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


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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Figure 1: Characterization of spp1 and spp3 in S. viridis and Zmaux1-0 in maize.
Figure 2: BSA mapping and variation of SvAUX1 and ZmAUX1 alleles.


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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




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.

Corresponding author

Correspondence to Thomas P. Brutnell.

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The authors declare no competing financial interests.

Supplementary information

Supplementary Information

Supplementary Figures 1–5. (PDF 1644 kb)

Supplementary Table 1

Mutant families and BSA pools that have been sequenced. (XLSX 26 kb)

Supplementary Table 2

Annotations of homozygous disruptive mutations in NMU00629, spp1 (line number exceeds 51 because of multiple transcripts for some genes). (XLSX 14 kb)

Supplementary Table 3

Annotations of homozygous disruptive mutations in NMU00933, spp3 (line number exceeds 98 because of multiple transcripts for some genes). (XLSX 13 kb)

Supplementary Table 4

Primers used in this study. (XLSX 11 kb)

File S1

Error-prone SNP calls from NMU mutants. (TXT 9831 kb)

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Huang, P., Jiang, H., Zhu, C. et al. Sparse panicle1 is required for inflorescence development in Setaria viridis and maize. Nature Plants 3, 17054 (2017).

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