Validation of KASP-SNP markers in cassava germplasm for marker-assisted selection of increased carotenoid content and dry matter content
Provitamin A biofortification and increased dry matter content are important breeding targets in cassava improvement programs worldwide. Biofortified varieties contribute to the alleviation of provitamin A deficiency, a leading cause of preventable blindness common among pre-school children and preg...
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| Format: | Article |
| Language: | English |
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Frontiers Media S.A.
2022-10-01
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| Series: | Frontiers in Plant Science |
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| Online Access: | https://www.frontiersin.org/articles/10.3389/fpls.2022.1016170/full |
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| author | Adenike D. Ige Adenike D. Ige Bunmi Olasanmi Guillaume J. Bauchet Ismail S. Kayondo Edwige Gaby Nkouaya Mbanjo Ruth Uwugiaren Ruth Uwugiaren Sharon Motomura-Wages Joanna Norton Chiedozie Egesi Chiedozie Egesi Elizabeth Y. Parkes Peter Kulakow Hernán Ceballos Ibnou Dieng Ismail Y. Rabbi |
| author_facet | Adenike D. Ige Adenike D. Ige Bunmi Olasanmi Guillaume J. Bauchet Ismail S. Kayondo Edwige Gaby Nkouaya Mbanjo Ruth Uwugiaren Ruth Uwugiaren Sharon Motomura-Wages Joanna Norton Chiedozie Egesi Chiedozie Egesi Elizabeth Y. Parkes Peter Kulakow Hernán Ceballos Ibnou Dieng Ismail Y. Rabbi |
| author_sort | Adenike D. Ige |
| collection | DOAJ |
| description | Provitamin A biofortification and increased dry matter content are important breeding targets in cassava improvement programs worldwide. Biofortified varieties contribute to the alleviation of provitamin A deficiency, a leading cause of preventable blindness common among pre-school children and pregnant women in developing countries particularly Africa. Dry matter content is a major component of dry yield and thus underlies overall variety performance and acceptability by growers, processors, and consumers. Single nucleotide polymorphism (SNP) markers linked to these traits have recently been discovered through several genome-wide association studies but have not been deployed for routine marker-assisted selection (MAS). This is due to the lack of useful information on markers’ performances in diverse genetic backgrounds. To overcome this bottleneck, technical and biological validation of the loci associated with increased carotenoid content and dry matter content were carried out using populations independent of the marker discovery population. In the present study, seven previously identified markers for these traits were converted to a robust set of uniplex allele-specific polymerase chain reaction (PCR) assays and validated in two independent pre-breeding and breeding populations. These assays were efficient in discriminating marker genotypic classes and had an average call rate greater than 98%. A high correlation was observed between the predicted and observed carotenoid content as inferred by root yellowness intensity in the breeding (r = 0.92) and pre-breeding (r = 0.95) populations. On the other hand, dry matter content-markers had moderately low predictive accuracy in both populations (r< 0.40) due to the more quantitative nature of the trait. This work confirmed the markers’ effectiveness in multiple backgrounds, therefore, further strengthening their value in cassava biofortification to ensure nutritional security as well as dry matter content productivity. Our study provides a framework to guide future marker validation, thus leading to the more routine use of markers in MAS in cassava improvement programs. |
| first_indexed | 2024-04-11T10:10:53Z |
| format | Article |
| id | doaj.art-97c7663829314fed891a8cef380b13c2 |
| institution | Directory Open Access Journal |
| issn | 1664-462X |
| language | English |
| last_indexed | 2024-04-11T10:10:53Z |
| publishDate | 2022-10-01 |
| publisher | Frontiers Media S.A. |
| record_format | Article |
| series | Frontiers in Plant Science |
| spelling | doaj.art-97c7663829314fed891a8cef380b13c22022-12-22T04:30:07ZengFrontiers Media S.A.Frontiers in Plant Science1664-462X2022-10-011310.3389/fpls.2022.10161701016170Validation of KASP-SNP markers in cassava germplasm for marker-assisted selection of increased carotenoid content and dry matter contentAdenike D. Ige0Adenike D. Ige1Bunmi Olasanmi2Guillaume J. Bauchet3Ismail S. Kayondo4Edwige Gaby Nkouaya Mbanjo5Ruth Uwugiaren6Ruth Uwugiaren7Sharon Motomura-Wages8Joanna Norton9Chiedozie Egesi10Chiedozie Egesi11Elizabeth Y. Parkes12Peter Kulakow13Hernán Ceballos14Ibnou Dieng15Ismail Y. Rabbi16International Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, NigeriaPan African University Life and Earth Sciences Institute (including Health and Agriculture), University of Ibadan, Ibadan, NigeriaDepartment of Crop and Horticultural Sciences, University of Ibadan, Ibadan, NigeriaBoyce Thompson Institute, Ithaca, NY, United