Letter

Sparse panicle1 is required for inflorescence development in Setaria viridis and maize

  • Nature Plants 3, Article number: 17054 (2017)
  • doi:10.1038/nplants.2017.54
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Abstract

Setaria viridis is a rapid-life-cycle model panicoid grass. To identify genes that may contribute to inflorescence architecture and thus have the potential to influence grain yield in related crops such as maize, we conducted an N-nitroso-N-methylurea (NMU) mutagenesis of S. viridis and screened for visible inflorescence mutant phenotypes. Of the approximately 2,700 M2 families screened, we identified four recessive sparse panicle mutants (spp1–spp4) characterized by reduced and uneven branching of the inflorescence. To identify the gene underlying the sparse panicle1 (spp1) phenotype, we performed bulked segregant analysis and deep sequencing to fine map it to an approximately 1 Mb interval. Within this interval, we identified disruptive mutations in two genes. Complementation tests between spp1 and spp3 revealed they were allelic, and deep sequencing of spp3 identified an independent disruptive mutation in SvAUX1 (AUXIN1), one of the two genes in the 1 Mb interval and the only gene disruption shared between spp1 and spp3. SvAUX1 was found to affect both inflorescence development and root gravitropism in S. viridis. A search for orthologous mutant alleles in maize confirmed a very similar role of ZmAUX1 in maize, which highlights the utility of S. viridis in accelerating functional genomic studies in maize.

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Acknowledgements

The authors thank A. Bray for his help in maize root gravitropism assay, C. Shyu for her help in qRT–PCR, and the DDPSC greenhouse staff for plant care. The work conducted by the US Department of Energy Joint Genome Institute was supported by the Office of Science of the US Department of Energy under contract number DE-AC02-05CH11231. This work was also supported by a Department of Energy grant to T.B.P. (DE-SC0008769), and a National Science Foundation grant to E.A.K. (IOS-1413824).

Author information

Author notes

    • Pu Huang
    •  & Hui Jiang

    These authors contributed equally to this work.

Affiliations

  1. Donald Danforth Plant Science Center, 975 N Warson Road, St. Louis, Missouri 63132, USA

    • Pu Huang
    • , Hui Jiang
    • , Chuanmei Zhu
    • , Mathew S. Box
    • , Elizabeth A. Kellogg
    •  & Thomas P. Brutnell
  2. Department of Energy Joint Genome Institute, Walnut Creek, California 94598, USA

    • Kerrie Barry
    • , Laura Sandor
    •  & Jeremy Schmutz
  3. HudsonAlpha Institute for Biotechnology, Huntsville, Alabama 35806, USA

    • Jerry Jenkins
    •  & Jeremy Schmutz

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Contributions

P.H., H.J. and T.P.B. conceived and designed the study. H.J. performed the screen, crosses and DNA extraction. P.H. and H.J. performed bulked segregant analysis. K.B., J.J., L.S. and J.S. performed library construction and sequencing. P.H. performed sequencing and other data analysis. P.H., H.J., C.Z. and M.S.B. performed phenotypic characterizations in S. viridis and maize. P.H., H.J., C.Z., E.A.K. and T.P.B. wrote the manuscript.

Competing interests

The authors declare no competing financial interests.

Corresponding author

Correspondence to Thomas P. Brutnell.

Supplementary information

PDF files

  1. 1.

    Supplementary Information

    Supplementary Figures 1–5.

Excel files

  1. 1.

    Supplementary Table 1

    Mutant families and BSA pools that have been sequenced.

  2. 2.

    Supplementary Table 2

    Annotations of homozygous disruptive mutations in NMU00629, spp1 (line number exceeds 51 because of multiple transcripts for some genes).

  3. 3.

    Supplementary Table 3

    Annotations of homozygous disruptive mutations in NMU00933, spp3 (line number exceeds 98 because of multiple transcripts for some genes).

  4. 4.

    Supplementary Table 4

    Primers used in this study.

Text files

  1. 1.

    File S1

    Error-prone SNP calls from NMU mutants.