scholarly journals Field cress genome mapping: Integrating linkage and comparative maps with cytogenetic analysis for rDNA carrying chromosomes

2019 ◽  
Vol 9 (1) ◽  
Author(s):  
Zeratsion Abera Desta ◽  
Bozena Kolano ◽  
Zeeshan Shamim ◽  
Susan J. Armstrong ◽  
Monika Rewers ◽  
...  
Keyword(s):  
Positional Cloning ◽  
Genome Mapping ◽  
Flow Cytometric Analysis ◽  
Genetic Maps ◽  
Cytogenetic Map ◽  
Comparative Maps ◽  
Chromosome Staining ◽  
Genome Assemblies ◽  
Future Work ◽  
Field Cress

AbstractField cress (Lepidium campestre L.), despite its potential as a sustainable alternative oilseed plant, has been underutilized, and no prior attempts to characterize the genome at the genetic or molecular cytogenetic level have been conducted. Genetic maps are the foundation for anchoring and orienting annotated genome assemblies and positional cloning of candidate genes. Our principal goal was to construct a genetic map using integrated approaches of genetic, comparative and cytogenetic map analyses. In total, 503 F2 interspecific hybrid individuals were genotyped using 7,624 single nucleotide polymorphism markers. Comparative analysis demonstrated that ~57% of the sequenced loci in L. campestre were congruent with Arabidopsis thaliana (L.) genome and suggested a novel karyotype, which predates the ancestral crucifer karyotype. Aceto-orcein chromosome staining and fluorescence in situ hybridization (FISH) analyses confirmed that L. campestre, L. heterophyllum Benth. and their hybrids had a chromosome number of 2n = 2x = 16. Flow cytometric analysis revealed that both species possess 2C roughly 0.4 picogram DNA. Integrating linkage and comparative maps with cytogenetic map analyses assigned two linkage groups to their particular chromosomes. Future work could incorporate FISH utilizing A. thaliana mapped BAC clones to allow the chromosomes of field cress to be identified reliably.

scholarly journals A Chromosome-Based Model for Estimating the Number of Conserved Segments Between Pairs of Species From Comparative Genetic Maps

Genetics ◽  
2000 ◽  
Vol 154 (1) ◽  
pp. 323-332
Author(s):  
David Waddington ◽  
Anthea J Springbett ◽  
David W Burt
Keyword(s):  
Maximum Likelihood ◽  
Dna Sequences ◽  
Common Ancestor ◽  
Length Distribution ◽  
Genetic Maps ◽  
Segment Length ◽  
Syntenic Block ◽  
Comparative Maps

Abstract Comparative genetic maps of two species allow insights into the rearrangements of their genomes since divergence from a common ancestor. When the map details the positions of genes (or any set of orthologous DNA sequences) on chromosomes, syntenic blocks of one or more genes may be identified and used, with appropriate models, to estimate the number of chromosomal segments with conserved content conserved between species. We propose a model for the distribution of the lengths of unobserved segments on each chromosome that allows for widely differing chromosome lengths. The model uses as data either the counts of genes in a syntenic block or the distance between extreme members of a block, or both. The parameters of the proposed segment length distribution, estimated by maximum likelihood, give predictions of the number of conserved segments per chromosome. The model is applied to data from two comparative maps for the chicken, one with human and one with mouse.

Linking porcine microsatellite markers to known genome regions by identifying their human orthologs

Genome ◽  
2003 ◽  
Vol 46 (5) ◽  
pp. 798-808 ◽  
Author(s):  
Zhihua Jiang ◽  
Jennifer J Michal
Keyword(s):  
Microsatellite Markers ◽  
Positional Cloning ◽  
Genome Mapping ◽  
Joint Analysis ◽  
Porcine Genome ◽  
Gene Markers ◽  
Human Orthologs ◽  
Human Genomic ◽  
Rh Panel ◽  
Simple Sequence

