Abstract
Rice false smut (RFS), caused by Ustilaginoidea virens, is one of the most destructive grain diseases in rice production worldwide. Hence, to increase the ability of rice resistance to U. virens is a major breeding goal of rice breeders. However, it is difficult to evaluate rice resistance to U. virens. Hence, to clarify the RFS-resistance genetic mechanism is of great significance. In this study, a diversity panel landrace comprising of 315 accessions was identified for resistance against U. virens at reproductive stage in 2017 and 2018. Totally, 58 significant SNPs were distributed on the rice whole genome except chromosome 7, and 3 SNPs associated with three RFS-related traits were identified in 2 years. Haplotype block structure analysis predicted that a total of 15 candidate genes for U. virens resistance were screened based on significant SNPs with minimum P value (− log10P = 13.86). Of which, LOC_Os01g15580, a plant NBS-LRR protein coding gene near the significant SNP chr01_8738751 (12.3 kb), was considered a candidate for key resistance factor in the disease. These findings might provide a new insight into the genetic basis of resistance to rice false smut.
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References
Andargie M, Li LY, Feng AQ, Zhu XY, Li JX (2018) Mapping of the quantitative trait locus (QTL) conferring resistance to rice false smut disease. Curr Plant Biol 15:38–43. https://doi.org/10.1016/j.cpb.2018.11.003
Ashizawa T, Takahashi M, Moriwaki J, Hirayae K (2011) A refined inoculation method to evaluate false smut resistance in rice. J Gen Plant Pathol 77(1):10–16. https://doi.org/10.1007/s10327-010-0279-5
Biswas A (2001) Field reaction of hybrid rice varieties to false smut (FSm) and kernel smut (KSm) diseases in West Bengal, India. Environ Ecol 19(1):229–230
Brown JKM (2015) Durable resistance of crops to disease: a Darwinian perspective. Annu Rev Phytopathol 53:513–539. https://doi.org/10.1146/annurev-phyto-102313-045914
Chen J, Zhang F, Zhao C, Lv G, Sun C, Pan Y, Guo X, Chen F (2019) Genome-wide association study of six quality traits reveals the association of the TaRPP13L1 gene with flour colour in Chinese bread wheat. Plant Biotechnol J 17:2106–2122. https://doi.org/10.1111/pbi.13126
Chib H, Tikoo M, Kalha C, Gupta B, Singh S, Raina P (1992) Effect of false smut on yield of rice. J Mycol Plant Pathol 22(3):278–280
Fujita Y, Sonoda R, Yaegashi H (1989) Inoculation with conidiospores of false smut fungus to rice panicles at the booting stage. J Phytopathol 55(5):629–634
Guo W (1992) Studies on the infection period and the infection gate of the chlamydospores of Ustilaginoidea virens (Cooke)TAK. on rice. Acta Phytophylacica Sin 19:97–100
Guo X, Li Y, Fan J, Liang L, Huang F, Wenming W (2012) Progress in the study of false smut disease in rice. J Agric Sci Technol (1939–1250):1211–1217
Huang XH, Wei XH, Sang T, Zhao QA, Feng Q, Zhao Y, Li CY, Zhu CR, Lu TT, Zhang ZW, Li M, Fan DL, Guo YL, Wang A, Wang L, Deng LW, Li WJ, Lu YQ, Weng QJ, Liu KY, Huang T, Zhou TY, Jing YF, Li W, Lin Z, Buckler ES, Qian QA, Zhang QF, Li JY, Han B (2010) Genome-wide association studies of 14 agronomic traits in rice landraces. Nat Genet 42(11):961–976. https://doi.org/10.1038/ng.695
Jiang Z, Jiang Z, Jiang Z, Zhang G (2009) Effect of false smut ball number on yield of rice. Northern Rice 3
Jin S, Dai G, Runmei H, Qian D, Xue H (2015) Resistance evaluation of 11 rice (Oryza sativa) varieties to Ustilaginoidea virens. J SHANGHAI JIAOTONG UNIV SCI 23(3)
Koiso Y, Morisaki N, Yamashita Y, Mitsui Y, Shirai R, Hashimoto Y, Iwasaki S (1998) Isolation and structure of an antimitotic cyclic peptide, Ustiloxin F: chemical interrelation with a homologous peptide, Ustiloxin B. J Antibiot 51(4):418–422. https://doi.org/10.7164/antibiotics.51.418
Li Y, Zhang Y, Zhu Z, Zhao L, Wang C (2008) QTL analysis for resistance to rice false smut by using recombinant inbred lines in rice. Chin J Rice Sci 22(5):472–576. https://doi.org/10.16819/j.1001
Li Y, Shi J, Xiang ZF, Hu RP, Shi SP, Peng T, Liu DY, Huang TY (2017) Analysis of the resistance to rice blast and false smut of 18 varieties of hybrid rice in Sichuan Province, China. Int J Agric Biol 19(4):880–886. https://doi.org/10.17957/Ijab/15.0384
