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Your search keyword '"Karen S. Aitken"' showing total 2 results
Start Over Author "Karen S. Aitken" Journal bmc genomics
2 results on '"Karen S. Aitken"'

1. A linkage disequilibrium-based approach to position unmapped SNPs in crop species

Author

Seema Yadav, Elizabeth M. Ross, Karen S. Aitken, Lee T. Hickey, Owen Powell, Xianming Wei, Kai P. Voss-Fels, and Ben J. Hayes

Subjects
Genetic map, Linkage disequilibrium, Single nucleotide polymorphism, Biotechnology, TP248.13-248.65, Genetics, QH426-470
Abstract

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.

Published
2021
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2. A comprehensive genetic map of sugarcane that provides enhanced map coverage and integrates high-throughput Diversity Array Technology (DArT) markers

Author

Meredith D. McNeil, Peter C Bundock, Jingchuan Li, Scott Hermann, Katarzyna Heller-Uszynska, Andrzej Kilian, Robert J Henry, and Karen S. Aitken

Subjects
Genetic Markers, Polyploid, Genetic mapping, Polymorphism, Single Nucleotide, Genome, SNP markers, Saccharum officinarum, Gene mapping, Genetic variation, Genetics, Amplified Fragment Length Polymorphism Analysis, biology, DArT sugarcane array, Chromosome Mapping, Genetic Variation, food and beverages, Chromosome, biology.organism_classification, Saccharum, Genetic marker, Evolutionary biology, Amplified fragment length polymorphism, Restriction fragment length polymorphism, Genome, Plant, Research Article, Microsatellite Repeats, Biotechnology
Abstract

Background Sugarcane genetic mapping has lagged behind other crops due to its complex autopolyploid genome structure. Modern sugarcane cultivars have from 110-120 chromosomes and are in general interspecific hybrids between two species with different basic chromosome numbers: Saccharum officinarum (2n = 80) with a basic chromosome number of 10 and S. spontaneum (2n = 40-128) with a basic chromosome number of 8. The first maps that were constructed utilised the single dose (SD) markers generated using RFLP, more recent maps generated using AFLP and SSRs provided at most 60% genome coverage. Diversity Array Technology (DArT) markers are high throughput allowing greater numbers of markers to be generated. Results Progeny from a cross between a sugarcane variety Q165 and a S. officinarum accession IJ76-514 were used to generate 2467 SD markers. A genetic map of Q165 was generated containing 2267 markers, These markers formed 160 linkage groups (LGs) of which 147 could be placed using allelic information into the eight basic homology groups (HGs) of sugarcane. The HGs contained from 13 to 23 LGs and from 204 to 475 markers with a total map length of 9774.4 cM and an average density of one marker every 4.3 cM. Each homology group contained on average 280 markers of which 43% were DArT markers 31% AFLP, 16% SSRs and 6% SNP markers. The multi-allelic SSR and SNP markers were used to place the LGs into HGs. Conclusions The DArT array has allowed us to generate and map a larger number of markers than ever before and consequently to map a larger portion of the sugarcane genome. This larger number of markers has enabled 92% of the LGs to be placed into the 8 HGs that represent the basic chromosome number of the ancestral species, S. spontaneum. There were two HGs (HG2 and 8) that contained larger numbers of LGs verifying the alignment of two sets of S. officinarum chromosomes with one set of S. spontaneum chromosomes and explaining the difference in basic chromosome number between the two ancestral species. There was also evidence of more complex structural differences between the two ancestral species. Electronic supplementary material The online version of this article (doi:10.1186/1471-2164-15-152) contains supplementary material, which is available to authorized users.

Published
2014
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