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Beshera KA, Harris PM, Michael SK. Relative Genetic Homogeneity within a Phenotypically Diverse group: The Case of Lake Tana Labeobarbus (Cyprinidae) Species Flock, Ethiopia. Zootaxa 2023; 5301:182-198. [PMID: 37518566 DOI: 10.11646/zootaxa.5301.2.2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/07/2023] [Indexed: 08/01/2023]
Abstract
The Lake Tana Labeobarbus species flock represents one of the world's most famous examples of lacustrine species radiations. Previous studies of this group have resulted in the description of at least 15 species based on their differences in functional morphology and definition of two clades (lacustrine and riverine spawning clades) based on life history traits. A total of 166 fish representing 14 Labeobarbus species were genotyped using 10 lineage-specific hexaploid microsatellite loci. Six of these loci were developed for this study based on DNA sequence contigs derived from a microsatellite-enriched genomic library of Labeobarbus intermedius from Lake Tana; the remaining four loci were obtained from a previous study. The genotypes of the 10 loci were analyzed to examine genetic diversity and population structure within Lake Tana Labeobarbus. Overall mean allelic richness (NA) was 17.6 alleles per locus and observed (Ho) and expected (He) heterozygosities were 0.84 ± 0.14 and 0.73 ± 0.09, respectively, across all Lake Tana Labeobarbus samples examined. Our analyses reveal that there is little genetic differentiation among species (FST = 0.020-0.099; only 10 of 91 species comparisons were significant), but moderate differentiation (FST = 0.11, p < 0.05) between lacustrine and riverine spawning populations. Relative to previous phylogenetic hypotheses, our phenetic analysis employing the R-based Analysis of Phylogenetics and Evolution (APE) program seems to perform marginally better in revealing lineages within Lake Tana Labeobarbus. Herein, our results are compared to a previous microsatellite-based study of the same populations.
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Affiliation(s)
- Kebede A Beshera
- Department of Biological Sciences and Chemistry; Southern University and Agricultural & Mechanical College; 801 Harding Blvd; Baton Rouge; LA 70807; USA.
| | - Phillip M Harris
- Biodiversity and Systematics; Department of Biological Sciences; The University of Alabama; Tuscaloosa; AL 35487-0345; USA.
| | - Semhar K Michael
- Department of Mathematics and Statistics; South Dakota State University; Box 2225; Brookings; SD.
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2
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Zhang H, Tang Y, Li Q, Zhao S, Zhang Z, Chen Y, Shen Z, Chen C. Genetic and epigenetic variation separately contribute to range expansion and local metalliferous habitat adaptation during invasions of Chenopodium ambrosioides into China. ANNALS OF BOTANY 2022; 130:1041-1056. [PMID: 36413156 PMCID: PMC9851312 DOI: 10.1093/aob/mcac139] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/21/2022] [Accepted: 11/18/2022] [Indexed: 06/16/2023]
Abstract
BACKGROUND AND AIMS Invasive plants often colonize wide-ranging geographical areas with various local microenvironments. The specific roles of epigenetic and genetic variation during such expansion are still unclear. Chenopodium ambrosioides is a well-known invasive alien species in China that can thrive in metalliferous habitats. This study aims to comprehensively understand the effects of genetic and epigenetic variation on the successful invasion of C. ambrosioides. METHODS We sampled 367 individuals from 21 heavy metal-contaminated and uncontaminated sites with a wide geographical distribution in regions of China. We obtained environmental factors of these sampling sites, including 13 meteorological factors and the contents of four heavy metals in soils. Microsatellite markers were used to investigate the demographic history of C. ambrosioides populations in China. We also analysed the effect of epigenetic variation on metalliferous microhabitat adaptation using methylation-sensitive amplified polymorphism (MSAP) markers. A common garden experiment was conducted to compare heritable phenotypic variations among populations. KEY RESULTS Two distinct genetic clusters that diverged thousands of years ago were identified, suggesting that the eastern and south-western C. ambrosioides populations in China may have originated from independent introduction events without recombination. Genetic variation was shown to be a dominant determinant of phenotypic differentiation relative to epigenetic variation, and further affected the geographical distribution pattern of invasive C. ambrosioides. The global DNA unmethylation level was reduced in metalliferous habitats. Dozens of methylated loci were significantly associated with the heavy metal accumulation trait of C. ambrosioides and may contribute to coping with metalliferous microenvironments. CONCLUSIONS Our study of C. ambrosioides highlighted the dominant roles of genetic variation in large geographical range expansion and epigenetic variation in local metalliferous habitat adaptation.
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Affiliation(s)
- Hanchao Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Yongwei Tang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Quanyuan Li
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Shangjun Zhao
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Zhou Zhang
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Yahua Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
- Jiangsu Collaborative Innovation Centre for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Zhenguo Shen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
- Jiangsu Collaborative Innovation Centre for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
| | - Chen Chen
- College of Life Sciences, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
- Jiangsu Collaborative Innovation Centre for Solid Organic Waste Resource Utilization, Nanjing Agricultural University, Nanjing, Jiangsu, PR China
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3
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Assessment of the Genetic Distinctiveness and Uniformity of Pre-Basic Seed Stocks of Italian Ryegrass Varieties. Genes (Basel) 2022; 13:genes13112097. [DOI: 10.3390/genes13112097] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/30/2022] [Revised: 11/03/2022] [Accepted: 11/09/2022] [Indexed: 11/16/2022] Open
Abstract
Lolium multiflorum Lam., commonly known as Italian ryegrass, is a forage grass mostly valued for its high palatability and digestibility, along with its high productivity. However, Italian ryegrass has an outbreeding nature and therefore has high genetic heterogeneity within each variety. Consequently, the exclusive use of morphological descriptors in the existing varietal identification and registration process based on the Distinctness, Uniformity, and Stability (DUS) test results in an inadequately precise assessment. The primary objective of this work was to effectively test whether the uniformity observed at the phenological level within each population of Italian ryegrass was confirmed at the genetic level through an SSR marker analysis. In this research, using 12 polymorphic SSR loci, we analyzed 672 samples belonging to 14 different Italian ryegrass commercial varieties to determine the pairwise genetic similarity (GS), verified the distribution of genetic diversity within and among varieties, and investigated the population structure. Although the fourteen commercial varieties did not show elevated genetic differentiation, with only 13% of the total variation attributable to among-cultivar genetic variation, when analyzed as a core, each variety constitutes a genetic cluster on its own, resulting in distinct characteristics from the others, except for two varieties. In this way, by combining a genetic tool with the traditional morphological approach, we were able to limit biases linked to the environmental effect of field trials, assessing the real source of diversity among varieties and concretely answering the key requisites of the Plant Variety Protection (PVP) system.
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4
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Preston R, Blomster J, Schagerström E, Seppä P. Clonality, polyploidy and spatial population structure in Baltic Sea
Fucus vesiculosus. Ecol Evol 2022; 12:e9336. [PMID: 36188503 PMCID: PMC9486819 DOI: 10.1002/ece3.9336] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/11/2022] [Revised: 08/25/2022] [Accepted: 08/30/2022] [Indexed: 01/16/2023] Open
Affiliation(s)
- Roxana Preston
- Ecosystems and Environment Research Programme Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland
- Tvärminne Zoological Station University of Helsinki Hanko Finland
| | - Jaanika Blomster
- Ecosystems and Environment Research Programme Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland
| | - Ellen Schagerström
- Department of Ecology, Environment and Plant Sciences Stockholm University Stockholm Sweden
- Stockholm University Baltic Sea Centre Stockholm University Stockholm Sweden
| | - Perttu Seppä
- Organismal and Evolutionary Biology Research Programme Faculty of Biological and Environmental Sciences University of Helsinki Helsinki Finland
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5
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Varela-Álvarez E, Meirmans PG, Guiry MD, Serrão EA. Biogeographic Population Structure of Chimeric Blades of Porphyra in the Northeast Atlantic Reveals Southern Rich Gene Pools, Introgression and Cryptic Plasticity. FRONTIERS IN PLANT SCIENCE 2022; 13:818368. [PMID: 35283864 PMCID: PMC8908385 DOI: 10.3389/fpls.2022.818368] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/19/2021] [Accepted: 02/04/2022] [Indexed: 06/14/2023]
Abstract
The genus Porphyra sensu lato (Bangiaceae, Rhodophyta), an important seaweed grown in aquaculture, is the most genetically diverse group of the Class Bangiophyceae, but has poorly understood genetic variability linked to complex evolutionary processes. Genetic studies in the last decades have largely focused on resolving gene phylogenies; however, there is little information on historical population biogeography, structure and gene flow in the Bangiaceae, probably due to their cryptic nature, chimerism and polyploidy, which render analyses challenging. This study aims to understand biogeographic population structure in the two abundant Porphyra species in the Northeast Atlantic: Porphyra dioica (a dioecious annual) and Porphyra linearis (protandrous hermaphroditic winter annual), occupying distinct niches (seasonality and position on the shore). Here, we present a large-scale biogeographic genetic analysis across their distribution in the Northeast Atlantic, using 10 microsatellites and cpDNA as genetic markers and integrating chimerism and polyploidy, including simulations considering alleles derived from different ploidy levels and/or from different genotypes within the chimeric blade. For P. linearis, both markers revealed strong genetic differentiation of north-central eastern Atlantic populations (from Iceland to the Basque region of Northeast Iberia) vs. southern populations (Galicia in Northwest Iberia, and Portugal), with higher genetic diversity in the south vs. a northern homogenous low diversity. For. P. dioica, microsatellite analyses also revealed two genetic regions, but with weaker differentiation, and cpDNA revealed little structure with all the haplotypes mixed across its distribution. The southern cluster in P. linearis also included introgressed individuals with cpDNA from P. dioica and a winter form of P. dioica occurred spatially intermixed with P. linearis. This third entity had a similar morphology and seasonality as P. linearis but genomes (either nuclear or chloroplast) from P. dioica. We hypothesize a northward colonization from southern Europe (where the ancestral populations reside and host most of the gene pool of these species). In P. linearis recently established populations colonized the north resulting in homogeneous low diversity, whereas for P. dioica the signature of this colonization is not as obvious due to hypothetical higher gene flow among populations, possibly linked to its reproductive biology and annual life history.
