Chinese Bulletin of Botany ›› 2016, Vol. 51 ›› Issue (6): 737-742.DOI: 10.11983/CBB15204

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Genome-wide Association Study of Genes Related to Waxiness in Oryza sativa

Xinghai Yang1,2, Baoxuan Nong1,2, Xiuzhong Xia1,2, Zongqiong Zhang1,2, Yu Zeng1,2, Kaiqiang Liu3, Guofu Deng3, Danting Li1,2*   

  1. 1Rice Research Institute, Guangxi Academy of Agricultural Science, Nanning 530007, China
    2Guangxi Key Laboratory of Rice Research Genetics and Breeding, Nanning 530007, China
    3Guangxi Academy of Agricultural Science, Nanning 530007, China
  • Received:2015-11-11 Accepted:2016-03-25 Online:2016-11-01 Published:2016-12-02
  • Contact: Li Danting
  • About author:

    # Co-first authors

Abstract: We examined rice waxiness by genome-wide association study based on genotyping 1 090 071 single nucleotide polymorphism (SNP) variants across landraces in the core collection of 419 rice germplasm derived from Guangxi. We identified 45 significant associated loci located on chromosome 6 at P<4.72×10-8 (4.72E-8) in the compressed mixed linear model. Screening the genes in the candidate regions about 150 kb upstream and downstream of each significant loci revealed 305 candidate genes, including Wx and SSIIa related to starch synthase. Furthermore, 4 significant SNPs associated with waxiness were intensively located in the region of 5.69-5.89 Mb on chromosome 6. This region may be an important candidate region related to waxiness in rice.