Abstract
Acid lime (Citrus aurantifolia) is the fourth largest fruit crop in terms of cultivated area and production in Oman. However, over half a million lime trees were lost in Oman over the past 35 years due to witches’ broom disease of lime (WBDL) which is caused by Candidatus phytoplasma aurantifolia. This study was conducted to examine genetic diversity of acid lime in Oman. AFLP analysis of 143 acid lime samples from Oman, 2 from Brazil and one from Pakistan using 4 primer pair combinations produced 980 polymorphic loci (100 %) and 146 AFLP genotypes. Despite the long history of acid lime cultivation in Oman, populations of lime from different districts were found to have low levels of genetic diversity (0.0888–0.2284). AMOVA analysis indicated the existence of high level of genetic differentiation (F ST = 0.271) among populations of acid lime from Oman and Brazil, which indicates that both populations have evolved independently for a considerably long period of time. On the other hand, AMOVA analysis showed that only 11 % of the genetic variation exists among populations from the 18 different districts in Oman. This suggests frequent exchange of acid lime planting material across geographical regions in Oman. Findings from this study suggest that the low level of genetic diversity of acid lime in Oman and frequent movement of acid lime planting material across districts are two main factors which contributed to the rapid spread and high susceptibility of acid limes to WBDL in the country.
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1007%2Fs10681-012-0728-7/MediaObjects/10681_2012_728_Fig1_HTML.gif)
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1007%2Fs10681-012-0728-7/MediaObjects/10681_2012_728_Fig2_HTML.jpg)
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1007%2Fs10681-012-0728-7/MediaObjects/10681_2012_728_Fig3_HTML.gif)
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1007%2Fs10681-012-0728-7/MediaObjects/10681_2012_728_Fig4_HTML.gif)
![](http://media.springernature.com/m312/springer-static/image/art%3A10.1007%2Fs10681-012-0728-7/MediaObjects/10681_2012_728_Fig5_HTML.gif)
Similar content being viewed by others
References
Abkenar AA, Isshiki S (2003) Molecular characterization and genetic diversity among Japanese acid citrus (Citrus spp.) based on RAPD markers. J Hortic Sci Biotechnol 78:108–112
Alhudaib K, Arocha Y, Wilson M, Jones P (2009) Molecular identification, potential vectors and alternative hosts of the phytoplasma associated with a lime decline disease in Saudi Arabia. Crop Protection 28:13–18
Alpaa K, Gopal K, Gopi V, Aliya S, Sreenivasulu B, Purushotham K (2010) Fingerprinting of acid lime varieties and clones having varied resistance to bacterial canker, using RAPD marker. Arch Phytopathol Plant Prot 43:624–633
Al-Saadi AM, Khan IA, Deadman ML (2004) Economic losses caused by witches’ broom disease of lime and some management aspects in Shinas area of Oman. In: 10th international citrus congress, Morocco, 15–20 February 2004, pp 817–818
Al-Sa'di AM, Drenth A, Deadman ML, Aitken EAB (2008a) Genetic diversity, aggressiveness and metalaxyl sensitivity of Pythium aphanidermatum populations infecting cucumber in Oman. Plant Pathol 57:45–56
Al-Sa'di AM, Drenth A, Deadman ML, de Cock AWAM, Al-Said FA, Aitken EAB (2008b) Genetic diversity, aggressiveness and metalaxyl sensitivity of Pythium spinosum infecting cucumber in Oman. J Phytopathol 156:29–35
Al-Sadi AM, Al-Masoudi RS, Al-Habsi N, Al-Said FA, Al-Rawahy SA, Ahmed M, Deadman ML (2010) Effect of salinity on Pythium dam**-off of cucumber and on the tolerance of Pythium aphanidermatum. Plant Pathol 59:112–120
