ArticleBMC plant biology2015
Genome-wide Association Study (GWAS) of mesocotyl elongation based on re-sequencing approach in rice.
Article in BMC plant biology, 2015. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 52 papers.
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Who cites it
52 citing papers in PubMed.
- Genome-wide association study uncovers the genetic loci for yield-related traits in waxy rice.Journal of applied genetics · 2026Article
- BloomSight: An ultra-high-frequency phenotyping framework for diurnal flowering dynamics inPlant phenomics (Washington, D.C.) · 2026Article
- Genome-wide association analysis and molecular marker development for effective tiller number in rice natural population.BMC plant biology · 2026Article
- Amino-acid-transporter-mediated assembly of rhizosphere microbiota enhances soil organic nitrogen acquisition in rice.Nature plants · 2026Article
- Genome-wide association analysis of wheat quality traits in Qinghai Province.BMC plant biology · 2026Article
- Dissection of genomic regions underlying early seedling vigour in chickpea through genome-wide association mapping.BMC plant biology · 2025Article
- Genetic loci and functional genes conferring deep-sowing tolerance across multiple environments in soybean.TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik · 2025Article
- Phenomics-assisted genetic dissection and molecular design of drought resistance in rice.Plant communications · 2025Article
- Identification of key genes associated with mesocotyl length through a genome-wide association study in rice.Frontiers in plant science · 2025Article
- Enhanced antioxidant activity improves deep-sowing tolerance in maize.BMC plant biology · 2024Article
- Discovering New QTNs and Candidate Genes Associated with Rice-Grain-Related Traits within a Collection of Northeast Core Set and Rice Landraces.Plants (Basel, Switzerland) · 2024Article
- Genome-Wide Association Study Identifies Quantitative Trait Loci and Candidate Genes Involved in Deep-Sowing Tolerance in Maize (Plants (Basel, Switzerland) · 2024Article
- Development of Novel KASP Markers for Improved Germination in Deep-Sown Direct Seeded Rice.Rice (New York, N.Y.) · 2024Article
- Article
- The transcription factor MYB110 regulates plant height, lodging resistance, and grain yield in rice.The Plant cell · 2024Article
- Unveiling genetic basis of seedling emergence from deep soil depth under dry direct- seeded conditions in rice (Frontiers in plant science · 2024Article
- Identification of Genetic Loci for Rice Seedling Mesocotyl Elongation in Both Natural and Artificial Segregating Populations.Plants (Basel, Switzerland) · 2023Article
- Article
- 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
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17 authors.
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Abstract
backgroundMechanized dry seeded rice can save both labour and water resources. Rice seedling establishment is sensitive to sowing depth while mesocotyl elongation facilitates the emergence of deeply sown seeds.
resultsA set of 270 rice accessions, including 170 from the mini-core collection of Chinese rice germplasm (C Collection) and 100 varieties used in a breeding program for drought resistance (D Collection), was screened for mesocotyl lengths of seedlings grown in water (MLw) in darkness and in 5 cm sand culture (MLs). Twenty six accessions (10.53 %) have MLw longer than 1.0 cm. Eleven accessions had the highest mesocotyl lengths, i.e. 1.4 - 5.05 cm of MLw and 3.0 - 6.4 cm in 10 cm sand culture, including 7 upland landraces or varieties. The genotypic data of 1,019,883 SNPs were developed by re-sequencing of those accessions. A whole-genome SNP array (Rice SNP50) was used to genotype 24 accessions as a validation panel, giving 98.41 % of consistent SNPs with the re-sequencing data in average. GWAS based on compressed mixed linear model was conducted using GAPIT. Based on a threshold of -log(P) ≥8.0, 13 loci were associated to MLw on rice chromosome 1, 3, 4, 5, 6 and 9, respectively. Three associated loci, on chromosome 3, 6, and 10, were detected for MLs. A set of 99 associated SNPs for MLw, based on a compromised threshold (-log(P) ≥7.0), located in intergenic regions or different positions of 36 annotated genes, including one cullin and one growth regulating factor gene.
conclusionsHigher proportion and extension of elongated mesocotyls were observed in the mini-core collection of rice germplasm and upland rice landraces or varieties, possibly causing the correlation between mesocotyl elongation and drought resistance. GWAS found 13 loci for mesocotyl length measured in dark germination that confirmed the previously reported co-location of two QTLs across populations and experiments. Associated SNPs hit 36 annotated genes including function-matching candidates like cullin and GRF. The germplasm with elongated mesocotyl, especially upland landraces or varieties, and the associated SNPs could be useful in further studies and breeding of mechanized dry seeded rice.
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