Haplotype analysis in multiple crosses to identify a QTL gene

Identifying quantitative trait locus (QTL) genes is a challenging task. Herein, we report using a two-step process to identify Apoa2 as the gene Underlying Hdlq5, a QTL for plasma high-density lipoprotein cholesterol (HDL) levels on mouse chromosome 1. First, we performed a sequence analysis of the Apoa2 coding region in 46 genetically diverse mouse strains and found five different APOA2 protein variants, which we named APOA2(a) to APOA2(e). Second, we conducted a haplotype analysis of the strains in 21 crosses that have so far detected HDL QTLs; we found that Hdlq5 was detected only in the nine crosses where one parent had the APOA2(b) protein variant characterized by an Ala(61)-to-Val(61) substitution. We then found that strains with the APOA2(b) variant had significantly higher (P less than or equal to 0.002) plasma HDL levels than those with either the APOA2(a) or the APOA2(c) variant. These findings Support Apoa2 as the underlying Hdlq5 gene and suggest the Apoa2 polymorphisms responsible for the Hdlq5 phenotype. Therefore, haplotype analysis in multiple crosses can be Used to support a candidate QTL gene.