ArticlePloS one2013
Analysis and optimization of bulk DNA sampling with binary scoring for germplasm characterization.
Article in PloS one, 2013. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 16 papers.
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16 citing papers in PubMed.
- Large scale sampling of Mexican maize landraces for the presence of transgenes.Transgenic research · 2023Article
- Genotyping of DNA pools identifies untapped landraces and genomic regions to develop next-generation varieties.Plant biotechnology journal · 2023Article
- Genetic diversity and population structure of Uganda's yam (Dioscorea spp.) genetic resource based on DArTseq.PloS one · 2023Article
- Maize dispersal patterns associated with different types of endosperm and migration of indigenous groups in lowland South America.Annals of botany · 2022Article
- RAD-seq as an effective strategy for heterogenous variety identification in plants-a case study in Italian Ryegrass (Lolium multiflorum).BMC plant biology · 2022Article
- Development of 50 InDel-based barcode system for genetic identification of tartary buckwheat resources.PloS one · 2021Article
- Fingerprint identification of white clover cultivars based on SSR molecular markers.Molecular biology reports · 2020Article
- Comparisons of sampling methods for assessing intra- and inter-accession genetic diversity in three rice species using genotyping by sequencing.Scientific reports · 2020Article
- An information theory approach to biocultural complexity.Scientific reports · 2020Article
- Deciphering the Genetic Diversity of Landraces With High-Throughput SNP Genotyping of DNA Bulks: Methodology and Application to the Maize 50k Array.Frontiers in plant science · 2020Article
- Genetic variability evaluation and cultivar identification of tetraploid annual ryegrass using SSR markers.PeerJ · 2019Article
- An informational view of accession rarity and allele specificity in germplasm banks for management and conservation.PloS one · 2018Article
- An SSR-based approach incorporating a novel algorithm for identification of rare maize genotypes facilitates criteria for landrace conservation in Mexico.Ecology and evolution · 2017Article
- Barcode System for Genetic Identification of Soybean [Frontiers in plant science · 2017Article
- Insight into the genetic variability analysis and cultivar identification of tall fescue by using SSR markers.Hereditas · 2016Article
- Linkage disequilibrium and population-structure analysis among Capsicum annuum L. cultivars for use in association mapping.Molecular genetics and genomics : MGG · 2014Article
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6 authors.
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Abstract
The strategy of bulk DNA sampling has been a valuable method for studying large numbers of individuals through genetic markers. The application of this strategy for discrimination among germplasm sources was analyzed through information theory, considering the case of polymorphic alleles scored binarily for their presence or absence in DNA pools. We defined the informativeness of a set of marker loci in bulks as the mutual information between genotype and population identity, composed by two terms: diversity and noise. The first term is the entropy of bulk genotypes, whereas the noise term is measured through the conditional entropy of bulk genotypes given germplasm sources. Thus, optimizing marker information implies increasing diversity and reducing noise. Simple formulas were devised to estimate marker information per allele from a set of estimated allele frequencies across populations. As an example, they allowed optimization of bulk size for SSR genotyping in maize, from allele frequencies estimated in a sample of 56 maize populations. It was found that a sample of 30 plants from a random mating population is adequate for maize germplasm SSR characterization. We analyzed the use of divided bulks to overcome the allele dilution problem in DNA pools, and concluded that samples of 30 plants divided into three bulks of 10 plants are efficient to characterize maize germplasm sources through SSR with a good control of the dilution problem. We estimated the informativeness of 30 SSR loci from the estimated allele frequencies in maize populations, and found a wide variation of marker informativeness, which positively correlated with the number of alleles per locus.
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