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Identification of QTL regions for seedling root traits and their effect on nitrogen use efficiency in wheat (Triticum aestivum L.)

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QTL for a wheat ideotype root system and its plasticity to nitrogen deficiency were characterized.


Root system architecture-related traits (RRTs) and their plasticity to nitrogen availability are important for nitrogen acquisition and yield formation in wheat (Triticum aestivum L.). In this study, quantitative trait loci (QTL) analysis was conducted under different nitrogen conditions, using the seedlings of 188 recombinant inbred lines derived from a cross between Kenong 9204 and Jing 411. Fifty-three QTL for seven RRTs and fourteen QTL for the plasticity of these RRTs to nitrogen deficiency were detected. Thirty of these QTL were mapped in nine clusters on chromosomes 2B, 2D, 3A, 3D, 6B, 6D, 7A and 7B. Six of these nine clusters were also colocated with loci for nitrogen use efficiency (NUE)-related traits (NRTs). Among them, three QTL clusters (C2B, C6D and C7B) were highlighted, considering that they individually harbored three stable robust QTL (i.e., QMrl-2B.1, QdRs-6D and QMrl-7B). C2B and C7B stably contributed to the optimal root system, and C6D greatly affected the plasticity of RRTs in response to nitrogen deficiency. However, strong artificial selection was only observed for C7B in 574 derivatives of Kenong 9204. Covariance analysis identified QMrl-7B as the major contributor in C7B that affected the investigated NRTs in mature plants. Phenotypic analysis indicated that thousand kernel weight might represent a “concomitant” above-ground trait of the “hidden” RRTs controlled by C7B, which are used for breeding selection. Dissecting these QTL regions with potential breeding value will ultimately facilitate the selection of donor lines with both high yield and NUE in wheat breeding programs.

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Root system architecture


Root system architecture-related traits


Maximum root length


Root dry weight


Total root length


Root surface area


Root volume


Root diameter


Root tip number


Phenotypic difference values of RRTs between low nitrogen treatment and control treatment


Nitrogen use efficiency


Nitrogen use efficiency-related traits


NUE based on grain yield


Nitrogen uptake content


Nitrogen concentration


Yield-related traits


Spikelet number per spike


Kernel number per spike


Grain yield


Thousand kernel weight


Recombinant inbred line population derived from the cross between Kenong 9204 and Jing 411


Marker-assisted selection


Single-nucleotide polymorphism


Confidence interval


Quantitative trait loci


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This research was supported by grants from the National Key Research and Development Program of China (2016YFD0100706), the National Natural Science Foundation of China (31601809), West Light Foundation of the Chinese Academy of Sciences (2016XBZG_XBQNXZ_B_002), Shandong Provincial Science Foundation for Outstanding Youth (ZR2017JL017), Hebei Provincial Science and Technology Research and Development Project (16226320D) and China Agriculture Research System (CARS-03).

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Correspondence to Fa Cui, Tao Wang or Junming Li.

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Fan, X., Zhang, W., Zhang, N. et al. Identification of QTL regions for seedling root traits and their effect on nitrogen use efficiency in wheat (Triticum aestivum L.). Theor Appl Genet 131, 2677–2698 (2018).

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