scholarly journals GenoTypeMapper: graphical genotyping on genetic and sequence-based maps

Plant Methods ◽  
2020 ◽  
Vol 16 (1) ◽  
Author(s):  
Mathieu Deblieck ◽  
Andrii Fatiukha ◽  
Norbert Grundman ◽  
Lianne Merchuk-Ovnat ◽  
Yehoshua Saranga ◽  
...  
Keyword(s):  
Drought Stress ◽  
Genetic Maps ◽  
Wild Emmer ◽  
Linkage Drag ◽  
Single Individual ◽  
Physical Maps ◽  
Software Packages ◽  
Breeding Populations ◽  
Physical Scale ◽  
Future Work

Abstract Background The rising availability of assemblies of large genomes (e.g. bread and durum wheat, barley) and their annotations deliver the basis to graphically present genome organization of parents and progenies on a physical scale. Genetic maps are a very important tool for breeders but often represent distorted models of the actual chromosomes, e.g., in centromeric and telomeric regions. This biased picture might lead to imprecise assumptions and estimations about the size and complexity of genetic regions and the selection of suitable molecular markers for the incorporation of traits in breeding populations or near-isogenic lines (NILs). Some software packages allow the graphical illustration of genotypic data, but to the best of our knowledge, suitable software packages that allow the comparison of genotypic data on the physical and genetic scale are currently unavailable. Results We developed a simple Java-based-software called GenoTypeMapper (GTM) for comparing genotypic data on genetic and physical maps and tested it for effectiveness on data of two NILs that carry QTL-regions for drought stress tolerance from wild emmer on chromosome 2BS and 7AS. Both NILs were more tolerant to drought stress than their recurrent parents but exhibited additional undesirable traits such as delayed heading time. Conclusions In this article, we illustrate that the software easily allows users to display and identify additional chromosomal introgressions in both NILs originating from the wild emmer parent. The ability to detect and diminish linkage drag can be of particular interest for pre-breeding purposes and the developed software is a well-suited tool in this respect. The software is based on a simple allele-matching algorithm between the offspring and parents of a crossing scheme. Despite this simple approach, GTM seems to be the only software that allows us to analyse, illustrate and compare genotypic data of offspring of different crossing schemes with up to four parents in two different maps. So far, up to 500 individuals with a maximum number of 50,000 markers can be examined with the software. The main limitation that hampers the performance of the software is the number of markers that are examined in parallel. Since each individual must be analysed separately, a maximum of ten individuals can currently be displayed in a single run. On a computer with an Intel five processor of the 8th generation, GTM can reliably either analyse a single individual with up to 12,000 markers or ten individuals with up to 3,600 markers in less than five seconds. Future work aims to improve the performance of the software so that more complex crossing schemes with more parents and more markers can be analysed.

scholarly journals Heterogeneity in Rates of Recombination Across the Mouse Genome

Genetics ◽  
1996 ◽  
Vol 142 (2) ◽  
pp. 537-548 ◽  
Author(s):  
Michael W Nachman ◽  
Gary A Churchill
Keyword(s):  
Linkage Map ◽  
Genetic Map ◽  
Large Scale ◽  
Physical Map ◽  
Genetic Maps ◽  
Recombination Rates ◽  
Physical Maps ◽  
Genomic Patterns ◽  
Mary Lyon ◽  
Microsatellite Linkage

Abstract If loci are randomly distributed on a physical map, the density of markers on a genetic map will be inversely proportional to recombination rate. First proposed by MARY LYON, we have used this idea to estimate recombination rates from the Drosophila melanogaster linkage map. These results were compared with results of two other studies that estimated regional recombination rates in D. melanogaster using both physical and genetic maps. The three methods were largely concordant in identifying large-scale genomic patterns of recombination. The marker density method was then applied to the Mus musculus microsatellite linkage map. The distribution of microsatellites provided evidence for heterogeneity in recombination rates. Centromeric regions for several mouse chromosomes had significantly greater numbers of markers than expected, suggesting that recombination rates were lower in these regions. In contrast, most telomeric regions contained significantly fewer markers than expected. This indicates that recombination rates are elevated at the telomeres of many mouse chromosomes and is consistent with a comparison of the genetic and cytogenetic maps in these regions. The density of markers on a genetic map may provide a generally useful way to estimate regional recombination rates in species for which genetic, but not physical, maps are available.

