Multi-environment BSA-seq using large F3 populations is able to achieve reliable QTL mapping with high power and resolution: An experimental demonstration in rice

作     者：Yan Zheng Ei Ei Khine Khin Mar Thi Ei Ei Nyein Likun Huang Lihui Lin Xiaofang Xie Min Htay Wai Lin Khin Than Oo Myat Myat Moe San San Aye Weiren Wu Yan Zheng;Ei Ei Khine;Khin Mar Thi;Ei Ei Nyein;Likun Huang;Lihui Lin;Xiaofang Xie;Min Htay Wai Lin;Khin Than Oo;Myat Myat Moe;San San Aye;Weiren Wu

作者机构：College of Life SciencesFujian Agriculture and Forestry UniversityFuzhou 350002FujianChina Fujian Provincial Key Laboratory of Crop Breeding by DesignFujian Agriculture and Forestry UniversityFuzhou 350002FujianChina Key Laboratory of GeneticsBreeding and Multiple Utilization of CropsMinistry of EducationFujian Agriculture and Forestry UniversityFuzhou 350002FujianChina Department of BotanyMawlamyine UniversityMon StateMawlamyineMyanmar Department of BotanyDagon UniversityNorth DagonYangonMyanmar 

出 版 物：《The Crop Journal》 (作物学报（英文版）)

年 卷 期：2024年第12卷第2期

页      面：549-557页

核心收录：

学科分类：09[农学] 0901[农学-作物学] 

基　　金：supported by Natural Science Foundation of Fujian Province (CN) (2020I0009, 2022J01596) Cooperation Project on University Industry-Education-Research of Fujian Provincial Science and Technology Plan (CN) (2022N5011) Lancang-Mekong Cooperation Special Fund (2017-2020) International Sci-Tech Cooperation and Communication Program of Fujian Agriculture and Forestry University (KXGH17014) 

主　　题：BSA-seq QTL mapping Large F3 population Multi-environment experiment Cross-validation 

摘      要：Bulked-segregant analysis by deep sequencing(BSA-seq) is a widely used method for mapping QTL(quantitative trait loci) due to its simplicity, speed, cost-effectiveness, and efficiency. However, the ability of BSA-seq to detect QTL is often limited by inappropriate experimental designs, as evidenced by numerous practical studies. Most BSA-seq studies have utilized small to medium-sized populations, with F2populations being the most common choice. Nevertheless, theoretical studies have shown that using a large population with an appropriate pool size can significantly enhance the power and resolution of QTL detection in BSA-seq, with F_(3)populations offering notable advantages over F2populations. To provide an experimental demonstration, we tested the power of BSA-seq to identify QTL controlling days from sowing to heading(DTH) in a 7200-plant rice F_(3)population in two environments, with a pool size of approximately 500. Each experiment identified 34 QTL, an order of magnitude greater than reported in most BSA-seq experiments, of which 23 were detected in both experiments, with 17 of these located near41 previously reported QTL and eight cloned genes known to control DTH in rice. These results indicate that QTL mapping by BSA-seq in large F_(3)populations and multi-environment experiments can achieve high power, resolution, and reliability.