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Affiliation(s)
| | - Patrick G. Meirmans
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, Netherlands
| | - Michael D. Guiry
- AlgaeBase, Ryan Institute, National University of Ireland, Galway, Ireland
| | - Ester A. Serrão
- CCMAR Centro de Ciências do Mar, CIMAR, Universidade do Algarve, Faro, Portugal
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6
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Wilson S, Malosetti M, Maliepaard C, Mulder HA, Visser RGF, van Eeuwijk F. Training Set Construction for Genomic Prediction in Auto-Tetraploids: An Example in Potato. FRONTIERS IN PLANT SCIENCE 2021; 12:771075. [PMID: 34899794 PMCID: PMC8651708 DOI: 10.3389/fpls.2021.771075] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/05/2021] [Accepted: 10/20/2021] [Indexed: 06/14/2023]
Abstract
Training set construction is an important prerequisite to Genomic Prediction (GP), and while this has been studied in diploids, polyploids have not received the same attention. Polyploidy is a common feature in many crop plants, like for example banana and blueberry, but also potato which is the third most important crop in the world in terms of food consumption, after rice and wheat. The aim of this study was to investigate the impact of different training set construction methods using a publicly available diversity panel of tetraploid potatoes. Four methods of training set construction were compared: simple random sampling, stratified random sampling, genetic distance sampling and sampling based on the coefficient of determination (CDmean). For stratified random sampling, population structure analyses were carried out in order to define sub-populations, but since sub-populations accounted for only 16.6% of genetic variation, there were negligible differences between stratified and simple random sampling. For genetic distance sampling, four genetic distance measures were compared and though they performed similarly, Euclidean distance was the most consistent. In the majority of cases the CDmean method was the best sampling method, and compared to simple random sampling gave improvements of 4-14% in cross-validation scenarios, and 2-8% in scenarios with an independent test set, while genetic distance sampling gave improvements of 5.5-10.5% and 0.4-4.5%. No interaction was found between sampling method and the statistical model for the traits analyzed.
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Affiliation(s)
- Stefan Wilson
- Biometris, Wageningen University & Research, Wageningen, Netherlands
| | - Marcos Malosetti
- Biometris, Wageningen University & Research, Wageningen, Netherlands
| | - Chris Maliepaard
- Plant Breeding, Wageningen University & Research, Wageningen, Netherlands
| | - Han A. Mulder
- Wageningen University & Research, Animal Breeding and Genomics, Wageningen, Netherlands
| | | | - Fred van Eeuwijk
- Biometris, Wageningen University & Research, Wageningen, Netherlands
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7
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Cui X, Li C, Qin S, Huang Z, Gan B, Jiang Z, Huang X, Yang X, Li Q, Xiang X, Chen J, Zhao Y, Rong J. High-throughput sequencing-based microsatellite genotyping for polyploids to resolve allele dosage uncertainty and improve analyses of genetic diversity, structure and differentiation: A case study of the hexaploid Camellia oleifera. Mol Ecol Resour 2021; 22:199-211. [PMID: 34260828 DOI: 10.1111/1755-0998.13469] [Citation(s) in RCA: 3] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/03/2020] [Revised: 07/08/2021] [Accepted: 07/12/2021] [Indexed: 11/30/2022]
Abstract
Conventional microsatellite (simple sequence repeat, SSR) genotyping methods cannot accurately identify polyploid genotypes leading to allele dosage uncertainty, introducing biases in population genetic analysis. Here, a new SSR genotyping method was developed to directly infer accurate polyploid genotypes. The frequency distribution of SSR sequences was obtained based on deep-coverage high-throughput sequencing data. Corrections were performed accounting for the "stutter peak" and amplification efficiency of SSR sequences. Perl scripts and an online SSR genotyping tool "SSRSeq" were provided to process the sequencing data and output genotypes with corrected allele dosages. Hexaploid Camellia oleifera is the dominant woody oilseed crop in China. Understanding the geographical pattern of genetic variation in wild C. oleifera is essential for the conservation and utilization of genetic resources. Six wild C. oleifera populations were sampled across geographical ranges in subtropical evergreen broadleaf forests of China. Using 35 SSR markers, the high-throughput sequencing-based SSRSeq method was applied to obtain accurate hexaploid genotypes of wild C. oleifera. The results demonstrated that the new method could resolve allele dosage uncertainty and considerably improve genetic diversity, structure and differentiation analyses for polyploids. The genetic variation patterns of wild C. oleifera across geographical ranges agree with the "central-marginal hypothesis", stating that genetic diversity is high in the central population and declines from the central to the peripheral populations, and genetic differentiation increases from the centre to the periphery. This method and findings can facilitate the utilization of wild C. oleifera genetic resources for the breeding of cultivated C. oleifera.
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Affiliation(s)
- Xiangyan Cui
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Caihua Li
- Center for Genetic & Genomic Analysis, Genesky Biotechnologies Inc, Shanghai, China
| | - Shengyuan Qin
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Zebin Huang
- Center for Genetic & Genomic Analysis, Genesky Biotechnologies Inc, Shanghai, China
| | - Bin Gan
- Center for Genetic & Genomic Analysis, Genesky Biotechnologies Inc, Shanghai, China
| | | | - Xiaomao Huang
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Xiaoqiang Yang
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Qin Li
- Fudan Development Institute, Fudan University, Shanghai, China
| | - Xiaoguo Xiang
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China
| | - Jiakuan Chen
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China.,Fudan Development Institute, Fudan University, Shanghai, China
| | - Yao Zhao
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China.,Lushan Botanical Garden, Chinese Academy of Sciences, Lushan, China
| | - Jun Rong
- Jiangxi Province Key Laboratory of Watershed Ecosystem Change and Biodiversity, Center for Watershed Ecology, Institute of Life Science and School of Life Sciences, Nanchang University, Nanchang, China.,Lushan Botanical Garden, Chinese Academy of Sciences, Lushan, China
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8
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Development of novel microsatellite marker panel in threatened tetraploid mahseer, Tor tor (Hamilton 1822) for insights into its genetic diversity and population structure. Meta Gene 2021. [DOI: 10.1016/j.mgene.2021.100880] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/21/2022] Open
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9
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Breidenbach N, Gailing O, Krutovsky KV. Genetic structure of coast redwood (Sequoia sempervirens [D. Don] Endl.) populations in and outside of the natural distribution range based on nuclear and chloroplast microsatellite markers. PLoS One 2020; 15:e0243556. [PMID: 33306715 PMCID: PMC7732113 DOI: 10.1371/journal.pone.0243556] [Citation(s) in RCA: 8] [Impact Index Per Article: 2.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2020] [Accepted: 11/24/2020] [Indexed: 11/18/2022] Open
Abstract
Coast redwood (Sequoia sempervirens) naturally growing in southern Oregon and northern California is one of the few conifer tree species that are polyploid. Despite its unique ecological and economic importance, its population genetic structure is still insufficiently studied. To obtain additional data on its population genetic structure we genotyped 317 samples collected from populations in California (data set C) and 144 trees growing in a provenance trial in France (data set F) using 12 nuclear (five random nuclear genomic nSSRs and seven expressed sequence tag EST-SSRs) and six chloroplast (cpSSRs) microsatellite or simple sequence repeat (SSR) markers, respectively. These data sets were also used as reference to infer the origin of 147 coast redwood trees growing in Germany (data set G). Coast redwood was introduced to Europe, including Germany as an ornamental species, decades ago. Due to its fast growth and high timber quality, it could be considered as a potential commercial timber species, especially in perspective to climate warming that makes more regions in Germany suitable for its growing. The well performing trees in colder Germany could be potential frost resistant genotypes, but their genetic properties and origin are mostly unknown. Within the natural range in southern Oregon and northern California, only two relatively weak clusters were identified, one northern and one southern, separated by the San Francisco Bay. High genetic diversity, but low differentiation was found based on the 12 nuclear SSR markers for all three data sets F, C and G. We found that investigated 147 German trees represented only 37 different genotypes. They showed genetic diversity at the level less than diversity observed within the natural range in the northern or southern cluster, but more similar to the diversity observed in the southern cluster. It was difficult to assign German trees to the original single native populations using the six cpSSR markers, but rather to either the northern or southern cluster. The high number of haplotypes found in the data sets based on six cpSSR markers and low genetic differentiation based on 12 nuclear SSRs found in this study helps us study and better understand population genetic structure of this complex polyploid tree and supports the selection of potential genotypes for German forestry.
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Affiliation(s)
- Natalie Breidenbach
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Göttingen, Germany
| | - Oliver Gailing
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Göttingen, Germany
- Center for Integrated Breeding Research, Georg-August University of Göttingen, Göttingen, Germany
| | - Konstantin V. Krutovsky
- Department of Forest Genetics and Forest Tree Breeding, Georg-August University of Göttingen, Göttingen, Germany
- Center for Integrated Breeding Research, Georg-August University of Göttingen, Göttingen, Germany
- Laboratory of Population Genetics, Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia
- Laboratory of Forest Genomics, Genome Research and Education Center, Institute of Fundamental Biology and Biotechnology, Siberian Federal University, Krasnoyarsk, Russia
- Department of Ecosystem Sciences and Management, Texas A&M University, College Station, Texas, United States of America
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10
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Gemenet DC, Lindqvist-Kreuze H, De Boeck B, da Silva Pereira G, Mollinari M, Zeng ZB, Craig Yencho G, Campos H. Sequencing depth and genotype quality: accuracy and breeding operation considerations for genomic selection applications in autopolyploid crops. TAG. THEORETICAL AND APPLIED GENETICS. THEORETISCHE UND ANGEWANDTE GENETIK 2020; 133:3345-3363. [PMID: 32876753 PMCID: PMC7567692 DOI: 10.1007/s00122-020-03673-2] [Citation(s) in RCA: 12] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/01/2020] [Accepted: 08/21/2020] [Indexed: 05/06/2023]
Abstract
KEY MESSAGE Polypoid crop breeders can balance resources between density and sequencing depth, dosage information and fewer highly informative SNPs recommended, non-additive models and QTL advantages on prediction dependent on trait architecture. The autopolyploid nature of potato and sweetpotato ensures a wide range of meiotic configurations and linkage phases leading to complex gene-action and pose problems in genotype data quality and genomic selection analyses. We used a 315-progeny biparental F1 population of hexaploid sweetpotato and a diversity panel of 380 tetraploid potato, genotyped using different platforms to answer the following questions: (i) do polyploid crop breeders need to invest more for additional sequencing depth? (ii) how many markers are required to make selection decisions? (iii) does considering non-additive genetic effects improve predictive ability (PA)? (iv) does considering dosage or quantitative trait loci (QTL) offer significant improvement to PA? Our results show that only a small number of highly informative single nucleotide polymorphisms (SNPs; ≤ 1000) are adequate for prediction in the type of populations we analyzed. We also show that considering dosage information and models considering only additive effects had the best PA for most traits, while the comparative advantage of considering non-additive genetic effects and including known QTL in the predictive model depended on trait architecture. We conclude that genomic selection can help accelerate the rate of genetic gains in potato and sweetpotato. However, application of genomic selection should be considered as part of optimizing the entire breeding program. Additionally, since the predictions in the current study are based on single populations, further studies on the effects of haplotype structure and inheritance on PA should be studied in actual multi-generation breeding populations.
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Affiliation(s)
- Dorcus C Gemenet
- International Potato Center, ILRI Campus, P.O. Box 25171-00603, Nairobi, Kenya.
