Publications by authors named "Juan Viruel"

19 Publications

  • Page 1 of 1

Patterns of transmission and horizontal gene transfer in the Dioscorea sansibarensis leaf symbiosis revealed by whole-genome sequencing.

Curr Biol 2021 Apr 8. Epub 2021 Apr 8.

Laboratory of Microbiology, Ghent University, 9000 Ghent, Belgium; LIPME, Université de Toulouse, INRAE, CNRS, 31320 Castanet-Tolosan, France. Electronic address:

Leaves of the wild yam species Dioscorea sansibarensis display prominent forerunner or "drip" tips filled with extracellular bacteria of the species Orrella dioscoreae. This species of yam is native to Madagascar and tropical Africa and reproduces mainly asexually through aerial bulbils and underground tubers, which also contain a small population of O. dioscoreae. Despite apparent vertical transmission, the genome of O. dioscoreae does not show any of the hallmarks of genome erosion often found in hereditary symbionts (e.g., small genome size and accumulation of pseudogenes). We investigated here the range and distribution of leaf symbiosis between D. sansibarensis and O. dioscoreae using preserved leaf samples from herbarium collections that were originally collected from various locations in Africa. We recovered DNA from the extracellular symbiont in all samples, showing that the symbiosis is widespread throughout continental Africa and Madagascar. Despite the degraded nature of this DNA, we constructed 17 symbiont genomes using de novo methods without relying on a reference. Phylogenetic and genomic analyses revealed that horizontal transmission of symbionts and horizontal gene transfer have shaped the evolution of the symbiont. These mechanisms could help explain lack of signs of reductive genome evolution despite an obligate host-associated lifestyle. Furthermore, phylogenetic analysis of D. sansibarensis based on plastid genomes revealed a strong geographical clustering of samples and provided evidence that the symbiosis originated at least 13 mya, earlier than previously estimated..
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1016/j.cub.2021.03.049DOI Listing
April 2021

Biogeography and genome size evolution of the oldest extant vascular plant genus, Equisetum (Equisetaceae).

Ann Bot 2021 Apr;127(5):681-695

Royal Botanic Gardens, Kew, Richmond, UK.

Background And Aims: Extant plant groups with a long fossil history are key elements in understanding vascular plant evolution. Horsetails (Equisetum, Equisetaceae) have a nearly continuous fossil record dating back to the Carboniferous, but their phylogenetic and biogeographic patterns are still poorly understood. We use here the most extensive phylogenetic analysis to date as a framework to evaluate their age, biogeography and genome size evolution.

Methods: DNA sequences of four plastid loci were used to estimate divergence times and investigate the biogeographic history of all extant species of Equisetum. Flow cytometry was used to study genome size evolution against the framework of phylogenetic relationships in Equisetum.

Key Results: On a well-supported phylogenetic tree including all extant Equisetum species, a molecular clock calibrated with multiple fossils places the node at which the outgroup and Equisetum diverged at 343 Mya (Early Carboniferous), with the first major split among extant species occurring 170 Mya (Middle Jurassic). These dates are older than those reported in some other recent molecular clock studies but are largely in agreement with a timeline established by fossil appearance in the geological record. Representatives of evergreen subgenus Hippochaete have much larger genome sizes than those of deciduous subgenus Equisetum, despite their shared conserved chromosome number. Subgenus Paramochaete has an intermediate genome size and maintains the same number of chromosomes.

Conclusions: The first divergences among extant members of the genus coincided with the break-up of Pangaea and the resulting more humid, warmer climate. Subsequent tectonic activity most likely involved vicariance events that led to species divergences combined with some more recent, long-distance dispersal events. We hypothesize that differences in genome size between subgenera may be related to the number of sperm flagellae.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1093/aob/mcab005DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC8052921PMC
April 2021

Phenolic Compounds Content and Genetic Diversity at Population Level across the Natural Distribution Range of Bearberry (, Ericaceae) in the Iberian Peninsula.

Plants (Basel) 2020 Sep 22;9(9). Epub 2020 Sep 22.

Departamento of Ciencias Agrarias y del Medio Natural, Instituto Universitario de Ciencias Ambientales, Universidad de Zaragoza, Escuela Politécnica Superior, Ctra. Cuarte s.n., 22071 Huesca, Spain.