Al-Sadi A, Al-Hilali S, Al-Yahyai R, Al-Said F, Deadman M, Al-Mahmooli I, Nolasco G (2012a) Molecular characterization and potential sources of Citrus Tristeza Virus in Oman. Plant Pathol. doi:10.1111/j.1365-3059.2011.02553.x
Al-Sadi AM, Al-Ghaithi AG, Al-Balushi ZM, Al-Jabri AH (2012b) Analysis of diversity in Pythium aphanidermatum populations from a single greenhouse reveals phenotypic and genotypic changes over 2006 to 2011. Plant Dis 96:852–858
Bove JM (1995) Virus and virus-like disease of citrus in the near east region. FAO, Rome
Bove JM, Danet JL, Bananej K, Hassanzadeh N, Taghizadeh M, Salehi M, Garnier M (2000) Witches’ broom disease of lime (WBDL) in Iran. In: Paper presented at the proceedings of the fourteenth conference of IOCV
Chung KR, Khan IA, Brlansky RH (2009) Citrus diseases exotic to Florida: witches’ broom disease of lime (WBDL). EDIS Publications, University of Florida, Gainesville, PP228, pp 1-3
Corazza-Nunes MJ, Machado MA, Nunes WMC, Cristofani MN, Targon MLP (2002) Assesment of genetic variability in grapefruits (Citrus paradise Macf.) and pummelos (C. maxima (Burm) Merr.) using RAPD and SSR markers. Euphytica 126:169–176
Culley T, Wolfe A (2001) Population genetic structure of the clestogamous plant species Viola pubescens Aiton (Violaceae), as indicated by allozyme and ISSR molecular markers. Heredity 86:545–556
Davies FS, Albrigo LG (1994) Citrus. CAB International, United Kingdom
Dehesdtani A, Kazemitabar SK, Rahimian H (2007) Assessment of genetic diversity of Navel sweet orange cultivars grown in Mazandaran Province using RAPD markers. Asian J Plant Sci 6:1119–1124
Deng SJ, Hiruki C (1991) Genetic relatedness between two non-culturable mycoplasmalike organisms revealed by nucleic acid hybridization and polymerase chain reaction. Phytopathology 81:1475–1479
EL-Mouei R, Choumane W, Dway F (2011) Molecular characterization and genetic diversity in Genus Citrus from Syria. Int J Agric Biol 13:351–356
Excoffier L, Laval G, Schneider S (2005) Arlequin (version 3.0): an integrated software package for population genetics data analysis. Evol Bioinf 1:47–50
Fang DQ, Roos ML, Krueger RR, Federic CT (1997) Fingerprintiing trifoliate orange germplasm accessions with isozymes RFLPs and inter-simple sequence repeat markers. Theor Appl Genetics 95:211–219
FAOSTAT-Agriculture (2011) http://faostat.fao.org/site/567/default.aspx#ancor
Garnier M, Zreik L, Bové JM (1991) Witches’ broom, a lethal mycoplasmal disease of lime trees in the Sultanate of Oman and the United Arab Emirates. Plant Dis 75:546–551
Geleta M, Bryngelsson T, Bekele E (2008) Assessment of genetic diversity of Guizotia abyssinica (L.f.) Cass. (Asteraceae) from Ethiopia using amplified fragment length polymorphism. Plant Genetic Resour Character Util 6 (1):41–51
Ghosh DK, Das AK, Singh S, Singh SJ, Ahlawat YA (1999) Occurrence of witches’ broom, a new phytoplasma disease of acid lime (Citrus aurantifolia) in India. Plant Dis 83:302
Grünwald NJ, Goodwin SB, Milgroom MG, Fry WE (2003) Anlaysis of genotypic diversity data for populations of microorganisms. Phytopathology 93:738–746
Gundersen DE, Lee IM (1996) Ultrasensitive detection of phytoplasmas by nested PCR assay using two universal primer pairs. Phytopathol Mediterr 35:144–151
Hodgson RW (1967) Horticultural varieties of citrus. In: Reuther W, Batchelor LD, Webber HD (eds) The citrus Industry. Univeristy of California Press, Berkeley, pp 431–591
Jannati M, Fotouhi R, Abad AP, Salehi Z (2009) Genetic diversity analysis of Iranian citrus varieties using micro satellite (SSR) based markers. J Hortic For 1:120–125
