QTL

Quantitative trait locus (QTL) is a locus in the genome that correlates with variation in a quantitative trait, such as height, yield, or flowering time. QTLs are detected through statistical associations between phenotypic variation and genetic markers in a segregating population. Because most quantitative traits are controlled by multiple loci and influenced by the environment, individual QTLs typically have small to moderate effects.

To map QTLs, researchers cross individuals with contrasting phenotypes to produce mapping populations, including F2, backcross, recombinant inbred lines, or advanced populations like MAGIC. The populations are genotyped with markers (such as SNPs or SSRs) and phenotyped for the trait. QTL detection can use linkage mapping or association mapping (genome-wide association studies). Significance is assessed with LOD scores and permutation tests to establish thresholds. Methods such as interval mapping, composite interval mapping, and multiple interval mapping help localize QTLs to genomic regions. The estimated effect of a QTL may be additive, dominance, or involve epistasis, and the proportion of phenotypic variance explained is reported as the effect size. QTL intervals often contain many genes; fine mapping and candidate gene analysis are used to identify causal genes.

Applications include marker-assisted selection and genomic selection in breeding programs, enabling the transfer of favorable alleles. QTL information supports functional studies and can be integrated with gene expression data (eQTL). Limitations include environmental influence, population size, and the often small effect of many QTLs, which can reduce mapping resolution and transfer accuracy.