Bearberry () is a medicinal plant traditionally employed for the treatment of urinary tract infections due to high contents of arbutin (hydroquinone β-D-glucoside), which is now mainly used as a natural skin-whitening agent in cosmetics. Bearberry has also been proposed as a natural antioxidant additive due to the high contents of phenolic compounds in leaves. We studied the variation on phenolic compounds in 42 wild populations of bearberry, aiming to elucidate if intrinsic biological, climatic, and/or geographic factors affect phenolic contents across its natural distribution in the Iberian Peninsula. Bearberry leaves were collected during autumn over a three-year period (2014-2016) in populations across a latitude and altitude gradient. Methanolic extracts showed a wide range of variation in total phenols content, and different phenolic profiles regarding arbutin (levels of this major constituent varied from 87 to 232 mg/g dr wt), but also catechin and myricetin contents, which were affected by geographic and climatic factors. Moderate levels of variation on genome size-assessed by flow cytometry-and on two plastid DNA regions were also detected among populations. Genetic and cytogenetic differentiation of populations was weakly but significantly associated to phytochemical diversity. Elite bearberry genotypes with higher antioxidant capacity were subsequently identified.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/plants9091250DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7570137PMC
September 2020

Toward Unifying Global Hotspots of Wild and Domesticated Biodiversity.

Plants (Basel) 2020 Aug 31;9(9). Epub 2020 Aug 31.

Royal Botanic Gardens, Kew, Richmond TW93AQ, UK.

Global biodiversity hotspots are areas containing high levels of species richness, endemism and threat. Similarly, regions of agriculturally relevant diversity have been identified where many domesticated plants and animals originated, and co-occurred with their wild ancestors and relatives. The agro-biodiversity in these regions has, likewise, often been considered threatened. Biodiversity and agro-biodiversity hotspots partly overlap, but their geographic intricacies have rarely been investigated together. Here we review the history of these two concepts and explore their geographic relationship by analysing global distribution and human use data for all plants, and for major crops and associated wild relatives. We highlight a geographic continuum between agro-biodiversity hotspots that contain high richness in species that are intensively used and well known by humanity (i.e., major crops and most viewed species on Wikipedia) and biodiversity hotspots encompassing species that are less heavily used and documented (i.e., crop wild relatives and species lacking information on Wikipedia). Our contribution highlights the key considerations needed for further developing a unifying concept of agro-biodiversity hotspots that encompasses multiple facets of diversity (including genetic and phylogenetic) and the linkage with overall biodiversity. This integration will ultimately enhance our understanding of the geography of human-plant interactions and help guide the preservation of nature and its contributions to people.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3390/plants9091128DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7569820PMC
August 2020

Museomics Unveil the Phylogeny and Biogeography of the Neglected Juan Fernandez Archipelago and Endemic Grasses and Their Connection With Relict Pampean-Ventanian Fescues.

Front Plant Sci 2020 26;11:819. Epub 2020 Jun 26.

Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, Huesca, Spain.

Oceanic islands constitute natural laboratories to study plant speciation and biogeographic patterns of island endemics. Juan Fernandez is a southern Pacific archipelago consisting of three small oceanic islands located 600-700 km west of the Chilean coastline. Exposed to current cold seasonal oceanic climate, these 5.8-1 Ma old islands harbor a remarkable endemic flora. All known Fernandezian endemic grass species belong to two genera, and , of uncertain taxonomic adscription. Classical and modern classifications have placed them either in Bromeae (), Duthieinae, Aveneae/Poeae, or Loliinae (fine-leaved ); however, none of them have clarified their evolutionary relationships with respect to their closest relatives. includes four species, which are endemic to Masatierra (Robinson Crusoe island) ( and ) and to Masafuera (Alejandro Selkirk island) ( and ). The monotypic is a rare endemic species to Masatierra which is only known from its type locality and is currently considered extinct. We have used museomic approaches to uncover the challenging evolutionary history of these endemic grasses and to infer the divergence and dispersal patterns from their ancestors. Genome skimming data were produced from herbarium samples of and , and the 164 years old type specimen of , as well as for a collection of 33 species representing the main broad- and fine-leaved Loliinae lineages. Paired-end reads were successfully mapped to plastomes and nuclear ribosomal cistrons of reference species and used to reconstruct phylogenetic trees. Filtered ITS and TLF sequences from these genomes were further combined with our large Loliinae data sets for accurate biogeographic reconstruction. Nuclear and plastome data recovered a strongly supported fine-leaved Fernandezian clade where was resolved as sister to . Bayesian divergence dating and dispersal-extinction-cladogenesis range evolution analyses estimated the split of the Fernandezian clade from its ancestral southern American Pampas-Ventanian Loliinae lineage in the Miocene-Pliocene transition, following a long distance dispersal from the continent to the uplifted volcanic palaeo-island of Santa Clara-Masatierra. Consecutive Pliocene-Pleistocene splits and a Masatierra-to-Masafuera dispersal paved the way for speciation of and taxa.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fpls.2020.00819DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7333454PMC
June 2020

Microsatellite marker development in the crop wild relative using genome skimming.