Martinez-Castillo J, Colunga-GraciaMarin P, Zizumbo-Villarreal D (2008) Genetic erosion and in situ conservation of lima bean (Phaseolus lunatus L.) landraces in its Mesoamerican diversity center. Genet Resour Crop Evol 55:1065–1077
Moghal SM, Shivanathan P, Mani A, Al-Zidjali AD, Al-Zidjali TS, Al-Raeesy YM (1993) Status of pests and diseases in Oman: series 1: plant diseases in the Batinah. Ministry of Agriculture and Fisheries, Muscat
Nei M (1973) Analysis of gene diversity in subdivided populations. Proc Nat Acad Sci 70:3321–3323
Nei M (1978) Estimation of average heterozygosity and genetic distance from a small number of individuals. Genetics 89:583–590
Novelli VM, Cristofani M, Souza AA, Machado MA (2006) Development and charaterization of polymorphic microsatellite markers for the sweet orange (Citrus sinensis L. Osbeck). Genetics Mol Biol 29(1):90–96
Pang X-M, Hu C-G, Deng X–X (2007) Phylogentic relationships within Citrus and its related genera as inferred from AFLP markers. Genet Resour Crop Evol 54:429–436
Robles-Gonzalez MM, Medina-Urrutia VM, Velazquez-Monreal JJ, Simpson J (2008) Field performance and molecular profiles of Mexican lime selection. Euphytica 161:401–411
Salehi M, Izadpanah K, Siampour M, Bagheri A, Faghihi SM (2007) Transmission of ‘Candidatus phytoplasma aurantifolia’ to Bakraee (Citrus reticulata Hybrid) by Feral Hishimonus phycitis leafhoppers in Iran. Plant Dis 91:466
Schneider B, Seemuller E, Smart CD, Kirkpatrick BC (1995) Phylogenetic classification of plant pathogenic mycoplasmalike organisms or phytoplasmas. In: Raszin S, Tully JG (eds) Molecular and diagnostic procedures in mycoplasmology, vol 2. Academic Press, New York, pp 369–380
Stoddart JA, Taylor JF (1988) Genotypic diversity: estimation and prediction in samples. Genetics 118:705–711
Strange RN, Scott PR (2005) Plant disease: a threat to global food security. Annu Rev Phytopathol 43:83–116
Vose P, Hogers R, Bleeker M, Reijans M, van de Lee T, Hornes M, Frijters A, Pot J, Peleman J, Kuiper M, Zabeau M (1995) AFLP: a new technique for DNA fingerprinting. Nucleic Acids Res 23:4407–4414
Waller JM, Bridge J (1978) Plant diseases and nematodes in the Sultanate of Oman. Proc Am Nat Sci 24:313–326
Yang Y, Pan Y, Gong X, Fan M (2010) Genetic variation in the endangered Rutaceae species Citrus hongheensis based on ISSR fingerprinting. Genet Resour Crop Evol 57:1239–1248
Yeh RC, Boyle TJB (1997) Population genetic analysis of co-dominant and dominant markers and quantitative traits. Belg J Bot 129:157
Yong L, De-Chung L, Bo W, Zhong-Hai S (2006) Genetic diversity of pummelo (Citrus grandis Osbeck) and its relatives based on simple sequence repeat markers. Chin J Agric Biotechnol 3:119–126
Acknowledgments
Authors would like to acknowledge Prof. Claudine Carvalho (Brazil) and Prof. Mumtaz Khan (Pakistan) for providing the acid lime sample. Thanks are due to lime growers for their help in sample collections and to research assistants and Issa Al-Mahmooli for help in technical work. We acknowledge Sultan Qaboos University for funding this study through the Strategic Research Project: Rejuvenating lime production in Oman: resolving current challenges (SR/AGR/CROP/08/01).
Author information
Authors and Affiliations
Corresponding author
Rights and permissions
About this article
Cite this article
Al-Sadi, A.M., Al-Moqbali, H.S., Al-Yahyai, R.A. et al. AFLP data suggest a potential role for the low genetic diversity of acid lime (Citrus aurantifolia Swingle) in Oman in the outbreak of witches’ broom disease of lime. Euphytica 188, 285–297 (2012). https://doi.org/10.1007/s10681-012-0728-7
Received:
Accepted:
Published:
Issue Date:
DOI: https://doi.org/10.1007/s10681-012-0728-7