Simulation-based optimization of genomic selection scheme for accelerating genetic gain while preventing inbreeding...

Area of Science:

• Plant breeding
• Genetics
• Quantitative genetics

Background:

• Genomic selection (GS) accelerates genetic gain in plant breeding.
• Onion (Allium cepa L.) is an out-crossing crop susceptible to inbreeding depression, complicating breeding programs.
• Contamination of self-pollinated seeds is a common issue in onion breeding.

Purpose of the Study:

• To simulate and compare breeding programs with and without genomic selection (GS) in onion.
• To develop and evaluate novel GS schemes to mitigate inbreeding depression while maximizing genetic gain.
• To assess the long-term efficiency of different GS strategies in onion breeding.

Main Methods:

• Simulation of 10-year breeding programs under various GS scenarios.
• Implementation of general GS, GS with shortened generation time, and a proposed GS scheme.
• The proposed scheme integrates shortened generation time, prediction model updates, and avoidance of co-selecting close relatives.

Main Results:

• General GS with shortened generation time initially provided the highest genetic gain but led to rapid inbreeding.
• The proposed GS scheme demonstrated superior performance in later years, achieving substantial genetic gain with significantly lower inbreeding levels.
• Onion breeding benefits from GS, with optimal scheme selection dependent on the desired breeding period.

Conclusions:

• Genomic selection is a valuable tool for enhancing onion breeding programs.
• A tailored GS strategy combining shortened generation time and updated prediction models is crucial for sustainable long-term breeding.
• Careful selection of GS schemes is necessary to balance genetic gain and control inbreeding depression in onion.