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Mohd Rodzik FF, Sudirman NA, Teh CK, Ong AL, Heng HY, Yaakop S, Mohd-Assaad N, Ong-Abdullah M, Ata N, Amit S, Saragih B, Appleton DR, Kulaveerasingam H. Development of Nuclear DNA Markers for Applications in Genetic Diversity Study of Oil Palm-Pollinating Weevil Populations. Insects 2023; 14:157. [PMID: 36835726 PMCID: PMC9967927 DOI: 10.3390/insects14020157] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 11/10/2022] [Revised: 12/19/2022] [Accepted: 12/20/2022] [Indexed: 06/18/2023]
Abstract
The oil palm-pollinating weevil (Elaeidobius kamerunicus Faust) was introduced from Cameroon, West Africa, to Malaysia in 1981, and subsequently, to other oil palm-growing countries as well. This study aims to develop a set of robust E. kamerunicus-specific nuclear DNA markers to directly assess the genetic diversity of the weevil populations. A total of 19,148 SNP and 223,200 SSR were discovered from 48 weevils representing three origins (Peninsular Malaysia, Sabah, and Riau) using RAD tag sequencing. Subsequent filtering steps further reduced these to 1000 SNP and 120 SSR. The selected 220 SNP exhibited a polymorphism information content (PIC) of 0.2387 (±0.1280), and 8 SSR had the PIC of 0.5084 (±0.1928). These markers were found to show sufficient polymorphism, making it possible to assign 180 weevils into three major clusters from Ghana, Cameroon, and Southeast Asia (mainly in Malaysia and Indonesia). These DNA markers successfully confirmed the Cameroon origin of the Southeast Asian cluster. However, the presence of null alleles in the SSR markers, due to limited flexibility of the probe design on the short RAD tags, led to an underestimation of heterozygosity within the populations. Hence, the developed SNP markers turned out to be more efficient than the SSR markers in the genetic diversity assessment of the E. kamerunicus populations. The genetic information provides useful insight into developing guidelines for the genetic monitoring and conservation planning of E. kamerunicus.
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Affiliation(s)
- Fairuz Farhana Mohd Rodzik
- Sime Darby Plantation R&D Centre, Serdang 43400, Selangor, Malaysia
- Centre for Insect Systematics, Department of Biological Science and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Nurshazwani Amalina Sudirman
- Sime Darby Plantation R&D Centre, Serdang 43400, Selangor, Malaysia
- Centre for Insect Systematics, Department of Biological Science and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Chee-Keng Teh
- Sime Darby Plantation R&D Centre, Serdang 43400, Selangor, Malaysia
| | - Ai-Ling Ong
- Sime Darby Plantation R&D Centre, Serdang 43400, Selangor, Malaysia
| | - Huey-Ying Heng
- Sime Darby Plantation R&D Centre, Serdang 43400, Selangor, Malaysia
| | - Salmah Yaakop
- Centre for Insect Systematics, Department of Biological Science and Biotechnology, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
| | - Norfarhan Mohd-Assaad
- Department of Applied Physics, Faculty of Science and Technology, Universiti Kebangsaan Malaysia (UKM), Bangi 43600, Selangor, Malaysia
- Institute of Systems Biology (INBIOSIS), Universiti Kebangsaan Malaysia, Bangi 43600, Selangor, Malaysia
| | - Meilina Ong-Abdullah
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), 6 Persiaran Institusi, Bandar Baru Bangi, Kajang 43000, Selangor, Malaysia
| | - Nabeel Ata
- Advanced Biotechnology and Breeding Centre, Malaysian Palm Oil Board (MPOB), 6 Persiaran Institusi, Bandar Baru Bangi, Kajang 43000, Selangor, Malaysia
| | - Samsudin Amit
- Sime Darby Plantation R&D Centre, Serdang 43400, Selangor, Malaysia
| | - Burhanuddin Saragih
- Sime Darby Plantation R&D Centre, Serdang 43400, Selangor, Malaysia
- Minamas Research Centre Pekanbaru, Jalan Baru Bakal, Tualang Timur, Kecamatan Tualang, Kabupaten Siak, Perawang 28772, Provinsi Riau, Indonesia
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Teh CK, Ong AL, Mayes S, Massawe F, Appleton DR. Major QTLs for Trunk Height and Correlated Agronomic Traits Provide Insights into Multiple Trait Integration in Oil Palm Breeding. Genes (Basel) 2020; 11:genes11070826. [PMID: 32708151 PMCID: PMC7397176 DOI: 10.3390/genes11070826] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.8] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 05/07/2020] [Revised: 06/16/2020] [Accepted: 06/16/2020] [Indexed: 11/26/2022] Open
Abstract
Superior oil yield is always the top priority of the oil palm industry. Short trunk height (THT) and compactness traits have become increasingly important to improve harvesting efficiency since the industry started to suffer yield losses due to labor shortages. Breeding populations with low THT and short frond length (FL) are actually available, such as Dumpy AVROS pisifera (DAV) and Gunung Melayu dura (GM). However, multiple trait stacking still remains a challenge for oil palm breeding, which usually requires 12–20 years to complete a breeding cycle. In this study, yield and height increment in the GM × GM (GM-3341) and the GM × DAV (GM-DAV-3461) crossing programs were evaluated and palms with good yield and smaller height increment were identified. In the GM-3341 family, non-linear THT growth between THT_2008 (seven years old) and THT_2014 (13 years old) was revealed by a moderate correlation, suggesting that inter-palm competition becomes increasingly important. In total, 19 quantitative trait loci (QTLs) for THT_2008 (8), oil per palm (O/P) (7) and FL (4) were localized on the GM-3341 linkage map, with an average mapping interval of 2.01 cM. Three major QTLs for THT_2008, O/P and FL are co-located on chromosome 11 and reflect the correlation of THT_2008 with O/P and FL. Multiple trait selection for high O/P and low THT (based on the cumulative effects of positive alleles per trait) identified one palm from 100 palms, but with a large starting population of 1000–1500 seedling per cross, this low frequency could be easily compensated for during breeding selection.