StatesInternational Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, NigeriaInternational Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, NigeriaInternational Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, NigeriaMolecular Plant Sciences program, Washington State University, Pullman, WA, United StatesCollege of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Hilo, HI, United StatesCollege of Tropical Agriculture and Human Resources, University of Hawaii at Manoa, Hilo, HI, United StatesInternational Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, NigeriaCornell University, Ithaca, NY, United StatesInternational Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, NigeriaInternational Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, NigeriaThe Alliance of Bioversity International and the International Center for Tropical Agriculture (CIAT), Cali, ColombiaInternational Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, NigeriaInternational Institute of Tropical Agriculture (IITA), Ibadan, Oyo State, NigeriaProvitamin A biofortification and increased dry matter content are important breeding targets in cassava improvement programs worldwide. Biofortified varieties contribute to the alleviation of provitamin A deficiency, a leading cause of preventable blindness common among pre-school children and pregnant women in developing countries particularly Africa. Dry matter content is a major component of dry yield and thus underlies overall variety performance and acceptability by growers, processors, and consumers. Single nucleotide polymorphism (SNP) markers linked to these traits have recently been discovered through several genome-wide association studies but have not been deployed for routine marker-assisted selection (MAS). This is due to the lack of useful information on markers’ performances in diverse genetic backgrounds. To overcome this bottleneck, technical and biological validation of the loci associated with increased carotenoid content and dry matter content were carried out using populations independent of the marker discovery population. In the present study, seven previously identified markers for these traits were converted to a robust set of uniplex allele-specific polymerase chain reaction (PCR) assays and validated in two independent pre-breeding and breeding populations. These assays were efficient in discriminating marker genotypic classes and had an average call rate greater than 98%. A high correlation was observed between the predicted and observed carotenoid content as inferred by root yellowness intensity in the breeding (r = 0.92) and pre-breeding (r = 0.95) populations. On the other hand, dry matter content-markers had moderately low predictive accuracy in both populations (r< 0.40) due to the more quantitative nature of the trait. This work confirmed the markers’ effectiveness in multiple backgrounds, therefore, further strengthening their value in cassava biofortification to ensure nutritional security as well as dry matter content productivity. Our study provides a framework to guide future marker validation, thus leading to the more routine use of markers in MAS in cassava improvement programs.https://www.frontiersin.org/articles/10.3389/fpls.2022.1016170/fullcassava (Manihot esculenta Crantz)provitamin A contentdry matter contentallele-specific PCRpredictive accuracymarker-assisted selection |
| spellingShingle | Adenike D. Ige Adenike D. Ige Bunmi Olasanmi Guillaume J. Bauchet Ismail S. Kayondo Edwige Gaby Nkouaya Mbanjo Ruth Uwugiaren Ruth Uwugiaren Sharon Motomura-Wages Joanna Norton Chiedozie Egesi Chiedozie Egesi Elizabeth Y. Parkes Peter Kulakow Hernán Ceballos Ibnou Dieng Ismail Y. Rabbi Validation of KASP-SNP markers in cassava germplasm for marker-assisted selection of increased carotenoid content and dry matter content Frontiers in Plant Science cassava (Manihot esculenta Crantz) provitamin A content dry matter content allele-specific PCR predictive accuracy marker-assisted selection |
| title | Validation of KASP-SNP markers in cassava germplasm for marker-assisted selection of increased carotenoid content and dry matter content |
| title_full | Validation of KASP-SNP markers in cassava germplasm for marker-assisted selection of increased carotenoid content and dry matter content |
| title_fullStr | Validation of KASP-SNP markers in cassava germplasm for marker-assisted selection of increased carotenoid content and dry matter content |
| title_full_unstemmed | Validation of KASP-SNP markers in cassava germplasm for marker-assisted selection of increased carotenoid content and dry matter content |
| title_short | Validation of KASP-SNP markers in cassava germplasm for marker-assisted selection of increased carotenoid content and dry matter content |
| title_sort | validation of kasp snp markers in cassava germplasm for marker assisted selection of increased carotenoid content and dry matter content |
| topic | cassava (Manihot esculenta Crantz) provitamin A content dry matter content allele-specific PCR predictive accuracy marker-assisted selection |
| url | https://www.frontiersin.org/articles/10.3389/fpls.2022.1016170/full |
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