Stochastic simulations to optimize genomic selection for laying hens: Impact of generation interval and genotyping in the context of extended laying period

Extending the productive lifespan of laying hens is a key objective for sustainable egg production. Achieving this goal requires improving egg production and quality traits expressed late in life. Genomic selection offers opportunities to increase accuracy of selection for such traits, while shorter generation intervals can accelerate genetic progress. However, both strategies may affect inbreeding, and their combined impact in the context of extended laying cycles has not yet been quantified. Stochastic simulations were performed to evaluate seven breeding programs for layers, based on real genotype data and six quantitative traits (egg weight, egg shell strength, and laying rate, each at 60 and 90 weeks). Programs differed by generation interval (L, 60, 45, or 30 weeks) and two selection method were applied to each scenario: single-step GBLUP using male genotypes (ssGBLUPm), or single-step GBLUP using both male and female genotypes (ssGBLUPmf). A control PBLUP based scenario with a 60 weeks L was also performed. Each scenario was replicated 30 times, and results were compared for annual genetic gain (∆G), prediction accuracy (r), and inbreeding rate (∆F). Genomic evaluations using a generation interval of 60 weeks improved both ∆G and ∆F, especially when both sexes were genotyped. Reducing the generation interval to 30 weeks maximized ∆G (up to 1.17 SD/year) but increased ∆F above 1%/year. Overlapping generation schemes (45-week interval) provided an intermediate outcome, improving ∆G compared with conventional 60-week generation interval schemes while limiting ∆F compared with 30-week generation interval schemes. Including female genotypes was particularly beneficial for late-recorded traits at 90 weeks, where accuracy increased by up to 38%. Shortening generation interval and implementing genomic selection substantially increased annual genetic gain, especially for persistency traits expressed late in life. However, these strategies also raised inbreeding, with overlapping generations offering a valuable compromise. Full genotyping of both sexes enhanced accuracy and reduced the increase in ΔF per ΔG unit, highlighting the relevance of genomic selection in breeding programs aiming to extend laying periods sustainably.