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Fine mapping and genetic analysis identified a C2H2-type zinc finger as a candidate gene for heading date regulation in wheat

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Abstract

Key message

A minor-effect QTL, Qhd.2AS, that affects heading date in wheat was mapped to a genomic interval of 1.70-Mb on 2AS, and gene analysis indicated that the C2H2-type zinc finger protein gene TraesCS2A02G181200 is the best candidate for Qhd.2AS.

Abstract

Heading date (HD) is a complex quantitative trait that determines the regional adaptability of cereal crops, and identifying the underlying genetic elements with minor effects on HD is important for improving wheat production in diverse environments. In this study, a minor QTL for HD that we named Qhd.2AS was detected on the short arm of chromosome 2A by Bulked Segregant Analysis and validated in a recombinant inbred population. Using a segregating population of 4894 individuals, Qhd.2AS was further delimited to an interval of 0.41 cM, corresponding to a genomic region spanning 1.70 Mb (from 138.87 to 140.57 Mb) that contains 16 high-confidence genes based on IWGSC RefSeq v1.0. Analyses of sequence variations and gene transcription indicated that TraesCS2A02G181200, which encodes a C2H2-type zinc finger protein, is the best candidate gene for Qhd.2AS that influences HD. Screening a TILLING mutant library identified two mutants with premature stop codons in TraesCS2A02G181200, both of which exhibited a delay in HD of 2–4 days. Additionally, variations in its putative regulatory sites were widely present in natural accession, and we also identified the allele which was positively selected during wheat breeding. Epistatic analyses indicated that Qhd.2AS-mediated HD variation is independent of VRN-B1 and environmental factors. Phenotypic investigation of homozygous recombinant inbred lines (RILs) and F2:3 families showed that Qhd.2AS has no negative effect on yield-related traits. These results provide important cues for refining HD and therefore improving yield in wheat breeding programs and will deepen our understanding of the genetic regulation of HD in cereal plants.

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Data availability

The datasets generated during and/or analyzed during the current study are available from the corresponding author on reasonable request.

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Acknowledgements

This work was financially supported by the National Natural Science Foundation of China (Grant No. 32172040), the Crop Varietal Improvement and Insect Pests Control by Nuclear Radiation, the China Agriculture Research System of MOF and MARA (Grant No. CARS-03), and the Agricultural Science and Technology Innovation Program (Grant No. CAAS-ZDRW202002).

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  1. Yuting Li and Hongchun Xiong have contributed equally to this work.

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  1. MARA Key Laboratory of Sustainable Crop Production in the Middle Reaches of the Yangtze River (Co-Construction By Ministry and Province), College of Agriculture, Yangtze University, Jingzhou, 434025, China

    Yuting Li & Zhengwu Fang

  2. National Engineering Laboratory of Crop Molecular Breeding/National Center of Space Mutagenesis for Crop Improvement, Institute of Crop Sciences, Chinese Academy of Agricultural Sciences, Beijing, China

    Yuting Li, Hongchun Xiong, Huijun Guo, Chunyun Zhou, Meiyu Fu, Yongdun Xie, Linshu Zhao, Jiayu Gu, Shirong Zhao, Yuping Ding, Chaojie Wang, Ahsan Irshad & Luxiang Liu

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Conceptualization, LL and ZF; formal analysis YL, HX, HG, CZ, and MF; methodology: YL, HX, YX, LZ, SZ, and YD; resources: HG, JG, CW, and AI; Writing—original draft: YL and HX; Writing—review & editing: LL; supervision, LL; funding acquisition: LL. All authors have read and approved the final manuscript.

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Fig. S1

Distribution of HDs in the RILs that were homozygous for the dominant and recessive VRN-B1 alleles (TIF 7046 KB)

Fig. S2

a Frequency distribution of HDs in the secondary segregating population for Qhd.2AS. b Comparison of HDs in plants with different Qhd.2AS genotypes (TIF 7131 KB)

Fig. S3

a Geographical distribution of the representative SNP-140361804. b Frequency distribution of the SNP-140361773 and SNP-140361804 in wheat landraces and modern cultivars (TIF 14063 KB)

Fig. S4

Multiple sequence alignment of the promoter sequences of TraesCS2A02G181200 and its homeologues (TIF 39149 KB)

Fig. S5

Haplotype analysis of Qhd.2AS in the MCC panel. a Scatter plot of KASP marker assays for genotyping the MCC panel with four closely-linked markers. b Frequency distributions of haplotypes Hap-1-4 in wheat accessions with different growth habits and c in landraces and modern cultivars (TIF 6863 KB)

Fig. S6

Interaction graphs of VRN-B1 and Qhd.2AS in the RIL population. Error bars represent the standard errors of the means. **p < 0.01, *p < 0.05 (TIF 7171 KB)

Fig. S7

Evaluation of the effect of Qhd.2AS on important agronomic traits in the secondary segregating population (TIF 2945 KB)

Supplementary file8 (DOCX 43 KB)

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Li, Y., Xiong, H., Guo, H. et al. Fine mapping and genetic analysis identified a C2H2-type zinc finger as a candidate gene for heading date regulation in wheat. Theor Appl Genet 136, 140 (2023). https://doi.org/10.1007/s00122-023-04363-5

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