Quantitative Trait Loci (QTL) Detection and Heritability in Plant and Animal Genetics

Quantitative Genetics: Heritability and QTL Detection

Introduction to Quantitative Genetics

Quantitative genetics studies the inheritance of traits that are determined by multiple genes, often influenced by environmental factors. These traits, such as height, milk yield, or meat quality, show continuous variation rather than discrete categories.

• Quantitative Trait: A measurable phenotype that depends on the cumulative actions of many genes and the environment.

• Examples: Milk production in cattle, crop yield in plants, body weight in pigs.

Heritability

Heritability quantifies the proportion of total phenotypic variance in a population that is attributable to genetic variance, specifically the additive genetic component.

• Definition: The proportion of total variance that is additive genetic and can be transmitted from parent to offspring.

• Symbol: $h^2$

• Formula:

$h^2 = \frac{\sigma^2_A}{\sigma^2_P}$

• $\sigma^2_A$ = Additive genetic variance

• $\sigma^2_P$ = Total phenotypic variance

• Interpretation: Higher heritability means a greater proportion of the trait is determined by genetics rather than environment.

Genetic Architecture of Quantitative Traits

Quantitative traits are typically influenced by many loci (genes), each contributing a small effect. Occasionally, some loci have a larger, detectable effect.

• Traits may involve tens, hundreds, or thousands of loci.

• Most loci have small effects and are difficult to detect individually.

• Some loci with larger effects can be identified and studied.

QTL Detection

Definition and Goal

QTL (Quantitative Trait Loci): Genomic regions that are statistically associated with variation in a quantitative trait.

• Goal: Find a polymorphism in the genome that is associated with a distinct difference in phenotype.

• Concept: Simple in theory, but complex in execution due to the polygenic nature of most traits.

Genotyping for QTL Detection

• Individual Locus Genotyping: Uses marker loci (e.g., M and m) and QTL alleles (e.g., Q and q).

• Most QTL are discovered using genetic markers, which are often neutral polymorphisms rather than the causative variant itself.

Approaches to QTL Detection

• Candidate Gene Approach:

  • Select a gene based on physiological or biochemical relevance.

  • Identify a polymorphism within the gene.

  • Selective and targeted; analyzes one gene at a time.

• Anonymous Marker Panel Approach:

  • Develop a panel of markers (e.g., SNPs, microsatellites).

  • Scan a region, chromosome, or the entire genome for associations.

  • Allows for high-throughput, genome-wide analysis.

Technologies / Methods

Candidate Gene Approach	Anonymous Marker Panel Approach
Genotyping individuals by PCR Sequencing specific genes/markers	Genotyping by high-density marker panels Whole genome sequencing

Examples of QTL Databases and Applications

Large databases, such as Animal QTLdb, collect and curate QTL information for various livestock species. These databases are essential for research and breeding programs.

• Species Covered: Cattle, pig, chicken, horse, sheep, catfish, rainbow trout, etc.

• Traits: Meat quality, milk yield, disease resistance, growth rate, etc.

Sample Table: Top QTL Traits in Pigs and Cattle

Pig Traits	Number of QTL	Cattle Traits	Number of QTL
Drip loss	1,069	Age at puberty	10,941
Average daily gain	528	Scrotal circumference	3,561
Muscle thickness	502	Milk fat yield	3,496
Backfat thickness	324	Percentage normal sperm	2,591
Meat color	240	Milk protein yield	2,455
Shear force	189	Milk yield	1,874

Case Studies: Genes Affecting Livestock Traits

• Calpastatin (CAST) Gene:

  • Associated with meat quality, tenderness, and juiciness in cattle.

  • Calpastatin inhibits calpain, an enzyme involved in muscle protein breakdown post-mortem.

• Halothane Gene in Pigs:

  • Makes pigs more susceptible to stress (Porcine Stress Syndrome, PSS).

  • Associated with high carcass yield but poor meat quality.

  • Genotypes: NN (normal), Nn/nn (susceptible to PSS).

Summary Table: QTL Detection Approaches

Approach	Key Features	Technologies
Candidate Gene	Targeted, hypothesis-driven, one gene at a time	PCR, gene sequencing
Anonymous Marker Panel	Genome-wide, high-throughput, unbiased	High-density marker panels, whole genome sequencing

Additional info:

• QTL mapping is a foundational tool in animal and plant breeding, allowing for marker-assisted selection and genomic selection strategies.

• Understanding heritability helps breeders predict the response to selection and optimize breeding programs.