Appl Plant Sci 2020 May 26;8(5):e11349. Epub 2020 May 26.

School of Biological Sciences University of Portsmouth PO1 2DY Portsmouth United Kingdom.

Premise: Nuclear microsatellite markers were developed for , the sister species of the crop , to provide molecular genetic tools for the investigation of genetic diversity and structure.

Methods And Results: Fifty microsatellite loci were identified in by means of genome skimming, and 44 loci successfully amplified. Of these, 16 loci evenly spread across the reference nuclear genome were used for genotyping six 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 .

Conclusions: The 16 microsatellite loci developed here can be used for population genetic studies in , and 28 additional loci that successfully amplified are available for further testing.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/aps3.11349DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7249271PMC
May 2020

Strategies for reducing per-sample costs in target capture sequencing for phylogenomics and population genomics in plants.

Appl Plant Sci 2020 Apr 14;8(4):e11337. Epub 2020 Apr 14.

Department of Biological Sciences Texas Tech University Lubbock Texas 79409 USA.

The reduced cost of high-throughput sequencing and the development of gene sets with wide phylogenetic applicability has led to the rise of sequence capture methods as a plausible platform for both phylogenomics and population genomics in plants. An important consideration in large targeted sequencing projects is the per-sample cost, which can be inflated when using off-the-shelf kits or reagents not purchased in bulk. Here, we discuss methods to reduce per-sample costs in high-throughput targeted sequencing projects. We review the minimal equipment and consumable requirements for targeted sequencing while comparing several alternatives to reduce bulk costs in DNA extraction, library preparation, target enrichment, and sequencing. We consider how each of the workflow alterations may be affected by DNA quality (e.g., fresh vs. herbarium tissue), genome size, and the phylogenetic scale of the project. We provide a cost calculator for researchers considering targeted sequencing to use when designing projects, and identify challenges for future development of low-cost sequencing in non-model plant systems.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/aps3.11337DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC7186906PMC
April 2020

Characterization of sequence variability hotspots in Cranichideae plastomes (Orchidaceae, Orchidoideae).

PLoS One 2020 28;15(1):e0227991. Epub 2020 Jan 28.

Royal Botanic Gardens, Kew, Richmond, Surrey, England, United Kingdom.

This study reports complete plastome sequences for six species of Neotropical Cranichideae and focuses on identification of the most variable regions (hotspots) in this group of orchids. These structure of these six plastomes is relatively conserved, exhibiting lengths ranging between 142,599 to 154,562 bp with 36.7% GC on average and exhibiting typical quadripartite arrangement (LSC, SSC and two IRs). Variation detected in the LSC/IR and SSC/IR junctions is explained by the loss of ndhF and ycf1 length variation. For the two genera of epiphytic clade in Spiranthinae, almost whole sets of the ndh-gene family were missing. Eight mutation hotspots were identified based on nucleotide diversity, sequence variability and parsimony-informative sites. Three of them (rps16-trnQ, trnT-trnL, rpl32-trnL) seem to be universal hotspots in the family, and the other five (trnG-trnR, trnR-atpA, trnP-psaJ, rpl32-infA, and rps15-ycf1) are described for the first time as orchid molecular hotspots. These regions have much more variation than all those used previously in phylogenetics of the group and offer useful plastid markers for phylogenetic, barcoding and population genetic studies. The use of whole plastomes or exclusive no-gap matrices also positioned with high support the holomycotrophic Rhizanthella among Orchidoideae plastomes in model-based analyses, showing the utility of plastomes for phylogenetic placement of this unusual genus.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0227991PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6986716PMC
April 2020

A Target Capture-Based Method to Estimate Ploidy From Herbarium Specimens.

Front Plant Sci 2019 24;10:937. Epub 2019 Jul 24.

Royal Botanic Gardens, Kew, Richmond, United Kingdom.

