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Mathias-Ramwell M, Pavez V, Meneses M, Fernández F, Valdés A, Lobos I, Silva M, Saldaña R, Hinrichsen P. Phenotypic and genetic characterization of an Avena sativa L. germplasm collection of diverse origin: implications for food-oat breeding in Chile. FRONTIERS IN PLANT SCIENCE 2023; 14:1298591. [PMID: 38179484 PMCID: PMC10764548 DOI: 10.3389/fpls.2023.1298591] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/21/2023] [Accepted: 12/05/2023] [Indexed: 01/06/2024]
Abstract
Oats are known for their nutritional value and also for their beneficial properties on human health, such as the reduction of cholesterol levels and risk of coronary heart disease; they are an important export product for Chile. During the last decade (2010-2022) over 90% of the oat cultivated area in Chile has been covered with Avena sativa L. cv. Supernova INIA. This lack of genetic diversity in a context of climate change could limit the long-term possibility of growing oats in Chile. The present study is a phenotypic and genetic analysis of 132 oat cultivars and pure lines of diverse origin that can be considered as potential breeding material. The germplasm was evaluated for 28 traits and analyzed with 14 SSR markers. The effects of genotypes on phenotype were significant over all traits (P ≤ 0.05). Most traits exhibited moderate to high broad-sense heritability with exceptions such as yield (H2 = 0.27) and hulls staining (H2 = 0.32). Significant undesirable correlations between traits were generally of small biological importance, which is auspicious for achieving breeding objectives. Some of the heritability data and correlations provided here have not been previously reported. The overall phenotypic diversity was high (H' = 0.68 ± 0.18). The germplasm was grouped into three phenotypic clusters, differing in their qualities for breeding. Twenty-six genotypes outperforming Supernova INIA were identified for breeding of conventional food-oats. The genetic diversity of the germplasm was moderate on average (He = 0.58 ± 0.03), varying between 0.32 (AM22) and 0.77 (AME178). Two genetic subpopulations supported by the Structure algorithm exhibited a genetic distance of 0.24, showing low divergence of the germplasm. The diversity and phenotypic values found in this collection of oat genotypes are promising with respect to obtaining genetic gain in the short term in breeding programs. However, the similar genetic diversity, higher phenotypic diversity, and better phenotypic performance of the germplasm created in Chile compared to foreign germplasm suggest that germplasm harboring new genetic diversity will be key to favor yield and quality in new oat cultivars in the long term.
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Affiliation(s)
- Mónica Mathias-Ramwell
- Programa de mejoramiento genético de avena, Instituto de Investigaciones Agropecuarias (INIA), Centro Regional de Investigación Carillanca, Temuco, Chile
| | - Valentina Pavez
- Laboratorio de Análisis Genético, Instituto de Investigaciones Agropecuarias, Centro Regional de Investigación La Platina, Santiago, Chile
| | - Marco Meneses
- Laboratorio de Análisis Genético, Instituto de Investigaciones Agropecuarias, Centro Regional de Investigación La Platina, Santiago, Chile
| | - Feledino Fernández
- Programa de mejoramiento genético de avena, Instituto de Investigaciones Agropecuarias (INIA), Centro Regional de Investigación Carillanca, Temuco, Chile
| | - Adriana Valdés
- Facultad de Recursos Naturales, Universidad Católica de Temuco, Temuco, Chile
| | - Iris Lobos
- Laboratorio de Espectroscopía Infrarrojo Cercano, Instituto de Investigaciones Agropecuarias, Centro Regional de Investigación Remehue, Osorno, Chile
| | - Mariela Silva
- Laboratorio de Espectroscopía Infrarrojo Cercano, Instituto de Investigaciones Agropecuarias, Centro Regional de Investigación Remehue, Osorno, Chile
| | - Rodolfo Saldaña
- Laboratorio de Nutrición Animal y Medio Ambiente, Instituto de Investigaciones Agropecuarias, Centro Regional de Investigación Remehue, Osorno, Chile
| | - Patricio Hinrichsen
- Laboratorio de Análisis Genético, Instituto de Investigaciones Agropecuarias, Centro Regional de Investigación La Platina, Santiago, Chile
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Choquet M, Lizano AM, Le Moan A, Ravinet M, Dhanasiri AKS, Hoarau G. Unmasking microsatellite deceptiveness and debunking hybridization with SNPs in four marine copepod species of Calanus. Mol Ecol 2023; 32:6854-6873. [PMID: 37902127 DOI: 10.1111/mec.17183] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Grants] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/19/2023] [Revised: 10/06/2023] [Accepted: 10/16/2023] [Indexed: 10/31/2023]
Abstract
