Identification of a walnut (Juglans regia L.) germplasm collection and evaluation of their genetic variability by microsatellite markers

L. Ruiz-Garcia, G. Lopez-Ortega, A. Fuentes Denia, D. Frutos Tomas

Abstract


The characterization and evaluation of walnut (Juglans regia) germplasm constitute important aspects of taxonomic analysis and are valuable tools for breeding programs. In this work, a collection of 57 common walnut cultivars, mainly coming from Spain and the USA, has been studied with microsatellite markers. To carry out this work, 32 primer pairs flanking simple sequence repeats previously developed in Juglans nigra were screened to select the loci that presented high polymorphism and that were easier to score. The 19 selected microsatellite markers allowed the discrimination of the studied cultivars, with a total of 97 alleles detected and an average of 5 alleles per locus, confirming that these markers are more suitable tools for walnut identification than other molecular markers studied previously. The genetic similarity estimated from the molecular data clearly separated the Spanish walnuts from the Californian genotypes. Allelic data are presented for use as size standards to assist in correcting laboratory-tolaboratory variation of allele size calling. Some of them are compared with previous results published and the discrepancies found are discussed.


Keywords


cultivar discrimination; genetic relationships; molecular characterization; plant breeding; polymorphism

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References


Andreakis N., Piccirillo P., Santangelo I., Di Vaio C., Monti Sabia L., 2002. Diversitâ molecolare di biotipi di noce provenienti da semenzali e innesti Della cv. 'Sorrento'. Riv Frutticolt Ortofloricolt 64, 71-79. [In Italian].

Arulsekar S., Mcgranahan G.H., Parfitt D.E., 1986. Inheritance of phosphoglucomutase and esterase isozymes in Persian walnut. J Hered 77, 220-221.

Bai W.N., Liao W.J., Zhang D.Y., 2010. Nuclear and chloroplast DNA phylogeography reveal two refuge areas with asymmetrical gene flow in a temperate walnut tree from East Asia. New Phytologist 188, 892-901. http://dx.doi.org/10.1111/j.1469-8137.2010.03407.x PMid:20723077

Ballouche A., Damblon F., 1988. Nouvelles données palynologiques sur la végétation holocène du Maroc. Travaux de la section scientifique et technique. Inst Fr Pondichéry, Trav Sec Sci Tech 25, 83-90. [In French].

Bayazit S., Kazan K., Gülbitti S., Cevik V., Ayanoglu H., Ergül A., 2007. AFLP analysis of genetic diversity in low chill requiring walnut (Juglans regia L.) genotypes from Hatay, Turkey. Sci Hortic 111, 394-398. http://dx.doi.org/10.1016/j.scienta.2006.11.006

Beede R.H., Hasey J.K., 1998. History of the walnut in California. In: Walnut production manual (Ramos D.E., ed). Division of Agriculture and Natural Resources, University of California, Oakland, CA. pp. 8-15.

Berg L.S., 1937. Natural regions of the USSR (Translated by Titelbaum O.A.). MacMillan Co, NY, USA. 480 pp.

Bottema S., 1980. On the history of the walnut (Juglans regia L.) in shoutheastern Europe. Acta Bot Neerl 29, 343-349.

Bowcock A.M., Ruiz-Linares A., Tomfohrde J., Minch E., Kidd J.R., Cavalli-Sforza L.L., 1994. High resolution of human evolutionary trees with polymorphic microsatellites. Nature 368, 455-457. http://dx.doi.org/10.1038/368455a0 PMid:7510853

Browicz K., 1976. Juglandaceae. In: Flora iranica (Rechinger K.H., ed). Akademische, Druck-u Verlagsanstalt, Austria. Vol 121, pp. 1-5.

Brownstein M.J., Carpten J.D., Smith J.R., 1996. Modulation of nontemplated addition by Taq polymerase: primer modifications that facilitated genotyping. Biotech 20, 1004-1010.

Callen D.F., Thompson A.D., Shen Y., Phillips H.A., Richards R.I., Mulley J.C., 1993. Incidence and origin of «null» alleles in the (AC)n microsatellite markers. Am J Hum Genet 52, 922-927. PMid:8488841 PMCid:1682051

Carrión J.S., Sanchéz-Gómez P., 1992. Palinological data in support of the survival of walnut (Juglans regia L.) in the western Mediterranean area during last glacial times. J Biogeogr 19, 623-630. http://dx.doi.org/10.2307/2845705

Ciarmiello L.F., Piccirillo P., Pontecorvo G., De Luca A., Kafantaris I., Woodrow P., 2011. A PCR based SNPs marker for specific characterization of English walnut (Juglans regia L.) cultivars. Mol Biol Rep 38, 1237-1249. http://dx.doi.org/10.1007/s11033-010-0223-y PMid:20577817

Dangl G.S., Woeste K., Aradhya M.K., Koehmstedt A., Simon C., Potter D., Leslie C.A., Mcgranahan G., 2005. Characterization of 14 microsatellite markers for genetic analysis and cultivar identification of walnut. J Amer Soc Hort Sci 130, 348-354.

