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

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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Genetic analysis and genome mapping in Raphanus

Genome ◽

10.1139/g03-026 ◽

2003 ◽

Vol 46 (3) ◽

pp. 423-430 ◽

Cited By ~ 31

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.

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Restriction site-associated DNA sequencing for SNP discovery and high-density genetic map construction in southern catfish ( Silurus meridionalis )

Royal Society Open Science ◽

10.1098/rsos.172054 ◽

2018 ◽

Vol 5 (5) ◽

pp. 172054 ◽

Cited By ~ 5

Author(s):

Mimi Xie ◽

Yao Ming ◽

Feng Shao ◽

Jianbo Jian ◽

Yaoguang Zhang ◽

...

Keyword(s):

Linkage Map ◽

Genetic Map ◽

Restriction Site ◽

Genome Structure ◽

High Density ◽

Genetic Maps ◽

High Quality ◽

Silurus Meridionalis ◽

Map Construction ◽

High Density Linkage Map

Single-nucleotide polymorphism (SNP) markers and high-density genetic maps are important resources for marker-assisted selection, mapping of quantitative trait loci (QTLs) and genome structure analysis. Although linkage maps in certain catfish species have been obtained, high-density maps remain unavailable in the economically important southern catfish ( Silurus meridionalis ). Recently developed restriction site-associated DNA (RAD) markers have proved to be a promising tool for SNP detection and genetic map construction. The objective of the present study was to construct a high-density linkage map using SNPs generated by next-generation RAD sequencing in S. meridionalis for future genetic and genomic studies. An F1 population of 100 individuals was obtained by intraspecific crossing of two wild heterozygous individuals. In total, 77 634 putative high-quality bi-allelic SNPs between the parents were discovered by mapping the parents' paired-end RAD reads onto the reference contigs from both parents, of which 54.7% were transitions and 45.3% were transversions (transition/transversion ratio of 1.2). Finally, 26 714 high-quality RAD markers were grouped into 29 linkage groups by using de novo clustering methods (Stacks). Among these markers, 4514 were linked to the female genetic map, 23 718 to the male map and 6715 effective loci were linked to the integrated map spanning 5918.31 centimorgans (cM), with an average marker interval of 0.89 cM. High-resolution genetic maps are a useful tool for both marker-assisted breeding and various genome investigations in catfish, such as sequence assembly, gene localization, QTL detection and genome structure comparison. Hence, such a high-density linkage map will serve as a valuable resource for comparative genomics and fine-scale QTL mapping in catfish species.

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Chromonomer: a tool set for repairing and enhancing assembled genomes through integration of genetic maps and conserved synteny

10.1101/2020.02.04.934711 ◽

2020 ◽

Cited By ~ 2

Author(s):

Julian Catchen ◽

Angel Amores ◽

Susan Bassham

Keyword(s):

Genetic Map ◽

Reference Genome ◽

Genome Structure ◽

Orthologous Gene ◽

Genetic Maps ◽

Conserved Synteny ◽

Sequencing Technologies ◽

Sequencing Library ◽

Tool Set ◽

And Function

AbstractThe pace of the sequencing and computational assembly of novel reference genomes is accelerating. Though DNA sequencing technologies and assembly software tools continue to improve, biological features of genomes such as repetitive sequence as well as molecular artifacts that often accompany sequencing library preparation can lead to fragmented or chimeric assemblies. If left uncorrected, defects like these trammel progress on understanding genome structure and function, or worse, positively mislead such research. Fortunately, integration of additional, independent streams of information, such as a genetic map – particularly a marker-dense map from RADseq, for example – and conserved orthologous gene order from related taxa can be used to scaffold together unlinked, disordered fragments and to restructure a reference genome where it is incorrectly joined. We present a tool set for automating these processes, one that additionally tracks any changes to the assembly and to the genetic map, and which allows the user to scrutinize these changes with the help of web-based, graphical visualizations. Chromonomer takes a user-defined reference genome, a map of genetic markers, and, optionally, conserved synteny information to construct an improved reference genome of chromosome models: a “chromonome”. We demonstrate Chromonomer’s performance on genome assemblies and genetic maps that have disparate characteristics and levels of quality.