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Affiliation(s)
- Chee-Keng Teh
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Serdang 43400, Selangor State, Malaysia; (A.-L.O.); (D.R.A.)
- School of Biosciences, University of Nottingham Malaysia, Semenyih 43500, Selangor State, Malaysia;
- Correspondence:
| | - Ai-Ling Ong
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Serdang 43400, Selangor State, Malaysia; (A.-L.O.); (D.R.A.)
- School of Biosciences, University of Nottingham Malaysia, Semenyih 43500, Selangor State, Malaysia;
| | - Sean Mayes
- School of Biosciences, University of Nottingham, Sutton Bonington Campus, Leicestershire LE12 5RD, UK;
| | - Festo Massawe
- School of Biosciences, University of Nottingham Malaysia, Semenyih 43500, Selangor State, Malaysia;
| | - David Ross Appleton
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Serdang 43400, Selangor State, Malaysia; (A.-L.O.); (D.R.A.)
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Teh CK, Lee HL, Abidin H, Ong AL, Mayes S, Chew FT, Appleton D. A practical genome-enabled legitimacy assay for oil palm breeding and seed production. BMC Plant Biol 2019; 19:470. [PMID: 31690276 PMCID: PMC6833287 DOI: 10.1186/s12870-019-2062-x] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/23/2019] [Accepted: 10/09/2019] [Indexed: 05/02/2023]
Abstract
BACKGROUND Legitimacy in breeding and commercial crop production depends on optimised protocols to ensure purity of crosses and correct field planting of material. In oil palm, the presence of three fruit forms permits these assumptions to be tested, although only after field planting. The presence of incorrect fruit forms in a cross is a clear sign of illegitimacy. Given that tenera forms produce 30% more oil for the same weight of fruit as dura, the presence of low levels of dura contamination can have major effect during the economic lifespan of an oil palm, which is around 25 years. We evaluated two methods for legitimacy test 1) The use of SHELL markers to the gene that determines the shell-thickness trait 2) The use of SNP markers, to determine the legitimacy of the cross. RESULTS Our results indicate that the SHELL markers can theoretically reduce the major losses due to dura contamination of tenera planting material. However, these markers cannot distinguish illegitimate tenera, which reduces the value of having bred elite tenera for commercial planting and in the breeding programme, where fruit form is of limited utility, and incorrect identity could lead to significant problems. We propose an optimised approach using SNPs for routine quality control. CONCLUSIONS Both dura and tenera contamination can be identified and removed at or before the nursery stage. An optimised legitimacy assay using SNP markers coupled with a suitable sampling scheme is now ready to be deployed as a standard control for seed production and breeding in oil palm. The same approach will also be an effective solution for other perennial crops, such as coconut and date palm.
