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.

Collinearity between a 30-centimorgan segment of Arabidopsis thaliana chromosome 4 and duplicated regions within the Brassica napus genome

Genome ◽  
1998 ◽  
Vol 41 (1) ◽  
pp. 62-69 ◽  
Author(s):  
A C Cavell ◽  
D J Lydiate ◽  
IAP Parkin ◽  
C Dean ◽  
M Trick
Keyword(s):  
Arabidopsis Thaliana ◽  
Brassica Napus ◽  
Physical Map ◽  
Brassica Species ◽  
Single Copy ◽  
Genetic Maps ◽  
Haploid Genome ◽  
Chromosome 4 ◽  
Crop Species ◽  
Brassica Crop

Arabidopsis thaliana (the model dicotyledonous plant) is closely related to Brassica crop species. Genome collinearity, or conservation of marker order, between Brassica napus (oilseed rape) and A. thaliana was assessed over a 7.5-Mbp region of the long arm of A. thaliana chromosome 4, equivalent to 30 cM. Estimates of copy number indicated that sequences present in a single copy in the haploid genome of A. thaliana (n = 5) were present in 2-8 copies in the haploid genome of B. napus (n = 19), while sequences present in multiple copies in A. thaliana were present in over 10 copies in B. napus. Genetic mapping in B. napus of DNA markers derived from a segment of A. thaliana chromosome 4 revealed duplicated homologous segments in the B. napus genome. Physical mapping in A. thaliana of homologues of Brassica clones derived from these regions confirmed the identity of six duplicated segments with substantial homology to the 7.5-Mbp region of chromosome 4 in A. thaliana. These six duplicated Brassica regions (on average 22cM in length) are collinear, except that two of the six copies contain the same large internal inversion. These results have encouraging implications for the feasibility of shuttling between the physical map of A. thaliana and genetic maps of Brassica species, for identifying candidate genes and for map based gene cloning in Brassica crops.

scholarly journals A linkage disequilibrium-based approach to position unmapped SNPs in crop species

BMC Genomics ◽  
2021 ◽  
Vol 22 (1) ◽  
Author(s):  
Seema Yadav ◽  
Elizabeth M. Ross ◽  
Karen S. Aitken ◽  
Lee T. Hickey ◽  
Owen Powell ◽  
...  
Keyword(s):  
Linkage Disequilibrium ◽  
Genetic Map ◽  
Association Studies ◽  
Genetic Maps ◽  
Data Sets ◽  
Genome Wide Association Studies ◽  
Crop Species ◽  
Wide Range ◽  
The Mean ◽  
Genome Assemblies

Abstract Background High-density SNP arrays are now available for a wide range of crop species. Despite the development of many tools for generating genetic maps, the genome position of many SNPs from these arrays is unknown. Here we propose a linkage disequilibrium (LD)-based algorithm to allocate unassigned SNPs to chromosome regions from sparse genetic maps. This algorithm was tested on sugarcane, wheat, and barley data sets. We calculated the algorithm’s efficiency by masking SNPs with known locations, then assigning their position to the map with the algorithm, and finally comparing the assigned and true positions. Results In the 20-fold cross-validation, the mean proportion of masked mapped SNPs that were placed by the algorithm to a chromosome was 89.53, 94.25, and 97.23% for sugarcane, wheat, and barley, respectively. Of the markers that were placed in the genome, 98.73, 96.45 and 98.53% of the SNPs were positioned on the correct chromosome. The mean correlations between known and new estimated SNP positions were 0.97, 0.98, and 0.97 for sugarcane, wheat, and barley. The LD-based algorithm was used to assign 5920 out of 21,251 unpositioned markers to the current Q208 sugarcane genetic map, representing the highest density genetic map for this species to date. Conclusions Our LD-based approach can be used to accurately assign unpositioned SNPs to existing genetic maps, improving genome-wide association studies and genomic prediction in crop species with fragmented and incomplete genome assemblies. This approach will facilitate genomic-assisted breeding for many orphan crops that lack genetic and genomic resources.