Don R.H., Cox P.T., Wainwrigth B.J., Baker K., Mattick J.S., 1991. Touchdown PCR to circumvent spurious priming during gene amplification. Nucl Acids Res 19, 4008. http://dx.doi.org/10.1093/nar/19.14.4008 PMid:1861999 PMCid:328507

Fjellstrom R.G., Parfitt D.E., Mcgranahan G.H., 1994. Genetic relationship and characterization of Persian walnut (Juglans regia L.) cultivars using restriction fragment length polymorphisms (RFLPs). J Amer Soc Hort Sci 119, 833-839.

Foroni I., Rao R., Woeste K., Gallitelli M., 2005. Characterization of Juglans regia L. with SSR markers and evaluation of genetic relationships among cultivars and the 'Sorrento' landrace. J Hort Sci Biotech 80, 49-53.

Foroni I., Woeste K., Monti L.M., Rao R., 2006. Identification of 'Sorrento'walnut using simple sequence repeats (SSRs). Genet Resour Crop Evol 54, 1081-1094. http://dx.doi.org/10.1007/s10722-006-9187-0

Frutos D., 2000. Temperate fruit crops in warm climates. In: Walnuts (Juglans regia L.) in the Mediterranean warm climates (Erez A., ed). Kluwer Acad. Publ, The Netherlands. pp. 405-427.

Gunn B.F., Aradhya M., Salick J.M., Miller A.J., Yongping Y., Lin L., Xian H., 2010. Genetic variation in walnuts (Juglans regia and J. sigillata; Juglandaceae): species distinctions, human impacts, and the conservation of agrobiodiversity in Yunnan, China1. Am J Bot 97, 660-671. http://dx.doi.org/10.3732/ajb.0900114 PMid:21622428

Gupta P.K., Balyan H.S., Sharma P.C., Ramesh B., 1996. Microsatellites in plants: a new class of molecular markers. Curr Sci 70, 45-54.

Kafkas S., Ozkan H., Sutyemez M., 2005. DNA polymorphism and assessment of genetic relationships in walnut genotypes based on AFLP and SAMPL markers. J Amer Soc Hort Sci 130, 585-590.

Kalinowski S.T., Taper M.L., Marshall T.C., 2007. Revising how the computer program CERVUS accommodates genotyping error increases success in paternity assignment. Mol Ecol 16, 1099-1006. http://dx.doi.org/10.1111/j.1365-294X.2007.03089.x PMid:17305863

Kloosterman A.D., Budowle B., Daselaar P., 1993. PCR-amplification and detection of the human DIS80 VNTR locus. Amplification conditions, population genetics and application in forensic analysis. Intl J Legal Med 105, 257-264. http://dx.doi.org/10.1007/BF01370382 PMid:8471543

Kumar S., Tamura K., Nei M., 1994. MEGA: molecular evolutionary genetics analysis software for microcomputers. Comput Appl Biosci 10, 189-191. PMid:8019868

Langella O., 1999. CNRS UPR9034 Populations. 1228 pp. Available in http://www.cnrs.gif.fr/pge. [12/5/2002].

McGranahan G., Leslie C., 1990. Walnuts (Juglans). Genetic resources of temperate fruit and nut crops (Moore J.N., Ballington J.R., eds). Int Soc Hortic Sci, Wageningen. The Netherlands. 907 pp.

McGranahan G., Leslie C., 2009. Breeding walnuts (Juglans Regia). In: Breeding plantation tree crops: temperate species (Jain S.M., Priyadarshan P.M., eds). Springer NY. pp. 254-294. http://dx.doi.org/10.1007/978-0-387-71203-1_8

Nekrassowa V.L., 1927. The genus Juglans in Turkestan. Bull Appl Bot Plant Breed 18, 303-360.

Nicese F.P., Hormaza J.I., Mcgranahan G.H., 1998. Molecular characterization and genetic relatedness among walnut (Juglans regia L.) genotypes based on RAPD markers. Euphytica 101, 199-206. http://dx.doi.org/10.1023/A:1018390120142

Ninot A., Aletà N., 2003. Identification and genetic relationship of Persian walnut genotypes using isozyme markers. J Am Pomol Soc 57, 106-114.

