Dynamic Genome-Wide Association Analysis and Identification of Candidate Genes Involved in Anaerobic Germination Tolerance in Rice

Abstract

Background: In 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.Results: In 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 YZX 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-based target metabolite detection technology were used to verify the expression levels of these four candidate genes and the contents of the metabolites they regulate, which specifically responded to AG.Conclusion: The 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.

Genome-wide association analysis for emergence of deeply sown rice (Oryza sativa) reveals novel aus-specific phytohormone candidate genes for adaptation to dry-direct seeding in the field

“…Prior genome-wide association studies (GWAS) on germplasm panels and genetic mapping studies on biparental populations have been conducted to identify quantitative trait loci (QTLs) for phenotypes associated with deep-sowing tolerance in rice, including mesocotyl length (Wu et al, 2015a;Zhao et al, 2018;Liu et al, 2020), seedling vigor (Guo et al, 2019), and anaerobic germination (Yang et al, 2019;Rohilla et al, 2020;Su et al, 2020). From five GWAS studies of mesocotyl length using rice diversity panels ranging in size from 147 to 621 individuals, ~64 marker-trait associations (18 QTLs and 46 loci) have been reported, with overlap among some traitassociated genomic regions from different studies yielding a minimum of eleven uniquely identified QTL/loci overall (Wu et al, 2015a;Lu et al, 2016;Zhao et al, 2018;Liu et al, 2020;Wang et al, 2021b).…”