Interspecific hybridization events are on the rise in natural systems due to climate change disrupting species barriers. Across taxa, microsatellites have long been the molecular markers of choice to identify admixed individuals. However, with the advent of high-throughput sequencing easing the generation of genome-wide datasets, incorrect reports of hybridization resulting from microsatellite technical artefacts have been uncovered in a growing number of taxa. In the marine zooplankton genus Calanus (Copepoda), whose species are used as climate change indicators, microsatellite markers have suggested hybridization between C. finmarchicus and C. glacialis, while other nuclear markers (InDels) never detected any admixed individuals, leaving the scientific community divided. Here, for the first time, we investigated the potential for hybridization among C. finmarchicus, C. glacialis, C. helgolandicus and C. hyperboreus using two large and independent SNP datasets. These were derived firstly from a protocol of target-capture applied to 179 individuals collected from 17 sites across the North Atlantic and Arctic Oceans, including sympatric areas, and second from published RNA sequences. All SNP-based analyses were congruent in showing that Calanus species are distinct and do not appear to hybridize. We then thoroughly re-assessed the microsatellites showing hybrids, with the support of published transcriptomes, and identified technical issues plaguing eight out of 10 microsatellites, including size homoplasy, paralogy, potential for null alleles and even two primer pairs targeting the same locus. Our study illustrates how deceptive microsatellites can be when applied to the investigation of hybridization.
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Affiliation(s)
- Marvin Choquet
- Natural History Museum, University of Oslo, Oslo, Norway
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Apollo M Lizano
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
| | - Alan Le Moan
- CNRS-Sorbonne Université, Station Biologique de Roscoff, Roscoff, France
| | - Mark Ravinet
- School of Life Sciences, University of Nottingham, Nottingham, UK
| | - Anusha K S Dhanasiri
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
- Department of Paraclinical Sciences, Faculty of Veterinary Medicine, Norwegian University of Life Sciences (NMBU), Oslo, Norway
| | - Galice Hoarau
- Faculty of Biosciences and Aquaculture, Nord University, Bodø, Norway
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Lepais O, Aissi A, Véla E, Beghami Y. Joint analysis of microsatellites and flanking sequences enlightens complex demographic history of interspecific gene flow and vicariance in rear-edge oak populations. Heredity (Edinb) 2022; 129:169-182. [PMID: 35725763 PMCID: PMC9411615 DOI: 10.1038/s41437-022-00550-0] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 07/13/2021] [Revised: 06/10/2022] [Accepted: 06/10/2022] [Indexed: 12/25/2022] Open
Abstract
Inference of recent population divergence requires fast evolving markers and necessitates to differentiate shared genetic variation caused by ancestral polymorphism and gene flow. Theoretical research shows that the use of compound marker systems integrating linked polymorphisms with different mutational dynamics, such as a microsatellite and its flanking sequences, can improve estimation of population structure and inference of demographic history, especially in the case of complex population dynamics. However, empirical application in natural populations has so far been limited by lack of suitable methods for data collection. A solution comes from the development of sequence-based microsatellite genotyping which we used to study molecular variation at 36 sequenced nuclear microsatellites in seven Quercus canariensis and four Q. faginea rear-edge populations across Algeria. We aim to decipher their taxonomic relationship, past evolutionary history and recent demographic trajectory. First, we compare the estimation of population genetics parameters and simulation-based inference of demographic history from microsatellite sequence alone, flanking sequence alone or the combination of linked microsatellite and flanking sequence variation. Second, we apply random forest approximate Bayesian computation to identify which of these sequence types is most informative. Whereas analysing microsatellite variation alone indicates recent interspecific gene flow, additional information gained by integrating nucleotide variation in flanking sequences, by reducing homoplasy, suggests ancient interspecific gene flow followed by drift in isolation instead. The weight of each polymorphism in the inference also demonstrates the value of linked variations with contrasted mutation dynamic to improve estimation of both demographic and mutational parameters.