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Chromonomer: A Tool Set for Repairing and Enhancing Assembled Genomes Through Integration of Genetic Maps and Conserved Synteny

G3 Genes|Genome|Genetics ◽

10.1534/g3.120.401485 ◽

2020 ◽

Vol 10 (11) ◽

pp. 4115-4128 ◽

Cited By ~ 1

Author(s):

Julian Catchen ◽

Angel Amores ◽

Susan Bassham

Keyword(s):

Genetic Map ◽

Reference Genome ◽

Genome Structure ◽

Orthologous Gene ◽

Genetic Maps ◽

Conserved Synteny ◽

Sequencing Technologies ◽

Sequencing Library ◽

Tool Set ◽

And Function

The pace of the sequencing and computational assembly of novel reference genomes is accelerating. Though DNA sequencing technologies and assembly software tools continue to improve, biological features of genomes such as repetitive sequence as well as molecular artifacts that often accompany sequencing library preparation can lead to fragmented or chimeric assemblies. If left uncorrected, defects like these trammel progress on understanding genome structure and function, or worse, positively mislead this research. Fortunately, integration of additional, independent streams of information, such as a marker-dense genetic map and conserved orthologous gene order from related taxa, can be used to scaffold together unlinked, disordered fragments and to restructure a reference genome where it is incorrectly joined. We present a tool set for automating these processes, one that additionally tracks any changes to the assembly and to the genetic map, and which allows the user to scrutinize these changes with the help of web-based, graphical visualizations. Chromonomer takes a user-defined reference genome, a map of genetic markers, and, optionally, conserved synteny information to construct an improved reference genome of chromosome models: a “chromonome”. We demonstrate Chromonomer’s performance on genome assemblies and genetic maps that have disparate characteristics and levels of quality.

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Heterogeneity in Rates of Recombination Across the Mouse Genome

Genetics ◽

10.1093/genetics/142.2.537 ◽

1996 ◽

Vol 142 (2) ◽

pp. 537-548 ◽

Cited By ~ 2

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.

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An enhanced molecular marker based genetic map of perennial ryegrass (Lolium perenne) reveals comparative relationships with other Poaceae genomes

Genome ◽

10.1139/g01-144 ◽

2002 ◽

Vol 45 (2) ◽

pp. 282-295 ◽

Cited By ~ 175

Author(s):

Elizabeth S Jones ◽

Natalia L Mahoney ◽

Michael D Hayward ◽

Ian P Armstead ◽

J Gilbert Jones ◽

...

Keyword(s):

Molecular Marker ◽

Linkage Map ◽

Genetic Map ◽

Lolium Perenne ◽

Perennial Ryegrass ◽

Genetic Linkage Map ◽

Population Based ◽

Genetic Maps ◽

Linkage Groups ◽

Integrated Genetic Map

A molecular-marker linkage map has been constructed for perennial ryegrass (Lolium perenne L.) using a one-way pseudo-testcross population based on the mating of a multiple heterozygous individual with a doubled haploid genotype. RFLP, AFLP, isoenzyme, and EST data from four collaborating laboratories within the International Lolium Genome Initiative were combined to produce an integrated genetic map containing 240 loci covering 811 cM on seven linkage groups. The map contained 124 codominant markers, of which 109 were heterologous anchor RFLP probes from wheat, barley, oat, and rice, allowing comparative relationships between perennial ryegrass and other Poaceae species to be inferred. The genetic maps of perennial ryegrass and the Triticeae cereals are highly conserved in terms of synteny and colinearity. This observation was supported by the general agreement of the syntenic relationships between perennial ryegrass, oat, and rice and those between the Triticeae and these species. A lower level of synteny and colinearity was observed between perennial ryegrass and oat compared with the Triticeae, despite the closer taxonomic affinity between these species. It is proposed that the linkage groups of perennial ryegrass be numbered in accordance with these syntenic relationships, to correspond to the homoeologous groups of the Triticeae cereals.Key words: Lolium perenne, genetic linkage map, RFLP, AFLP, conserved synteny.

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A physical map with yeast artificial chromosome (YAC) clones covering 63% of the 12 rice chromosomes

Genome ◽

10.1139/g00-076 ◽

2001 ◽

Vol 44 (1) ◽

pp. 32-37 ◽

Cited By ~ 11

Author(s):

Shoko Saji ◽

Yosuke Umehara ◽

Baltazar A Antonio ◽

Hiroko Yamane ◽

Hiroshi Tanoue ◽

...

