Association studies using family pools of outcrossing crops based on allele-frequency estimates from DNA sequencing.

ABSTRACT:

Key message

We propose a method in which GBS data can be conveniently analyzed without calling genotypes. F2 families are frequently used in breeding of outcrossing species, for instance to obtain trait measurements on plots. We propose to perform association studies by obtaining a matching "family genotype" from sequencing a pooled sample of the family, and to directly use allele frequencies computed from sequence read-counts for mapping. We show that, under additivity assumptions, there is a linear relationship between the family phenotype and family allele frequency, and that a regression of family phenotype on family allele frequency will estimate twice the allele substitution effect at a locus. However, medium-to-low sequencing depth causes underestimation of the true allele s

SUBMITTER: Ashraf BH 

PROVIDER: S-EPMC4035547 | biostudies-literature | 2014 Jun

REPOSITORIES: biostudies-literature