Chin Bull Bot ›› 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:2016-12-02 Published:2016-11-01
  • Contact: Li Danting E-mail:lidanting@gxaas.net
  • 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.

Figure 1

Genome-wide association studies of waxy traits in rice(A) Manhattan plots of compresses mixed linear model for waxy trait; (B) Quantitle-quantitle plot of compresses mixed linear model for waxy trait"

Table 1

Significantly associated SNPs of waxiness in rice"

Chromosome Position Allele Major allele Minor allele P-value Known loci
6 921039 A, T 455 75 2.32E-12
6 945908 G, T 455 73 6.02E-09
6 945924 G, A 455 73 6.02E-09
6 1179280 C, A 516 32 2.60E-08
6 1457896 C, A 465 339 1.42E-09
6 1512757 G, C 381 197 3.57E-09
6 1512819 A, G 384 198 3.38E-09
6 1592445 G, C 593 231 1.20E-13
6 1597045 G, A 470 236 9.37E-09
6 1607061 T, A 559 247 1.61E-19
6 1654904 G, T 297 161 2.12E-10
6 1661829 A, C 587 241 1.69E-21
6 1684538 A, G 407 171 3.63E-09
6 1684543 C, T 444 136 4.13E-17
6 1684784 T, C 431 155 7.26E-13
6 1694761 G, C 481 231 3.78E-22
6 1694808 A, G 482 230 9.55E-21
6 1694818 T, C 455 251 8.14E-15
6 1703886 T, G 574 264 3.20E-21
6 1720764 A, G 533 269 4.73E-15
6 1720799 G, A 561 241 3.70E-23
6 1720821 C, T 560 240 4.80E-23
6 1745339 C, T 338 134 1.00E-08
6 1754453 A, T 561 253 1.75E-22
6 1756202 T, C 552 264 1.79E-21
6 1756454 A, G 556 262 2.45E-23
6 1780293 T, C 482 248 4.08E-23
6 1780336 C, A 483 249 2.81E-23
6 1780519 C, T 479 251 3.96E-09
6 1792217 C, T 557 241 3.29E-24 Wx
6 1797551 C, T 571 253 1.32E-23
6 1807558 A, G 295 159 9.55E-14
6 1807737 T, C 272 166 8.98E-12
6 1807778 G, T 279 159 1.67E-13
6 1807797 A, G 534 250 1.38E-20
6 1822395 T, C 525 219 1.12E-20
6 1865861 G, A 543 137 3.62E-10
6 1958767 T, C 405 211 2.23E-11
6 2256752 G, A 578 34 2.85E-12
6 5688919 T, G 581 211 5.68E-09
6 5711650 C, T 664 34 1.17E-08
6 5843510 G, A 763 49 2.79E-10
6 5881999 T, C 784 48 3.34E-08
6 6879531 A, G 488 272 1.62E-09 SSIIa
6 6879731 C, G 486 274 2.07E-09

Table 2

Summary of 3 significantly associated loci and candidate genes"

Position Candidate gene Annotation
Chr06_1792217 Os06g0133000 Wx
Chr06_5843510 Os06g0214900 FAD-dependent pyridine nucleotide-disulphide oxidoreductase domain containing protein
Chr06_5843510 Os06g0215000 Hypothetical protein
Chr06_5843510 Os06g0215100 Protein of unknown function DUF1645 family protein
Chr06_5843510 Os06g0214850 Similar to gibberellin receptor GID1L2
Chr06_5843510 Os06g0214800 Alpha/beta hydrolase fold-3 domain containing protein
Chr06_5843510 Os06g0214300 Alpha/beta hydrolase fold-3 domain containing protein
Chr06_6879531 Os06g0229800 SSIIa
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