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Identification and candidate gene mining of HvSS1, a novel qualitative locus on chromosome 6H, regulating the uppermost internode elongation in barley (Hordeum vulgare L.)

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Abstract

Key message

A novel qualitative locus regulating the uppermost internode elongation of barley was identified and mapped on 6H, and the candidate gene mining was performed by employing various barley genomic resources.

Abstract

The stem of grass crops, such as barley and wheat, is composed of several interconnected internodes. The extent of elongation of these internodes determines stem height, and hence lodging, canopy architecture, and grain yield. The uppermost internode (UI) is the last internode to elongate. Its elongation contributes largely to stem height and facilitates spike exsertion, which is crucial for final grain yield. Despite the molecular mechanism underlying regulation of UI elongation was extensively investigated in rice, little is known in barley. In this study, we characterized a barley spontaneous mutant, Sheathed Spike 1 (SS1), showing significantly shortened UI and sheathed spike (SS). The extension of UI parenchyma cell in SS1 was significantly suppressed. Exogenous hormone treatments and RNA-seq analysis indicated that the suppression of UI elongation is possibly related to insufficient content of endogenous bioactive gibberellin. Genetic analysis showed that SS1 is possibly controlled by a qualitative dominant nuclear factor. Bulked segregant analysis and further molecular marker mapping identified a novel major locus, HvSS1, in a recombination cold spot expanding 173.44–396.33 Mb on chromosome 6H. The candidate gene mining was further conducted by analyzing sequence differences, spatiotemporal expression patterns, and variant distributions of genes in the candidate interval by employing various barley genomic resources of worldwide collections of barley accessions. This study made insight into genetic control of UI elongation in barley and laid a solid foundation for further gene cloning and functional characterization. The results obtained here also provided valuable information for similar research in wheat.

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Acknowledgments

This work is supported by the Science and Technology Support Project of Sichuan Province, China (2016NZ0103), the Science and Technology Service Network Initiative of the Chinese Academy of Sciences (KFJ-STS-QYZD-2021-22-001), the Major Tibet Science and Technology Projects (XZ2021NA01), and the Innovation Team of Triticeae Crops of Sichuan Province.

Funding

Science and Technology Support Project (2016NZ0103) by Department of Science and Technology of Sichuan Province; Science and Technology Service Network Initiative (KFJ-STS-QYZD-2021-22-001) by Chinese Academy of Sciences; Major Tibet Science and Technology Projects (XZ2021NA01) by Science and Technology Department of Tibet; Innovation Team of Triticeae Crops of Sichuan Province by Sichuan Provincial Department of Agriculture and Rural Affairs;

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  1. Xi Pu and Yanyan Tang are contributed equally to this work.

Authors and Affiliations

  1. Chengdu Institute of Biology, Chinese Academy of Sciences, Chengdu, 610041, Sichuan, People’s Republic of China

    Xi Pu, Yanyan Tang, Meihao Zhang, Tao Li, Xvebing Qiu, Juanyu Zhang, Jinhui Wang, Lilan Li, Zhao Yang, Yan Su, Haili Zhang, Junjun Liang, Maoqun Yu, Guangbing Deng & Hai Long

  2. University of Chinese Academy of Sciences, Beijing, People’s Republic of China

    Xi Pu, Yanyan Tang, Meihao Zhang, Tao Li, Xvebing Qiu, Juanyu Zhang & Zhao Yang

  3. Tibet Academy of Agricultural and Animal Husbandry Sciences, Lhasa, Tibet, People’s Republic of China

    Yawei Tang

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Contributions

XP, YT, MZ, GD, LL, YS, XQ, JW, and ZY participated in the field trials, sampling and phenotyping; YT, MZ, GD, and XP developed populations and YT (Yawei Tang) provided barley germplasm; XP, MZ, JZ performed genotyping; XP, HL, MZ, and TL analyzed data; XP, HL, HZ, JL, and MY discussed results; PX and HL wrote the manuscript; HL, PX, and XQ revised manuscript; HL, GD, and YT (Yawei Tang) acquired funding. HL conceived and designed the study, and all authors reviewed the manuscript.

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Correspondence to Hai Long.

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The authors declare that this research has no human and animal participants and that the experiments comply with the current laws of China.

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All sequence data generated and used in this study has been deposited in The Genome Sequence Archive (GSA) (CRA004088), Beijing Institute of Genomics, Chinese Academy of Sciences, and is publicly available.

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Communicated by Takao Komatsuda.

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Pu, X., Tang, Y., Zhang, M. et al. Identification and candidate gene mining of HvSS1, a novel qualitative locus on chromosome 6H, regulating the uppermost internode elongation in barley (Hordeum vulgare L.). Theor Appl Genet 134, 2481–2494 (2021). https://doi.org/10.1007/s00122-021-03837-8

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