Analysis of the Genetic Diversity in Citrus (Citrus spp.) Species Using SSR Markers

Document Type : Research Paper

Abstract

Abstract
Determination of genetic diversity level is important in clarifying genetic relationships, characterizing germplasm and the registration of new cultivars. In this study, genetic variation among 56 accessions (G1~G56) of Citrus including several undefined local or native genotypes and some known varieties in Jiroft, Kerman province, Iran was investigated using SSR markers. In total, 12 SSR primers produced 54 alleles. The lowest number of alleles was observed on cAGG9 locus with 2 alleles and the highest number of alleles was observed in TAA41 locus with 8 alleles. Polymorphic Information Content (PIC) varied from 0.19 to 0.37 with mean of 0.28. The percentage of heterozygosity per marker detected in our samples ranged from 25% to 96% with an average of 67%. Grouping of the accessions using Jaccard similarity coefficient and based on the Neighbor-Joining method assigned the 56 accessions into four major clusters. The SSR data indicated a high relationship between G2 and G41 (unknown natural types) with grapefruits (Citrus paradisi) (G50 and G51), G17 (unknown natural type) with orange (C. sinensis) (G56) and G40 (unknown natural type) with pummelo (C. grandis) (G49). Unidentified genotype G43 in a single-accession cluster didn’t show any close molecular similarity to control samples [mandarin (C. reticulata), pummelo, sweet orange, sour orange (C. aurantium), etc.]. Mandarin, pummelo and citron (C. medica) were clustered into three particular groups as major species of Citrus. Also, our results demonstrated that SSR markers can be useful in evaluating citrus genetic diversity and in classifying accessions to phylogenetic groups based on their genetic similarity values.
 

