利用全基因體關聯性分析探討優良燕麥品系與燕麥地方種種子活力之遺傳結構

Genome-wide Association Study Reveals the Genetic Architecture of Seed Vigour in Elite Oat Lines and Landraces

黃敬廷(Ching-Ting Huang)

指導教授 ： 黃永芬

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/NTU201901702

摘要

種子活力對作物萌芽、苗期植株建立甚至後期的產量、品質都有重要影響。對芻料作物而言，優良的種子活力有助提高作物與雜草的競爭優勢、降低田間管理的成本。燕麥（Avena sativa L.）是世界上重要的芻料作物之一，然而，燕麥種子活力的遺傳結構至今仍未被深入研究。本研究以來自Collaborative Oat Research Enterprise (CORE) 的650個優良燕麥品系及來自美國農業部 National Small Grain Collection (NSGC) 的378個燕麥地方品系為材料，調查兩個族群種子活力的相關性狀並藉由全基因體關聯性分析（genome-wide association study）探討其遺傳結構。本研究建立藉影像分析調查種子活力相關性狀的流程；量測性狀包含：種子根數目、根面積、芽長以及根和芽的生長速率等。調查結果發現大部分的性狀在兩個族群中皆有相當大的變異，並且近似常態分布。全基因體關聯性分析發現42與17個分子標誌在錯誤發現率（False discovery rate, FDR）低於0.1的狀況下分別與根及芽的相關性狀有顯著關聯性。在59個顯著相關的標誌中，22個標誌落在燕麥基因體中七組同源序列片段（homeologous region）、5個標誌的序列在水稻、二穗短柄草、玉米基因體上有高度相似的片段（E-value < 10-10），其中4個標誌位在已知的基因序列中。標誌avgbs_cluster_41284.1.50對應之異種同源基因（orthologous gene）Os06g0146400參與木膠的生合成，而標誌avgbs2_183559.1.25對應之異種同源基因Zm00001d036145則與植物的苗期生長有關。本研究為首次利用全基因體關聯性分析探討燕麥種子活力之遺傳結構，研究所發現顯著相關的位點值得深入研究，以進一步了解燕麥種子活力之遺傳機制。

關鍵字

燕麥（Avena sativa L.） ； 種子活力 ； 全基因體關聯性分析

並列摘要

Seed vigour is crucial for crop germination and early establishment and influences further biomass production. It is especially important for forage production. Oat (Avena sativa L.) is one of the important forage crops in the world. However, little is known about the genetic architecture of seed vigour in oats. In order to investigate the genetic architecture of seed vigour in oats, we used genome-wide association study (GWAS) based on two diversity panels, one consisted of 650 elite oat lines from Collaborative Oat Research Enterprise (CORE), and the other consisted of 378 landraces from National Small Grains Collection (NSGC). We have developed an image-based phenotyping pipeline to assess oat seed vigour traits, including root number, root surface area, shoot length and growth rates were derived from initial measurements. Most traits showed great variation following the normal distribution. We have identified 42 and 17 markers significantly associated with root and shoot traits at false discovery rate < 0.1, respectively. Twenty-two trait-associated markers fell into seven sets of homeologous regions. Context sequences of five trait-associated markers showed similarity (E-value < 10-10) to gene models from rice, Brachypodium and maize, among which four were located within known gene models. Marker avgbs_cluster_41284.1.50 matched to Os06g0146400, which encoded a glucuronosyltransferase and is involved in the biosynthesis of lignin. Marker avgbs2_183559.1.25 matched to Zm00001d036145, which coded for an iron-sulfur assembly protein and was hypothesize to be related to seedling growth. This study presents the first GWAS on oat seed vigour; loci identified in this study merit further investigation to gain insight of the genetics of oat seed vigour.

並列關鍵字

Oat (Avena sativa L.) ； Seed vigour ； Genome-wide association study

參考文獻

Altschul SF, Madden TL, Schäffer AA, Zhang J, Zhang Z, Miller W, Lipman DJ (1997) Gapped BLAST and PSI-BLAST: a new generation of protein database search programs. Nucleic acids research 25:3389-3402

Arsenault J, Poulcur S, Messier C, Guay RJH (1995) WinRHlZO™, a root-measuring system with a unique overlap correction method. HortScience 30:906-906

Atkinson JA, Wingen LU, Griffiths M, Pound MP, Gaju O, Foulkes MJ, Le Gouis J, Griffiths S, Bennett MJ, King J, Wells DM (2015) Phenotyping pipeline reveals major seedling root growth QTL in hexaploid wheat. J Exp Bot 66:2283-2292

Bekele WA, Wight CP, Chao S, Howarth CJ, Tinker NA (2018) Haplotype-based genotyping-by-sequencing in oat genome research. Plant Biotechnol J 16:1452-1463

Burton AL, Brown KM, Lynch JP (2013) Phenotypic diversity of root anatomical and architectural traits in species. Crop Science 53:1042-1055