Whole genome duplication (WGD) events are common in many plant lineages, but the ploidy status and possible occurrence of intraspecific ploidy variation are unknown for most species. Standard methods for ploidy determination are chromosome counting and flow cytometry approaches. While flow cytometry approaches typically use fresh tissue, an increasing number of studies have shown that recently dried specimens can be used to yield ploidy data. Recent studies have started to explore whether high-throughput sequencing (HTS) data can be used to assess ploidy levels by analyzing allelic frequencies from single copy nuclear genes. Here, we compare different approaches using a range of yam () tissues of varying ages, drying methods and quality, including herbarium tissue. Our aims were to: (1) explore the limits of flow cytometry in estimating ploidy level from dried samples, including herbarium vouchers collected between 1831 and 2011, and (2) optimize a HTS-based method to estimate ploidy by considering allelic frequencies from nuclear genes obtained using a target-capture method. We show that, although flow cytometry can be used to estimate ploidy levels from herbarium specimens collected up to fifteen years ago, success rate is low (5.9%). We validated our HTS-based estimates of ploidy using 260 genes by benchmarking with dried samples of species of known ploidy (, , and ). Subsequently, we successfully applied the method to the 85 herbarium samples analyzed with flow cytometry, and successfully provided results for 91.7% of them, comprising species across the phylogenetic tree of . We also explored the limits of using this HTS-based approach for identifying high ploidy levels in herbarium material and the effects of heterozygosity and sequence coverage. Overall, we demonstrated that ploidy diversity within and between species may be ascertained from historical collections, allowing the determination of polyploidization events from samples collected up to two centuries ago. This approach has the potential to provide insights into the drivers and dynamics of ploidy level changes during plant evolution and crop domestication.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3389/fpls.2019.00937DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6667659PMC
July 2019

A customized nuclear target enrichment approach for developing a phylogenomic baseline for yams (Dioscoreaceae).

Appl Plant Sci 2019 Jun 13;7(6):e11254. Epub 2019 Jun 13.

Royal Botanic Gardens Kew, Richmond Surrey TW9 3DS United Kingdom.

Premise: We developed a target enrichment panel for phylogenomic studies of , an economically important genus with incompletely resolved relationships.

Methods: Our bait panel comprises 260 low- to single-copy nuclear genes targeted to work in , assessed here using a preliminary taxon sampling that includes both distantly and closely related taxa, including several yam crops and potential crop wild relatives. We applied coalescent-based and maximum likelihood phylogenomic inference approaches to the pilot taxon set, incorporating new and published transcriptome data from additional species.

Results: The custom panel retrieved ~94% of targets and >80% of full gene length from 88% and 68% of samples, respectively. It has minimal gene overlap with existing panels designed for angiosperm-wide studies and generally recovers longer and more variable targets. Pilot phylogenomic analyses consistently resolve most deep and recent relationships with strong support across analyses and point to revised relationships between the crop species and candidate crop wild relatives.

Discussion: Our customized panel reliably retrieves targeted loci from , is informative for resolving relationships in denser samplings, and is suitable for refining our understanding of the independent origins of cultivated yam species; the panel likely has broader promise for phylogenomic studies across Dioscoreales.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/aps3.11254DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6580989PMC
June 2019

Advances in genotyping microsatellite markers through sequencing and consequences of scoring methods for (Leguminosae).

Appl Plant Sci 2018 Dec 11;6(12):e01201. Epub 2018 Dec 11.

Institut Méditerranéen de Biodiversité et d'Ecologie marine et continentale (IMBE) [IMBE is sponsored by Aix Marseille University, Avignon University, Centre National de la Recherche Scientifique (CNRS), and Institut de Recherche pour le Développement (IRD)] Station marine d'Endoume, Chemin de la Batterie des Lions FR-13007 Marseille France.

Premise Of The Study: Simple sequence repeat (SSR) or microsatellite markers have been used in a broad range of studies mostly scoring alleles on the basis of amplicon size as a proxy for the number of repeat units of an SSR motif. However, additional sources of variation within the SSR or in the flanking regions have largely remained undetected.

Methods: In this study, we implemented a next-generation sequencing-based genotyping approach in a newly characterized set of 18 nuclear SSR markers for the carob tree, . Our aim was to evaluate the effect of three different methods of scoring molecular variation present within microsatellite markers on the genetic diversity and structure results.

