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Ting NC, Chan PL, Buntjer J, Ordway JM, Wischmeyer C, Ooi LCL, Low ETL, Marjuni M, Sambanthamurthi R, Singh R. High-resolution genetic linkage map and height-related QTLs in an oil palm ( Elaeis guineensis) family planted across multiple sites. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2023; 29:1301-1318. [PMID: 38024957 PMCID: PMC10678900 DOI: 10.1007/s12298-023-01360-2] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Grants] [Track Full Text] [Subscribe] [Scholar Register] [Received: 04/23/2023] [Revised: 09/09/2023] [Accepted: 09/14/2023] [Indexed: 12/01/2023]
Abstract
A refined SNP array containing 92,459 probes was developed and applied for chromosome scanning, construction of a high-density genetic linkage map and QTL analysis in a selfed Nigerian oil palm family (T128). Genotyping of the T128 mapping family generated 76,447 good quality SNPs for detailed scanning of aberration and homozygosity in the individual pseudo-chromosomes. Of them, 25,364 polymorphic SNPs were used for linkage analysis resulting in an 84.4% mapping rate. A total of 21,413 SNPs were mapped into 16 linkage groups (LGs), covering a total map length of 1364.5 cM. This genetic map is 16X denser than the previous version used to establish pseudo-chromosomes of the oil palm reference genome published in 2013. The QTLs associated with height, height increment and rachis length were identified in LGs TT05, 06, 08, 15 and 16. The present QTLs as well as those published previously were tagged to the reference genome to determine their chromosomal locations. Almost all the QTLs identified in this study were either close to or co-located with those reported in other populations. Determining the QTL position on chromosomes was also helpful in mining for the underlying candidate genes. In total, 55 putative genes and transcription factors involved in the biosynthesis, conjugation and signalling of the major phytohormones, especially for gibberellins and cell wall morphogenesis were found to be present in the identified genomic QTL regions, and their potential roles in plant dwarfism are discussed. Supplementary Information The online version contains supplementary material available at 10.1007/s12298-023-01360-2.
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Affiliation(s)
- Ngoot-Chin Ting
- Malaysian Palm Oil Board (MPOB), Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Pek-Lan Chan
- Malaysian Palm Oil Board (MPOB), Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | | | | | | | - Leslie Cheng-Li Ooi
- Malaysian Palm Oil Board (MPOB), Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Eng Ti Leslie Low
- Malaysian Palm Oil Board (MPOB), Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Marhalil Marjuni
- Malaysian Palm Oil Board (MPOB), Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Ravigadevi Sambanthamurthi
- Malaysian Palm Oil Board (MPOB), Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
| | - Rajinder Singh
- Malaysian Palm Oil Board (MPOB), Advanced Biotechnology and Breeding Centre, 6, Persiaran Institusi, Bandar Baru Bangi, 43000 Kajang, Selangor Malaysia
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Ithnin M, Othman A, Tahir NIM, Banisetti KB, Abd Halim MA, Rajesh MK. Oil Palm: Genome Designing for Improved Nutritional Quality. COMPENDIUM OF CROP GENOME DESIGNING FOR NUTRACEUTICALS 2023:1-41. [DOI: 10.1007/978-981-19-3627-2_22-1] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Track Full Text] [Subscribe] [Scholar Register] [Received: 12/09/2022] [Accepted: 12/10/2022] [Indexed: 09/02/2023]
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Kim HU, Li D. Editorial: Dissection of the molecular basis of fatty acid composition in oil crops and molecular breeding of oil crops with improved fatty acid composition. FRONTIERS IN PLANT SCIENCE 2022; 13:1053735. [PMID: 36340413 PMCID: PMC9632414 DOI: 10.3389/fpls.2022.1053735] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 09/26/2022] [Accepted: 09/30/2022] [Indexed: 06/16/2023]
Affiliation(s)
- Hyun Uk Kim
- Department of Bioindustry and Bioresource Engineering, Plant Engineering Research Institute, Sejong University, Seoul, South Korea
| | - Dongdong Li
- College of Tropical Crops, Hainan University, Haikou, China
