Glossary of Terms

Glossary Term	Definition
Accession	Accessions are germplasm for genotyping.
BLUE	Best Linear Unbiased Estimator
BLUP	Best Linear Unbiased Predictor
Breeding Management System (BMS)	The Breeding Management System (BMS) is an information management system developed by the Integrated Breeding Platform to help breeders manage the breeding process, from project planning to decision-making.
Breeding View	Breeding View is the Breeding Management System’s (BMS) field trial and QTL statistical analysis tool.  Breeding View is integrated with your project database, allowing data selected within the Workbench to move seamlessly to field trial analysis.  Breeding View can also operate as a standalone application for the analysis of data stored outside the project database and for QTL (quantitative trait loci) identification.
Breeding View (BV)	Breeding View (BV) is the Breeding Management System’s statistical analysis tool. BV can perform phenotypic data analyses and identify quantitative trait loci (QTL).
Checks	Checks are control germplasm with known phenotypes.  Checks are included in field designs because deviations from previously characterized phenotypes may indicate confounding environmental factors.
Diplotype	Diplotype is the phased genotype of a diploid organism.
DMS	See Study Data Management System (DMS)
Double Haploid (DH)	Double haploids are homozygous at all loci. Double haploid zygotes are created when a gamete is induced to double its genome.
Factor	A factor is a controlled independent variable.  Factors can include blocking factors and treatments with levels.
Field Map	Field maps describe the planting layout for fields and nurseries.
Flapjack	Flapjack is a tool for graphical genotyping and haplotype visualization.
G X E Interaction	Genotype by environment (G x E) interaction can be calculated when phenotype is measured in multiple environments.
Genotype	Genotype is a genetic signature.  Genotype can refer to DNA or marker-based information, but can also refer to other genetic grouping, like germplasm identifiers and pedigree-based family groupings.
Germplasm ID (GID)	Germplasm ID (GID) is a unique numeric identifier assigned to all germplasm in public crop databases.
GMS	See Genealogy Management System (GMS)
Integrated Breeding Platform	[The Integrated Breeding Platform (http://www.integratedbreeding.net) connects registered users access to Breeding Management System software, comprehensive technical support, and training resources.
Haplotype	Haplotype is the phased genotype of a haploid or the gamete of diploid organism.
Ideotype	Ideotype is the target genotype that represents the end goal of marker assisted selection (MAS).
Inbred Line	An inbreed line contains individuals with similar genotypes and high levels of homozygosity.  Inbreed lines can be created by self-pollination or through crosses between close relatives.
Incomplete Block Design	An incomplete block design contains blocks with only a subset of the treatments.
Marker-Assisted Backcross Breeding (MABC)	Marker-assisted backcross (MABC) uses molecular markers to track the introgression of a few favourable alleles, such as for disease resistance, from a donor parent into a recurrent parent that has otherwise favourable genetics. Markers spread throughout the donor parent’s genome are also used to select against the unfavourable donor genome.
Marker-Assisted Gene Pyramiding	Marker-assisted gene pyramiding uses molecular markers to track and predict the transmission of desired genes from multiple individuals into offspring containing all genes of interest.
Marker-Assisted Recurrent Selection (MARS)	Marker-assisted recurrent selection (MARS) begins by associating phenotypic variance in a population of interest to quantitative trait loci (QTL).  Once QTL are identified, linked genetic markers can be used to inform and speed the process of selecting the best individuals, and recombining these selected individuals to form the next generation or cycle of selection.
Marker-Assisted Selection (MAS)	Marker-assisted selection (MAS) is the use of genetic markers inform selections. In contrast to phenotypic selection, markers linked to a trait of interest are selected. MAS has the potential to speed the breeding process by increasing the frequency of favourable alleles and decreasing the frequency of unfavourable alleles in breeding populations.
Molecular Breeding Planner	The Molecular Breeding Planner, also known as the Breeding Planner, develops breeding schemes, including timelines and optimal population sizes, to improve the efficiency of genetic gains using genetic markers.
Molecular Markers	Molecular markers are DNA sequences that can be used to differentiate individuals, families, and populations.
Multiparental Population	A multiparental population can trace a pedigree back to multiple parents.
Multi-Site Analysis	See GxE
Ontology	The Breeding Management System’s crop ontology management tool uses a structured vocabulary to allow descriptors to act as variables in database queries and statistical analyses.
Polymorphic Markers	Markers differing between germplasm.
Quantitative Trait Loci (QTL)	Quantitative trait loci (QTL) are genomic regions that contribute to the expression of quantitative traits.
Randomized Complete Block Design	A randomized block design fully replicates all germplasm, or treatments, in grouped homogeneous blocks.  Location is often a blocking factor.
Recombinant Inbred Line (RIL)	A recombinant inbreed line (RIL) is created by numerous cycle of selfing and single seed descent. Individual members of RIL populations are fixed, or homozygous, at almost all loci. Adequately sized RIL populations contain almost all of the parental genetic diversity and recombinants.
Row-Column Design	A row-column design can be used when two environmental gradients are expected to influence phenotypes between rows and columns in a field trial.  Soil, irrigation, and elevation gradients can all be expected to introduce error in phenotypic measure.  Row-Column designs, like Latin Square designs, can reduce the error introduced to phenotypic measurements by bidirectional field gradients.
Single Site Analysis Pipeline	The single site analysis pipeline in Breeding View can be used to analyze phenotypic data from single sites when no blocking is for location or year.
Workbench	The Workbench is the Breeding Management System (BMS) user interface, and can launch all breeding tools and access associated crop databases. The Dashboard of the Workbench is where new project databases can be created and previously started project databases browsed and opened.