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Affiliation(s)
- Olivier Lepais
- Univ. Bordeaux, INRAE, BIOGECO, F-33610, Cestas, France.
| | | | - Errol Véla
- AMAP, Université de Montpellier/CIRAD/CNRS/INRA/IRD, Montpellier, France
| | - Yassine Beghami
- LAPAPEZA, Université Batna 1 Hadj Lakhdar, ISVSA, Batna, Algeria
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Baumel A, Nieto Feliner G, Médail F, La Malfa S, Di Guardo M, Bou Dagher Kharrat M, Lakhal-Mirleau F, Frelon V, Ouahmane L, Diadema K, Sanguin H, Viruel J. Genome-wide footprints in the carob tree (Ceratonia siliqua) unveil a new domestication pattern of a fruit tree in the Mediterranean. Mol Ecol 2022; 31:4095-4111. [PMID: 35691023 PMCID: PMC9541536 DOI: 10.1111/mec.16563] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.5] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 09/21/2021] [Revised: 05/13/2022] [Accepted: 06/08/2022] [Indexed: 12/22/2022]
Abstract
Intense research efforts over the last two decades have renewed our understanding of plant phylogeography and domestication in the Mediterranean basin. Here we aim to investigate the evolutionary history and the origin of domestication of the carob tree (Ceratonia siliqua), which has been cultivated for millennia for food and fodder. We used >1000 microsatellite genotypes to delimit seven carob evolutionary units (CEUs). We investigated genome‐wide diversity and evolutionary patterns of the CEUs with 3557 single nucleotide polymorphisms generated by restriction‐site associated DNA sequencing (RADseq). To address the complex wild vs. cultivated status of sampled trees, we classified 56 sampled populations across the Mediterranean basin as wild, seminatural or cultivated. Nuclear and cytoplasmic loci were identified from RADseq data and separated for analyses. Phylogenetic analyses of these genomic‐wide data allowed us to resolve west‐to‐east expansions from a single long‐term refugium probably located in the foothills of the High Atlas Mountains near the Atlantic coast. Our findings support multiple origins of domestication with a low impact on the genetic diversity at range‐wide level. The carob was mostly domesticated from locally selected wild genotypes and scattered long‐distance westward dispersals of domesticated varieties by humans, concomitant with major historical migrations by Romans, Greeks and Arabs. Ex situ efforts to preserve carob genetic resources should prioritize accessions from both western and eastern populations, with emphasis on the most differentiated CEUs situated in southwest Morocco, south Spain and eastern Mediterranean. Our study highlights the relevance of wild and seminatural habitats in the conservation of genetic resources for cultivated trees.
