Identification and validation of a key genomic region on chromosome 6 for resistance to Fusarium stalk rot in tropical maize
Fusarium stalk rot (FSR) of maize is an economically important post-flowering stalk rot (PFSR) disease caused by Fusarium verticillioides. The pathogen invades the plant individually, or in combination with other stalk rot pathogens or secondary colonizers, thereby making it difficult to make accurate selection for resistance. For identification and validation of genomic regions associated with FSR resistance, a genome-wide association study (GWAS) was conducted with 342 maize lines. The panel was screened for FSR in three environments using standard artificial inoculation methodology. GWAS using the mixed linear model corrected for population structure and kinship was done, in which 290,626 SNPs from genotyping-by-sequencing were used. A total of 7 SNPs, five on chromosome 6 showing strong LD at 168 Mb, were identified to be associated with FSR. Haplotype regression analysis identified 32 haplotypes with a significant effect on the trait. In a QTL mapping experiment in two populations for validating the identified variants, QTLs were identified with confidence intervals having overlapped physical coordinates in both the populations on chromosome 6, which was closely located to the GWAS-identified variants on chromosome 6. It makes this genomic region a crucial one to further investigate the possibility of developing trait markers for deployment in breeding pipelines. It was noted that previously reported QTLs for other stalk rots in maize mapped within the same physical intervals of several haplotypes identified for FSR resistance in this study. The possibility of QTLs controlling broad-spectrum resistance for PFSR in general requires further investigation.
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Subjects: | AGRICULTURAL SCIENCES AND BIOTECHNOLOGY, Genome-Wide Association Study, Fusarium Stalk Rot, FUSARIUM, MAIZE, DISEASE RESISTANCE, QUANTITATIVE TRAIT LOCI MAPPING, |
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dig-cimmyt-10883-222762023-10-27T15:17:38Z Identification and validation of a key genomic region on chromosome 6 for resistance to Fusarium stalk rot in tropical maize Rashid, Z. Babu, V. Sharma, S.S. Singh, P.K. Nair, S.K. AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genome-Wide Association Study Fusarium Stalk Rot FUSARIUM MAIZE DISEASE RESISTANCE QUANTITATIVE TRAIT LOCI MAPPING Fusarium stalk rot (FSR) of maize is an economically important post-flowering stalk rot (PFSR) disease caused by Fusarium verticillioides. The pathogen invades the plant individually, or in combination with other stalk rot pathogens or secondary colonizers, thereby making it difficult to make accurate selection for resistance. For identification and validation of genomic regions associated with FSR resistance, a genome-wide association study (GWAS) was conducted with 342 maize lines. The panel was screened for FSR in three environments using standard artificial inoculation methodology. GWAS using the mixed linear model corrected for population structure and kinship was done, in which 290,626 SNPs from genotyping-by-sequencing were used. A total of 7 SNPs, five on chromosome 6 showing strong LD at 168 Mb, were identified to be associated with FSR. Haplotype regression analysis identified 32 haplotypes with a significant effect on the trait. In a QTL mapping experiment in two populations for validating the identified variants, QTLs were identified with confidence intervals having overlapped physical coordinates in both the populations on chromosome 6, which was closely located to the GWAS-identified variants on chromosome 6. It makes this genomic region a crucial one to further investigate the possibility of developing trait markers for deployment in breeding pipelines. It was noted that previously reported QTLs for other stalk rots in maize mapped within the same physical intervals of several haplotypes identified for FSR resistance in this study. The possibility of QTLs controlling broad-spectrum resistance for PFSR in general requires further investigation. 4549-4563 2022-12-07T20:29:29Z 2022-12-07T20:29:29Z 2022 Article Published Version https://hdl.handle.net/10883/22276 10.1007/s00122-022-04239-0 English Nutrition, health & food security Accelerated Breeding Plant Health Genetic Innovation Resilient Agrifood Systems CGIAR Research Program on Maize One CGIAR https://hdl.handle.net/10568/126434 CIMMYT manages Intellectual Assets as International Public Goods. The user is free to download, print, store and share this work. In case you want to translate or create any other derivative work and share or distribute such translation/derivative work, please contact CIMMYT-Knowledge-Center@cgiar.org indicating the work you want to use and the kind of use you intend; CIMMYT will contact you with the suitable license for that purpose Open Access Berlin (Germany) Springer 135 0040-5752 Theoretical and Applied Genetics |
