QTG-Seq Accelerates QTL Fine Mapping through QTL Partitioning and Whole-Genome Sequencing of Bulked Segregant Samples

• Published in: Molecular plant 2019-03, Vol.12 (3), p.426-437
• Main Authors: Zhang, Hongwei, Wang, Xi, Pan, Qingchun, Li, Pei, Liu, Yunjun, Lu, Xiaoduo, Zhong, Wanshun, Li, Minqi, Han, Linqian, Li, Juan, Wang, Pingxi, Li, Dongdong, Liu, Yan, Li, Qing, Yang, Fang, Zhang, Yuan-Ming, Wang, Guoying, Li, Lin
• Format: Article
• Language: English
• Subjects: plant height; QTL; QTL fine-mapping; quantitative trait locus; whole genome sequencing
• ISSN: 1674-2052; 1752-9867
• DOI: 10.1016/j.molp.2018.12.018

Deciphering the genetic mechanisms underlying agronomic traits is of great importance for crop improvement. Most of these traits are controlled by multiple quantitative trait loci (QTLs), and identifying the underlying genes by conventional QTL fine-mapping is time-consuming and labor-intensive. Here, we devised a new method, named quantitative trait gene sequencing (QTG-seq), to accelerate QTL fine-mapping. QTG-seq combines QTL partitioning to convert a quantitative trait into a near-qualitative trait, sequencing of bulked segregant pools from a large segregating population, and the use of a robust new algorithm for identifying candidate genes. Using QTG-seq, we fine-mapped a plant-height QTL in maize (Zea mays L.), qPH7, to a 300-kb genomic interval and verified that a gene encoding an NF-YC transcription factor was the functional gene. Functional analysis suggested that qPH7-encoding protein might influence plant height by interacting with a CO-like protein and an AP2 domain-containing protein. Selection footprint analysis indicated that qPH7 was subject to strong selection during maize improvement. In summary, QTG-seq provides an efficient method for QTL fine-mapping in the era of “big data”. QTG-seq was devised for rapid fine-mapping of QTL in plants. As a proof of concept, the robustness of QTG-seq was proved by successfully identifying the causal gene underlying a plant-height QTL, qPH7, in maize. Furthermore, simulation analyses suggested that QTG-seq can be widely adopted for QTL fine-mapping in plants.