- CGIAR Excellence in Breeding Platform, International Maize and Wheat Improvement Center (CIMMYT), ICRAF Campus, 1041-00621, Nairobi, Kenya.
| | | | - Bert De Boeck
- International Potato Center, Av. La Molina 1895, Lima, Peru
| | | | | | - Zhao-Bang Zeng
- North Carolina State University, Raleigh, NC, 27695, USA
| | - G Craig Yencho
- North Carolina State University, Raleigh, NC, 27695, USA
| | - Hugo Campos
- International Potato Center, Av. La Molina 1895, Lima, Peru
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11
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Understanding the genetic diversity of the guayabillo (Psidium galapageium), an endemic plant of the Galapagos Islands. Glob Ecol Conserv 2020. [DOI: 10.1016/j.gecco.2020.e01350] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 02/04/2023] Open
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12
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Eckert S, Herden J, Stift M, Joshi J, van Kleunen M. Manipulation of cytosine methylation does not remove latitudinal clines in two invasive goldenrod species in Central Europe. Mol Ecol 2020; 30:222-236. [PMID: 33150604 DOI: 10.1111/mec.15722] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Journal Information] [Subscribe] [Scholar Register] [Received: 10/10/2019] [Revised: 10/03/2020] [Accepted: 10/23/2020] [Indexed: 12/23/2022]
Abstract
Invasive species frequently differentiate phenotypically in novel environments within a few generations, often even with limited genetic variation. For the invasive plants Solidago canadensis and S. gigantea, we tested whether such differentiation might have occurred through heritable epigenetic changes in cytosine methylation. In a 2-year common-garden experiment, we grew plants from seeds collected along a latitudinal gradient in their non-native Central European range to test for trait differentiation and whether differentiation disappeared when seeds were treated with the demethylation agent zebularine. Microsatellite markers revealed no population structure along the latitudinal gradient in S. canadensis, but three genetic clusters in S. gigantea. Solidago canadensis showed latitudinal clines in flowering phenology and growth. In S. gigantea, the number of clonal offspring decreased with latitude. Although zebularine had a significant effect on early growth, probably through effects on cytosine methylation, latitudinal clines remained (or even got stronger) in plants raised from seeds treated with zebularine. Thus, our experiment provides no evidence that epigenetic mechanisms by selective cytosine methylation contribute to the observed phenotypic differentiation in invasive goldenrods in Central Europe.
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Affiliation(s)
- Silvia Eckert
- Biodiversity Research/Systematic Botany, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany
| | - Jasmin Herden
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Marc Stift
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany
| | - Jasmin Joshi
- Biodiversity Research/Systematic Botany, Institute of Biochemistry and Biology, University of Potsdam, Potsdam, Germany.,Institute for Landscape and Open Space, Eastern Switzerland University of Applied Sciences, Rapperswil, Switzerland.,Berlin-Brandenburg Institute of Advanced Biodiversity Research (BBIB), Berlin, Germany
| | - Mark van Kleunen
- Ecology, Department of Biology, University of Konstanz, Konstanz, Germany.,Zhejiang Provincial Key Laboratory of Plant Evolutionary Ecology and Conservation, Taizhou University, Taizhou, China
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13
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Gargiulo R, Worswick G, Arnold C, Pike LJ, Cowan RS, Hardwick KA, Chapman T, Fay MF. Conservation of the Threatened Species, Pulsatilla vulgaris Mill. (Pasqueflower), is Aided by Reproductive System and Polyploidy. J Hered 2020; 110:618-628. [PMID: 31102445 DOI: 10.1093/jhered/esz035] [Citation(s) in RCA: 6] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/25/2019] [Accepted: 05/16/2019] [Indexed: 11/13/2022] Open
Abstract
Population loss due to habitat disturbance is a major concern in biodiversity conservation. Here we investigate the genetic causes of the demographic decline observed in English populations of Pulsatilla vulgaris and the consequences for conservation. Using 10 nuclear microsatellite markers, we compare genetic variation in wild populations with restored and seed-regenerated populations (674 samples). Emergence of genetic structure and loss of allelic variation in natural populations are not as evident as expected from demographic trends. Restored populations show genetic variation comparable to their source populations and, in general, to the wild ones. Genetic homogeneity is observed in regeneration trials, although some alleles not captured in source populations are detected. We infer that polyploidy, longevity, and clonal reproduction have provided P. vulgaris with the standing genetic variation necessary to make the species resilient to the effects of demographic decline, suggesting that the use of multiple sources for reintroduction may be beneficial to mimic natural gene flow and the availability of multiple allele copies typical of polyploid species.
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Affiliation(s)
| | | | | | | | | | - Kate A Hardwick
- Royal Botanic Gardens, Kew, Millennium Seed Bank, Ardingly, UK
| | - Ted Chapman
- Royal Botanic Gardens, Kew, Millennium Seed Bank, Ardingly, UK
| | - Michael F Fay
- Royal Botanic Gardens, Kew, Richmond, UK.,School of Plant Biology, University of Western Australia, Crawley, Western Australia, Australia
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14
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Beirinckx L, Vanschoenwinkel B, Triest L. Hidden Hybridization and Habitat Differentiation in a Mediterranean Macrophyte, the Euryhaline Genus Ruppia. FRONTIERS IN PLANT SCIENCE 2020; 11:830. [PMID: 32754168 PMCID: PMC7366321 DOI: 10.3389/fpls.2020.00830] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 12/02/2019] [Accepted: 05/22/2020] [Indexed: 06/11/2023]
Abstract
In many aquatic plant taxa, classification based on morphology has always been difficult. Molecular markers revealed that the complexity in several of these aquatic taxa could be addressed to recurrent hybridization events and cryptic species diversity. The submerged macrophyte genus Ruppia is one of these aquatic genera with a complex taxonomy due to the absence of clear distinguishable traits and several hybridization events. Two species co-exist throughout Europe, R. maritima and R. spiralis (previously known as R. cirrhosa), but recent molecular studies also found several indications of hybridization, introgression and chloroplast capture between these species. However, the full extent and frequency of hybridization and introgression in this genus has not been studied so far, nor is it clear how these hybrid lineages can co-exist locally with their parental species. In this paper, we wanted to detect whether a single coastal wetland where both species co-exist can act as a Ruppia hybrid zone. As a case study, we chose the Camargue, a Mediterranean coastal wetland that harbors a wide diversity in aquatic habitats, especially in terms of salinity and hydro-regime. We sampled several Ruppia populations within this wetland. To identify each sample and reconstruct the local genetic structure of the two parental species and their hybrids, we used both chloroplast and nuclear microsatellite markers. Afterward, we tested whether different species had different habitat preferences. Our results confirmed that R. maritima and R. spiralis are two strongly divergent species with different reproductive ecologies and different habitat preferences. This prevents frequent hybridization and consequently we could not detect any trace of a recent hybridization event. However, we found several populations of later-generation hybrids, including a population of R. maritima x hybrid backcrosses. The hybrid populations occupy a different habitat and are genetically distinct from their parental species, although they tend to be morphological similar to parental R. maritima. Although local hybridization and introgression in Ruppia is less frequent than we expected, the taxonomy of Ruppia is complicated due to ancient hybridizations and several back-crossings.
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Affiliation(s)
- Lise Beirinckx
- Ecology and Biodiversity Research Group, Plant Biology and Nature Management, Vrije Universiteit Brussel (VUB), Brussels, Belgium
| | - Bram Vanschoenwinkel
- Community Ecology Laboratory, Department of Biology, Vrije Universiteit Brussel (VUB), Brussels, Belgium
- Centre for Environmental Management, University of the Free State, Bloemfontein, South Africa
| | - Ludwig Triest
- Ecology and Biodiversity Research Group, Plant Biology and Nature Management, Vrije Universiteit Brussel (VUB), Brussels, Belgium
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15
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Meirmans PG. genodive version 3.0: Easy-to-use software for the analysis of genetic data of diploids and polyploids. Mol Ecol Resour 2020; 20:1126-1131. [PMID: 32061017 PMCID: PMC7496249 DOI: 10.1111/1755-0998.13145] [Citation(s) in RCA: 128] [Impact Index Per Article: 32.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/19/2019] [Revised: 01/09/2020] [Accepted: 02/10/2020] [Indexed: 12/28/2022]
Abstract
genodive version 3.0 is a user-friendly program for the analysis of population genetic data. This version presents a major update from the previous version and now offers a wide spectrum of different types of analyses. genodive has an intuitive graphical user interface that allows direct manipulation of the data through transformation, imputation of missing data, and exclusion and inclusion of individuals, population and/or loci. Furthermore, genodive seamlessly supports 15 different file formats for importing or exporting data from or to other programs. One major feature of genodive is that it supports both diploid and polyploid data, up to octaploidy (2n = 8x) for some analyses, but up to hexadecaploidy (2n = 16x) for other analyses. The different types of analyses offered by genodive include multiple statistics for estimating population differentiation (φST , FST , F'ST , GST , G'ST , G''ST , Dest , RST , ρ), analysis of molecular variance-based K-means clustering, Hardy-Weinberg equilibrium, hybrid index, population assignment, clone assignment, Mantel test, Spatial Autocorrelation, 23 ways of calculating genetic distances, and both principal components and principal coordinates analyses. A unique feature of genodive is that it can also open data sets with nongenetic variables, for example environmental data or geographical coordinates that can be included in the analysis. In addition, genodive makes it possible to run several external programs (lfmm, structure, instruct and vegan) directly from its own user interface, avoiding the need for data reformatting and use of the command line. genodive is available for computers running Mac OS X 10.7 or higher and can be downloaded freely from: http://www.patrickmeirmans.com/software.
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Affiliation(s)
- Patrick G Meirmans
- Institute for Biodiversity and Ecosystem Dynamics (IBED), University of Amsterdam, Amsterdam, The Netherlands
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16
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Huang K, Dunn DW, Ritland K, Li B. polygene: Population genetics analyses for autopolyploids based on allelic phenotypes. Methods Ecol Evol 2019. [DOI: 10.1111/2041-210x.13338] [Citation(s) in RCA: 20] [Impact Index Per Article: 4.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/01/2022]
Affiliation(s)
- Kang Huang
- Shaanxi Key Laboratory for Animal Conservation College of Life Sciences Northwest University Xi’an China
- Department of Forest and Conservation Sciences University of British Columbia Vancouver Canada
| | - Derek W. Dunn
- Shaanxi Key Laboratory for Animal Conservation College of Life Sciences Northwest University Xi’an China
| | - Kermit Ritland
- Department of Forest and Conservation Sciences University of British Columbia Vancouver Canada
| | - Baoguo Li
- Shaanxi Key Laboratory for Animal Conservation College of Life Sciences Northwest University Xi’an China
- Center for Excellence in Animal Evolution and Genetics Chinese Academy of Sciences Kunming China
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17
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Genotypic Frequencies at Equilibrium for Polysomic Inheritance Under Double-Reduction. G3-GENES GENOMES GENETICS 2019; 9:1693-1706. [PMID: 30910817 PMCID: PMC6505158 DOI: 10.1534/g3.119.400132] [Citation(s) in RCA: 18] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 12/19/2022]
Abstract
Polyploids are organisms whose genomes consist of more than two complete sets of chromosomes. Both autopolyploids and allopolyploids may display polysomic inheritance. A peculiarity of polysomic inheritance is multivalent formation during meiosis resulting in double-reduction, which occurs when sister chromatid fragments segregate into the same gamete. Double-reduction can result in gametes carrying identical-by-descent alleles and slightly increasing homozygosity. This will cause the genotypic frequencies to deviate from expected values and will thus bias the results of standard population genetic analytical methods used in molecular ecology and selective breeding. In this study, we extend existing double-reduction models to account for any even level of ploidy, and derive the symbolic expressions for genotypic frequencies via two methods. Inbreeding coefficients and heterozygosity under double-reduction and inbreeding are also calculated. Numerical solutions obtained by computer simulations are compared with analytical solutions predicted by the model to validate the model.
