Patterns on nucleotide diversity in Meisa1 and G3PHD in wild and cultivated cassava
The distribution and frequency of single nucleotide polymorphisms (SNPs) is an excellent tool for discerning evolutionary relatedness between cultivated and wild plant genomes. This type of information is scanty for the genus Manihot, and thus limiting systematic approaches in the genetic improvemen...
| Autores principales: | , , , , , , , , |
|---|---|
| Formato: | Journal Article |
| Lenguaje: | Inglés |
| Publicado: |
2013
|
| Materias: | |
| Acceso en línea: | https://hdl.handle.net/10568/77418 |
| _version_ | 1855523487112757248 |
|---|---|
| author | Beyene, D. Mukasa, S.B. Jansson, C. Villiers, Etienne P. de Ferguson, Morag E. Rabbi, Ismail Y. Kyamanywa, S. Sebuliba, J. Baguma, Yona K. |
| author_browse | Baguma, Yona K. Beyene, D. Ferguson, Morag E. Jansson, C. Kyamanywa, S. Mukasa, S.B. Rabbi, Ismail Y. Sebuliba, J. Villiers, Etienne P. de |
| author_facet | Beyene, D. Mukasa, S.B. Jansson, C. Villiers, Etienne P. de Ferguson, Morag E. Rabbi, Ismail Y. Kyamanywa, S. Sebuliba, J. Baguma, Yona K. |
| author_sort | Beyene, D. |
| collection | Repository of Agricultural Research Outputs (CGSpace) |
| description | The distribution and frequency of single nucleotide polymorphisms (SNPs) is an excellent tool for discerning evolutionary relatedness between cultivated and wild plant genomes. This type of information is scanty for the genus Manihot, and thus limiting systematic approaches in the genetic improvement of cassava. Here, we present a detailed description of the comparative patterns of SNPs in Isoamylase1 (Meisa1) and Glyceraldehyde-3-phosphate dehydrogenase (G3pdh) in 10 accessions of wild (Manihot esculenta subsp. flabellifolia) and 12 accessions of cultivated cassava (M. esculenta). The results show that Meisa1 is more variable in cultivated cassava than that in subspecies flabellifolia, where the 954 bp sequence region differs at 1 in 111 and 250 nucleotides of cultivated and wild species, respectively. Frequency analysis shows that SNP occurs once every 42 bp in cultivated and every 70 bp in wild. Tajima’s D test statistics showed that Meisa1 has been evolving under different selection pressures, diversifying in cultivated and purifying in wild. G3pdh is under diversifying selection in both populations. This may indicate the importance for isoamylase1 in starch quality traits in cassava, a trait that is likely to have been the target for artificial selection by farmers and breeders, in addition to natural selection. This study also suggests that G3pdh may be a good marker for phylogeny study while Meisa1 may be useful for intra and inter-cultivar diversity studies. The non-synonymous SNPs that changed the amino acid property were identified and the potential implication of the change in protein function was analyzed and discussed. |
| format | Journal Article |
| id | CGSpace77418 |
| institution | CGIAR Consortium |
| language | Inglés |
| publishDate | 2013 |
| publishDateRange | 2013 |
| publishDateSort | 2013 |
| record_format | dspace |
| spelling | CGSpace774182025-10-16T09:52:51Z Patterns on nucleotide diversity in Meisa1 and G3PHD in wild and cultivated cassava Beyene, D. Mukasa, S.B. Jansson, C. Villiers, Etienne P. de Ferguson, Morag E. Rabbi, Ismail Y. Kyamanywa, S. Sebuliba, J. Baguma, Yona K. cassava starch genetic improvement hybrids genotypes enzymes isoamylase nucleotides The distribution and frequency of single nucleotide polymorphisms (SNPs) is an excellent tool for discerning evolutionary relatedness between cultivated and wild plant genomes. This type of information is scanty for the genus