Pangenomics for Agricultural Breeding: Construction Strategies, Evidence Integration, and Translational Constraints

Area of Science:

• Genomics
• Bioinformatics
• Agricultural Science

Background:

• Pangenomics offers a comprehensive view of genetic diversity beyond single reference genomes.
• It is crucial for understanding structural variants (SVs), copy number variations (CNVs), and presence/absence variations (PAVs) in agricultural species.
• These variations influence domestication, adaptation, and breeding traits.

Purpose of the Study:

• To review advancements in pangenomics for livestock and crops.
• To compare different technical approaches for pangenome construction and analysis.
• To discuss the application and limitations of pangenome resources in breeding.

Main Methods:

• Summarizing progress in long-read sequencing, telomere-to-telomere (T2T) assembly, and graph-based genome analysis.
• Comparing variant integration, reference-guided iterative graph construction, and reference-free graph construction methods.
• Evaluating methods based on accuracy, scalability, reference bias, and computational demand.

Main Results:

• Pangenome resources facilitate discovery of hidden variants, interpretation of quantitative trait loci (QTL) and genome-wide association studies (GWAS), and environmental adaptation analysis.
• Different pangenome construction strategies yield varying results in terms of accuracy, consistency, and computational requirements.
• Unresolved limitations include graph complexity, pipeline-dependent variant calls, and challenges in functional annotation and cross-study comparability.

Conclusions:

• Pangenome studies are valuable but non-equivalent, with resource-building, method development, and trait-focused studies offering different insights.
• Inconsistencies across studies often reflect differences in sampling, genome complexity, and methodology rather than simple disagreements.
• Further development is needed to overcome current limitations and fully leverage pangenomics for agricultural breeding.