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Gan ST, Teo CJ, Manirasa S, Wong WC, Wong CK. Assessment of genetic diversity and population structure of oil palm (Elaeis guineensis Jacq.) field genebank: A step towards molecular-assisted germplasm conservation. PLoS One 2021; 16:e0255418. [PMID: 34324602 PMCID: PMC8320974 DOI: 10.1371/journal.pone.0255418] [Citation(s) in RCA: 2] [Impact Index Per Article: 0.7] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 02/25/2021] [Accepted: 07/15/2021] [Indexed: 11/19/2022] Open
Abstract
Oil palm (Elaeis guineensis) germplasm is exclusively maintained as ex situ living collections in the field for genetic conservation and evaluation. However, this is not for long term and the maintenance of field genebanks is expensive and challenging. Large area of land is required and the germplasms are exposed to extreme weather conditions and casualty from pests and diseases. By using 107 SSR markers, this study aimed to examine the genetic diversity and relatedness of 186 palms from a Nigerian-based oil palm germplasm and to identify core collection for conservation. On average, 8.67 alleles per SSR locus were scored with average effective number of alleles per population ranging from 1.96 to 3.34 and private alleles were detected in all populations. Mean expected heterozygosity was 0.576 ranging from 0.437 to 0.661 and the Wright's fixation index calculated was -0.110. Overall moderate genetic differentiation among populations was detected (mean pairwise population FST = 0.120, gene flow Nm = 1.117 and Nei's genetic distance = 0.466) and this was further confirmed by AMOVA analysis. UPGMA dendogram and Bayesian structure analysis concomitantly clustered the 12 populations into eight genetic groups. The best core collection assembled by Core Hunter ver. 3.2.1 consisted of 58 palms accounting for 31.2% of the original population, which was a smaller core set than using PowerCore 1.0. This core set attained perfect allelic coverage with good representation, high genetic distance between entries, and maintained genetic diversity and structure of the germplasm. This study reported the first molecular characterization and validation of core collections for oil palm field genebank. The established core collection via molecular approach, which captures maximum genetic diversity with minimum redundancy, would allow effective use of genetic resources for introgression and for sustainable oil palm germplasm conservation. The way forward to efficiently conserve the field genebanks into next generation without losing their diversity was further discussed.
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Affiliation(s)
- Siou Ting Gan
- Biotechnology Section, Advanced Agriecological Research Sdn. Bhd. (AAR), AAR-UNMC Biotechnology Research Centre, Semenyih, Selangor, Malaysia
| | - Chin Jit Teo
- Plant Breeding Section, Advanced Agriecological Research Sdn. Bhd. (AAR), Paloh, Johor, Malaysia
| | - Shobana Manirasa
- Biotechnology Section, Advanced Agriecological Research Sdn. Bhd. (AAR), AAR-UNMC Biotechnology Research Centre, Semenyih, Selangor, Malaysia
| | - Wei Chee Wong
- Biotechnology Section, Advanced Agriecological Research Sdn. Bhd. (AAR), AAR-UNMC Biotechnology Research Centre, Semenyih, Selangor, Malaysia
| | - Choo Kien Wong
- Plant Breeding Section, Advanced Agriecological Research Sdn. Bhd. (AAR), Paloh, Johor, Malaysia
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Camacho-Villalobos A, Serna F, Flores J, Flores H, Manrique P, Bendezu J. Morphological and molecular characterization of an Elaeis oleifera (H.B.K) Cortes germplasm collection located in Ucayali, Peru. PLoS One 2021; 16:e0250445. [PMID: 33956829 PMCID: PMC8101761 DOI: 10.1371/journal.pone.0250445] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [MESH Headings] [Grants] [Track Full Text] [Download PDF] [Figures] [Journal Information] [Subscribe] [Scholar Register] [Received: 06/17/2020] [Accepted: 04/07/2021] [Indexed: 12/05/2022] Open
Abstract
