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Nucleotide Diversity and Molecular Evolution of the ALK Gene in Cultivated Rice and its Wild Relatives

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Abstract

Gelatinization temperature (GT), an important parameter for rice cooking quality, is mainly regulated by the ALK gene encoding starch synthase IIa. Here, we reported the nucleotide diversity of the ALK gene in 122 cultivated accessions and 199 wild rice accessions that were collected around the Pearl River Basin in China. A total of 93 single nucleotide ploymorphisms (SNPs) were identified, with an average of one SNP per 40 bp. Tajima D statistics revealed that the DNA sequences covering the last exon have probably evolved under balancing selection. Based on two functional SNPs (an A to G substitution at 4198 bp and a GC to TT dinucleotide substitution at 4330/4331 bp), three haplotypes, G/GC, G/TT, and A/GC, were identified in both wild and cultivated accessions, with the G/GC haplotype being predominant. Interestingly, the A/GC haplotype was exclusively found in the wild accessions from Guangdong province, while the G/TT haplotype was only present in the wild accessions from Jiangxi province and Hainan Island. This suggests that the G/TT and A/GC variants may have arisen independently and undergone balancing selection on separate haplotypes in multiple populations. Our result supports earlier hypothesis that cultivated rice was independently domesticated from multiple domestication events in China. Our study aids in the understanding of the domestication process that led to the improvement of rice grain quality.

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Acknowledgments

This research was jointly supported by the CAS Strategic Priority Research Program (grant no. XDA05130403), and Overseas Construction Plan for Science and Education Base, China-Africa Center for Research and Education, Chinese Academy of Sciences (grant no. SAJC201327).

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Authors and Affiliations

  1. Key Laboratory of Plant Germplasm Enhancement and Specialty Agriculture, Wuhan Botanical Garden of the Chinese Academy of Sciences, Wuhan, 430074, People’s Republic of China

    Ying Zhou, Hongyu Zheng, Guochao Wei, Hui Zhou, Yanni Han & Yuepeng Han

  2. Graduate University of Chinese Academy of Sciences, 19A Yuquanlu, Beijing, 100049, People’s Republic of China

    Hongyu Zheng, Guochao Wei, Hui Zhou & Yanni Han

  3. National Key Laboratory of Crop Genetic Improvement and National Center of Plant Gene Research (Wuhan), Huazhong Agricultural University, Wuhan, 430070, People’s Republic of China

    Xufeng Bai & Yongzhong Xing

  4. Sino-African Joint Research Center, Chinese Academy of Sciences, Wuhan, 430074, People’s Republic of China

    Yuepeng Han

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  1. Ying Zhou
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Correspondence to Yuepeng Han.

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Zhou, Y., Zheng, H., Wei, G. et al. Nucleotide Diversity and Molecular Evolution of the ALK Gene in Cultivated Rice and its Wild Relatives. Plant Mol Biol Rep 34, 923–930 (2016). https://doi.org/10.1007/s11105-016-0975-1

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