Insights into maydis leaf blight resistance in maize: a comprehensive genome-wide association study in sub-tropics of India
Background: In the face of contemporary climatic vulnerabilities and escalating global temperatures, the prevalence of maydis leaf blight (MLB) poses a potential threat to maize production. This study endeavours to discern marker-trait associations and elucidate the candidate genes that underlie res...
| Main Authors: | , , , , , , , |
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| Format: | Journal Article |
| Language: | Inglés |
| Published: |
BioMed Central
2024
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| Subjects: | |
| Online Access: | https://hdl.handle.net/10568/151860 |
| _version_ | 1855520074341810176 |
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| author | Wajhat Un Nisa Sandhu, Surinder Nair, Sudha Krishnan Kaur, Harleen Kumar, Ashok Rashid, Zerka Gajanan Saykhedkar Vikal, Yogesh |
| author_browse | Gajanan Saykhedkar Kaur, Harleen Kumar, Ashok Nair, Sudha Krishnan Rashid, Zerka Sandhu, Surinder Vikal, Yogesh Wajhat Un Nisa |
| author_facet | Wajhat Un Nisa Sandhu, Surinder Nair, Sudha Krishnan Kaur, Harleen Kumar, Ashok Rashid, Zerka Gajanan Saykhedkar Vikal, Yogesh |
| author_sort | Wajhat Un Nisa |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Background: In the face of contemporary climatic vulnerabilities and escalating global temperatures, the prevalence of maydis leaf blight (MLB) poses a potential threat to maize production. This study endeavours to discern marker-trait associations and elucidate the candidate genes that underlie resistance to MLB in maize by employing a diverse panel comprising 336 lines. The panel was screening for MLB across four environments, employing standard artificial inoculation techniques. Genome-wide association studies (GWAS) and haplotype analysis were conducted utilizing a total of 128,490 SNPs obtained from genotyping-by-sequencing (GBS). Results: GWAS identified 26 highly significant SNPs associated with MLB resistance, among the markers examined. Seven of these SNPs, reported in novel chromosomal bins (9.06, 5.01, 9.01, 7.04, 4.06, 1.04, and 6.05) were associated with genes: bzip23, NAGS1, CDPK7, aspartic proteinase NEP-2, VQ4, and Wun1, which were characterized for their roles in diminishing fungal activity, fortifying defence mechanisms against necrotrophic pathogens, modulating phyto-hormone signalling, and orchestrating oxidative burst responses. Gene mining approach identified 22 potential candidate genes associated with SNPs due to their functional relevance to resistance against necrotrophic pathogens. Notably, bin 8.06, which hosts five SNPs, showed a connection to defense-regulating genes against MLB, indicating the potential formation of a functional gene cluster that triggers a cascade of reactions against MLB. In silico studies revealed gene expression levels exceeding ten fragments per kilobase million (FPKM) for most genes and demonstrated coexpression among all candidate genes in the coexpression network. Haplotype regression analysis revealed the association of 13 common significant haplotypes at Bonferroni <= 0.05. The phenotypic variance explained by these significant haplotypes ranged from low to moderate, suggesting a breeding strategy that combines multiple resistance alleles to enhance resistance to MLB. Additionally, one particular haplotype block (Hap_8.3) was found to consist of two SNPs (S8_152715134, S8_152460815) identified in GWAS with 9.45% variation explained (PVE). Conclusion: The identified SNPs/ haplotypes associated with the trait of interest contribute to the enrichment of allelic diversity and hold direct applicability in Genomics Assisted Breeding for enhancing MLB resistance in maize. |
| format | Journal Article |
| id | CGSpace151860 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2024 |
| publishDateRange | 2024 |
| publishDateSort | 2024 |
| publisher | BioMed Central |
| publisherStr | BioMed Central |
| record_format | dspace |
