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Acta Agronomica Sinica ›› 2021, Vol. 47 ›› Issue (6): 1114-1123.doi: 10.3724/SP.J.1006.2021.02047


Genome-wide association study of blast resistance loci in the core germplasm of rice landraces from Guangxi

CHEN Can(), NONG Bao-Xuan(), XIA Xiu-Zhong, ZHANG Zong-Qiong, ZENG Yu, FENG Rui, GUO Hui, DENG Guo-Fu, LI Dan-Ting*(), YANG Xing-Hai*()   

  1. Rice Research Institute, Guangxi Academy of Agricultural Sciences/Guangxi Key Laboratory of Rice Genetics and Breeding, Nanning 530007, Guangxi, China
  • Received:2020-07-12 Accepted:2020-12-01 Online:2021-06-12 Published:2020-12-28
  • Contact: LI Dan-Ting,YANG Xing-Hai E-mail:chencan129@126.com;nongbaoxuan88@gxaas.net;ricegl@163.com;yangxinghai514@163.com
  • Supported by:
    The Special Fund of Local Science and Technology Development for the Central Guidance(桂科ZY19183020);The Guangxi Special Fund for Innovation-Driven Development(AA17204045-1);The Guangxi Natural Science Fund(2020GXNSFAA259041);The Guangxi Natural Science Fund(2018GXNSFAA138124);The Guangxi Natural Science Fund(2017GXNSFBA198210);The Opening Project of Major Science and Technology Innovation Base for Guangxi(2018-05-Z06-CX04);The Development Fund of Guangxi Academy of Agricultural Sciences(桂农科2019Z08)


Blast disease is one of the most important rice diseases, which seriously affects the yield and quality in rice. In general, breeding resistant varieties is the most economical, environmental, and friendly way to control rice blast. Identification and mining of blast resistance genes are the basis and premise of disease resistance breeding. In our previous study, 419 core germplasms from Guangxi rice landraces were sequenced using specific-locus amplified fragment sequencing (SLAF-seq) technology, and 208,993 high-quality SNPs were identified. Spray inoculation at seedling stage was used to evaluate the resistance of the 419 germplasms to 7 strains. According to phenotype and genotype data, genome-wide association study (GWAS) for rice blast was performed using general linear model (GLM) and mixed linear model (MLM). A total of 20 loci were detected under the two models, including 20 loci detected by GLM and 1 locus detected by MLM. Chr12_10803913 locus was detected in both models. There were 17 loci, overlapping with previously reported genes/QTLs, while the remaining three loci were the first reported, including Chr3_18302718, Chr3_18302744, and Chr5_10379127. A total of 323 candidate genes were screened out in the genomic regions of 150 kb upstream and downstream of 20 significantly associated loci. Eight candidate genes were preliminarily determined to be related to disease resistance. Among them, both LOC_Os12g18360 (Pita) and LOC_Os12g18729 (Ptr) were known cloned genes, LOC_Os03g32100, LOC_Os03g32180, and LOC_Os05g18090 were selected as candidate genes near the three loci. The results provided the scientific basis for the mining of rice blast resistance loci and gene cloning.

Key words: rice, blast disease, genome-wide association study (GWAS), candidate genes

Table 1

Statistical analysis of leaf blast resistance of rice seedlings inoculated with different rice blast strains"

CV (%)
ZA9 1-9 5.03±1.49 29.62
ZA13 1-8 5.72±1.36 23.78
ZB1 1-7 4.29±1.44 33.57
ZB9 1-8 4.83±1.54 31.88
ZB13 1-7 3.80±1.53 40.26
ZC3 1-8 4.84±1.62 33.47
ZC13 1-7 2.93±1.40 47.78

Fig. 1

Distribution of resistance levels of leaf blast among the associated population inoculated with seven strains"

Fig. 2

Genome-wide association study of rice blast resistance to three strains A, B, and C represent Manhattan plot of GLM model ZB9, ZC3, and ZC13, respectively. D represents Manhattan plot ZC3 in MLM model. D, E, and F represent Quantitle-Quantitle plot of GLM model ZB9, ZC3, and ZC13, respectively. H represents Quantitle-Quantitle plot ZC3 in MLM model. The solid inverse triangle in the figure is the significant correlation point in this study."