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Affiliation(s)
- Alex Baumel
- Aix Marseille University, Avignon University, CNRS, IRD, IMBE, Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Faculté des Sciences et Techniques St-Jérôme, Marseille, France
| | | | - Frédéric Médail
- Aix Marseille University, Avignon University, CNRS, IRD, IMBE, Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Faculté des Sciences et Techniques St-Jérôme, Marseille, France
| | - Stefano La Malfa
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Mario Di Guardo
- Department of Agriculture, Food and Environment (Di3A), University of Catania, Catania, Italy
| | - Magda Bou Dagher Kharrat
- Laboratoire Biodiversité et Génomique Fonctionnelle, Faculté des Sciences, Université Saint-Joseph, Campus Sciences et Technologies, Beirut, Lebanon
| | - Fatma Lakhal-Mirleau
- Aix Marseille University, Avignon University, CNRS, IRD, IMBE, Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Faculté des Sciences et Techniques St-Jérôme, Marseille, France
| | - Valentine Frelon
- Aix Marseille University, Avignon University, CNRS, IRD, IMBE, Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale, Faculté des Sciences et Techniques St-Jérôme, Marseille, France
| | - Lahcen Ouahmane
- Faculté des Sciences Semlalia, Laboratoire de Biotechnologies Microbiennes Agrosciences et Environnement, Université Cadi Ayyad Marrakech, Marrakech, Morocco
| | - Katia Diadema
- Conservatoire Botanique National Méditerranéen de Porquerolles (CBNMed), Hyères, France
| | - Hervé Sanguin
- CIRAD, UMR PHIM, Montpellier, France.,PHIM, Univ Montpellier, CIRAD, INRAE, Institut Agro, IRD, Montpellier, France
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Bersweden L, Viruel J, Schatz B, Harland J, Gargiulo R, Cowan RS, Calevo J, Juan A, Clarkson JJ, Leitch AR, Fay MF. Microsatellites and petal morphology reveal new patterns of admixture in Orchis hybrid zones. AMERICAN JOURNAL OF BOTANY 2021; 108:1388-1404. [PMID: 34418070 DOI: 10.1002/ajb2.1710] [Citation(s) in RCA: 4] [Impact Index Per Article: 1.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 09/30/2020] [Revised: 02/20/2021] [Accepted: 02/23/2021] [Indexed: 05/23/2023]
Abstract
PREMISE The genetic structure of hybrid zones provides insight into the potential for gene flow to occur between plant taxa. Four closely related European orchid species (Orchis anthropophora, O. militaris, O. purpurea, and O. simia) hybridize when they co-occur. We aimed to characterize patterns of hybridization in O. militaris-O. purpurea, O. purpurea-O. simia, and O. anthropophora-O. simia hybrid zones using molecular and morphological data. METHODS We used 11 newly isolated nuclear microsatellites to genotype 695 individuals collected from seven hybrid zones and six allopatric parental populations in France. Geometric morphometric analysis was conducted using 15 labellum landmarks to capture the main aspects of petal shape. RESULTS Backcrossing was asymmetric toward O. militaris in multiple O. militaris-O. purpurea hybrid zones. Hybrids in O. purpurea-O. simia and O. anthropophora-O. simia hybrid zones were largely limited to F1 and F2 generations, but further admixture had occurred. These patterns were reflected in labellum geometric morphometric data, which correlated strongly with nuclear microsatellite data in all three species combinations. CONCLUSIONS The coexistence of parental and admixed individuals in these Orchis hybrid zones implies they are likely to be tension zones being maintained by a balance between gene flow into the hybrid zone and selection acting against admixed individuals. The pattern of admixture in the three species combinations suggests intrinsic selection acting on the hybrids is weaker in more closely related taxa.
