Genomic analysis of the Ixworth chicken: insights into a local dual-purpose breed

Intensive genetic selection in commercial poultry has greatly enhanced productivity, but it has also caused substantial genetic erosion, affecting long-term sustainability. Body weight and growth rate as well as egg production are considered antagonistic traits, leading to highly specialized broiler and layer lines with further loss of diversity. Local breeds, such as the British Ixworth dual-purpose chicken, are vital reservoirs of biodiversity, yet the genomic basis of their balanced traits remains poorly understood. At the same time, ethical concerns regarding male chick culling have led several European countries to ban the practice in recent years, renewing interest in dual-purpose systems in which both sexes can be viably utilized. By addressing both genetic erosion and chick culling, dual-purpose chickens can contribute to more sustainable poultry production. To investigate the genetic architecture of the Ixworth chicken, we conducted high-resolution whole-genome sequencing, and compared it with its wild progenitor and specialized commercial lines for layers and broilers. Our analyses identify the Ixworth chicken as genetically distinct, with moderate nucleotide diversity, low inbreeding, and rapid decay of linkage disequilibrium, suggesting limited historical selection despite possible recent bottlenecks associated with its critical status. Its genetic architecture further revealed distinguished selection signatures balancing meat productivity (chromosomes 1, 6, 28) with egg-laying performance (chromosomes 1, 3, 10), contrasting with the narrow selection for growth in broilers and reproductive efficiency in layers. Notably, we discovered a distinct selective sweep on chromosome 4 (90.10–90.30 Mb) that harbors the developmental regulator CYP26B1, the exocytosis regulator EXOC6B, regulatory long non-coding RNAs, and co-localizes with QTLs for cooking loss and fatty acid composition. This alignment provides a compelling genomic basis for the breed’s historical reputation for superior table quality, a trait likely selected either deliberately or as a fortunate consequence of selection on a linked developmental pathway. This study uncovers the complex genetic legacy of the British Ixworth dual-purpose breed, offering insights into population parameters and positive selection signatures that may help to enhance biodiversity and animal welfare in future breeding programs and guide conservation efforts of the breed.