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.

scholarly journals Identification and Physical Localization of Useful Genes and Markers to a Major Gene-Rich Region on Wheat Group1SChromosomes

Genetics ◽  
2001 ◽  
Vol 157 (4) ◽  
pp. 1735-1747 ◽  
Author(s):  
Devinder Sandhu ◽  
Julie A Champoux ◽  
Svetlana N Bondareva ◽  
Kulvinder S Gill
Keyword(s):  
Dna Analysis ◽  
Major Gene ◽  
Rflp Markers ◽  
Rich Region ◽  
Wheat Group ◽  
Marker Loci ◽  
Group 1 Chromosomes ◽  
Gene Rich Region ◽  
Homeologous Group ◽  
Group 1

AbstractThe short arm of Triticeae homeologous group 1 chromosomes is known to contain many agronomically important genes. The objectives of this study were to physically localize gene-containing regions of the group 1 short arm, enrich these regions with markers, and study the distribution of genes and recombination. We focused on the major gene-rich region (“1S0.8 region”) and identified 75 useful genes along with 93 RFLP markers by comparing 35 different maps of Poaceae species. The RFLP markers were tested by gel blot DNA analysis of wheat group 1 nullisomic-tetrasomic lines, ditelosomic lines, and four single-break deletion lines for chromosome arm 1BS. Seventy-three of the 93 markers mapped to group 1 and detected 91 loci on chromosome 1B. Fifty-one of these markers mapped to two major gene-rich regions physically encompassing 14% of the short arm. Forty-one marker loci mapped to the 1S0.8 region and 10 to 1S0.5 region. Two cDNA markers mapped in the centromeric region and the remaining 24 loci were on the long arm. About 82% of short arm recombination was observed in the 1S0.8 region and 17% in the 1S0.5 region. Less than 1% recombination was observed for the remaining 85% of the physical arm length.

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.

Development of a Brassica seed cDNA microarray

Genome ◽  
2008 ◽  
Vol 51 (3) ◽  
pp. 236-242 ◽  
Author(s):  
Daoquan Xiang ◽  
Raju Datla ◽  
Fengling Li ◽  
Adrian Cutler ◽  
Meghna R. Malik ◽  
...  
Keyword(s):  
Expression Patterns ◽  
Cdna Array ◽  
Brassica Species ◽  
Crop Species ◽  
Rna Targets ◽  
Associated Functions ◽  
Leaf Tissues ◽  
Germinating Seeds ◽  
Signal Intensities

Brassica species represent several important crops including canola ( Brassica napus ). Understanding of genetic elements that contribute to seed-associated functions will impact future improvements in the canola crop. Brassica species share a very close taxonomic and molecular relationship with Arabidopsis thaliana. However, there are several subtle but distinct seed-associated agronomic characteristics that differ among the oil seed crop species. To address these, we have generated 67 535 ESTs predominately from Brassica seeds, analyzed these sequences, and identified 10 642 unigenes for the preparation of a targeted seed cDNA array. A set of 10 642 PCR primer pairs was designed and corresponding amplicons were produced for spotting, along with relevant controls. Critical quality control tests produced satisfactory results for use of this microarray in biological experiments. The microarray was also tested with specific RNA targets from embryos, germinating seeds, and leaf tissues. The hybridizations, signal intensities, and overall quality of these slides were consistent and reproducible. Additionally, there are 429 ESTs represented on the array that show no homology with any A. thaliana annotated gene or any gene in the Brassica genome databases or other plant databases; however, all of these probes hybridized to B. napus transcripts, indicating that the array also will be useful in defining expression patterns for genes so far unique to Brassica species.