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Affiliation(s)
- Leif Bersweden
- Jodrell Laboratory, Royal Botanic Gardens, Kew TW9 3DS, UK
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Juan Viruel
- Jodrell Laboratory, Royal Botanic Gardens, Kew TW9 3DS, UK
| | - Bertrand Schatz
- Centre for Ecology and Evolution, University of Montpellier, Montpellier 34090, France
| | - Joanna Harland
- Faculty of Biological Sciences, University of Leeds, Leeds LS2 9JT, UK
| | | | - Robyn S Cowan
- Jodrell Laboratory, Royal Botanic Gardens, Kew TW9 3DS, UK
| | - Jacopo Calevo
- Department of Life Sciences and Systems Biology, University of Turin, Turin 10125, Italy
| | - Ana Juan
- Department of Environmental Sciences & Natural Resources, University of Alicante, San Vicente, Alicante 03690, Spain
| | | | - Andrew R Leitch
- School of Biological and Chemical Sciences, Queen Mary University of London, Mile End Road, London E1 4NS, UK
| | - Michael F Fay
- Jodrell Laboratory, Royal Botanic Gardens, Kew TW9 3DS, UK
- School of Plant Biology, University of Western Australia, Crawley, WA 6009, Australia
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Wolf KKE, Hoppe CJM, Leese F, Weiss M, Rost B, Neuhaus S, Gross T, Kühne N, John U. Revealing environmentally driven population dynamics of an Arctic diatom using a novel microsatellite PoolSeq barcoding approach. Environ Microbiol 2021; 23:3809-3824. [PMID: 33559305 DOI: 10.1111/1462-2920.15424] [Citation(s) in RCA: 5] [Impact Index Per Article: 1.7] [Reference Citation Analysis] [Abstract] [Track Full Text] [Journal Information] [Subscribe] [Scholar Register] [Received: 04/07/2020] [Revised: 02/01/2021] [Accepted: 02/02/2021] [Indexed: 11/28/2022]
Abstract
Ecological stability under environmental change is determined by both interspecific and intraspecific processes. Particularly for planktonic microorganisms, it is challenging to follow intraspecific dynamics over space and time. We propose a new method, microsatellite PoolSeq barcoding (MPB), for tracing allele frequency changes in protist populations. We successfully applied this method to experimental community incubations and field samples of the diatom Thalassiosira hyalina from the Arctic, a rapidly changing ecosystem. Validation of the method found compelling accuracy in comparison with established genotyping approaches within different diversity contexts. In experimental and environmental samples, we show that MPB can detect meaningful patterns of population dynamics, resolving allelic stability and shifts within a key diatom species in response to experimental treatments as well as different bloom phases and years. Through our novel MPB approach, we produced a large dataset of populations at different time-points and locations with comparably little effort. Results like this can add insights into the roles of selection and plasticity in natural protist populations under stable experimental but also variable field conditions. Especially for organisms where genotype sampling remains challenging, MPB holds great potential to efficiently resolve eco-evolutionary dynamics and to assess the mechanisms and limits of resilience to environmental stressors.
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Affiliation(s)
- Klara K E Wolf
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Clara J M Hoppe
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Florian Leese
- Faculty of Biology, Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
| | - Martina Weiss
- Faculty of Biology, Aquatic Ecosystem Research, University of Duisburg-Essen, Essen, Germany
| | - Björn Rost
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,University of Bremen, FB2, Bremen, Germany
| | - Stefan Neuhaus
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Thilo Gross
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,University of Oldenburg, ICBM, Oldenburg, Germany.,Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
| | - Nancy Kühne
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany
| | - Uwe John
- Alfred Wegener Institute, Helmholtz Centre for Polar and Marine Research, Bremerhaven, Germany.,Helmholtz Institute for Functional Marine Biodiversity, Oldenburg, Germany
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Kyratzis AC, Antoniou C, Papayiannis LC, Graziani G, Rouphael Y, Kyriacou MC. Pod Morphology, Primary and Secondary Metabolite Profiles in Non-grafted and Grafted Carob Germplasm Are Configured by Agro-Environmental Zone, Genotype, and Growing Season. FRONTIERS IN PLANT SCIENCE 2021; 11:612376. [PMID: 33519870 PMCID: PMC7838365 DOI: 10.3389/fpls.2020.612376] [Citation(s) in RCA: 7] [Impact Index Per Article: 2.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 10/08/2020] [Accepted: 12/15/2020] [Indexed: 05/17/2023]
Abstract