Results: The analysis of the sequences of 77 multilocus genotypes from four populations revealed SSR variation and additional sources of polymorphism in 87% of the loci analyzed (42 single-nucleotide polymorphisms and five insertion/deletion polymorphisms), as well as divergent paralog copies in two loci. Ignoring sequence variation under standard amplicon size genotyping resulted in incorrect identification of 69% of the alleles, with important effects on the genetic diversity and structure estimates.

Discussion: Next-generation sequencing allows the detection and scoring of SSRs, single-nucleotide polymorphisms, and insertion/deletion polymorphisms to increase the resolution of population genetic studies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1002/aps3.1201DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC6303155PMC
December 2018

Genome wide association analysis of cold tolerance at germination in temperate japonica rice (Oryza sativa L.) varieties.

PLoS One 2017 17;12(8):e0183416. Epub 2017 Aug 17.

Cooperativa de Productores de Semillas de Arroz, Sueca, Valencia, Spain.

A pool of 200 traditional, landraces and modern elite and old cultivars of rice, mainly japonica varieties adapted to temperate regions, have been used to perform a genome wide association study to detect chromosome regions associated to low temperature germination (LTG) regulation using a panel of 1672 SNP markers. Phenotyping was performed by determining growth rates when seeds were germinated at 25° and 15°C in order to separate the germination vigorousness from cold tolerance effects. As expected, the ability to produce viable seedlings varied widely among rice cultivars and also depended greatly on temperature. Furthermore, we observed a differential response during seed germination and in coleoptile elongation. Faster development at 15°C was observed in seeds from varieties traditionally used as cold tolerant parents by breeders, along with other potentially useful cultivars, mainly of Italian origin. When phenotypic data were combined with the panel of SNPs for japonica rice cultivars, significant associations were detected for 31 markers: 7 were related to growth rate at 25°C and 24 to growth rates at 15°. Among the latter, some chromosome regions were associated to LTG while others were related to coleoptile elongation. Individual effects of the associated markers were low, but by combining favourable alleles in a linear regression model we estimated that 27 loci significantly explained the observed phenotypic variation. From these, a core panel of 13 markers was selected and, furthermore, two wide regions of chromosomes 3 and 6 were consistently associated to rice LTG. Varieties with higher numbers of favourable alleles for the panels of associated markers significantly correlated with increased phenotypic values at both temperatures, thus corroborating the utility of the tagged markers for marker assisted selection (MAS) when breeding japonica rice for LTG.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0183416PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5560564PMC
October 2017

Diversification into novel habitats in the Africa clade of Dioscorea (Dioscoreaceae): erect habit and elephant's foot tubers.

BMC Evol Biol 2016 11 8;16(1):238. Epub 2016 Nov 8.

African Centre for DNA Barcoding, Department of Botany & Plant Biotechnology, University of Johannesburg, PO Box 524, Auckland Park, Johannesburg, Gauteng, 2006, South Africa.

Background: Dioscorea is a widely distributed and highly diversified genus in tropical regions where it is represented by ten main clades, one of which diversified exclusively in Africa. In southern Africa it is characterised by a distinct group of species with a pachycaul or "elephant's foot" structure that is partially to fully exposed above the substrate. In contrast to African representatives of the genus from other clades, occurring mainly in forest or woodland, the pachycaul taxa and their southern African relatives occur in diverse habitats ranging from woodland to open vegetation. Here we investigate patterns of diversification in the African clade, time of transition from forest to more open habitat, and morphological traits associated with each habitat and evaluate if such transitions have led to modification of reproductive organs and mode of dispersal.

Results: The Africa clade originated in the Oligocene and comprises four subclades. The Dioscorea buchananii subclade (southeastern tropical Africa and South Africa) is sister to the East African subclade, which is respectively sister to the recently evolved sister South African (e. g., Cape and Pachycaul) subclades. The Cape and Pachycaul subclades diversified in the east of the Cape Peninsula in the mid Miocene, in an area with complex geomorphology and climate, where the fynbos, thicket, succulent karoo and forest biomes meet.

Conclusions: Diversification out of forest is associated with major shifts in morphology of the perennial tuber (specifically an increase in size and orientation which presumably led them to become pachycaul) and rotation of stem (from twining to non-twining). The iconic elephant's foot morphology, observed in grasslands and thicket biomes, where its corky bark may offer protection against fire and herbivory, evolved since mid Miocene. A shift in pollination trait is observed within the forest, but entry into open habitat does not show association with reproductive morphology, except in the seed wing, which has switched from winged all round the seed margin to just at the base or at the apex of it, or has been even replaced by an elaiosome.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12862-016-0812-zDOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5100304PMC
November 2016

Genetic Diversity and Population Structure of Rice Varieties Cultivated in Temperate Regions.

