ArticleGenes2019
Genome-wide Association Study (GWAS) for Mesocotyl Elongation in Rice (
Article in Genes, 2019. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 25 papers.
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Who cites it
25 citing papers in PubMed.
- Genetic architecture of phenological, morphological, and phytochemical traits in Cannabis landraces.The plant genome · 2026Article
- An evolutionarily diverged CCD4 enzyme negatively regulates mesocotyl elongation in rice.The New phytologist · 2026Article
- Unlocking genetic hotspots: GWAS reveals key nitrogen responsive genomic regions and key genes for root and yield traits in indica rice.Molecular genetics and genomics : MGG · 2025Article
- Genome-wide association analysis in identification of superior haplotypes for vegetative stage drought stress tolerance in rice.Physiology and molecular biology of plants : an international journal of functional plant biology · 2025Article
- Identification of key genes associated with mesocotyl length through a genome-wide association study in rice.Frontiers in plant science · 2025Article
- Comparative Analysis of Mesocotyl Elongation Ability among Maize Inbred Lines.International journal of molecular sciences · 2024Article
- Article
- Long non-coding RNAs and their potential function in response to postharvest senescence of Sparassis latifolia during cold storage.Scientific reports · 2024Article
- Antimalarial drug discovery: progress and approaches.Nature reviews. Drug discovery · 2023Review
- Article
- Identification of Genetic Loci for Rice Seedling Mesocotyl Elongation in Both Natural and Artificial Segregating Populations.Plants (Basel, Switzerland) · 2023Article
- Comprehensive investigation of long non-coding RNAs in an endophytic fungus Calcarisporium arbuscula NRRL 3705.Archives of microbiology · 2023Article
- Screening germplasm and detecting QTLs for mesocotyl elongation trait in rice (Oryza sativa L.) by association mapping.BMC genomic data · 2023Article
- Genome-wide association analysis for emergence of deeply sown rice (Frontiers in plant science · 2023Article
- Validation of genes affecting rice mesocotyl length through candidate association analysis and identification of the superior haplotypes.Frontiers in plant science · 2023Article
- GWAS with principal component analysis identify QTLs associated with main peanut flavor-related traits.Frontiers in plant science · 2023Article
- Transcriptome-guided annotation and functional classification of long non-coding RNAs in Arabidopsis thaliana.Scientific reports · 2022Article
- The Combination of Conventional QTL Analysis, Bulked-Segregant Analysis, and RNA-Sequencing Provide New Genetic Insights into Maize Mesocotyl Elongation under Multiple Deep-Seeding Environments.International journal of molecular sciences · 2022Article
- Primary Root and Mesocotyl Elongation in Maize Seedlings: Two Organs with Antagonistic Growth below the Soil Surface.Plants (Basel, Switzerland) · 2021Review
- Proofing Direct-Seeded Rice with Better Root Plasticity and Architecture.International journal of molecular sciences · 2021Review
Corrections and comments
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Authors and funding
8 authors.
Funding
No grant is acknowledged in the PubMed record.
Abstract
Mesocotyl is a crucial organ for pushing buds out of soil, which plays a vital role in seedling emergence and establishment in dry direct-seeded rice. However, the genetic mechanisms of mesocotyl elongation remains unclear. In our study, 208 rice accessions were used to identify the SNPs significantly associated with mesocotyl length under various culture conditions, including sand, water and soil. The mesocotyl length ranges from 0 to 4.88 cm, 0 to 3.99 cm and 0 to 4.51 cm in sand, water and soil covering, respectively. A total of 2,338,336 SNPs were discovered by re-sequencing of 208 rice accessions. Genome-wide association study (GWAS) based on mixed linear model (MLM) was conducted and 16 unique loci were identified on chromosomes 1, 2 (2), 3, 4, 5 (2), 6 (2), 7, 8, 9 (2) and 12 (3), respectively, explaining phenotypic variations ranging from 6.3 to 15.9%. Among these loci, 12 were stable across two or more environments. Ten out of the sixteen loci coincided with known genes or quantitative trait locus (QTL), whereas the other six were potentially novel loci. Furthermore, five high-confidence candidate genes related to mesocotyl elongation were identified on chromosomes 1, 3, 5, 9 and 12. Moreover, qRT-PCR analysis showed that all the five genes showed significant expression difference between short-mesocotyl accessions and long-mesocotyl accessions. This study provides new insights into the genetic architecture of rice mesocotyl, the associated SNPs and germplasms with long mesocotyl could be useful in the breeding of mechanized dry direct-seeded rice.
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