A Review of Methods for the Geometric Post-Processing of Topology Optimized Models

2020 ◽  
Vol 20 (6) ◽  
Author(s):  
Subodh C. Subedi ◽  
Chaman Singh Verma ◽  
Krishnan Suresh
Keyword(s):  
Design Space ◽  
Poor Quality ◽  
Industrial Applications ◽  
Post Processing ◽  
Design Validation ◽  
Element Mesh ◽  
Parametric Control ◽  
Software Packages ◽  
Future Work ◽  
Testing Design

Abstract Topology optimization (TO) has rapidly evolved from an academic exercise into an exciting discipline with numerous industrial applications. Various TO algorithms have been established, and several commercial TO software packages are now available. However, a major challenge in TO is the post-processing of the optimized models for downstream applications. Typically, optimal topologies generated by TO are faceted (triangulated) models, extracted from an underlying finite element mesh. These triangulated models are dense, poor quality, and lack feature/parametric control. This poses serious challenges to downstream applications such as prototyping/testing, design validation, and design exploration. One strategy to address this issue is to directly impose downstream requirements as constraints in the TO algorithm. However, this not only restricts the design space, it may even lead to TO failure. Separation of post-processing from TO is more robust and flexible. The objective of this paper is to provide a critical review of various post-processing methods and categorize them based both on targeted applications and underlying strategies. The paper concludes with unresolved challenges and future work.

scholarly journals A gap-free tomato genome built from complementary PacBio and Nanopore long DNA sequences reveals extensive linkage drag during breeding

2021 ◽  
Author(s):  
Willem M. J. van Rengs ◽  
Maximilian H.-W. Schmidt ◽  
Sieglinde Effgen ◽  
Yazhong Wang ◽  
Mohd Waznul Adly Mohd Zaidan ◽  
...  
Keyword(s):  
Dna Sequences ◽  
Genetic Material ◽  
Genetic Maps ◽  
Linkage Drag ◽  
Chromosome Conformation ◽  
Long Read ◽  
Commercial Breeding ◽  
Related Wild Species ◽  
Rapid Generation ◽  
Pandemic Strains

The assembly and scaffolding of plant crop genomes facilitates the characterization of genetically diverse cultivated and wild germplasm. The cultivated tomato has been improved through the introgression of genetic material from related wild species, including resistance to pandemic strains of Tobacco Mosaic virus (TMV) from Solanum peruvianum. Here we applied PacBio HiFi and ONT nanopore sequencing to develop independent, highly contiguous and complementary assemblies of an inbred TMV-resistant tomato variety. We merged the HiFi and ONT assemblies to generate a long-read-only assembly where all twelve chromosomes were represented as twelve contiguous sequences (N50=68.5 Mbp). The merged assembly was validated by chromosome conformation capture data and is highly consistent with previous tomato assemblies that made use of genetic maps and HiC for scaffolding. Our long-read-only assembly reveals that a complex series of structural variants linked to the TMV resistance gene likely contributed to linkage drag of a 64.1 Mbp region of the S. peruvianum genome during tomato breeding. We show that this minimal introgression region is present in six cultivated tomato hybrid varieties developed in three commercial breeding programs. Our results suggest that complementary long read technologies can facilitate the rapid generation of near complete genome sequences.

scholarly journals First Chromosomal Restriction Map ofActinobacillus pleuropneumoniae and Localization of Putative Virulence-Associated Genes

1999 ◽  
Vol 181 (14) ◽  
pp. 4161-4169 ◽  
Author(s):  
Winfried Oswald ◽  
Denis V. Konine ◽  
Judith Rohde ◽  
Gerald-F. Gerlach
Keyword(s):  
Southern Blot ◽  
Reference Strain ◽  
Housekeeping Genes ◽  
Actinobacillus Pleuropneumoniae ◽  
Genetic Maps ◽  
Restriction Map ◽  
Physical Maps ◽  
Serotype 1 ◽  
Reference Strains ◽  
Fragment Excision

