Genome-wide association analysis for tuber dry matter and oxidative browning in water yam (Dioscorea alata L.)
Yam (Dioscorea spp.) is a nutritional and medicinal staple tuber crop grown in the tropics and sub-tropics. Among the food yam species, water yam (Dioscorea alata L.) is the most widely distributed and cultivated species worldwide. Tuber dry matter content (DMC) and oxidative browning (OxB) are impo...
| Autores principales: | , , , , , , , |
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| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
MDPI
2020
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| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/114380 |
| _version_ | 1855519336838463488 |
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| author | Gatarira, C. Agre, P. Matsumoto, R. Edemodu, A. Adetimirin, Victor O. Bhattacharjee, Ranjana Asiedu, R. Asfaw, A. |
| author_browse | Adetimirin, Victor O. Agre, P. Asfaw, A. Asiedu, R. Bhattacharjee, Ranjana Edemodu, A. Gatarira, C. Matsumoto, R. |
| author_facet | Gatarira, C. Agre, P. Matsumoto, R. Edemodu, A. Adetimirin, Victor O. Bhattacharjee, Ranjana Asiedu, R. Asfaw, A. |
| author_sort | Gatarira, C. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | Yam (Dioscorea spp.) is a nutritional and medicinal staple tuber crop grown in the tropics and sub-tropics. Among the food yam species, water yam (Dioscorea alata L.) is the most widely distributed and cultivated species worldwide. Tuber dry matter content (DMC) and oxidative browning (OxB) are important quality attributes that determine cultivar acceptability in water yam. This study used a single nucleotide polymorphism (SNP) assay from a diversity arrays technology (DArT) platform for a genome-wide association study (GWAS) of the two quality traits in a panel of 100 water yam clones grown in three environments. The marker–trait association analysis identified significant SNPs associated with tuber DMC on chromosomes 6 and 19 and with OxB on chromosome 5. The significant SNPs cumulatively explained 45.87 and 12.74% of the total phenotypic variation for the tuber DMC and OxB, respectively. Gene annotation for the significant SNP loci identified important genes associated in the process of the proteolytic modification of carbohydrates in the dry matter accumulation pathway as well as fatty acid β-oxidation in peroxisome for enzymatic oxidation. Additional putative genes were also identified in the peak SNP sites for both tuber dry matter and enzymatic oxidation with unknown functions. The results of this study provide valuable insight for further dissection of the genetic architecture of tuber dry matter and enzymatic oxidation in water yam. They also highlight SNP variants and genes useful for genomics-informed selection decisions in the breeding process for improving food quality traits in water yam. |
| format | Journal Article |
| id | CGSpace114380 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2020 |
| publishDateRange | 2020 |
| publishDateSort | 2020 |
| publisher | MDPI |
| publisherStr | MDPI |
| record_format | dspace |
| spelling | CGSpace1143802025-11-11T10:08:44Z Genome-wide association analysis for tuber dry matter and oxidative browning in water yam (Dioscorea alata L.) Gatarira, C. Agre, P. Matsumoto, R. Edemodu, A. Adetimirin, Victor O. Bhattacharjee, Ranjana Asiedu, R. Asfaw, A. genes bibliographic information yams dry matter tubers quality ecology Yam (Dioscorea spp.) is a nutritional and medicinal staple tuber crop grown in the tropics and sub-tropics. Among the food yam species, water yam (Dioscorea alata L.) is the most widely distributed and cultivated species worldwide. Tuber dry matter content (DMC) and oxidative browning (OxB) are important quality attributes that determine cultivar acceptability in water yam. This study used a single nucleotide polymorphism (SNP) assay from a diversity arrays technology (DArT) platform for a genome-wide association study (GWAS) of the two quality traits in a panel of 100 water yam clones grown in three environments. The marker–trait association analysis identified significant SNPs associated with tuber DMC on chromosomes 6 and 19 and with OxB on chromosome 5. The significant SNPs cumulatively explained 45.87 and 12.74% of the total phenotypic variation for the tuber DMC and OxB, respectively. Gene annotation for the significant SNP loci identified important genes associated in the process of the proteolytic modification of carbohydrates in the dry matter accumulation pathway as well as fatty acid β-oxidation in peroxisome for enzymatic oxidation. Additional putative genes were also identified in the peak SNP sites for both tuber dry matter and enzymatic oxidation with unknown functions. The results of this study provide valuable insight for further dissection of the genetic architecture of tuber dry matter and enzymatic oxidation in water yam. They also highlight SNP variants and genes useful for genomics-informed selection decisions in the breeding process for improving food quality traits in water yam. 2020 2021-07-26T08:34:55Z 2021-07-26T08:34:55Z Journal Article https://hdl.handle.net/10568/114380 en Open Access application/pdf MDPI Gatarira, C., Agre, P., Matsumoto, R., Edemodu, A., Adetimirin, V., Bhattacharjee, R., ... & Asfaw, A. (2020). Genome-wide association analysis for tuber dry matter and oxidative browning in water yam (Dioscorea alata L.). Plants, 9(8), 969: 1-19. |
| spellingShingle | genes bibliographic information yams dry matter tubers quality ecology Gatarira, C. Agre, P. Matsumoto, R. Edemodu, A. Adetimirin, Victor O. Bhattacharjee, Ranjana Asiedu, R. Asfaw, A. Genome-wide association analysis for tuber dry matter and oxidative browning in water yam (Dioscorea alata L.) |
| title | Genome-wide association analysis for tuber dry matter and oxidative browning in water yam (Dioscorea alata L.) |
| title_full | Genome-wide association analysis for tuber dry matter and oxidative browning in water yam (Dioscorea alata L.) |
| title_fullStr | Genome-wide association analysis for tuber dry matter and oxidative browning in water yam (Dioscorea alata L.) |
| title_full_unstemmed | Genome-wide association analysis for tuber dry matter and oxidative browning in water yam (Dioscorea alata L.) |
| title_short | Genome-wide association analysis for tuber dry matter and oxidative browning in water yam (Dioscorea alata L.) |
| title_sort | genome wide association analysis for tuber dry matter and oxidative browning in water yam dioscorea alata l |
| topic | genes bibliographic information yams dry matter tubers quality ecology |
| url | https://hdl.handle.net/10568/114380 |
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