The African oil palm (Elaeis guineensis Jacq) is a crop that is widely distributed in tropical regions around the world; however, this crop is subject to limitations such as rapid trunk growth and susceptibility to bud rot and red ring diseases particularly in South America. To overcome these limitations, national breeding and conservation programs have been established, and there is a need to identify parental palms from natural populations of the American oil palm (E. oleifera H.B.K. Cortes) with desirable yield and morphological traits (i.e., yield production and bunch number) and with high genetic diversity. However, in Peru the morphological and genetic data related to this important crop is limited. In this study, we characterized the morphological and yield and estimated the genetic diversity using 12 neutral microsatellite markers (simple sequence repeats, SSRs) across 72 oil palm individuals belonging to the E. oleifera germplasm collection located in the tropical region of Ucayali, Peru. Our results showed that morphological and yield traits explained approximately 40.39% of the variability within the Peruvian germplasm. Furthermore, Yield Production was highly correlated with two yield traits: Bunch Number (0.67) and Average weight per bunch (0.78). Based on the yield and morphological traits, a clustering analysis was performed and three phenotypic groups were identified (1, 2 and 3) in which groups 1 and 3 showed high scores associated primarily with yield traits. Microsatellite markers revealed 143 alleles, 11.92 ± 4.72 alleles per locus (A) and an expected heterozygosity (He) of 0.69 ± 0.045. A structural analysis identified three populations (k = 3), that were not related to the phenotypic groups. Interestingly, a multiple allele background was identified within the groups using multilocus and phylogenetic relationship analyses. This is the first Peruvian report regarding E. oleifera that shows preliminary data of the morphological and yield traits and genetic data, and highlight the importance of this information to set up future steps to national breeding strategies and improve the conservation of genetic material of E. oleifera. Overall, these novel findings could contribute to the development of the local oil palm industry in Peru.
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Affiliation(s)
- Alina Camacho-Villalobos
- Estación Experimental Agraria Pucallpa, Dirección de Desarrollo Tecnológico Agrario, Instituto Nacional de Innovación Agraria (INIA), Coronel Portillo, Ucayali, Perú
| | - Fernando Serna
- Centro Experimental La Molina, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Lima, Perú
| | - Jhofre Flores
- Facultad de Ciencias Agropecuarias, Universidad Nacional de Ucayali (UNU), Coronel Portillo, Ucayali, Perú
| | - Hector Flores
- Centro Experimental La Molina, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Lima, Perú
| | | | - Jorge Bendezu
- Estación Experimental Agraria Pucallpa, Dirección de Recursos Genéticos y Biotecnología, Instituto Nacional de Innovación Agraria (INIA), Coronel Portillo, Ucayali, Perú
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Sarimana U, Herrero J, Erika P, Indarto N, Wendra F, Santika B, Ritter E, Sembiring Z, Asmono D. Analysis of genetic diversity and discrimination of Oil Palm DxP populations based on the origins of pisifera elite parents. BREEDING SCIENCE 2021; 71:134-143. [PMID: 34377061 PMCID: PMC8329876 DOI: 10.1270/jsbbs.20043] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Download PDF] [Figures] [Subscribe] [Scholar Register] [Received: 04/08/2020] [Accepted: 09/29/2020] [Indexed: 06/13/2023]
Abstract
A total of 251 Dura cross Pisifera (DxP) hybrid palms from six populations descending from six parental African Pisifera origins and involving 12 progenies were analyzed with 19 selected Simple Sequence Repeats (SSR) markers. A total of 110 alleles were produced, ranging from three to eight per SSR, with a mean of 5.8 alleles per SSR locus. Of these, 68.5% were considered shared alleles by more than one population and the remaining 31.5% were population specific alleles. They generated between six and 21 haplotypes in all populations, and depending on the SSR marker, between one and 10 haplotypes within populations. Various parameters for analyzing genetic variability, differentiation and genetic structure were computed using GenAlEx, Structure and Darwin software. The obtained results confirmed microsatellites as a robust, feasible and trustful method for obtaining DNA fingerprints, tracing the source of oil palm samples. With respect to the authenticity of materials or for solving legitimacy issues, accession belonging to each population by SSR markers could be distinguished, but additional SSR should be screened for improving this process.
