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Title: Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation

item WARD, JUDSON - Cornell University
item BHANGOO, JASBIR - Sector 18
item MOORE, PATRICK - Washington State University Extension Service
item SWANSON, J - Salve Regina University
item VIOLA, ROBERTO - Iasma Research Center
item VELASCO, RICARDO - Iasma Research Center
item Bassil, Nahla
item WEBER, COURTNEY - Cornell University
item SARGENT, DANIEL - Iasma Research Center

Submitted to: BMC Genomics
Publication Type: Peer Reviewed Journal
Publication Acceptance Date: 12/4/2012
Publication Date: 1/16/2013
Citation: Ward, J.A., Bhangoo, J., Fernandez-Fernandez, F., Moore, P., Swanson, J.D., Viola, R., Velasco, R., Bassil, N.V., Weber, C.A., Sargent, D.J. 2013. Saturated linkage map construction in Rubus idaeus using genotyping by sequencing and genome-independent imputation. Biomed Central (BMC) Genomics. 14:2 DOI:10.1186/1471-2164-14-2.

Interpretive Summary: New DNA marker technologies have developed and are very useful to fill genetic maps in crops. One of these techniques, Genotyping by sequencing (GBS) was used to produce a high density DNA map for red raspberry. Certain regions of the map had a low coverage and many missing poitns. However, a new method of interpreting and replacing missing data overcame this challenge, and enabled construction of more complete maps. The two resulting parental maps contained over 2300 molecular markers for the seven red raspberry chromosomes. GBS together with genome-independent interpretation for replacement of missing data provided a rapid method for genetic map construction in raspberries and can be applied to other crops.

Technical Abstract: Rapid 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. Genotyping 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. GBS 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.