Skip to main page content
U.S. flag

An official website of the United States government

Dot gov

The .gov means it’s official.
Federal government websites often end in .gov or .mil. Before sharing sensitive information, make sure you’re on a federal government site.

Https

The site is secure.
The https:// ensures that you are connecting to the official website and that any information you provide is encrypted and transmitted securely.

Access keys NCBI Homepage MyNCBI Homepage Main Content Main Navigation
. 2024 Feb 28:15:1272326.
doi: 10.3389/fpls.2024.1272326. eCollection 2024.

Superior haplotypes towards the development of blast and bacterial blight-resistant rice

Shamshad Alam  1 , Krishna Tesman Sundaram  1 , Uma Maheshwar Singh  2 , Madamshetty Srinivas Prasad  3 , Gouri Sankar Laha  3 , Pallavi Sinha  1 , Vikas Kumar Singh  1
Affiliations

Superior haplotypes towards the development of blast and bacterial blight-resistant rice

Shamshad Alam et al. Front Plant Sci. .

Abstract

Rice blast and bacterial leaf blight, are major disease, significantly threatens rice yield in all rice growing regions under favorable conditions and identification of resistance genes and their superior haplotypes is a potential strategy for effectively managing and controlling this devastating disease. In this study, we conducted a genome-wide association study (GWAS) using a diverse set of 147 rice accessions for blast and bacterial blight diseases in replications. Results revealed 23 (9 for blast and 14 for BLB) significant marker-trait associations (MTAs) that corresponded to 107 and 210 candidate genes for blast and BLB, respectively. The haplo-pheno analysis of the candidate genes led to the identification of eight superior haplotypes for blast, with an average SES score ranging from 0.00 to 1.33, and five superior haplotypes for BLB, with scores ranging from 1.52cm to 4.86cm superior haplotypes. Among these, superior haplotypes LOC_OS12G39700-H4 and LOC_Os06g30440-H33 were identified with the lowest average blast scores of 0.00-0.67, and superior haplotype LOC_Os02g12660-H39 exhibited the lowest average lesion length (1.88 - 2.06cm) for BLB. A total of ten accessions for blast and eight accessions for BLB were identified carrying superior haplotypes were identified. These haplotypes belong to aus and indx subpopulations of five countries (Bangladesh, Brazil, India, Myanmar, and Pakistan). For BLB resistance, eight accessions from six countries (Bangladesh, China, India, Myanmar, Pakistan, and Sri Lanka) and four subpopulations (aus, ind1A, ind2, and ind3) were identified carrying superior haplotypes. Interestingly, four candidate genes, LOC_Os06g21040, LOC_Os04g23960, LOC_Os12g39700, and LOC_Os01g24640 encoding transposon and retrotransposon proteins were among those with superior haplotypes known to play a crucial role in plant defense responses. These identified superior haplotypes have the potential to be combined into a single genetic background through haplotype-based breeding for a broader resistance spectrum against blast and bacterial blight diseases.

Keywords: BLB; GWAS; blast; haplo-pheno; rice; superior haplotype.

PubMed Disclaimer

Conflict of interest statement

The authors declare that the research was conducted in the absence of any commercial or financial relationships that could be construed as a potential conflict of interest.

Figures

Figure 1
Figure 1
(A) Circular Manhattan and QQ-plot for MTAs associated with resistance to BLAST (B) Circular Manhattan and QQ-plot for MTAs associated with resistance to BLB.
Figure 2
Figure 2
Haplotype analysis of LOC_OS12G39700 across the sub-set panel. (A) Haplotypic variation of LOC_OS12G39700, a gene associated with blast resistance. (B) Boxplot showing variation in blast resistance among 147 accessions of 3K RGP (C) The geographical distribution of superior haplotype.
Figure 3
Figure 3
Haplotype analysis of LOC_Os02g12660 across the sub-set panel. (A) Haplotypic variation of LOC_Os02g12660, a gene associated with BLB resistance. (B) Boxplot showing variation in BLB resistance among 147 accessions of 3K RGP (C) The geographical distribution of superior haplotype.
Figure 4
Figure 4
Towards developing tailored made rice with superior haplotypes for blast and BLB resistance. (A, C) The most inferior haplotype combination for blast and BLB resistance (B, D) the most superior haplotype combination for enhanced blast resistance. Through haplotype-based breeding, new breeding lines can be developed with the most superior haplotype combination.
See this image and copyright information in PMC

References

    1. 3,000 rice genomes project (2014). The 3,000 rice genomes project. GigaScience 3, 7. doi: 10.1186/2047-217X-3-7 - DOI - PMC - PubMed
    1. AbuQamar S., Chai M. F., Luo H., Song F., Mengiste T. (2008). Tomato protein kinase 1b mediates signaling of plant responses to necrotrophic fungi and insect herbivory. Plant Cell 20, 1964–1983. doi: 10.1105/tpc.108.059477 - DOI - PMC - PubMed
    1. Alam S., Imam J., Nitin M., Prasad C., Variar M. (2017). Molecular screening of Blast Resistance Gene Pi2 in Indian rice landraces (Oryza sativa L.) and its verification by virulence analysis. Proc. Natl. Acad. Sciences India Section B 87, 67–72. doi: 10.1007/s40011-015-0548-3 - DOI
    1. Ao Y., Li Z., Feng D., Xiong F., Liu J., Li J. F., et al. . (2014). OsCERK1 and OsRLCK176 play important roles in peptidoglycan and chitin signaling in rice innate immunity. Plant Journal: Cell Mol. Biol. 80, 1072–1084. doi: 10.1111/tpj.12710 - DOI - PubMed
    1. Ashkani S., Rafii M. Y., Shabanimofrad M., Ghasemzadeh A., Ravanfar S. A., Latif M. A. (2016). Molecular progress on the mapping and cloning of functional genes for blast disease in rice (Oryza sativa L.): Current status and future considerations. Crit. Rev. Biotechnol. 36, 353–367. doi: 10.3109/07388551.2014.961403 - DOI - PubMed