Table 2

SNP locus of significant association of rice blast and located genes/QTLs"

Upstream loci
Downstream loci
Known genes/QTLs
ZB9 1 10,443,043 1.63E-06 10,293,043 10,593,043 GLM Pi-h2(t)
ZC3 1 8,116,727 1.54E-07 7,966,727 8,266,727 GLM Pi-sj9
ZC3 1 8,116,887 2.91E-07 7,966,887 8,266,887 GLM Pi-sj9
ZC3 3 18,302,718 3.60E-08 18,152,718 18,452,718 GLM
ZC3 3 18,302,744 1.35E-08 18,152,744 18,452,744 GLM
ZC3 5 10,379,127 2.32E-07 10,229,127 10,529,127 GLM
ZB9 8 6,776,078 4.99E-07 6,626,078 6,926,078 GLM Pizh, Pi42
Upstream loci
Downstream loci
Known genes/QTLs
ZC13 12 10,917,077 9.44E-08 10,767,077 11,067,077 GLM Pi12, Pi157, Pi19(t), Pi20, Pi31(t), Pi42(t), Pi6(t), Pita, Pita2, Pi67, Pi39(t), Pi58(t), Pi57, Ptr
ZC13 12 10,919,541 3.98E-07 10,769,541 11,069,541 GLM
ZC3 12 10,629,609 6.56E-08 10,479,609 107,79,609 GLM
ZC3 12 10,796,961 1.84E-07 10,646,961 10,946,961 GLM
ZC3 12 10,801,871 1.30E-07 10,651,871 10,951,871 GLM
ZC3 12 10,803,744 7.39E-09 10,653,744 10,953,744 GLM
ZC3 12 10,803,791 3.45E-08 10,653,791 10,953,791 GLM
ZC3 12 10,803,913 9.20E-10 10,653,913 10,953,913 GLM
ZC3 12 10,816,142 4.90E-09 10,666,142 10,966,142 GLM
ZC3 12 10,816,145 8.24E-09 10,666,145 10,966,145 GLM
ZC3 12 10,816,166 8.24E-09 10,666,166 10,966,166 GLM
ZC3 12 10,816,338 8.01E-09 10,666,338 10,966,338 GLM
ZC3 12 10,926,790 2.35E-07 10,776,790 11,076,790 GLM
ZC3 12 10,803,913 3.93E-07 10,653,913 10,953,913 MLM

Table 3

Information of candidate genes"

Gene name
Physical position
Gene annotation
LOC_Os01g14550 8,159,849-8,161,554 Pathogen-related protein, putative, expressed
LOC_Os01g14590 8,175,375-8,177,889 Pathogen-related protein, putative, expressed
LOC_Os03g32100 18,367,156-18,368,378 Spotted leaf 11, putative, expressed
LOC_Os03g32180 18,410,063-18,411,482 Polygalacturonase inhibitor 1 precursor, putative, expressed
LOC_Os05g18090 10,404,235-10,407,571 SHR5-receptor-like kinase, putative, expressed
LOC_Os12g18360 10,606,359-10,612,068 NB-ARC domain containing protein, expressed
LOC_Os12g18374 10,624,037-10,633,368 NB-ARC domain containing protein, expressed
LOC_Os12g18729 10,822,534-10,833,768 Expressed protein

Fig. 3

Identified blast resistance genes and their associated loci An inverted triangle refers to the region of an association point or associated bit. A: the rice blast genes located on chromosome 1; B: the rice blast genes on chromosome 12 overlapped with the significantly associated locus region."

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