Evidence map›Paper›PMID 39779777›Full record

ArticleScientific reports2025

Pre-breeding in alfalfa germplasm develops highly differentiated populations, as revealed by genome-wide microhaplotype markers.

Cesar A Medina, Dongyan Zhao, Meng Lin, Manoj Sapkota, Alexander M Sandercock, Craig T Beil, Moira J Sheehan, Brian M Irish, Long-Xi Yu, Hari Poudel and 10 more

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In one paragraph

Article in Scientific reports, 2025. The graph could read no effect estimate from its abstract, so it casts no vote on the map. An erratum has been issued. Cited by 6 papers.

0numbers the graph read from it
0cells of the map it votes in
6citing papers in PubMed
–field-weighted citation impact
1 · What the graph read from it

What it found

Each row is one number read from the abstract, on the scale the paper reported it, with its interval. Left of the dashed line favours the treatment, right favours the comparator. Under each row is the sentence it came from. New to these charts? A ten-minute tutorial.

The abstract states no effect estimate the extractor could read, or names no intervention and outcome on the map, so this paper lights no cell and moves no belief. It is still indexed, cited and linked below.

2 · The registry

The trial behind it

Trials whose registry record cites this paper, or whose number appears in the abstract. A trial that started after this paper was published is citing it as background, not reporting it.

Neither the registry nor the abstract names a trial number. If this is a trial report, that itself is worth knowing.

3 · Its place in the literature

Who cites it

6 citing papers in PubMed.

  1. Standardized microhaplotype databases and frameworks for assessing and mining crop genetic diversity.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2026
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4 · The record

Corrections and comments

5 · Who and what money

Authors and funding

20 authors.

Cesar A MedinaPlant Science Research Unit, USDA-ARS, St. Paul, MN, USA.
Dongyan ZhaoBreeding Insight, Cornell University, Ithaca, NY, USA.
Meng LinBreeding Insight, Cornell University, Ithaca, NY, USA.
Manoj SapkotaBreeding Insight, Cornell University, Ithaca, NY, USA.
Alexander M SandercockBreeding Insight, Cornell University, Ithaca, NY, USA.
Craig T BeilBreeding Insight, Cornell University, Ithaca, NY, USA.
Moira J SheehanBreeding Insight, Cornell University, Ithaca, NY, USA.
Brian M IrishPlant Germplasm Introduction and Testing Research Unit, USDA-ARS, Prosser, WA, USA.
Long-Xi YuPlant Germplasm Introduction and Testing Research Unit, USDA-ARS, Prosser, WA, USA.
Hari PoudelLethbridge Research and Development Center, Agriculture and Agri-Food Canada, Lethbridge, AB, Canada.
Annie ClaessensQuebec Research and Development Centre, Agriculture and Agri-Food Canada, Québec, QC, Canada.
Virginia MooreSchool of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY, USA.
Jamie CrawfordSchool of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY, USA.
Julie HansenSchool of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY, USA.
Donald ViandsSchool of Integrative Plant Science, Plant Breeding and Genetics Section, Cornell University, Ithaca, NY, USA.
Michael D PeelForage and Range Research Unit, USDA-ARS, Logan, UT, USA.
Neal TilhouDairy Forage Research Center, USDA-ARS, Madison, WI, US, USA.
Heathcliffe RidayDairy Forage Research Center, USDA-ARS, Madison, WI, US, USA.
E Charles BrummerDepartment of Plant Sciences, University of California Davis, Davis, CA, USA.
Zhanyou XuPlant Science Research Unit, USDA-ARS, St. Paul, MN, USA. zhanyou.xu@usda.gov.

Funding

Agricultural Research Service 2019-70005-30361 to ECB, HR, DV/VM, and BIAgricultural Research Service 5062-12210-004-000DHatch Multistate Research Project NE-2210 (formerly NE-1710)
6 · The paper itself

Abstract

Plant genebanks contain large numbers of germplasm accessions that likely harbor useful alleles or genes absent in commercial plant breeding programs. Broadening the genetic base of commercial alfalfa germplasm with these valuable genetic variations can be achieved by screening the extensive genetic diversity in germplasm collections and enabling maximal recombination among selected genotypes. In this study, we assessed the genetic diversity and differentiation of germplasm pools selected in northern U.S. latitudes (USDA Plant Hardiness Zone 7 or below) originating from Eurasian germplasm. The germplasm evaluated included four BASE populations (C0) from different geographical origins (Central Asia, Northeastern Europe, Balkans-Turkey-Black Sea, and Siberia/Mongolia), 20 cycle-one populations (C1) derived from each of the four BASE populations selected across five locations in the U.S. and Canada, and four commercial cultivars. Using a panel of 3,000 Diversity Array Technologies (DArTag) marker loci, we retrieved 2,994 target SNPs and approximately 12,000 microhaplotypes. Microhaplotypes exhibited higher genetic diversity values than target SNPs. Principal component analysis and discriminant analysis of principal components revealed significant population structure among the alfalfa populations based on geographical origin, while the check cultivars formed a central cluster. Inbreeding coefficients (F

Indexed as

Medicago sativaPlant BreedingPolymorphism, Single NucleotideGenetic MarkersGenetics, PopulationGenetic VariationGenome, PlantGenotypeHaplotypesGenetic MarkersAlfalfaDArTagGenetic diversityMicrohaplotypes

Identifiers

PMID39779777
PMCPMC11711157

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Read under generation 80e0d062 · epoch 390. Bibliography from PubMed, PubMed Central and OpenAlex; grants from NIH RePORTER; trial links from ClinicalTrials.gov; estimates, votes and beliefs from the OpenQuestion graph.