ABSTRACT Combined physical and genetic maps of the genomes ofActinobacillus pleuropneumoniae AP76 (serotype 7 clinical isolate) and of A. pleuropneumoniae ATCC 27088 (serotype 1 reference strain) were constructed by using the restriction endonucleases ApaI, AscI, NotI, andSalI. The chromosome sizes as determined by the addition of estimated fragment sizes were 2.4 Mbp, and both maps had a resolution of approximately 100 kbp. The linkages between the ApaI,AscI, NotI, and SalI fragments and their relative positions were determined by (i) fragment excision and redigestion and (ii) partial digests of defined fragments and Southern blot using end-standing probes. The single SalI site within the chromosome of strain A. pleuropneumoniae AP76 was defined as position 1 of the map; for the map of A. pleuropneumoniae ATCC 27088, the corresponding SalI site was chosen. Putative virulence-associated genes (apx,omlA, sodA, tbpBA,ureC, and a repeat element) and housekeeping genes (glyA, metJ, recA, andrhoAP) were positioned on the physical maps and located on the ApaI and NotI fragments of A. pleuropneumoniae serotype reference strains.

Correlating the Genetic and Physical Map of Barley Chromosome 3H Revealed Limitations of the FISH-Based Mapping of Nearby Single-Copy Probes Caused by the Dynamic Structure of Metaphase Chromosomes

2017 ◽  
Vol 152 (2) ◽  
pp. 90-96 ◽  
Author(s):  
Fernanda O. Bustamante ◽  
Lala Aliyeva-Schnorr ◽  
Jörg Fuchs ◽  
Sebastian Beier ◽  
Andreas Houben
Keyword(s):  
Dna Sequences ◽  
Physical Map ◽  
Dynamic Structure ◽  
Single Copy ◽  
Physical Distance ◽  
Genetic Distances ◽  
Genetic Maps ◽  
Metaphase Chromosomes ◽  
Physical Maps

Genetic maps are based on the recombination frequency of molecular markers which often show different positions in comparison to the corresponding physical maps. To decipher the position and order of DNA sequences genetically mapped to terminal and interstitial regions of barley (Hordeum vulgare) chromosome 3H, fluorescence in situ hybridization (FISH) on mitotic metaphase chromosomes was performed with 16 genomic single-copy probes derived from fingerprinted BAC contigs. Long genetic distances at subterminal regions translated into short physical distances, confirming that recombination events occur more often at distal regions of chromosome 3H. Nonoverlapping FISH signals were frequently obtained for probes with a physical distance of at least 30-60 kb. Only 8% of the analyzed chromosomes showed a symmetric order of FISH signals on both sister chromatids. Due to the dynamic packing of metaphase chromatin, the order of 2 adjacent single-copy signals along the chromosome arms outside the (peri)centromeric region can only reliably be determined if the cytological distance is approximately 3%, corresponding to 21.6 Mb.

scholarly journals Development of New Candidate Gene and EST-Based Molecular Markers for Gossypium Species

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Ramesh Buyyarapu ◽  
Ramesh V. Kantety ◽  
John Z. Yu ◽  
Sukumar Saha ◽  
Govind C. Sharma
Keyword(s):  
Molecular Markers ◽  
Candidate Gene ◽  
Candidate Genes ◽  
Genetic Maps ◽  
Physical Maps ◽  
Polymorphism Detection ◽  
A Genome ◽  
Species Cluster ◽  
Gene Based Markers ◽  
Integrated Genetic Maps

