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The molecular basis of mutations at the Waxy locus from Amaranthus caudatus L.: evolution of the waxy phenotype in three species of grain amaranth

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Abstract

Polymorphisms at the Waxy locus of Amaranthus caudatus L. collected from a wide range of regions were used to investigate genetic diversity and mutation sites. A comparison of the Waxy locus revealed a very high level of sequence conservation. This result clearly showed low environmental and evolutionary variability in the Waxy gene. We also performed screening to confirm the mutation sites in the coding sequences of all accessions. The results indicate that one insertion in the coding region of Waxy genes was responsible for the change in perisperm starch leading to the waxy phenotype in all accessions of this species, and thus that a single mutation event altered the regulation of the Waxy gene during the domestication of this crop. In addition, phylogenetic analysis showed that waxy phenotypes within each of three species, A. caudatus, A. cruentus and A. hypochondriacus, originated separately or differentiated from nonwaxy phenotypes of each species through a single mutational event (i.e., a frame shift or base substitution). We also compared obvious structural features of the coding sequence of waxy and nonwaxy phenotypes with those of low-amylose phenotypes in A. caudatus. The Waxy coding sequences of low-amylose phenotypes do not show polymorphisms and are identical with those of waxy phenotypes. This could mean that there is another gene that encodes a key enzyme responsible for amylose synthesis as the elementary quantity in tissues other than perisperm in A. caudatus.

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Acknowledgments

We express our sincere thanks to Dr. D. Brenner of USDA-ARS-MWA-PIRU, Iowa State University, USA, for providing the accessions used in this experiment. We also would like to thank Ms. Sachiko Ohashi for expert technical assistance. This research was supported by the grant-in-aid for Japan Society for the Promotion of Science (JSPS) fellows relating to JSPS Postdoctoral Fellowship for Foreign Researchers (ID No. P 11212).

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Authors and Affiliations

  1. Genetic Resources Center, National Institute of Agrobiological Sciences, 2-1-2 Tsukuba, Ibaraki, 305-8602, Japan

    Young-Jun Park, Tomotaro Nishikawa & Norihiko Tomooka

  2. Graduate School of Agriculture, Shinshu University, 8304 Minamiminowa, Nagano, 399-4598, Japan

    Kazuhiro Nemoto

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  1. Young-Jun Park
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  2. Tomotaro Nishikawa
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  3. Norihiko Tomooka
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  4. Kazuhiro Nemoto
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Correspondence to Young-Jun Park.

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Park, YJ., Nishikawa, T., Tomooka, N. et al. The molecular basis of mutations at the Waxy locus from Amaranthus caudatus L.: evolution of the waxy phenotype in three species of grain amaranth. Mol Breeding 30, 511–520 (2012). https://doi.org/10.1007/s11032-011-9640-4

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