Evidence map›Paper›PMID 36411593›Full record

ArticleThe plant genome2023

Development of molecular inversion probes for soybean progeny genomic selection genotyping.

Haichuan Wang, Benjamin Campbell, Mary Happ, Samantha McConaughy, Aaron Lorenz, Keenan Amundsen, Qijian Song, Vincent Pantalone, David Hyten

Open access · goldAbstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in The plant genome, 2023. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 5 papers.

0numbers the graph read from it
0cells of the map it votes in
5citing papers in PubMed
1.3field-weighted citation impact, top 17% of its field
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

5 citing papers in PubMed, 6 citations in OpenAlex.

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4 · The record

Corrections and comments

PubMed lists nothing against this paper. Absence here is not a guarantee, only a check that was made.

5 · Who and what money

Authors and funding

9 authors at 4 institutions in 1 country.

Haichuan WangDep. of Agronomy and Horticulture, Univ. of Nebraska-Lincoln, Lincoln, NE, USA.
Benjamin CampbellDep. of Agronomy and Plant Genetics, Univ. of Minnesota, St. Paul, MN, USA.
Mary HappDep. of Agronomy and Horticulture, Univ. of Nebraska-Lincoln, Lincoln, NE, USA.ORCID 0000-0002-5897-2617
Samantha McConaughyDep. of Agronomy and Horticulture, Univ. of Nebraska-Lincoln, Lincoln, NE, USA.
Aaron LorenzDep. of Agronomy and Plant Genetics, Univ. of Minnesota, St. Paul, MN, USA.ORCID 0000-0002-4361-1683
Keenan AmundsenDep. of Agronomy and Horticulture, Univ. of Nebraska-Lincoln, Lincoln, NE, USA.
Qijian SongUSDA-ARS, Soybean Genomics and Improvement Lab, Beltsville, MD, USA.
Vincent PantaloneDep. of Plant Sciences, Univ. of Tennessee, Knoxville, TN, USA.
David HytenDep. of Agronomy and Horticulture, Univ. of Nebraska-Lincoln, Lincoln, NE, USA.ORCID 0000-0001-6324-9389
University of Nebraska–Lincoln · USUniversity of Minnesota · USAgricultural Research Service · USUniversity of Tennessee at Knoxville · US

Funding

No grant is acknowledged in the PubMed record.

6 · The paper itself

Abstract

Increasing rate of genetic gain for key agronomic traits through genomic selection requires the development of new molecular methods to run genome-wide single-nucleotide polymorphisms (SNPs). The main limitation of current methods is the cost is too high to screen breeding populations. Molecular inversion probes (MIPs) are a targeted genotyping-by-sequencing (GBS) method that could be used for soybean [Glycine max (L.) Merr.] that is both cost-effective, high-throughput, and provides high data quality to screen breeder's germplasm for genomic selection. A 1K MIP SNP set was developed for soybean with uniformly distributed markers across the genome. The SNPs were selected to maximize the number of informative markers in germplasm being tested in soybean breeding programs located in the northern-central and middle-southern regions of the United States. The 1K SNP MIP set was tested on diverse germplasm and a recombinant inbred line (RIL) population. Targeted sequencing with MIPs obtained an 85% enrichment for the targeted SNPs. The MIP genotyping accuracy was 93% overall, whereas homozygous call accuracy was 98% with <10% missing data. The accuracy of MIPs combined with its low per-sample cost makes it a powerful tool to enable genomic selection within soybean breeding programs.

Indexed as

Genome, PlantGenomicsGenotyping TechniquesGlycine maxMolecular ProbesMolecular Probe TechniquesSelection, GeneticData AnalysisGenotypeHeterozygotePlant BreedingPolymorphism, Single NucleotideReproducibility of ResultsSequence AlignmentUnited StatesWorkflowMolecular Probes

Identifiers

PMID36411593
PMCPMC12807013
OpenAlexW4309659657

What OpenQuestion holds

Textmetadata
Read underepoch 390

Registered trials

None linked

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.