建立水稻核心收集系的演算法比較

Abstract

核心收集系為少量、最小重覆，具有代表性的一組收集系。本研究使用96個以台灣栽培種為主的水稻收集系，以雙重限制酶切位相關序列定序 (double digest Restriction Associated DNA sequencing , ddRAD) 產生的1960筆SNP資料，轉換為遺傳距離後以不同的方法建立測試用核心收集系，在具有明確族群結構的水稻比較各個方法的優缺點，並以水稻44K SNP晶片413個收集系的36901筆SNP資料驗證結果。主要使用的方法為隨機取樣法、各種分層取樣法 (stratified sampling) 、以遺傳距離為基礎的Marita法、genetic distance optimization (GDOpt) 法以及以隨機局部搜索法 (stochastic local search) 建立核心收集系的軟體的 Core hunter (version 2.0)，使用的主要評量標準為非核心的收集系與最近核心收集系的遺傳距離 (Average distance between each accession and nearest entry, A-NE) 以及核心收集系與其最近核心收集系的遺傳距離 (Average distance between each entry and the nearest neighboring entry, E-NE) ，A-NE在兩筆資料的表現上以GDOpt表現的最好，而E-NE則是以軟體Core hunter表現的最佳。但是E-NE數值容易受到次族群之間可能有基因組混雜的收集系影響，不適合用於具有強烈族群結構的水稻，而以A-NE及主成分分析各個次族群取樣到核心收集系的分佈總結，GDOpt為最適合用於建立水稻核心收集系的方法。

Core collection is a limited subset of accessions representing the spectrum of the whole collection with minimum repetitiveness. In this study, 96 rice accessions were sequenced by double digest Restriction Associated DNA sequencing (ddRAD) and resulted 1960 Single Nucleotide Polymorphism (SNP) markers. Methods for constructing core collections include random sampling, stratified sampling, Marita’s method, genetic distance sampling (GDOpt) and Core hunter (version 2.0). Average distance between each accession and nearest entry (A-NE) and the average distance between each entry and the nearest neighboring entry (E-NE) are used as criteria for evaluating the effectiveness of the methods tested. The results indicate that while GDOpt performed best in A-NE, Core hunter performed best in E-NE. However, core collections constructed by Core hunter favored accessions that are outbreeds between rice subpopulations and thus E-NE may not be an appropriate criterion when subpopulations were evident in the accessions. As the A-NE being the sole criterion, GDOpt is the method of choice for construction of core collection even when subpopulations exist as in the case of rice. The results of 413 diverse accessions based on the publicly available data of 44K SNP chip study also agree with the conclusion above.