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18
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polyRAD: Genotype Calling with Uncertainty from Sequencing Data in Polyploids and Diploids. G3-GENES GENOMES GENETICS 2019; 9:663-673. [PMID: 30655271 PMCID: PMC6404598 DOI: 10.1534/g3.118.200913] [Citation(s) in RCA: 45] [Impact Index Per Article: 9.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Indexed: 11/18/2022]
Abstract
Low or uneven read depth is a common limitation of genotyping-by-sequencing (GBS) and restriction site-associated DNA sequencing (RAD-seq), resulting in high missing data rates, heterozygotes miscalled as homozygotes, and uncertainty of allele copy number in heterozygous polyploids. Bayesian genotype calling can mitigate these issues, but previously has only been implemented in software that requires a reference genome or uses priors that may be inappropriate for the population. Here we present several novel Bayesian algorithms that estimate genotype posterior probabilities, all of which are implemented in a new R package, polyRAD. Appropriate priors can be specified for mapping populations, populations in Hardy-Weinberg equilibrium, or structured populations, and in each case can be informed by genotypes at linked markers. The polyRAD software imports read depth from several existing pipelines, and outputs continuous or discrete numerical genotypes suitable for analyses such as genome-wide association and genomic prediction.
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19
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Plue J, Aavik T, Cousins SAO. Grazing networks promote plant functional connectivity among isolated grassland communities. DIVERS DISTRIB 2018. [DOI: 10.1111/ddi.12842] [Citation(s) in RCA: 11] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 12/24/2022] Open
Affiliation(s)
- Jan Plue
- Biogeography and Geomatics; Department of Physical Geography; Stockholm University; Stockholm Sweden
- Natural Sciences, Technology and Environmental Studies; Södertörn University; Stockholm Sweden
- Plant Conservation and Population Biology; University of Leuven; Heverlee Belgium
| | - Tsipe Aavik
- Institute of Ecology and Earth Sciences; Tartu University; Tartu Estonia
| | - Sara A. O Cousins
- Biogeography and Geomatics; Department of Physical Geography; Stockholm University; Stockholm Sweden
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20
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Ferretti L, Ribeca P, Ramos-Onsins SE. The Site Frequency/Dosage Spectrum of Autopolyploid Populations. Front Genet 2018; 9:480. [PMID: 30405691 PMCID: PMC6207136 DOI: 10.3389/fgene.2018.00480] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.8] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/20/2018] [Accepted: 09/28/2018] [Indexed: 01/15/2023] Open
Abstract
The Site Frequency Spectrum (SFS) and the heterozygosity of allelic variants are among the most important summary statistics for population genetic analysis of diploid organisms. We discuss the generalization of these statistics to populations of autopolyploid organisms in terms of the joint Site Frequency/Dosage Spectrum and its expected value for autopolyploid populations that follow the standard neutral model. Based on these results, we present estimators of nucleotide variability from High-Throughput Sequencing (HTS) data of autopolyploids and discuss potential issues related to sequencing errors and variant calling. We use these estimators to generalize Tajima's D and other SFS-based neutrality tests to HTS data from autopolyploid organisms. Finally, we discuss how these approaches fail when the number of individuals is small. In fact, in autopolyploids there are many possible deviations from the Hardy–Weinberg equilibrium, each reflected in a different shape of the individual dosage distribution. The SFS from small samples is often dominated by the shape of these deviations of the dosage distribution from its Hardy–Weinberg expectations.
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21
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Zhou J, Dudash MR, Zimmer EA, Fenster CB. Comparison of population genetic structures of the plant Silene stellata and its obligate pollinating seed predator moth Hadena ectypa. ANNALS OF BOTANY 2018; 122:593-603. [PMID: 29850821 PMCID: PMC6153480 DOI: 10.1093/aob/mcy091] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/05/2017] [Accepted: 05/03/2018] [Indexed: 05/29/2023]
Abstract
BACKGROUND AND AIMS Population genetic structures and patterns of gene flow of interacting species provide important insights into the spatial scale of their interactions and the potential for local co-adaptation. We analysed the genetic structures of the plant Silene stellata and the nocturnal moth Hadena ectypa. Hadena ectypa acts as one of the important pollinators of S. stellata as well as being an obligate seed parasite on the plant. Although H. ectypa provides a substantial pollination service to S. stellata, this system is largely considered parasitic due to the severe seed predation by the Hadena larvae. Previous research on this system has found variable interaction outcomes across space, indicating the potential for a geographical selection mosaic. METHODS Using 11 microsatellite markers for S. stellata and nine markers for H. ectypa, we analysed the population genetic structure and the patterns and intensity of gene flow within and among three local populations in the Appalachians. KEY RESULTS We found no spatial genetic structure in the moth populations, while significant differentiation was detected among the local plant populations. Additionally, we observed that gene flow rates among H. ectypa populations were more uniform and that the mean gene flow rate in H. ectypa was twice as large as that in S. stellata. CONCLUSIONS Our results suggest that although the moths move frequently among populations, long-distance pollen carryover only happens occasionally. The difference in gene flow rates between S. stellata and H. ectypa could prevent strict local co-adaptation. Furthermore, higher gene flow rates in H. ectypa could also increase resistance of the local S. stellata populations to the parasitic effect of H. ectypa and therefore help to stabilize the Silene-Hadena interaction dynamics.
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Affiliation(s)
- Juannan Zhou
- Simons Center for Quantitative Biology, Cold Spring Harbor Laboratory, Cold Spring Harbor, NY, USA
| | - Michele R Dudash
- Department of Natural Resource Management, South Dakota State University, Brookings, SD, USA
| | - Elizabeth A Zimmer
- Department of Botany, National Museum of Natural History, MRC 166, Smithsonian Institution, Washington, DC, USA
| | - Charles B Fenster
- Department of Biology and Microbiology, South Dakota State University, Brookings, SD, USA
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22
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Pérez‐Alquicira J, Weller SG, Domínguez CA, Molina‐Freaner FE, Tsyusko OV. Different patterns of colonization of Oxalis alpina in the Sky Islands of the Sonoran desert via pollen and seed flow. Ecol Evol 2018; 8:5661-5673. [PMID: 29938082 PMCID: PMC6010862 DOI: 10.1002/ece3.4096] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/21/2018] [Revised: 03/09/2018] [Accepted: 03/13/2018] [Indexed: 11/08/2022] Open
Abstract
Historical factors such as climatic oscillations during the Pleistocene epoch have dramatically impacted species distributions. Studies of the patterns of genetic structure in angiosperm species using molecular markers with different modes of inheritance contribute to a better understanding of potential differences in colonization and patterns of gene flow via pollen and seeds. These markers may also provide insights into the evolution of reproductive systems in plants. Oxalis alpina is a tetraploid, herbaceous species inhabiting the Sky Island region of the southwestern United States and northern Mexico. Our main objective in this study was to analyze the influence of climatic oscillations on the genetic structure of O. alpina and the impact of these oscillations on the evolutionary transition from tristylous to distylous reproductive systems. We used microsatellite markers and compared our results to a previous study using chloroplast genetic markers. The phylogeographic structure inferred by both markers was different, suggesting that intrinsic characteristics including the pollination system and seed dispersal have influenced patterns of gene flow. Microsatellites exhibited low genetic structure, showed no significant association between geographic and genetic distances, and all individual genotypes were assigned to two main groups. In contrast, chloroplast markers exhibited a strong association between geographic and genetic distance, had higher levels of genetic differentiation, and were assigned to five groups. Both types of DNA markers showed evidence of a northward expansion as a consequence of climate warming occurring in the last 10,000 years. The data from both types of markers support the hypothesis for several independent transitions from tristyly to distyly.
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Affiliation(s)
- Jessica Pérez‐Alquicira
- Departamento de Botánica y ZoologíaCONACYT – Laboratorio Nacional de Identificación y Caracterización VegetalCentro Universitario de Ciencias Biológicas y AgropecuariasUniversidad de GuadalajaraZapopanMexico
| | - Stephen G. Weller
- Department of Ecology and Evolutionary BiologyUniversity of CaliforniaIrvineCalifornia
| | - César A. Domínguez
- Departamento de Ecología EvolutivaInstituto de EcologíaUniversidad Nacional Autónoma de MéxicoCiudad de MéxicoMéxico
| | - Francisco E. Molina‐Freaner
- Departamento de Ecología de la Biodiversidad, Estación Regional del NoroesteInstituto de EcologíaUniversidad Nacional Autónoma de MéxicoHermosilloMéxico
| | - Olga V. Tsyusko
- Department of Plant and Soil SciencesUniversity of KentuckyLexingtonKentucky
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23
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24
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Jighly A, Lin Z, Forster JW, Spangenberg GC, Hayes BJ, Daetwyler HD. Insights into population genetics and evolution of polyploids and their ancestors. Mol Ecol Resour 2018; 18:1157-1172. [PMID: 29697892 DOI: 10.1111/1755-0998.12896] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.2] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/12/2017] [Accepted: 03/13/2018] [Indexed: 01/10/2023]
Abstract
We have developed the first comprehensive simulator for polyploid genomes (PolySim) and demonstrated its value by performing large-scale simulations to examine the effect of different population parameters on the evolution of polyploids. PolySim is unlimited in terms of ploidy, population size or number of simulated loci. Our process considered the evolution of polyploids from diploid ancestors, polysomic inheritance, inbreeding, recombination rate change in polyploids and gene flow from lower to higher ploidies. We compared the number of segregating single nucleotide polymorphisms, minor allele frequency, heterozygosity, R2 and average kinship relatedness between different simulated scenarios, and to real data from polyploid species. As expected, allotetraploid populations showed no difference from their ancestral diploids when population size remained constant and there was no gene flow or multivalent (MV) pairing between subgenomes. Autotetraploid populations showed significant differences from their ancestors for most parameters and diverged from their ancestral populations faster than allotetraploids. Autotetraploids can have significantly higher heterozygosity, relatedness and extended linkage disequilibrium compared with allotetraploids. Interestingly, autotetraploids were more sensitive to increasing selfing rate and decreasing population size. MV formation can homogenize allotetraploid subgenomes, but this homogenization requires a higher MV rate than previously proposed. Our results can be considered as the first building block to understand polyploid population evolutionary dynamics. PolySim can be used to simulate a wide variety of polyploid organisms that mimic empirical populations, which, in combination with quantitative genetics tools, can be used to investigate the power of genomewide association, genomic selection or breeding programme designs in these species.
