BAYERO UNIVERSITY, KANO
Department of Agronomy
POSTGRADUATE LECTURE NOTE
Course: Advanced Plant Breeding
MATING SYSTEMS IN PLANT BREEDING:
Genetic and Phenotypic Assortative and Disassortative Mating, and Their Genetic
Consequences
1.0 Learning Objectives
By the end of this lecture, students should be able to:
1. Define mating systems and distinguish random mating from non-random mating in plant populations.
2. Differentiate genetic (genotypic) assortative mating from phenotypic assortative mating.
3. Distinguish positive assortative mating from negative (disassortative) mating and identify natural plant
mechanisms that enforce each.
4. Derive and interpret the genetic consequences of assortative and disassortative mating on allele
frequency, genotype frequency, genetic variance, and correlation between relatives.
5. Distinguish the effects of assortative mating from those of inbreeding.
6. Apply knowledge of mating systems to practical plant breeding decisions, including parent selection,
heterosis breeding, and hybrid seed production.
2.0 The Concept of Mating Systems
A mating system describes the pattern by which individuals in a population pair to produce the next
generation — that is, who mates with whom with respect to genotype, phenotype, and relatedness. Mating
systems are central to plant breeding because they determine how genetic variation present in a base
population is reorganised into the genotypes of progeny, and therefore how quickly and in what direction a
population can respond to selection.
Mating systems in plant populations are broadly classified as follows:
• Random mating (panmixia) – any individual has an equal probability of mating with any other
individual in the population, irrespective of genotype or phenotype.
• Inbreeding – mating between relatives (individuals related by descent), including self-fertilisation as
the most intense form.
• Positive assortative mating – mating between individuals that resemble each other more than
expected by chance (“like mates with like”).
• Negative assortative mating (disassortative mating) – mating between individuals that are more
dissimilar than expected by chance (“like avoids like”; “unlike mates with unlike”).
Note: Inbreeding is mating based on relatedness/ancestry (identity by descent), whereas assortative/disassortative
mating is based on resemblance in genotype or phenotype and does not necessarily imply any pedigree relationship
between mates. The two systems can, however, occur together and their effects can be confused if not carefully
distinguished, as shown later in this note.
2.1 Mechanisms That Enforce Non-Random Mating in Plants
Because plants are sessile, mating patterns are strongly influenced by floral biology, breeding structure, and
pollination vectors. Important natural mechanisms include:
• Self-incompatibility (SI) systems – gametophytic SI (e.g., Solanaceae, Poaceae grasses) and sporophytic
SI (e.g., Brassicaceae) prevent fertilisation between plants sharing the same S-allele, enforcing
outcrossing and a form of genetic disassortative mating at the S-locus.
• Heterostyly – e.g., pin and thrum floral morphs in Primula and Fagopyrum (buckwheat); legitimate,
fertile pollinations occur mainly between different morphs, another natural disassortative system.
• Dichogamy (protandry/protogyny) and herkogamy – spatial or temporal separation of anthers and
stigma promotes outcrossing and reduces self-pollination.
• Dioecy and monoecy with self-incompatibility – physical separation of sexes, obligating cross-
pollination.
• Flowering time and plant-height synchrony – in wind- and insect-pollinated species, plants that flower
at the same time or have similar height/architecture are more likely to exchange pollen, generating
phenotypic positive assortative mating for phenological and morphological traits even without any
deliberate choice mechanism.
3.0 Random Mating as the Reference System
Random mating is the baseline against which all other mating systems are compared. Under random mating,
with no selection, mutation, or migration, a locus with two alleles A and a at frequencies p and q (p + q = 1)
reaches Hardy–Weinberg equilibrium in a single generation, with genotype frequencies:
AA = p² Aa = 2pq aa = q²
Under random mating, allele and genotype frequencies remain constant across generations (in the absence
of other evolutionary forces), and there is zero correlation between the genotypes or phenotypes of mating
pairs. Departures from these expectations — specifically, a correlation between the genotypes/phenotypes
of mates — signal assortative or disassortative mating.
4.0 Assortative Mating (Positive Assortative Mating)
Assortative mating occurs when mating pairs resemble each other for a given trait more than would be
expected under random mating, generating a positive correlation, r, between the genotypic or phenotypic
values of mates. Two forms are recognised in genetics: genetic (genotypic) assortative mating and
phenotypic assortative mating.
4.1 Genetic (Genotypic) Assortative Mating
Genetic assortative mating occurs when mates are chosen directly on the basis of genotype at a specific
locus (or, more realistically, when phenotype is a perfect or near-perfect reflection of genotype, as with a
simply inherited, fully penetrant qualitative trait). This is the classical case treated in early population-
genetic models: like genotypes preferentially mate with like genotypes — for example, AA with AA, and aa
with aa, more often than chance.
