Construction of bovine whole-genome radiation hybrid and linkage maps using high-throughput genotyping.
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ABSTRACT:
SUBMITTER: McKay SD
PROVIDER: S-EPMC2063635 | biostudies-literature |
REPOSITORIES: biostudies-literature
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Project description:BackgroundBovine whole genome linkage disequilibrium maps were constructed for eight breeds of cattle. These data provide fundamental information concerning bovine genome organization which will allow the design of studies to associate genetic variation with economically important traits and also provides background information concerning the extent of long range linkage disequilibrium in cattle.ResultsLinkage disequilibrium was assessed using r2 among all pairs of syntenic markers within eight breeds of cattle from the Bos taurus and Bos indicus subspecies. Bos taurus breeds included Angus, Charolais, Dutch Black and White Dairy, Holstein, Japanese Black and Limousin while Bos indicus breeds included Brahman and Nelore. Approximately 2670 markers spanning the entire bovine autosomal genome were used to estimate pairwise r2 values. We found that the extent of linkage disequilibrium is no more than 0.5 Mb in these eight breeds of cattle.ConclusionLinkage disequilibrium in cattle has previously been reported to extend several tens of centimorgans. Our results, based on a much larger sample of marker loci and across eight breeds of cattle indicate that in cattle linkage disequilibrium persists over much more limited distances. Our findings suggest that 30,000-50,000 loci will be needed to conduct whole genome association studies in cattle.
| S-EPMC2174945 | biostudies-literature
Project description:BackgroundHigh resolution radiation hybrid (RH) maps can facilitate genome sequence assembly by correctly ordering genes and genetic markers along chromosomes. The objective of the present study was to generate high resolution RH maps of bovine chromosomes 19 (BTA19) and 29 (BTA29), and compare them with the current 7.1X bovine genome sequence assembly (bovine build 3.1). We have chosen BTA19 and 29 as candidate chromosomes for mapping, since many Quantitative Trait Loci (QTL) for the traits of carcass merit and residual feed intake have been identified on these chromosomes.ResultsWe have constructed high resolution maps of BTA19 and BTA29 consisting of 555 and 253 Single Nucleotide Polymorphism (SNP) markers respectively using a 12,000 rad whole genome RH panel. With these markers, the RH map of BTA19 and BTA29 extended to 4591.4 cR and 2884.1 cR in length respectively. When aligned with the current bovine build 3.1, the order of markers on the RH map for BTA19 and 29 showed inconsistencies with respect to the genome assembly. Maps of both the chromosomes show that there is a significant internal rearrangement of the markers involving displacement, inversion and flips within the scaffolds with some scaffolds being misplaced in the genome assembly. We also constructed cattle-human comparative maps of these chromosomes which showed an overall agreement with the comparative maps published previously. However, minor discrepancies in the orientation of few homologous synteny blocks were observed.ConclusionThe high resolution maps of BTA19 (average 1 locus/139 kb) and BTA29 (average 1 locus/208 kb) presented in this study suggest that by the incorporation of RH mapping information, the current bovine genome sequence assembly can be significantly improved. Furthermore, these maps can serve as a potential resource for fine mapping QTL and identification of causative mutations underlying QTL for economically important traits.
| S-EPMC2064936 | biostudies-literature
Project description:BackgroundGenotyping-by-sequencing (GBS) provides affordable methods for genotyping hundreds of individuals using millions of markers. However, this challenges bioinformatic procedures that must overcome possible artifacts such as the bias generated by polymerase chain reaction duplicates and sequencing errors. Genotyping errors lead to data that deviate from what is expected from regular meiosis. This, in turn, leads to difficulties in grouping and ordering markers, resulting in inflated and incorrect linkage maps. Therefore, genotyping errors can be easily detected by linkage map quality evaluations.ResultsWe developed and used the Reads2Map workflow to build linkage maps with simulated and empirical GBS data of diploid outcrossing populations. The workflows run GATK, Stacks, TASSEL, and Freebayes for single-nucleotide polymorphism calling and updog, polyRAD, and SuperMASSA for genotype calling, as well as OneMap and GUSMap to build linkage maps. Using simulated data, we observed which genotype call software fails in identifying common errors in GBS sequencing data and proposed specific filters to better handle them. We tested whether it is possible to overcome errors in a linkage map using genotype probabilities from each software or global error rates to estimate genetic distances with an updated version of OneMap. We also evaluated the impact of segregation distortion, contaminant samples, and haplotype-based multiallelic markers in the final linkage maps. Through our evaluations, we observed that some of the approaches produce different results depending on the dataset (dataset dependent) and others produce consistent advantageous results among them (dataset independent).ConclusionsWe set as default in the Reads2Map workflows the approaches that showed to be dataset independent for GBS datasets according to our results. This reduces the number of required tests to identify optimal pipelines and parameters for other empirical datasets. Using Reads2Map, users can select the pipeline and parameters that best fit their data context. The Reads2MapApp shiny app provides a graphical representation of the results to facilitate their interpretation.
