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 imputation require a reference genome and thus are not an option for most species.ResultsGenotyping by Sequencing (GBS) was used to produce highly saturated maps for a R. idaeus pseudo-testcross progeny. While low coverage and high variance in sequencing resulted in a large number of missing values for some individuals, a novel method of imputation based on maximum likelihood marker ordering from initial marker segregation overcame the challenge of missing values, and made map construction computationally tractable. The two resulting parental maps contained 4521 and 2391 molecular markers spanning 462.7 and 376.6 cM respectively over seven linkage groups. Detection of precise genomic regions with segregation distortion was possible because of map saturation. Microsatellites (SSRs) linked these results to published maps for cross-validation and map comparison.ConclusionsGBS together with genome-independent imputation provides a rapid method for genetic map construction in any pseudo-testcross progeny. Our method of imputation estimates the correct genotype call of missing values and corrects genotyping errors that lead to inflated map size and reduced precision in marker placement. Comparison of SSRs to published R. idaeus maps showed that the linkage maps constructed with GBS and our method of imputation were robust, and marker positioning reliable. The high marker density allowed identification of genomic regions with segregation distortion in R. idaeus, which may help to identify deleterious alleles that are the basis of inbreeding depression in the species.

Genome-wide SNP discovery and genetic linkage map construction in sunflower (Helianthus annuus L.) using a genotyping by sequencing (GBS) approach

“…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).…”

“…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…”

“…To date, the GBS approach has been popular and applied to many plant species for SNP discovery and genotyping. These species include barley (Elshire et al 2011), Miscanthus sinensis (Ma et al 2012), Rubus idaeus (Ward et al 2013) and maize (Romay et al 2013). Also GBS was applied in an F 2 population of oil palm to identify 21,471 SNPs and to construct a linkage map containing 1085 SNPs (Pootakham et al 2015).…”

Breeding rootstocks for Prunus species: Advances in genetic and genomics of peach and cherry as a model

“…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).…”

Characterizing Uncertainty in High-Density Maps from Multiparental Populations

“…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).…”