymorphic SSR loci to infer genetic diversity and population structure among 112 S. splendens accessions. Based on the developed gene-associated SSRs, clustering analyses consistently revealed two distinct genetic groups within the core collection of S. splendens cultivars. This work developed and characterized an exhaustive set of genome-wide gene-associated SSR markers for scarlet sage. These SSRs can provide species identification, genetic diversity and population structure information for S. splendens, and will therefore be important tools for the management and protection of S. splendens germplasm.
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Affiliation(s)
- Si-Qian Jiao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, 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
| | - Ai-Xiang Dong
- Beijing Key Laboratory of Greening Plants Breeding, Beijing Institute of Landscape Architecture, Beijing, China
| | - Tian-Le Shi
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, 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
| | - Hui Liu
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, 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
| | - Ilga Porth
- Département des Sciences du Bois et de la Forêt, Pavillon Charles-Eugène-Marchand, Université Laval, Québec, QC, Canada
| | - Hai-Bo Xin
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, 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.,Beijing Key Laboratory of Greening Plants Breeding, Beijing Institute of Landscape Architecture, Beijing, China
| | - Jian-Feng Mao
- Beijing Advanced Innovation Center for Tree Breeding by Molecular Design, National Engineering Laboratory for Tree Breeding, 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
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Hartvig I, So T, Changtragoon S, Tran HT, Bouamanivong S, Ogden R, Senn H, Vieira FG, Turner F, Talbot R, Theilade I, Nielsen LR, Kjær ED. Conservation genetics of the critically endangered Siamese rosewood (Dalbergia cochinchinensis): recommendations for management and sustainable use. CONSERV GENET 2020. [DOI: 10.1007/s10592-020-01279-1] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/30/2022]
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Ranathunge C, Wheeler GL, Chimahusky ME, Perkins AD, Pramod S, Welch ME. Transcribed microsatellite allele lengths are often correlated with gene expression in natural sunflower populations. Mol Ecol 2020; 29:1704-1716. [PMID: 32285554 DOI: 10.1111/mec.15440] [Citation(s) in RCA: 10] [Impact Index Per Article: 2.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/16/2018] [Revised: 03/15/2020] [Accepted: 04/02/2020] [Indexed: 12/23/2022]
Abstract
Microsatellites are common in genomes of most eukaryotic species. Due to their high mutability, an adaptive role for microsatellites has been considered. However, little is known concerning the contribution of microsatellites towards phenotypic variation. We used populations of the common sunflower (Helianthus annuus) at two latitudes to quantify the effect of microsatellite allele length on phenotype at the level of gene expression. We conducted a common garden experiment with seed collected from sunflower populations in Kansas and Oklahoma followed by an RNA-Seq experiment on 95 individuals. The effect of microsatellite allele length on gene expression was assessed across 3,325 microsatellites that could be consistently scored. Our study revealed 479 microsatellites at which allele length significantly correlates with gene expression (eSTRs). When irregular allele sizes not conforming to the motif length were removed, the number of eSTRs rose to 2,379. The percentage of variation in gene expression explained by eSTRs ranged from 1%-86% when controlling for population and allele-by-population interaction effects at the 479 eSTRs. Of these eSTRs, 70.4% are in untranslated regions (UTRs). A gene ontology (GO) analysis revealed that eSTRs are significantly enriched for GO terms associated with cis- and trans-regulatory processes. Our findings suggest that a substantial number of transcribed microsatellites can influence gene expression.
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Affiliation(s)
- Chathurani Ranathunge
- Department of Biological Sciences, Mississippi State University, Starkville, MS, USA
| | - Gregory L Wheeler
- Department of Biological Sciences, Mississippi State University, Starkville, MS, USA
| | - Melody E Chimahusky
- Department of Biological Sciences, Mississippi State University, Starkville, MS, USA
| | - Andy D Perkins
- Department of Computer Science and Engineering, Mississippi State University, Starkville, MS, USA
| | - Sreepriya Pramod
- Department of Biological Sciences, Mississippi State University, Starkville, MS, USA
| | - Mark E Welch
- Department of Biological Sciences, Mississippi State University, Starkville, MS, USA
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