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Wang Y, Zou J, Zhao J, Zheng Y, Li D. EgmiR5179 Regulates Lipid Metabolism by Targeting EgMADS16 in the Mesocarp of Oil Palm ( Elaeis guineensis). FRONTIERS IN PLANT SCIENCE 2021; 12:722596. [PMID: 34381490 PMCID: PMC8350733 DOI: 10.3389/fpls.2021.722596] [Citation(s) in RCA: 0] [Impact Index Per Article: 0] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Figures] [Subscribe] [Scholar Register] [Received: 06/09/2021] [Accepted: 07/07/2021] [Indexed: 06/13/2023]
Abstract
EgMADS16, one of the MADS-box transcription factors in oil palm, has a high expression level in the late fruit development of the oil palm fruit mesocarp. At the same time, it is also predicted to be the target gene of EgmiR5179, which has been identified in previous research. In this paper, we focused on the function and regulatory mechanism of the EgMADS16 gene in oil palm lipid metabolism. The results indicated that the transcription level of EgMADS16 was highest in the fourth stage, and a dual-luciferase reporter assay proved that the EgMADS16 expression level was downregulated by EgmiR5179. In both the OXEgMADS16 Arabidopsis seeds and oil palm embryonic calli, the total lipid contents were significantly decreased, but the contents of C18:0 and C18:3 in OXEgMADS16 lines were significantly increased. As expected, EgmiR5179 weakened the inhibitory effect of EgMADS16 on the oil contents in transgenic Arabidopsis plants that coexpressed EgmiR5179 and EgMADS16 (OXEgmiR5179-EgMADS16). Moreover, yeast two-hybrid and BiFC analyses suggested that there was an interaction between the EgMADS16 protein and EgGLO1 protein, which had been proven to be capable of regulating fatty acid synthesis in our previous research work. In summary, a model of the molecular mechanism by which miRNA5179 targets EgMADS16 to regulate oil biosynthesis was hypothesized, and the research results provide new insight into lipid accumulation and molecular regulation in oil palm.
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Affiliation(s)
- Yifei Wang
- College of Tropical Crops, Hainan University, Haikou, China
| | - Jixin Zou
- College of Tropical Crops, Hainan University, Haikou, China
- Rubber Research Institute of Chinese Academy of Tropical Agricultural Sciences (CATAS), Haikou, China
| | - Jin Zhao
- College of Tropical Crops, Hainan University, Haikou, China
| | - Yusheng Zheng
- College of Tropical Crops, Hainan University, Haikou, China
| | - Dongdong Li
- College of Tropical Crops, Hainan University, Haikou, China
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B KB, Mathur RK, M V B V, Shil S, G R, P A, H P B. Genome-wide association study (GWAS) of major QTLs for bunch and oil yield related traits in Elaeis guineensis L. PLANT SCIENCE : AN INTERNATIONAL JOURNAL OF EXPERIMENTAL PLANT BIOLOGY 2021; 305:110810. [PMID: 33691957 DOI: 10.1016/j.plantsci.2020.110810] [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: 06/19/2020] [Revised: 12/23/2020] [Accepted: 12/29/2020] [Indexed: 06/12/2023]
Abstract
Oil palm (Elaeis guineensis Jacq.) is a long breeding cycle perennial crop with a genome size of 1.8 Gb. This is the first report of GWAS on large number of 310 African germplasm using 400 SSR markers till date. Highly significant correlation was found between leaf area (LA) and rachis length (RL) (0.75) followed by bunch weight (BW) and bunch index (BI) (0.65), whereas negative correlation was observed between bunch number (BN) and average bunch weight (ABW). First two principal component analysis (PCA) together explained maximum amount of variation (84.5 %). The PCA1 revealed that group 2 (Guinea Bissau and Cameroon) and group 4 (Zambia and Cameroon) genotypes are best suitable for BN, BI and BW traits. GWAS of six bunch yield and seven bunch oil yield traits with SSRs resulted in the identification 43 significant quantitative trait loci (QTLs) by mixed linear model (MLM) approach. Seven SSR loci were found to be linked to oil to dry mesocarp (ODM) on chromosomes 1,4,7,10,12 and 15. The SSR locus mEgCIR1753 for ODM was significantly linked at a p of ≤0.05 which explained 34.6 % of phenotypic variance. The important parameters like ODM, OWM and OB were located on 4, 10, 11 and 15 chromosomes. The leaf area and ODM were associated with candidate genes representing of low-temperature-induced 65 kDa proteins. The identified markers can be effectively used for marker assisted selection of high yielding oil palm genotypes.
