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Size homoplasy and mutational behavior of chloroplast simple sequence repeats (cpSSRs) inferred from intra- and interspecific variations in four chloroplast regions of diploid and polyploid Triticum and Aegilops species

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Abstract

Chloroplast simple sequence repeats (cpSSRs) are widely distributed in the chloroplast genomes of all plant species, and are frequently employed for genotypic and phylogenetic analysis. However, information on intra- and interspecies variation in cpSSRs is lacking. In this study, we sequenced four intergenic (non-coding) chloroplast DNA regions in 57 accessions of 12 tetraploid, and 16 accessions of 4 hexaploid species of Triticum and Aegilops. These sequence data added to our previous data for diploid species in the same chloroplast regions. Intra- and interspecific genetic variation was analyzed for a total of 189 accessions of 13 diploid, 12 tetraploid, and 4 hexaploid species of Triticum and Aegilops, such that all species were represented by multiple accessions. The data were used to infer phylogenetic relationships within and among Triticum and Aegilops species. Based on this robust phylogenetic tree, seven of eight cpSSR loci clearly exhibited “size homoplasy,” referring to the fact that cpSSRs of identical size and DNA sequence can arise even if the alleles are not descended from a common ancestor. These data indicate that cpSSRs should be used with caution in phylogenetic analyzes. Interestingly, as observed from several previous studies, our data also suggest that observed mutation rates may increase significantly when mononucleotide (homopolymer) repeat numbers reach or exceed 9 bp. In the present report, using this sequence data set involving cpSSRs, 81 unique haplotypes among 189 accessions were detected, and five tetraploid Triticum and Aegilops species were successfully identified and genotyped. Our results indicate that combinations of nucleotide substitutions, indels and SSRs of chloroplast nucleotide sequences are available for genoty** at the species accession level.

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Acknowledgements

We are also grateful to K. Kobayashi, Gifu University, for her essential support. We also thank M. Sumi, Gifu University, and H. Uto, Osaka Prefectural University for their support. This research was partly supported by a grant from the Ministry of Culture, Education and Technology, the National BioResource Project KOMUGI.

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  1. Laboratory of Plant Breeding and Genetics, Faculty of Applied Biological Sciences, Gifu University, 1-1, Yanagido, Gifu City, Gifu, 501-1193, Japan

    Kyoko Yamane

  2. Laboratory of Crop Evolution, Graduate School of Agriculture, Kyoto University, 1, Nakajo, Mozume, Muko, 617-0001, Japan

    Kyoko Yamane & Taihachi Kawahara

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  1. Kyoko Yamane
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Correspondence to Kyoko Yamane.

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Yamane, K., Kawahara, T. Size homoplasy and mutational behavior of chloroplast simple sequence repeats (cpSSRs) inferred from intra- and interspecific variations in four chloroplast regions of diploid and polyploid Triticum and Aegilops species. Genet Resour Crop Evol 65, 727–743 (2018). https://doi.org/10.1007/s10722-017-0567-4

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