Comparison of genetic linkage maps constructed using three reference genomes in autotetraploid alfalfa

This study aimed to compare genetic maps constructed using SNP markers derived from genotyping-by-sequencing, based on three distinct alfalfa reference genomes: (1) the monoploid assembly of ZhongmuNo.1 (Map 1), (2) the first homolog from the allele-aware XinJiang DaYe assembly (Map 2), and (3) a stable FASTA representation of a graph-based pangenome built using ZhongmuNo.1 as the backbone, incorporating four additional assemblies (Map 3). The alfalfa mapping population included 165 F1 individuals, and each final map was resolved into four haplotypes spanning eight linkage groups.