Microsatellites, or tandem simple sequence repeats (SSRs), have become one of the most popular molecular markers in genome mapping because of their abundance across genomes and because of their high levels of polymorphism. However, information on which genes surround or flank them has remained very limited for most SSRs, especially in livestock species. In this study, an in silico comparative mapping approach was developed to link porcine SSRs to known genome regions by identifying their human orthologs. From a total of 1321 porcine microsatellites used in this study, 228 were found to have blocks in alignment with human genomic sequences. These 228 SSRs span about 1459 cM of the porcine genome, but with uneven distributions, ranging from 2 on SSC12 to 24 on SSC14. Linking these porcine SSRs to the known genome regions in the human genome also revealed 16 new putative synteny groups between these two species. Fifteen SSRs on SSC3 with identified human orthologs were typed on a pig-hamster radiation hybrid (RH) panel and used in a joint analysis with 80 known gene markers previously mapped on SSC3 using the same panel. The analysis revealed that they were all highly linked to either one or both adjacent markers. These results indicated that assigning the porcine SSRs to known genome regions by identifying their human orthologs is a reliable approach. The process will provide a foundation for positional cloning of causative genes for economically important traits.Key words: pig, microsatellite markers, human orthologs, RH mapping.

scholarly journals AFLAP: Assembly-Free Linkage Analysis Pipeline using k-mers from whole genome sequencing data

2020 ◽  
Author(s):  
Kyle Fletcher ◽  
Lin Zhang ◽  
Juliana Gil ◽  
Rongkui Han ◽  
Keri Cavanaugh ◽  
...  
Keyword(s):  
Linkage Analysis ◽  
Whole Genome Sequencing ◽  
Genome Sequencing ◽  
Genetic Map ◽  
Genotyping By Sequencing ◽  
Genetic Maps ◽  
Whole Genome ◽  
Sequencing Data ◽  
Analysis Pipeline ◽  
Genome Assemblies

AbstractBackgroundGenetic maps are an important resource for validation of genome assemblies, trait discovery, and breeding. Next generation sequencing has enabled production of high-density genetic maps constructed with 10,000s of markers. Most current approaches require a genome assembly to identify markers. Our Assembly Free Linkage Analysis Pipeline (AFLAP) removes this requirement by using uniquely segregating k-mers as markers to rapidly construct a genotype table and perform subsequent linkage analysis. This avoids potential biases including preferential read alignment and variant calling.ResultsThe performance of AFLAP was determined in simulations and contrasted to a conventional workflow. We tested AFLAP using 100 F2 individuals of Arabidopsis thaliana, sequenced to low coverage. Genetic maps generated using k-mers contained over 130,000 markers that were concordant with the genomic assembly. The utility of AFLAP was then demonstrated by generating an accurate genetic map using genotyping-by-sequencing data of 235 recombinant inbred lines of Lactuca spp. AFLAP was then applied to 83 F1 individuals of the oomycete Bremia lactucae, sequenced to >5x coverage. The genetic map contained over 90,000 markers ordered in 19 large linkage groups. This genetic map was used to fragment, order, orient, and scaffold the genome, resulting in a much-improved reference assembly.ConclusionsAFLAP can be used to generate high density linkage maps and improve genome assemblies of any organism when a mapping population is available using whole genome sequencing or genotyping-by-sequencing data. Genetic maps produced for B. lactucae were accurately aligned to the genome and guided significant improvements of the reference assembly.

scholarly journals A new decade and new data at SoyBase, the USDA-ARS soybean genetics and genomics database

2020 ◽  
Vol 49 (D1) ◽  
pp. D1496-D1501
Author(s):  
Anne V Brown ◽  
Shawn I Conners ◽  
Wei Huang ◽  
Andrew P Wilkey ◽  
David Grant ◽  
...  
Keyword(s):  
Soybean Genome ◽  
Genetic Maps ◽  
Pedigree Information ◽  
Data Sets ◽  
Visualization System ◽  
Interactive Tools ◽  
Genome Viewer ◽  
Reference Quality ◽  
Soybean Genetics ◽  
Genome Assemblies

Abstract SoyBase, a USDA genetic and genomics database, holds professionally curated soybean genetic and genomic data, which is integrated and made accessible to researchers and breeders. The site holds several reference genome assemblies, as well as genetic maps, thousands of mapped traits, expression and epigenetic data, pedigree information, and extensive variant and genotyping data sets. SoyBase displays include genetic, genomic, and epigenetic maps of the soybean genome. Gene expression data is presented in the genome viewer as heat maps and pictorial and tabular displays in gene report pages. Millions of sequence variants have been added, representing variations across various collections of cultivars. This variant data is explorable using new interactive tools to visualize the distribution of those variants across the genome, between selected accessions. SoyBase holds several reference-quality soybean genome assemblies, accessible via various query tools and browsers, including a new visualization system for exploring the soybean pan-genome. SoyBase also serves as a nexus of announcements pertinent to the greater soybean research community. The database also includes a soybean-specific anatomic and biochemical trait ontology. The database can be accessed at https://soybase.org.

