Linkage disequilibrium across the zebra finch genome

Linkage disequilibrium (LD) plays an important role in evolutionary biology. It can reveal much about past demography, patterns of recombination and it has important implications in gene mapping. Recent studies in humans demonstrate that LD is highly structured, forming discrete blocks of LD separated by recombination hotspots. Such variable patterns of LD have important implications for gene mapping and for our interpretation of factors governing genetic variation in natural systems. The aim of this study was to investigate genome-wide LD in the zebra finch using 876 SNPs and construct LD maps to investigate patterns of LD across chromosomes.

A striking pattern was identified with respect to the two types of chromosomes present in birds. As predicted on the microchromosomes, which have a higher recombination rate, LD declined more rapidly with physical distance compared to the macrochromsomes. Interestingly, the distribution of recombination and pattern of LD also differed dramatically between the macro and microchromosomes. On microchromosomes the distribution of LD is mostly uniform, but on the macrochromosomes recombination rate is localized to the distal ends of the chromosomes, and large blocks of LD were present in the centre of the macrochromosomes. This pattern is independent of the position of the centromere. These results suggest that for future mapping studies marker densities will need to vary between micro and macrochromosomes, but also with respect to their position on the macrochromosomes. These results also have implications for our interpretation of patterns of genetic variation along chromosomes.

 

LD covaried with GC content and gene density, but not heterozygosity.

 

 

 

 

 

 

Related publications

Stapley J, Birkhead TR, Burke T, Slate J. (2010) Pronounced inter- and intrachromosomal variation in linkage disequilibrium across the zebra finch genome, Genome Research 20:496-502.

This project is funded by the Biotechnology and Biological Sciences Research Council.