水稻於淹水逆境下缺氧發芽之遺傳分析

本研究針對153個水稻種原及144個重組自交系進行淹水情況下缺氧發芽性狀之調查，由調查結果可觀察到稉稻品種於淹水環境下芽鞘延長之速率明顯地較秈稻品種快。在全基因體關聯性分析 (genome wide association study, GWAS) 中，共偵測到88個單一核苷酸多型性 (single nucleotide polymorphism, SNP) 與水稻的缺氧發芽顯著相關，且有10個基因體片段與前人利用雙親本雜交族群之遺傳研究互相呼應。而在本篇研究的雙親本雜交族群中，我們偵測到唯一且主效 (~30%) 的數量性狀基因座 (QTL) ，在此基因座中緊鄰著最顯著的SNP位點，存在一可能影響水稻缺氧發芽的候選基因─hexokinase 6 (HXK6, LOC_Os01g53930)。針對此基因座附近變異所做之Haplotype analysis指出此基因座的變異與水稻次族群有明顯關聯性；定序HXK6，同樣的可以看到明顯之秈稉分化，且在此基因之啟動子 (promoter) 序列中，可以找到位於預測轉錄因子接合位上的變異，此變異可能影響HXK6在淹水情況下之基因表現，進而改變水稻幼苗對於淹水之耐受性，然而仍需更多的研究來證實此一假設。GWAS能夠有效率的偵測到水稻種原中基因體變異與外表性狀間的關係，不過，對於與次族群結構相依之性狀卻缺乏辨別力；然而，跨次族群之雙親本雜交族群能夠輕易地打破族群結構，以偵測次族群間的對偶基因型差異。在本篇研究中，我們利用了兩個研究方法之互補性，有效率的解析複雜農藝性狀之遺傳結構。另一方面，利用針對不同水稻種原之比較轉錄體分析，我們得到了一組在耐淹品種與不耐品種間存在不同調控機制之基因，這些基因對於耐淹水品系可能扮演著重要的角色；我們也能夠看到在一些極端耐淹品系中，可能存在其獨特之對偶基因或是調控機制以造就其更進一步之耐受性。結合遺傳與基因表現之研究，我們期待能對水稻如何在淹水環境下發芽且正常生長能有更全面性的深入了解，並應用這些獲得的知識於水稻品種之改良。

關鍵字

水稻；缺氧發芽；全基因組關聯性分析；數量性狀基因座定位； RNA定序；淹水逆境

並列摘要

In this research, 153 diverse rice accessions and 144 recombinant inbred lines (RILs) were screened for their responses to submergence. Differential anaerobic response was observed between Japonica and Indica varieties. Total 88 SNPs identified from genome-wide association studies (GWAS) were associated with anaerobic germination, and 10 genomic regions were repeatedly detected in this study and previous bi-parental QTL studies. A unique and strong signal explaining ~30% of the phenotypic variation was only detected in the RILs population, in this interval, a hexokinase gene (HXK6) adjacent to the peak SNP was considered a potential candidate to control the phenotypic variation of anaerobic germination. Haplotype analysis around this gene across the diverse rice accessions indicated a significant Japonica — Indica divergence. Sequence analysis identified a SNP at a predicted transcription factor binding site in the promoter region of the HXK6 gene, suggesting the expression of HXK6 might be responsible for the variation of anaerobic response, while further experiments are needed to confirm the functions of HXK6. GWAS detected phenotype-genotype association with higher resolution, while bi-parental mapping was able to identify subpopulation-related variants not captured by GWAS. This study demonstrated these two approaches are complementary for dissecting the genetic architecture of complex traits in rice. By comparative transcriptomic analysis in different rice genotypes with contrasting tolerance to submergence, we identified a core set of genes being differentially regulated under submergence between tolerant and sensitive rice genotypes. These differential modulations could contribute to the fundamental tolerance in the moderate tolerant and tolerant rice genotypes. Rare allele-specific gene regulations and genotype-specific adaptive mechanisms could further promote the submergence tolerance in those genotypes with extremely adaptive phenotype. Through genetic and comparative transcriptomic aspects, we expected to have more comprehensive insights about how rice seedlings of different genotypes to germinate and survive under the oxygen/energy deficit led by submergence and utilize the knowledge in the improvement of submergence tolerance in modern rice cultivars.

並列關鍵字

rice ； anaerobic germination ； GWAS ； QTL mapping ； RNA-Seq ； submergence

參考文獻

Alexandrov, N., Tai, S., Wang, W., Mansueto, L., Palis, K., Fuentes, R.R., Ulat, V.J., Chebotarov, D., Zhang, G., Li, Z., et al. (2015). SNP-Seek database of SNPs derived from 3000 rice genomes. Nucleic Acids Res. 43, D1023–D1027.

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國際替代計量

水稻於淹水逆境下缺氧發芽之遺傳分析

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