Rice (N Y) 2016 Dec 20;9(1):58. Epub 2016 Oct 20.

Centro de Genómica, Instituto Valenciano de Investigaciones Agrarias, Carretera CV 315 Km 10,7 (Carretera Moncada - Náquera Km 4.5), 46113, Moncada, Spain.

Background: After its domestication, rice cultivation expanded from tropical regions towards northern latitudes with temperate climate in a progressive process to overcome limiting photoperiod and temperature conditions. This process has originated a wide range of diversity that can be regarded as a valuable resource for crop improvement. In general, current rice breeding programs have to deal with a lack of both germplasm accessions specifically adapted to local agro-environmental conditions and adapted donors carrying desired agronomical traits. Comprehensive maps of genome variability and population structure would facilitate genome-wide association studies of complex traits, functional gene investigations and the selection of appropriate donors for breeding purposes.

Results: A collection of 217 rice varieties mainly cultivated in temperate regions was generated. The collection encompasses modern elite and old cultivars, as well as traditional landraces covering a wide genetic diversity available for rice breeders. Whole Genome Sequencing was performed on 14 cultivars representative of the collection and the genomic profiles of all cultivars were constructed using a panel of 2697 SNPs with wide coverage throughout the rice genome, obtained from the sequencing data. The population structure and genetic relationship analyses showed a strong substructure in the temperate rice population, predominantly based on grain type and the origin of the cultivars. Dendrogram also agrees population structure results.

Conclusions: Based on SNP markers, we have elucidated the genetic relationship and the degree of genetic diversity among a collection of 217 temperate rice varieties possessing an enormous variety of agromorphological and physiological characters. Taken together, the data indicated the occurrence of relatively high gene flow and elevated rates of admixture between cultivars grown in remote regions, probably favoured by local breeding activities. The results of this study significantly expand the current genetic resources available for temperate varieties of rice, providing a valuable tool for future association mapping studies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.1186/s12284-016-0130-5DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5073090PMC
December 2016

Computer-assisted sperm morphometry fluorescence-based analysis has potential to determine progeny sex.

Asian J Androl 2016 Nov-Dec;18(6):858-862

TECNOGAM research group, Environmental Sciences Institute (IUCA), Department of Animal Production and Food Sciences, Higher Polytechnic School, University of Zaragoza, Ctra. Cuarte S/N 22071 Huesca, Spain.

This study was designed to determine the ability of computer-assisted sperm morphometry analysis (CASA-Morph) with fluorescence to discriminate between spermatozoa carrying different sex chromosomes from the nuclear morphometrics generated and different statistical procedures in the bovine species. The study was divided into two experiments. The first was to study the morphometric differences between X- and Y-chromosome-bearing spermatozoa (SX and SY, respectively). Spermatozoa from eight bulls were processed to assess simultaneously the sex chromosome by FISH and sperm morphometry by fluorescence-based CASA-Morph. SX cells were larger than SY cells on average (P < 0.001) although with important differences between bulls. A simultaneous evaluation of all the measured features by discriminant analysis revealed that nuclear area and average fluorescence intensity were the variables selected by stepwise discriminant function analysis as the best discriminators between SX and SY. In the second experiment, the sperm nuclear morphometric results from CASA-Morph in nonsexed (mixed SX and SY) and sexed (SX) semen samples from four bulls were compared. FISH allowed a successful classification of spermatozoa according to their sex chromosome content. X-sexed spermatozoa displayed a larger size and fluorescence intensity than nonsexed spermatozoa (P < 0.05). We conclude that the CASA-Morph fluorescence-based method has the potential to find differences between X- and Y-chromosome-bearing spermatozoa in bovine species although more studies are needed to increase the precision of sex determination by this technique.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.4103/1008-682X.187578DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC5109876PMC
March 2017

Characterization of nuclear microsatellite markers for Rumex bucephalophorus (Polygonaceae) using 454 sequencing.

Appl Plant Sci 2015 Dec 15;3(12). Epub 2015 Dec 15.

Departamento Biología Vegetal y Ecología, Universidad de Sevilla, Avda. Reina Mercedes, 41012 Seville, Spain.

