Gene function & annotation

Genetic Architecture of Growth-Related Traits and Transcript Isoform Diversity in an F34 Advanced Intercross Chicken Line

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Abstract

Identifying genetic variants underlying growth-related traits in livestock remains challenging due to the highly polygenic nature of these traits and the predominance of regulatory variation. Here, we characterize the genetic architecture of growth-related traits and transcript isoform diversity in an F34 Advanced Intercross Line (AIL) of chickens derived from modern broiler and Fayoumi founder lines. This population exhibits extensive recombination, reduced linkage disequilibrium (LD), and substantial phenotypic variation, providing improved resolution for genetic mapping. Low-pass whole-genome sequencing (~0.8×) was performed on 376 F34 individuals, followed by genotype imputation using BaseVar and STITCH. After quality control filtering (call rate >95%, INFO >0.4, minor allele frequency >0.01), 4,087,445 autosomal SNPs were retained for genome-wide association analyses of growth-related traits. In parallel, long-read RNA sequencing was conducted on liver, muscle, and jejunum tissues from individuals within the same population, generating more than 3.4 billion mapped reads across 1,104 samples. Transcriptome assembly identified 24,112 expressed genes and 125,072 transcript isoforms, corresponding to an average of approximately 5.2 isoforms per gene, revealing extensive transcriptomic complexity across growth-relevant tissues. A substantial number of previously unannotated isoforms and alternative splicing events were detected, including complex transcript structures at key growth-related loci and long structural genes such as TTN. Comparison of LD decay across populations showed a marked reduction in LD in the F34 AIL relative to the founder lines and a previously characterized F18 AIL generation, consistent with increased mapping resolution in the advanced intercross population. Together, these results provide a detailed description of the genetic architecture of growth-related traits and the transcript isoform landscape across key tissues in the F34 AIL. This dataset establishes a foundation for future studies aimed at linking genetic associations with regulatory mechanisms affecting gene expression and transcript structure in poultry growth traits.

Keywords: 2026

How to Cite:

Cheng, H., Fang, L., Gu, S., Guan, D., Lamont, S., Liang, D., Prowse-Wilkins, C., Van Goor, A., Wang, Y., Wei, Y. & Zhou, H., (2026) “Genetic Architecture of Growth-Related Traits and Transcript Isoform Diversity in an F34 Advanced Intercross Chicken Line”, World Congress on Genetics Applied to Livestock Production Digital Archive 2026(1): 2295820. doi: https://doi.org/10.31274/wcgalp.24375

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