Microsatellite discovery from BAC end sequences and genetic mapping to anchor the soybean physical and genetic maps

Genome ◽  
2008 ◽  
Vol 51 (4) ◽  
pp. 294-302 ◽  
Author(s):  
Randy C. Shoemaker ◽  
David Grant ◽  
Terry Olson ◽  
Wesley C. Warren ◽  
Rod Wing ◽  
...  
Keyword(s):  
Genetic Map ◽  
Physical Map ◽  
Genetic Maps ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Dinucleotide Repeats ◽  
Length Polymorphisms ◽  
Glycine Max L ◽  
Physical And Genetic Map ◽  
End Sequences

Whole-genome sequencing of the soybean ( Glycine max (L.) Merr. ‘Williams 82’) has made it important to integrate its physical and genetic maps. To facilitate this integration of maps, we screened 3290 microsatellites (SSRs) identified from BAC end sequences of clones comprising the ‘Williams 82’ physical map. SSRs were screened against 3 mapping populations. We found the AAT and ACT motifs produced the greatest frequency of length polymorphisms, ranging from 17.2% to 32.3% and from 11.8% to 33.3%, respectively. Other useful motifs include the dinucleotide repeats AG, AT, and AG, with frequency of length polymorphisms ranging from 11.2% to 18.4% (AT), 12.4% to 20.6% (AG), and 11.3% to 16.4% (GT). Repeat lengths less than 16 bp were generally less useful than repeat lengths of 40–60 bp. Two hundred and sixty-five SSRs were genetically mapped in at least one population. Of the 265 mapped SSRs, 60 came from BAC singletons not yet placed into contigs of the physical map. One hundred and ten originated in BACs located in contigs for which no genetic map location was previously known. Ninety-five SSRs came from BACs within contigs for which one or more other BACs had already been mapped. For these fingerprinted contigs (FPC) a high percentage of the mapped markers showed inconsistent map locations. A strategy is introduced by which physical and genetic map inconsistencies can be resolved using the preliminary 4× assembly of the whole genome sequence of soybean.

scholarly journals Development ofa Physical and Genetic Map of the Virulent WolbachiaStrainwMelPop

2003 ◽  
Vol 185 (24) ◽  
pp. 7077-7084 ◽  
Author(s):  
Ling V. Sun ◽  
Markus Riegler ◽  
Scott L. O'Neill
Keyword(s):  
Genetic Map ◽  
Gel Electrophoresis ◽  
Southern Hybridization ◽  
Gene Organization ◽  
Pulsed Field Gel Electrophoresis ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Restriction Fragments ◽  
Chromosome Fragments ◽  
Physical And Genetic Map

ABSTRACT We report here the construction of a physical and genetic map of the virulent Wolbachia strain, wMelPop. This map was determined by ordering 28 chromosome fragments that resulted from digestion with the restriction endonucleases FseI, ApaI, SmaI, and AscI and were resolved by pulsed-field gel electrophoresis. Southern hybridization was done with 53 Wolbachia-specific genes as probes in order to determine the relative positions of these restriction fragments and use them to serve as markers. Comparison of the resulting map with the whole genome sequence of the closely related benign Wolbachia strain, wMel, shows that the two genomes are largely conserved in gene organization with the exception of a single inversion in the chromosome.

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 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.

A physical and genetic map of theMycoplasma hyopneumoniaestrain J genome

2000 ◽  
Vol 46 (9) ◽  
pp. 832-840 ◽  
Author(s):  
Walter A Blank ◽  
Gerald W Stemke
Keyword(s):  
Genetic Map ◽  
Dna Hybridization ◽  
Gel Electrophoresis ◽  
Type Strain ◽  
Physical Map ◽  
Mycoplasma Hyopneumoniae ◽  
Pulsed Field Gel Electrophoresis ◽  
Cosmid Library ◽  
Physical And Genetic Map ◽  
Genomic Map

A macrorestriction map of the genome of Mycoplasma hyopneumoniae strain J, the type strain of the causative agent of enzootic pneumonia in pigs, was constructed using pulsed-field gel electrophoresis (PFGE) and DNA hybridization. The size of the genome as determined by PFGE was approximately 1070 kb. Assembly of the M. hyopneumoniae genomic map was facilitated and complimented by the simultaneous construction of an ordered cosmid library. Five contigs of overlapping cosmids were assembled, which together represent coverage of approximately 728 kb. Forty-two genetic markers (including three types of repeated elements) were placed on the M. hyopneumoniae map. Closer examination of an ApaI restriction fragment contained entirely within a single cosmid insert suggests that the genome size may be overestimated by PFGE.Key words: Mycoplasma hyopneumoniae, mollicutes, physical map, genetic map.

scholarly journals Vibrio cholerae O139 Bengal: Combined Physical and Genetic Map and Comparative Analysis with the Genome of V. cholerae O1