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Affiliation(s)
- Chee-Keng Teh
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Banting, Selangor Malaysia
- School of Biosciences, University of Nottingham Malaysia, Semenyih, Selangor Malaysia
| | - Heng-Leng Lee
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Banting, Selangor Malaysia
| | - Hafiza Abidin
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Banting, Selangor Malaysia
| | - Ai-Ling Ong
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Banting, Selangor Malaysia
- School of Biosciences, University of Nottingham Malaysia, Semenyih, Selangor Malaysia
| | - Sean Mayes
- School of Biosciences, University of Nottingham, Nottingham, UK
| | - Fook-Tim Chew
- Department of Biological Sciences, National University of Singapore, Lower Kent Ridge Rd, Singapore, Singapore
| | - David Appleton
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Banting, Selangor Malaysia
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Affiliation(s)
- Chee-Keng Teh
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor, 43400, Malaysia
| | - Ai-Ling Ong
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor, 43400, Malaysia
| | - Qi-Bin Kwong
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor, 43400, Malaysia
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Teh CK, Muaz SD, Tangaya P, Fong PY, Ong AL, Mayes S, Chew FT, Kulaveerasingam H, Appleton D. Characterizing haploinsufficiency of SHELL gene to improve fruit form prediction in introgressive hybrids of oil palm. Sci Rep 2017; 7:3118. [PMID: 28596562 PMCID: PMC5465187 DOI: 10.1038/s41598-017-03225-7] [Citation(s) in RCA: 6] [Impact Index Per Article: 0.9] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 12/01/2016] [Accepted: 04/21/2017] [Indexed: 11/22/2022] Open
Abstract
The fundamental trait in selective breeding of oil palm (Eleais guineensis Jacq.) is the shell thickness surrounding the kernel. The monogenic shell thickness is inversely correlated to mesocarp thickness, where the crude palm oil accumulates. Commercial thin-shelled tenera derived from thick-shelled dura × shell-less pisifera generally contain 30% higher oil per bunch. Two mutations, shMPOB (M1) and shAVROS (M2) in the SHELL gene – a type II MADS-box transcription factor mainly present in AVROS and Nigerian origins, were reported to be responsible for different fruit forms. In this study, we have tested 1,339 samples maintained in Sime Darby Plantation using both mutations. Five genotype-phenotype discrepancies and eight controls were then re-tested with all five reported mutations (shAVROS, shMPOB, shMPOB2, shMPOB3 and shMPOB4) within the same gene. The integration of genotypic data, pedigree records and shell formation model further explained the haploinsufficiency effect on the SHELL gene with different number of functional copies. Some rare mutations were also identified, suggesting a need to further confirm the existence of cis-compound mutations in the gene. With this, the prediction accuracy of fruit forms can be further improved, especially in introgressive hybrids of oil palm. Understanding causative variant segregation is extremely important, even for monogenic traits such as shell thickness in oil palm.
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Affiliation(s)
- Chee-Keng Teh
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor, Malaysia.
| | - Siti Dalila Muaz
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor, Malaysia
| | - Praveena Tangaya
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor, Malaysia
| | - Po-Yee Fong
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor, Malaysia
| | - Ai-Ling Ong
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor, Malaysia
| | - Sean Mayes
- School of Biosciences, University of Nottingham, Nottingham, UK
| | - Fook-Tim Chew
- Department of Biological Sciences, National University of Singapore, Singapore, Singapore
| | | | - David Appleton
- Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, Selangor, Malaysia
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Ithnin M, Teh CK, Ratnam W. Genetic diversity of Elaeis oleifera (HBK) Cortes populations using cross species SSRs: implication's for germplasm utilization and conservation. BMC Genet 2017; 18:37. [PMID: 28420332 PMCID: PMC5395919 DOI: 10.1186/s12863-017-0505-7] [Citation(s) in RCA: 7] [Impact Index Per Article: 1.0] [Reference Citation Analysis] [What about the content of this article? (0)] [Affiliation(s)] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 11/15/2016] [Accepted: 04/12/2017] [Indexed: 11/25/2022] Open
Abstract
Background The Elaeis oleifera genetic materials were assembled from its center of diversity in South and Central America. These materials are currently being preserved in Malaysia as ex situ living collections. Maintaining such collections is expensive and requires sizable land. Information on the genetic diversity of these collections can help achieve efficient conservation via maintenance of core collection. For this purpose, we have applied fourteen unlinked microsatellite markers to evaluate 532 E. oleifera palms representing 19 populations distributed across Honduras, Costa Rica, Panama and Colombia. Results In general, the genetic diversity decreased from Costa Rica towards the north (Honduras) and south-east (Colombia). Principle coordinate analysis (PCoA) showed a single cluster indicating low divergence among palms. The phylogenetic tree and STRUCTURE analysis revealed clusters based on country of origin, indicating considerable gene flow among populations within countries. Based on the values of the genetic diversity parameters, some genetically diverse populations could be identified. Further, a total of 34 individual palms that collectively captured maximum allelic diversity with reduced redundancy were also identified. High pairwise genetic differentiation (Fst > 0.250) among populations was evident, particularly between the Colombian populations and those from Honduras, Panama and Costa Rica. Crossing selected palms from highly differentiated populations could generate off-springs that retain more genetic diversity. Conclusion The results attained are useful for selecting palms and populations for core collection. The selected materials can also be included into crossing scheme to generate offsprings that capture greater genetic diversity for selection gain in the future. Electronic supplementary material The online version of this article (doi:10.1186/s12863-017-0505-7) contains supplementary material, which is available to authorized users.
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Affiliation(s)
- Maizura Ithnin
- Malaysian Palm Oil Board (MPOB), P.O.Box 10620, 50720, Kuala Lumpur, Malaysia.
| | - Chee-Keng Teh
- Malaysian Palm Oil Board (MPOB), P.O.Box 10620, 50720, Kuala Lumpur, Malaysia.,Present Address: Biotechnology & Breeding Department, Sime Darby Plantation R&D Centre, 43400, Selangor, Malaysia
| | - Wickneswari Ratnam
- School of Environmental and Natural Resource Sciences, Faculty of Science and Technology, Universiti Kebangsaan Malaysia, 43600, Bangi, Selangor, Malaysia
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