<b>Passport data and phenotypic characterization of sequenced accessions</b>

<i>Bromus auleticus</i>, a valuable forage grass native to the Pampa biome, is currently suffering genetic erosion. Therefore, it is central to assess the appropriate methodologies for developing population genomic studies and contributing to the conservation of this plant genetic resource. This study evaluated five accessions using two genotyping strategies: individual sequencing (ind-seq) and pooled sequencing (pool-seq). To compare their efficacy, was investigated the correlation between allele frequencies calculated using each approach. Geneticdiversity and population structure were also analyzed using both methods. These comparisons explicitly accounted for the potential effects of one or more of the following parameters: sample size, missing data, sequencing depth, and minor allele frequencies. Notably, the highest concordance and percentage of common SNPs between ind-seq and pool-seq was achieved using 30 to 60 plants per accession, with a maximum missing data threshold of 10% and a more tolerant minimum allele frequency threshold for pool-seq (0.01) compared to ind-seq (0.05). Reaching maximum similarity in allele frequencies also required a higher sequencing depth for pool-seq (4.8 million reads-Mr) than for ind-seq (0.9 Mr). Pools of 50 individuals yielded the highest number of polymorphic sites, averaging over 9,000 across all accessions at a sequencing depth of 4.8 Mr. Under these conditions, pool-seq consistently yielded a means across all accessions of 0.09 higher expected heterozygosity and 0.24 lower allelic richness compared to ind-seq across all accessions. The population structure detected with both methodologies showed agreement, aligning with the outcrossing nature of <i>B. auleticus</i> and the geographical origin of each accession. The average inbreeding coefficient of 0.2 indicates signs of inbreeding, highlighting the importance of conservation efforts of this valuable plant genetic resource. Based on these findings, two workflows were proposed to carry out population genomics studies of <i>Bromus auleticus</i>.潘帕斯草原原生的优质饲草博氏雀麦（Bromus auleticus）目前正面临遗传侵蚀风险。因此，开发适用于该物种的群体基因组学研究方法、助力其植物遗传资源保护，已成为当前的核心任务。本研究采用两种基因分型策略对5份种质资源进行评估：个体测序（ind-seq）与混池测序（pool-seq）。为比较二者的应用效能，本研究探究了两种方法计算得到的等位基因频率之间的相关性，并同时利用两种方法分析了遗传多样性与群体结构。上述比较分析明确考量了以下一项或多项参数的潜在影响：样本量、缺失数据、测序深度以及次要等位基因频率。值得注意的是，当每份种质的样本量设置为30~60株、最大缺失数据阈值设为10%，且混池测序的最小等位基因频率阈值（0.01）较个体测序（0.05）更为宽松时，个体测序与混池测序间的一致性及共有单核苷酸多态性（SNP）位点占比达到最高。要实现等位基因频率的最高相似性，混池测序所需的测序深度（4.8百万读长，Mr）同样高于个体测序（0.9 Mr）。每份种质使用50个个体构建的混池，在4.8 Mr测序深度下可获得最多的多态性位点，所有种质的平均多态性位点数量超过9000个。在此条件下，相较于个体测序，混池测序得到的所有种质平均预期杂合度高出0.09，而等位基因丰富度则降低0.24。两种方法检测到的群体结构结果一致，与博氏雀麦的异交特性及每份种质的地理起源相符。平均近交系数为0.2，这表明该物种存在近交迹象，凸显了对这一优质植物遗传资源开展保护工作的重要性。基于上述研究结果，本研究提出了两套适用于博氏雀麦群体基因组学研究的实验流程。