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Sequence-Related Amplified Polymorphism (SRAP) Markers Based Genetic Diversity and Population Structure Analysis of Oil Palm (Elaeis guineensis Jacq.)

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Abstract

Oil palm (Elaeis guineensis Jacq.) is the key vegetable oil yielded crop and widely distributed in the southern region of China. The present study aimed at analyzing the genetic diversity and population structure of 223 oil palm accessions collected from four provinces of China by using the sequence-related amplified polymorphism (SRAP) markers. A set of 33 SRAP molecular markers were employed to analyze genetic diversity as well as population structure across 223 oil palm accessions. Out of 514 amplified bands, 487 (94.75%) bands were found to be polymorphic. The PIC value (polymorphic information content) of detected bands was from 0.38 to 0.51, with 0.46 of average. The STRUCTURE analysis categorized the 223 oil palm accessions into three subpopulations. The UPGMA based clustering classified them into three major clusters. The correlation between the population subdivisions and the genetic relationships among oil palm accessions was revealed by UPGMA and Bayesian STRUCTURE analyses. The principal coordinate analysis also confirmed a similar grouping of accessions as revealed by the UPGMA dendrogram and STRUCTURE analysis. AMOVA analysis also revealed the variance of 24% among subpopulations and 76% within subpopulations. The present investigation provided valuable information on population structure and genetic diversity of oil palm populations in China for molecular breeding research in oil palm.

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Data Availability

The SRAP (Sequence related amplified polymorphism) primers and SRAP data are available in the article and oil palm accessions used in this study are given in the supplementary table.

Abbreviations

SRAP:

Sequence-Related Amplified Polymorphism

DNA:

deoxyribonucleic acid

References

  • Agbagwa I, Patil P, Datta S, Nadarajan N (2014) Comparative efficiency of SRAP, SSR and AFLP-RGA markers in resolving genetic diversity in pigeon pea (Cajanus sp.). Ind J Biotech 13:486–495

    CAS  Google Scholar 

  • Agyenim-Boateng KG, Lu JN, Shi YZ, Zhang D, Yin XG (2019) SRAP analysis of the genetic diversity of wild castor (Ricinus communis L.) in South China. PLoS One 14(7):e0219667

    CAS  PubMed  PubMed Central  Google Scholar 

  • Bai B, Wang L, Zhang YJ, Lee M, Rahmadsyah R, Alfiko Y, Ye BQ, Purwantomo S, Suwanto A, Chua NH, Yue GH (2018) Developing genome-wide SNPs and constructing an ultrahigh-density linkage map in oil palm. Sci Rep 8:691–695

    PubMed  PubMed Central  Google Scholar 

  • Bhatt J, Kumar S, Patel S, Solanki R (2017) Sequence-related amplified polymorphism (SRAP) markers based genetic diversity analysis of cumin genotypes. Ann Agrar Sci 15:434–438

    Google Scholar 

  • Ding C, Lin WF (2010) ISSR analysis on genetic diversity of new oil palm germplasm. J Anhui Agric Sci 38(4):2202–2205

    CAS  Google Scholar 

  • Ding C, Lang NJ, Lin WF (2012) Study on genetic diversity of 12 oil palm varieties introduced newly. J Chin Cereals Oils Assoc 27(5):60–69

    CAS  Google Scholar 

  • Evanno G, Regnaut S, Goudet J (2005) Detecting the number of clusters of individuals using the software STRUCTURE: a simulation study. Mol Ecol 14:2611–2620

    CAS  PubMed  Google Scholar 

  • Frankel OH, Brown AHD (1984) Plant genetic resources today: a critical appraisal. In: Holden JHW, Williams JT (eds) Crop genetic resources: conservation and evaluation. Academic, London, pp 249–257

    Google Scholar 

  • Ganesh SK, Thangavelu S (1995) Genetic divergence in sesame (Sesamum indicum L.). Madras Agric J 82:263–265

    Google Scholar 

  • Govindaraj M, Vetriventhan M, Srinivasan M (2015) Importance of genetic diversity assessment in crop plants and its recent advances: An overview of its analytical perspectives. Genet Res Inter 43:1487

    Google Scholar 

  • Hanna BB, Malgorzate T, Leszek B, Andrzej K, Monika RT (2014) Genome-wide characterization of genetic diversity and population structure in Secale. BMC Plant Biol 14:184–198

    Google Scholar 

  • Lei XT, Cao HX (2013) Oil palm. China Agricult Press, Beijing

    Google Scholar 

  • Li G, Quiros CF (2001) Sequence-related amplified polymorphism (SRAP), a new marker system based on a simple PCR reaction: its application to mapping and gene tagging in Brassica. Theor App Genet 103:455–461