1998 ◽  
Vol 180 (17) ◽  
pp. 4516-4522 ◽  
Author(s):  
Gopal Khetawat ◽  
Rupak K. Bhadra ◽  
Sujata Kar ◽  
Jyotirmoy Das
Keyword(s):  
Vibrio Cholerae ◽  
Genetic Map ◽  
Physical Map ◽  
Hypervariable Regions ◽  
Restriction Sites ◽  
Vibrio Cholerae O139 ◽  
Physical And Genetic Map ◽  
Dna Restriction ◽  
Enzyme I ◽  
Fragment Excision

ABSTRACT A combined physical and genetic map of the genome of strain SG24 ofVibrio cholerae O139 Bengal, a novel non-O1 strain having epidemic potential, has been constructed by using the enzymesNotI, SfiI, and CeuI. The genome of SG24 is circular, and the genome size is about 3.57 Mb. The linkages between 47 NotI and 32 SfiI fragments ofV. cholerae SG24 genomic DNA were determined by combining two approaches: (i) identification of fragments produced by enzyme I in fragments produced by enzyme II by the method of fragment excision, redigestion, and end labeling and (ii) use of the linking clone libraries generated from the genome of classical O1 strain 569B. The linkages between nine CeuI fragments were determined primarily by analyses of partial fragments of theCeuI-digested genome. More than 80 cloned homologous and heterologous genes, including several operons, have been positioned on the physical map. The map of the SG24 genome represents the second map of a V. cholerae genome, and a comparison of this map with that of classical O1 strain 569B revealed considerable diversity in DNA restriction sites and allowed identification of hypervariable regions. Several genetic markers, including virulence determinant genes, are in different positions in the SG24 and 569B genomes.

scholarly journals Identification and High-Density Mapping of Gene-Rich Regions in Chromosome Group 1 of Wheat

Genetics ◽  
1996 ◽  
Vol 144 (4) ◽  
pp. 1883-1891 ◽  
Author(s):  
Kulvinder S Gill ◽  
Bikram S Gill ◽  
Takashi R Endo ◽  
Teri Taylor
Keyword(s):  
Genetic Map ◽  
Physical Map ◽  
Average Distance ◽  
High Density ◽  
Genetic Maps ◽  
Cdna Clones ◽  
Density Mapping ◽  
Physical Maps ◽  
Group 1 Chromosomes ◽  
Group 1

We studied the distribution of genes and recombination in wheat (Triticum aestivum) group 1 chromosomes by comparing high-density physical and genetic maps. Physical maps of chromosomes 1A, 1B, and 1D were generated by mapping 50 DNA markers on 56 single-break deletion lines. A consensus physical map was compared with the 1D genetic map of Triticum tauschii (68 markers) and a Triticeae group 1 consensus map (288 markers) to generate a cytogenetic ladder map (CLM). Most group 1 markers (86%) were present in five clusters that encompassed only 10% of the group 1 chromosome. This distribution may reflect that of genes because more than half of the probes were cDNA clones and 30% were PstI genomic. All 14 agronomically important genes in group 1 chromosomes were present in these clusters. Most recombination occurred in gene-cluster regions. Markers fell at an average distance of 244 kb in these regions. The CLM involving the Triticeae consensus genetic map revealed that the above distribution of genes and recombination is the same in other Triticeae species. Because of a significant number of common markers, our CLM can be used for comparative mapping and to estimate physical distances among markers in many Poaceae species including rice and maize.

scholarly journals Repertoire of SSRs in the Castor Bean Genome and Their Utilization in Genetic Diversity Analysis inJatropha curcas

2011 ◽  
Vol 2011 ◽  
pp. 1-9 ◽  
Author(s):  
Arti Sharma ◽  
Rajinder Singh Chauhan
Keyword(s):  
Linkage Mapping ◽  
Castor Bean ◽  
Seed Oil ◽  
Polymorphic Information Content ◽  
Whole Genome Sequence ◽  
Whole Genome ◽  
Dinucleotide Repeats ◽  
Whole Genome Analysis ◽  
Diversity Studies ◽  
Germplasm Analysis

Castor bean andJatrophacontain seed oil of industrial importance, share taxonomical and biochemical similarities, which can be explored for identifying SSRs in the whole genome sequence of castor bean and utilized inJatropha curcas. Whole genome analysis of castor bean identified 5,80,986 SSRs with a frequency of 1 per 680 bp. Genomic distribution of SSRs revealed that 27% were present in the non-genic region whereas 73% were also present in the putative genic regions with 26% in 5′UTRs, 25% in introns, 16% in 3′UTRs and 6% in the exons. Dinucleotide repeats were more frequent in introns, 5′UTRs and 3′UTRs whereas trinucleotide repeats were predominant in the exons. The transferability of randomly selected 302 SSRs, from castor bean to 49J. curcasgenotypes and 8Jatrophaspecies other thanJ. curcas, showed that 211 (~70%) amplified onJatrophaout of which 7.58% showed polymorphisms inJ. curcasgenotypes and 12.32% inJatrophaspecies. The higher rate of transferability of SSR markers from castor bean toJatrophacoupled with a good level of PIC (polymorphic information content) value (0.2 inJ. curcasgenotypes and 0.6 inJatrophaspecies) suggested that SSRs would be useful in germplasm analysis, linkage mapping, diversity studies and phylogenetic relationships, and so forth, inJ. curcasas well as otherJatrophaspecies.

