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Insertion of a transposable element in Less Shattering1 (SvLes1) gene is not always involved in foxtail millet (Setaria italica) domestication

Abstract

Recently, the less Shattering1 gene (SvLes1), an MYB transcription factor on chromosome V, in Setaria viridis, was reported to control the degree of seed shattering within S. viridis. SvLes1-1 and SvLes1-2 are the wild type (high shattering) allele and the reduced shattering allele, respectively. In addition to these two alleles, the loss-of-function allele through a transposable-element (TE) insertion in exon 2 was found in foxtail millet, a domesticated type of S. viridis, and was designated as SiLes1-TE. This gene is considered to be a domestication gene in foxtail millet. We screened 131 accessions of foxtail millet and found that 16 landraces (12.2%) of foxtail millet do not have the TE, despite expression of the non-shattering phenotype. We sequenced the SvLes1 gene of these 16 accessions and classified them into three alleles, SvLes1-1, SvLes1-2, and a new allele, SvLes1-3. The geographical distribution of these three alleles was different, suggesting that foxtail millet domestication and differentiation are more complex than expected.

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Acknowledgements

We are grateful to the NARO Genebank, Japan, the USDA genebank, and Iwate Agricultural Research Center for providing plant materials. This work was supported by JSPS KAKENHI Grant Number 20K06098.

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Correspondence to Kenji Fukunaga.

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Supplementary Information

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10722_2021_1165_MOESM1_ESM.docx

Supplemental Figure 1. Sequence of SvLes1 gene of A10.1 and primers used for this study. Primer directions are indicated by arrows. (DOCX 41 kb)

10722_2021_1165_MOESM2_ESM.docx

Supplemental Figure 2. Alignment of the SiLes-TE allele among five accessions, Yugu1, JP71640, JP3913, Otsuchi10, and Nisatai-zairai. Sequences of other four landraces were retrieved from the whole genome sequences determined in this study. Exons were highlighted in light blue. Red arrows and large arrows indicate starts and ends of TE sequences and LTRs, respectively. Red arrows indicate primers used for genotyping and their directions. *Nisatai-zairai (DOCX 80 kb)

Supplemental Table 1. Plant materials used for this study and their alleles in SvLes1 gene (XLSX 16 kb)

Supplemental Table 2. Primers used for amplification, genotyping, and sequencing (XLSX 11 kb)

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Fukunaga, K., Matsuyama, S., Abe, A. et al. Insertion of a transposable element in Less Shattering1 (SvLes1) gene is not always involved in foxtail millet (Setaria italica) domestication. Genet Resour Crop Evol 68, 2923–2930 (2021). https://doi.org/10.1007/s10722-021-01165-w

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Keyword

  • Domestication
  • Foxtail millet
  • Seed shattering
  • Setaria viridis
  • Transposable elements