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AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genome-Wide Association Study Fusarium Stalk Rot FUSARIUM MAIZE DISEASE RESISTANCE QUANTITATIVE TRAIT LOCI MAPPING AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genome-Wide Association Study Fusarium Stalk Rot FUSARIUM MAIZE DISEASE RESISTANCE QUANTITATIVE TRAIT LOCI MAPPING |
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AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genome-Wide Association Study Fusarium Stalk Rot FUSARIUM MAIZE DISEASE RESISTANCE QUANTITATIVE TRAIT LOCI MAPPING AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genome-Wide Association Study Fusarium Stalk Rot FUSARIUM MAIZE DISEASE RESISTANCE QUANTITATIVE TRAIT LOCI MAPPING Rashid, Z. Babu, V. Sharma, S.S. Singh, P.K. Nair, S.K. Identification and validation of a key genomic region on chromosome 6 for resistance to Fusarium stalk rot in tropical maize |
description |
Fusarium stalk rot (FSR) of maize is an economically important post-flowering stalk rot (PFSR) disease caused by Fusarium verticillioides. The pathogen invades the plant individually, or in combination with other stalk rot pathogens or secondary colonizers, thereby making it difficult to make accurate selection for resistance. For identification and validation of genomic regions associated with FSR resistance, a genome-wide association study (GWAS) was conducted with 342 maize lines. The panel was screened for FSR in three environments using standard artificial inoculation methodology. GWAS using the mixed linear model corrected for population structure and kinship was done, in which 290,626 SNPs from genotyping-by-sequencing were used. A total of 7 SNPs, five on chromosome 6 showing strong LD at 168 Mb, were identified to be associated with FSR. Haplotype regression analysis identified 32 haplotypes with a significant effect on the trait. In a QTL mapping experiment in two populations for validating the identified variants, QTLs were identified with confidence intervals having overlapped physical coordinates in both the populations on chromosome 6, which was closely located to the GWAS-identified variants on chromosome 6. It makes this genomic region a crucial one to further investigate the possibility of developing trait markers for deployment in breeding pipelines. It was noted that previously reported QTLs for other stalk rots in maize mapped within the same physical intervals of several haplotypes identified for FSR resistance in this study. The possibility of QTLs controlling broad-spectrum resistance for PFSR in general requires further investigation. |
format |
Article |
topic_facet |
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genome-Wide Association Study Fusarium Stalk Rot FUSARIUM MAIZE DISEASE RESISTANCE QUANTITATIVE TRAIT LOCI MAPPING |
author |
Rashid, Z. Babu, V. Sharma, S.S. Singh, P.K. Nair, S.K. |
author_facet |
Rashid, Z. Babu, V. Sharma, S.S. Singh, P.K. Nair, S.K. |
author_sort |
Rashid, Z. |
title |
Identification and validation of a key genomic region on chromosome 6 for resistance to Fusarium stalk rot in tropical maize |
title_short |
Identification and validation of a key genomic region on chromosome 6 for resistance to Fusarium stalk rot in tropical maize |
title_full |
Identification and validation of a key genomic region on chromosome 6 for resistance to Fusarium stalk rot in tropical maize |
title_fullStr |
Identification and validation of a key genomic region on chromosome 6 for resistance to Fusarium stalk rot in tropical maize |
title_full_unstemmed |
Identification and validation of a key genomic region on chromosome 6 for resistance to Fusarium stalk rot in tropical maize |
title_sort |
identification and validation of a key genomic region on chromosome 6 for resistance to fusarium stalk rot in tropical maize |
publisher |
Springer |
publishDate |
2022 |
url |
https://hdl.handle.net/10883/22276 |
work_keys_str_mv |
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_version_ |
1781883769900236800 |