| spelling | CGSpace1518602025-05-04T09:21:29Z Insights into maydis leaf blight resistance in maize: a comprehensive genome-wide association study in sub-tropics of India Wajhat Un Nisa Sandhu, Surinder Nair, Sudha Krishnan Kaur, Harleen Kumar, Ashok Rashid, Zerka Gajanan Saykhedkar Vikal, Yogesh maize genome-wide association studies single nucleotide polymorphisms haplotype analysis Background: In the face of contemporary climatic vulnerabilities and escalating global temperatures, the prevalence of maydis leaf blight (MLB) poses a potential threat to maize production. This study endeavours to discern marker-trait associations and elucidate the candidate genes that underlie resistance to MLB in maize by employing a diverse panel comprising 336 lines. The panel was screening for MLB across four environments, employing standard artificial inoculation techniques. Genome-wide association studies (GWAS) and haplotype analysis were conducted utilizing a total of 128,490 SNPs obtained from genotyping-by-sequencing (GBS). Results: GWAS identified 26 highly significant SNPs associated with MLB resistance, among the markers examined. Seven of these SNPs, reported in novel chromosomal bins (9.06, 5.01, 9.01, 7.04, 4.06, 1.04, and 6.05) were associated with genes: bzip23, NAGS1, CDPK7, aspartic proteinase NEP-2, VQ4, and Wun1, which were characterized for their roles in diminishing fungal activity, fortifying defence mechanisms against necrotrophic pathogens, modulating phyto-hormone signalling, and orchestrating oxidative burst responses. Gene mining approach identified 22 potential candidate genes associated with SNPs due to their functional relevance to resistance against necrotrophic pathogens. Notably, bin 8.06, which hosts five SNPs, showed a connection to defense-regulating genes against MLB, indicating the potential formation of a functional gene cluster that triggers a cascade of reactions against MLB. In silico studies revealed gene expression levels exceeding ten fragments per kilobase million (FPKM) for most genes and demonstrated coexpression among all candidate genes in the coexpression network. Haplotype regression analysis revealed the association of 13 common significant haplotypes at Bonferroni <= 0.05. The phenotypic variance explained by these significant haplotypes ranged from low to moderate, suggesting a breeding strategy that combines multiple resistance alleles to enhance resistance to MLB. Additionally, one particular haplotype block (Hap_8.3) was found to consist of two SNPs (S8_152715134, S8_152460815) identified in GWAS with 9.45% variation explained (PVE). Conclusion: The identified SNPs/ haplotypes associated with the trait of interest contribute to the enrichment of allelic diversity and hold direct applicability in Genomics Assisted Breeding for enhancing MLB resistance in maize. 2024 2024-08-26T15:30:27Z 2024-08-26T15:30:27Z Journal Article https://hdl.handle.net/10568/151860 en Open Access application/pdf BioMed Central Nisa, W. U., Sandhu, S., Nair, S. K., Kaur, H., Kumar, A., Rashid, Z., Saykhedkar, G., & Vikal, Y. (2024). Insights into maydis leaf blight resistance in maize: a comprehensive genome-wide association study in sub-tropics of India. BMC Genomics, 25(1), 760. https://doi.org/10.1186/s12864-024-10655-x |
| spellingShingle | maize genome-wide association studies single nucleotide polymorphisms haplotype analysis Wajhat Un Nisa Sandhu, Surinder Nair, Sudha Krishnan Kaur, Harleen Kumar, Ashok Rashid, Zerka Gajanan Saykhedkar Vikal, Yogesh Insights into maydis leaf blight resistance in maize: a comprehensive genome-wide association study in sub-tropics of India |
| title | Insights into maydis leaf blight resistance in maize: a comprehensive genome-wide association study in sub-tropics of India |
| title_full | Insights into maydis leaf blight resistance in maize: a comprehensive genome-wide association study in sub-tropics of India |
| title_fullStr | Insights into maydis leaf blight resistance in maize: a comprehensive genome-wide association study in sub-tropics of India |
| title_full_unstemmed | Insights into maydis leaf blight resistance in maize: a comprehensive genome-wide association study in sub-tropics of India |
| title_short | Insights into maydis leaf blight resistance in maize: a comprehensive genome-wide association study in sub-tropics of India |
| title_sort | insights into maydis leaf blight resistance in maize a comprehensive genome wide association study in sub tropics of india |
| topic | maize genome-wide association studies single nucleotide polymorphisms haplotype analysis |
| url | https://hdl.handle.net/10568/151860 |
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