scholarly journals The First Genetic Map for a Psoraleoid Legume (Bituminaria bituminosa) Reveals Highly Conserved Synteny with Phaseoloid Legumes

Plants ◽  
2020 ◽  
Vol 9 (8) ◽  
pp. 973
Author(s):  
Matthew N. Nelson ◽  
Jafar S. Jabbari ◽  
Rust Turakulov ◽  
Aneeta Pradhan ◽  
Maria Pazos-Navarro ◽  
...  
Keyword(s):  
Genetic Map ◽  
Divergence Time ◽  
Genotyping By Sequencing ◽  
Chromosome Count ◽  
Forage Legume ◽  
Linkage Groups ◽  
Closely Related Species ◽  
Drought Tolerant ◽  
Bituminaria Bituminosa ◽  
Pharmaceutical Properties

We present the first genetic map of tedera (Bituminaria bituminosa (L.) C.H. Stirton), a drought-tolerant forage legume from the Canary Islands with useful pharmaceutical properties. It is also the first genetic map for any species in the tribe Psoraleeae (Fabaceae). The map comprises 2042 genotyping-by-sequencing (GBS) markers distributed across 10 linkage groups, consistent with the haploid chromosome count for this species (n = 10). Sequence tags from the markers were used to find homologous matches in the genome sequences of the closely related species in the Phaseoleae tribe: soybean, common bean, and cowpea. No tedera linkage groups align in their entirety to chromosomes in any of these phaseoloid species, but there are long stretches of collinearity that could be used in tedera research for gene discovery purposes using the better-resourced phaseoloid species. Using Ks analysis of a tedera transcriptome against five legume genomes provides an estimated divergence time of 17.4 million years between tedera and soybean. Genomic information and resources developed here will be invaluable for breeding tedera varieties for forage and pharmaceutical purposes.

scholarly journals Adaptive Divergence under Gene Flow along an Environmental Gradient in Two Coexisting Stickleback Species

Genes ◽  
2021 ◽  
Vol 12 (3) ◽  
pp. 435
Author(s):  
Thijs M. P. Bal ◽  
Alejandro Llanos-Garrido ◽  
Anurag Chaturvedi ◽  
Io Verdonck ◽  
Bart Hellemans ◽  
...  
Keyword(s):  
Gene Flow ◽  
Brackish Water ◽  
Environmental Gradient ◽  
Spatial Scales ◽  
Morphological Differentiation ◽  
Genotyping By Sequencing ◽  
Adaptive Divergence ◽  
Linkage Groups ◽  
Closely Related Species ◽  
Genomic Patterns

There is a general and solid theoretical framework to explain how the interplay between natural selection and gene flow affects local adaptation. Yet, to what extent coexisting closely related species evolve collectively or show distinctive evolutionary responses remains a fundamental question. To address this, we studied the population genetic structure and morphological differentiation of sympatric three-spined and nine-spined stickleback. We conducted genotyping-by-sequencing and morphological trait characterisation using 24 individuals of each species from four lowland brackish water (LBW), four lowland freshwater (LFW) and three upland freshwater (UFW) sites in Belgium and the Netherlands. This combination of sites allowed us to contrast populations from isolated but environmentally similar locations (LFW vs. UFW), isolated but environmentally heterogeneous locations (LBW vs. UFW), and well-connected but environmentally heterogenous locations (LBW vs. LFW). Overall, both species showed comparable levels of genetic diversity and neutral genetic differentiation. However, for all three spatial scales, signatures of morphological and genomic adaptive divergence were substantially stronger among populations of the three-spined stickleback than among populations of the nine-spined stickleback. Furthermore, most outlier SNPs in the two species were associated with local freshwater sites. The few outlier SNPs that were associated with the split between brackish water and freshwater populations were located on one linkage group in three-spined stickleback and two linkage groups in nine-spined stickleback. We conclude that while both species show congruent evolutionary and genomic patterns of divergent selection, both species differ in the magnitude of their response to selection regardless of the geographical and environmental context.

scholarly journals Chromosomal Map of the Model LegumeLotus japonicus

Genetics ◽  
2002 ◽  
Vol 161 (4) ◽  
pp. 1661-1672 ◽  
Author(s):  
Andrea Pedrosa ◽  
Niels Sandal ◽  
Jens Stougaard ◽  
Dieter Schweizer ◽  
Andreas Bachmair
Keyword(s):  
Repetitive Sequences ◽  
Lotus Japonicus ◽  
Chromosome Complement ◽  
Linkage Groups ◽  
Closely Related Species ◽  
F1 Hybrid ◽  
Bac Clones ◽  
Genomic Regions ◽  
Chromosomal Map