Premise Of The Study: Nuclear microsatellite markers were developed in Rumex bucephalophorus subsp. canariensis (Polygonaceae) to investigate its genetic diversity and structure.

Methods And Results: Sixteen polymorphic microsatellite markers were obtained using 454 next-generation sequencing with di-, tri-, and tetranucleotide repeats. The average number of alleles was 5.688 and 3.813 for R. bucephalophorus subsp. canariensis var. canariensis and var. fruticescens, respectively. Slightly higher levels of mean genetic diversity were found in var. canariensis (expected heterozygosity = 0.600) than in var. fruticescens (expected heterozygosity = 0.514). Cross-amplifications in related taxa within R. bucephalophorus showed good amplification and polymorphic patterns.

Conclusions: These 16 novel nuclear microsatellite markers are the first in the genus Rumex and may serve as valuable tools to carry out studies on genetic diversity and structure as well as progeny studies.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3732/apps.1500088DOI Listing
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4683044PMC
December 2015

Latitudinal environmental niches and riverine barriers shaped the phylogeography of the Central Chilean endemic Dioscorea humilis (Dioscoreaceae).

PLoS One 2014 8;9(10):e110029. Epub 2014 Oct 8.

Departamento de Ecología, Centro de Investigaciones sobre Desertificación (CIDE), Consejo Superior de Investigaciones Científicas (CSIC), Moncada, Valencia, Spain.

The effects of Pleistocene glaciations and geographical barriers on the phylogeographic patterns of lowland plant species in Mediterranean-climate areas of Central Chile are poorly understood. We used Dioscorea humilis (Dioscoreaceae), a dioecious geophyte extending 530 km from the Valparaíso to the Bío-Bío Regions, as a case study to disentangle the spatio-temporal evolution of populations in conjunction with latitudinal environmental changes since the Last Inter-Glacial (LIG) to the present. We used nuclear microsatellite loci, chloroplast (cpDNA) sequences and environmental niche modelling (ENM) to construct current and past scenarios from bioclimatic and geographical variables and to infer the evolutionary history of the taxa. We found strong genetic differentiation at nuclear microsatellite loci between the two subspecies of D. humilis, probably predating the LIG. Bayesian analyses of population structure revealed strong genetic differentiation of the widespread D. humilis subsp. humilis into northern and southern population groups, separated by the Maipo river. ENM revealed that the ecological niche differentiation of both groups have been maintained up to present times although their respective geographical distributions apparently fluctuated in concert with the climatic oscillations of the Last Glacial Maximum (LGM) and the Holocene. Genetic data revealed signatures of eastern and western postglacial expansion of the northern populations from the central Chilean depression, whereas the southern ones experienced a rapid southward expansion after the LGM. This study describes the complex evolutionary histories of lowland Mediterranean Chilean plants mediated by the summed effects of spatial isolation caused by riverine geographical barriers and the climatic changes of the Quaternary.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0110029PLOS
http://www.ncbi.nlm.nih.gov/pmc/articles/PMC4190404PMC
October 2015

New microsatellite loci in the dwarf yams Dioscorea group Epipetrum (Dioscoreaceae).

Am J Bot 2010 Nov 8;97(11):e121-3. Epub 2010 Oct 8.

Departamento de Agricultura y Economía Agraria, Escuela Politécnica Superior de Huesca, Universidad de Zaragoza, C/ Carretera de Cuarte Km 1, E22071, Huesca (Huesca), Spain.

Unlabelled:

Premise Of The Study: Microsatellite loci were isolated and characterized from enriched genomic libraries of two taxa of the Chilean Epipetrum group of Dioscorea to assess their levels of genetic diversity and population differentiation. •

Methods And Results: Eleven microsatellite loci were identified. Six out of nine microsatellites from D. biloba amplified in D. humilis, and the two microsatellites from D. humilis amplified in both taxa. Two different sets of eight loci amplified in each of the two tested taxa, D. biloba and D. humilis. The average number of alleles was 5.75 and 5 for D. biloba and D. humilis, respectively. Higher levels of mean genetic diversity were found in D. biloba (H(E) = 0.639) than in D. humilis (H(E) = 0.414). •

Conclusions: These microsatellite primers will be useful in population genetic studies and to establish conservation strategies in the endangered taxa of the Epipetrum group of Dioscorea.
View Article and Find Full Text PDF

Download full-text PDF

Source
http://dx.doi.org/10.3732/ajb.1000304DOI Listing
November 2010