Single nucleotide Polymorphism (SNP) identification, genetic diversity, and population structure of Ryegrass from the northeastern highlands of Peru

Ryegrass (Lolium multiflorum) is a combined forage used in livestock support systems in temperate climates. Its favorable characteristics include high nutritional value, rapid regrowth, and remarkable environmental adaptability. Understanding its genetic diversity is essential for guiding conservation strategies and creating improved cultivars. This study aimed to identify single nucleotide polymorphisms (SNPs) and evaluate the genetic diversity and structure of 64 ryegrass lines from northeastern Peru. DNA was extracted and genotyped using the genotyping-by-sequencing (GBS) technique, followed by bioinformatic analysis using the Stacks pipeline and population genetics tools. A total of 12,199 high-quality single nucleotide polymorphisms (SNPs) were identified, evenly distributed across seven chromosomes, with an average density of 5.4 SNPs/Mb. A proportion of these markers were located in coding regions, which had a functionally significant impact on functionally significant genes, thu..., 1.1.Plant material
During 2024, ryegrass samples were collected from the genebank  of the National Institute of Agrarian Innovation (INIA) in Peru. The collection involved randomly sampling various ryegrass populations to ensure a genetically representative background for each population. The samples correspond to material originally collected in 2002 in the Cajamarca Region, from the following locations: Cutervo (5), Tacabamba (7), Sendamal (5), Micuypampa (4), Paccha (4), El Agrario (4), Calquis (4), Bambamarca (4), Campiña (3), Santa Cruz (2), Cochan (4), and Baños del Inca (4).
Additionally, 14 commercial ryegrass genotypes were collected from materials currently established at the Chachapoyas Agrarian Experimental Station, within the agrostological garden in the Amazonas region. These include the following cultivars: Wanca Grass (3), Bison II (3), Inglés (2), Max (4), and the AGP Ecotype (2) (Table 1 - uploaded as (Identification_of_experimental_lines.csv).
1.2.DNA extraction ..., # Single nucleotide Polymorphism (SNP) identification, genetic diversity, and population structure of Ryegrass from the northeastern highlands of Peru

[Access this dataset on Dryad](https://doi.org/10.5061/dryad.jh9w0vtpg)

This dataset contains a high-quality SNP matrix (n = 12,199) obtained through genotyping-by-sequencing (GBS) of 64 ryegrass (Lolium multiflorum) lines collected from the northeastern highlands of Peru. The data support the genetic diversity and population structure analyses described in the study “Single Nucleotide Polymorphism (SNP) Identification, Genetic Diversity, and Population Structure of Ryegrass from the Northeastern Highlands of Peru”.

The SNP matrix was generated by aligning raw sequencing reads to the reference genome 'Rabiosa' (L. multiflorum), followed by bioinformatic filtering to ensure data quality, representativeness, and removal of linkage disequilibrium.

## Data Structure and File Description

The file `SNP_matrix_coded_ryegrass.csv` contains t...,