Lippert C, Listgarten J, Liu Y, Kadie CM, Davidson RI, Heckerman D (2011) FaST linear mixed models for genome-wide association studies. Nat Methods 8(10):833–835. https://doi.org/10.1038/nmeth.1681
Lu SQ, Sun WB, Meng JJ, Wang A, Wang XH, Tian J, Fu XX, Dai JG, Liu Y, Lai DW, Zhou LG (2015) Bioactive Bis-naphtho-gamma-pyrones from rice false smut pathogen Ustilaginoidea virens. J Agric Food Chem 63(13):3501–3508. https://doi.org/10.1021/acs.jafc.5b00694
Meng JJ, Sun WB, Mao ZL, Xu D, Wang XH, Lu SQ, Lai DW, Liu Y, Zhou LG, Zhang GZ (2015) Main ustilaginoidins and their distribution in rice false smut balls. Toxins 7(10):4023–4034. https://doi.org/10.3390/toxins7104023
Mundt CC (2014) Durable resistance: a key to sustainable management of pathogens and pests. Infect Genet Evol 27:446–455. https://doi.org/10.1016/j.meegid.2014.01.011
Nielsen R, Paul JS, Albrechtsen A, Song YS (2011) Genotype and SNP calling from next-generation sequencing data. Nat Rev Genet 12(6):443–451. https://doi.org/10.1038/nrg2986
Price AL, Patterson NJ, Plenge RM, Weinblatt ME, Shadick NA, Reich D (2006) Principal components analysis corrects for stratification in genome-wide association studies. Nat Genet 38(8):904–909. https://doi.org/10.1038/ng1847
Purcell S, Neale B, Todd-Brown K, Thomas L, Ferreira MAR, Bender D, Maller J, Sklar P, de Bakker PIW, Daly MJ, Sham PC (2007) PLINK: a tool set for whole-genome association and population-based linkage analyses. Am J Hum Genet 81(3):559–575. https://doi.org/10.1086/519795
Yang L, Chen L, Xu J, Liu J, Ding K (2012) Estimation of yield loss caused by rice false smut. J Anhui Agric Univ 39:474–477. https://doi.org/10.13610/j.cnki.1672-352x.2012.03.020
Yano K, Yamamoto E, Aya K, Takeuchi H, Lo PC, Hu L, Yamasaki M, Yoshida S, Kitano H, Hirano K, Matsuoka M (2016) Genome-wide association study using whole-genome sequencing rapidly identifies new genes influencing agronomic traits in rice. Nat Genet 48(8):927–934. https://doi.org/10.1038/ng.3596
Zhang C, Hu B, Zhu K, Zhang H, Leng Y, Tang S, Gu M, Liu Q (2013) QTL mapping for rice RVA properties using high-throughput re-sequenced chromosome segment substitution lines. Rice Sci 20(6):407–414. https://doi.org/10.1016/s1672-6308(13)60131-6
Zhang C, Zhu J, Chen S, Fan X, Li Q, Lu Y, Wang M, Yu H, Yi C, Tang S, Gu M, Liu Q (2019) Wx(lv), the ancestral allele of rice waxy gene. Mol Plant 12:1157–1166. https://doi.org/10.1016/j.molp.2019.05.011
Zhao K, Tung CW, Eizenga GC, Wright MH, Ali ML, Price AH, Norton GJ, Islam MR, Reynolds A, Mezey J, McClung AM, Bustamante CD, McCouch SR (2011) Genome-wide association mapping reveals a rich genetic architecture of complex traits in Oryza sativa. Nat Commun 2:ARTN 46728. https://doi.org/10.1038/ncomms1467
Zheng T, Yu H, Zhang H, Wu Z, Wang W, Tai S, Chi L, Ruan J, Wei C, Shi J, Gao Y, Fu B, Zhou Y, Zhao X, Zhang F, McNally KL, Li Z, Zhang G, Li J, Zhang D, Xu J, Li Z (2015) Rice functional genomics and breeding database (RFGB): 3K-rice SNP and InDel sub-database. Chin Sci Bull (Chinese Version) 60(4):367–371. https://doi.org/10.1360/n972014-01231
Zhou X (2017) A unified framework for variance component estimation with summary statistics in genome-wide association studies. Ann Appl Stat 11(4):2027–2051. https://doi.org/10.1214/17-Aoas1052
Zhou YL, Xie XW, Zhang F, Wang S, Liu XZ, Zhu LH, Xu JL, Gao YM, Li ZK (2014) Detection of quantitative resistance loci associated with resistance to rice false smut (Ustilaginoidea virens) using introgression lines. Plant Pathol 63(2):365–372. https://doi.org/10.1111/ppa.12091
Funding
This work was partly granted from the National Transgenic Research Program (2016ZX08001004-001-002), the National Key Research and Development Program (2016YFD0100903), the National Nature Science Foundation (31870322) of China, and Huanghe Patent Program of Wuhan City.
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Weixiong Long and Shaoqing Li designed the experiment and wrote the manuscript.
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Long, W., Yuan, Z., Fan, F. et al. Genome-wide association analysis of resistance to rice false smut. Mol Breeding 40, 46 (2020). https://doi.org/10.1007/s11032-020-01130-y
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DOI: https://doi.org/10.1007/s11032-020-01130-y