Peakall R., Smouse P.E., 2006. GENALEX 6: genetic analysis in Excel. Population genetic software for teaching and research. Mol Ecol Notes. 6, 288-295. Available in http://www.anu.edu.au/BoZo/GenAlEx/ [25/8/2010]. http://dx.doi.org/10.1111/j.1471-8286.2005.01155.x

Pollegioni P., Woeste K., Mugnozza G.S., Malvolti M.E., 2009. Retrospective identification of hybridogenic walnut plants by SSR fingerprinting and parentage analysis. Mol Breed 24, 321-335. http://dx.doi.org/10.1007/s11032-009-9294-7

Potter D., Fangyou G., Aiello G., Leslie G., Mcgranahan G., 2002. Intersimple sequences repeat markers for fingerprinting and determining genetic relationships of walnut (Juglans regia) cultivars. J Amer Soc Hort Sci 127, 75-81.

Rice W.R., 1989. Analyzing tables of statistical tests. Evol 43, 223-225. http://dx.doi.org/10.2307/2409177

Robichaud R.L., Glaubitz J.C., Rhodes O.E., Woeste K., 2006. A robust set of black walnut microsatellites for parentage and clonal identification. New Forest 32, 179-196. http://dx.doi.org/10.1007/s11056-005-5961-7

Sánchez-Goñi M.F., 1988. A propos de la présence du pollen de Castanea et de Juglans dans les sédiments archéologiques würmiens anciens du Pays Basque espagnol. Inst Fr Pondichéry, Trav Sec Sci Tech 25, 73-82. [In French].

Solar A., Smole J., Stampar F., Virscekmarn M., 1994. Characterization of isozyme variation in walnut (Juglans regia L.). Euphytica 77, 105-112. http://dx.doi.org/10.1007/BF02551471

Stirling D., 2003. Multiplex amplification refractory mutation system for the 20 detection of prothrombotic polymorphisms. In: PCR protocols (Bartlett J.M.S., Stirling D., eds). Humana, New Jersey. Vol 226, pp. 323-325. http://dx.doi.org/10.1385/1-59259-384-4:323 PMid:12958516

This P., Jung A., Boccacci P., Borrego J., Botta R., 2004. Development of a standard set of micro satellite reference alleles for identification of grape cultivars. Theor Appl Genet 109, 1448-1458. http://dx.doi.org/10.1007/s00122-004-1760-3 PMid:15565426

Tulecke W., Mcgranahan G.H., 1994. The walnut germplasm collection at the University of California, Davis: a description of the collections and a history of the breeding program of Eugene F. Serr and Harold I. Forde. Rpt 13. Univ Calif Genet Resour Conserv Program, Davis

Van Den Brinks M., Janssen C.R., 1985. The effect of human activities during cultural phases on the development of montane vegetation in the Serra da Estrela, Portugal. Revue Paleobot Palynol 44, 193-215. http://dx.doi.org/10.1016/0034-6667(85)90016-8

Victory E., Glaubitz J., Rhodes O.E., Woeste K., 2006. Genetic homogeneity in Juglans nigra (Juglandaceae) at nuclear microsatellites. Am J Bot 93, 118-126. http://dx.doi.org/10.3732/ajb.93.1.118

Vyas D., Sharma S.K., Sharma D.R., 2003. Genetic structure of walnut genotypes using leaf isozymes as variability measure. Sci Hort 97, 141-152. http://dx.doi.org/10.1016/S0304-4238(02)00129-2

Wang H., Pei D., Gu R.S., Wang B.Q., 2008. Genetic diversity and structure of walnut populations in central and Southwestern China revealed by microsatellite markers. J Amer Soc Hort Sci 133, 197-203.

Warburton M.L., Bliss F.A., 1996. Genetic diversity in peach (Prunus persica L. Batch) revealed by randomly amplified polymorphic DNA (RAPD) markers and compared to inbreeding coefficients. J Amer Soc Hort Sci 121, 1012-1019.

Woeste K., Burns R., Rhodes O., Michler C., 2002. Thirty polymorphic nuclear microsatellite loci from black walnut. J Hered 93, 58-60. http://dx.doi.org/10.1093/jhered/93.1.58 PMid:12011179

Wright S., 1950. Genetical structure of populations. Nature 166, 247-249. http://dx.doi.org/10.1038/166247a0 PMid:15439261

Zohary D., 1970. Centers of diversity and centers of origin. In: Genetic resources in plants (Frankel O.H., Bennett E., eds). Blackwell. Oxford, UK. pp. 33-42.

Zohary D., Hopf M., 1988. Domestication of plants in the Old World. Clarendon Press, Oxford, UK. 249 pp




DOI: 10.5424/sjar/20110901-227-10