Bulk sequencing	The sequencing of a pool of nuclear DNA from many cells belonging to an individual.
centiMorgan	A map unit for measuring recombination to infer relative distances between linked markers.
Crossover	Large reciprocal exchanges of DNA between homologous chromosomes which produce recombinant chromatids. Crossovers are required for the correct segregation of chromosomes during meiosis.
Crossover interference	A biological phenomenon where one meiotic crossover reduces the probability of a crossover at an adjacent internal, in the same meiosis, in a distance-dependent manner.
DNA double-strand break (DSB)	Programmed DNA double-strand breaks are formed to initiate homologous recombination in meiosis I and are essential to make crossovers.
Genetic distance	A measure of the likelihood of a crossover occurring between two genetic markers. The smaller the genetic distance between markers, the more likely they will be inherited together.
Genome-wide association study	An approach to link genetic variants with traits.
Haplotype	A group of alleles that tend to segregate together and are inherited from one parent.
Heterochiasmy	Difference in the frequency and location of crossovers occurring between sexes of the same species.
Hidden Markov model	Markov process models random system where the future is independent of the past given the current status. Hidden Markov model applies to systems with Markov property, with unobservable (hidden) variable. It consists of two layers of stochastic processes including Markovian transitions between hidden states (transition model) along sequential time steps and the distribution of observable data (emission model) over hidden states.
Individual genetic map (iMap)	The genetic map derived from an individual’s gametes.
Mapping functions	Haldane, cM = − 0.5 × ln(1 − 2r) × 100 Kosambi, cM = 0.25 × ln ((1 + 2r)/(1 − 2r)) × 100 r is the recombination fraction. The Haldane mapping function adds mathematical adjustments to the recombination fraction. It assumes that crossover events are random and independent along the chromosome, and the number of crossover events between two loci follows a Poisson distribution. Haldane’s mapping function adjusts underestimated crossover rate in larger intervals that are likely to have unobserved even number of crossovers. Kosambi’s mapping function was derived based on Haldane’s and takes consideration of crossover interference.
Markers	Polymorphic DNA sequences that are located at known positions in the genome and used as genetic features to distinguish sequences between people/populations.
Markov chain	A stochastic system which models the transitioning among states. The probability of transitioning to any particular state is dependent solely on the current state and time elapsed.
Non-crossover	A type of homologous recombination used in the repair of DNA double-strand breaks, which does not result in a crossover. The repair between two homologs is non-reciprocal.
Physical distance	An absolute measure of DNA length in nucleotide base pairs.
Quantitative trait locus (QTL)	A genomic region that contributes to a trait of interest. QTL mapping often aims to identify the gene that controls the measurable trait.
Single-cell sequencing	The sequencing of nucleic acids from an individual cell using optimized short-read sequencing technology. Sequencing single gametes of an individual overcomes the necessity of recruiting thousands of family trios to generate a reference genetic map that is not a representation of any individual.
Single-nucleotide polymorphism (SNP)	Alteration of a single nucleotide at a specific position in the genome that is present in a large fraction of the population.
Structural variation (SV)	Large genomic alterations, which can include inversions, duplications, translocations, insertions, and deletions. The minimum size is arbitrary, but in this review, SV refers to events > 50 kb unless specified otherwise.