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Affiliation(s)
- Abdulqader Jighly
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Vic., Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Vic., Australia
| | - Zibei Lin
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Vic., Australia
| | - John W Forster
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Vic., Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Vic., Australia
| | - German C Spangenberg
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Vic., Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Vic., Australia
| | - Ben J Hayes
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Vic., Australia
- Queensland Alliance for Agriculture and Food Innovation, Centre for Animal Science, University of Queensland, St Lucia, Qld, Australia
| | - Hans D Daetwyler
- Agriculture Victoria, AgriBio, Centre for AgriBiosciences, Bundoora, Vic., Australia
- School of Applied Systems Biology, La Trobe University, Bundoora, Vic., Australia
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25
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Meirmans PG, Liu S, van Tienderen PH. The Analysis of Polyploid Genetic Data. J Hered 2018; 109:283-296. [DOI: 10.1093/jhered/esy006] [Citation(s) in RCA: 110] [Impact Index Per Article: 18.3] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 08/28/2017] [Accepted: 01/20/2018] [Indexed: 12/14/2022] Open
Affiliation(s)
- Patrick G Meirmans
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
| | - Shenglin Liu
- Department of Bioscience, Aarhus University, Aarhus, Denmark
| | - Peter H van Tienderen
- Institute for Biodiversity and Ecosystem Dynamics, University of Amsterdam, Amsterdam, the Netherlands
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26
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Field DL, Broadhurst LM, Elliott CP, Young AG. Population assignment in autopolyploids. Heredity (Edinb) 2017; 119:389-401. [PMID: 28976495 DOI: 10.1038/hdy.2017.51] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/22/2017] [Revised: 07/07/2017] [Accepted: 07/24/2017] [Indexed: 11/09/2022] Open
Abstract
Understanding the patterns of contemporary gene dispersal within and among populations is of critical importance to population genetics and in managing populations for conservation. In contrast to diploids, there are few studies of gene dispersal in autopolyploids, in part due to complex polysomic inheritance and genotype ambiguity. Here we develop a novel approach for population assignment for codominant markers for autotetraploids and autohexaploids. This method accounts for polysomic inheritance, unreduced gametes and unknown allele dosage. It can also utilise information regarding the origin and genotype of one parent for population assignment of maternal or paternal parents. Using simulations, we demonstrate that our approach achieves high levels of accuracy for assignment even when population divergence is low (FST~0.06) and with only 12 microsatellite loci. We also show that substantially higher accuracy is achieved when known maternal information is utilised, regardless of whether allele dosage is known. Although this novel method exhibited near identical levels of accuracy to Structure when population divergence was high, it performed substantially better for most parameters at moderate (FST=0.06) to low levels of divergence (FST=0.03). These methods fill an important gap in the toolset for autopolyploids and pave the way for investigating contemporary gene dispersal in a widespread group of organisms.
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Affiliation(s)
- D L Field
- Department of Botany and Biodiversity Research, University of Vienna, Faculty of Life Sciences, Vienna, Austria
| | | | - C P Elliott
- Biodiversity Conservation Centre, Kings Park, Western Australia, Australia
| | - A G Young
- CSIRO Plant Industry, Canberra, ACT, Australia
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27
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Clark LV, Schreier AD. Resolving microsatellite genotype ambiguity in populations of allopolyploid and diploidized autopolyploid organisms using negative correlations between allelic variables. Mol Ecol Resour 2017; 17:1090-1103. [DOI: 10.1111/1755-0998.12639] [Citation(s) in RCA: 26] [Impact Index Per Article: 3.7] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/14/2015] [Revised: 11/06/2016] [Accepted: 11/16/2016] [Indexed: 01/16/2023]
Affiliation(s)
- Lindsay V. Clark
- Department of Crop Sciences University of Illinois, Urbana‐Champaign 1201 W. Gregory Drive Urbana IL 61801 USA
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28
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Laport RG, Minckley RL, Ramsey J. Ecological distributions, phenological isolation, and genetic structure in sympatric and parapatric populations of the Larrea tridentata polyploid complex. AMERICAN JOURNAL OF BOTANY 2016; 103:1358-1374. [PMID: 27440793 DOI: 10.3732/ajb.1600105] [Citation(s) in RCA: 17] [Impact Index Per Article: 2.1] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 03/06/2016] [Accepted: 05/20/2016] [Indexed: 06/06/2023]
Abstract
PREMISE OF THE STUDY Polyploidy is widely recognized as a mechanism of diversification. Contributions of polyploidy to specific pre- and postzygotic barriers-and classifications of polyploid speciation as "ecological" vs. "non-ecological"-are more contentious. Evaluation of these issues requires comprehensive studies that test ecological characteristics of cytotypes as well as the coincidence of genetic structure with cytotype distributions. METHODS We investigated a classical example of autopolyploid speciation, Larrea tridentata, at multiple areas of cytotype co-occurrence. Habitat and phenological differences were compared between diploid, tetraploid, and hexaploid populations on the basis of edaphic, community composition, and flowering time surveys. Frequency of hybridization between diploids and tetraploids was investigated using a diploid-specific chloroplast DNA (cpDNA) marker; genetic structure for all cytotypes was assessed using amplified fragment length polymorphisms (AFLPs). KEY RESULTS Across contact zones, we found cytotypes in habitats distinguished by soil and vegetation. We observed modest differences in timing and production of flowers, indicating a degree of assortative mating that was asymmetric between cytotypes. Nonetheless, cpDNA analyses in diploid-tetraploid contact zones suggested that ∼5% of tetraploid plants had hybrid origins involving unilateral sexual polyploidization. Genetic structure of AFLPs largely coincided with cytotype distributions in diploid-tetraploid contact zones. In contrast, there was little structure in areas of contact between tetraploids and hexaploids, suggesting intercytotype gene flow or recurrent hexaploid formation. CONCLUSIONS Diploid, tetraploid, and hexaploid cytotypes of L. tridentata are segregated by environmental distributions and flowering phenology in contact zones, with diploid and tetraploid populations having corresponding differences in genetic structure.
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Affiliation(s)
- Robert G Laport
- University of Nebraska-Lincoln, School of Biological Sciences, Lincoln, Nebraska 68588 USA
| | - Robert L Minckley
- University of Rochester, Department of Biology, River Campus, Rochester, New York 14627 USA
| | - Justin Ramsey
- Black Hills State University, School of Natural Sciences, Spearfish, South Dakota 57799 USA
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29
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Marques I, Montgomery SA, Barker MS, Macfarlane TD, Conran JG, Catalán P, Rieseberg LH, Rudall PJ, Graham SW. Transcriptome-derived evidence supports recent polyploidization and a major phylogeographic division in Trithuria submersa (Hydatellaceae, Nymphaeales). THE NEW PHYTOLOGIST 2016; 210:310-323. [PMID: 26612464 DOI: 10.1111/nph.13755] [Citation(s) in RCA: 3] [Impact Index Per Article: 0.4] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 06/28/2015] [Accepted: 10/12/2015] [Indexed: 06/05/2023]
Abstract
Relatively little is known about species-level genetic diversity in flowering plants outside the eudicots and monocots, and it is often unclear how to interpret genetic patterns in lineages with whole-genome duplications. We addressed these issues in a polyploid representative of Hydatellaceae, part of the water-lily order Nymphaeales. We examined a transcriptome of Trithuria submersa for evidence of recent whole-genome duplication, and applied transcriptome-derived microsatellite (expressed-sequence tag simple-sequence repeat (EST-SSR)) primers to survey genetic variation in populations across its range in mainland Australia. A transcriptome-based Ks plot revealed at least one recent polyploidization event, consistent with fixed heterozygous genotypes representing underlying sets of homeologous loci. A strong genetic division coincides with a trans-Nullarbor biogeographic boundary. Patterns of 'allelic' variation (no more than two variants per EST-SSR genotype) and recently published chromosomal evidence are consistent with the predicted polyploidization event and substantial homozygosity underlying fixed heterozygote SSR genotypes, which in turn reflect a selfing mating system. The Nullarbor Plain is a barrier to gene flow between two deep lineages of T. submersa that may represent cryptic species. The markers developed here should also be useful for further disentangling species relationships, and provide a first step towards future genomic studies in Trithuria.
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Affiliation(s)
- Isabel Marques
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, 6804 Marine Drive SW, Vancouver, BC, V6T 1Z4, Canada
- Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, C/Carretera de Cuarte Km 1, Huesca, E22071, Spain
| | - Sean A Montgomery
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, 6804 Marine Drive SW, Vancouver, BC, V6T 1Z4, Canada
| | - Michael S Barker
- Department of Ecology and Evolutionary Biology, University of Arizona, Tucson, AZ, 85721, USA
| | - Terry D Macfarlane
- Western Australian Herbarium, Science and Conservation Division, Department of Parks and Wildlife, Locked Bag 104, Bentley Delivery Centre, Bentley, WA, 6983, Australia
| | - John G Conran
- School of Biological Sciences, Australian Centre for Evolutionary Biology and Biodiversity & Sprigg Geobiology Centre, The University of Adelaide, Benham Bldg DX 650 312, Adelaide, SA, 5005, Australia
| | - Pilar Catalán
- Department of Agricultural and Environmental Sciences, High Polytechnic School of Huesca, University of Zaragoza, C/Carretera de Cuarte Km 1, Huesca, E22071, Spain
- Department of Botany, Institute of Biology, Tomsk State University, Lenin Av. 36, Tomsk, 634050, Russia
| | - Loren H Rieseberg
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
| | - Paula J Rudall
- Royal Botanic Gardens, Kew, Richmond, Surrey, TW9 3AB, UK
| | - Sean W Graham
- Department of Botany, University of British Columbia, 6270 University Boulevard, Vancouver, BC, V6T 1Z4, Canada
- UBC Botanical Garden & Centre for Plant Research, University of British Columbia, 6804 Marine Drive SW, Vancouver, BC, V6T 1Z4, Canada
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Balao F, Tannhäuser M, Lorenzo MT, Hedrén M, Paun O. Genetic differentiation and admixture between sibling allopolyploids in the Dactylorhiza majalis complex. Heredity (Edinb) 2016; 116:351-61. [PMID: 26604189 PMCID: PMC4787024 DOI: 10.1038/hdy.2015.98] [Citation(s) in RCA: 21] [Impact Index Per Article: 2.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 03/11/2015] [Revised: 10/17/2015] [Accepted: 10/20/2015] [Indexed: 12/24/2022] Open
Abstract
Allopolyploidization often happens recurrently, but the evolutionary significance of its iterative nature is not yet fully understood. Of particular interest are the gene flow dynamics and the mechanisms that allow young sibling polyploids to remain distinct while sharing the same ploidy, heritage and overlapping distribution areas. By using eight highly variable nuclear microsatellites, newly reported here, we investigate the patterns of divergence and gene flow between 386 polyploid and 42 diploid individuals, representing the sibling allopolyploids Dactylorhiza majalis s.s. and D. traunsteineri s.l. and their parents at localities across Europe. We make use in our inference of the distinct distribution ranges of the polyploids, including areas in which they are sympatric (that is, the Alps) or allopatric (for example, Pyrenees with D. majalis only and Britain with D. traunsteineri only). Our results show a phylogeographic signal, but no clear genetic differentiation between the allopolyploids, despite the visible phenotypic divergence between them. The results indicate that gene flow between sibling Dactylorhiza allopolyploids is frequent in sympatry, with potential implications for the genetic patterns across their entire distribution range. Limited interploidal introgression is also evidenced, in particular between D. incarnata and D. traunsteineri. Altogether the allopolyploid genomes appear to be porous for introgression from related diploids and polyploids. We conclude that the observed phenotypic divergence between D. majalis and D. traunsteineri is maintained by strong divergent selection on specific genomic areas with strong penetrance, but which are short enough to remain undetected by genotyping dispersed neutral markers.
