Molecular Breeding

, 39:114 | Cite as

Use of genomic selection in breeding rice (Oryza sativa L.) for resistance to rice blast (Magnaporthe oryzae)

  • Mao Huang
  • Elias G. Balimponya
  • Emmanuel M. Mgonja
  • Leah K. McHale
  • Ashura Luzi-Kihupi
  • Guo-Liang Wang
  • Clay H. SnellerEmail author


Rice blast (RB), caused by the fungal pathogen Magnaporthe oryzae, is a major disease in rice (Oryzae sativa L.) with resistance controlled by major and minor genes. Genomic selection (GS) is a breeding technology applicable for selecting traits controlled by many genes. Our objective was to assess the utility of GS in improving RB resistance. A population of 161 accessions from Africa and another population of 162 accessions from the USA were evaluated for resistance to six and eight RB isolates, respectively. Each rice population was genotyped with single nucleotide polymorphism (SNP) markers. The accuracy of GS was determined using seven models: genomic best linear unbiased prediction (gBLUP), gBLUP with some markers as fixed effects (fgBLUP), gBLUP model with population structure as a covariate (sgBLUP), multitrait gBLUP (mgBLUP), Bayesian (BayesA and BayesC) models, and a multiple linear regression model using significant markers (MLR). Each set of population had accessions with good resistance to multiple isolates. Using cross-validation, the accuracy of gBLUP ranged from 0.15 to 0.72; the gBLUP, sgBLUP, mgBLUP, and Bayesian methods had similar accuracy, while fgBLUP gave the greatest accuracy. Without cross-validation, gBLUP, sgBLUP, fgBLUP, and Bayesian methods were similar and were superior to mgBLUP and MLR. In general, a GS model built on data from one isolate was able to predict the phenotypes generated from other isolates, suggesting common genes controlling resistance across isolates. Our results demonstrate that GS may be a very useful method to improve RB resistance. The fgBLUP model could be used to effectively select for both durable and resistance traits conferred by major genes.


Rice blast Genomic selection Accuracy Genotype by sequencing Resistant Susceptible 



The authors are also grateful to Dr. Sneller’s and Wang’s labs at the Ohio State University (OSU) and Dr. Bo Zhou’s Lab at the International Rice Research Institute (IRRI) for their technical assistance.

Funding information

The authors are grateful to the Norman E. Borlaug Leadership Enhancement in Agriculture Program (Borlaug LEAP) and Innovative Agricultural Research Initiative (iAGRI) project of the USAID for providing grants to support this project.

Supplementary material

11032_2019_1023_MOESM1_ESM.docx (57 kb)
ESM 1 (DOCX 56 kb)
11032_2019_1023_MOESM2_ESM.docx (181 kb)
ESM 2 (DOCX 180 kb)


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Copyright information

© Springer Nature B.V. 2019

Authors and Affiliations

  • Mao Huang
    • 1
  • Elias G. Balimponya
    • 2
  • Emmanuel M. Mgonja
    • 3
  • Leah K. McHale
    • 4
  • Ashura Luzi-Kihupi
    • 5
  • Guo-Liang Wang
    • 3
  • Clay H. Sneller
    • 1
    Email author
  1. 1.Department of Horticulture and Crop ScienceThe Ohio State UniversityWoosterUSA
  2. 2.Tanzania Official Seed Certification InstituteMtwaraTanzania
  3. 3.Department of Plant PathologyThe Ohio State UniversityColumbusUSA
  4. 4.Department of Horticulture and Crop ScienceThe Ohio State UniversityColumbusUSA
  5. 5.Department of Crop Science and HorticultureSokoine University of AgricultureMorogoroTanzania

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