Carob is a predominantly rainfed tree crop of high nutritive value and a long history of adaptation to the edaphoclimatic stress conditions of the Mediterranean. However, declining attention to the carob tree in recent decades has aggravated genetic erosion. The extant in situ germplasm varies both in terms of pod morphology and composition, reflecting the genetic and physiological divide chiefly among grafted and non-grafted material, and possibly the impact of variable agro-environments. Accordingly, the present study aimed to establish a systematic categorization of the genetic and phenotypic diversity encountered across carob germplasm identified in situ throughout Cyprus, a historical center of production and genetic diversity for the species. Linking pod morphology, primary and secondary metabolite profiles with genotyped source material originating in different agro-environments and crop seasons would provide a framework for interpreting (a) the interaction of these factors in configuring carob pod physicochemical constitution, and (b) the relative stability of phenotypic traits against environmental and seasonal variation. Microsatellite analysis discriminated 36 genotypes out of the 124 trees located in nine traditional agro-environmental zones and revealed low genetic diversity within the grafted germplasm. Two landraces were identified: "Tillyria," which is widespread and predominant, and "Kountourka," which is mainly localized to the northeastern peninsula of Karpasia. Morphological traits, such as seeds-to-pod weight ratio, pod width and thickness were principally under genetic control. Contrarily, compositional traits, particularly total phenolic content-including condensed tannins, in vitro antioxidant capacity and to a lesser extent gallic acid, organic acids and minerals were under agro-environmental control. Agro-environmental zone also modulated principally fructose and glucose; sucrose was modulated equally by genotype and agro-environment, while total sugars were under genetic control. Statistically significant differences between seasons were detected for all traits except for the seeds-to-pod weight ratio, pod length and width. Hierarchical cluster analysis corroborates that Cyprus may be divided into two major agro-environmental zones modulating the compositional properties of the carob pulp. The present study provides a comprehensive insight into the extant carob genetic resources of Cyprus and advances our understanding of how genetic, agro-environmental and seasonal factors interact in shaping carob pod morphology and composition.
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Affiliation(s)
- Angelos C. Kyratzis
- Agricultural Research Institute, Ministry of Agriculture, Rural Development and Environment, Nicosia, Cyprus
| | - Chrystalla Antoniou
- Agricultural Research Institute, Ministry of Agriculture, Rural Development and Environment, Nicosia, Cyprus
| | - Lambros C. Papayiannis
- Agricultural Research Institute, Ministry of Agriculture, Rural Development and Environment, Nicosia, Cyprus
| | - Giulia Graziani
- Department of Pharmacy, University of Naples Federico II, Naples, Italy
| | - Youssef Rouphael
- Department of Agricultural Sciences, University of Naples Federico II, Portici, Italy
| | - Marios C. Kyriacou
- Agricultural Research Institute, Ministry of Agriculture, Rural Development and Environment, Nicosia, Cyprus
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Lepais O, Chancerel E, Boury C, Salin F, Manicki A, Taillebois L, Dutech C, Aissi A, Bacles CF, Daverat F, Launey S, Guichoux E. Fast sequence-based microsatellite genotyping development workflow. PeerJ 2020; 8:e9085. [PMID: 32411534 PMCID: PMC7204839 DOI: 10.7717/peerj.9085] [Citation(s) in RCA: 17] [Impact Index Per Article: 4.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 01/03/2020] [Accepted: 04/08/2020] [Indexed: 12/21/2022] Open
Abstract
Application of high-throughput sequencing technologies to microsatellite genotyping (SSRseq) has been shown to remove many of the limitations of electrophoresis-based methods and to refine inference of population genetic diversity and structure. We present here a streamlined SSRseq development workflow that includes microsatellite development, multiplexed marker amplification and sequencing, and automated bioinformatics data analysis. We illustrate its application to five groups of species across phyla (fungi, plant, insect and fish) with different levels of genomic resource availability. We found that relying on previously developed microsatellite assay is not optimal and leads to a resulting low number of reliable locus being genotyped. In contrast, de novo ad hoc primer designs gives highly multiplexed microsatellite assays that can be sequenced to produce high quality genotypes for 20-40 loci. We highlight critical upfront development factors to consider for effective SSRseq setup in a wide range of situations. Sequence analysis accounting for all linked polymorphisms along the sequence quickly generates a powerful multi-allelic haplotype-based genotypic dataset, calling to new theoretical and analytical frameworks to extract more information from multi-nucleotide polymorphism marker systems.
