Genome-wide association study identified candidate genes controlling continuous storage root formation and bulking in hexaploid sweetpotato
Abstract Background Continuous storage root formation and bulking (CSRFAB) in sweetpotato is an important trait from agronomic and biological perspectives. Information about the molecular mechanisms underlying CSRFAB traits is lacking. Results Here, as a first step toward understanding the genetic b...
| Main Authors: | , , , , , , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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BMC
2020-01-01
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| Series: | BMC Plant Biology |
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| Online Access: | https://doi.org/10.1186/s12870-019-2217-9 |
| _version_ | 1818426084477108224 |
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| author | Astère Bararyenya Bode A. Olukolu Phinehas Tukamuhabwa Wolfgang J. Grüneberg Wellington Ekaya Jan Low Mildred Ochwo-Ssemakula Thomas L. Odong Herbert Talwana Arfang Badji Martina Kyalo Yao Nasser Dorcus Gemenet Mercy Kitavi Robert O. M. Mwanga |
| author_facet | Astère Bararyenya Bode A. Olukolu Phinehas Tukamuhabwa Wolfgang J. Grüneberg Wellington Ekaya Jan Low Mildred Ochwo-Ssemakula Thomas L. Odong Herbert Talwana Arfang Badji Martina Kyalo Yao Nasser Dorcus Gemenet Mercy Kitavi Robert O. M. Mwanga |
| author_sort | Astère Bararyenya |
| collection | DOAJ |
| description | Abstract Background Continuous storage root formation and bulking (CSRFAB) in sweetpotato is an important trait from agronomic and biological perspectives. Information about the molecular mechanisms underlying CSRFAB traits is lacking. Results Here, as a first step toward understanding the genetic basis of CSRFAB in sweetpotato, we performed a genome-wide association study (GWAS) using phenotypic data from four distinct developmental stages and 33,068 single nucleotide polymorphism (SNP) and insertion-deletion (indel) markers. Based on Bonferroni threshold (p-value < 5 × 10− 7), we identified 34 unique SNPs that were significantly associated with the complex trait of CSRFAB at 150 days after planting (DAP) and seven unique SNPs associated with discontinuous storage root formation and bulking (DCSRFAB) at 90 DAP. Importantly, most of the loci associated with these identified SNPs were located within genomic regions (using Ipomoea trifida reference genome) previously reported for quantitative trait loci (QTL) controlling similar traits. Based on these trait-associated SNPs, 12 and seven candidate genes were respectively annotated for CSRFAB and DCSRFAB traits. Congruent with the contrasting and inverse relationship between discontinuous and continuous storage root formation and bulking, a DCSRFAB-associated candidate gene regulates redox signaling, involved in auxin-mediated lateral root formation, while CSRFAB is enriched for genes controlling growth and senescence. Conclusion Candidate genes identified in this study have potential roles in cell wall remodeling, plant growth, senescence, stress, root development and redox signaling. These findings provide valuable insights into understanding the functional networks to develop strategies for sweetpotato yield improvement. The markers as well as candidate genes identified in this pioneering research for CSRFAB provide important genomic resources for sweetpotato and other root crops. |
| first_indexed | 2024-12-14T14:24:13Z |
| format | Article |
| id | doaj.art-36567ed2f77c4596bf9018170201dc26 |
| institution | Directory Open Access Journal |
| issn | 1471-2229 |
| language | English |
| last_indexed | 2024-12-14T14:24:13Z |
| publishDate | 2020-01-01 |
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| series | BMC Plant Biology |
