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Definition
| Incomplete dominance where the heterozygote has a phenotype in the exact middle between each homozygote. |
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Definition
| Affect quantitative traits due to the average per copy effects of alleles in genetic loci. |
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Definition
| Calculated by adding the proportion of homozygotes to half the proportion of heterozygotes. All allele frequencies should add up to one. Remain the same after a generation of random mating. |
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Definition
| Cultivars are genetically identical clones. |
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Term
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Definition
| An examination of a genome-wide set of variants in different individuals to see if any variant is associated with a trait. Requires genetic markers, phenotypic trait data, a diverse and large population of individuals, and analysis of population structure. May be applied in humans, animals, plants, and others. Detecting associations can depend on the population structure; larger number of markers are required. If population structure is not taken into account, it can lead to false marker associations. Uses thousands of SNPs to identify differences in the phenotypic trait of an individual. Uses the locations of SNP markers where individuals possessing the desired trait have a different allele frequency than those without the desired trait. All SNPs across the entire genome are plotted in a Manhattan plot. Has immediate applications in plant breeding (marker assisted selection). |
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Definition
| A dominance effect. The heterozygote has an equal phenotype to one of the homozygotes. |
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Term
| Compressed mixed linear model (CMLM) |
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Definition
| A method used by GAPIT software. |
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Definition
| Sexually reproducing species. Cultivars may be a hybrid, synthetic, or other levels of open pollination. Allele and genotype frequencies tend to stay stable over time, with both homozygotes and heterozygotes. |
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Definition
| Result from only one generation of meiosis. Help to preserve linkage. |
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Term
| Efficient mixed model association (EMMA) |
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Definition
| A method used by GAPIT software. |
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Term
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Definition
| Affect quantitative traits. Associated with two or more alleles at two or more loci. Expression of a gene at one locus affects the phenotypic expression of another locus. |
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Definition
| Food is a human right: "The right for people to feed themselves in dignity". The availability of sufficient food. People must have the means to access food that meets the individual's dietary needs. Plant breeding is involved with food security. |
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Term
| Genome association prediction integrated tool (GAPIT) |
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Definition
| A software tool that uses EMMA, CMLM, and P3D. Operated in R. Uses 6 libraries from R. Produces outputs in two formats: csv files for tabular results and pdf files for graphics. |
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Term
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Definition
| A format for inputting data into GAPIT software. A common format for genetic data. |
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Term
| Hardy-Weinberg equilibrium |
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Definition
In 1908, G.H. Hardy, a British mathematician, and W. Weinberg, a German physician, independently deduced the relationship between allele frequencies and genotype frequencies under random mating. Allele and genotype frequencies remain constant. The square of the array of allele frequencies is equal to the array of genotype frequencies.
(p + g)2 = p2 + 2pq + q2
(p1 + p2 + p3)2 = p12 + 2p1p2 + 2p1p3 + p22 + 2p2p3 + p32 |
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Term
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Definition
| Results in increased frequency of recombination. |
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Term
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Definition
| A dominance effect. Includes additive, partial, and over-dominance. |
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Definition
| Affect quantitative traits. Associated with pairs of alleles at the same locus. Includes complete and incomplete dominance. |
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Term
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Definition
| When the loci are on different chromosomes. 50% recombination is considered unlinked. |
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Term
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Definition
| The sister software to MapQTL. Creates genetic linkage maps for diploid species and experimental populations, which can be inputted into MapQTL. |
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Definition
| Can be generated by GAPIT as a heatmap. May be imported as a table into GAPIT. |
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Term
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Definition
Gamete disequilibrium
When loci are on the same chromosome. Non-random association of alleles at two or more loci that descend from a single ancestral chromosome. Each generation of meiosis provides opportunities for chromosomal crossovers and therefore disruption of linkage. Each gene independently is at Hardy-Weinberg equilibrium. Can have independent assortment if the loci are far enough apart for recombination to occur frequently enough (50%). Includes coupling linkage and repulsion linkage. May be advantageous or disadvantageous to breeders. After t generations of random mating:
D = p(A1B1) - (p(A1)p(B1)) = ((1 - r)t)(D0) |
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Term
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Definition
| A plot used in association mapping where SNPs across the entire genome are plotted against the negative logarithm of the association p-value. Chromosomes are along the X axis, and the Y axis is the log of the p-value. Areas with peaks likely have association in that area of the genome. The log threshold value is plotted as a line on the Y-axis; anything above the threshold is considered to have an association with the trait. |
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Term
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Definition
| Software created for mapping QTLs. A sister software to Joinmap. Requires linkage maps from a Joinmap linkage genotype file to identify QTL positions. |
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Term
| Marker assisted selection (MAS) |
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Definition
| Allows for identification of superior individuals based on genotype. Can lead to the identification of genes responsible for agronomic traits. Uses marker data from association mapping. |
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Term
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Definition
| Incomplete dominance where the heterozygote has a phenotype that surpasses both homozygotes. |
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Term
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Definition
| Incomplete dominance where the heterozygote has a phenotype between each homozygote, but closer to one of the homozygotes than the other. |
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Term
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Definition
| The genetic improvement of plants for human benefit. A science, art, and business. About food production in a global context. Deals with food security. Stages include developing genetic variation, developing and selecting genotypes from breeding populations, and synthesizing elite genotypes into cultivars. |
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Term
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Definition
| A group of interbreeding individuals that exist together in time and space. Distribution of a trait value in a population can be fully described by mean and variance. Can be characterized in terms of its genotype and allele frequencies. |
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Term
| Population parameters previously determined (P3D) |
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Definition
| A method used by GAPIT software. |
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Term
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Definition
| Exemplified in Mendel's garden peas. Have phenotypes that fall into distinct categories. Controlled by one or few genes. Limited environmental influence. Studied by analyzing phenotypic ratios and inheritance patterns. |
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Term
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Definition
| Characterized by a continuum of phenotypes. "Of degree rather than of kind" - Falconer (1981). Controlled by the joint action of many genes. Greatly influenced by environment. By necessity studied within the context of a population. Studied with measures of central tendency (mean) and dispersion (variance). Genetic improvements are achieved despite not knowing the genes that control it. Unknown features of such genes include: number of loci (QTL), genomic location, and effect of each locus. Effects include additive, dominance, and epistatic. |
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Term
| Quantitative trait loci (QTL) |
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Definition
| Loci which affect quantitative traits. Mapped in MapQTL. |
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Term
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Definition
| An environment for statistical computing. GAPIT software runs on R. |
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Definition
| The conditions under which the Hardy-Weinberg equilibrium is true. The population must be large, with no selection, no mutation, and no migration. Allele frequencies stay stable over time. |
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Definition
| Sexually reproducing species. Cultivars are often a single inbred line. Allele and genotype frequencies tend toward homozygosity over time. |
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Term
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Definition
| Includes self-pollinated and cross-pollinated species, which lead to vastly different population structures. |
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Term
| Single nucleotide polymorphism (SNP) |
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Definition
| A marker consisting of a single base pair change. |
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Term
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Definition
| Software which helps generate population structure data that can be inputted into GAPIT as a covariate. |
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