AbstractLotus japonicus is a model plant for the legume family. To facilitate map-based cloning approaches and genome analysis, we performed an extensive characterization of the chromosome complement of the species. A detailed karyotype of L. japonicus Gifu was built and plasmid and BAC clones, corresponding to genetically mapped markers (see the accompanying article by Sandal  et al. 2002, this issue), were used for FISH to correlate genetic and chromosomal maps. Hybridization of DNA clones from 32 different genomic regions enabled the assignment of linkage groups to chromosomes, the comparison between genetic and physical distances throughout the genome, and the partial characterization of different repetitive sequences, including telomeric and centromeric repeats. Additional analysis of L. filicaulis and its F1 hybrid with L. japonicus demonstrated the occurrence of inversions between these closely related species, suggesting that these chromosome rearrangements are early events in speciation of this group.

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

Genome ◽  
2002 ◽  
Vol 45 (2) ◽  
pp. 282-295 ◽  
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.

Genetic map of eight microsatellite markers comprising two linkage groups on rat chromosome 6

1995 ◽  
Vol 68 (1-2) ◽  
pp. 107-111 ◽  
Author(s):  
Y. Du ◽  
E.F. Remmers ◽  
H. Zha ◽  
E.A. Goldmuntz ◽  
P. Mathern ◽  
...  
Keyword(s):  
Microsatellite Markers ◽  
Genetic Map ◽  
Chromosome 6 ◽  
Linkage Groups

scholarly journals Centromere-Linkage Analysis and Consolidation of the Zebrafish Genetic Map

Genetics ◽  
1996 ◽  
Vol 142 (4) ◽  
pp. 1277-1288
Author(s):  
Stephen L Johnson ◽  
Michael A Gates ◽  
Michele Johnson ◽  
William S Talbot ◽  
Sally Horne ◽  
...  
Keyword(s):  
Linkage Group ◽  
Linkage Analysis ◽  
Genetic Analysis ◽  
Linkage Map ◽  
Rapid Method ◽  
Genetic Map ◽  
Dna Polymorphisms ◽  
Linkage Groups

Abstract The ease of isolating mutations in zebrafish will contribute to an understanding of a variety of processes common to all vertebrates. To facilitate genetic analysis of such mutations, we have identified DNA polymorphisms closely linked to each of the 25 centromeres of zebrafish, placed centromeres on the linkage map, increased the number of mapped PCR-based markers to 652, and consolidated the number of linkage groups to the number of chromosomes. This work makes possible centromere-linkage analysis, a novel, rapid method to assign mutations to a specific linkage group using half-tetrads.

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.

Genetic map of 16 polymorphic markers forming three linkage groups assigned to rat Chromosome 4

1995 ◽  
Vol 6 (7) ◽  
pp. 459-463 ◽  
Author(s):  
E. A. Goldmuntz ◽  
E. F. Remmers ◽  
Y. Du ◽  
H. Zha ◽  
P. Mathern ◽  
...  
Keyword(s):  
Genetic Map ◽  
Polymorphic Markers ◽  
Chromosome 4 ◽  
Linkage Groups

scholarly journals Large-scale SNP discovery and construction of a high-density genetic map of Colossoma macropomum through genotyping-by-sequencing

2017 ◽  
Vol 7 (1) ◽  
Author(s):  
José de Ribamar da Silva Nunes ◽  
Shikai Liu ◽  
Fábio Pértille ◽  
Caio Augusto Perazza ◽  
Priscilla Marqui Schmidt Villela ◽  
...  
Keyword(s):  
Genetic Map ◽  
Large Scale ◽  
Genotyping By Sequencing ◽  
High Density ◽  
Snp Discovery ◽  
Colossoma Macropomum

scholarly journals Construction of a high-density genetic map: genotyping by sequencing (GBS) to map purple seed coat color (Psc) in hulless barley

Hereditas ◽  
2018 ◽  
Vol 155 (1) ◽  
Author(s):  
Xiaohua Yao ◽  
Kunlun Wu ◽  
Youhua Yao ◽  
Yixiong Bai ◽  
Jingxiu Ye ◽  
...  
Keyword(s):  
Genetic Map ◽  
Seed Coat ◽  
Coat Color ◽  
Genotyping By Sequencing ◽  
High Density ◽  
Seed Coat Color ◽  
Hulless Barley
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