Keyword(s):

Genetic Map ◽

Dna Markers ◽

Yeast Artificial Chromosome ◽

Physical Map ◽

Genome Structure ◽

Rice Genome ◽

Artificial Chromosome ◽

Physical Length ◽

Rice Chromosomes ◽

Yac Contig

A new YAC (yeast artificial chromosome) physical map of the 12 rice chromosomes was constructed utilizing the latest molecular linkage map. The 1439 DNA markers on the rice genetic map selected a total of 1892 YACs from a YAC library. A total of 675 distinct YACs were assigned to specific chromosomal locations. In all chromosomes, 297 YAC contigs and 142 YAC islands were formed. The total physical length of these contigs and islands was estimated to 270 Mb which corresponds to approximately 63% of the entire rice genome (430 Mb). Because the physical length of each YAC contig has been measured, we could then estimate the physical distance between genetic markers more precisely than previously. In the course of constructing the new physical map, the DNA markers mapped at 0.0-cM intervals were ordered accurately and the presence of potentially duplicated regions among the chromosomes was detected. The physical map combined with the genetic map will form the basis for elucidation of the rice genome structure, map-based cloning of agronomically important genes, and genome sequencing.Key words: physical mapping, YAC contig, rice genome, rice chromosomes.

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

10.1101/2020.09.14.296525 ◽

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.

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The genetic and RFLP characterization of the left end of linkage group III in Caenorhabditis elegans

Genome ◽

10.1139/g93-096 ◽

1993 ◽

Vol 36 (4) ◽

pp. 712-724 ◽

Cited By ~ 2

Author(s):

Dave Pilgrim

Keyword(s):

Caenorhabditis Elegans ◽

Linkage Group ◽

Genetic Map ◽

Physical Map ◽

Group Iii ◽

C Elegans ◽

Genomic Regions ◽

Caenorhabditis Elegans Genome ◽

Selection Of

A genetic approach was taken to identify new transposable element Tc1 -dependent polymorphisms on the left end of linkage group III in the nematode Caenorhabditis elegans. The cloning of the genomic DNA surrounding the Tc1 allowed the selection of overlapping clones (from the collection being used to assemble the physical map of the C. elegans genome). A contig of approximately 600–800 kbp in the region has been identified, the genetic map of the region has been refined, and 10 new RFLPs as well as at least four previously characterized genetic loci have been positioned onto the physical map, to the resolution of a few cosmids. This analysis demonstrated the ability to combine physical and genetic mapping for the rapid analysis of large genomic regions (0.5–1 Mbp) in genetically amenable eukaryotes.Key words: Caenorhabditis elegans, genome analysis, RFLP, physical map, genetic map.

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Identification of QTLs for Stripe Rust Resistance in a Recombinant Inbred Line Population

International Journal of Molecular Sciences ◽

10.3390/ijms20143410 ◽

2019 ◽

Vol 20 (14) ◽

pp. 3410 ◽

Cited By ~ 6

Author(s):

Manyu Yang ◽

Guangrong Li ◽

Hongshen Wan ◽

Liping Li ◽

Jun Li ◽

...

Keyword(s):

Genetic Map ◽

Stripe Rust ◽

Resistance Genes ◽

Phenotypic Variation ◽

Recombinant Inbred ◽

Rust Resistance ◽

High Density ◽

Genetic Maps ◽

Stripe Rust Resistance ◽

Resistance Locus

Stripe rust, caused by Puccinia striiformis f. sp. tritici (Pst), is one of the most devastating fungal diseases of wheat worldwide. It is essential to discover more sources of stripe rust resistance genes for wheat breeding programs. Specific locus amplified fragment sequencing (SLAF-seq) is a powerful tool for the construction of high-density genetic maps. In this study, a set of 200 recombinant inbred lines (RILs) derived from a cross between wheat cultivars Chuanmai 42 (CH42) and Chuanmai 55 (CH55) was used to construct a high-density genetic map and to identify quantitative trait loci (QTLs) for stripe rust resistance using SLAF-seq technology. A genetic map of 2828.51 cM, including 21 linkage groups, contained 6732 single nucleotide polymorphism markers (SNP). Resistance QTLs were identified on chromosomes 1B, 2A, and 7B; Qyr.saas-7B was derived from CH42, whereas Qyr.saas-1B and Qyr.saas-2A were from CH55. The physical location of Qyr.saas-1B, which explained 6.24–34.22% of the phenotypic variation, overlapped with the resistance gene Yr29. Qyr.saas-7B accounted for up to 20.64% of the phenotypic variation. Qyr.saas-2A, a minor QTL, was found to be a likely new stripe rust resistance locus. A significant additive effect was observed when all three QTLs were combined. The combined resistance genes could be of value in breeding wheat for stripe rust resistance.

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