New source of molecular markers accelerate the efforts in improving cotton fiber traits and aid in developing high-density integrated genetic maps. We developed new markers based on candidate genes and G. arboreum EST sequences that were used for polymorphism detection followed by genetic and physical mapping. Nineteen gene-based markers were surveyed for polymorphism detection in 26 Gossypium species. Cluster analysis generated a phylogenetic tree with four major sub-clusters for 23 species while three species branched out individually. CAP method enhanced the rate of polymorphism of candidate gene-based markers between G. hirsutum and G. barbadense. Two hundred A-genome based SSR markers were designed after datamining of G. arboreum EST sequences (Mississippi Gossypium arboreum  EST-SSR: MGAES). Over 70% of MGAES markers successfully produced amplicons while 65 of them demonstrated polymorphism between the parents of G. hirsutum and G. barbadense RIL population and formed 14 linkage groups. Chromosomal localization of both candidate gene-based and MGAES markers was assisted by euploid and hypoaneuploid CS-B analysis. Gene-based and MGAES markers were highly informative as they were designed from candidate genes and fiber transcriptome with a potential to be integrated into the existing cotton genetic and physical maps.

scholarly journals Meta-Analysis of Quantitative Traits Loci (QTL) Identified in Drought Response in Rice (Oryza sativa L.)

Plants ◽  
2021 ◽  
Vol 10 (4) ◽  
pp. 716
Author(s):  
Nurhanis Selamat ◽  
Kalaivani K. Nadarajah
Keyword(s):  
Drought Stress ◽  
Drought Tolerance ◽  
Qtl Analysis ◽  
Oryza Sativa L ◽  
Genetic Maps ◽  
Chromosome 1 ◽  
Chromosome 2 ◽  
Consensus Map ◽  
Breeding Programs ◽  
Stable Qtls

Rice is an important grain that is the staple food for most of the world’s population. Drought is one of the major stresses that negatively affects rice yield. The nature of drought tolerance in rice is complex as it is determined by various components and has low heritability. Therefore, to ensure success in breeding programs for drought tolerant rice, QTLs (quantitative trait loci) of interest must be stable in a variety of plant genotypes and environments. This study identified stable QTLs in rice chromosomes in a variety of backgrounds and environments and conducted a meta-QTL analysis of stable QTLs that have been reported by previous research for use in breeding programs. A total of 653 QTLs for drought tolerance in rice from 27 genetic maps were recorded for analysis. The QTLs recorded were related to 13 traits in rice that respond to drought. Through the use of BioMercartor V4.2, a consensus map containing QTLs and molecular markers were generated using 27 genetic maps that were extracted from the previous 20 studies and meta-QTL analysis was conducted on the consensus map. A total of 70 MQTLs were identified and a total of 453 QTLs were mapped into the meta-QTL areas. Five meta-QTLs from chromosome 1 (MQTL 1.5 and MQTL 1.6), chromosome 2 (MQTL2.1 and MQTL 2.2) and chromosome 3 (MQTL 3.1) were selected for functional annotation as these regions have high number of QTLs and include many traits in rice that respond to drought. A number of genes in MQTL1.5 (268 genes), MQTL1.6 (640 genes), MQTL 2.1 (319 genes), MQTL 2.2 (19 genes) and MQTL 3.1 (787 genes) were annotated through Blast2GO. Few major proteins that respond to drought stress were identified in the meta-QTL areas which are Abscisic Acid-Insensitive Protein 5 (ABI5), the G-box binding factor 4 (GBF4), protein kinase PINOID (PID), histidine kinase 2 (AHK2), protein related to autophagy 18A (ATG18A), mitochondrial transcription termination factor (MTERF), aquaporin PIP 1-2, protein detoxification 48 (DTX48) and inositol-tetrakisphosphate 1-kinase 2 (ITPK2). These proteins are regulatory proteins involved in the regulation of signal transduction and gene expression that respond to drought stress. The meta-QTLs derived from this study and the genes that have been identified can be used effectively in molecular breeding and in genetic engineering for drought resistance/tolerance in rice.

scholarly journals Mapping and Tagging by DNA Markers of Wild Emmer Alleles that Improve Quantitative Traits in Common Wheat

2001 ◽  
Author(s):  
Moshe Feldman ◽  
Eitan Millet ◽  
Calvin O. Qualset ◽  
Patrick E. McGuire
Keyword(s):  
Wild Species ◽  
Protein Concentration ◽  
Quantitative Traits ◽  
Genetic Maps ◽  
Wild Emmer ◽  
Substitution Lines ◽  
Group 4 ◽  
Chromosome Arm ◽  
End Use

