Genomic selection in commercial perennial crops: Applicability and improvement in oil palm (Elaeis guineensis Jacq.)
Genomic selection (GS) uses genome-wide markers to select individuals with the desired overall combination of breeding traits. A total of 1,218 individuals from a commercial population of Ulu Remis x AVROS (UR x AVROS) were genotyped using the OP200K array. The traits of interest included: Shell-to-...
| Main Authors: | , , , , , , , , , |
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| Format: | Article |
| Language: | English |
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Nature Publishing Group
2017
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| Online Access: | http://eprints.um.edu.my/17536/1/KwongQB_%282017%29.pdf |
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| author | Kwong, Q.B. Ong, A.L. Teh, C.K. Chew, F.T. Tammi, M. Mayes, S. Kulaveerasingam, H. Yeoh, H.S. Harikrishna, J.A. Appleton, D.R. |
| author_facet | Kwong, Q.B. Ong, A.L. Teh, C.K. Chew, F.T. Tammi, M. Mayes, S. Kulaveerasingam, H. Yeoh, H.S. Harikrishna, J.A. Appleton, D.R. |
| author_sort | Kwong, Q.B. |
| collection | UM |
| description | Genomic selection (GS) uses genome-wide markers to select individuals with the desired overall combination of breeding traits. A total of 1,218 individuals from a commercial population of Ulu Remis x AVROS (UR x AVROS) were genotyped using the OP200K array. The traits of interest included: Shell-to-fruit ratio (S/F, %), mesocarp-to-fruit ratio (M/F, %), kernel-to-fruit ratio (K/F, %), fruit per bunch (F/B, %), oil per bunch (O/B, %) and oil per palm (O/P, kg/palm/year). Genomic heritabilities of these traits were estimated to be in the range of 0.40 to 0.80. GS methods assessed were RR-BLUP, Bayes A (BA), CÏ € (BC), Lasso (BL) and Ridge Regression (BRR). All methods resulted in almost equal prediction accuracy. The accuracy achieved ranged from 0.40 to 0.70, correlating with the heritability of traits. By selecting the most important markers, RR-BLUP B has the potential to outperform other methods. The marker density for certain traits can be further reduced based on the linkage disequilibrium (LD). Together with in silico breeding, GS is now being used in oil palm breeding programs to hasten parental palm selection. |
| first_indexed | 2024-03-06T05:42:48Z |
| format | Article |
| id | um.eprints-17536 |
| institution | Universiti Malaya |
| language | English |
| last_indexed | 2024-03-06T05:42:48Z |
| publishDate | 2017 |
| publisher | Nature Publishing Group |
| record_format | dspace |
| spelling | um.eprints-175362017-07-20T03:12:20Z http://eprints.um.edu.my/17536/ Genomic selection in commercial perennial crops: Applicability and improvement in oil palm (Elaeis guineensis Jacq.) Kwong, Q.B. Ong, A.L. Teh, C.K. Chew, F.T. Tammi, M. Mayes, S. Kulaveerasingam, H. Yeoh, H.S. Harikrishna, J.A. Appleton, D.R. QH301 Biology Genomic selection (GS) uses genome-wide markers to select individuals with the desired overall combination of breeding traits. A total of 1,218 individuals from a commercial population of Ulu Remis x AVROS (UR x AVROS) were genotyped using the OP200K array. The traits of interest included: Shell-to-fruit ratio (S/F, %), mesocarp-to-fruit ratio (M/F, %), kernel-to-fruit ratio (K/F, %), fruit per bunch (F/B, %), oil per bunch (O/B, %) and oil per palm (O/P, kg/palm/year). Genomic heritabilities of these traits were estimated to be in the range of 0.40 to 0.80. GS methods assessed were RR-BLUP, Bayes A (BA), CÏ € (BC), Lasso (BL) and Ridge Regression (BRR). All methods resulted in almost equal prediction accuracy. The accuracy achieved ranged from 0.40 to 0.70, correlating with the heritability of traits. By selecting the most important markers, RR-BLUP B has the potential to outperform other methods. The marker density for certain traits can be further reduced based on the linkage disequilibrium (LD). Together with in silico breeding, GS is now being used in oil palm breeding programs to hasten parental palm selection. Nature Publishing Group 2017 Article PeerReviewed application/pdf en http://eprints.um.edu.my/17536/1/KwongQB_%282017%29.pdf Kwong, Q.B. and Ong, A.L. and Teh, C.K. and Chew, F.T. and Tammi, M. and Mayes, S. and Kulaveerasingam, H. and Yeoh, H.S. and Harikrishna, J.A. and Appleton, D.R. (2017) Genomic selection in commercial perennial crops: Applicability and improvement in oil palm (Elaeis guineensis Jacq.). Scientific Reports, 7 (1). pp. 1-9. ISSN 2045-2322, DOI https://doi.org/10.1038/s41598-017-02602-6 <https://doi.org/10.1038/s41598-017-02602-6>. https://www.nature.com/articles/s41598-017-02602-6 doi: 10.1038/s41598-017-02602-6 |
| spellingShingle | QH301 Biology Kwong, Q.B. Ong, A.L. Teh, C.K. Chew, F.T. Tammi, M. Mayes, S. Kulaveerasingam, H. Yeoh, H.S. Harikrishna, J.A. Appleton, D.R. Genomic selection in commercial perennial crops: Applicability and improvement in oil palm (Elaeis guineensis Jacq.) |
| title | Genomic selection in commercial perennial crops: Applicability and improvement in oil palm (Elaeis guineensis Jacq.) |
| title_full | Genomic selection in commercial perennial crops: Applicability and improvement in oil palm (Elaeis guineensis Jacq.) |
| title_fullStr | Genomic selection in commercial perennial crops: Applicability and improvement in oil palm (Elaeis guineensis Jacq.) |
| title_full_unstemmed | Genomic selection in commercial perennial crops: Applicability and improvement in oil palm (Elaeis guineensis Jacq.) |
| title_short | Genomic selection in commercial perennial crops: Applicability and improvement in oil palm (Elaeis guineensis Jacq.) |
| title_sort | genomic selection in commercial perennial crops applicability and improvement in oil palm elaeis guineensis jacq |
| topic | QH301 Biology |
| url | http://eprints.um.edu.my/17536/1/KwongQB_%282017%29.pdf |
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