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A SNP-based GWAS and functional haplotype-based GWAS of flag leaf-related traits and their influence on the yield of bread wheat (Triticum aestivum L.)

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Abstract

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The genetic architecture of five flag leaf morphology traits was dissected by the functional haplotype-based GWAS and a standard SNP-based GWAS in a diverse population consisting of 197 varieties.

Abstract

Flag leaf morphology (FLM) is a critical factor affecting plant architecture and grain yield in wheat. The genetic architecture of FLM traits has been extensively studied with QTL mapping in bi-parental populations, while few studies exploited genome-wide association studies (GWAS) in diverse populations. In this study, a panel of 197 elite and historical varieties from China was evaluated for five FLM traits including the length (FLL), width (FLW), ratio (FLR), area (FLA) and angle (FLANG) as well as yield in nine environments. Based on the phenotypic correlation between yield and FLL (-0.43), FLA (− 0.32) and FLW (0.11), an empirical FLM index combining the three FLM traits proved to be a good predictor for yield. Two GWAS approaches were applied to dissect the genetic architecture of five FLM traits with a Wheat660K SNP array. The functional haplotype-based GWAS revealed 6, 5 and 7 QTL for FLANG, FLL and FLR, respectively, whereas two QTL for FLW and one for FLR were identified by the standard SNP-based GWAS. Due to co-localization, there were 18 independent QTL and 10 of them were close to known ones. One co-localized QTL on chromosome 5A was associated with FLL, FLANG and FLR. Moreover, both GWAS approaches identified a novel QTL for FLR on chromosome 6B which was not reported in previous studies. This study provides new insights into the relationship between FLM and yield and broadens our understanding of the genetic architecture of FLM traits in wheat.

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Abbreviations

BLUE:

Best linear unbiased estimation

GWAS:

Genome-wide association study

YHW:

Yellow and Huai Valley Winter Wheat Region

FH-GWAS:

Functional haplotype-based GWAS

FLL:

Flag leaf length

FLW:

Flag leaf width

FLANG:

Flag leaf angle

FLR:

Flag leaf ratio

FLA:

Flag leaf area

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Acknowledgements

The authors thank Pro. Thorsten Schnurbusch (IPK) for support, advice and revisions regarding this manuscript. We thank Yusuf Yilmaz Ata and Roop Kamel for their help in GWAS. And we also show our appreciation for the China Scholarship Council (CSC) for sponsoring Shulin Chen as guest scientist studying in Leibniz Institute of Plant Genetics and Crop Plant Research (IPK).

Funding

The design of the study and collection, analysis and interpretation of data were supported by the Scientific and technological research projects (30602021) and the National Basic Research Program of China (2014CB138105).

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Author notes

  1. Shulin Chen and Fang Liu contributed equally to this work.

Authors and Affiliations

  1. College of Agronomy, Henan Agricultural University, Zhengzhou, 450002, China

    Shulin Chen, Wenxue Wu & Kehui Zhan

  2. Leibniz Institute of Plant Genetics and Crop Plant Research (IPK), Corrensstr. 3, 06466, Stadt Seeland OT Gatersleben, Germany

    Fang Liu & Yong Jiang

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  1. Shulin Chen
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Contributions

K.Z. and Y.J. conceived the project and planned the trials. S.C. and F.L. analysed the data and were a major contributor in writing the manuscript. W.W. performed the statistical analyses and edited the manuscript. All authors have read and approved the final manuscript.

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Correspondence to Kehui Zhan.

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Chen, S., Liu, F., Wu, W. et al. A SNP-based GWAS and functional haplotype-based GWAS of flag leaf-related traits and their influence on the yield of bread wheat (Triticum aestivum L.). Theor Appl Genet 134, 3895–3909 (2021). https://doi.org/10.1007/s00122-021-03935-7

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