The general goal was to identify, map, and tag, with DNA markers, segments of chromosomes of a wild species (wild emmer wheat, the progenitor of cultivated wheat) determining the number, chromosomal locations, interactions, and effects of genes that control quantitative traits when transferred to a cultivated plant (bread wheat). Slight modifications were introduced and not all objectives could be completed within the human and financial resources available, as noted with the specific objectives listed below: 1. To identify the genetic contribution of each of the available wild emmer chromosome-arm substitution lines (CASLs) in the bread wheat cultivar Bethlehem for quantitative traits, including grain yield and its components and grain protein concentration and yield, and the effect of major loci affecting the quality of end-use products. [The quality of end-use products was not analyzed.] 2. To determine the extent and nature of genetic interactions (epistatic effects) between and within homoeologous groups 1 and 7 for the chromosome arms carrying "wild" and "cultivated" alleles as expressed in grain and protein yields and other quantitative traits. [Two experiments were successful, grain protein concentration could not be measured; data are partially analyzed.] 3. To derive recombinant substitution lines (RSLs) for the chromosome arms of homoeologous groups 1 and 7 that were found previously to promote grain and protein yields of cultivated wheat. [The selection of groups 1 and 7 tons based on grain yield in pot experiments. After project began, it was decided also to derive RSLs for the available arms of homoeologous group 4 (4AS and 4BL), based on the apparent importance of chromosome group 4, based on early field trials of the CASLs.] 4. To characterize the RSLs for quantitative traits as in objective 1 and map and tag chromosome segments producing significant effects (quantitative trait loci, QTLs by RFLP markers. [Producing a large population of RSLs for each chromosome arm and mapping them proved more difficult than anticipated, low numbers of RSLs were obtained for two of the chromosome arms.] 5. To construct recombination genetic maps of chromosomes of homoeologous groups 1 and 7 and to compare them to existing maps of wheat and other cereals [Genetic maps are not complete for homoeologous groups 4 and 7.] The rationale for this project is that wild species have characteristics that would be valuable if transferred to a crop plant. We demonstrated the sequence of chromosome manipulations and genetic tests needed to confirm this potential value and enhance transfer. This research has shown that a wild tetraploid species harbors genetic variability for quantitative traits that is interactive and not simply additive when introduced into a common genetic background. Chromosomal segments from several chromosome arms improve yield and protein in wheat but their effect is presumably enhanced when combination of genes from several segments are integrated into a single genotype in order to achieve the benefits of genes from the wild species. The interaction between these genes and those in the recipient species must be accounted for. The results of this study provide a scientific basis for some of the disappointing results that have historically obtained when using wild species as donors for crop improvement and provide a strategy for further successes.

scholarly journals Core Collapse in Rotating Massive Stars and LGRBs

2011 ◽  
Vol 7 (S279) ◽  
pp. 154-158
Author(s):  
Aldo Batta
Keyword(s):  
Gravitational Interaction ◽  
Three Dimensions ◽  
Core Collapse ◽  
Disk Formation ◽  
Physical Conditions ◽  
Physical Scale ◽  
Accretion Rates ◽  
Self Gravity ◽  
Relativistic Potential ◽  
Future Work

AbstractThe collapse of massive rotating stellar cores and the associated accretion is thought to power long GRBs. The physical scale and dynamics of the accretion disk are initially set by the angular momentum distribution in the progenitor, and the physical conditions make neutrino emission the main cooling agent in the flow. We have carried out an initial set of calculations of the collapse of rotating polytropic cores in three dimensions, making use of a pseudo-relativistic potential and a simplified cooling prescription. We focus on the effects of self gravity and cooling on the overall morphology and evolution of the flow for a given rotation rate in the context of the collapsar model. For the typical cooling times expected in such a scenario we observe the appearance of strong instabilities on a time scale, tcool, following disk formation. Such instabilities and their gravitational interaction with the black hole (BH) produce significant variability in the energy loss and accretion rates, which would translate into neutrino cooling variations when a more realistic neutrino cooling scheme is implemented in future work.

Sign in / Sign up

Export Citation Format

Share Document