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Affiliation(s)
- F Balao
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - M Tannhäuser
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - M T Lorenzo
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
| | - M Hedrén
- Department of Biology, Lund University, Lund, Sweden
| | - O Paun
- Department of Botany and Biodiversity Research, University of Vienna, Vienna, Austria
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31
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Blischak PD, Kubatko LS, Wolfe AD. Accounting for genotype uncertainty in the estimation of allele frequencies in autopolyploids. Mol Ecol Resour 2015; 16:742-54. [PMID: 26607217 DOI: 10.1111/1755-0998.12493] [Citation(s) in RCA: 31] [Impact Index Per Article: 3.4] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/02/2015] [Revised: 11/17/2015] [Accepted: 11/18/2015] [Indexed: 01/03/2023]
Abstract
Despite the increasing opportunity to collect large-scale data sets for population genomic analyses, the use of high-throughput sequencing to study populations of polyploids has seen little application. This is due in large part to problems associated with determining allele copy number in the genotypes of polyploid individuals (allelic dosage uncertainty-ADU), which complicates the calculation of important quantities such as allele frequencies. Here, we describe a statistical model to estimate biallelic SNP frequencies in a population of autopolyploids using high-throughput sequencing data in the form of read counts. We bridge the gap from data collection (using restriction enzyme based techniques [e.g. GBS, RADseq]) to allele frequency estimation in a unified inferential framework using a hierarchical Bayesian model to sum over genotype uncertainty. Simulated data sets were generated under various conditions for tetraploid, hexaploid and octoploid populations to evaluate the model's performance and to help guide the collection of empirical data. We also provide an implementation of our model in the R package polyfreqs and demonstrate its use with two example analyses that investigate (i) levels of expected and observed heterozygosity and (ii) model adequacy. Our simulations show that the number of individuals sampled from a population has a greater impact on estimation error than sequencing coverage. The example analyses also show that our model and software can be used to make inferences beyond the estimation of allele frequencies for autopolyploids by providing assessments of model adequacy and estimates of heterozygosity.
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Affiliation(s)
- Paul D Blischak
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, 318 W. 12th Avenue, Columbus, OH, 43210, USA
| | - Laura S Kubatko
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, 318 W. 12th Avenue, Columbus, OH, 43210, USA.,Department of Statistics, Ohio State University, 1958 Neil Avenue, Columbus, OH, 43210, USA
| | - Andrea D Wolfe
- Department of Evolution, Ecology and Organismal Biology, Ohio State University, 318 W. 12th Avenue, Columbus, OH, 43210, USA
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32
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Kvist L, Aminian L, Rouger R, Kreivi M, Laurila M, Hyvärinen M, Aspi J, Markkola A. A climatic relict or a long distance disperser: conservation genetics of an Arctic disjunct polyploid plant. CONSERV GENET 2015. [DOI: 10.1007/s10592-015-0756-7] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/23/2022]
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33
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van der Meer S, Jacquemyn H. Genetic Diversity and Spatial Genetic Structure of the Grassland Perennial Saxifraga granulata along Two River Systems. PLoS One 2015; 10:e0130463. [PMID: 26079603 PMCID: PMC4469588 DOI: 10.1371/journal.pone.0130463] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/24/2015] [Accepted: 05/20/2015] [Indexed: 11/18/2022] Open
Abstract
Due to changes in land use, the natural habitats of an increasing number of plant species have become more and more fragmented. In landscapes that consist of patches of suitable habitat, the frequency and extent of long-distance seed dispersal can be expected to be an important factor determining local genetic diversity and regional population structure of the remaining populations. In plant species that are restricted to riparian habitats, rivers can be expected to have a strong impact on the dynamics and spatial genetic structure of populations as they may enable long-distance seed dispersal and thus maintain gene flow between fragmented populations. In this study, we used polymorphic microsatellite markers to investigate the genetic diversity and the spatial genetic structure of 28 populations of Saxifraga granulata along two rivers in central Belgium. We hypothesized that rivers might be essential for gene flow among increasingly isolated populations of this species. Genetic diversity was high (HS = 0.68), which to a certain extent can be explained by the octoploid nature of S. granulata in the study area. Populations along the Dijle and Demer rivers were also highly differentiated (G"ST = 0.269 and 0.164 and DEST = 0.190 and 0.124, respectively) and showed significant isolation-by-distance, indicating moderate levels of gene flow primarily between populations that are geographically close to each other. Along the river Demer population genetic diversity was higher upstream than downstream, suggesting that seed dispersal via the water was not the primary mode of dispersal. Overall, these results indicate that despite increasing fragmentation populations along both rivers were highly genetically diverse. The high ploidy level and longevity of S. granulata have most likely buffered negative effects of fragmentation on genetic diversity and the spatial genetic structure of populations in riparian grasslands.
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Affiliation(s)
- Sascha van der Meer
- KU Leuven, Laboratory of Plant Conservation and Population Biology, Kasteelpark Arenberg 31- bus 02435, Heverlee, Belgium
| | - Hans Jacquemyn
- KU Leuven, Laboratory of Plant Conservation and Population Biology, Kasteelpark Arenberg 31- bus 02435, Heverlee, Belgium
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34
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Hardy OJ. Population genetics of autopolyploids under a mixed mating model and the estimation of selfing rate. Mol Ecol Resour 2015; 16:103-17. [PMID: 25981126 DOI: 10.1111/1755-0998.12431] [Citation(s) in RCA: 27] [Impact Index Per Article: 3.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/11/2014] [Revised: 05/07/2015] [Accepted: 05/12/2015] [Indexed: 11/27/2022]
Abstract
Nowadays, the population genetics analysis of autopolyploid species faces many difficulties due to (i) limited development of population genetics tools under polysomic inheritance, (ii) difficulties to assess allelic dosage when genotyping individuals and (iii) a form of inbreeding resulting from the mechanism of 'double reduction'. Consequently, few data analysis computer programs are applicable to autopolyploids. To contribute bridging this gap, this article first derives theoretical expectations for the inbreeding and identity disequilibrium coefficients under polysomic inheritance in a mixed mating model. Moment estimators of these coefficients are proposed when exact genotypes or just markers phenotypes (i.e. allelic dosage unknown) are available. This led to the development of estimators of the selfing rate based on adult genotypes or phenotypes and applicable to any even-ploidy level. Their statistical performances and robustness were assessed by numerical simulations. Contrary to inbreeding-based estimators, the identity disequilibrium-based estimator using phenotypes is robust (absolute bias generally < 0.05), even in the presence of double reduction, null alleles or biparental inbreeding due to isolation by distance. A fairly good precision of the selfing rate estimates (root mean squared error < 0.1) is already achievable using a sample of 30-50 individuals phenotyped at 10 loci bearing 5-10 alleles each, conditions reachable using microsatellite markers. Diallelic markers (e.g. SNP) can also perform satisfactorily in diploids and tetraploids but more polymorphic markers are necessary for higher ploidy levels. The method is implemented in the software SPAGeDi and should contribute to reduce the lack of population genetics tools applicable to autopolyploids.
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Affiliation(s)
- Olivier J Hardy
- Evolutionary Biology and Ecology-CP 160/12, Faculté des Sciences, Université Libre de Bruxelles, 50 Av. F. Roosevelt, 1050, Brussels, Belgium
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35
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Spielmann A, Harris SA, Boshier DH, Vinson CC. orchard: Paternity program for autotetraploid species. Mol Ecol Resour 2015; 15:915-20. [PMID: 25581442 DOI: 10.1111/1755-0998.12370] [Citation(s) in RCA: 9] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/25/2013] [Revised: 01/02/2015] [Accepted: 01/07/2015] [Indexed: 11/30/2022]
Abstract
Advances in molecular marker technology have provided new opportunities to study the population genetics of polyploid taxa. Paternity analysis using microsatellite markers can be used in detection of gene flow between individuals and populations, in mating system analysis, to identify factors that influence fecundity and fertility, to identify behaviour of parent-offspring relationships and in the analysis of the reproductive success of different ecological groups. As there is no specific program for carrying out paternity analysis in tetraploid species, specialized software was designed for the assignment of paternity for autotetraploid species. orchard is a novel implementation of exclusion and likelihood statistics for carrying out paternity analysis of autotetraploids. First, the program performs an exclusion method, and then, a likelihood statistic is used with nonexcluded candidate fathers. Optional features include estimation of allele dosage of known mother trees and the estimation of pollen flow distances. orchard was tested using a data set of microsatellite data of Dipteryx odorata, a tetraploid Amazonian tree species.
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Affiliation(s)
| | - S A Harris
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - D H Boshier
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
| | - C C Vinson
- Department of Plant Sciences, University of Oxford, South Parks Road, Oxford, OX1 3RB, UK
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36
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De Silva NH, Gea L, Lowe R. Genetic analysis of resistance to Pseudomonas syringae pv. actinidiae (Psa) in a kiwifruit progeny test: an application of generalised linear mixed models (GLMMs). SPRINGERPLUS 2014; 3:547. [PMID: 26034671 PMCID: PMC4447754 DOI: 10.1186/2193-1801-3-547] [Citation(s) in RCA: 7] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 08/28/2014] [Accepted: 09/15/2014] [Indexed: 11/24/2022]
Abstract
Linear Mixed models (LMMs) that incorporate genetic and spatial covariance structures have been used for many years to estimate genetic parameters and to predict breeding values in animal and plant breeding. Although the theoretical aspects for extending LMM to generalised linear mixed models (GLMMs) have been around for some time, suitable software has been developed only within the last decade or so. The GLIMMIX procedure in SAS® is becoming popular for fitting GLMMs in various disciplines. Applications of GLMMs to genetic analysis have been limited, probably because of the complexity of the models used. This is particularly so for Proc GLIMMIX because, unlike ASReml software, it is not specifically tailored for analysis of breeding data and some pre-procedure coding is necessary. Binary data that fits the GLMM framework is commonly encountered in breeding experiments, such as when evaluating individuals for resistance by observing the presence or absence of disease. Bacterial canker (Psa) caused by Pseudomonas syringae pv. actinidiae is a serious disease of kiwifruit in New Zealand and other kiwifruit-producing countries. Data from a progeny test trial was available to identify parents with high breeding values for resistance. We successfully applied the GLIMMIX procedure for this purpose. Heritability for resistance was moderate, and we identified two parents and their family as having high potential for Psa resistance breeding. There are several potential pitfalls when using GLMMs with binary data and these are briefly discussed.
