Genomic insights into <em>Lolium multiflorum</em> diversity for forage breeding in Andean livestock systems

Understanding the genetic diversity of Lolium multiflorum is essential for strengthening breeding programs and enhancing the sustainability of Andean livestock systems. This study evaluated the genomic variability and population structure of 27 accessions of Lolium multiflorum from the Cajamarca region and the INIA Amazonas germplasm bank (Peru), using the genotyping-by-sequencing (GBS) technique. DNA extracted from young leaves was sequenced on an Illumina NovaSeq 6000 platform, and reads were processed with bioinformatic tools (FastQC, BWA, GATK, VCFtools, BCFtools, and scikit-allel). After stringent filtering, 2,070 SNPs were obtained across seven chromosomes, with heterogeneous SNP distribution across the seven chromosomes. Principal Coordinate Analysis (PCoA) and phylogenetic analysis (UPGMA) revealed two distinct genetic groups, indicating a complex structure shaped by gene flow and local selection. AMOVA showed that 90.01% of the genetic variation occurs within populations, whereas 9.99% corresponds to interregional differences (PhiPT = 0.099, p &lt; 0.006). The negative FIS values (Cajamarca = -0.2312; Amazonas = -0.5489) indicate an excess of heterozygotes, a pattern typically associated with predominantly allogamous species. Moreover, the high levels of observed heterozygosity (Ho &gt; 0.57) point to possible hybrid vigor and suggest that these populations may be maintaining a stable genetic equilibrium. These results confirm that Peruvian L. multiflorum maintains a broad genetic base, shaped by historical germplasm exchange and local environmental adaptation. This genetic diversity provides essential insights for conservation planning and supports breeding initiatives to improve forage resilience and productivity in high-Andean ecosystems.