2013
DOI: 10.1186/1471-2164-14-2
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Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation

Abstract: BackgroundRapid development of highly saturated genetic maps aids molecular breeding, which can accelerate gain per breeding cycle in woody perennial plants such as Rubus idaeus (red raspberry). Recently, robust genotyping methods based on high-throughput sequencing were developed, which provide high marker density, but result in some genotype errors and a large number of missing genotype values. Imputation can reduce the number of missing values and can correct genotyping errors, but current methods of imputa… Show more

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Cited by 170 publications
(192 citation statements)
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“…Although the numbers of sequence reads and percentages of uniquely aligned reads were variable in previous work, comparison indicates that the sunflower GBS performed in this study was efficient in terms of read number. For example, total reads of Rubus idaeus generated by GBS (135,776,036) (Ward et al 2013) were lower than those we obtained for sunflower. In addition, the percentage of reads that passed filtration and uniquely aligned to the genome in our study (29.2 %) was higher than for GBS analysis of Miscanthus sinensis (23 %) for which many more reads were obtained (415,694,046) (Ma et al 2012).…”
Section: Gbs and Snp Identificationcontrasting
confidence: 43%
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“…Although the numbers of sequence reads and percentages of uniquely aligned reads were variable in previous work, comparison indicates that the sunflower GBS performed in this study was efficient in terms of read number. For example, total reads of Rubus idaeus generated by GBS (135,776,036) (Ward et al 2013) were lower than those we obtained for sunflower. In addition, the percentage of reads that passed filtration and uniquely aligned to the genome in our study (29.2 %) was higher than for GBS analysis of Miscanthus sinensis (23 %) for which many more reads were obtained (415,694,046) (Ma et al 2012).…”
Section: Gbs and Snp Identificationcontrasting
confidence: 43%
“…Differences in read numbers among studies can be due to the number of individuals used in GBS and/or technical performance of the sequencing chemistry. GBS of Miscanthus sinensis used 192 individuals (Ma et al 2012) while our study and that of Rubus idaeus (Ward et al 2013) used 95 individuals. In another study, GBS analysis of an oil palm F 2 population consisting of 108 individuals generated a much higher LG 1 212 86 2.47…”
Section: Gbs and Snp Identificationmentioning
confidence: 99%
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“…A number of methods to identify SNPs have been described (Ganal et al, 2009): by searching expressed sequence tag (EST) databases (Batley et al, 2003), amplicon re-sequencing (Choi et al, 2007), complete sequence of a genome (Velasco et al, 2007), and more recently, high throughput sequencing technology (Barbazuk et al, 2007). Advances in next-generation techniques have reduced the cost of DNA sequencing to the point where it is now feasible to perform genotypingby-sequencing (GBS) to analyze small-and large-sized genomes with high diversity and allow the identification of thousands of markers for a species (Elshire et al, 2011;Poland et al, 2012;Ward et al, 2013;Guajardo et al, 2015). Future applications of GBS in genetic improvement will allow breeders to perform genomic selection of new germplasm or species without having to first develop a molecular tool, which is needed with other types of molecular markers; it will also allow conservation biologists to determine population structure without needing previous knowledge of the genome or diversity of the species under study (Elshire et al, 2011).…”
Section: Molecular Markersmentioning
confidence: 99%
“…For humans and many other species, high-density consensus maps have been published and used across multiple mapping studies (Murray et al 1994;Dietrich et al 1996;Chowdhary and Raudsepp 2006;Bult et al 2008;Cox et al 2009;Wong et al 2010). However, efforts to increase the saturation of genetic maps with high-throughput genotyping are still being made in many plant species (Poland et al 2012;Ward et al 2013;Wang et al 2014).…”
mentioning
confidence: 99%