Genomic insights into Lolium multiflorum diversity for forage breeding in Andean livestock systems

Understanding the genetic diversity of Lolium multiflorum is essential for developing targeted breeding programs that can effectively support pasture-based livestock systems in the Peruvian Andean. This study assessed genomic variability and population structure in 27 L. multiflorum accessions 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. After bioinformatic processing, 2,070 single nucleotide polymorphisms (SNPs) with heterogeneous distribution were obtained across seven chromosomes. A Principal Coordinate and an Unweighted Pair Group Method with Arithmetic Mean analyses revealed two distinct genetic groups were identified, reflecting a complex structure shaped by gene flow and local selection. The analysis of molecular variance showed that 90% of the genetic variation occurs within populations, whereas the remaining 10% corresponds to interregional differences (PhiPT = 0.099, p < 0.006). The negative Inbreeding Coefficient (F_IS) values (Cajamarca = -0.2312; Amazonas = -0.5489) indicate an excess of heterozygotes, a pattern typically associated with predominantly outcrossing species. Additionally, high observed heterozygosity (Ho > 0.57) points to potential hybrid vigor and indicates that these populations may maintain stable genetic equilibrium. Collectively, these findings demonstrate that Peruvian L. multiflorum harbors a broad genetic base, shaped by historical germplasm exchange and local environmental adaptation. This diversity provides critical insights for conservation strategies and can supports breeding programs aimed at enhancing forage resilience and productivity in high-Andean ecosystems.