Genome-wide association study of Northern corn leaf blight (NCLB) resistance using temperate and subtropical maize recombinant inbred lines
Abstract Background Northern corn leaf blight (NCLB) is a foliar disease in maize caused by the fungus Setosphaeria turcica, which severely impacts maize production. Genetic studies can help mitigate the effects of NCLB by developing maize resistant varieties and enhancing overall crop yield. Result...
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BMC
2025-07-01
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| Series: | BMC Genomics |
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| Online Access: | https://doi.org/10.1186/s12864-025-11806-4 |
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| author | Xiaodong Gong Fuyan Jiang Ranjan K. Shaw Jiachen Sun Tao Dai Yaqi Bi Yanhui Pan Jiao Kong Haiyang Zong Xiaoping Yang Babar Ijaz Xingming Fan |
| author_facet | Xiaodong Gong Fuyan Jiang Ranjan K. Shaw Jiachen Sun Tao Dai Yaqi Bi Yanhui Pan Jiao Kong Haiyang Zong Xiaoping Yang Babar Ijaz Xingming Fan |
| author_sort | Xiaodong Gong |
| collection | DOAJ |
| description | Abstract Background Northern corn leaf blight (NCLB) is a foliar disease in maize caused by the fungus Setosphaeria turcica, which severely impacts maize production. Genetic studies can help mitigate the effects of NCLB by developing maize resistant varieties and enhancing overall crop yield. Results In this study, a multi-parent population (MPP) was constructed using two temperate maize inbred lines (Zheng58 and HuangC) and one subtropical inbred line (AN20) as the female parents, with the elite temperate maize inbred line Ye107 as the common male parent. The MPP consisted of three recombinant inbred line (RIL) subpopulations, comprising a total of 529 F8 RILs. Genotyping-by-sequencing (GBS) generated 549,531 single nucleotide polymorphisms (SNPs), which were used for genome-wide association studies (GWAS). GWAS analysis identified 14 SNPs significantly associated with NCLB resistance. Candidate genes were screened within a 100 Kb region upstream and downstream of the significant SNPs, identifying two novel candidate genes, Zm00001d034918 and Zm00001d024406, that regulate NCLB resistance in maize. These genes encode proteins involved in energy metabolism and protein interactions, both of which play key roles in maize defense responses against NCLB. qRT-PCR results confirmed that after artificial inoculation with Setosphaeria turcica, both genes were significantly upregulated in the parental line Zheng58. Conclusions This study identifies two candidate genes associated with NCLB resistance through a genome-wide association analysis using 529 recombinant inbred lines evaluated across subtropical and tropical environments. The candidate genes were further validated through preliminary qRT-PCR analysis. These findings provide valuable genomic resources for breeding NCLB-resistant maize varieties and enhances our understanding of the genetic mechanisms underlying NCLB resistance in maize. |
| format | Article |
| id | doaj-art-071276dc1cd24f00a1af4db2a342a99d |
| institution | Kabale University |
| issn | 1471-2164 |
| language | English |
| publishDate | 2025-07-01 |
| publisher | BMC |
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| series | BMC Genomics |
| spelling | doaj-art-071276dc1cd24f00a1af4db2a342a99d2025-08-20T04:01:18ZengBMCBMC Genomics1471-21642025-07-0126111610.1186/s12864-025-11806-4Genome-wide association study of Northern corn leaf blight (NCLB) resistance using temperate and subtropical maize recombinant inbred linesXiaodong Gong0Fuyan Jiang1Ranjan K. Shaw2Jiachen Sun3Tao Dai4Yaqi Bi5Yanhui Pan6Jiao Kong7Haiyang Zong8Xiaoping Yang9Babar Ijaz10Xingming Fan11Institute of Food Crops, Yunnan Academy of Agricultural SciencesInstitute of Food Crops, Yunnan Academy of Agricultural SciencesInstitute of Food Crops, Yunnan Academy of Agricultural SciencesInstitute of Food Crops, Yunnan Academy of