| spelling | doaj.art-36567ed2f77c4596bf9018170201dc262022-12-21T22:57:59ZengBMCBMC Plant Biology1471-22292020-01-0120111610.1186/s12870-019-2217-9Genome-wide association study identified candidate genes controlling continuous storage root formation and bulking in hexaploid sweetpotatoAstère Bararyenya0Bode A. Olukolu1Phinehas Tukamuhabwa2Wolfgang J. Grüneberg3Wellington Ekaya4Jan Low5Mildred Ochwo-Ssemakula6Thomas L. Odong7Herbert Talwana8Arfang Badji9Martina Kyalo10Yao Nasser11Dorcus Gemenet12Mercy Kitavi13Robert O. M. Mwanga14Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere UniversityDepartment of Entomology and Plant Pathology, University of TennesseeDepartment of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere UniversityInternational Potato Center (CIP)International Livestock Research InstituteInternational Potato Center (CIP)Department of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere UniversityDepartment of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere UniversityDepartment of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere UniversityDepartment of Agricultural Production, College of Agricultural and Environmental Sciences, Makerere UniversityInternational Livestock Research InstituteInternational Livestock Research InstituteInternational Potato Center (CIP)International Potato Center (CIP)International Potato Center (CIP)Abstract Background Continuous storage root formation and bulking (CSRFAB) in sweetpotato is an important trait from agronomic and biological perspectives. Information about the molecular mechanisms underlying CSRFAB traits is lacking. Results Here, as a first step toward understanding the genetic basis of CSRFAB in sweetpotato, we performed a genome-wide association study (GWAS) using phenotypic data from four distinct developmental stages and 33,068 single nucleotide polymorphism (SNP) and insertion-deletion (indel) markers. Based on Bonferroni threshold (p-value < 5 × 10− 7), we identified 34 unique SNPs that were significantly associated with the complex trait of CSRFAB at 150 days after planting (DAP) and seven unique SNPs associated with discontinuous storage root formation and bulking (DCSRFAB) at 90 DAP. Importantly, most of the loci associated with these identified SNPs were located within genomic regions (using Ipomoea trifida reference genome) previously reported for quantitative trait loci (QTL) controlling similar traits. Based on these trait-associated SNPs, 12 and seven candidate genes were respectively annotated for CSRFAB and DCSRFAB traits. Congruent with the contrasting and inverse relationship between discontinuous and continuous storage root formation and bulking, a DCSRFAB-associated candidate gene regulates redox signaling, involved in auxin-mediated lateral root formation, while CSRFAB is enriched for genes controlling growth and senescence. Conclusion Candidate genes identified in this study have potential roles in cell wall remodeling, plant growth, senescence, stress, root development and redox signaling. These findings provide valuable insights into understanding the functional networks to develop strategies for sweetpotato yield improvement. The markers as well as candidate genes identified in this pioneering research for CSRFAB provide important genomic resources for sweetpotato and other root crops.https://doi.org/10.1186/s12870-019-2217-9DArTseqGenotyping-by-sequencingGWASCSRFABGBSappPolyploid |
| spellingShingle | Astère Bararyenya Bode A. Olukolu Phinehas Tukamuhabwa Wolfgang J. Grüneberg Wellington Ekaya Jan Low Mildred Ochwo-Ssemakula Thomas L. Odong Herbert Talwana Arfang Badji Martina Kyalo Yao Nasser Dorcus Gemenet Mercy Kitavi Robert O. M. Mwanga Genome-wide association study identified candidate genes controlling continuous storage root formation and bulking in hexaploid sweetpotato BMC Plant Biology DArTseq Genotyping-by-sequencing GWAS CSRFAB GBSapp Polyploid |
| title | Genome-wide association study identified candidate genes controlling continuous storage root formation and bulking in hexaploid sweetpotato |
| title_full | Genome-wide association study identified candidate genes controlling continuous storage root formation and bulking in hexaploid sweetpotato |
| title_fullStr | Genome-wide association study identified candidate genes controlling continuous storage root formation and bulking in hexaploid sweetpotato |
| title_full_unstemmed | Genome-wide association study identified candidate genes controlling continuous storage root formation and bulking in hexaploid sweetpotato |
| title_short | Genome-wide association study identified candidate genes controlling continuous storage root formation and bulking in hexaploid sweetpotato |
| title_sort | genome wide association study identified candidate genes controlling continuous storage root formation and bulking in hexaploid sweetpotato |
| topic | DArTseq Genotyping-by-sequencing GWAS CSRFAB GBSapp Polyploid |
| url | https://doi.org/10.1186/s12870-019-2217-9 |
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