from Dave Matthews, 3/16/94 [Actually there is no template for QTL data yet. But here's a start on it, an answer to a potential donor's question about submitting just the scores from a QTL study, as opposed to the QTL analysis and results.] > we have 5 location X years ... four datapoints per entry x location x year. For this kind of data the basic record type in GrainGenes is the 'Trait_scores'. The first Trait_scores example below, "Sprouting at Caldwell 1990" shows how this is used to present the mean scores for all entries at one Environment. (An Environment is one location x year.) The second example, "Sprouting averaged", shows how to present an average over all Environments if you want to do that. If you want to load each of your four datapoints separately instead of the mean score at each Environment, you could make four Trait_scores objects, "Dormancy at Environment 1, Replicate 1", "Dormancy at Environment 1, Replicate 2", etc. In addition, four other record types are needed: - an Environment record for each of the five Environments, - a Germplasm record for each parent, - a Map record giving the segregation of molecular markers for these entries, in the same order as listed in your Trait_scores records, - one Trait_Study object, e.g. "Dormancy, Blake94", which points to all your Trait_scores records and gives additional information about the study as a whole. Examples are below. Note that these records all point to each other by name, e.g. Trait_Study to Map (under the field Mapping_data), Map to Germplasm (under the fields Female_parent and Male_parent). If some of the information is already in the database, you don't need to put it in again, just make your pointers to the correct names. E.g. if this is for the Steptoe x Morex population, just enter "Barley, SxM" in the Mapping_data field. These examples don't encompass all the options you have, so don't let them stifle your creativity. First, I can add more fields if you have data that aren't accommodatable yet. Second, there are already more fields available than are shown in these examples, expecially for the Environment, Germplasm, and Trait_scores record types. To see the full list of fields for all record types, consult the Gopher "GrainGenes administrative information" / "Current GrainGenes models.wrm file". :::::::: Trait_scores : "Sprouting at Caldwell 1990" Environment "Caldwell 1990" Comment "Scores standardized to mean of 1.0. In order of genotypes" Scores "0.920 1.025 1.030 0.655 1.040 1.485 1.560 0.115 0.420 0.340 1.050 \ 1.995 0.370 0.605 1.260 1.055 1.650 1.705 0.980 0.345 1.395 1.055 0.655 \ 1.050 1.365 0.915 0.865 0.655 0.290 0.600 1.400 1.850 0.715 1.480 1.710 \ 0.340 0.285 1.165 0.320 0.885 1.480 0.295 0.430 1.390 1.890 0.320 1.650 \ 0.030 0.310 1.450 1.595 1.420 0.825 1.075 1.595 0.530 1.455 1.320 0.400 \ 1.225 0.910 0.385 0.625 2.020 0.275 0.630 0.425 0.460 0.910 0.855 1.215 \ 1.055 1.115 1.680 0.500 1.340 1.520 0.635" Trait_scores : "Sprouting averaged" Trait_study "Sprouting, Anderson93" Environment "Caldwell 1990" Environment "Helfer 1990" Environment "Ketola 1990" Environment "Caldwell 1991" Environment "Ketola 1991" Environment "Snyder 1991" Comment "Scores standardized to mean of 1.0, then averaged over all \ environments. In order of genotypes" Scores "0.9434 0.9692 0.892 0.6857 0.9945 1.1717 1.5199 0.4634 0.4871 0.6886 \ 0.9848 1.7353 0.7325 0.9905 0.8532 0.8885 0.9065 1.0787 1.0443 0.8375 \ 1.3833 1.0403 0.8206 0.6021 1.5345 0.7449 0.7669 0.5157 0.3115 0.7711 \ 1.201 1.6234 0.9171 1.2002 1.5592 0.3814 0.4892 1.1173 0.3839 0.9247 1.447 \ 0.4568 0.9076 1.2542 1.8675 0.2711 1.6361 0.4655 0.4989 1.1075 1.3798 \ 1.5909 0.7322 0.7058 1.5801 0.6386 1.6116 0.9853 0.7341 1.5147 1.2959 \ 0.3746 1.239 1.4953 0.7925 0.6977 0.6114 0.9855 0.9772 0.6931 1.3452 \ 0.9639 1.1036 1.509 0.4715 1.1107 0.926 0.6978" Environment : "Caldwell 1990" Year 1990 Location "Caldwell Farm, Ithaca, NY, USA" Experimental_design RCB Replications 3 Germplasm : "NY6432-18" Species "T. aestivum" Market_class "White Winter" Pedigree "Heine's VII /2/ Arthur Sib / Talbot" Map : "Wheat sprouting markers" Genetic Species "T. aestivum" Female_parent "NY6432-18" Male_parent "Clark's Cream" Map_units "cM, Haldane" Reference "CRS-33-453" Contact "Anderson, James A." Contact "Sorrells, Mark E." Remarks "78 F5-derived recombinant inbred lines. Evaluation based on a bulk \ of 5 to 10 plants per line. Clones were chosen from a wheat chromosomal arm \ map to sample all chromosome arms. Additional clones, not previously located \ to chromosome arm, were utilized to give 195 clones surveyed for polymorphism \ with 4 restriction enzymes. RI lines were probed with 37 of the polymorphic \ clones." gMap "Ta-Anderson-1A" 45 gMap "Ta-Anderson-2" 10 Locus WG180 313331333310113313311133330113113131133331111113311133333113333131311333331331 Locus BCD98 303111113110313111331131310311311011113111311030311110131311310111313101331131 ... Trait_Study : "Sprouting, Anderson93" Trait "Wheat sprouting" Reference "CRS-33-453" Protocol "Five physiologically mature spikes examined under artificial \ rainfall rated on 0 to 9 scale for degree of sprouting. Data was transformed \ so that all genotypes harvested from the same environment on the same day \ were equalized to an average of 1.0. Lower numbers indicate more resistance \ to preharvest sprouting." Parental_description "NY6432-18" "Moderate resistance" Parental_description "Clark's Cream" "High resistance" Parental_Mean_SD "NY6432-18" 0.89 0.40 Parental_Mean_SD "Clark's Cream" 0.38 0.21 Mapping_data "Wheat sprouting markers" Population_size 78 Population_type "F5-derived recombinant inbred lines" QTL_analysis_method "Single-factor ANOVA" Statistics "Population mean 0.97" Statistics "C.V. = 22.6 Statistics "LSD (0.05) = 0.61" Statistics "Experimental error mean square = 0.1448" Statistics "ANOVA for RI lines: Statistics " df = 77 Statistics " mean square = 2.71 Statistics " Prob. < 0.001 Statistics "ANOVA for RI lines x Env. interaction: Statistics " df = 385 Statistics " mean square = 0.43 Statistics " Prob. < 0.001 Heritability 0.84 "line mean basis" Heritability 0.35 "per plot basis" Type_I_error_rate_per_locus 0.05 Number_of_markers_tested 37 QTLs_found 4 Phenotypic_R2 0.37 Genetic_R2 0.44 R2_definition "R-squared is the proportion of the total phenotypic or genetic \ variance explained by a multiple regression model containing the significant \ QTL and their interactions." QTL "Sprouting 1" QTL "Sprouting 2" QTL "Sprouting 3" QTL "Sprouting 4" Trait_scores "Sprouting at Caldwell 1990" Trait_scores "Sprouting at Helfer 1990" Trait_scores "Sprouting at Ketola 1990" Trait_scores "Sprouting at Caldwell 1991" Trait_scores "Sprouting at Ketola 1991" Trait_scores "Sprouting at Snyder 1991"