Candidate gene sequencing and validation of SNP markers linked to carotenoid content in cassava (Manihot esculenta Crantz)
Cassava is a widely grown staple in Sub-Saharan Africa and consumed as a cheap source of calories, but the crop is deficient in micronutrients including pro-vitamin A carotenoids. This challenge is currently being addressed through biofortification breeding that relies on phenotypic selection. Geneb...
| Autores principales: | , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
Springer
2017
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/83509 |
| _version_ | 1855542531308126208 |
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| author | Udoh, L.I. Gedil, Melaku A Parkes, Elizabeth Y. Kulakow, Peter A. Adesoye, A.I. Nwuba, C. Rabbi, Ismail Y. |
| author_browse | Adesoye, A.I. Gedil, Melaku A Kulakow, Peter A. Nwuba, C. Parkes, Elizabeth Y. Rabbi, Ismail Y. Udoh, L.I. |
| author_facet | Udoh, L.I. Gedil, Melaku A Parkes, Elizabeth Y. Kulakow, Peter A. Adesoye, A.I. Nwuba, C. Rabbi, Ismail Y. |
| author_sort | Udoh, L.I. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Cassava is a widely grown staple in Sub-Saharan Africa and consumed as a cheap source of calories, but the crop is deficient in micronutrients including pro-vitamin A carotenoids. This challenge is currently being addressed through biofortification breeding that relies on phenotypic selection. Genebased markers linked to pro-vitamin A content variation are expected to increase the rate of genetic gain for this critical trait. We sequenced four candidate carotenoid genes from 167 cassava accessions representing the diversity of elite breeder lines from IITA. Total carotenoid content was determined using spectrophotometer and total β-carotene was quantified by highperformance liquid chromatography. Storage root yellowness due to carotenoid pigmentation was
assessed. We carried out candidate gene association analysis that accounts for population structure and kinship using genome-wide single nucleotide polymorphisms (SNPs) generated through genotyping-by-sequencing. Significant SNPs were used to design competitive allele-specific PCR assays and validated on the larger population for potential use in markerassisted
selection breeding. Candidate gene sequencing of the genes β-carotene hydroxylase (crtRB), phytoene synthase (PSY2), lycopene epsilon cyclase (lcyE), and lycopene beta cyclase (lcyB) yielded a total of 37 SNPs. Total carotenoid content, total β-carotene, and color parameters were significantly associated with markers in the PSY2 gene. The SNPs from lcyE were significantly associated with color while those of lcyB and crtRB were not significantly associated with carotenoids or color parameters. These validated and breeder-friendly markers have potential to enhance the efficiency of selection for high β-carotene cassava, thus accelerating genetic gain. |
| format | Journal Article |
| id | CGSpace83509 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2017 |
| publishDateRange | 2017 |
| publishDateSort | 2017 |
| publisher | Springer |
| publisherStr | Springer |
| record_format | dspace |
| spelling | CGSpace835092024-03-06T10:16:43Z Candidate gene sequencing and validation of SNP markers linked to carotenoid content in cassava (Manihot esculenta Crantz) Udoh, L.I. Gedil, Melaku A Parkes, Elizabeth Y. Kulakow, Peter A. Adesoye, A.I. Nwuba, C. Rabbi, Ismail Y. cassava vitamin a carotinoids marker-assisted selection candidate gene association biofortification Cassava is a widely grown staple in Sub-Saharan Africa and consumed as a cheap source of calories, but the crop is deficient in micronutrients including pro-vitamin A carotenoids. This challenge is currently being addressed through biofortification breeding that relies on phenotypic selection. Genebased markers linked to pro-vitamin A content variation are expected to increase the rate of genetic gain for this critical trait. We sequenced four candidate carotenoid genes from 167 cassava accessions representing the diversity of elite breeder lines from IITA. Total carotenoid content was determined using spectrophotometer and total β-carotene was quantified by highperformance liquid chromatography. Storage root yellowness due to carotenoid pigmentation was assessed. We carried out candidate gene association analysis that accounts for population structure and kinship using genome-wide single nucleotide polymorphisms (SNPs) generated through genotyping-by-sequencing. Significant SNPs were used to design competitive allele-specific PCR assays and validated on the larger population for potential use in markerassisted selection breeding. Candidate gene sequencing of the genes β-carotene hydroxylase (crtRB), phytoene synthase (PSY2), lycopene epsilon cyclase (lcyE), and lycopene beta cyclase (lcyB) yielded a total of 37 SNPs. Total carotenoid content, total β-carotene, and color parameters were significantly associated with markers in the PSY2 gene. The SNPs from lcyE were significantly associated with color while those of lcyB and crtRB were not significantly associated with carotenoids or color parameters. These validated and breeder-friendly markers have potential to enhance the efficiency of selection for high β-carotene cassava, thus accelerating genetic gain. 2017-10 2017-09-14T15:01:25Z 2017-09-14T15:01:25Z Journal Article https://hdl.handle.net/10568/83509 en Limited Access Springer Udo, L.I., Gedil, M., Parkes, E.Y., Kulakow, P., Adesoye, A., Nwuba, C. & Rabbi, I.Y. (2017). Candidate gene sequencing and validation of SNP markers linked to carotenoid content in cassava (Manihot esculenta Crantz). Molecular Breeding, 37(123), 1-12. |
| spellingShingle | cassava vitamin a carotinoids marker-assisted selection candidate gene association biofortification Udoh, L.I. Gedil, Melaku A Parkes, Elizabeth Y. Kulakow, Peter A. Adesoye, A.I. Nwuba, C. Rabbi, Ismail Y. Candidate gene sequencing and validation of SNP markers linked to carotenoid content in cassava (Manihot esculenta Crantz) |
| title | Candidate gene sequencing and validation of SNP markers linked to carotenoid content in cassava (Manihot esculenta Crantz) |
| title_full | Candidate gene sequencing and validation of SNP markers linked to carotenoid content in cassava (Manihot esculenta Crantz) |
| title_fullStr | Candidate gene sequencing and validation of SNP markers linked to carotenoid content in cassava (Manihot esculenta Crantz) |
| title_full_unstemmed | Candidate gene sequencing and validation of SNP markers linked to carotenoid content in cassava (Manihot esculenta Crantz) |
| title_short | Candidate gene sequencing and validation of SNP markers linked to carotenoid content in cassava (Manihot esculenta Crantz) |
| title_sort | candidate gene sequencing and validation of snp markers linked to carotenoid content in cassava manihot esculenta crantz |
| topic | cassava vitamin a carotinoids marker-assisted selection candidate gene association biofortification |
| url | https://hdl.handle.net/10568/83509 |
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