Consequences of genetic assortative mating at a single locus:
• Allele frequencies (p and q) are unchanged, because assortative mating does not, by itself, favour
survival or transmission of one allele over another — it only changes how alleles are combined into
genotypes.
• Genotype frequencies deviate from Hardy–Weinberg proportions: homozygote classes (AA and aa)
increase in frequency at the expense of heterozygotes (Aa).
• Over successive generations, heterozygosity at the locus declines and the population moves toward a
bimodal structure with two increasingly distinct homozygous classes, resembling (but mechanistically
distinct from) the effect of inbreeding.
• Complete (perfect) positive assortative mating for a single dominant/recessive pair can, at equilibrium,
eliminate the heterozygous class from matings between phenotypically distinguishable classes, though
mating within the heterozygous class itself continues to segregate 1:2:1.
4.2 Phenotypic Assortative Mating
In practice, most traits of interest to plant breeders — yield, maturity, plant height, seed size — are
quantitative (polygenic) traits controlled by many loci with small individual effects, together with
environmental variation. Phenotypic assortative mating occurs when individuals mate on the basis of
phenotypic resemblance for such a trait, e.g., tall plants pollinating tall plants, early-flowering plants
pollinating early-flowering plants. Because phenotype is an imperfect indicator of genotype (P = G + E),
phenotypic assortative mating has weaker, but qualitatively similar, genetic effects to genotypic assortative
mating, and its consequences must be modelled through the correlation between mates and the heritability
of the trait.
4.2.1 Modelling Phenotypic Assortative Mating
Let r be the phenotypic correlation between mates for the trait, and h² the narrow-sense heritability of the
trait in the population. The correlation between the breeding values (additive genetic values) of mates,
sometimes called the genetic correlation induced by assortment, is approximately:
rₘ (mates, additive genotype) ≈ h² × r
This shows that phenotypic assortative mating translates into genetic assortative mating only to the extent
that the trait is heritable; for a trait with low heritability, even strong phenotypic assortment (high r)
produces only a weak correlation between the actual breeding values of mates, and correspondingly weak
genetic consequences.
5.0 Genetic Consequences of Positive Assortative Mating
The genetic consequences of sustained positive assortative mating for a quantitative trait, developed
originally by Sewall Wright and Fisher, and extended by Falconer and Mackay in the classical quantitative-
genetics framework, are as follows:
5.1 No Change in Allele or Overall Mean
As with genotypic assortative mating, phenotypic assortative mating does not change allele frequencies at
the loci controlling the trait, and (in the absence of directional selection) it does not change the population
mean. Its principal effect is on the variance and covariance structure of the population, not on the average
genetic value.
5.2 Increase in Additive Genetic Variance
Assortative mating increases the additive genetic variance (Vₐ) of the trait relative to random mating,
because it creates positive covariances between the alleles at different loci that jointly influence the trait (a
form of induced linkage disequilibrium among trait loci, even between loci on different chromosomes). Each
generation of assortative mating adds to this covariance until an equilibrium variance is reached. The
classical approximation (Wright, Fisher) for the equilibrium additive variance under a constant mating
correlation r among parents is:
Vₐ(equilibrium) ≈ Vₐ(random mating) / (1 − r h²/2)
(Different sources express the equilibrating series slightly differently, but all agree qualitatively: the additive
variance rises above the random-mating value and approaches a new, higher equilibrium after several
generations of consistent assortative mating, rather than increasing without bound.)
5.3 Excess of Homozygotes and Increased Phenotypic Variance
• At the loci underlying the assorted trait, homozygote frequencies increase and heterozygote
frequencies decrease relative to Hardy–Weinberg expectation, in the same direction as genetic
assortative mating, but to a lesser degree proportional to h².
• Because more genetic variance is expressed, phenotypic variance for the trait also increases across
generations, and the population distribution tends to spread out (and may become platykurtic or even
bimodal under strong assortment).
5.4 Increased Correlation Between Relatives
Positive assortative mating increases the resemblance (phenotypic and genetic correlation) between
relatives for the assorted trait — for example, between full sibs, half sibs, and parent–offspring pairs —
above the values expected under random mating. This occurs because mates are no longer genetically
independent samples of the population; a degree of positive genetic covariance is introduced between the
two parents themselves, which is transmitted to their joint offspring and to comparisons among offspring.
