The OWB population – how big is it?
Patrick Hayes, Victoria Carollo-Blake, Yada Chutimanitsakun, Luis Cistue, Alfonso Cuesta-Marcos, Andreas Graner, and Kazuhiro Sato
The original set of OWB lines, used for construction of a linkage map by Costa et al. 2001, consists of 94 doubled haploid (DH) lines. The DH lines are numbered consecutively 1 – 94.
The OWB mapping population used by Szucs et al. (2009) and Close et al. (2009) consists of 93 DH lines due to a DNA quality and quantity issue leading to the removal of DH # 12 . In the n = 93 map data file on GrainGenes (http://wheat.pw.usda.gov/ggpages/maps/OWB/ - “OWB OPA 2008 mapdata”), DH # 12 is missing and the DH lines are numbered 1 - 11 and 13 - 94.
The OWB mapping population used by Chutimanitsakun et al. (submitted, 2010) consists of 82 DH lines. Eleven lines were dropped because we identified nine sets of identical lines. Specifically, the following sets of lines are identical: set 1 = DH 1, 4, 27, 62; set 2 = DH 16, 71; set 3 = DH 5, 18; set 4 = DH 31, 58; set 5 = 35, 50; set 6 = DH 15, 47; set 7 = DH 61, 88; set 8 = DH 22, 70; set 9 = DH 80, 77. One representative was kept from each set and DH #1, 5, 15, 22, 27, 50, 58, 62, 71, 80 and 88 were removed. Removing these lines, along with DH 12, leads to a population size of n = 82.
The members of each set were not identified as identical in previous iterations of the map (e.g. Costa et al. , 2001) because they were different from one another at multiple loci. These loci have been progressively removed from the data set based on quality control criteria. In other words, the lines were thought to be similar but not identical but the differences were due to scoring errors. The lines within each set are identical for all the Illumina SNPs and other loci included in the Szűcs et al. (2009) map. The lines within each set are also identical for all RAD loci reported by Chutimanitsakun et al. (submitted 2010). The most likely explanation for the presence of these identical sets of lines is that multiple haploids were inadvertently advanced from callus regenerated from a single embryo. These haploids were successfully doubled and advanced.
Using the 2383 locus data set, we empirically determined the effects of the duplicated lines on map construction and QTL analysis by comparing results of analyses based on n = 82 and n = 93. As shown in Table 1, map lengths with the n = 82 and n = 93 populations are comparable. There were no changes in locus order between maps. Estimates of QTL number, location and effect are comparable. The results from n = 93 are shown in Table 2, and these can be compared to n = 82 as reported in Chutimanitsakun et al. (submitted, 2010).
Henceforth, we will distribute the set of 82 lines, and the two parents. For future reference, this set of lines will be referred to as OWB_Hb_82. H.b. refers to the Hordeum bulbosum – the method of doubled haploid production. This nomenclature involving method of doubled haploid production is necessary due to the development of additional set of 93 DH lines by anther culture.
Cistue et al. (submitted 2010) reported the development and mapping of an additional 93 OWB DH lines. These lines, developed by anther culture (A.C.), are numbered starting with 801 and ending with 914. The numbering is non-consecutive, due to removal of numbered plants due to sterility, poor seed production, and/or insufficient DNA for genotyping. For future reference, this set of lines will be referred to as OWB_A.C. _93. As reported by Cistue et al. (submitted 2010) the H.b. and A.C. linkage maps (built with BOPA 1 and 2 SNPs only) are quite similar, and the two data sets can be seamlessly integrated. There are no duplicate lines in the A.C. data set.
Therefore, we are confident that the presence of the duplicated lines in the H.b. lines has not compromised prior analyses, and we are pleased to offer the research community an additional 93 genotyped lines.
Seed sets of the OWB_A.C._93 and OWB_H.b._82 will be available from: Oregon State University (Corvallis, Oregon, USA), the Leibniz Institute of Plant Genetics and Crop Plant Research (IPK) (Gatersleben, Germany), and the Barley Germplasm Center, Resource Institute for Bioresources (Kurashiki, Japan). Please see http://barleyworld.org/oregonwolfebarleys/gettingseeds.php for ordering procedures. When ordering, please be sure to specify which seed sets are desired (e.g. OWB_H.b._82, OWB_A.C._93, or and OWB_H.b._82 + OWB_A.C._93).
Genotype and phenotype data sets are available for the H.b and A.C. “subpopulations”, and the full population, from GrainGenes (http://wheat.pw.usda.gov/ggpages/maps/OWB/). For further information, please contact:
Dr. Patrick Hayes
Crop Science Bldg.
3050 Campus Way
Oregon State University
Corvallis, OR 97331 USA
Costa, J.M., S. Kramer, C. Jobet, R. Wolfe, A. Kleinhofs, D. Kudrna, A. Corey, S. McCoy, O. Riera-Lizarazu, K. Sato, T. Toojinda, I. Vales, P. Szucs, and P. M. Hayes. 2001. Molecular mapping of the Oregon Wolfe Barleys: an exceptionally polymorphic doubled-haploid population. Theor. Appl. Genet.103:415-424.
Chutimanitsakun, Y., R.W. Nipper, A. Cuesta-Marcos, E.A. Johnson, and P.M. Hayes. Submitted. Construction and application of a Restriction Site Associated DNA (RAD) linkage map in barley. BMC Genomics
Cistué, L., S. Chao, Y. Chutimanitsakun, A. Corey, A. Cuesta-Marcos, B. Echávarri , T. Filichkina, N. Garcia-Mariño, I. Romagosa and P.M. Hayes. Submitted. Comparative mapping of the Oregon Wolfe Barley using doubled haploid lines derived from female and male gametes. Theor. Appl. Genet.
Close, T.J., P. R. Bhat, S. Lonardi, Y. Wu, N. Rostoks, L.Ramsay, A. Druka, N.Stein, J.T Svensson, S. Wanamaker, S. Bozdag , M. L. Roose, M.J. Moscou, S. Chao, R.Varshney, P. Szucs , K. Sato, P. M. Hayes , D. E. Matthews , A. Kleinhofs , G. J. Muehlbauer , J. DeYoung , D. F. Marshall, K. Madishetty, R. D .Fenton, P. Condamine, A. Graner and R. Waugh. 2009. Development and implementation of high-throughput SNP genotyping in barley. BMC Genomics 10:582doi:10.1186/1471-2164-10-582
Szűcs, P., V. Blake, P.R. Bhat, S. Chao, T.J. Close, A. Cuesta-Marcos, G.J. Muehlbauer, L. Ramsay, R. Waugh, and P. M. Hayes. 2009. An integrated resource for barley linkage map and malting quality QTL alignment. The Plant Genome. 2:134-140.