Combination of linkage mapping, GWAS, and GP to dissect the genetic basis of common rust resistance in tropical maize germplasm
Common rust (CR) caused by Puccina sorghi is one of the destructive fungal foliar diseases of maize and has been reported to cause moderate to high yield losses. Providing CR resistant germplasm has the potential to increase yields. To dissect the genetic architecture of CR resistance in maize, asso...
| Autores: | , , , , , , , , , , , |
|---|---|
| Tipo de documento: | artigo |
| Estado: | Versão publicada |
| Data de publicação: | 2020 |
| País: | México |
| Recursos: | Centro Internacional de Mejoramiento de Maíz y Trigo |
| Repositório: | Repositorio Institucional de Publicaciones Multimedia del CIMMYT |
| OAI Identifier: | oai:repository.cimmyt.org:10883/21136 |
| Acesso em linha: | https://hdl.handle.net/10883/21136 |
| Access Level: | Acceso aberto |
| Palavra-chave: | AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genome-Wide Association Study Genomic Prediction Joint Linkage Association Mapping Genotyping by Sequencing Common Rust GENOMICS GENOTYPES RESISTANCE RUSTS MAIZE CHROMOSOME MAPPING DNA SEQUENCE |
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Combination of linkage mapping, GWAS, and GP to dissect the genetic basis of common rust resistance in tropical maize germplasmKibe, M.Nyaga, C.Nair, S.K.Beyene, Y.Das, B.Suresh, L.M.Jumbo, M.BMakumbi, D.Kinyua, J.Olsen, M.Prasanna, B.M.Gowda, M.AGRICULTURAL SCIENCES AND BIOTECHNOLOGYGenome-Wide Association StudyGenomic PredictionJoint Linkage Association MappingGenotyping by SequencingCommon RustGENOMICSGENOTYPESRESISTANCERUSTSMAIZECHROMOSOME MAPPINGDNA SEQUENCECommon rust (CR) caused by Puccina sorghi is one of the destructive fungal foliar diseases of maize and has been reported to cause moderate to high yield losses. Providing CR resistant germplasm has the potential to increase yields. To dissect the genetic architecture of CR resistance in maize, association mapping, in conjunction with linkage mapping, joint linkage association mapping (JLAM), and genomic prediction (GP) was conducted on an association-mapping panel and five F3 biparental populations using genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs). Analysis of variance for the biparental populations and the association panel showed significant genotypic and genotype x environment (GXE) interaction variances except for GXE of Pop4. Heritability (h2) estimates were moderate with 0.37–0.45 for the individual F3 populations, 0.45 across five populations and 0.65 for the association panel. Genome-wide association study (GWAS) analyses revealed 14 significant marker-trait associations which individually explained 6–10% of the total phenotypic variances. Individual population-based linkage analysis revealed 26 QTLs associated with CR resistance and together explained 14–40% of the total phenotypic variances. Linkage mapping revealed seven QTLs in pop1, nine QTL in pop2, four QTL in pop3, five QTL in pop4, and one QTL in pop5, distributed on all chromosomes except chromosome 10. JLAM for the 921 F3 families from five populations detected 18 QTLs distributed in all chromosomes except on chromosome 8. These QTLs individually explained 0.3 to 3.1% and together explained 45% of the total phenotypic variance. Among the 18 QTL detected through JLAM, six QTLs, qCR1-78, qCR1-227, qCR3-172, qCR3-186, qCR4-171, and qCR7-137 were also detected in linkage mapping. GP within population revealed low to moderate correlations with a range from 0.19 to 0.51. Prediction correlation was high with r = 0.78 for combined analysis of the five F3 populations. Prediction of biparental populations by using association panel as training set reveals positive correlations ranging from 0.05 to 0.22, which encourages to develop an independent but related population as a training set which can be used to predict diverse but related populations. The findings of this study provide valuable information on understanding the genetic basis of CR resistance and the obtained information can be used for developing functional molecular markers for marker-assisted selection and for implementing GP to improve CR resistance in tropical maize.MDPI2021-01-23T01:05:13Z2021-01-23T01:05:13Z2020Published Versioninfo:eu-repo/semantics/publishedVersioninfo:eu-repo/semantics/articleapplication/pdfhttps://hdl.handle.net/10883/2113610.3390/ijms2118651818211422-0067International Journal of Molecular Sciences6518reponame:Repositorio Institucional de Publicaciones Multimedia del CIMMYTinstname:Centro Internacional de Mejoramiento de Maíz y Trigoinstacron:CIMMYTEnglishhttps://www.mdpi.com/1422-0067/21/18/6518#supplementaryBasel (Switzerland)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 purposeOpen Accessinfo:eu-repo/semantics/openAccessoai:repository.cimmyt.org:10883/211362024-10-11T19:58:02Z |
| dc.title.none.fl_str_mv |
Combination of linkage mapping, GWAS, and GP to dissect the genetic basis of common rust resistance in tropical maize germplasm |
| title |
Combination of linkage mapping, GWAS, and GP to dissect the genetic basis of common rust resistance in tropical maize germplasm |
| spellingShingle |
Combination of linkage mapping, GWAS, and GP to dissect the genetic basis of common rust resistance in tropical maize germplasm Kibe, M. AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genome-Wide Association Study Genomic Prediction Joint Linkage Association Mapping Genotyping by Sequencing Common Rust GENOMICS GENOTYPES RESISTANCE RUSTS MAIZE CHROMOSOME MAPPING DNA SEQUENCE |
| title_short |
Combination of linkage mapping, GWAS, and GP to dissect the genetic basis of common rust resistance in tropical maize germplasm |
| title_full |
Combination of linkage mapping, GWAS, and GP to dissect the genetic basis of common rust resistance in tropical maize germplasm |
| title_fullStr |