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Affiliation(s)
- Nihal H De Silva
- The New Zealand Institute for Plant & Food Research Limited (PFR), Mt Albert Research Centre, 120 Mt Albert Road, Auckland, 1142 New Zealand
| | - Luis Gea
- PFR, Te Puke Research Centre, 412 No. 1 Road, RD 2, Te Puke, 3182 New Zealand
| | - Russell Lowe
- PFR, Te Puke Research Centre, 412 No. 1 Road, RD 2, Te Puke, 3182 New Zealand
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37
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Dufresne F, Stift M, Vergilino R, Mable BK. Recent progress and challenges in population genetics of polyploid organisms: an overview of current state-of-the-art molecular and statistical tools. Mol Ecol 2013; 23:40-69. [DOI: 10.1111/mec.12581] [Citation(s) in RCA: 248] [Impact Index Per Article: 22.5] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/26/2013] [Revised: 10/29/2013] [Accepted: 10/30/2013] [Indexed: 12/19/2022]
Affiliation(s)
- France Dufresne
- Département de Biologie; Université du Québec à Rimouski; Québec QC Canada G5L 3A1
| | - Marc Stift
- Department of Biology; University of Konstanz; Konstanz D 78457 Germany
| | - Roland Vergilino
- Department of Integrative Biology; University of Guelph; Guelph ON Canada N1G 2W1
| | - Barbara K. Mable
- Institute of Biodiversity; Animal Health and Comparative Medicine; College of Medical, Veterinary and Life Sciences; University of Glasgow; Glasgow UK
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38
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Origins and distribution of invasive Rubus fruticosus L. agg. (Rosaceae) clones in the Western United States. Biol Invasions 2012. [DOI: 10.1007/s10530-012-0369-8] [Citation(s) in RCA: 12] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 10/27/2022]
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39
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Aguirre AA, Wollenweber B, Frei UK, Lübberstedt T. PollenCALC: software for estimation of pollen compatibility of self-incompatible allo- and autotetraploid species. BMC Bioinformatics 2012; 13:125. [PMID: 22676372 PMCID: PMC3439690 DOI: 10.1186/1471-2105-13-125] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.1] [Reference Citation Analysis] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/18/2012] [Accepted: 06/07/2012] [Indexed: 11/30/2022] Open
Abstract
Background Self-incompatibility (SI) is a biological mechanism to avoid inbreeding in allogamous plants. In grasses, this mechanism is controlled by a two-locus system (S-Z). Calculation of male and female gamete frequencies is complex for tetraploid species. We are not aware of any software available for predicting pollen haplotype frequencies and pollen compatibility in tetraploid species. Results PollenCALC is a software tool written in C++ programming language that can predict pollen compatibility percentages for polyploid species with a two-locus (S, Z) self-incompatibility system. The program predicts pollen genotypes and frequencies based on defined meiotic parameters for allo- or autotetraploid species with a gametophytic S-Z SI system. These predictions can be used to obtain expected values for for diploid and for (allo- or autotetraploidy SI grasses. Conclusion The information provided by this calculator can be used to predict compatibility of pair-crosses in plant breeding applications, to analyze segregation distortion for S and Z genes, as well as linked markers in mapping populations, hypothesis testing of the number of S and Z alleles in a pair cross, and the underlying genetic model.
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40
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Köhnemann S, Nedele J, Schwotzer D, Morzfeld J, Pfeiffer H. The validation of a 15 STR multiplex PCR for Cannabis species. Int J Legal Med 2012; 126:601-6. [PMID: 22573357 DOI: 10.1007/s00414-012-0706-6] [Citation(s) in RCA: 18] [Impact Index Per Article: 1.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/31/2012] [Accepted: 04/26/2012] [Indexed: 10/28/2022]
Abstract
Trade and acquisition of Cannabis drugs are illegal in many countries worldwide; nevertheless, crimes related with these drugs are a major problem for the investigative authorities. With this manuscript, we want to introduce a 15 short tandem repeat (STR) Cannabis marker set that can be amplified in one PCR reaction. This multiplex PCR is specific to Cannabis species and combines highly informative STR markers. The 15 STR multiplex is easy to use and was validated according to common laboratory quality standards. Due to the fact that a lot of Cannabis plants are cultivated by clonal propagation and may show aneuploidy, polyploidy or multiple gene loci, it is not possible to apply biostatistics that follow the Hardy-Weinberg law. However, this multiplex will help the police to trace back trade routes of drug syndicates or dealers and it can help to link Cannabis plants to a crime scene.
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Affiliation(s)
- Stephan Köhnemann
- Institute of Legal Medicine, Röntgenstr. 23, 48149, Münster, Germany.
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41
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Jørgensen MH, Ehrich D, Schmickl R, Koch MA, Brysting AK. Interspecific and interploidal gene flow in Central European Arabidopsis (Brassicaceae). BMC Evol Biol 2011; 11:346. [PMID: 22126410 PMCID: PMC3247304 DOI: 10.1186/1471-2148-11-346] [Citation(s) in RCA: 47] [Impact Index Per Article: 3.6] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/06/2011] [Accepted: 11/29/2011] [Indexed: 01/02/2023] Open
Abstract
BACKGROUND Effects of polyploidisation on gene flow between natural populations are little known. Central European diploid and tetraploid populations of Arabidopsis arenosa and A. lyrata are here used to study interspecific and interploidal gene flow, using a combination of nuclear and plastid markers. RESULTS Ploidal levels were confirmed by flow cytometry. Network analyses clearly separated diploids according to species. Tetraploids and diploids were highly intermingled within species, and some tetraploids intermingled with the other species, as well. Isolation with migration analyses suggested interspecific introgression from tetraploid A. arenosa to tetraploid A. lyrata and vice versa, and some interploidal gene flow, which was unidirectional from diploid to tetraploid in A. arenosa and bidirectional in A. lyrata. CONCLUSIONS Interspecific genetic isolation at diploid level combined with introgression at tetraploid level indicates that polyploidy may buffer against negative consequences of interspecific hybridisation. The role of introgression in polyploid systems may, however, differ between plant species, and even within the small genus Arabidopsis, we find very different evolutionary fates when it comes to introgression.
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Affiliation(s)
- Marte H Jørgensen
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, P.O. Box 1066 Blindern, NO-0316 Oslo, Norway
| | - Dorothee Ehrich
- Institute for Arctic and Marine Biology, University of Tromsø, NO-9037 Tromsø, Norway
| | - Roswitha Schmickl
- Centre for Organismal Studies (COS) Heidelberg, Department of Biodiversity and Plant Systematics, University of Heidelberg, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Marcus A Koch
- Centre for Organismal Studies (COS) Heidelberg, Department of Biodiversity and Plant Systematics, University of Heidelberg, Im Neuenheimer Feld 345, D-69120 Heidelberg, Germany
| | - Anne K Brysting
- Centre for Ecological and Evolutionary Synthesis (CEES), Department of Biology, University of Oslo, P.O. Box 1066 Blindern, NO-0316 Oslo, Norway
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42
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Trapnell DW, Hamrick JL, Parker KC, Braungart KW, Glenn TC. Evaluating the utility of microsatellites for investigations of autopolyploid taxa. J Hered 2011; 102:473-8. [PMID: 21670174 DOI: 10.1093/jhered/esr045] [Citation(s) in RCA: 13] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/14/2022] Open
Abstract
Autopolyploid taxa present numerous challenges for population genetic analyses due to difficulties determining allele dosage. Dosage ambiguity hinders accurate assessment of allele frequencies, multilocus genotypes (MLGTs), as well as levels and patterns of clonality. The pervasiveness of polyploidy in the evolutionary history of plant taxa makes this a recurring problem. Whereas diploidization of loci may occur over time, duplication of at least some loci is still frequently evident. Fortunately, with high-quality allozyme gels, it is possible to accurately infer allele dosage and, thus, determine exact MLGTs. However, accurately assessing dosage of microsatellite peaks is nearly impossible when studying wild populations with a large number of alleles per locus. Even if precise knowledge of genotypes is not required, for comparable numbers of alleles per locus and loci, the number of "phenotypes" is always lower with microsatellites than allozymes due to the inability to assess allele dosage. Microsatellite loci typically have more alleles per locus relative to allozymes although fewer loci are generally employed. Here, we present a mathematical model for comparing the relative utility of simple sequence repeat (SSR) versus allozyme markers to discriminate MLGTs. For example, the average plant allozyme study (2.6 alleles per locus, 10 polymorphic loci) has better discriminating power than SSR markers with 10 alleles at each of 3 loci, 9 alleles at 4 loci, 6 alleles at 5 loci, 5 alleles at 6 loci, and 4 alleles at 8 loci, demonstrating the value of assessing the relative discriminating power of these markers.
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Affiliation(s)
- Dorset W Trapnell
- Department of Plant Biology, University of Georgia, Athens, GA 30602, USA.
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43
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Pfeiffer T, Roschanski AM, Pannell JR, Korbecka G, Schnittler M. Characterization of microsatellite loci and reliable genotyping in a polyploid plant, Mercurialis perennis (Euphorbiaceae). ACTA ACUST UNITED AC 2011; 102:479-88. [PMID: 21576288 DOI: 10.1093/jhered/esr024] [Citation(s) in RCA: 45] [Impact Index Per Article: 3.5] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022]
Abstract
For many applications in population genetics, codominant simple sequence repeats (SSRs) may have substantial advantages over dominant anonymous markers such as amplified fragment length polymorphisms (AFLPs). In high polyploids, however, allele dosage of SSRs cannot easily be determined and alleles are not easily attributable to potentially diploidized loci. Here, we argue that SSRs may nonetheless be better than AFLPs for polyploid taxa if they are analyzed as effectively dominant markers because they are more reliable and more precise. We describe the transfer of SSRs developed for diploid Mercurialis huetii to the clonal dioecious M. perennis. Primers were tested on a set of 54 male and female plants from natural decaploid populations. Eight of 65 tested loci produced polymorphic fragments. Binary profiles from 4 different scoring routines were used to define multilocus lineages (MLLs). Allowing for fragment differences within 1 MLL, all analyses revealed the same 14 MLLs without conflicting with merigenet, sex, or plot assignment. For semiautomatic scoring, a combination of as few as 2 of the 4 most polymorphic loci resulted in unambiguous discrimination of clones. Our study demonstrates that microsatellite fingerprinting of polyploid plants is a cost efficient and reliable alternative to AFLPs, not least because fewer loci are required than for diploids.