5.5 Assortative Mating Is Not Inbreeding
Although both inbreeding and strong positive assortative mating increase homozygosity and reduce the
proportion of heterozygotes, the two processes are genetically distinct and should not be conflated:
Feature Inbreeding Positive Assortative Mating
Basis of mating Relatedness / identity by descent Phenotypic or genotypic
resemblance
Loci affected All loci genome-wide, equally Only loci that influence the assorted
trait (and loci linked/correlated with
them)
Effect on homozygosity Increases genome-wide Increases only at trait-relevant loci
Inbreeding depression Expected, from genome-wide Not generally expected, since
exposure of deleterious recessives unrelated loci remain in Hardy–
Weinberg proportions
Effect on additive variance Can increase among-family variance Increases additive genetic variance
but reduces within-family variance; for the assorted trait specifically
total population variance effects
differ from assortative mating
Table 1. Key distinctions between inbreeding and positive assortative mating.
6.0 Disassortative (Negative Assortative) Mating
Disassortative mating occurs when mating pairs are less alike than expected by chance for a given trait,
producing a negative correlation (r < 0) between the genotypic or phenotypic values of mates. As with
positive assortment, this may operate at the genetic (genotypic) level or the phenotypic level.
6.1 Genetic Disassortative Mating in Plants
• Self-incompatibility (SI) systems – in both gametophytic SI (e.g., many Solanaceae, Poaceae, Fabaceae)
and sporophytic SI (e.g., Brassicaceae), pollen carrying an S-allele identical to one carried by the
recipient pistil is rejected. This is a textbook case of genetic disassortative mating maintained at the S-
locus, and it is one of the classical examples of balancing selection in population genetics: the rejection
of like alleles actively favours rare S-alleles, maintaining very high allelic diversity (sometimes dozens of
S-alleles) in outcrossing populations.
• Heterostyly – in distylous species such as Primula and Fagopyrum esculentum (buckwheat), only
pollinations between the pin and thrum floral morphs (controlled by the S-supergene) are fully fertile;
pollinations within the same morph are largely incompatible. This enforces disassortative mating with
respect to floral morph.
6.2 Phenotypic Disassortative Mating
Phenotypic disassortative mating for continuously varying (quantitative) traits is comparatively rare as a
spontaneous natural phenomenon in plants, because pollen vectors typically do not actively “choose”
dissimilar partners for morphometric traits the way some animals do. However, plant breeders deliberately
impose phenotypic and genetic disassortment when they intentionally cross genetically or phenotypically
dissimilar parents — for instance, in heterosis (hybrid vigour) breeding, where genetically divergent inbred
lines or heterotic groups are deliberately intercrossed rather than allowed to mate at random or
assortatively.
7.0 Genetic Consequences of Disassortative Mating
• Increased heterozygosity: at loci governing the disassorted trait, heterozygote frequency rises above
Hardy–Weinberg expectation, and homozygote frequencies fall — the opposite pattern to assortative
mating and to inbreeding.
• Reduced additive genetic variance for the disassorted trait: because dissimilar genotypes/phenotypes
are combined, the progeny generation is genetically “averaged” toward the population mean more
than under random mating, narrowing the distribution of genetic values over generations.
• Maintenance of polymorphism: strong genetic disassortative mating, as at self-incompatibility loci, is a
powerful balancing-selection mechanism because it confers a mating (fitness) advantage on individuals
carrying rare alleles, actively preserving allelic diversity that would otherwise be lost to drift.
• Negative correlation between relatives: because parents are genetically dissimilar by design, the
covariance structure among relatives for the disassorted trait is reduced relative to random mating,
and can, at the extreme, become negative for parent–offspring comparisons involving the assorted
character.
• No change in allele frequency: as with assortative mating, disassortative mating alone (absent
selection) does not change allele frequencies; it redistributes existing alleles into different genotypic
and phenotypic combinations.
8.0 Comparative Summary of Mating Systems
Mating System Mate correlation (r) Effect on Heterozygosity Effect on Genetic Variance
Random mating r=0 Hardy–Weinberg Baseline (reference) variance
proportions maintained
Positive assortative r>0 Decreases at trait loci Increases additive variance for
mating (more homozygotes) the trait, to a new equilibrium
Negative r<0 Increases at trait loci (more Decreases additive variance for
(dis)assortative mating heterozygotes) the trait
Inbreeding Not defined by Decreases genome-wide, at Redistributes variance among vs
phenotypic r; based all loci within families; can expose
on deleterious recessives
pedigree/relatedness (inbreeding depression)
(F)
Table 2. Comparative summary of random mating, assortative mating, disassortative mating, and inbreeding.
