Evidence map›Paper›PMID 38791258›Full record

ArticleInternational journal of molecular sciences2024

Genetic Diversity and Genome-Wide Association Analysis of the Hulled/Naked Trait in a Barley Collection from Shanghai Agricultural Gene Bank.

Zhiwei Chen, Zhenzhu Guo, Luli Li, Nigel G Halford, Guimei Guo, Shuwei Zhang, Yingjie Zong, Shiseng Liu, Chenghong Liu, Longhua Zhou

Abstract read
PubMed Full text at PMC Publisher
In one paragraph

Article in International journal of molecular sciences, 2024. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 1 paper.

0numbers the graph read from it
0cells of the map it votes in
1citing 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

1 citing paper in PubMed.

  1. Article
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

10 authors.

Zhiwei ChenShanghai Key Laboratory of Agricultural Genetics and Breeding (21DZ2271900), Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms of Ministry of Agriculture and Rural Affairs (Shanghai), Shanghai Agricultural Biosafety Evaluation and Testing Professional Technical Service Platform (23DZ2290700), Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.ORCID 0000-0002-0478-4880
Zhenzhu GuoShanghai Key Laboratory of Agricultural Genetics and Breeding (21DZ2271900), Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms of Ministry of Agriculture and Rural Affairs (Shanghai), Shanghai Agricultural Biosafety Evaluation and Testing Professional Technical Service Platform (23DZ2290700), Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.
Luli LiShanghai Key Laboratory of Agricultural Genetics and Breeding (21DZ2271900), Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms of Ministry of Agriculture and Rural Affairs (Shanghai), Shanghai Agricultural Biosafety Evaluation and Testing Professional Technical Service Platform (23DZ2290700), Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.
Nigel G HalfordRothamsted Research, Harpenden AL5 2JQ, UK.ORCID 0000-0001-6488-2530
Guimei GuoShanghai Key Laboratory of Agricultural Genetics and Breeding (21DZ2271900), Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms of Ministry of Agriculture and Rural Affairs (Shanghai), Shanghai Agricultural Biosafety Evaluation and Testing Professional Technical Service Platform (23DZ2290700), Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.
Shuwei ZhangShanghai Key Laboratory of Agricultural Genetics and Breeding (21DZ2271900), Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms of Ministry of Agriculture and Rural Affairs (Shanghai), Shanghai Agricultural Biosafety Evaluation and Testing Professional Technical Service Platform (23DZ2290700), Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.
Yingjie ZongShanghai Key Laboratory of Agricultural Genetics and Breeding (21DZ2271900), Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms of Ministry of Agriculture and Rural Affairs (Shanghai), Shanghai Agricultural Biosafety Evaluation and Testing Professional Technical Service Platform (23DZ2290700), Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.
Shiseng LiuShanghai Key Laboratory of Agricultural Genetics and Breeding (21DZ2271900), Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms of Ministry of Agriculture and Rural Affairs (Shanghai), Shanghai Agricultural Biosafety Evaluation and Testing Professional Technical Service Platform (23DZ2290700), Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.
Chenghong LiuShanghai Key Laboratory of Agricultural Genetics and Breeding (21DZ2271900), Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms of Ministry of Agriculture and Rural Affairs (Shanghai), Shanghai Agricultural Biosafety Evaluation and Testing Professional Technical Service Platform (23DZ2290700), Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.
Longhua ZhouShanghai Key Laboratory of Agricultural Genetics and Breeding (21DZ2271900), Key Laboratory for Safety Assessment (Environment) of Agricultural Genetically Modified Organisms of Ministry of Agriculture and Rural Affairs (Shanghai), Shanghai Agricultural Biosafety Evaluation and Testing Professional Technical Service Platform (23DZ2290700), Biotechnology Research Institute of Shanghai Academy of Agricultural Sciences, Shanghai 201106, China.

Funding

Biotechnology and Biological Sciences Research Council BB/P016855/1the Climbing Plan PG22211the ear-marked fund for CARS CARS-05-01A-02the Shanghai Agriculture Applied Technology Development Program 2019-02-08-00-08-F01109
6 · The paper itself

Abstract

Barley is one of the most important cereal crops in the world, and its value as a food is constantly being revealed, so the research into and the use of barley germplasm are very important for global food security. Although a large number of barley germplasm samples have been collected globally, their specific genetic compositions are not well understood, and in many cases their origins are even disputed. In this study, 183 barley germplasm samples from the Shanghai Agricultural Gene Bank were genotyped using genotyping-by-sequencing (GBS) technology, SNPs were identified and their genetic parameters were estimated, principal component analysis (PCA) was preformed, and the phylogenetic tree and population structure of the samples were also analyzed. In addition, a genome-wide association study (GWAS) was carried out for the hulled/naked grain trait, and a KASP marker was developed using an associated SNP. The results showed that a total of 181,906 SNPs were identified, and these barley germplasm samples could be roughly divided into three categories according to the phylogenetic analysis, which was generally consistent with the classification of the traits of row type and hulled/naked grain. Population structure analysis showed that the whole barley population could be divided into four sub-populations (SPs), the main difference from previous classifications being that the two-rowed and the hulled genotypes were sub-divided into two SPs. The GWAS analysis of the hulled/naked trait showed that many associated loci were unrelated to the

Indexed as

Genome-Wide Association StudyHordeumPhylogenyPolymorphism, Single NucleotideChinaGenetic VariationGenome, PlantGenotypePhenotypePrincipal Component AnalysisQuantitative Trait LociSeed Bankgenome-wide association studies (GWAS)genotyping-by-sequencing (GBS)Hordeum vulgare L.Kompetitive Allele Specific PCR (KASP)naked trait

Identifiers

PMID38791258
PMCPMC11120781

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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.