ArticleTAG. Theoretical and applied genetics. Theoretische und angewandte Genetik2012
Retention of agronomically important variation in germplasm core collections: implications for allele mining.
Article in TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik, 2012. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 17 papers.
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Who cites it
17 citing papers in PubMed.
- Understanding the root of the problem for tackling pea root rot disease.Frontiers in microbiology · 2024Review
- Uncovering natural allelic and structural variants of OsCENH3 gene by targeted resequencing and in silico mining in genus Oryza.Scientific reports · 2023Article
- A pan-genome data structure induced by pooled sequencing facilitates variant mining in heterogeneous germplasm.Molecular breeding : new strategies in plant improvement · 2022Article
- Whole genome re-sequencing reveals the genetic diversity and evolutionary patterns of Eucommia ulmoides.Molecular genetics and genomics : MGG · 2022Article
- Genomics Enabled Breeding Strategies for Major Biotic Stresses in Pea (Frontiers in plant science · 2022Review
- Genetic diversity and evolutionary patterns ofEcology and evolution · 2021Article
- Molecular diversity assessment of a world collection of safflower genotypes by SRAP and SCoT molecular markers.Physiology and molecular biology of plants : an international journal of functional plant biology · 2018Article
- A Review of Living Collections with Special Emphasis on Sustainability and Its Impact on Research Across Multiple Disciplines.Biopreservation and biobanking · 2017Review
- Towards new sources of resistance to the currant-lettuce aphid (Molecular breeding : new strategies in plant improvement · 2017Article
- Principal components analysis--K-means transposon element based foxtail millet core collection selection method.BMC genetics · 2016Article
- Variations in DREB1A and VP1.1 Genes Show Association with Salt Tolerance Traits in Wild Tomato (Solanum pimpinellifolium).PloS one · 2015Article
- Carotenoids gene markers for sweetpotato (Ipomoea batatas L. Lam): applications in genetic mapping, diversity evaluation and cross-species transference.Molecular genetics and genomics : MGG · 2014Article
- Article
- Geographical gradient of the eIF4E alleles conferring resistance to potyviruses in pea (Pisum) germplasm.PloS one · 2014Article
- A strategy for finding the optimal scale of plant core collection based on Monte Carlo simulation.TheScientificWorldJournal · 2014Article
- Article
- Establishing an efficient way to utilize the drought resistance germplasm population in wheat.TheScientificWorldJournal · 2013Article
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3 authors.
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Abstract
The primary targets of allele mining efforts are loci of agronomic importance. Agronomic loci typically exhibit patterns of allelic diversity that are consistent with a history of natural or artificial selection. Natural or artificial selection causes the distribution of genetic diversity at such loci to deviate substantially from the pattern found at neutral loci. The germplasm utilized for allele mining should contain maximum allelic variation at loci of interest, in the smallest possible number of samples. We show that the popular core collection assembly procedure "M" (marker allele richness), which leverages variation at neutral loci, performs worse than random assembly for retaining variation at a locus of agronomic importance in sugar beet (Beta vulgaris L. subsp. vulgaris) that is under selection. We present a corrected procedure ("M+") that outperforms M. An extensive coalescent simulation was performed to demonstrate more generally the retention of neutral versus selected allelic variation in core subsets assembled with M+. A negative correlation in level of allelic diversity between neutral and selected loci was observed in 42% of simulated data sets. When core collection assembly is guided by neutral marker loci, as is the current common practice, enhanced allelic variation at agronomically important loci should not necessarily be expected.
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