scholarly journals Telomere-to-telomere gapless chromosomes of banana using nanopore sequencing

2021 ◽  
Vol 4 (1) ◽  
Author(s):  
Caroline Belser ◽  
Franc-Christophe Baurens ◽  
Benjamin Noel ◽  
Guillaume Martin ◽  
Corinne Cruaud ◽  
...  
Keyword(s):  
Musa Acuminata ◽  
Genetic Maps ◽  
Nanopore Sequencing ◽  
Genome Coverage ◽  
Long Reads ◽  
Oxford Nanopore ◽  
A Genome ◽  
Long Read ◽  
Genome Assemblies ◽  
First Time

AbstractLong-read technologies hold the promise to obtain more complete genome assemblies and to make them easier. Coupled with long-range technologies, they can reveal the architecture of complex regions, like centromeres or rDNA clusters. These technologies also make it possible to know the complete organization of chromosomes, which remained complicated before even when using genetic maps. However, generating a gapless and telomere-to-telomere assembly is still not trivial, and requires a combination of several technologies and the choice of suitable software. Here, we report a chromosome-scale assembly of a banana genome (Musa acuminata) generated using Oxford Nanopore long-reads. We generated a genome coverage of 177X from a single PromethION flowcell with near 17X with reads longer than 75 kbp. From the 11 chromosomes, 5 were entirely reconstructed in a single contig from telomere to telomere, revealing for the first time the content of complex regions like centromeres or clusters of paralogous genes.

scholarly journals Genetic analysis of phenotype in Trypanosoma brucei : a classical approach to potentially complex traits

2002 ◽  
Vol 357 (1417) ◽  
pp. 89-99 ◽  
Author(s):  
Andy Tait ◽  
Dan Masiga ◽  
Johnstone Ouma ◽  
Annette MacLeod ◽  
Juergen Sasse ◽  
...  
Keyword(s):  
Genetic Mapping ◽  
Trypanosoma Brucei ◽  
Complex Traits ◽  
Positional Cloning ◽  
Genetic Maps ◽  
Linkage Groups ◽  
Physical Size ◽  
Large Numbers ◽  
Number Of Genes ◽  
Allelic Segregation

The genome of the African trypanosome, Trypanosoma brucei , is currently being sequenced, raising the question of how the data generated can be used to determine the function of the large number of genes that will be identified. There is a range of possible approaches, and in this paper we discuss the use of a classical genetic approach coupled with positional cloning based on the ability of trypanosomes to undergo genetic exchange. The genetics of these parasites is essentially similar to a conventional diploid Mendelian system with allelic segregation and an independent assortment of markers on different chromosomes. Data are presented showing that recombination occurs between markers on the same chromosome allowing the physical size of the unit of recombination to be determined. Analysis of the available progeny clones from a series of crosses shows that, in principal, large numbers of progeny can readily be isolated from existing cryopreserved products of mating and, taking these findings together, it is clear that genetic mapping of variable phenotypes is feasible. The available phenotypes for analysis are outlined and most are relevant to the transmission and pathogenesis of the parasite. Genetic maps from two crosses are presented based on the use of the technique of AFLP; these maps comprise 146 and 139 markers in 30 and 21 linkage groups respectively. Segregation distortion is exhibited by some of the linkage groups and the possible reasons for this are discussed. The general conclusion, from the results presented, is that a genetic-mapping approach is feasible and will, in the future, allow the genes determining a number of important traits to be identified.

Differential transferability of EST-SSR primers developed from the diploid species Pseudoroegneria spicata, Thinopyrum bessarabicum, and Thinopyrum elongatum

Genome ◽  
2017 ◽  
Vol 60 (6) ◽  
pp. 530-536 ◽  
Author(s):  
Richard R.-C. Wang ◽  
Steve R. Larson ◽  
Kevin B. Jensen
Keyword(s):  
Expressed Sequence Tag ◽  
Genome Mapping ◽  
Diploid Species ◽  
Genetic Maps ◽  
Pseudoroegneria Spicata ◽  
Ssr Primers ◽  
Polymorphic Species ◽  
Thinopyrum Bessarabicum ◽  
Species Specific ◽  
Thinopyrum Elongatum

