SSR mining in oil palm EST database: application in oil palm germplasm diversity studies.
This study reports on the detection of additional expressed sequence tags (EST) derived simple sequence repeat (SSR) markers for the oil palm. A large collection of 19243 Elaeis guineensis ESTs were assembled to give 10258 unique sequences, of which 629 ESTs were found to contain 722 SSRs with a var...
| Main Authors: | , , , , , , , |
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| Format: | Article |
| Language: | English English |
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Indian Academy of Sciences
2010
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| Subjects: | |
| Online Access: | http://psasir.upm.edu.my/id/eprint/16819/1/SSR%20mining%20in%20oil%20palm%20EST%20database.pdf |
| _version_ | 1825945889677508608 |
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| author | Ngoot-Chin, Ting Mohd Zaki, Noorhariza Rosli, Rozana Eng-Ti , Leslie Low Ithnin, Maizura Suan-Choo , Chia Soon-Guan , Tan Rajinder, Singh |
| author_facet | Ngoot-Chin, Ting Mohd Zaki, Noorhariza Rosli, Rozana Eng-Ti , Leslie Low Ithnin, Maizura Suan-Choo , Chia Soon-Guan , Tan Rajinder, Singh |
| author_sort | Ngoot-Chin, Ting |
| collection | UPM |
| description | This study reports on the detection of additional expressed sequence tags (EST) derived simple sequence repeat (SSR) markers for the oil palm. A large collection of 19243 Elaeis guineensis ESTs were assembled to give 10258 unique sequences, of which 629 ESTs were found to contain 722 SSRs with a variety of motifs. Dinucleotide repeats formed the largest group(45.6%) consisting of 66.9% AG/CT, 21.9% AT/AT, 10.9% AC/GT and 0.3% CG/CG motifs. This was followed by trinucleotide repeats, which is the second most abundant repeat types (34.5%) consisting of AAG/CTT (23.3%), AGG/CCT
(13.7%), CCG/CGG (11.2%), AAT/ATT (10.8%), AGC/GCT (10.0%), ACT/AGT (8.8%), ACG/CGT (7.6%), ACC/GGT(7.2%), AAC/GTT (3.6%) and AGT/ACT (3.6%) motifs. Primer pairs were designed for 405 unique EST-SSRs and 15 of these were used to genotype 105 E. guineensis and 30 E. oleifera accessions. Fourteen SSRs were polymorphic in at least one
germplasm revealing a total of 101 alleles. The high percentage (78.0%) of alleles found to be specific for either E. guineensis or E. oleifera has increased the power for discriminating the two species. The estimates of genetic differentiation detected by EST-SSRs were compared to those reported previously. The transferability across palm taxa to two Cocos nucifera and six exotic palms is also presented. The polymerase chain reaction (PCR) products of three primer-pairs detected in E. guineensis,
E. oleifera, C. nucifera and Jessinia bataua were cloned and sequenced. Sequence alignments showed mutations within the SSR site and the flanking regions. Phenetic analysis based on the sequence data revealed that C. nucifera is closer to oil palm compared to J. bataua; consistent with the taxanomic classification. |
| first_indexed | 2024-03-06T07:38:33Z |
| format | Article |
| id | upm.eprints-16819 |
| institution | Universiti Putra Malaysia |
| language | English English |
| last_indexed | 2024-03-06T07:38:33Z |
| publishDate | 2010 |
| publisher | Indian Academy of Sciences |
| record_format | dspace |
| spelling | upm.eprints-168192015-12-18T02:50:53Z http://psasir.upm.edu.my/id/eprint/16819/ SSR mining in oil palm EST database: application in oil palm germplasm diversity studies. Ngoot-Chin, Ting Mohd Zaki, Noorhariza Rosli, Rozana Eng-Ti , Leslie Low Ithnin, Maizura Suan-Choo , Chia Soon-Guan , Tan Rajinder, Singh This study reports on the detection of additional expressed sequence tags (EST) derived simple sequence repeat (SSR) markers for the oil palm. A large collection of 19243 Elaeis guineensis ESTs were assembled to give 10258 unique sequences, of which 629 ESTs were found to contain 722 SSRs with a variety of motifs. Dinucleotide repeats formed the largest group(45.6%) consisting of 66.9% AG/CT, 21.9% AT/AT, 10.9% AC/GT and 0.3% CG/CG motifs. This was followed by trinucleotide repeats, which is the second most abundant repeat types (34.5%) consisting of AAG/CTT (23.3%), AGG/CCT (13.7%), CCG/CGG (11.2%), AAT/ATT (10.8%), AGC/GCT (10.0%), ACT/AGT (8.8%), ACG/CGT (7.6%), ACC/GGT(7.2%), AAC/GTT (3.6%) and AGT/ACT (3.6%) motifs. Primer pairs were designed for 405 unique EST-SSRs and 15 of these were used to genotype 105 E. guineensis and 30 E. oleifera accessions. Fourteen SSRs were polymorphic in at least one germplasm revealing a total of 101 alleles. The high percentage (78.0%) of alleles found to be specific for either E. guineensis or E. oleifera has increased the power for discriminating the two species. The estimates of genetic differentiation detected by EST-SSRs were compared to those reported previously. The transferability across palm taxa to two Cocos nucifera and six exotic palms is also presented. The polymerase chain reaction (PCR) products of three primer-pairs detected in E. guineensis, E. oleifera, C. nucifera and Jessinia bataua were cloned and sequenced. Sequence alignments showed mutations within the SSR site and the flanking regions. Phenetic analysis based on the sequence data revealed that C. nucifera is closer to oil palm compared to J. bataua; consistent with the taxanomic classification. Indian Academy of Sciences 2010 Article PeerReviewed application/pdf en http://psasir.upm.edu.my/id/eprint/16819/1/SSR%20mining%20in%20oil%20palm%20EST%20database.pdf Ngoot-Chin, Ting and Mohd Zaki, Noorhariza and Rosli, Rozana and Eng-Ti , Leslie Low and Ithnin, Maizura and Suan-Choo , Chia and Soon-Guan , Tan and Rajinder, Singh (2010) SSR mining in oil palm EST database: application in oil palm germplasm diversity studies. Journal of Genetics, 89 (2 ). pp. 1-11. ISSN 0022-1333 Oil palm - Germplasm resources. Genetic variation. Oil-palm - Breeding. English |
| spellingShingle | Oil palm - Germplasm resources. Genetic variation. Oil-palm - Breeding. Ngoot-Chin, Ting Mohd Zaki, Noorhariza Rosli, Rozana Eng-Ti , Leslie Low Ithnin, Maizura Suan-Choo , Chia Soon-Guan , Tan Rajinder, Singh SSR mining in oil palm EST database: application in oil palm germplasm diversity studies. |
| title | SSR mining in oil palm EST database: application in oil palm germplasm diversity studies. |
| title_full | SSR mining in oil palm EST database: application in oil palm germplasm diversity studies. |
| title_fullStr | SSR mining in oil palm EST database: application in oil palm germplasm diversity studies. |
| title_full_unstemmed | SSR mining in oil palm EST database: application in oil palm germplasm diversity studies. |
| title_short | SSR mining in oil palm EST database: application in oil palm germplasm diversity studies. |
| title_sort | ssr mining in oil palm est database application in oil palm germplasm diversity studies |
| topic | Oil palm - Germplasm resources. Genetic variation. Oil-palm - Breeding. |
| url | http://psasir.upm.edu.my/id/eprint/16819/1/SSR%20mining%20in%20oil%20palm%20EST%20database.pdf |
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