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QTL-seq for rapid identification of candidate genes for flowering time in broccoli × cabbage

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A major QTL controlling early flowering in broccoli × cabbage was identified by marker analysis and next-generation sequencing, corresponding to GRF6 gene conditioning flowering time in Arabidopsis.

Abstract

Flowering is an important agronomic trait for hybrid production in broccoli and cabbage, but the genetic mechanism underlying this process is unknown. In this study, segregation analysis with BC1P1, BC1P2, F2, and F2:3 populations derived from a cross between two inbred lines “195” (late-flowering) and “93219” (early flowering) suggested that flowering time is a quantitative trait. Next, employing a next-generation sequencing-based whole-genome QTL-seq strategy, we identified a major genomic region harboring a robust flowering time QTL using an F2 mapping population, designated Ef2.1 on cabbage chromosome 2 for early flowering. Ef2.1 was further validated by indel (insertion or deletion) marker-based classical QTL mapping, explaining 51.5% (LOD = 37.67) and 54.0% (LOD = 40.5) of the phenotypic variation in F2 and F2:3 populations, respectively. Combined QTL-seq and classical QTL analysis narrowed down Ef1.1 to a 228-kb genomic region containing 29 genes. A cabbage gene, Bol024659, was identified in this region, which is a homolog of GRF6, a major gene regulating flowering in Arabidopsis, and was designated BolGRF6. qRT-PCR study of the expression level of BolGRF6 revealed significantly higher expression in the early flowering genotypes. Taken together, our results provide support for BolGRF6 as a possible candidate gene for early flowering in the broccoli line 93219. The identified candidate genomic regions and genes may be useful for molecular breeding to improve broccoli and cabbage flowering times.

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Acknowledgments

This work was supported by the National Natural Science Foundation of China (Grant No. 31372067), the China Agriculture Research System (Grant No. CARS-25-A), the Key Projects in the National Science and Technology Pillar Program of China (Grant No. 2013BAD01B04), the Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, P.R. China, and the Science and Technology Innovation Program of the Chinese Academy of Agricultural Sciences (Grant No. CAAS-ASTIP-IVFCAAS). We thank Tom Buckle, MSc, from Liwen Bianji, Edanz Group China (http://www.liwenbianji.cn/ac), for editing the English text of a draft of this manuscript.

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  1. Institute of Vegetables and Flowers, Chinese Academy of Agricultural Sciences, Key Laboratory of Biology and Genetic Improvement of Horticultural Crops, Ministry of Agriculture, 12 Zhongguancun Nandajie Street, Beijing, 100081, China

    Jinshuai Shu, Yumei Liu, Lili Zhang, Zhansheng Li, Zhiyuan Fang, Limei Yang, Mu Zhuang, Yangyong Zhang & Honghao Lv

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  1. Jinshuai Shu
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  2. Yumei Liu
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Correspondence to Yumei Liu.

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Shu, J., Liu, Y., Zhang, L. et al. QTL-seq for rapid identification of candidate genes for flowering time in broccoli × cabbage. Theor Appl Genet 131, 917–928 (2018). https://doi.org/10.1007/s00122-017-3047-5

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