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 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.

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.

中文翻译：

---

水稻全基因组动态关联分析及候选基因耐缺氧萌发鉴定

背景

在亚洲大米生产中，由于成本上升，劳动力短缺和水短缺，现在有越来越多的国家选择直接播种模式。水稻种子经历无氧萌发（AG）的能力在直接播种的成功中起着重要作用。

结果

在这项研究中，我们基于重测序使用了2,123,725个单核苷酸多态性（SNP）标记，对209个天然稻群体进行了胚芽鞘长度（CL）和胚芽鞘直径（CD）的动态全基因组关联研究（GWAS）。在这两个表型中总共检测到26个SNP位点，其中5个与先前报告的位点（S1_ 39674301，S6_20797781，S7_ 18722403，S8_ 9946213，S11_ 19165397）重叠，并且在不同时间点重复检测到两个位点（S3_ 24689629和S5_ 27918754）。我们建议将这7个基因座（-log ₁₀（P）值> 7.3271）是影响AG耐受性的关键位置。为了更有效地筛选候选基因，我们在六个关键阶段（包括厌氧（AN）和氧转化点（AN-A））对耐潮品种R151的转录组进行了测序，并获得了高质量的差异表达谱。确定了四个可靠的候选基因：Os01g0911700（OsVP1），Os05g0560900（OsGA2ox8），Os05g0562200（OsDi19-1）和Os06g0548200。然后使用qRT-PCR和LC-MS / MS靶向代谢物检测技术进一步验证了这四个候选基因的上调表达与AG密切相关。

结论

这四个新的候选基因在缺氧条件下与赤霉素（GA）和脱落酸（ABA）的调控以及细胞壁代谢有关，并促进胚芽鞘伸长，同时避免了不良反应，使胚芽鞘获得氧气，摆脱了低氧环境并迅速发芽。这项研究的结果加深​​了我们对水稻种子中AG的遗传基础的了解，这有助于选择适合直接播种的耐潮品种。