Simple sequence repeat technology based on expressed sequence tag (EST-SSR) is a useful genomic tool for genome mapping, characterizing plant species relationships, elucidating genome evolution, and tracing genes on alien chromosome segments. EST-SSR primers developed from three perennial diploid species of Triticeae, Pseudoroegneria spicata (Pursh) Á. Löve (having St genome), Thinopyrum bessarabicum (Savul. & Rayss) Á. Löve (Jb = Eb = J), and Thinopyrum elongatum (Host) D.R. Dewey (Je = Ee = E), were used to produce amplicons in these three species to (i) assess relative transferability, (ii) identify polymorphic species-specific markers, and (iii) determine genome relationships among the three species. Because of the close relationship between Jb and Je genomes, EST-SSR primers derived from Th. bessarabicum and Th. elongatum had greater transferability to each other than those derived from the St-genome P. spicata. A large number of polymorphic species- and genome-specific EST-SSR amplicons were identified that will be used for construction of genetic maps of these diploid species, and tracing economically useful genes in breeding or gene transfer programs in various species of Triticeae.

Genetic analysis and genome mapping in Raphanus

Genome ◽  
2003 ◽  
Vol 46 (3) ◽  
pp. 423-430 ◽  
Author(s):  
Kirstin E Bett ◽  
Derek J Lydiate
Keyword(s):  
Genetic Map ◽  
Comparative Mapping ◽  
Genome Mapping ◽  
Brassica Species ◽  
Genetic Maps ◽  
Rflp Markers ◽  
Raphanus Raphanistrum ◽  
Crop Species ◽  
Marker Loci ◽  
Reference Map

The first genetic map of the Raphanus genome was developed based on meiosis in a hybrid between Raphanus sativus (cultivated radish) and Raphanus raphanistrum (wild radish). This hybrid was used to produce a BC1 population of 54 individuals and an F2 population of 85 individuals. A total of 236 marker loci were assayed in these populations using a set of 144 informative Brassica RFLP probes previously used for genetic mapping in other crucifer species. The genetic maps derived from the BC1 and F2 populations were perfectly collinear and were integrated to produce a robust Raphanus map. Cytological observations demonstrated strict bivalent pairing in the R. sativus × R. raphanistrum hybrids. Productive pairing along the length of each chromosome was confirmed by the identification of nine extensive linkage groups and the lack of clustering of marker loci. Indeed, the distributions of both marker loci and crossovers was more random than those reported for other crop species. The genetic markers and the reference map of Raphanus will be of considerable value for future trait mapping and marker-assisted breeding in this crop, as well as in the intergenomic transfer of Raphanus genes into Brassica crops. The future benefits of comparative mapping with Arabidopsis and Brassica species are also discussed.Key words: radish, genetic map, RFLP markers, comparative mapping, segregation distortion.

scholarly journals Genome Mapping in Capsicum and the Evolution of Genome Structure in the Solanaceae

Genetics ◽  
1999 ◽  
Vol 152 (3) ◽  
pp. 1183-1202 ◽  
Author(s):  
Kevin D Livingstone ◽  
Vincent K Lackney ◽  
James R Blauth ◽  
Rik van Wijk ◽  
Molly Kyle Jahn
Keyword(s):  
Genetic Map ◽  
Genome Mapping ◽  
Genome Structure ◽  
Genetic Maps ◽  
Tomato Genome ◽  
F2 Population ◽  
Pericentric Inversions ◽  
Pepper Genome ◽  
Genomic Regions ◽  
Paracentric Inversions

Abstract We have created a genetic map of Capsicum (pepper) from an interspecific F2 population consisting of 11 large (76.2–192.3 cM) and 2 small (19.1 and 12.5 cM) linkage groups that cover a total of 1245.7 cM. Many of the markers are tomato probes that were chosen to cover the tomato genome, allowing comparison of this pepper map to the genetic map of tomato. Hybridization of all tomato-derived probes included in this study to positions throughout the pepper map suggests that no major losses have occurred during the divergence of these genomes. Comparison of the pepper and tomato genetic maps showed that 18 homeologous linkage blocks cover 98.1% of the tomato genome and 95.0% of the pepper genome. Through these maps and the potato map, we determined the number and types of rearrangements that differentiate these species and reconstructed a hypothetical progenitor genome. We conclude there have been 30 breaks as part of 5 translocations, 10 paracentric inversions, 2 pericentric inversions, and 4 disassociations or associations of genomic regions that differentiate tomato, potato, and pepper, as well as an additional reciprocal translocation, nonreciprocal translocation, and a duplication or deletion that differentiate the two pepper mapping parents.

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