Fine Mapping of Collagen-Induced Arthritis Quantitative Trait Loci in an Advanced Intercross Line

Abstract

The generation of advanced intercross lines (AIL) is a powerful approach for high-resolution fine mapping of quantitative trait loci (QTLs), because they accumulate much more recombination events compared with conventional F2 intercross and N2 backcross. However, the application of this approach is severely hampered by the requirements of excessive resources to maintain such crosses, i.e., in terms of animal care, space, and time. Therefore, in this study, we produced an AIL to fine map collagen-induced arthritis (CIA) QTLs using comparatively limited resources. We used only 308 (DBA/1 × FVB/N)F11/12 AIL mice to refine QTLs controlling the severity and onset of arthritis as well as the Ab response and T cell subset in CIA, namely Cia2, Cia27, and Trmq3. These QTLs were originally identified in (DBA/1 × FVB/N)F2 progeny. The confidence intervals of the three QTLs were refined from 40, 43, and 48 Mb to 12, 4.1, and 12 Mb, respectively. The data were complemented by the use of another QTL fine-mapping approach, haplotype analysis, to further refine Cia2 into a 2-Mb genomic region. To aid in the search for candidate genes for the QTLs, genome-wide expression profiling was performed to identify strain-specific differentially expressed genes within the confidence intervals. Of the 1396 strain-specific differentially expressed genes, 3, 3, and 12 genes were within the support intervals of the Cia2, Cia27, and Trmq3, respectively. In addition, this study revealed that Cia27 and Trmq3 controlling anti-CII IgG2a Ab and CD4:CD8 T cell ratio, respectively, also regulated CIA clinical phenotypes.

Using an advanced intercross line to identify quantitative trait loci controlling immune response during collagen-induced arthritis

“…However, it was successfully used to refine three QTLs previously identified in the F2 progeny, indicating that this AIL could be used for QTL high-resolution mapping. 11,12 Then, we examined the heterogeneity and recombination frequencies, which are important parameters for QTL mapping accuracy. Heterogeneity was tested to investigate the allele distribution on four chromosomes and it was estimated from the percentage of DBA/1 allele of the markers used for genotyping.…”

“…11,12 In this study, in order to test the possibility of identifying QTLs directly in AIL, we genotyped 308 F11/12 AIL mice with 109 genetic markers covering four chromosomes, with an average intermarker distance of 5.5 Mb. Several normally distributed immune-response quantitative traits, such as antibodies to collagen type II and T-cell subset proportions in lymph nodes as well as reactive oxygen species (ROS) were investigated.…”

Contribution of genetic studies in rodent models of autoimmune arthritis to understanding and treatment of rheumatoid arthritis

“…70,71 To generate these lines, heterozygous offspring from the parental inbred strains are intercrossed for several generations avoiding brother-sister mating. This approach requires large numbers of offspring and generates an increased number of recombination events.…”

Fine-Scale Analysis of Parasite Resistance Genes in the Red Flour Beetle, Tribolium castaneum

“…2-cM range or less to facilitate candidate gene identification (Yu et al 2006). However, the QTL that we identified were positioned within large marker intervals due to the dominant AFLP markers used in the linkage analysis (Adarichev et al 2003).…”

“…Fine-mapping of QTL can be achieved by increasing marker density within the chromosomal region of interest, increasing the number of individuals for which phenotypic information can be obtained, or by increasing the accuracy of assigning QTL genotypes (Nezer et al 2003). QTL should be defined by informative, codominant markers within a 1-to 2-cM range or less to facilitate candidate gene identification (Yu et al 2006). However, the QTL that we identified were positioned within large marker intervals due to the dominant AFLP markers used in the linkage analysis (Adarichev et al 2003).…”