Aixin Ni

Heterosis, or hybrid vigor, refers to the phenomenon that performance in hybrids is superior to the average performance of their parents. Utilization of heterosis has been adopted around 100 years ago in animal breeding, yet its genetic and molecular mechanisms remain incompletely understood. At present, most eggs, chicken meat, and pork are produced from hybrid animals. Among those, egg-laying performance is both economically important and genetically complex. This thesis focuses on hybrids between the indigenous Beijing-You chickens and the commercial White Leghorns layers, aiming to characterize their heterosis across the laying period, and to uncover the genetic variants underlying heterosis for egg-laying performance through an integrated genomic and transcriptomic approach.

A full diallel cross was constructed, and a comprehensive phenotypic dataset comprising nearly 80 traits, including egg weights, egg production, and egg quality traits, was recorded from the onset of laying to 100 weeks of age. Analyses of heritability, phenotypic and genetic correlations, heterosis, and reciprocal cross differences revealed substantial heterosis for egg-laying performance, with crossbreds showing improved persistency, and in some cases, even exceeding the better parent. To investigate the genetic basis of these patterns, whole-genome sequencing data from 1,004 chickens were combined with ovarian transcriptome data from a subset of individuals.

Additive-dominance model based genome-wide association study (GWAS) identified loci for cumulative egg number where dominance contributed to trait variation. Moreover, expression quantitative trait loci (eQTL) mapping, transcriptome-wide association study (TWAS), and Mendelian randomization revealed candidate genes related to egg number, providing evidence for potential causal relationships. The thesis further examined the genetic architectures of egg weight and egg quality traits, applying GWAS additive-dominance model, conditional analyses, and fine-mapping to identify secondary signals and potential causal variants. Results showed that dominance played a limited role in heterosis for these traits, with additive effects dominating the genetic architecture. Several promising candidate genes for egg weights and eggshell color were identified in proximity to GWAS peak signals. Overall, this work provided new insights into the genetic and transcriptomic mechanisms of heterosis in laying hens, and informed crossbreeding strategies that enhance egg-laying performance.