| S-EPMC10603770 | biostudies-literature
Project description:The next-generation sequencing technology coupled with the growing number of genome sequences opens the opportunity to redesign genotyping strategies for more effective genetic mapping and genome analysis. We have developed a high-throughput method for genotyping recombinant populations utilizing whole-genome resequencing data generated by the Illumina Genome Analyzer. A sliding window approach is designed to collectively examine genome-wide single nucleotide polymorphisms for genotype calling and recombination breakpoint determination. Using this method, we constructed a genetic map for 150 rice recombinant inbred lines with an expected genotype calling accuracy of 99.94% and a resolution of recombination breakpoints within an average of 40 kb. In comparison to the genetic map constructed with 287 PCR-based markers for the rice population, the sequencing-based method was approximately 20x faster in data collection and 35x more precise in recombination breakpoint determination. Using the sequencing-based genetic map, we located a quantitative trait locus of large effect on plant height in a 100-kb region containing the rice "green revolution" gene. Through computer simulation, we demonstrate that the method is robust for different types of mapping populations derived from organisms with variable quality of genome sequences and is feasible for organisms with large genome sizes and low polymorphisms. With continuous advances in sequencing technologies, this genome-based method may replace the conventional marker-based genotyping approach to provide a powerful tool for large-scale gene discovery and for addressing a wide range of biological questions.
| S-EPMC2694477 | biostudies-literature
Project description:BackgroundBovine chromosome (BTA) 15 contains a quantitative trait loci (QTL) for meat tenderness, as well as several breaks in synteny with human chromosome (HSA) 11. Both linkage and radiation hybrid (RH) maps of BTA 15 are available, but the linkage map lacks gene-specific markers needed to identify genes underlying the QTL, and the gene-rich RH map lacks associations with marker genotypes needed to define the QTL. Integrating the maps will provide information to further explore the QTL as well as refine the comparative map between BTA 15 and HSA 11. A recently developed approach to integrating linkage and RH maps uses both linkage and RH data to resolve a consensus marker order, rather than aligning independently constructed maps. Automated map construction procedures employing this maximum-likelihood approach were developed to integrate BTA RH and linkage data, and establish comparative positions of BTA 15 markers with HSA 11 homologs.ResultsThe integrated BTA 15 map represents 145 markers; 42 shared by both data sets, 36 unique to the linkage data and 67 unique to RH data. Sequence alignment yielded comparative positions for 77 bovine markers with homologs on HSA 11. The map covers approximately 32% of HSA 11 sequence in five segments of conserved synteny, another 15% of HSA 11 is shared with BTA 29. Bovine and human order are consistent in portions of the syntenic segments, but some rearrangement is apparent. Comparative positions of gene markers near the meat tenderness QTL indicate the region includes separate segments of HSA 11. The two microsatellite markers flanking the QTL peak are between defined syntenic segments.ConclusionsCombining data to construct an integrated map not only consolidates information from different sources onto a single map, but information contributed from each data set increases the accuracy of the map. Comparison of bovine maps with well annotated human sequence can provide useful information about genes near mapped bovine markers, but bovine gene order may be different than human. Procedures to connect genetic and physical mapping data, build integrated maps for livestock species, and connect those maps to more fully annotated sequence can be automated, facilitating the maintenance of up-to-date maps, and providing a valuable tool to further explore genetic variation in livestock.
| S-EPMC526187 | biostudies-literature
Project description:BackgroundThe recent availability of genomic sequences and BAC libraries for a large number of mammals provides an excellent opportunity for identifying comparatively-anchored markers that are useful for creating high-resolution radiation-hybrid (RH) and BAC-based comparative maps. To use these maps for multispecies genome comparison and evolutionary inference, robust bioinformatic tools are required for the identification of chromosomal regions shared between genomes and to localize the positions of evolutionary breakpoints that are the signatures of chromosomal rearrangements. Here we report an automated tool for the identification of homologous synteny blocks (HSBs) between genomes that tolerates errors common in RH comparative maps and can be used for automated whole-genome analysis of chromosome rearrangements that occur during evolution.FindingsWe developed an algorithm and software tool (SyntenyTracker) that can be used for automated definition of HSBs using pair-wise RH or gene-based comparative maps as input. To verify correct implementation of the underlying algorithm, SyntenyTracker was used to identify HSBs in the cattle and human genomes. Results demonstrated 96% agreement with HSBs defined manually using the same set of rules. A comparison of SyntenyTracker with the AutoGRAPH synteny tool was performed using identical datasets containing 14,380 genes with 1:1 orthology in human and mouse. Discrepancies between the results using the two tools and advantages of SyntenyTracker are reported.ConclusionSyntenyTracker was shown to be an efficient and accurate automated tool for defining HSBs using datasets that may contain minor errors resulting from limitations in map construction methodologies. The utility of SyntenyTracker will become more important for comparative genomics as the number of mapped and sequenced genomes increases.
