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Fine-mapping and validation of the major quantitative trait locus QFlANG-4B for flag leaf angle in wheat

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Abstract

Key message

This study precisely mapped and validated a quantitative trait locus (QTL) located on chromosome 4B for flag leaf angle in wheat.

Abstract

Flag leaf angle (FLANG) is closely related to crop architecture and yield. We previously identified the quantitative trait locus (QTL) QFLANG-4B for FLANG on chromosome 4B, located within a 14-cM interval flanked by the markers Xbarc20 and Xzyh357, using a mapping population of recombinant inbred lines (RILs) derived from a cross between Nongda3331 (ND3331) and Zang1817. In this study, we fine-mapped QFLANG-4B and validated its associated genetic effect. We developed a BC3F3 population using ND3331 as the recurrent parent through marker-assisted selection, as well as near-isogenic lines (NILs) by selfing BC3F3 plants carrying different heterozygous segments for the QFLANG-4B region. We obtained eight recombinant types for QFLANG-4B, narrowing its location down to a 5.3-Mb region. This region contained 76 predicted genes, 7 of which we considered to be likely candidate genes for QFLANG-4B. Marker and phenotypic analyses of individual plants from the secondary mapping populations and their progeny revealed that the FLANG of the ND3331 allele is significantly higher than that of the Zang1817 allele in multiple environments. These results not only provide a basis for the map-based cloning of QFLANG-4B, but also indicate that QFLANG-4B has great potential for marker-assisted selection in wheat breeding programs designed to improve plant architecture and yield.

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Data availability

RNA sequencing data are available at the Sequence Read Archive (SRA) under accession no. PRJNA1070335.

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Acknowledgements

This work was supported by National Natural Science Foundation of China (Grant no. 32125030, U22A20478), Pinduoduo-China Agricultural University Research Fund (PC2023A01003), Major Program of National Agricultural Science and Technology of China (NK20220607).

Funding

Fund was provided by National Natural Science Foundation of China, Grant No. 32125030, Yingyin Yao, Pinduoduo-China Agricultural University Research Fund, PC2023A01003, Yingyin Yao, Major Program of National Fund of Philosophy and Social Science of China, NK20220607, Jinkun Du.

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Authors and Affiliations

  1. Frontiers Science Center for Molecular Design Breeding, Key Laboratory of Crop Heterosis and Utilization (MOE), and Beijing Key Laboratory of Crop Genetic Improvement, China Agricultural University, Beijing, 100193, China

    Wenjia Zhang, Xinyi Chen, Kai Yang, Siyuan Chang, Xue Zhang, Mingde Liu, Longfei Wu, Mingming Xin, Zhaorong Hu, Jie Liu, Huiru Peng, Zhongfu Ni, Qixin Sun, Yingyin Yao & Jinkun Du

Authors
  1. Wenjia Zhang
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  2. Xinyi Chen
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Contributions

JD conceived the project; WZ performed the experiments; XC, KY, SC, and XZ provided technological assistance; ML and LW performed bioinformatics analysis; MX, ZH, JL, HP, ZN, QS, and YY provided theoretical contributions to the project; WZ and JD contributed to writing and revision of the manuscript.

Corresponding author

Correspondence to Jinkun Du.

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122_2024_4629_MOESM1_ESM.jpg

Phenotypic variations in the flag leaves of ND3331, Zang1817, and R53 during the flowering stage. Flag leaf angle (FLANG) is the angle between the stem immediately under the spike and the fag leaf midrib. Scale bars, 5 cm. (JPG 149 kb)

122_2024_4629_MOESM2_ESM.jpg

Fine-mapping of QFLANG-4B. (a) Genetic location of the QFLANG-4B mapping interval on chromosome 4B. (b) Diagram of the 14 recombinant genotypes from the BC3F3 population in the ND3331 background. Black, homozygous for ND3331; gray, heterozygous; white, homozygous Zang1817. (JPG 299 kb)

122_2024_4629_MOESM3_ESM.jpg

Effect of the genotype at the QFLANG-4B region in two bulks of from different NIL pairs on mean FLANG values. ***, P < 0.001 as determined by a two-tailed Student’s t test. (JPG 808 kb)

122_2024_4629_MOESM4_ESM.jpg

Colinearity analysis of the QFLANG-4B mapping interval between the Zang1817 and Chinese Spring genomes. The reference genome version IWGSC RefSeq v1.1 was used for Chinese Spring. The genes and lines of homologous gene pairs are grouped by their strength of relationship. Color priority: RBH (Reciprocal Best Hit) > SBH (Single-side Best Hit) > 1-to-many (all putative homologous genes). All homologous lines are grouped by score: 0–50, 50–70, and 70–100. (JPG 680 kb)

122_2024_4629_MOESM5_ESM.jpg

Distribution of single nucleotide polymorphisms (SNPs) on chromosomes. Sliding window method was used for reducing noise. (JPG 1147 kb)

122_2024_4629_MOESM6_ESM.jpg

Analysis of genes expressed at very low levels (TPM ≤ 1) (a) and with similar relative expression levels (b) in the two bulks of homozygous ND3331 and Zang1817 within the QFLANG-4B mapping interval at the heading stage. (JPG 1394 kb)

122_2024_4629_MOESM7_ESM.jpg

(a) Sequence variations of “r-e-z haploblock” between the parents ND3331 and Zang1817. Comparison of the genomic sequences between ND3331 and Zang1817 within the QTL region revealed a large fragment deletion (~500 kb) spanning three high confident genes including ZnF-B, EamA-B and Rht-B1a in ND3331. (b) Heatmap representing the transcriptional changes in TaSPL8’s three homoeoalleles on chromosome 2A, 2B and 2D in the bulk of homozygous Zang1817 for QFlANG-4B relative to the bulk of homozygous ND3331. Heat map illustrating the FPKM-based expression patterns of these genes. For each gene, the average FPKM values of three biological replicates for each sample were normalized using R and reported in the heatmap. (JPG 381 kb)

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Zhang, W., Chen, X., Yang, K. et al. Fine-mapping and validation of the major quantitative trait locus QFlANG-4B for flag leaf angle in wheat. Theor Appl Genet 137, 121 (2024). https://doi.org/10.1007/s00122-024-04629-6

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