Extensive linkage disequilibrium in a wild bird population

Area of Science:

• Population genetics
• Wildlife genomics
• Evolutionary biology

Background:

• Understanding linkage disequilibrium (LD) is crucial for insights into population demographics and identifying genetic bases of complex traits in wild populations.
• Data on LD patterns in non-model wild vertebrate species remain limited.

Purpose of the Study:

• To conduct a comprehensive examination of LD extent and patterns in a pedigreed wild bird population (Siberian jay).
• To assess the feasibility of LD mapping for phenotypic traits in this species.

Main Methods:

• Genotyping of Siberian jays using 97 autosomal and 6 gonosomal microsatellites.
• Utilizing a recently established linkage map for genetic analysis.
• Analyzing syntenic and nonsyntenic marker pair associations to determine LD patterns.

Main Results:

• High levels of LD were observed, extending over tens of centimorgans or several megabases, generally decaying with increasing intermarker distance.
• Significant LD was common between both syntenic and nonsyntenic markers.
• LD patterns varied across linkage groups, with lower levels on the Z-chromosome compared to autosomes.

Conclusions:

• The extensive LD in Siberian jays is likely influenced by small population size, genetic structure, and inbreeding.
• Long-range LD supports the feasibility of LD mapping for traits using low-density markers.
• The prevalence of nonsyntenic LD necessitates combining linkage and LD methods to avoid false-positive associations.