Family-based QTL mapping

Mapping QTLs is an important activity that plant breeders and geneticists routinely use to associate potential causal genes with phenotypes of interest.

Some of which include limited polymorphism rates, and no indication of marker effectiveness in multiple genetic backgrounds.

[2] Family-based QTL mapping removes this limitation by using existing plant breeding families.

[citation needed] Natural collection of individuals (considered unrelated) with unknown pedigree constitutes mapping populations.

[3][4] While conceptual underpinning of these approaches have been long known, advances in recent decades in molecular genetics, development in efficient algorithms, and computing power have enabled the large scale application of these methods.

These are complementary methods that, together, provide means to probe the genome and describe etiology of complex traits.

In linkage studies, we seek to identify the loci that cosegregate with a specific genomic region, tagged by polymorphic markers, within families.

Linkage disequilibrium (LD) and association mapping is receiving considerable attention in the plant genetics community for its potential to use existing genetic resources collections to fine map quantitative trait loci (QTL), validate candidate genes, and identify alleles of interest (Yu and Buckler, 2006).

The family-based, Tran-disequilibirum test (TDT) has gained wide popularity in recent years,[citation needed] this method also focuses on alleles transmitted to affect offispring, but it is formulated to take account of both the linkage and the disequilibrium that underlie the association.

Haplotypes refer to combinations of marker alleles which are located closely together on the same chromosome and which tend to be inherited together.

With availability of high density SNP makers, haplotypes play an important role in association studies.

First – haplotypes are critical to understanding the LD pattern across the genome, which is essential for association studies.

However the pedigree drawing in plants requires some additional features such as inbreeding, selfing, mutation, polyploidy etc.