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- Title
Multi-environment BSA-seq using large F<sub>3</sub> populations is able to achieve reliable QTL mapping with high power and resolution: An experimental demonstration in rice.
- Authors
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
- Abstract
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 F2 populations 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 F3 populations offering notable advantages over F2 populations. 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 F3 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 near 41 previously reported QTL and eight cloned genes known to control DTH in rice. These results indicate that QTL mapping by BSA-seq in large F3 populations and multi-environment experiments can achieve high power, resolution, and reliability.
- Subjects
RICE; GRAIN; EXPERIMENTAL design; COST effectiveness; POPULATION
- Publication
Crop Journal (2095-5421), 2024, Vol 12, Issue 2, p549
- ISSN
2095-5421
- Publication type
Article
- DOI
10.1016/j.cj.2024.01.009