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Affiliation(s)
- Kalyana Babu B
- ICAR-Indian Institute of Oil Palm Research, Pedavegi, 534 450, West Godavari (Dt), Andhra Pradesh, India.
| | - R K Mathur
- ICAR-Indian Institute of Oil Palm Research, Pedavegi, 534 450, West Godavari (Dt), Andhra Pradesh, India
| | - Venu M V B
- ICAR-Indian Institute of Oil Palm Research, Pedavegi, 534 450, West Godavari (Dt), Andhra Pradesh, India
| | - Sandip Shil
- ICAR-Indian Institute of Oil Palm Research, Pedavegi, 534 450, West Godavari (Dt), Andhra Pradesh, India
| | - Ravichandran G
- ICAR-Indian Institute of Oil Palm Research, Pedavegi, 534 450, West Godavari (Dt), Andhra Pradesh, India
| | - Anita P
- ICAR-Indian Institute of Oil Palm Research, Pedavegi, 534 450, West Godavari (Dt), Andhra Pradesh, India
| | - Bhagya H P
- ICAR-Indian Institute of Oil Palm Research, Pedavegi, 534 450, West Godavari (Dt), Andhra Pradesh, India
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Babu BK, Mathur RK, Anitha P, Ravichandran G, Bhagya HP. Phenomics, genomics of oil palm ( Elaeis guineensis Jacq.): way forward for making sustainable and high yielding quality oil palm. PHYSIOLOGY AND MOLECULAR BIOLOGY OF PLANTS : AN INTERNATIONAL JOURNAL OF FUNCTIONAL PLANT BIOLOGY 2021; 27:587-604. [PMID: 33854286 PMCID: PMC7981377 DOI: 10.1007/s12298-021-00964-w] [Citation(s) in RCA: 1] [Impact Index Per Article: 0.3] [Reference Citation Analysis] [Abstract] [Key Words] [Track Full Text] [Subscribe] [Scholar Register] [Received: 11/02/2020] [Revised: 02/26/2021] [Accepted: 03/02/2021] [Indexed: 05/17/2023]
Abstract
Oil palm (Elaeis guineensis Jacq.) is a heterogeneous, perennial crop having long breeding cycle with a genome size of 1.8 Gb. The demand for vegetable oil is steadily increasing, and expected that nearly 240-250 million tons of vegetable oil may be required by 2050. Genomics and next generation technologies plays crucial role in achieving the sustainable availability of oil palm with good yield and high quality. A successful breeding programme in oil palm depends on the availability of diverse gene pool, ex-situ conservation and their proper utilization for generating elite planting material. The major breeding methods adopted in oil palm are either modified recurrent selection or the modified reciprocal recurrent selection method. The QTLs of yield and related traits are chiefly located on chromosome 4, 10, 12 and 15 which is discussed in the current review. The probable chromosomal regions influencing the less height increment is observed to be on chromosomes 4, 10, 14 and 15. Advanced genomic approaches together with bioinformatics tools were discussed thoroughly for achieving sustainable oil palm where more efforts are needed. Major emphasis is given on oil palm crop improvement using holistic approaches of various genomic tools. Also a road map given on the milestones in the genomics and way forward for making oil palm to high yielding quality oil palm.
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Affiliation(s)
- B. Kalyana Babu
- ICAR-Indian Institute of Oil Palm Research, 534 450, Pedavegi, West Godavari (Dt), Andhra Pradesh India
| | - R. K. Mathur
- ICAR-Indian Institute of Oil Palm Research, 534 450, Pedavegi, West Godavari (Dt), Andhra Pradesh India
| | - P. Anitha
- ICAR-Indian Institute of Oil Palm Research, 534 450, Pedavegi, West Godavari (Dt), Andhra Pradesh India
| | - G. Ravichandran
- ICAR-Indian Institute of Oil Palm Research, 534 450, Pedavegi, West Godavari (Dt), Andhra Pradesh India
| | - H. P. Bhagya
- ICAR-Indian Institute of Oil Palm Research, 534 450, Pedavegi, West Godavari (Dt), Andhra Pradesh India
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