Anchored Reference Loci in Loblolly Pine (Pinus taeda L.) for Integrating Pine Genomics

Genetics ◽  
2001 ◽  
Vol 159 (2) ◽  
pp. 799-809 ◽  
Author(s):  
Garth R Brown ◽  
Edward E Kadel ◽  
Daniel L Bassoni ◽  
Kristine L Kiehne ◽  
Berhanu Temesgen ◽  
...  
Keyword(s):  
Pinus Taeda ◽  
Loblolly Pine ◽  
Comparative Mapping ◽  
Expressed Sequence Tag ◽  
Single Species ◽  
Douglas Fir ◽  
Genetic Maps ◽  
Multiple Sources ◽  
Primer Sets ◽  
Pinus Taeda L

Abstract Anchored reference loci provide a framework for comparative mapping. They are landmarks to denote conserved chromosomal segments, allowing the synthesis of genetic maps from multiple sources. We evaluated 90 expressed sequence tag polymorphisms (ESTPs) from loblolly pine (Pinus taeda L.) for this function. Primer sets were assayed for amplification and polymorphism in six pedigrees, representing two subgenera of Pinus and a distant member of the Pinaceae, Douglas-fir (Pseudotsuga menziesii [Mirb.] Franco). On average, 89% of primer sets amplified in four species of subgenus Pinus, 49% in one species of subgenus Strobus, and 22% in Douglas-fir. Polymorphisms were detected for 37–61% of the ESTPs within each pedigree. Comparative mapping in loblolly and slash pine (P. elliottii Englm.) revealed that ESTPs mapped to the same location. Disrupted synteny or significant disruptions in colinearity were not detected. Thirty-five ESTPs met criteria established for anchor loci. The majority of those that did not meet these criteria were excluded when map location was known in only a single species. Anchor loci provide a unifying tool for the community, facilitating the creation of a “generic” pine map and serving as a foundation for studies on genome organization and evolution.

scholarly journals Genome Assembly of the Popular Korean Soybean Cultivar Hwangkeum

2021 ◽  
Author(s):  
Myung-Shin Kim ◽  
Taeyoung Lee ◽  
Jeonghun Baek ◽  
Ji Hong Kim ◽  
Changhoon Kim ◽  
...  
Keyword(s):  
Reference Genome ◽  
De Novo ◽  
Anthocyanin Biosynthesis ◽  
Genetic Maps ◽  
Soybean Cultivar ◽  
Gene Arrangement ◽  
Nucleotide Polymorphisms ◽  
Sequencing Data ◽  
Crop Species ◽  
Satellite Repeats

AbstractMassive resequencing efforts have been undertaken to catalog allelic variants in major crop species including soybean, but the scope of the information for genetic variation often depends on short sequence reads mapped to the extant reference genome. Additional de novo assembled genome sequences provide a unique opportunity to explore a dispensable genome fraction in the pan-genome of a species. Here, we report the de novo assembly and annotation of Hwangkeum, a popular soybean cultivar in Korea. The assembly was constructed using PromethION nanopore sequencing data and two genetic maps, and was then error-corrected using Illumina short-reads and PacBio SMRT reads. The 933.12 Mb assembly was annotated 79,870 transcripts for 58,550 genes using RNA-Seq data and the public soybean annotation set. Comparison of the Hwangkeum assembly with the Williams 82 soybean reference genome sequence revealed 1.8 million single-nucleotide polymorphisms, 0.5 million indels, and 25 thousand putative structural variants. However, there was no natural megabase-scale chromosomal rearrangement. Incidentally, by adding two novel groups, we found that soybean contains four clearly separated groups of centromeric satellite repeats. Analyses of satellite repeats and gene content suggested that the Hwangkeum assembly is a high-quality assembly. This was further supported by comparison of the marker arrangement of anthocyanin biosynthesis genes and of gene arrangement at the Rsv3 locus. Therefore, the results indicate that the de novo assembly of Hwangkeum is a valuable additional reference genome resource for characterizing traits for the improvement of this important crop species.

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