ArticleRice (New York, N.Y.)2020
The Candidate Genes Underlying a Stably Expressed QTL for Low Temperature Germinability in Rice (Oryza sativa L.).
Article in Rice (New York, N.Y.), 2020. The graph could read no effect estimate from its abstract, so it casts no vote on the map. Cited by 12 papers.
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12 citing papers in PubMed, 37 citations in OpenAlex.
- Low temperature-induced profiling of transcription and alternative splicing during seed germination in rice.BMC genomics · 2026Article
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- A Novel Function of GW5 on Controlling the Early Growth Vigor and its Haplotype Effect on Shoot Dry Weight and Grain Size in Rice (Oryza sativa L.).Rice (New York, N.Y.) · 2024Article
- Impact of rice GENERAL REGULATORY FACTOR14h (GF14h) on low-temperature seed germination and its application to breeding.PLoS genetics · 2024Article
- Progress in the study of functional genes related to direct seeding of rice.Molecular breeding : new strategies in plant improvement · 2023Review
- Transcriptomic and QTL Analysis of Seed Germination Vigor under Low Temperature in Weedy Rice WR04-6.Plants (Basel, Switzerland) · 2023Article
- Gene expression variation explains maize seed germination heterosis.BMC plant biology · 2022Article
- Identification of OsPK5 involved in rice glycolytic metabolism and GA/ABA balance for improving seed germination via genome-wide association study.Journal of experimental botany · 2022Article
- Brassinosteroid biosynthesis geneFrontiers in plant science · 2022Article
- Article
- Integrative QTL Identification, Fine Mapping and Candidate Gene Analysis of a Major Locus qLTG3a for Seed Low-Temperature Germinability in Rice.Rice (New York, N.Y.) · 2021Article
- Association Mapping and Functional Analysis of Rice Cold Tolerance QTLs at the Bud Burst Stage.Rice (New York, N.Y.) · 2021Article
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14 authors at 1 institution in 1 country.
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Abstract
backgroundDirect seeding is an efficient cultivation technique in rice. However, poor low temperature germinability (LTG) of modern rice cultivars limits its application. Identifying the genes associated with LTG and performing molecular breeding is the fundamental way to address this issue. However, few LTG QTLs have been fine mapped and cloned so far.
resultsIn the present study, the LTG evaluation of 375 rice accessions selected from the Rice Diversity Panel 2 showed that there were large LTG variations within the population, and the LTG of Indica group was significantly higher than that of Japonica and Aus groups (p < 0.01). In total, eleven QTLs for LTG were identified through genome-wide association study (GWAS). Among them, qLTG_sRDP2-3/qLTG_JAP-3, qLTG_AUS-3 and qLTG_sRDP2-12 are first reported in the present study. The QTL on chromosome 10, qLTG_sRDP2-10a had the largest contribution to LTG variations in 375 rice accessions, and was further validated using single segment substitution line (SSSL). The presence of qLTG_sRDP2-10a could result in 59.8% increase in LTG under 15 °C low temperature. The expression analysis of the genes within qLTG_sRDP2-10a region indicated that LOC_Os10g22520 and LOC_Os10g22484 exhibited differential expression between the high and low LTG lines. Further sequence comparisons revealed that there were insertion and deletion sequence differences in the promoter and intron region of LOC_Os10g22520, and an about 6 kb variation at the 3' end of LOC_Os10g22484 between the high and low LTG lines, suggesting that the sequence variations of the two genes could be the cause for their differential expression in high and low LTG lines.
conclusionAmong the 11 QTLs identified in this study, qLTG_sRDP2-10a could also be detected in other three studies using different germplasm under different cold environments. Its large effect and stable expression make qLTG_sRDP2-10a particularly valuable in rice breeding. The two genes, LOC_Os10g22484 and LOC_Os10g22520, were considered as the candidate genes underlying qLTG_sRDP2-10a. Our results suggest that integrating GWAS and SSSL can facilitate identification of QTL for complex traits in rice. The identification of qLTG_sRDP2-10a and its candidate genes provide a promising source for gene cloning of LTG and molecular breeding for LTG in rice.
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