Combination of linkage mapping, GWAS, and GP to dissect the genetic basis of common rust resistance in tropical maize germplasm |
| title_full_unstemmed |
Combination of linkage mapping, GWAS, and GP to dissect the genetic basis of common rust resistance in tropical maize germplasm |
| title_sort |
Combination of linkage mapping, GWAS, and GP to dissect the genetic basis of common rust resistance in tropical maize germplasm |
| dc.creator.none.fl_str_mv |
Kibe, M. Nyaga, C. Nair, S.K. Beyene, Y. Das, B. Suresh, L.M. Jumbo, M.B Makumbi, D. Kinyua, J. Olsen, M. Prasanna, B.M. Gowda, M. |
| author |
Kibe, M. |
| author_facet |
Kibe, M. Nyaga, C. Nair, S.K. Beyene, Y. Das, B. Suresh, L.M. Jumbo, M.B Makumbi, D. Kinyua, J. Olsen, M. Prasanna, B.M. Gowda, M. |
| author_role |
author |
| author2 |
Nyaga, C. Nair, S.K. Beyene, Y. Das, B. Suresh, L.M. Jumbo, M.B Makumbi, D. Kinyua, J. Olsen, M. Prasanna, B.M. Gowda, M. |
| author2_role |
author author author author author author author author author author author |
| dc.subject.none.fl_str_mv |
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genome-Wide Association Study Genomic Prediction Joint Linkage Association Mapping Genotyping by Sequencing Common Rust GENOMICS GENOTYPES RESISTANCE RUSTS MAIZE CHROMOSOME MAPPING DNA SEQUENCE |
| topic |
AGRICULTURAL SCIENCES AND BIOTECHNOLOGY Genome-Wide Association Study Genomic Prediction Joint Linkage Association Mapping Genotyping by Sequencing Common Rust GENOMICS GENOTYPES RESISTANCE RUSTS MAIZE CHROMOSOME MAPPING DNA SEQUENCE |
| description |
Common rust (CR) caused by Puccina sorghi is one of the destructive fungal foliar diseases of maize and has been reported to cause moderate to high yield losses. Providing CR resistant germplasm has the potential to increase yields. To dissect the genetic architecture of CR resistance in maize, association mapping, in conjunction with linkage mapping, joint linkage association mapping (JLAM), and genomic prediction (GP) was conducted on an association-mapping panel and five F3 biparental populations using genotyping-by-sequencing (GBS) single-nucleotide polymorphisms (SNPs). Analysis of variance for the biparental populations and the association panel showed significant genotypic and genotype x environment (GXE) interaction variances except for GXE of Pop4. Heritability (h2) estimates were moderate with 0.37–0.45 for the individual F3 populations, 0.45 across five populations and 0.65 for the association panel. Genome-wide association study (GWAS) analyses revealed 14 significant marker-trait associations which individually explained 6–10% of the total phenotypic variances. Individual population-based linkage analysis revealed 26 QTLs associated with CR resistance and together explained 14–40% of the total phenotypic variances. Linkage mapping revealed seven QTLs in pop1, nine QTL in pop2, four QTL in pop3, five QTL in pop4, and one QTL in pop5, distributed on all chromosomes except chromosome 10. JLAM for the 921 F3 families from five populations detected 18 QTLs distributed in all chromosomes except on chromosome 8. These QTLs individually explained 0.3 to 3.1% and together explained 45% of the total phenotypic variance. Among the 18 QTL detected through JLAM, six QTLs, qCR1-78, qCR1-227, qCR3-172, qCR3-186, qCR4-171, and qCR7-137 were also detected in linkage mapping. GP within population revealed low to moderate correlations with a range from 0.19 to 0.51. Prediction correlation was high with r = 0.78 for combined analysis of the five F3 populations. Prediction of biparental populations by using association panel as training set reveals positive correlations ranging from 0.05 to 0.22, which encourages to develop an independent but related population as a training set which can be used to predict diverse but related populations. The findings of this study provide valuable information on understanding the genetic basis of CR resistance and the obtained information can be used for developing functional molecular markers for marker-assisted selection and for implementing GP to improve CR resistance in tropical maize. |
| publishDate |
2020 |
| dc.date.none.fl_str_mv |
2020 2021-01-23T01:05:13Z 2021-01-23T01:05:13Z |
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Published Version info:eu-repo/semantics/publishedVersion info:eu-repo/semantics/article |
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article |
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publishedVersion |
| dc.identifier.none.fl_str_mv |
https://hdl.handle.net/10883/21136 10.3390/ijms21186518 |
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https://hdl.handle.net/10883/21136 |
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10.3390/ijms21186518 |
| dc.language.none.fl_str_mv |
English |
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English |
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https://www.mdpi.com/1422-0067/21/18/6518#supplementary |
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Open Access info:eu-repo/semantics/openAccess |
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Open Access |
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openAccess |
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application/pdf |
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Basel (Switzerland) |
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MDPI |
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MDPI |
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18 21 1422-0067 International Journal of Molecular Sciences 6518 reponame:Repositorio Institucional de Publicaciones Multimedia del CIMMYT instname:Centro Internacional de Mejoramiento de Maíz y Trigo instacron:CIMMYT |
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Centro Internacional de Mejoramiento de Maíz y Trigo |
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