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Affiliation(s)
- Tanja Pfeiffer
- Institute of Botany and Landscape Ecology, Ernst-Moritz-Arndt-University Greifswald, Grimmer Str. 88, 17487 Greifswald, Germany.
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44
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CLARK LINDSAYV, JASIENIUK MARIE. polysat
: an R package for polyploid microsatellite analysis. Mol Ecol Resour 2011; 11:562-6. [DOI: 10.1111/j.1755-0998.2011.02985.x] [Citation(s) in RCA: 343] [Impact Index Per Article: 26.4] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/26/2022]
Affiliation(s)
- LINDSAY V. CLARK
- Department of Plant Sciences, Mail Stop 4, University of California, Davis, CA 95616, USA
| | - MARIE JASIENIUK
- Department of Plant Sciences, Mail Stop 4, University of California, Davis, CA 95616, USA
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45
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Garsmeur O, Charron C, Bocs S, Jouffe V, Samain S, Couloux A, Droc G, Zini C, Glaszmann JC, Van Sluys MA, D'Hont A. High homologous gene conservation despite extreme autopolyploid redundancy in sugarcane. THE NEW PHYTOLOGIST 2011; 189:629-42. [PMID: 21039564 DOI: 10.1111/j.1469-8137.2010.03497.x] [Citation(s) in RCA: 42] [Impact Index Per Article: 3.2] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/09/2023]
Abstract
Modern sugarcane (Saccharum spp.) is the leading sugar crop and a primary energy crop. It has the highest level of 'vertical' redundancy (2n=12x=120) of all polyploid plants studied to date. It was produced about a century ago through hybridization between two autopolyploid species, namely S. officinarum and S. spontaneum. In order to investigate the genome dynamics in this highly polyploid context, we sequenced and compared seven hom(oe)ologous haplotypes (bacterial artificial chromosome clones). Our analysis revealed a high level of gene retention and colinearity, as well as high gene structure and sequence conservation, with an average sequence divergence of 4% for exons. Remarkably, all of the hom(oe)ologous genes were predicted as being functional (except for one gene fragment) and showed signs of evolving under purifying selection, with the exception of genes within segmental duplications. By contrast, transposable elements displayed a general absence of colinearity among hom(oe)ologous haplotypes and appeared to have undergone dynamic expansion in Saccharum, compared with sorghum, its close relative in the Andropogonea tribe. These results reinforce the general trend emerging from recent studies indicating the diverse and nuanced effect of polyploidy on genome dynamics.
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Affiliation(s)
- Olivier Garsmeur
- CIRAD, UMR 1098 DAP, Avenue Agropolis, TA A96/03, F-34398 Montpellier Cedex 5, France
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Balao F, Valente LM, Vargas P, Herrera J, Talavera S. Radiative evolution of polyploid races of the Iberian carnation Dianthus broteri (Caryophyllaceae). THE NEW PHYTOLOGIST 2010; 187:542-551. [PMID: 20456054 DOI: 10.1111/j.1469-8137.2010.03280.x] [Citation(s) in RCA: 16] [Impact Index Per Article: 1.1] [Reference Citation Analysis] [Abstract] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Indexed: 05/27/2023]
Abstract
*The micro-evolutionary mechanisms that drive large-scale radiations are not completely understood, partly because of a shortage of population-level studies aimed at identifying putative causes of rapid evolutionary change. The Dianthus broteri complex, representing the largest polyploid series known to date for any species in the genus (2x, 4x, 6x and 12x cytotypes), belongs to a lineage that was recently found to have diversified at unusually rapid rates. *We used a combination of genome sequencing (internal transcribed spacer (ITS), plus chloroplast DNA (cpDNA) regions trnH-psbA, psbA-trnK and trnK-matK) and amplified fragment length polymorphism (AFLP) fingerprinting in 25 populations to infer the evolutionary history of extant polyploid races. *The haplotype, ribotype and AFLP reconstructions showed a star-shaped arrangement suggesting a pattern of radiative evolution. The major, widespread haplotype occurred at all ploidy levels, whereas 20 minor haplotypes were restricted to single populations and cytotypes. In addition, AFLP analyses retrieved well-supported cytogeographic groups: six clades were clearly differentiated in terms of ploidy level and geography. Molecular data indicate that gene flow among different cytotypes is rare or nonexistent. *Our study supports a scenario of rapid diversification in carnations in which autopolyploidy and allopolyploidy, in interaction with geography and/or isolation, have played prominent roles.
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Affiliation(s)
- Francisco Balao
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Apdo. 1095, E-41080 Sevilla, Spain
| | - Luis M Valente
- Real Jardín Botánico de Madrid, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain
| | - Pablo Vargas
- Real Jardín Botánico de Madrid, CSIC, Plaza de Murillo 2, 28014 Madrid, Spain
| | - Javier Herrera
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Apdo. 1095, E-41080 Sevilla, Spain
| | - Salvador Talavera
- Departamento de Biología Vegetal y Ecología, Universidad de Sevilla, Apdo. 1095, E-41080 Sevilla, Spain
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Korbecka G, Rymer PD, Harris SA, Pannell JR. Solving the Problem of Ambiguous Paralogy for Marker Loci: Microsatellite Markers with Diploid Inheritance in Allohexaploid Mercurialis annua (Euphorbiaceae). J Hered 2010; 101:504-11. [DOI: 10.1093/jhered/esq026] [Citation(s) in RCA: 12] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/13/2022] Open
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Vinson CC, Ribeiro DO, Harris SA, Sampaio I, Ciampi AY. Isolation of polymorphic microsatellite markers for the tetraploid Dipteryx odorata, an intensely exploited Amazonian tree species. Mol Ecol Resour 2009; 9:1542-4. [PMID: 21564953 DOI: 10.1111/j.1755-0998.2009.02694.x] [Citation(s) in RCA: 5] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/27/2022]
Abstract
Dipteryx odorata is an intensely exploited Amazonian tree legume. Microsatellite markers were developed to study the genetic structure, gene flow and reproductive biology of D. odorata. Eight highly polymorphic microsatellite markers were isolated from enriched repeat libraries screened for microsatellite repeats. An average of 16 alleles and 0.964 phenotype diversity per locus were found in 76 individuals from the Tapajos National Forest, in the state of Pará in the Brazilian Amazon.
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Affiliation(s)
- C C Vinson
- Universidade Federal do Pará, Campus de Bragança, Rua Leandro Ribeiro Aldeia, Bragança, Pará, CEP 68600 000, Brazil Department of Plant Sciences, University of Oxford, South Parks Road, Oxford OX1 3RB, UK Embrapa Recursos Genéticos e Biotecnologia, PqEB W5 Norte Final, Brasilia, DF, PO Box 02372, CEP 70770 900, Brazil
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Fredua-Agyeman R, Adamski D, Liao RJ, Morden C, Borthakur D. Development and characterization of microsatellite markers for analysis of population differentiation in the tree legume Acacia koa (Fabaceae: Mimosoideae) in the Hawaiian Islands. Genome 2009; 51:1001-15. [PMID: 19088813 DOI: 10.1139/g08-087] [Citation(s) in RCA: 13] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 11/22/2022]
Abstract
The aim of this research was to develop and use microsatellite markers to characterize the high-value timber tree Acacia koa (koa), which is endemic to the Hawaiian Islands. Genomic DNA fragments of 300-1000 bp were cloned and sequenced following enrichment for microsatellite motifs by PCR using 7 oligonucleotide repeat primers in separate reactions. Among 96 sequences analyzed, 63 contained unique microsatellite motifs flanked by variable sequences. A dual PCR method involving a primer walking step was used to develop 15 primer pairs. Another 16 primer pairs were developed directly from the variable sequences on both sides of the microsatellite motifs. These 31 primer pairs were tested on 172 koa plants representing 11 populations collected from 4 of the major Hawaiian Islands. Nine of the primers that identified polymorphic microsatellite loci and 3 that detected unique alleles exclusively in some populations were used for genetic diversity studies of koa. Cluster analysis and multidimensional scaling of the allelic phenotype data revealed that koa from Kauai formed a distinct group separate from koa of the neighboring islands of Oahu, Maui, and Hawaii. The oldest of the four islands, Kauai, also had the most diverse populations of koa.
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Affiliation(s)
- Rudolph Fredua-Agyeman
- Department of Molecular Biosciences & Bioengineering, University of Hawaii at Manoa, 1955 East-West Road, Agricultural Science 218, Honolulu, HI 96822, USA
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García-Verdugo C, Fay MF, Granado-Yela C, DE Casas RR, Balaguer L, Besnard G, Vargas P. Genetic diversity and differentiation processes in the ploidy series of Olea europaea L.: a multiscale approach from subspecies to insular populations. Mol Ecol 2008; 18:454-67. [PMID: 19143937 DOI: 10.1111/j.1365-294x.2008.04027.x] [Citation(s) in RCA: 68] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Indexed: 01/24/2023]
Abstract
Geographical isolation and polyploidization are central concepts in plant evolution. The hierarchical organization of archipelagos in this study provides a framework for testing the evolutionary consequences for polyploid taxa and populations occurring in isolation. Using amplified fragment length polymorphism and simple sequence repeat markers, we determined the genetic diversity and differentiation patterns at three levels of geographical isolation in Olea europaea: mainland-archipelagos, islands within an archipelago, and populations within an island. At the subspecies scale, the hexaploid ssp. maroccana (southwest Morocco) exhibited higher genetic diversity than the insular counterparts. In contrast, the tetraploid ssp. cerasiformis (Madeira) displayed values similar to those obtained for the diploid ssp. guanchica (Canary Islands). Geographical isolation was associated with a high genetic differentiation at this scale. In the Canarian archipelago, the stepping-stone model of differentiation suggested in a previous study was partially supported. Within the western lineage, an east-to-west differentiation pattern was confirmed. Conversely, the easternmost populations were more related to the mainland ssp. europaea than to the western guanchica lineage. Genetic diversity across the Canarian archipelago was significantly correlated with the date of the last volcanic activity in the area/island where each population occurs. At the island scale, this pattern was not confirmed in older islands (Tenerife and Madeira), where populations were genetically homogeneous. In contrast, founder effects resulted in low genetic diversity and marked genetic differentiation among populations of the youngest island, La Palma.
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Affiliation(s)
- C García-Verdugo
- Departamento de Biología Vegetal I, Universidad Complutense de Madrid, José Antonio Novais 2, 28040 Madrid, Spain.
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