    CAS  Google Scholar 

  • Li BJ, Wang JY, Liu ZJ, Zhuang XY, Huang JX (2018a) Genetic diversity and ex-situ conservation of loropetalum subcordatum, an endangered species endemic to China. BMC Genet 19:12

    PubMed  PubMed Central  Google Scholar 

  • Li SF, Lang XD, Liu WD, Ou GL, Xu H, Su JR (2018) The relationship between species richness and aboveground biomass in a primary Pinus kesiya forest of Yunnan, southwestern China. PLoS One 13:e0191140. https://doi.org/10.1371/journal.pone.0191140

    Article  CAS  PubMed  PubMed Central  Google Scholar 

  • Liu C, White M, Newell G, Pearson R (2013) Selecting thresholds for the prediction of species occurrence with presence-only data. J Biogeogra 40(4):778–789

    Google Scholar 

  • Liu L, Chen W, Zheng X, Li J, Yan DT, Liu L, Liu X, Wang YL (2016) Genetic diversity of Ulmus lamellosa by morphological traits and sequence-related amplified polymorphism (SRAP) markers. Biochem Syst Ecol 66:272–280

    CAS  Google Scholar 

  • Ma Y, Qu SQ, Xu XR, Liang TT, Zhang DK (2015) Genetic diversity analysis of Cotoneaster schantungensis Klotz. Using SRAP marker. Ameri J Plant Sci 6:2860–2866

    CAS  Google Scholar 

  • Mahendrasinh CT, Ranbir SF, Sushil K, Amar AS (2019) Sequence-related amplified polymorphism (SRAP) analysis of teak (Tectona grandis L.) germplasm. Eco Genet Genom 12:100041

    Google Scholar 

  • Maizura I, Rajanaidu N, Zakri AH (2006) Assessment of genetic diversity in oil palm (Elaeis guineensis Jacq.) using restriction fragment length polymorphism (RFLP). Genet Resour Crop Evol 53:187–195

    CAS  Google Scholar 

  • Mantel NA (1967) The detection of disease clustering and a generalized regression approach. Cancer Res 27:209–220

    CAS  PubMed  Google Scholar 

  • Moretzsohn MC, Nunes CDM, Ferreira ME (2000) RAPD linkage mapping of the shell thickness locus in oil palm (Elaeis guineensis). Theor Appl Genet 100(1):63–70

    CAS  Google Scholar 

  • Ong PW, Maizura I, Abdullah NA, Rafii MY, Ooi LC, Low ET, Singh R (2015) Development of SNP markers and their application for genetic diversity analysis in the oil palm (Elaeis guineensis). Genet Mol Res 14(4):12205–12216

    CAS  PubMed  Google Scholar 

  • Peakall ROD, Smouse PE (2006) GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes 6:288–295

    Google Scholar 

  • Premkrishnan BV, Arunachalam V (2012) In silico RAPD priming sites in expressed sequences and iSCAR markers for oil palm. Comp Funct Genomics 9:13709

    Google Scholar 

  • Pritchard JK, Stephens M, Donnelly P (2000) Inference of population structure using multilocus genotype data. Genetics 155:945–959

    CAS  PubMed  PubMed Central  Google Scholar 

  • Rance K, Mayes S, Price Z, Jack PL, Corley RHV (2001) Quantitative trait loci for yield components in oil palm (Elaeis guineensis Jacq.). Theor App Genet 103:1302–1310

    CAS  Google Scholar 

  • Rohlf FJ (2000) NTSYS-pc: Numerical Taxonomy and Multivariate Analysis System, Version 2.1. Exeter Software, Setauket

    Google Scholar 

  • Shaye NA, Migdadi H, Charbaji A, Alsayegh S, Daoud S, Al-Anazi W, Alghamdi S (2018) Genetic variation among saudi tomato (solanum lycopersicum L.) landraces studied using sds-page and srap markers. Saudi J Biol Sci 4:1–9

    Google Scholar 

  • Shevade VS, Loboda TV (2019) Oil palm plantations in Peninsular Malaysia: Determinants and constraints on expansion. PLoS One 14(2):e0210628

    CAS  PubMed  PubMed Central  Google Scholar 

  • Singh R, Nagappan J, Tan SG, Panandam JM, Cheah SC (2007) Development of simple sequence repeat (SSR) markers for oil palm and their application in genetic mapping and fingerprinting of tissue culture clones. Asia Pacific J Mol Biol biotech 15(3):121–131

    Google Scholar 

  • Stewart C, Via LE (1993) A rapid CTAB DNA isolation technique useful for RAPD fingerprinting and other PCR applications. Biotechniques 14:748–750

    CAS  PubMed  Google Scholar 

  • Tamaki I, Okada M (2014) Genetic admixing of two evergreen oaks, Quercus acuta and Q. sessilifolia (subgenus Cyclobalanopsis), is the result of interspecific introgressive hybridization. Tree Genet Genomes 10:989–999