Manihot, and thus limiting systematic approaches in the genetic improvement of cassava. Here, we present a detailed description of the comparative patterns of SNPs in Isoamylase1 (Meisa1) and Glyceraldehyde-3-phosphate dehydrogenase (G3pdh) in 10 accessions of wild (Manihot esculenta subsp. flabellifolia) and 12 accessions of cultivated cassava (M. esculenta). The results show that Meisa1 is more variable in cultivated cassava than that in subspecies flabellifolia, where the 954 bp sequence region differs at 1 in 111 and 250 nucleotides of cultivated and wild species, respectively. Frequency analysis shows that SNP occurs once every 42 bp in cultivated and every 70 bp in wild. Tajima’s D test statistics showed that Meisa1 has been evolving under different selection pressures, diversifying in cultivated and purifying in wild. G3pdh is under diversifying selection in both populations. This may indicate the importance for isoamylase1 in starch quality traits in cassava, a trait that is likely to have been the target for artificial selection by farmers and breeders, in addition to natural selection. This study also suggests that G3pdh may be a good marker for phylogeny study while Meisa1 may be useful for intra and inter-cultivar diversity studies. The non-synonymous SNPs that changed the amino acid property were identified and the potential implication of the change in protein function was analyzed and discussed. 2013 2016-10-27T08:30:24Z 2016-10-27T08:30:24Z Journal Article https://hdl.handle.net/10568/77418 en Limited Access Beyene, D., Mukasa, S.B., Jansson, C., de Villiers, E., Ferguson, M., Rabbi, I.Y., ... & Baguma, Y. (2013). Patterns of nucleotide diversity in Meisa1 and G3pdh in wild and cultivated cassava. SINET: Ethiopian Journal of Science, 36(2), 65-72. |
| spellingShingle | cassava starch genetic improvement hybrids genotypes enzymes isoamylase nucleotides Beyene, D. Mukasa, S.B. Jansson, C. Villiers, Etienne P. de Ferguson, Morag E. Rabbi, Ismail Y. Kyamanywa, S. Sebuliba, J. Baguma, Yona K. Patterns on nucleotide diversity in Meisa1 and G3PHD in wild and cultivated cassava |
| title | Patterns on nucleotide diversity in Meisa1 and G3PHD in wild and cultivated cassava |
| title_full | Patterns on nucleotide diversity in Meisa1 and G3PHD in wild and cultivated cassava |
| title_fullStr | Patterns on nucleotide diversity in Meisa1 and G3PHD in wild and cultivated cassava |
| title_full_unstemmed | Patterns on nucleotide diversity in Meisa1 and G3PHD in wild and cultivated cassava |
| title_short | Patterns on nucleotide diversity in Meisa1 and G3PHD in wild and cultivated cassava |
| title_sort | patterns on nucleotide diversity in meisa1 and g3phd in wild and cultivated cassava |
| topic | cassava starch genetic improvement hybrids genotypes enzymes isoamylase nucleotides |
| url | https://hdl.handle.net/10568/77418 |
| work_keys_str_mv | AT beyened patternsonnucleotidediversityinmeisa1andg3phdinwildandcultivatedcassava AT mukasasb patternsonnucleotidediversityinmeisa1andg3phdinwildandcultivatedcassava AT janssonc patternsonnucleotidediversityinmeisa1andg3phdinwildandcultivatedcassava AT villiersetiennepde patternsonnucleotidediversityinmeisa1andg3phdinwildandcultivatedcassava AT fergusonmorage patternsonnucleotidediversityinmeisa1andg3phdinwildandcultivatedcassava AT rabbiismaily patternsonnucleotidediversityinmeisa1andg3phdinwildandcultivatedcassava AT kyamanywas patternsonnucleotidediversityinmeisa1andg3phdinwildandcultivatedcassava AT sebulibaj patternsonnucleotidediversityinmeisa1andg3phdinwildandcultivatedcassava AT bagumayonak patternsonnucleotidediversityinmeisa1andg3phdinwildandcultivatedcassava |