Agricultural SciencesInstitute of Food Crops, Yunnan Academy of Agricultural SciencesInstitute of Food Crops, Yunnan Academy of Agricultural SciencesInstitute of Food Crops, Yunnan Academy of Agricultural SciencesInstitute of Food Crops, Yunnan Academy of Agricultural SciencesInstitute of Food Crops, Yunnan Academy of Agricultural SciencesInstitute of Food Crops, Yunnan Academy of Agricultural SciencesInstitute of Food Crops, Yunnan Academy of Agricultural SciencesInstitute of Food Crops, Yunnan Academy of Agricultural SciencesAbstract Background Northern corn leaf blight (NCLB) is a foliar disease in maize caused by the fungus Setosphaeria turcica, which severely impacts maize production. Genetic studies can help mitigate the effects of NCLB by developing maize resistant varieties and enhancing overall crop yield. Results In this study, a multi-parent population (MPP) was constructed using two temperate maize inbred lines (Zheng58 and HuangC) and one subtropical inbred line (AN20) as the female parents, with the elite temperate maize inbred line Ye107 as the common male parent. The MPP consisted of three recombinant inbred line (RIL) subpopulations, comprising a total of 529 F8 RILs. Genotyping-by-sequencing (GBS) generated 549,531 single nucleotide polymorphisms (SNPs), which were used for genome-wide association studies (GWAS). GWAS analysis identified 14 SNPs significantly associated with NCLB resistance. Candidate genes were screened within a 100 Kb region upstream and downstream of the significant SNPs, identifying two novel candidate genes, Zm00001d034918 and Zm00001d024406, that regulate NCLB resistance in maize. These genes encode proteins involved in energy metabolism and protein interactions, both of which play key roles in maize defense responses against NCLB. qRT-PCR results confirmed that after artificial inoculation with Setosphaeria turcica, both genes were significantly upregulated in the parental line Zheng58. Conclusions This study identifies two candidate genes associated with NCLB resistance through a genome-wide association analysis using 529 recombinant inbred lines evaluated across subtropical and tropical environments. The candidate genes were further validated through preliminary qRT-PCR analysis. These findings provide valuable genomic resources for breeding NCLB-resistant maize varieties and enhances our understanding of the genetic mechanisms underlying NCLB resistance in maize.https://doi.org/10.1186/s12864-025-11806-4MaizeNCLBSetosphaeria turcicaGWASQRT-PCR |
| spellingShingle | Xiaodong Gong Fuyan Jiang Ranjan K. Shaw Jiachen Sun Tao Dai Yaqi Bi Yanhui Pan Jiao Kong Haiyang Zong Xiaoping Yang Babar Ijaz Xingming Fan Genome-wide association study of Northern corn leaf blight (NCLB) resistance using temperate and subtropical maize recombinant inbred lines BMC Genomics Maize NCLB Setosphaeria turcica GWAS QRT-PCR |
| title | Genome-wide association study of Northern corn leaf blight (NCLB) resistance using temperate and subtropical maize recombinant inbred lines |
| title_full | Genome-wide association study of Northern corn leaf blight (NCLB) resistance using temperate and subtropical maize recombinant inbred lines |
| title_fullStr | Genome-wide association study of Northern corn leaf blight (NCLB) resistance using temperate and subtropical maize recombinant inbred lines |
| title_full_unstemmed | Genome-wide association study of Northern corn leaf blight (NCLB) resistance using temperate and subtropical maize recombinant inbred lines |
| title_short | Genome-wide association study of Northern corn leaf blight (NCLB) resistance using temperate and subtropical maize recombinant inbred lines |
| title_sort | genome wide association study of northern corn leaf blight nclb resistance using temperate and subtropical maize recombinant inbred lines |
| topic | Maize NCLB Setosphaeria turcica GWAS QRT-PCR |
| url | https://doi.org/10.1186/s12864-025-11806-4 |
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