How marker with trait association can be known?

Markers associated with traits can be identified through various genetic mapping approaches:

·         Linkage mapping: This method involves genotyping individuals from a mapping population (e.g., segregating populations, mapping panels) and phenotyping them for the trait of interest. Statistical analyses are then performed to identify markers that show significant linkage (co-segregation) with the trait.

·         Association mapping: Also known as linkage disequilibrium (LD) mapping, this method utilizes natural populations or breeding germplasm collections with historical recombination events. Genotypic data for markers and phenotypic data for the trait of interest are collected from a diverse population. Statistical methods, such as GWAS (Genome-Wide Association Studies), are used to identify markers that show significant association with the trait.

·         Candidate gene approach: In this approach, markers located within or near candidate genes known to be involved in the biological pathways underlying the trait are selected. Association between these markers and the trait is assessed through genotyping and phenotyping experiments.

·         Expression QTL (eQTL) mapping: This method identifies markers associated with variation in gene expression levels, which in turn may affect trait variation. It involves genotyping individuals and measuring gene expression levels, followed by statistical analysis to identify markers associated with expression levels of specific genes and, potentially, the trait of interest.

Once markers associated with the trait are identified through one or more of these approaches, they can be validated using independent populations or experimental designs to confirm their association with the trait. These validated markers can then be used in QTL mapping studies to identify genomic regions underlying the trait of interest.