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Affiliation(s)
- Olivier Lepais
- INRAE, Univ. Bordeaux, BIOGECO, Cestas, France
- INRAE, Université de Pau et Pays de l’Adour, ECOBIOP, Saint-Peé-sur-Nivelle, France
| | | | | | | | - Aurélie Manicki
- INRAE, Université de Pau et Pays de l’Adour, ECOBIOP, Saint-Peé-sur-Nivelle, France
| | - Laura Taillebois
- INRAE, Université de Pau et Pays de l’Adour, ECOBIOP, Saint-Peé-sur-Nivelle, France
| | | | | | - Cecile F.E. Bacles
- INRAE, Université de Pau et Pays de l’Adour, ECOBIOP, Saint-Peé-sur-Nivelle, France
| | | | - Sophie Launey
- INRAE, Agrocampus Ouest, ESE, Ecology and Ecosystem Health, Rennes, France
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Landoni B, Viruel J, Gómez R, Allaby RG, Brennan AC, Picó FX, Pérez‐Barrales R. Microsatellite marker development in the crop wild relative Linum bienne using genome skimming. APPLICATIONS IN PLANT SCIENCES 2020; 8:e11349. [PMID: 32477845 PMCID: PMC7249271 DOI: 10.1002/aps3.11349] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/27/2019] [Accepted: 01/26/2020] [Indexed: 05/10/2023]
Abstract
PREMISE Nuclear microsatellite markers were developed for Linum bienne, the sister species of the crop L. usitatissimum, to provide molecular genetic tools for the investigation of L. bienne genetic diversity and structure. METHODS AND RESULTS Fifty microsatellite loci were identified in L. bienne by means of genome skimming, and 44 loci successfully amplified. Of these, 16 loci evenly spread across the L. usitatissimum reference nuclear genome were used for genotyping six L. bienne populations. Excluding one monomorphic locus, the number of alleles per locus ranged from two to 12. Four out of six populations harbored private alleles. The levels of expected and observed heterozygosity were 0.076 to 0.667 and 0.000 to 1.000, respectively. All 16 loci successfully cross-amplified in L. usitatissimum. CONCLUSIONS The 16 microsatellite loci developed here can be used for population genetic studies in L. bienne, and 28 additional loci that successfully amplified are available for further testing.
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Affiliation(s)
- Beatrice Landoni
- School of Biological SciencesUniversity of PortsmouthPO1 2DYPortsmouthUnited Kingdom
| | - Juan Viruel
- Royal Botanic Gardens, KewTW9 3AERichmond, LondonUnited Kingdom
| | - Rocio Gómez
- Departamento de Ecología IntegrativaEstación Biológica de Doñana (EBD)Consejo Superior de Investigaciones Científicas (CSIC)41092SevilleSpain
| | - Robin G. Allaby
- School of Life SciencesUniversity of WarwickCV4 7ALWarwickUnited Kingdom
| | - Adrian C. Brennan
- Department of BiosciencesDurham UniversityStockton RoadDH1 3LEDurhamUnited Kingdom
| | - F. Xavier Picó
- Departamento de Ecología IntegrativaEstación Biológica de Doñana (EBD)Consejo Superior de Investigaciones Científicas (CSIC)41092SevilleSpain
| | - Rocio Pérez‐Barrales
- School of Biological SciencesUniversity of PortsmouthPO1 2DYPortsmouthUnited Kingdom
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