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Deploying QTL-seq rapid identification and separation of the major QTLs of tassel branch number for fine-mapping in advanced maize populations

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Abstract

The tassel competes with the ear for nutrients and shields the upper leaves, thereby reducing the yield of grain. The tassel branch number (TBN) is a pivotal determinant of tassel size, wherein the reduced TBN has the potential to enhance the transmission of light and reduce the consumption of nutrients, which should ultimately result in increased yield. Consequently, the TBN has emerged as a vital target trait in contemporary breeding programs that focus on compact maize varieties. In this study, QTL-seq technology and advanced population mapping were used to rapidly identify and dissect the major effects of the TBN on QTL. Advanced mapping populations (BC4F2 and BC4F3) were derived from the inbred lines 18–599 (8–11 TBN) and 3237 (0–1 TBN) through phenotypic recurrent selection. First, 13 genomic regions associated with the TBN were detected using quantitative trait locus (QTL)-seq and were located on chromosomes 2 and 5. Subsequently, validated loci within these regions were identified by QTL-seq. Three QTLs for TBN were identified in the BC4F2 populations by traditional QTL mapping, with each QTL explaining the phenotypic variation of 6.13–18.17%. In addition, for the major QTL (qTBN2-2 and qTBN5-1), residual heterozygous lines (RHLs) were developed from the BC4F2 population. These two major QTLs were verified in the RHLs by QTL mapping, with the phenotypic variation explained (PVE) of 21.57% and 30.75%, respectively. Near-isogenic lines (NILs) of qTBN2-2 and qTBN5-1 were constructed. There were significant differences between the NILs in TBN. These results will enhance our understanding of the genetic basis of TBN and provide a solid foundation for the fine-mapping of TBN.

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Data availability

The raw data and materials are available on request from the authors.

Abbreviations

TBN :

Tassel branch number

ICIM :

Inclusive composite interval mapping

QTL :

Quantitative trait locus

IM :

Inflorescence meristem

SPM :

Spikelet pair meristems

SM :

Spikelet meristems

PVE :

Phenotypic variation explained

BSA :

Bulked sample analysis

NGS :

Next-generation sequencing

RIL :

Recombinant inbred line

NILs :

Near-isogenic lines

GWAS :

Genome-wide association studies

SNP :

Single nucleotide polymorphism

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Acknowledgements

We would like to thank Shenzhen Huada Gene Technology Co., Ltd (https://www.genomics.cn/) for their whole-genome resequencing. We would also like to thank MogoEdit (http://www.mogoedit.com/) for their English language editing.

Funding

This work was supported by the National Basic Research Program of China (the “973” project, grant number: 2014CB138203), the National Natural Science Foundation of China (grant number: 31101161), the Sichuan Science and Technology Program (grant number: 2022NSFSC0151), and the Double-Support Plan of Sichuan Agricultural University.

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  1. Jixing Ni and Chong You contributed equally to the work.

Authors and Affiliations

  1. Maize Research Institute, Sichuan Agricultural University, No. 211 Huiming Road, Wenjiang District, Chengdu, 611130, Sichuan, China

    Jixing Ni, Chong You, Dengguo Tang, Haimei Wu, Wujiao Deng, Xueying Wang, Jinchang Yang, Ruifan Bao, Zhiqin Liu, Pengxu Meng, Tingzhao Rong & Jian Liu

  2. Sichuan Advanced Agricultural & Industrial Institute, China Agriculture University, No.8 Xingyuan Road, Xinjin District, Chengdu, 611430, Sichuan, China

    Zhengjie Chen

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Contributions

J. L. and T. R. conceived and designed the experiments. J. N., Y. C., Z. C., D. T., H. W., W. D., J. Y., X. W., R. B., Z. L., and P. M. conducted phenotyping measurement in the field trial and performed the experiments. J. N., Y. C., and Z. C. analyzed the data. J. N. and J. L. wrote and revised the manuscript.

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Correspondence to Jian Liu.

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Ni, J., You, C., Chen, Z. et al. Deploying QTL-seq rapid identification and separation of the major QTLs of tassel branch number for fine-mapping in advanced maize populations. Mol Breeding 43, 88 (2023). https://doi.org/10.1007/s11032-023-01431-y

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