9.0 Applications in Plant Breeding Practice
9.1 Parent Selection in Pedigree and Line Breeding
Breeders frequently practise phenotypic positive assortative mating, whether deliberately or by default,
when they select and intercross elite parents that resemble one another for target traits (e.g., crossing two
high-yielding, early-maturing lines). This accelerates fixation of favourable homozygous combinations and
can raise additive genetic variance available to selection in early segregating generations, but it also narrows
genetic diversity for the assorted trait over time, and should be balanced against the need to maintain
adequate genetic variability in the breeding population.
9.2 Self-Incompatibility and Hybrid Seed Production
Breeders exploit natural genetic disassortative mating systems (SI, male sterility) to enforce obligate
outcrossing in hybrid seed production, for example in Brassica oleracea, sunflower, and rye breeding
programmes, guaranteeing that seed harvested from a female parent line results from cross-pollination with
the desired male parent rather than self-pollination.
9.3 Heterosis Breeding and Heterotic Grouping
Deliberate crossing of genetically divergent inbred lines or heterotic groups (as in maize breeding, where
Stiff Stalk and non-Stiff Stalk groups are systematically intercrossed) is functionally a disassortative mating
strategy imposed at the level of the whole genome. It maximises heterozygosity and non-additive
(dominance) gene action in the F1, which underlies hybrid vigour, while the parent inbred lines themselves
are typically developed through repeated self-pollination (an extreme inbreeding system) to achieve the
homozygosity needed for uniform, stable hybrid parents.
9.4 Synchrony Selection
Selecting parents with matching flowering time or maturity (a form of phenotypic assortative mating for
phenology) is routinely used to ensure successful hybridisation in controlled crosses and to avoid
unintentional selfing or off-type contamination in open-pollinated seed production plots.
9.5 Implications for Recurrent Selection and Population Improvement
In recurrent selection schemes, breeders should be aware that intense phenotypic selection of parents for a
target trait can itself generate assortative mating for that trait (since selected parents tend to resemble one
another), inflating additive variance and apparent heritability estimates for the trait in later cycles.
Conversely, deliberately randomising or dissortatively pairing parents (e.g., through designed mating
schemes such as diallel or North Carolina designs with random pairing) helps breeders obtain unbiased
estimates of genetic variance components uncontaminated by assortment effects.
10.0 Summary
• A mating system describes non-random or random pairing of individuals for reproduction; it is distinct
from, but can co-occur with, inbreeding.
• Genetic (genotypic) assortative mating is direct mate choice by genotype; phenotypic assortative
mating is mate resemblance for a (usually polygenic) observable trait, and its genetic effect scales with
the trait's heritability.
• Positive assortative mating increases homozygosity and additive genetic variance for the assorted trait
and increases correlation between relatives, without changing allele frequencies and without causing
genome-wide inbreeding depression.
• Disassortative (negative assortative) mating, exemplified by plant self-incompatibility systems and
heterostyly, increases heterozygosity, decreases additive genetic variance for the trait, and helps
maintain allelic polymorphism through balancing selection.
• Plant breeders exploit both systems deliberately: assortative mating to fix favourable combinations in
pedigree breeding, and disassortative mating (via SI systems, male sterility, or divergent heterotic
groups) to enforce outcrossing and exploit heterosis.
11.0 Review Questions
7. Distinguish genetic (genotypic) assortative mating from phenotypic assortative mating, and explain
why heritability determines the strength of the genetic consequence of the latter.
8. Using Hardy–Weinberg proportions as a starting point, explain why positive assortative mating
increases homozygote frequency at trait loci without changing allele frequency.
9. Explain, with reference to self-incompatibility systems, how genetic disassortative mating can act as a
balancing-selection mechanism that maintains allelic diversity in plant populations.
10. Differentiate the genetic consequences of inbreeding from those of positive assortative mating, with
particular reference to inbreeding depression.
11. Discuss how a plant breeder might deliberately use both assortative and disassortative mating
strategies within the same breeding programme, giving one practical example of each.
12.0 Selected References for Further Reading
• Falconer, D.S. and Mackay, T.F.C. Introduction to Quantitative Genetics (relevant chapters on
assortative mating and correlation between relatives).
• Allard, R.W. Principles of Plant Breeding (chapters on mating systems and population structure).
• Wright, S. Evolution and the Genetics of Populations, Vol. 2: The Theory of Gene Frequencies
(foundational treatment of assortative mating theory).
• Acquaah, G. Principles of Plant Genetics and Breeding (sections on mating systems, self-
incompatibility, and heterosis).
• de Nettancourt, D. Incompatibility and Incongruity in Wild and Cultivated Plants (for self-
incompatibility mechanisms).