    Google Scholar 

  • Utomo C, Werner S, Niepold F, Deising HB (2005) Identification of Ganoderma, the causal agent of basal stem rot disease in oil palm using a molecular method. Mycopathol 159(1):159–170

    CAS  Google Scholar 

  • Wang D, Shen B, Gong H (2019) Genetic diversity of Simao pine in China revealed by SRAP markers. PeerJ 7:e6529

    PubMed  PubMed Central  Google Scholar 

  • Xia W, Luo TT, Zhang W, Mason AS, Huang DY, Huang XL, Tang WQ, Zhang CY, Xiao Y (2019) Development of high-density SNP markers and their application in evaluating genetic diversity and population structure in Elaeis guineensis. Front Plant Sci 10:130–141

    PubMed  PubMed Central  Google Scholar 

  • Xiao Y, Zhou LX, Xia W, Mason AS, Yang YD, Ma ZL, Peng ME (2014) Exploiting transcriptome data for the development and characterization of gene-based SSR markers related to cold tolerance in oil palm (Elaeis guineensis). BMC Plant Biol 14:384–397

    PubMed  PubMed Central  Google Scholar 

  • Yarra R, Jin L, Zhao Z, Cao H (2019) Progress in tissue culture and genetic transformation of oil palm: an overview. Int J Mol Sci 20(21):5353

    CAS  PubMed Central  Google Scholar 

  • Youssef M, James AC, Rivera-Madrid R et al (2011) Musa genetic diversity revealed by SRAP and AFLP. Mol Biotechnol 47:189–199

    CAS  PubMed  Google Scholar 

  • Yuan XY, Sun YW, Bai XR, Dang M, Feng XJ, Zulfiqar S, Zhao P (2018) Population structure, genetic diversity, and gene introgression of two closely related walnuts (Juglans regia and J. sigillata) in southwestern China revealed by EST-SSR markers. Forests 9:646

    Google Scholar 

  • Zagorcheva T, Stanev S, Rusanov K, Atanassov I (2020) SRAP markers for genetic diversity assessment of lavender (Lavandula angustifolia mill.) varieties and breeding lines. Biotechnol Biotechnol Equip 34:(1):303–308

    Google Scholar 

  • Zheng Y, Xu S, Liu J, Zhao Y, Liu J (2017) Genetic diversity and population structure of Chinese natural bermudagrass [Cynodon dactylon (L.) Pers.] germplasm based on SRAP markers. PLoS One 12(5):e0177508

    PubMed  PubMed Central  Google Scholar 

  • Zhou LX, Xiao Y, Xia W, Yang YD (2015) Analysis of genetic diversity and population structure of oil palm (Elaeis guineensis) from China and Malaysia based on species-specific simple sequence repeat markers. Genet Mol Res 14(4):16247–16254

    CAS  PubMed  Google Scholar 

  • Zhu SS, Zhu ZY, Wang HR, Wang L, Cheng LZ, Yuan YJ, Zheng YS, Li DD (2018) Characterization and functional analysis of a plastidial FAD6 gene and its promoter in the mesocarp of oil palm (Elaeis guineensis). Sci Hortic 239:163–170

    CAS  Google Scholar 

Download references

Acknowledgements

This work was supported by the Hainan Provincial Natural Science Foundation of China (319QN324), the Central public-interest scientific institution basal research fund for the Chinese Academy of Tropical Agricultural Sciences (No.1630152019001 and No.1630152017008), the fund for “The fund for species and varieties conservation of sector project of the Ministry of Agriculture and Rural Affairs”. (18200039).

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Authors and Affiliations

  1. Hainan Key Laboratory of Tropical Oil Crops Biology/Coconut Research Institute, Chinese Academy of Tropical Agricultural Sciences, Wenchang, Hainan, China

    Lixia Zhou, Rajesh Yarra, Hongxing Cao & Zhihao Zhao

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  1. Lixia Zhou
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  2. Rajesh Yarra
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  3. Hongxing Cao
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  4. Zhihao Zhao
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Contributions

LZ and HC conceived and designed the experiments. LZ and RY performed the experiments; LZ and RY validated the data, LZ and RY performed the formal analysis; LZ, RY and HC participated in original draft preparation; HC supervised the research.

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Correspondence to Hongxing Cao.

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Communicated by: Sithichoke Tangphatsornruang

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Zhou, L., Yarra, R., Cao, H. et al. Sequence-Related Amplified Polymorphism (SRAP) Markers Based Genetic Diversity and Population Structure Analysis of Oil Palm (Elaeis guineensis Jacq.). Tropical Plant Biol. 14, 63–71 (2021). https://doi.org/10.1007/s12042-020-09273-0

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