Abstract
BackgroundIn Asian rice production, an increasing number of countries now choose the direct seeding mode because of rising costs, labour shortages and water shortages. The ability of rice seeds to undergo anaerobic germination (AG) plays an important role in the success of direct seeding.ResultsIn this study, we used 2,123,725 single nucleotide polymorphism (SNP) markers based on resequencing to conduct a dynamic genome-wide association study (GWAS) of coleoptile length (CL) and coleoptile diameter (CD) in 209 natural rice populations. A total of 26 SNP loci were detected in these two phenotypes, of which 5 overlapped with previously reported loci (S1_ 39674301, S6_ 20797781, S7_ 18722403, S8_ 9946213, S11_ 19165397), and two sites were detected repeatedly at different time points (S3_ 24689629 and S5_ 27918754). We suggest that these 7 loci (−log10 (P) value > 7.3271) are the key sites that affect AG tolerance. To screen the candidate genes more effectively, we sequenced the transcriptome of the flooding-tolerant variety R151 in six key stages, including anaerobic (AN) and the oxygen conversion point (AN-A), and obtained high-quality differential expression profiles. Four reliable candidate genes were identified: Os01g0911700 (OsVP1), Os05g0560900 (OsGA2ox8), Os05g0562200 (OsDi19–1) and Os06g0548200. Then qRT-PCR and LC-MS/ MS targeting metabolite detection technology were used to further verify that the up-regulated expression of these four candidate genes was closely related to AG.ConclusionThe four novel candidate genes were associated with gibberellin (GA) and abscisic acid (ABA) regulation and cell wall metabolism under oxygen-deficiency conditions and promoted coleoptile elongation while avoiding adverse effects, allowing the coleoptile to obtain oxygen, escape the low-oxygen environment and germinate rapidly. The results of this study improve our understanding of the genetic basis of AG in rice seeds, which is conducive to the selection of flooding-tolerant varieties suitable for direct seeding.
Highlights
In Asian rice production, an increasing number of countries choose the direct seeding mode because of rising costs, labour shortages and water shortages
The purpose of this study was to detect genetic loci significantly associated with anaerobic germination (AG) in rice, to explore favourable single nucleotide polymorphism (SNP) alleles that may be used to breed rice suitable for direct seeding and to find reliable candidate genes to lay a foundation for future study of the molecular mechanism of AG in rice
coleoptile length (CL), coleoptile diameter (CD), coleoptile surface area (CSA) and coleoptile volume (CV) on the second, third and fourth days of germination were used as the indexes of submergence tolerance
Summary
In Asian rice production, an increasing number of countries choose the direct seeding mode because of rising costs, labour shortages and water shortages. Based on population growth, the Food and Agricultural Organization estimates that by 2050, the world rice requirement will be 524 MT with an annual increase of 2 MT from the present level of production (Jeon et al 2011). The current evidence shows a decline in grain yield productivity due to looming threats to natural resources, falling water tables, mounting labour shortages, energy scarcity, increasing input prices and changing climatic conditions (Singh et al 2013). The water-, energy-, and labour-intensive system of transplanted puddled rice is steadily being replaced by direct-seeded rice (DSR) due to the progressive scarcity of these resources (Miro et al 2017)
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