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Affiliation(s)
- Upit Sarimana
- Department Research and Development, PT Sampoerna Agro Tbk, Jln. Basuki Rahmat no. 788 Palembang 30127, Indonesia
| | - Javier Herrero
- NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Campus Agroalimentario de Arkaute s/n, 01192 Arkaute, Spain
| | - Pratiwi Erika
- Department Research and Development, PT Sampoerna Agro Tbk, Jln. Basuki Rahmat no. 788 Palembang 30127, Indonesia
| | - Nurcahyono Indarto
- Department Research and Development, PT Sampoerna Agro Tbk, Jln. Basuki Rahmat no. 788 Palembang 30127, Indonesia
| | - Fahmi Wendra
- Department Research and Development, PT Sampoerna Agro Tbk, Jln. Basuki Rahmat no. 788 Palembang 30127, Indonesia
| | - Baitha Santika
- Department Research and Development, PT Sampoerna Agro Tbk, Jln. Basuki Rahmat no. 788 Palembang 30127, Indonesia
| | - Enrique Ritter
- NEIKER - Basque Institute for Agricultural Research and Development, Basque Research and Technology Alliance (BRTA), Campus Agroalimentario de Arkaute s/n, 01192 Arkaute, Spain
| | - Zulhermana Sembiring
- Department Research and Development, PT Sampoerna Agro Tbk, Jln. Basuki Rahmat no. 788 Palembang 30127, Indonesia
| | - Dwi Asmono
- Department Research and Development, PT Sampoerna Agro Tbk, Jln. Basuki Rahmat no. 788 Palembang 30127, Indonesia
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Ithnin M, Vu WT, Shin MG, Suryawanshi V, Sherbina K, Zolkafli SH, Serdari NM, Amiruddin MD, Abdullah N, Mustaffa S, Marjuni M, Nookiah R, Kushairi A, Marjoram P, Nuzhdin SV, Chang PL, Singh R. Genomic diversity and genome-wide association analysis related to yield and fatty acid composition of wild American oil palm. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 304:110731. [PMID: 33568284 DOI: 10.1016/j.plantsci.2020.110731] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [MESH Headings] [Track Full Text] [Subscribe] [Scholar Register] [Received: 05/30/2020] [Revised: 10/13/2020] [Accepted: 10/15/2020] [Indexed: 05/15/2023]
Abstract
Existing Elaeis guineensis cultivars lack sufficient genetic diversity due to extensive breeding. Harnessing variation in wild crop relatives is necessary to expand the breadth of agronomically valuable traits. Using RAD sequencing, we examine the natural diversity of wild American oil palm populations (Elaeis oleifera), a sister species of the cultivated Elaeis guineensis oil palm. We genotyped 192 wild E. oleifera palms collected from seven Latin American countries along with four cultivated E. guineensis palms. Honduras, Costa Rica, Panama and Colombia palms are panmictic and genetically similar. Genomic patterns of diversity suggest that these populations likely originated from the Amazon Basin. Despite evidence of a genetic bottleneck and high inbreeding observed in these populations, there is considerable genetic and phenotypic variation for agronomically valuable traits. Genome-wide association revealed several candidate genes associated with fatty acid composition along with vegetative and yield-related traits. These observations provide valuable insight into the geographic distribution of diversity, phenotypic variation and its genetic architecture that will guide choices of wild genotypes for crop improvement.
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Affiliation(s)
- Maizura Ithnin
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Wendy T Vu
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Min-Gyoung Shin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Vasantika Suryawanshi
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Katrina Sherbina
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Siti Hazirah Zolkafli
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Norhalida Mohamed Serdari
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Mohd Din Amiruddin
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Norziha Abdullah
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Suzana Mustaffa
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Marhalil Marjuni
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Rajanaidu Nookiah
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Ahmad Kushairi
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia
| | - Paul Marjoram
- Department of Preventative Medicine, University of Southern California, Los Angeles, CA 90089, USA
| | - Sergey V Nuzhdin
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA
| | - Peter L Chang
- Department of Biological Sciences, University of Southern California, Los Angeles, CA 90089, USA.
| | - Rajinder Singh
- Malaysian Palm Oil Board, 6, Persiaran Institusi, Bandar Baru Bangi, Kajang, Selangor, 43000, Malaysia.
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