水稻幼苗耐旱相關性狀之數量性狀基因座探勘

Detection of Quantitative Trait Loci Associated with Rice Seedling Drought Tolerance Phenotypes

温宸欣(Chen-Hsin Wen)

指導教授 ： 董致韡

國立臺灣大學/生物資源暨農學院/農藝學研究所/碩士(2019年)

https://doi.org/10.6342/NTU201902357

摘要

水稻是餵養世界上一半人口的重要主食，而乾旱不論在高地或低地栽培環境下皆為顯著危害水稻產量的主要非生物逆境，特別是在未來乾旱頻率以及強度增加的趨勢下，育成耐旱水稻品種是現今必要的目標。由於植物的根部對於吸收土壤水分十分重要，根部系統結構（Root system architecture; RSA）因此被認為是乾旱耐受性中的重要性狀，根部系統結構是由許多不同的性狀共同決定，如根長、根生長角度以及根乾重等根部型態性狀。因此，為了提升水稻乾旱耐受性，針對根系進行適當的遺傳改良是具可行性的策略。本次研究採用聚乙二醇（polyethylene glycol 6000; PEG-6000）搭配水耕系統創造滲透勢壓力以模擬田間乾旱逆境，針對兩雙親本雜交族群，分別為一重組自交系（Recombinant inbred lines; RILs）和一F2族群，以及一自然種原，調查正常以及乾旱情況下的幼苗根部以及耐旱相關性狀。藉由聚乙二醇在Kimura溶液中所創造的低水勢能提供一個相對穩定的滲透勢逆境，且讓我們能針對根部相關性狀進行評估。三族群之基因型資料以測序基因分型（genotyping-by-sequencing; GBS） 技術取得單一核苷酸多型性（single nucleotide polymorphism; SNP）分子標誌。利用高密度SNP分子標誌針對各族群進行傳統的區間定位法（interval mapping; IM)、單點分析（single marker analysis; SMA）和全基因體關聯性分析（genome wide association study; GWAS），鑑定基因型和外表型的關聯。我們的定位結果顯示，針對偵測雙親本雜交族群的關聯性，使用高密度分子標誌進行單點分析可以達到區間定位法的解析度。在三個族群中共偵測到13個與根部性狀相關的染色體區間，且利用三個線上資料庫針對其中10個區間進行候選基因的探勘。根據基因功能，有一個基因被註解參與根部發育，而有三個已知基因已被證實具有調節根部生長的功能，這四個基因可以作為後續功能性分析的候選基因，以確認他們參與在根長度變化中的角色。在F2族群和自然種原中，我們偵測到數個與幼苗高度、葉捲曲程度和抽穗期相關的基因體片段。我們期望未來本研究結果所偵測到的顯著染色體片段和SNP分子標誌可應用於耐旱水稻品種之育種。

關鍵字

水稻 ； 乾旱逆境 ； 聚乙二醇 ； 根部 ； 數量性狀基因座分析 ； 全基因體關聯性分析

並列摘要

Rice is an important staple food feeding half of the world population. Drought as the major abiotic stress for rice greatly affects the yield production both in upland and lowland fields. In particular, with the increasing frequencies and severity of drought stress, breeding for drought-tolerant rice is necessary nowadays. Root system architecture (RSA) has been considered as a critical component in drought tolerance because of the important role of roots in water uptake from soil. Various traits contribute together to RSA, such as root morphology including root length, root growth angle and root dry weight, therefore, genetic improvement for an appropriate root system is another promising strategy to elevate drought resistance in rice. In this study, two bi-parental crosses-derived populations: a recombinant inbred lines (RILs) and a F2 population, and a diverse panel were evaluated for their root and drought-tolerant related traits at seedling stage under a hydroponic system with and without an osmotic-associated drought stress induced by polyethylene glycol 6000 (PEG-6000) treatment. Low water potential imposed by PEG in Kimura solution provided a relatively stable experimental condition and allowed us to measure the root-related traits. Single nucleotide polymorphism (SNP) markers of the three populations were obtained following the genotyping-by-sequencing (GBS) approach. With the high-density SNPs, traditional interval mapping (IM), single marker analysis (SMA), and genome wide association study (GWAS) were performed in respective population to identify the genotype-phenotype associations. Our mapping results showed the power of SMA in detecting associations in bi-parental population as compared to the resolution which simple interval mapping can achieve when using the high-density markers. Total 13 genomic regions associated with root-related traits were identified in the three populations, ten of them were searched for candidate genes using three online databases. According to the gene functions, one gene was predicted to be involved in root development and three were characterized to regulate root growth. These four genes are the candidates for future functional analysis to confirm their roles in controlling the root length. Several genomic regions associated with seedling height (SH), rolling score (RS), and heading date (HD) were detected in our F2 populations and diverse panel. We hope the significant regions and SNP markers identified in this study can be utilized in the breeding for drought-tolerant rice cultivars.

並列關鍵字

Oryza sativa ； Drought ； PEG ； Root ； QTL analysis ； Genome-wide association study

參考文獻

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