scholarly journals Construction of a High-Density Genetic Map for Pitaya Using the Whole Genome Resequencing Approach

Horticulturae ◽  
2021 ◽  
Vol 7 (12) ◽  
pp. 534
Author(s):  
Zhijiang Wu ◽  
Haiyan Deng ◽  
Guidong Liang ◽  
Xiaoying Ye ◽  
Yonghua Qin ◽  
...  
Keyword(s):  
Linkage Map ◽  
Genetic Map ◽  
Snp Markers ◽  
High Density ◽  
Genetic Maps ◽  
Fleshy Fruit ◽  
Whole Genome ◽  
Genome Resequencing ◽  
Hylocereus Undatus ◽  
Whole Genome Resequencing

Pitaya (Hylocereus undatus) is one of the most economic fleshy fruit tree crops. This study aimed at producing a high-density linkage genetic map of pitaya based on the whole genome resequencing (WGrS) approach. For this purpose, a bi-parental F1 population of 198 individuals was generated and genotyped by WGrS. High-quality polymorphic 6434 single polymorphism nucleotide (SNP) markers were extracted and used to construct a high-density linkage map. A total of 11 linkage groups were resolved as expected in accordance with the chromosome number. The map length was 14,128.7 cM with an average SNP interval of 2.2 cM. Homology with the sequenced reference genome was described, and the physical and genetic maps were compared with collinearity analysis. This linkage map in addition to the available genomic resources will help for quantitative trait mapping, evolutionary studies and marker-assisted selection in the important Hylocereus species.

scholarly journals Physical and Genetic Map of the Pasteurella multocida A:1 Chromosome

1998 ◽  
Vol 180 (22) ◽  
pp. 6054-6058 ◽  
Author(s):  
Meredith L. Hunt ◽  
Carmel G. Ruffolo ◽  
Kumar Rajakumar ◽  
Ben Adler
Keyword(s):  
Genetic Map ◽  
Pasteurella Multocida ◽  
Physical Map ◽  
Restriction Enzymes ◽  
Circular Chromosome ◽  
Restriction Sites ◽  
Physical And Genetic Map ◽  
Single Circular Chromosome

ABSTRACT A physical and genetic map of the Pasteurella multocidaA:1 genome was generated by using the restriction enzymesApaI, CeuI, and NotI. The positions of 23 restriction sites and 32 genes, including 5 rrnoperons, were localized on the 2.35-Mbp single circular chromosome. This report presents the first genetic and physical map for this genus.

scholarly journals Physical and Genetic Map of the Obligate Intracellular Bacterium Coxiella burnetii

1998 ◽  
Vol 180 (15) ◽  
pp. 3816-3822 ◽  
Author(s):  
H. Willems ◽  
Cornelie Jäger ◽  
Georg Baljer
Keyword(s):  
Genetic Map ◽  
Coxiella Burnetii ◽  
Physical Map ◽  
Gene Organization ◽  
Intracellular Bacterium ◽  
Rrna Gene ◽  
Obligate Intracellular Bacterium ◽  
Obligate Intracellular ◽  
Great Heterogeneity ◽  
Physical And Genetic Map

ABSTRACT Pulsed-field gel electrophoresis and PCR techniques have been used to construct a NotI macrorestriction map of the obligate intracellular bacterium Coxiella burnetii Nine Mile. The size of the chromosome has been determined to be 2,103 kb comprising 29NotI restriction fragments. The average resolution is 72.5 kb, or about 3.5% of the genome. Experimental data support the presence of a linear chromosome. Published genes were localized on the physical map by Southern hybridization. One gene, recognized as transposable element, was found to be present in at least nine sites evenly distributed over the whole chromosome. There is only one copy of a 16S rRNA gene. The putative oriC has been located on a 27.5-kb NotI fragment. Gene organization upstream theoriC is almost identical to that of Pseudomonas putida and Bacillus subtilis, whereas gene organization downstream the oriC seems to be unique among bacteria. The physical map will be helpful in investigations of the great heterogeneity in restriction fragment length polymorphism patterns of different isolates and the great variation in genome size. The genetic map will help to determine whether gene order in different isolates is conserved.

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