Zea mays Genome sequencing. Zea mays

Deciphering the genetic mechanisms underlying agronomic traits is of great importance for crop improvement and global food security. Most of these traits are controlled by multiple quantitative trait loci (QTL), and identifying the underlying genes by conventional QTL fine-mapping is time-consuming and labor-intensive. Here, we devised a new method we 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 in just one generation of selection, bulked segregant sequencing on a large segregating population with relatively deep coverage, and a robust new algorithm for identifying candidate genes. Using QTG-seq, we fine-mapped a major plant height QTL in maize (Zea mays L.), qPH7, to a 300-kb genomic interval and verified that a gene in that region encoding an NF-YC transcription factor was the functional gene. Notably, our new maximum likelihood method (smoothLOD) for detecting fine-mapping signal was able to map the QTG directly into that genic region. Molecular evidence suggested that qPH7 influences plant height by interacting with proteins encoded by a CO-like gene and an AP2 domain containing genes. Selection analysis indicated that qPH7 was subject to strong selection during maize domestication. In summary, QTG-seq provides an efficient method for QTL fine-mapping in the era of “big data”.解析农艺性状背后的遗传机制，对于作物遗传改良与全球粮食安全具有重要意义。这类性状大多由多个数量性状基因座（quantitative trait locus, QTL）调控，而通过传统QTL精细定位鉴定其内在功能基因往往耗时耗力。本研究开发了一种名为数量性状基因测序（quantitative trait gene sequencing, QTG-seq）的新方法，以加速QTL精细定位流程。QTG-seq整合了三项核心技术：其一，通过QTL分区策略，仅需一轮选择即可将数量性状转化为近质量性状；其二，对大样本分离群体开展相对高深度覆盖的集群分离测序；其三，开发了一套稳健的新型候选基因鉴定算法。利用QTG-seq，本研究将玉米（Zea mays L.）中的主效株高QTL qPH7精细定位至300kb的基因组区间，并验证该区间内一个编码NF-YC转录因子的基因为其功能基因。值得注意的是，本研究开发的用于检测精细定位信号的新型最大似然法（smoothLOD），可直接将数量性状基因（quantitative trait gene, QTG）定位至该基因区域。分子生物学证据表明，qPH7通过与类CO基因及AP2结构域包含基因编码的蛋白互作调控玉米株高。选择分析结果显示，qPH7在玉米驯化过程中受到了强烈的选择压。综上，QTG-seq为“大数据”时代下的QTL精细定位提供了高效解决方案。