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: shellto...
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| Format: | Article |
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Nature Publishing Group
2017
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| Online Access: | https://eprints.nottingham.ac.uk/43533/ |
| _version_ | 1848796707623534592 |
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| author | Kwong, Qi Bin Ong, Ai Ling Teh, Chee Keng Chew, Fook Tim Tammi, Martti Mayes, Sean Kulaveerasingam, Harikrishna Yeoh, Suat Hui Harikrishna, Jennifer Ann Appleton, David Ross |
| author_facet | Kwong, Qi Bin Ong, Ai Ling Teh, Chee Keng Chew, Fook Tim Tammi, Martti Mayes, Sean Kulaveerasingam, Harikrishna Yeoh, Suat Hui Harikrishna, Jennifer Ann Appleton, David Ross |
| author_sort | Kwong, Qi Bin |
| building | Nottingham Research Data Repository |
| collection | Online Access |
| 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: shellto- 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), Cπ (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 | 2025-11-14T19:52:16Z |
| format | Article |
| id | nottingham-43533 |
| institution | University of Nottingham Malaysia Campus |
| institution_category | Local University |
| last_indexed | 2025-11-14T19:52:16Z |
| publishDate | 2017 |
| publisher | Nature Publishing Group |
| recordtype | eprints |
| repository_type | Digital Repository |
| spelling | nottingham-435332020-05-04T18:49:09Z https://eprints.nottingham.ac.uk/43533/ Genomic selection in commercial perennial crops: applicability and improvement in oil palm (Elaeis guineensis Jacq.) Kwong, Qi Bin Ong, Ai Ling Teh, Chee Keng Chew, Fook Tim Tammi, Martti Mayes, Sean Kulaveerasingam, Harikrishna Yeoh, Suat Hui Harikrishna, Jennifer Ann Appleton, David Ross 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: shellto- 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), Cπ (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 2017-06-06 Article PeerReviewed Kwong, Qi Bin, Ong, Ai Ling, Teh, Chee Keng, Chew, Fook Tim, Tammi, Martti, Mayes, Sean, Kulaveerasingam, Harikrishna, Yeoh, Suat Hui, Harikrishna, Jennifer Ann and Appleton, David Ross (2017) Genomic selection in commercial perennial crops: applicability and improvement in oil palm (Elaeis guineensis Jacq.). Scientific Reports, 7 . 2872/1-2872/9. ISSN 2045-2322 http://www.nature.com/articles/s41598-017-02602-6 doi:10.1038/s41598-017-02602-6 doi:10.1038/s41598-017-02602-6 |
| spellingShingle | Kwong, Qi Bin Ong, Ai Ling Teh, Chee Keng Chew, Fook Tim Tammi, Martti Mayes, Sean Kulaveerasingam, Harikrishna Yeoh, Suat Hui Harikrishna, Jennifer Ann Appleton, David Ross 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.) |
| url | https://eprints.nottingham.ac.uk/43533/ https://eprints.nottingham.ac.uk/43533/ https://eprints.nottingham.ac.uk/43533/ |