Complex linkage disequilibrium and quantitative trait loci in chicken
- 1Genetics, Hebrew University of Jerusalem, Jerusalem, Israel
- 2Hy-Line International, Dallas Center, IA 50063 USA
- 3The Roslin Institute and Royal (Dick) School of Veterinary Studies R(D)SVS, University of Edinburgh, Easter Bush, Midlothian, EH25 9RG UK
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 ≥ r2 < 0.7) or high (r2 ≥ 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.
Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1038/s41598-026-64633-2.
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BibTeX
@article{lipkin2026complex,
title = {{Complex linkage disequilibrium and quantitative trait loci in chicken}},
author = {Ehud Lipkin and Janet E. Fulton and Jacqueline Smith and David W. Burt and Morris Soller},
journal = {Scientific Reports},
year = {2026},
month = aug,
doi = {10.1038/s41598-026-64633-2},
url = {https://doi.org/10.1038/s41598-026-64633-2},
note = {CC BY 4.0},
}
RIS
TY - JOUR
TI - Complex linkage disequilibrium and quantitative trait loci in chicken
AU - Ehud Lipkin
AU - Janet E. Fulton
AU - Jacqueline Smith
AU - David W. Burt
AU - Morris Soller
PY - 2026
DA - 2026/08/07
JO - Scientific Reports
DO - 10.1038/s41598-026-64633-2
UR - https://doi.org/10.1038/s41598-026-64633-2
AB - 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 ≥ r2 < 0.7) or high (r2 ≥ 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. Supplementary Information: The online version contains supplementary material available at https://doi.org/10.1038/s41598-026-64633-2.
SN - 2045-2322
ER -