Keywords

References

Arumuganathan K and Earle ED, 1991. Nuclear DNA content of some important plant species. Plant Mol Biol Rep 9: 208–218.
Barkley NA, Roose ML, Krueger RR and Federici CT, 2006. Assessing genetic diversity and population structure in a Citrus germplasm collection utilizing simple sequence repeat markers (SSRs). Theor Appl Genet 112: 1519-1531.
Barret HC and Rhodes AM, 1976. A numerical taxonomic study affinity relationships in cultivated Citrus and its close relatives. Syst Botany 1: 105-136.
Breto MP, Ruiz C, Pina JA and Asins MJ, 2001. The diversification of Citrus clementina. Hort. Ex Tan., a vegetatively propagated crop species. Mol Phyl and Evol  21: 285–293.
Corazza-Nunes MJC, Machado MA, Nunes WMC, Cristofani M and Targon MLPN, 2002. Assessment of genetic variability in grapefruits (Citrus paradisi Macf.) and pummelos (C. maxima (Burn.) Merr.) using RAPD and SSR markers. Euphytica 126: 169-176.
Fang DQ and Roose ML, 1997. Identification of closely related Citrus cultivars with inter-simple sequence repeat markers. Theor Appl Genet 95: 408–417.
FAO. 2010. Citrus Fruit, Fresh and Processed. Annual Statistics. CCP: CI/ST/2007/. FAO Commodities and Trade Division. Food and Agriculture Organization of the United Nations, Rome, Italy.
Federici CT, Fang DQ, Scora RW and Roose ML, 1998. Phylogenetic relationships within the genus Citrus (Rutaceae) and related genera as revealed by RFLP and RAPD analysis. Theor Appl Genet 94: 812–822.
Filho HDC, Machado MA, Targon MLPN, Moreira MCPQDG and Pompeu J, 1998. Analysis of the genetic diversity among mandarins (Citrus spp.) using RAPD markers. Euphytica 102: 133-139.
Golein B and Adouli B, 2011. Citrus. Novin Poya Press, Tehran, Iran (In Farsi).
Golein B, Bigonah M, Azadvar M and Golmohammadi M, 2012. Analysis of genetic relationship between ‛Bakraee’ (Citrus sp.) and some known Citrus genotypes through SSR and PCR-RFLP markers. Sci Hort 148:147-153.
Graham J, Mc Nicole RJ and Mc Nicole JW, 1996. A comparison of methods for the estimation of genetic diversity in strawberry cultivars. Theor Appl Genet 93: 402-406.
Green RM, Vardi A and Galun E, 1986. The plastome of Citrus: physical map, variation among Citrus cultivars and species and comparison with related genera. Theor Appl Genet 72: 170–177.
Gulsen O and Roose ML, 2001. Lemons: diversity and relationships with selected citrus genotypes as measured with nuclear genome markers. J Am Soc Hort Sci 126: 309–317.
Hokanson SC, Szewe-McFadden AK, Lamboy WF and McFerson JR, 1998. Microsatellites (SSR) markers reveal genetic identification, genetic diversity and relationship in Malus domestica Borkh, Core subset collection. Theor Appl Genet 97: 671-683.
Iwamasa M, Nito N and Ling JT, 1988. Intra and inter generic hybridization in the orange subfamily Aurantioideae. Proc Int Soc Citricult 1: 123-130.
Moore GA, 2001. Oranges and lemons: clues to the taxonomy of Citrus from molecular markers. Trends Genet 17: 536–540.
Murray MG and Thompson WF, 1980. Rapid isolation of high molecular weight plant DNA. Nucleic Acids Res 8: 4321-4325.
Naghavi MR, Ghariazi B and Hossini salekdeh G, 2005. Molecular Markers. Tehran University Press (In Farsi).
Nicolosi E, Deng Z, Gentile A, LaMalfa S, Continella G and Tribulato E, 2000. Citrus phylogeny and genetic origin of important species as investigated by molecular markers. Theor Appl Genet 100: 1155-1166.
Novelli VM, Cristofani M, Souza AA, Marcos A and Machado MA, 2006. Development and characterization of polymorphic microsatellite markers for the sweet orange (Citrus sinensis L. Osbeck). Genet Mol Biol 29: 90-96.
Pang X, Hu C and Deng X, 2003. Phylogenetic relationships among Citrus and its relatives as revealed by SSR markers. Acta Genetica Sinica 30:81-87.
Pejic I, Ajmone-Marsan P, Morgante M, Kozumplik V, Castiglioni P, Taramino G and Motto M, 1998. Comparative analysis of genetic similarity among maize inbred lines detected by RFLPs, RAPDs, SSRs, and AFLPs. Theor Appl Genet 97: 1248–1255.
Rouhi Ghorabaie HR, Fotouhi Ghazvini R, Golein B and Nabipour AR, 2010. Identification of some Citrus accessions in a Citrus germplasm utilizing simple sequence repeat markers (SSRs). Hort Environ Biotechnol 51: 343-347.
Scora RW, 1975. On the history and origin of Citrus. Bull Torr Bot Club 102: 369–375.
Scora RW, 1988. Biochemistry, taxonomy and evolution of modern cultivated Citrus. Proc Int Soc Citricult 1: 277-289.
Shahsavar AR, Izadpanah K, Tafazoli E and Sayed Tabatabaei BE. 2007. Characterization of Citrus germplasm including unknown variants by inter-simple sequence repeat (ISSR) markers. Sci Hort 112: 310-314.
Swingle WT and Reece PC, 1967. The botany of citrus and its wild relatives in the orange subfamily. Pp. 190-430. In: Reuther W, Webber HJ and Batchelor LD (Eds.). The Citrus Industry. University of California Press, Berkeley.
Torres AM, Soost RK and Mau-Lastovicka, T, 1982. Citrus isosymes: genetics and distinguishing nucellar from zegotic seedlings. J Hered 73: 335-339.
Van Berloo R, 1999. GGT: software for the display of graphical genotypes. J Hered 90: 328-329.
Webber HJ, 1943. Cultivated varieties of Citrus. Pp. 475-642. In: Webber HJ and Batchelor LD (Eds.), The Citrus Industry. University of California Press, Berkeley.
Weising K, Nybom H, Wolff  K and Kahl G, 2005. DNA Fingerprinting in Plants: Principles, Methods and Applications, 2nd ed. Taylor and Francis Group, Boca Raton, Florida.
Xu Q, Chen LL, Ruan X, Chen D, Zhu A, Chen C, Bertrand D, Jiao WB, Hao BH, Lyon MP, Chen J, Gao S, Xing F, Lan H, Chang JW, Ge X, Lei Y, Hu Q, Miao Y, Wang L, Xiao S, Biswas MK, Zeng W, Guo F, Cao H, Yang X, Xu XW, Cheng YJ, Xu J, Liu JH, Luo O, Tang Z, Guo WW, Kuang H, Zhang HY, Roose MR, Nagarajan N, Deng XX and Ruan Y, 2013. The draft genome of sweet orange (Citrus sinensis). Nature Genet 45: 59-68
Yamamoto M, Kobayashi S, Nakamura Y and Yamada Y, 1993. Phylogenic relationships of Citrus revealed by diversity of cytoplasmic genomes. Pp. 39-46. In: Hayashi T, Omura M and Scott NS (Eds). Techniques on gene diagnosis and breeding in fruit trees. Fruit Trees Research Station Press, Okitsu.
Zane L, Bargelloni L and Patarnello T, 2002. Strategies for microsatellite isolation: A review. Mol Ecol 11:1-16.
Journal of Plant Physiology and Breeding
Volume 3, Issue 2 - Serial Number 2
December 2013
Pages 41-49

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