ArticlePloS one2014
Development of an alfalfa SNP array and its use to evaluate patterns of population structure and linkage disequilibrium.
Article in PloS one, 2014. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 40 papers.
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Who cites it
40 citing papers in PubMed, 84 citations in OpenAlex.
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- Multi-variant GWAS and genomic prediction dissect the genetic architecture underlying tomato fruit weight.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026Article
- Exploring the genetic diversity of the IPK Medicago germplasm collection using GBS.Plant biology (Stuttgart, Germany) · 2026Article
- Phenotypic and genomic insights into alfalfa diversity: Identifying critical loci for enhanced resilience.The plant genome · 2025Article
- BIGapp: A user-friendly genomic tool kit identified quantitative trait loci for creeping rootedness in alfalfa (Medicago sativa L.).The plant genome · 2025Article
- Optimization of high-throughput marker systems for genomic prediction in alfalfa family bulks.The plant genome · 2025Article
- Pre-breeding in alfalfa germplasm develops highly differentiated populations, as revealed by genome-wide microhaplotype markers.Scientific reports · 2025Article
- Cell-weighted polygenic risk scores are associated with β-amyloid and tau biomarkers in Alzheimer's disease.Brain communications · 2025Article
- Transcriptome-wide association mapping provides insights into the genetic basis and candidate genes governing flowering, maturity and seed weight in rice bean (Vigna umbellata).BMC plant biology · 2024Article
- Genome-wide association study for in vitro digestibility and related traits in triticale forage.BMC plant biology · 2024Article
- Multi-trait modeling and machine learning discover new markers associated with stem traits in alfalfa.Frontiers in plant science · 2024Article
- Identification of genetic loci associated with five agronomic traits in alfalfa using multi-environment trials.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2023Article
- Genetic diversity and local adaption of alfalfa populations (Medicago sativa L.) under long-term grazing.Scientific reports · 2023Article
- Alfalfa genomic selection for different stress-prone growing regions.The plant genome · 2022Article
- Genomic prediction for canopy height and dry matter yield in alfalfa using family bulks.The plant genome · 2022Article
- Accuracy of genomic selection for alfalfa biomass yield in two full-sib populations.Frontiers in plant science · 2022Article
- Construction of a high-density genetic map and localization of grazing-tolerant QTLs inFrontiers in plant science · 2022Article
- Strategies to Increase Prediction Accuracy in Genomic Selection of Complex Traits in Alfalfa (Cells · 2021Review
- A Review of Unreduced Gametes and Neopolyploids in Alfalfa: How to Fill the Gap between Well-Established Meiotic Mutants and Next-Generation Genomic Resources.Plants (Basel, Switzerland) · 2021Review
- Integration of Infinium and Axiom SNP array data in the outcrossing species Malus × domestica and causes for seemingly incompatible calls.BMC genomics · 2021Article
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Authors and funding
8 authors at 3 institutions in 1 country.
Funding
No grant is acknowledged in the PubMed record.
Abstract
A large set of genome-wide markers and a high-throughput genotyping platform can facilitate the genetic dissection of complex traits and accelerate molecular breeding applications. Previously, we identified about 0.9 million SNP markers by sequencing transcriptomes of 27 diverse alfalfa genotypes. From this SNP set, we developed an Illumina Infinium array containing 9,277 SNPs. Using this array, we genotyped 280 diverse alfalfa genotypes and several genotypes from related species. About 81% (7,476) of the SNPs met the criteria for quality control and showed polymorphisms. The alfalfa SNP array also showed a high level of transferability for several closely related Medicago species. Principal component analysis and model-based clustering showed clear population structure corresponding to subspecies and ploidy levels. Within cultivated tetraploid alfalfa, genotypes from dormant and nondormant cultivars were largely assigned to different clusters; genotypes from semidormant cultivars were split between the groups. The extent of linkage disequilibrium (LD) across all genotypes rapidly decayed to 26 Kbp at r(2) = 0.2, but the rate varied across ploidy levels and subspecies. A high level of consistency in LD was found between and within the two subpopulations of cultivated dormant and nondormant alfalfa suggesting that genome-wide association studies (GWAS) and genomic selection (GS) could be conducted using alfalfa genotypes from throughout the fall dormancy spectrum. However, the relatively low LD levels would require a large number of markers to fully saturate the genome.
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