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A Wheat 660 K SNP array-based high-density genetic map facilitates QTL mapping of flag leaf-related traits in wheat

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Abstract

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A high-density genetic map containing 122,620 SNP markers was constructed, which facilitated the identification of eight major flag leaf-related QTL in relatively narrow intervals.

Abstract

The flag leaf plays an important role in photosynthetic capacity and yield potential in wheat. In this study, we used a recombinant inbred line population containing 188 lines derived from a cross between ‘Lankao86’ (LK86) and ‘Ermangmai’ to construct a genetic map using the Wheat 660 K single-nucleotide polymorphism (SNP) array. The high-density genetic map contains 122,620 SNP markers spanning 5185.06 cM. It shows good collinearity with the physical map of Chinese Spring and anchors multiple sequences of previously unplaced scaffolds onto chromosomes. Based on the high-density genetic map, we identified seven, twelve, and eight quantitative trait loci (QTL) for flag leaf length (FLL), width (FLW), and area (FLA) across eight environments, respectively. Among them, three, one, and four QTL for FLL, FLW, and FLA are major and stably express in more than four environments. The physical distance between the flanking markers for QFll.igdb-3B/QFlw.igdb-3B/QFla.igdb-3B is only 444 kb containing eight high confidence genes. These results suggested that we could directly map the candidate genes in a relatively small region by the high-density genetic map constructed with the Wheat 660 K array. Furthermore, the identification of environmentally stable QTL for flag leaf morphology laid a foundation for the following gene cloning and flag leaf morphology improvement.

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All data generated or analyzed during this study are included in the main text article and its supplementary files.

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Acknowledgements

This work jointly supported by grants from the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA24010104), the National Natural Science Foundation of China (Grant No. 31921005), and the Major Basic Research Program of Shandong Natural Science Foundation (ZR2019ZD15).

Funding

This work jointly supported by grants from the Strategic Priority Research Program of the Chinese Academy of Sciences (XDA24010104), the National Natural Science Foundation of China (Grant No. 31921005), and the Major Basic Research Program of Shandong Natural Science Foundation (ZR2019ZD15).

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  1. Jianqing Niu and Yaoqi Si have contributed equally to this work.

Authors and Affiliations

  1. Hainan Yazhou Bay Seed Lab, Sanya, Hainan, China

    Jianqing Niu, Shengwei Ma & Hong-Qing Ling

  2. State Key Laboratory of Plant Cell and Chromosome Engineering, Institute of Genetics and Developmental Biology, Innovative Academy of Seed Design, Chinese Academy of Sciences, Beijing, China

    Jianqing Niu, Yaoqi Si, Shuiquan Tian, Xiaolin Liu, Xiaoli Shi, Shengwei Ma, Hong-Qing Ling & Shusong Zheng

  3. College of Life Sciences, University of Chinese Academy of Sciences, Beijing, China

    Shuiquan Tian, Xiaolin Liu & Hong-Qing Ling

  4. National Key Laboratory of Crop Biology, College of Life Sciences, Shandong Agricultural University, Taian, China

    Zhongqing Yu

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Contributions

H-QL and SZ conceived the project; SZ collected the parental materials and developed the RIL population; JN conducted experiments, analyzed data, and wrote the manuscript. YS and ST assisted in data collection for the RIL population; YS, ST, XL, XS, and ZY assisted in field trials. H-QL, SZ, YS, ST, and SM revised the manuscript. All authors contributed to the study and approved the final version for submission.

Corresponding authors

Correspondence to Hong-Qing Ling or Shusong Zheng.

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Communicated by Susanne Dreisigacker.

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Supplementary Information

Supplementary Fig. 1 The distribution of different category SNPs. (a) The histogram of call rate (CR) for Wheat 660K array SNPs. (b) The bar plot of SNPs.

Supplementary Fig. 2 The distribution of SNP markers. (a) The distribution of mapped SNP markers on each chromosome. (b) The distribution of bin SNP markers on each chromosome.

Supplementary Fig. 3 The distribution pattern of bin markers in the physical map based on the reference of IWGSC RefSeq V1.0 (a) and RefSeq V2.1 (b).

Supplementary Fig. 4 The histogram distribution of gap distance.

Supplementary Fig. 5 The phenotypic performance of parents and the RIL population. The histograms of flag leaf length (a), width (b), and area (c). The boxplots of flag leaf length (d), width (e), and area (f) across eight environments. The bottom and upper lines of the each box denote 25th and 75th percentile, respectively. The middle lines in the box represent median. The upper whiskers stand for maximum or 1.5× the interquartile range (IQR). The bottom whiskers stand for minimum or 1.5× the interquartile range (IQR).

Supplementary Fig. 6 The expression pattern of the candidate gene TraesCS3B02G368000 in different tissues.

Supplementary Table 1 Information of growing environments

Supplementary Table 2 The genetic map of LK86&EMM

Supplementary Table 3 The distribution of different kinds of markers based on IWGSC RefSeq v1.0

Supplementary Table 4 The relationship of bin markers between genetic and physical position

Supplementary Table 5 The list of markers grouped in the genetic map but located in unknown chromosome in reference genome

Supplementary Table 6 The distribution of markers located in unknown chromosome

Supplementary Table 7 The partial genetic and physical map in chromosome 2A

Supplementary Table 8 The partial genetic and physical map in chromosome 2D

Supplementary Table 9 Statistic analysis of phenotypic for parents and RIL population

Supplementary Table 10 Analysis of variance (ANOVA) and broad sense heritability for LL and LW in RIL population from eight environments

Supplementary Table 11 QTLs identified in less than four, but more than two environments for flag leaf related traits in the LK86/EMM population

Supplementary Table 12 Putative function genes in the intervals of flag leaf related QTL

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Niu, J., Si, Y., Tian, S. et al. A Wheat 660 K SNP array-based high-density genetic map facilitates QTL mapping of flag leaf-related traits in wheat. Theor Appl Genet 136, 51 (2023). https://doi.org/10.1007/s00122-023-04248-7

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