Genome-wide association analysis reveals seed protein loci as determinants of variations in grain mold resistance in sorghum

Abstract

Key message

GWAS analysis revealed variations at loci harboring seed storage, late embryogenesis abundant protein, and a tannin biosynthesis gene associated with sorghum grain mold resistance.

Abstract

Grain mold is the most important disease of sorghum [Sorghum bicolor (L.) Moench]. It starts at the early stages of grain development due to concurrent infection by multiple fungal species. The genetic architecture of resistance to grain mold is poorly understood. Using a diverse set of 635 Ethiopian sorghum accessions, we conducted a multi-stage disease rating for resistance to grain mold under natural infestation in the field. Through genome-wide association analyses with 173,666 SNPs and multiple models, two novel loci were identified that were consistently associated with grain mold resistance across environments. Sequence variation at new loci containing sorghum KAFIRIN gene encoding a seed storage protein affecting seed texture and LATE EMBRYOGENESIS ABUNDANT 3 (LEA3) gene encoding a protein that accumulates in seeds, previously implicated in stress tolerance, were significantly associated with grain mold resistance. The KAFIRIN and LEA3 loci were also significant factors in grain mold resistance in accessions with non-pigmented grains. Moreover, we consistently detected the known SNP (S4_62316425) in TAN1 gene, a regulator of tannin accumulation in sorghum grain to be significantly associated with grain mold resistance. Identification of loci associated with new mechanisms of resistance provides fresh insight into genetic control of the trait, while the highly resistant accessions can serve as sources of resistance genes for breeding. Overall, our association data suggest the critical role of loci harboring seed protein genes and implicate grain chemical and physical properties in sorghum grain mold resistance.

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Abbreviations

ANOVA:

Analysis of variance

BLINK:

Bayesian-information and linkage-disequilibrium iteratively nested keyway

CMLM:

Compressed mixed liner model

DTF:

Days to flowering

FarmCPU:

Fixed and random model circulating probability unification

FGMR:

Field (plot) grain mold rating

GLM:

Generalized linear model

GWAS:

Genome-wide association study

LEA:

Late embryogenesis abundant

MLM:

Mixed linear model

PCA:

Principal components analysis

PGMR:

Panicle grain mold rating

PHT:

Plant height

SNP:

Single nucleotide polymorphism

TGMR:

Threshed grain mold rating

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Acknowledgements

This study was made possible through funding by the Feed the Future Innovation Lab for Collaborative Research on Sorghum and Millet through grants from American People provided to the United States Agency for International Development (USAID) under cooperative agreement No. AID-OAA-A-13-00047. The contents are the sole responsibility of the authors and do not necessarily reflect the views of USAID or the United States Government. We are grateful for technical support by sorghum research staffs at Melkassa, Bako and Jimma Agricultural Research Centers.

Funding

United States Agency for International Development (USAID) under cooperative agreement No. AID-OAA-A-13-00047.

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GE, TM conceived the project and supervised the research work; HN, GG, GE, TM initiated and designed field and genotyping experiments; HN, MM, AT, AS, TB, KD, CB, TS, GA, performed field experiments and prepared leaf tissue samples; HN, GG, TM analyzed data; HN conducted the experiments and wrote the manuscript; MM, AT, GG, TT, TM contributed to the project ideas and edited the manuscript; All authors have read and approved the final version of the manuscript.

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Correspondence to Tesfaye Mengiste.

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Communicated by Hai-Chun Jing.

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Nida, H., Girma, G., Mekonen, M. et al. Genome-wide association analysis reveals seed protein loci as determinants of variations in grain mold resistance in sorghum. Theor Appl Genet 134, 1167–1184 (2021). https://doi.org/10.1007/s00122-020-03762-2

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