Sequencing & Pangenomes

The use of Linkage Disequilibrium for the Construction of a Knotty Reference Genome Map of Gallus domesticus

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Abstract

The chicken genome is highly complex, characterized by numerous microchromosomes, repetitive sequences, and inconsistencies among published reference genome maps. These features complicate genome assembly and the accurate placement of contigs and scaffolds, particularly when assemblies rely on short-read sequencing data. In this study, we investigated whether linkage disequilibrium (LD) information derived from whole-genome sequencing (WGS) data can be used to improve the assignment of unmapped or mis-mapped contigs and scaffolds in the chicken reference genome. Whole-genome sequencing data from 279 hens belonging to six Spanish local chicken breeds were analyzed, yielding more than 1.1 million autosomal single nucleotide polymorphisms (SNPs) segregating in all breeds. LD was estimated between SNPs located on autosomes and SNPs located on unmapped contigs and scaffolds using a geometrical LD approach. Strong LD (r > 0.8) was detected between several contigs/scaffolds and specific autosomal regions, notably on chromosomes 2, 27, and 33. Sequence alignments revealed high local sequence identity, including base substitutions, insertions, and deletions, supporting the physical inclusion of previously unmapped scaffold fragments within autosomal regions. These results confirm the hypothesis that contigs and scaffolds showing high LD with autosomes may be mis-mapped in the current reference genome. Our findings demonstrate that LD-based approaches, combined with whole-genome sequencing data, provide a powerful framework for improving the accuracy of the chicken reference genome assembly. The proposed method is complementary to long-reads methods such as PacBio, which is currently used the de novo assembly of two local Spanish chicken breeds.

Keywords: 2026

How to Cite:

Garcà­a-Cabrero, A., Garcà­a-Ruiz, F., Gomez-Raya, L., Peiró-Pastor, R., Rauw, W. & Torres, O., (2026) “The use of Linkage Disequilibrium for the Construction of a Knotty Reference Genome Map of Gallus domesticus”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2285453. doi: https://doi.org/10.31274/wcgalp.23714

Rights: 1