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Origin and evolution of the waxy phenotype in Amaranthus hypochondriacus: evidence from the genetic diversity in the Waxy locus

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Abstract

The existence of polymorphism in the Waxy locus in a large gene pool of 53 strains with various waxy phenotypes from samples of Amaranthus hypochondriacus collected from different regions was investigated in an origin-and-evolution study. First, we screened all strains for a mutation point (G–A polymorphism in exon 6) by using PCR–RFLP and/or direct sequence analysis. The results showed that the nonsense mutation in the coding region (exon 6) of the Waxy gene was responsible for the change in perisperm starch, leading to a waxy phenotype in all strains. Second, phylogenetic analysis, which was based on the Waxy variation, indicated diverse waxy types occurring separately and independently in certain domesticated regions in Mexico. Finally, we designated nine molecular types by comparing obvious structural variations in the coding region of the Waxy gene. Among the molecular types, A. hypochondriacus contained Type III in three subtypes with the waxy phenotype, with evolutionary routes that could originate from Type II in accordance with G–A polymorphism. In addition, these types had the same mutation points by which the Waxy gene was converted into the waxy phenotype. Therefore, the present results showed that the nonsense mutation is a unique event in the evolution of waxy phenotypes in this crop. This study will provide useful information for understanding the evolutionary process of the waxy phenotype.

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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.

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Authors and Affiliations

  1. Department of Bioscience and Food Production Science, Interdisciplinary Graduate School of Science & Technology, Shinshu University, 8304 Minamiminowa, Nagano, 399-4598, Japan

    Young-Jun Park

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

    Kazuhiro Nemoto, Kenichi Matsushima & Mineo Minami

  3. Genebank, National Insitute of Agrobiological Sciences, 2-1-2 Tsukuba, Ibaraki, 305-8602, Japan

    Tomotaro Nishikawa & Makoto Kawase

Authors
  1. Young-Jun Park
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  2. Kazuhiro Nemoto
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  3. Tomotaro Nishikawa
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  4. Kenichi Matsushima
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  5. Mineo Minami
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  6. Makoto Kawase
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Correspondence to Young-Jun Park.

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Park, YJ., Nemoto, K., Nishikawa, T. et al. Origin and evolution of the waxy phenotype in Amaranthus hypochondriacus: evidence from the genetic diversity in the Waxy locus. Mol Breeding 29, 147–157 (2012). https://doi.org/10.1007/s11032-010-9533-y

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  • DOI: https://doi.org/10.1007/s11032-010-9533-y

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