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022			_a1932-6203 (Online)
024	8		_ahttps://doi.org/10.1371/journal.pone.0325548
040			_aMX-TxCIM
041			_aeng
100	1		_aGillman, L. _939651
245	1	0	_aOptimizing genomic diversity assessments for conservation of Bromus auleticus (Trinius ex Nees) using individual and pooled sequencing
260			_aSan Francisco, CA (United States of America) : _bPublic Library of Science, _c2025.
500			_aPeer review
500			_aOpen Access
520			_aBromus auleticus, a valuable forage grass native to the Pampa biome, is currently undergoing genetic erosion. Therefore, it is essential to assess appropriate methodologies for developing population genomic studies that will contribute to the conservation of this genetic resource. In this study, we evaluated five accessions using two genotyping strategies: individual sequencing (ind-seq) and pooled sequencing (pool-seq). To assess methodologies effectiveness, the correlation between allele frequencies calculated using each approach was investigated, as well as genetic diversity and population structure. These comparisons explicitly accounted for the potential effects of factors such as sample size, missing data, sequencing depth, and minor allele frequencies. The highest values of frequencies concordance and percentage of SNPs in common between ind-seq and pool-seq were achieved using a sample size of 30-60 plants per accession. These values were obtained with a maximum missing data threshold of 10% and a less strict minimum allele frequency threshold for pool-seq (0.01) compared to ind-seq (0.05). Pool-seq required a higher sequencing depth per accession (4.8 million reads) compared to ind-seq (0.9 million reads) to achieve similar allele frequencies. Pools of 50 individuals yielded the highest number of polymorphic sites, averaging over 9,000 per accession at a sequencing depth of 4.8 Mr. Under these conditions, pool-seq consistently resulted in an average of 0.09 higher expected heterozygosity and a 0.24 lower allelic richness compared to ind-seq in all accessions. Population structure inferred with both methodologies confirmed the outcrossing nature of B. auleticus and aligned with the geographical origin of each accession. The average inbreeding coefficient of 0.2 evidence inbreeding, which highlights the importance of conservation efforts for this valuable plant genetic resource. Based on these findings, we propose two workflows for conducting population genomics studies on Bromus auleticus.
546			_aText in English
597			_dAgencia Nacional de Investigación e Innovación (ANII) _dInstituto Nacional de Investigación Agropecuaria (INIA) _dCentro Universitario Regional del Este (CURE)
650		0	_aGenetic diversity (resource) _gAGROVOC _92974
650		7	_aGenotyping _2AGROVOC _922057
650		7	_aSequence analysis _2AGROVOC _939652
650		7	_aSingle nucleotide polymorphisms _2AGROVOC _910805
700	1		_aCondón, F. _939653
700	1		_aPetroli, C.D. _gGenetic Resources Program _8CPEC01 _91408
700	1		_aRivas, M. _939654
773	0		_tPLOS One _gv. 20, no. 6, art. e0325548 _dSan Francisco, CA (United States of America) : Public Library of Science, 2025. _wG94957 _x1932-6203
856	4		_yOpen Access through DSpace _uhttps://hdl.handle.net/10883/35801
942			_cJA _n0 _2ddc
999			_c69046 _d69038