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Genome-Wide Association Study to Identify Favorable SNP Allelic Variations and Candidate Genes That Control the Timing of Spring Bud Flush of Tea (Camellia sinensis) Using SLAF-seq

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    Genome-Wide Association Study to Identify Favorable SNP Allelic Variations and Candidate Genes That Control the Timing of Spring Bud Flush of Tea (Camellia sinensis) Using SLAF-seq
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    • Rang Jian Wang*
      Rang Jian Wang
      Institute of Tea, Fujian Academy of Agricultural Sciences, 1 Hutouyang Road, Shekou, Fu’an, Fujian 355015, China
      Fujian Branch, National Center for Tea Improvement, 1 Hutouyang Road, Shekou, Fu’an, Fujian 355015, China
      *E-mail: [email protected]. Phone: +86 593 6610388.
      More by Rang Jian Wang
      Orcidhttp://orcid.org/0000-0003-4447-7217
    • Xiang Feng Gao
      Xiang Feng Gao
      Institute of Tea, Fujian Academy of Agricultural Sciences, 1 Hutouyang Road, Shekou, Fu’an, Fujian 355015, China
      Fujian Branch, National Center for Tea Improvement, 1 Hutouyang Road, Shekou, Fu’an, Fujian 355015, China
      More by Xiang Feng Gao
    • Jun Yang
      Jun Yang
      Institute of Tea, Fujian Academy of Agricultural Sciences, 1 Hutouyang Road, Shekou, Fu’an, Fujian 355015, China
      Fujian Branch, National Center for Tea Improvement, 1 Hutouyang Road, Shekou, Fu’an, Fujian 355015, China
      More by Jun Yang
    • Xiang Rui Kong
      Xiang Rui Kong
      Institute of Tea, Fujian Academy of Agricultural Sciences, 1 Hutouyang Road, Shekou, Fu’an, Fujian 355015, China
      Fujian Branch, National Center for Tea Improvement, 1 Hutouyang Road, Shekou, Fu’an, Fujian 355015, China
      More by Xiang Rui Kong
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    Journal of Agricultural and Food Chemistry

    Cite this: J. Agric. Food Chem. 2019, 67, 37, 10380–10391
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    https://doi.org/10.1021/acs.jafc.9b03330
    Published August 29, 2019
    Copyright © 2019 American Chemical Society
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    Abstract

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    The timing of spring bud flush (TBF) is of economic importance for tea plant (Camellia sinensis) breeding. We employed a genome-wide association study (GWAS) to identify favorable single nucleotide polymorphism (SNP) allelic variations as well as candidate genes that control TBF of C. sinensis using specific-locus-amplified fragment sequencing (SLAF-seq) in a diversity panel comprising 151 tea plant germplasm resources. GWAS analysis revealed 26 SNPs associated with TBF in three years, and we eventually identified a final significant SNP for TBF. To identify candidate genes possibly related to TBF, we screened seven candidate genes within 100 kb regions surrounding the trait-related SNP loci. Furthermore, the favorable allelic variation, the “TT” genotype in the SNP loci, was discovered, and a derived cleaved amplified polymorphism (dCAPS) marker was designed that cosegregated with TBF, which could be used for marker-assisted selection (MAS) breeding in C. sinensis. The results obtained from this study can provide a theoretical and applied basis for the MAS of early breeding in tea plants in the future.

    Copyright © 2019 American Chemical Society

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    Supporting Information

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    The Supporting Information is available free of charge on the ACS Publications website at DOI: 10.1021/acs.jafc.9b03330.

    • Information for 151 C. sinensis accessions (XLSX)

    • Information for 40 registered tea cultivars (XLSX)

    • Information for 40 tea hybrids with extremely early and late TBF trait (XLSX)

    • Detailed primer sequence information of the dCAPS marker (XLSX)

    • Phenotypic data for 151 C. sinensis accessions (XLSX)

    • Sequencing data statistics of 151 C. sinensis accessions (XLSX)

    • SLAF tag statistics of 151 C. sinensis accessions (XLSX)

    • Polymorphic SLAF tags of 151 C. sinensis accessions (XLSX)

    • SNP statistics of 151 C. sinensis accessions (XLSX)

    • Expression profiles of five candidate genes surrounding the 100 kb of the TBF-associated SNP loci under cold stress using datasets from TPIA database; uncharacterized protein gene; calmodulin-binding protein gene; uridine 5′-monophosphate synthase gene; uncharacterized protein gene; and uncharacterized protein gene (PDF)

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    Journal of Agricultural and Food Chemistry

    Cite this: J. Agric. Food Chem. 2019, 67, 37, 10380–10391
    Click to copy citationCitation copied!
    https://doi.org/10.1021/acs.jafc.9b03330
    Published August 29, 2019
    Copyright © 2019 American Chemical Society
    Request reuse permissions

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