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Phylogenetic relationships among species of Setaria (Paniceae; Panicoideae; Poaceae) in Korea: insights from nuclear (ITS and kn1) and chloroplast DNA sequence data

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Abstract

The genus Setaria (tribe Paniceae, subfamily Panicoideae, family Poaceae) comprises approximately 125 species, including agriculturally important food crop (Setaria italica) and globally distributed weed species (S. viridis, S. faberi, S. verticillata, and S. pumila). As an ongoing attempt to determine phylogenetic relationships among species of Setaria in East Asia, we generated phylogeny of Setaria based on a total of 44 accessions representing all the species in Korea. We sequenced two nuclear loci (nrDNA ITS and kn1) and three chloroplast DNA non-coding regions (trnL-trnF, psbJ-petA, and trnQ-rps16) and conducted maximum parsimony, maximum likelihood and Bayesian Inference analyses. The results identified two groups of Setaria in Korea, i.e., S. glauca (=S. pumila) group and S. viridis–S. faberi complex (S. viridis, S. italica, S. faberi, and S. × pycnocoma) group. Only one representative perennial species (i.e., S. chondrachne) in Korea is sister to the S. viridis–S. faberi clade. A minimum of two independent origins of S. faberi, a putative allotetraploid, is suggested in this study, but the contribution from B genome (i.e., S. adhaerens) was not supported. The origin of tetraploid, perennial species of Setaria in Korea, S. chondrachne, is uncertain, but this study suggests possible autotetraploidy and close relationship of S. chondrachne with A genome type species in S. viridis–S. faberi clade. We also documented possible ancient gene flow between D genome (i.e., S. glauca var. dura) and A genome (e.g., S. viridis) in this study.

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Acknowledgments

We thank Yongseong Kim for his technical assistance. The anonymous reviewer’s comments and suggestions greatly improved the earlier version of this manuscript. We also thank Janice MS for editing English. This study was supported by a grant from the Cooperative Research Program for Agricultural Science & Technology Development (Project No. PJ008548) of the Rural Development Administration, Republic of Korea) to C-S Kim.

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Authors and Affiliations

  1. Department of Biological Sciences, Sungkyunkwan University, Suwon, 440-746, Korea

    Seonhee Kim, Myong-Suk Cho & Seung-Chul Kim

  2. National Academy of Agricultural Science, Suwon, 441-701, Korea

    Chang-Seok Kim, Jeongran Lee & In-Yong Lee

  3. Department of Life Science and Biotechnology, Shingyeong University, Hwasung, 445-741, Korea

    Young-Jae Chung

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  1. Seonhee Kim
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Correspondence to Seung-Chul Kim.

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S. Kim and C.-S. Kim contributed equally to this work.

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Kim, S., Kim, CS., Lee, J. et al. Phylogenetic relationships among species of Setaria (Paniceae; Panicoideae; Poaceae) in Korea: insights from nuclear (ITS and kn1) and chloroplast DNA sequence data. Plant Syst Evol 301, 725–736 (2015). https://doi.org/10.1007/s00606-014-1111-z

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