Complex linkage disequilibrium and quantitative trait loci in chicken

Abstract

Abstract Linkage disequilibrium (LD) underpins mapping studies of Quantitative Trait Loci Regions (QTLRs). A common yet misled assumption assumes the closest sites to a significant marker as causative mutation candidates. We studied chicken LD of mapped chicken QTLRs for Marek’s Disease resistance in numerous populations and estimated background LD by random sampling of non-syntenic and syntenic marker pairs from different or same chromosomes. We defined LD blocks as marker groups located on the same chromosome having significant moderate (0.15 ≥ r 2 < 0.7) or high (r 2 ≥ 0.7) LD, regardless of distance and excluding mixed markers with no LD as a part of the block. We studied QTLR LD using SNP markers within the QTLRs. We found very complex LD patterns, with fragmented and interdigitated LD blocks. Exceptional high LD was found between two particular QTLRs, with shared protein networks suggesting possible functional relationships. Thus, causative candidates could be found beyond non-LD sites, occasionally at a very large distance from a significant marker, even in another QTLR. Multiple effects might make LD extremely complex, thus limiting GWAS informativity and repeatability. Complex LD challenges practical use across populations, and must be accounted for while interpreting genetic mapping studies.