| S-EPMC2726151 | biostudies-literature
Project description:The availability of genomic resources including linkage information for camelids has been very limited. Here, we describe the construction of a set of two radiation hybrid (RH) panels (5000RAD and 15000RAD) for the dromedary (Camelus dromedarius) as a permanent genetic resource for camel genome researchers worldwide. For the 5000RAD panel, a total of 245 female camel-hamster radiation hybrid clones were collected, of which 186 were screened with 44 custom designed marker loci distributed throughout camel genome. The overall mean retention frequency (RF) of the final set of 93 hybrids was 47.7%. For the 15000RAD panel, 238 male dromedary-hamster radiation hybrid clones were collected, of which 93 were tested using 44 PCR markers. The final set of 90 clones had a mean RF of 39.9%. This 15000RAD panel is an important high-resolution complement to the main 5000RAD panel and an indispensable tool for resolving complex genomic regions. This valuable genetic resource of dromedary RH panels is expected to be instrumental for constructing a high resolution camel genome map. Construction of the set of RH panels is essential step toward chromosome level reference quality genome assembly that is critical for advancing camelid genomics and the development of custom genomic tools.
| S-EPMC5792482 | biostudies-literature
Project description:The sorghum-sudangrass hybrid is a vital annual gramineous herbage. Few reports exist on its ultra-high-density genetic map. In this study, we sought to create an ultra-high-density genetic linkage map for this hybrid to strengthen its functional genomics research and genetic breeding. We used 150 sorghum-sudangrass hybrid F2 individuals and their parents (scattered ear sorghum and red hull sudangrass) for high-throughput sequencing on the basis of whole genome resequencing. In total, 1,180.66 Gb of data were collected. After identification, filtration for integrity, and partial segregation, over 5,656 single nucleotide polymorphism markers of high quality were detected. An ultra-high-density genetic linkage map was constructed using these data. The markers covered approximately 2,192.84 cM of the map with average marker intervals of 0.39 cM. The length ranged from 115.39 cM to 264.04 cM for the 10 linkage groups. Currently, this represents the first genetic linkage map of this size, number of molecular markers, density, and coverage for sorghum-sudangrass hybrid. The findings of this study provide valuable genome-level information on species evolution and comparative genomics analysis and lay the foundation for further research on quantitative trait loci fine mapping and gene cloning and marker-assisted breeding of important traits in sorghum-sudangrass hybrids.
| S-EPMC9707794 | biostudies-literature
Project description:BACKGROUND: Orange-spotted grouper, Epinephelus coioides, is one of the most valuable fish species in China. Commercial production of orange-spotted grouper could be increased by developing higher growth rates and improving commercially important traits. Information on genetic markers associated with quantitative trait loci (QTL) can be used in breeding programs to identify and select individuals carrying desired traits. A high-density genetic linkage map is the basis for QTL study, and multiplexed shotgun genotyping (MSG) facilitates the development of single nucleotide polymorphisms (SNPs) and genotyping. In this study, the first high-density genetic linkage maps for groupers were generated on the basis of the MSG method. RESULTS: The sex-averaged map contained a total of 4,608 SNPs, which spanned 1581.7 cM, with a mean distance between SNPs of 0.34 cM. The 4,608 SNPs were located in 2,849 unique locations on the linkage map, with an average inter-location space at 0.56 cM. There were 2,516 SNPs on the female map, and the number of unique locus was 1,902. However, the male map contained more numbers of SNP (2,939) and unique locations (2,005). The total length of the female and male maps was 1,370.9 and 1,335.5 cM, respectively. CONCLUSIONS: The high-resolution genetic linkage maps will be very useful for QTL analyses and marker-assisted selection (MAS) for economically important traits in molecular breeding of the orange-spotted grouper.
| S-EPMC3890575 | biostudies-literature
Project description:Radiation hybrid (RH) mapping is limited by the inherent genomic instability of RH clones entailing both, limited DNA sample amounts and genomic heterogeneity of the clones. Here the instability of RH clones is quantified and the suitability of the multiple strand displacement whole genome amplification method (WGA) for radiation hybrid mapping is assessed. To quantify the instability of RH clones, eleven clones of a 10,000(Rad) rhesus macaque radiation hybrid panel were passaged ten times and analyzed by interspersed repeat sequence specific quantitative PCR and by genotyping of 46 macaque chromosome 5 STS markers. The quantitative PCR data indicate an average loss of 55% of the donor DNA over 10 passages. Over the same period, a dropout of 46.2% of the STS markers was observed. These data indicate a genome wide half-life of the donor DNA of 8.7 passages and of 10.6 passages for the chromosome 5 markers. The genotyping data of the genomic RH DNA were compared to three sets of WGA experiments: 1) single wgaDNA amplifications, 2) six WGA replicates, and 3) re-amplification of wga DNA. The assays demonstrated concordance rates of 97.6%, 98% and 99.3%, respectively, and indicated the marker specificity of some repeated WGA dropouts. The study confirms that WGA is suitable for RH mapping studies should enable the accurate analysis of almost an infinite numbers of markers. WGA will allow the analysis of earliest RH clone passages, thus limiting their heterogeneity and RH mapping artifacts.
| S-EPMC4706074 | biostudies-literature