QTL mapping for foxtail millet plant height in multi-environment using an ultra-high density bin map
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ORIGINAL ARTICLE
QTL mapping for foxtail millet plant height in multi‑environment using an ultra‑high density bin map Qiang He1 · Hui Zhi1 · Sha Tang1 · Lu Xing2 · Suying Wang2 · Haigang Wang3 · Aiying Zhang4 · Yuhui Li4 · Ming Gao5 · Haijin Zhang6 · Guoqiu Chen6 · Shutao Dai7 · Junxia Li7 · Junjun Yang1 · Huifang Liu1 · Wei Zhang1 · Yanchao Jia1 · Shujie Li5 · Jinrong Liu2 · Zhijun Qiao3 · Erhu Guo4 · Guanqing Jia1 · Jun Liu1 · Xianmin Diao1 Received: 19 May 2020 / Accepted: 23 October 2020 © Springer-Verlag GmbH Germany, part of Springer Nature 2020
Abstract Key message Using a fixed RIL population derived from a widely used foxtail millet backbone breeding line and an elite cultivar, we constructed a high-density bin map and identified six novel multi-environment effect QTLs and seven candidate genes for dwarf phenotype. Abstract Plant height is an important trait that determines tradeoffs between competition and resource allocation, which is crucial for yield potential. To improve the C4 model plant foxtail millet (Setaria italica) productivity, it is necessary to isolate plant height-related genes that contribute to ideal plant architecture in breeding. In the present study, we generated a foxtail millet population of 333 recombinant inbred lines (RILs) derived from a cross between a backbone line Ai 88 and an elite cultivar Liaogu 1. We evaluated plant height in 13 environmental conditions across 4 years, the mean plant height of the RIL population ranged from 89.5 to 149.9 cm. Using deep re-sequencing data, we constructed a high-density bin map with 3744 marker bins. Quantitative trait locus (QTL) mapping identified 26 QTLs significantly associated with plant height. Of these, 13 QTLs were repeatedly detected under multiple environments, including six novel QTLs that have not been reported before. Seita.1G242300, a gene encodes gibberellin 2-oxidase-8, which was detected in nine environments in a 1.54-Mb interval of qPH1.3, was considered as an important candidate gene. Moreover, other six genes involved in GA biosynthesis or signaling pathways, and fifteen genes encode F-box domain proteins which might function as E3 ligases, were also considered as candidate genes in different QTLs. These QTLs and candidate genes identified in this study will help to elucidate the genetic basis of foxtail millet plant height, and the linked markers will be useful for marker-assistant selection of varieties with ideal plant architecture and high yield potential.
Communicated by Ian D Godwin. Qiang He and Hui Zhi have contributed equally to this work. Electronic supplementary material The online version of this article (https://doi.org/10.1007/s00122-020-03714-w) contains supplementary material, which is available to authorized users. * Xianmin Diao [email protected] 1
Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, Haidian 100081, China
2
Anyang Academy of Agricultural Sciences, Anyang 455000, Henan, China
3
Institute of Crop Germplasm, Shanxi Academy of Agricultural Sci
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