Inbred strains are individuals of a particular species which are nearly identical to each other in genotype due to long inbreeding. A strain is inbred when it has undergone at least 20 generations of brother x sister or offspring x parent mating, at which point at least 98.6% of the loci in an individual of the strain will be homozygous, and each individual can be treated effectively as clones. Some inbred strains have been bred for over 150 generations, leaving individuals in the population to be isogenic in nature. Inbred strains of animals are frequently used in laboratories for experiments where for the reproducibility of conclusions all the test animals should be as similar as possible. However, for some experiments, genetic diversity in the test population may be desired. Thus outbred strains of most laboratory animals are also available, where an outbred strain is a strain of an organism that is effectively wildtype in nature, where there is as little inbreeding as possible.
A quantitative trait locus (QTL) is a locus that correlates with variation of a quantitative trait in the phenotype of a population of organisms. QTLs are mapped by identifying which molecular markers correlate with an observed trait. This is often an early step in identifying the actual genes that cause the trait variation.
A DNA segment is identical by state (IBS) in two or more individuals if they have identical nucleotide sequences in this segment. An IBS segment is identical by descent (IBD) in two or more individuals if they have inherited it from a common ancestor without recombination, that is, the segment has the same ancestral origin in these individuals. DNA segments that are IBD are IBS per definition, but segments that are not IBD can still be IBS due to the same mutations in different individuals or recombinations that do not alter the segment.
Genetic association is when one or more genotypes within a population co-occur with a phenotypic trait more often than would be expected by chance occurrence.
Marker assisted selection or marker aided selection (MAS) is an indirect selection process where a trait of interest is selected based on a marker linked to a trait of interest, rather than on the trait itself. This process has been extensively researched and proposed for plant- and animal- breeding.
In genomics, a genome-wide association study, is an observational study of a genome-wide set of genetic variants in different individuals to see if any variant is associated with a trait. GWA studies typically focus on associations between single-nucleotide polymorphisms (SNPs) and traits like major human diseases, but can equally be applied to any other genetic variants and any other organisms.
Population structure is the presence of a systematic difference in allele frequencies between subpopulations. In a randomly mating population, allele frequencies are expected to be roughly similar between groups. However, mating tends to be non-random to some degree, causing structure to arise. For example, a barrier like a river can separate two groups of the same species and make it difficult for potential mates to cross; if a mutation occurs, over many generations it can spread and become common in one subpopulation while being completely absent in the other.
In genetics, association mapping, also known as "linkage disequilibrium mapping", is a method of mapping quantitative trait loci (QTLs) that takes advantage of historic linkage disequilibrium to link phenotypes to genotypes, uncovering genetic associations.
Nested association mapping (NAM) is a technique designed by the labs of Edward Buckler, James Holland, and Michael McMullen for identifying and dissecting the genetic architecture of complex traits in corn. It is important to note that nested association mapping is a specific technique that cannot be performed outside of a specifically designed population such as the Maize NAM population, the details of which are described below.
In statistical genetics, inclusive composite interval mapping (ICIM) has been proposed as an approach to QTL mapping for populations derived from bi-parental crosses. QTL mapping is based on genetic linkage map and phenotypic data to attempt to locate individual genetic factors on chromosomes and to estimate their genetic effects.
GeneNetwork is a combined database and open-source bioinformatics data analysis software resource for systems genetics. This resource is used to study gene regulatory networks that link DNA sequence differences to corresponding differences in gene and protein expression and to variation in traits such as health and disease risk. Data sets in GeneNetwork are typically made up of large collections of genotypes and phenotypes from groups of individuals, including humans, strains of mice and rats, and organisms as diverse as Drosophila melanogaster, Arabidopsis thaliana, and barley. The inclusion of genotypes makes it practical to carry out web-based gene mapping to discover those regions of genomes that contribute to differences among individuals in mRNA, protein, and metabolite levels, as well as differences in cell function, anatomy, physiology, and behavior.
A recombinant inbred strain or recombinant inbred line (RIL) is an organism with chromosomes that incorporate an essentially permanent set of recombination events between chromosomes inherited from two or more inbred strains. F1 and F2 generations are produced by intercrossing the inbred strains; pairs of the F2 progeny are then mated to establish inbred strains through long-term inbreeding.
Drosophila Genetic Reference Panel (DGRP) is a suite of Drosophila melanogaster lines derived from an out-crossed population in Raleigh, North Carolina. The founders of these lineages were collected from the Raleigh State Farmer's Market 35.764254°N 78.662935°W. The suite consists of 205 fully sequenced lines which have been inbred to near homozygosity. The primary goal of the DGRP is to provide a common set of strain for quantitative genetics research in Drosophila. Each researcher who uses the lines from the DGRP will have access to other researchers' data, which will be stored in a publicly available database. This allows for analyses to be performed across studies without having to worry about complications arising from different labs using genomically different lines of fruit flies.
Quantitative trait loci mapping or QTL mapping is the process of identifying genomic regions that potentially contain genes responsible for important economic, health or environmental characters. Mapping QTLs is an important activity that plant breeders and geneticists routinely use to associate potential causal genes with phenotypes of interest. Family-based QTL mapping is a variant of QTL mapping where multiple-families are used.
Molecular breeding is the application of molecular biology tools, often in plant breeding and animal breeding. In the broad sense, molecular breeding can be defined as the use of genetic manipulation performed at the level of DNA to improve traits of interest in plants and animals, and it may also include genetic engineering or gene manipulation, molecular marker-assisted selection, and genomic selection. More often, however, molecular breeding implies molecular marker-assisted breeding (MAB) and is defined as the application of molecular biotechnologies, specifically molecular markers, in combination with linkage maps and genomics, to alter and improve plant or animal traits on the basis of genotypic assays.
Genomic Selection (GS) predicts the breeding values of an offspring in a population by associating their traits with their high-density genetic marker scores. GS is a method proposed to address deficiencies of marker-assisted selection (MAS) in breeding programs. However, GS is a form of MAS that differs from it by estimating, at the same time, all genetic markers, haplotypes or marker effects along the entire genome to calculate the values of genomic estimated breeding values (GEBV). The potentiality of GS is to explain the genetic diversity of a breeding program through a high coverage of genome-wide markers and to assess the effects of those markers to predict breeding values.
A diversity panel is a collection of genetic material or individual samples taken from a diverse population of a certain species. The idea is to illustrate the genetic and phenotypic diversity of the species.
Function Maize gene for first step in biosynthesis of benzoxazin, which aids in resistance to insect pests, pathogenic fungi and bacteria.
In the field of genetic sequencing, genotyping by sequencing, also called GBS, is a method to discover single nucleotide polymorphisms (SNP) in order to perform genotyping studies, such as genome-wide association studies (GWAS). GBS uses restriction enzymes to reduce genome complexity and genotype multiple DNA samples. After digestion, PCR is performed to increase fragments pool and then GBS libraries are sequenced using next generation sequencing technologies, usually resulting in about 100bp single-end reads. It is relatively inexpensive and has been used in plant breeding. Although GBS presents an approach similar to restriction-site-associated DNA sequencing (RAD-seq) method, they differ in some substantial ways.
Stephen Kresovich is a plant geneticist and the Coker Endowed Chair of Genetics in the Department of Plant and Environmental Sciences at Clemson University and professor in the School of Integrative Plant Science in the College of Agriculture and Life Sciences at Cornell University. Since 2019 he has served as director of the Feed the Future Innovation Lab for Crop Improvement.
