ArticlePhysiology and molecular biology of plants : an international journal of functional plant biology2022
Meta-analysis of QTLs and candidate genes associated with seed germination in rice (
Article in Physiology and molecular biology of plants : an international journal of functional plant biology, 2022. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 3 papers.
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3 citing papers in PubMed, 5 citations in OpenAlex.
- GWAS Combined with Meta-Analysis Identifies OsDREB6 as a Regulator of Coleoptile Elongation Under Anaerobic Conditions in Rice.Rice (New York, N.Y.) · 2025Article
- Biocuration of a Transcription Factors Network Involved in Submergence Tolerance during Seed Germination and Coleoptile Elongation in Rice (Plants (Basel, Switzerland) · 2023Article
- Identification of novel candidate loci and genes for seed vigor-related traits in upland cotton (Frontiers in plant science · 2023Article
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Authors and funding
3 authors at 1 institution in 1 country.
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Abstract
Seed germination is one of the critical stages of plant life, and many quantitative trait loci (QTLs) control this complex trait. Meta-analysis of QTLs is a powerful computational technique for estimating the most stable QTLs regardless of the population's genetic background. Besides, this analysis effectively narrows down the confidence interval (CI) to identify candidate genes (CGs) and marker development. In the current study, a comprehensive genome-wide meta-analysis was performed on QTLs associated with germination in rice. This analysis was conducted based on the data reported over the last two decades. In this case, various analyses were performed, including seed germination rate, plumule length, radicle length, germination percentage, coleoptile length, coleorhiza length, radicle fresh weight, germination potential, and germination index. A total of 67 QTLs were projected onto a reference map for these traits and then integrated into 32 meta-QTLs (MQTLs) to provide a genetic framework for seed germination. The average CI of MQTLs was considerably reduced from 15.125 to 8.73 cM compared to the initial QTLs. This situation identified 728 well-known functionally characterized genes and novel putative CGs for investigated traits. The fold change calculation demonstrated that 155 CGs had significant changes in expression analysis. In this case, 112 and 43 CGs were up-regulated and down-regulated during germination, respectively. This study provides an overview and compares genetic loci controlling traits related to seed germination in rice. The findings can bridge the gap between QTLs and CGs for seed germination. Supplementary Information: The online version contains supplementary material available at 10.1007/s12298-022-01232-1.
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