ArticleGenes2024
The Effect of Genome Parametrization and SNP Marker Subsetting on Genomic Selection in Autotetraploid Alfalfa.
Article in Genes, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 10 papers.
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Who cites it
10 citing papers in PubMed.
- Alfalfa andPhysiology and molecular biology of plants : an international journal of functional plant biology · 2026Article
- White Lupin Genomic Selection for Adaptation to Drought or Moderately Calcareous Soil: A Proof-of-Concept Study.International journal of molecular sciences · 2026Article
- Characterization of Genetic Diversity and Genomic Prediction of Secondary Metabolites in Pea Genetic Resources.Plants (Basel, Switzerland) · 2026Article
- Implications of morphological and molecular distinctness on the registration of alfalfa candidate varieties issued by a breeding program: a case study.Frontiers in plant science · 2026Article
- Genotyping by sequencing reveals a chromosome A04 QTL governing whitefly resistance in upland cotton.Scientific reports · 2025Article
- Genetic Variation and Genome-Enabled Prediction of White Lupin Frost Resistance in Different Reference Populations.International journal of molecular sciences · 2025Article
- Genetic variation and genome-enabled selection of white lupin for key seed quality traits.BMC genomics · 2025Article
- Targeted genotyping (90K-SPET) facilitates genome-wide association studies and the prediction of yield-related traits in faba bean (Vicia faba L.).BMC plant biology · 2025Article
- Molecular markers enhance substantially the distinctness of alfalfa varieties for registration and protection.The plant genome · 2025Article
- Genome-Wide Association and Genomic Prediction of Alfalfa (International journal of molecular sciences · 2025Article
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Authors and funding
5 authors.
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No grant is acknowledged in the PubMed record.
Abstract
backgroundAlfalfa, the most economically important forage legume worldwide, features modest genetic progress due to long selection cycles and the extent of the non-additive genetic variance associated with its autotetraploid genome.
methodsTo improve the efficiency of genomic selection in alfalfa, we explored the effects of genome parametrization (as tetraploid and diploid dosages, plus allele ratios) and SNP marker subsetting (all available SNPs, only genic regions, and only non-genic regions) on genomic regressions, together with various levels of filtering on reading depth and missing rates. We used genotyping by sequencing-generated data and focused on traits of different genetic complexity, i.e., dry biomass yield in moisture-favorable (FE) and drought stress (SE) environments, leaf size, and the onset of flowering, which were assessed in 143 genotyped plants from a genetically broad European reference population and their phenotyped half-sib progenies.
resultsOn average, the allele ratio improved the predictive ability compared with other genome parametrizations (+7.9% vs. tetraploid dosage, +12.6% vs. diploid dosage), while using all the SNPs offered an advantage compared with any specific SNP subsetting (+3.7% vs. genic regions, +7.6% vs. non-genic regions). However, when focusing on specific traits, different combinations of genome parametrization and subsetting achieved better performances. We also released
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