Genetic Structure and Diversity Among Radish Varieties As Inferred from AFLP and ISSR Analyses Jasmina Muminović, Andrea Merz, and Albrecht E
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J. AMER. SOC. HORT. SCI. 130(1):79–87. 2005. Genetic Structure and Diversity among Radish Varieties as Inferred from AFLP and ISSR Analyses Jasmina Muminović, Andrea Merz, and Albrecht E. Melchinger University of Hohenheim, Institute of Plant Breeding, Seed Science, and Population Genetics, 70593 Stuttgart-Hohenheim, Germany Thomas Lübberstedt1 Danish Institute of Agricultural Sciences, 4200 Slagelse, Denmark ADDITIONAL INDEX WORDS. cluster analysis, genetic similarity, genetic structure, principal coordinate analysis, Raphanus sativus ABSTRACT. Twelve amplifi ed fragment length polymorphism (AFLP) primer combinations and 10 inter-simple sequence repeat (ISSR) primers were applied to estimate genetic diversity among 68 varieties of cultivated radish (Raphanus sativus L.). The material consisted of open-pollinated varieties, inbred lines, diploid and a few tetraploid hybrid vari- eties of garden radish [R. sativus var. sativus DC. convar. radicula (DC.) Alef.] and black radish [R. sativus var. niger (Mill.) Pers.]. Two accessions of uncultivated relatives of radish that as weeds cause serious contamination during the process of hybrid radish production were added to the analyses. Polymorphic fragments were scored for calculation of Jaccardʼs coeffi cient of genetic similarity (GS). Substantial level of genetic variability (average AFLP-based GS = 0.70; average ISSR-based GS = 0.61) was detected in the available germplasm of cultivated radish. Cluster analyses separated two weedy species from the cultivated germplasm. Within cultivated material, black radish and french breakfast radish types formed separate clusters. Based on AFLP data, a principal coordinate analysis (PCoA) and model-based approach revealed the genetic structure within cultivated radish germplasm and indicated the existence of divergent pools. Although the model-based approach did not separate black radish from french breakfast radish varieties, it offered a clear sub-division within garden radish germplasm. The results of this study may be relevant for hybrid radish breeding. Radish is an important commercial vegetable, consumed varieties in Germany are F1 hybrids, which indicates a signifi cant worldwide. It is an ancient domesticate, initially cultivated in increase during the period of last 15 years (Bundessortenamt, China and Korea (Kaneko and Matsuzawa, 1993). The fi rst 1986, 2001). Most breeding work is aimed at further adaptation European variety of cultivated radish was recorded in the 16th to different growing conditions, improved resistance to pests century (George and Evans, 1981; Wein, 1964). Based on the [Peronospora parasitica Tul. and Albugo candida (Pers.) Kuntze], latest available information, the production of radish in Europe and improved marketing conditions (Vogel, 1996). Specifi c market amounts to 120 000 t (Vogel, 1996). preferences strongly infl uence the selection of morphological Taxonomy classifi es radish within the family Brassicaceae traits of root considered in the breeding process of radish (A. into the section Raphanis DC. (Kaneko and Matsuzawa, 1993). Schieder, personal communication). Thus, garden radish is bred Of six species in the section, only garden radish and black radish for round, light-red colored roots, french breakfast radish type are cultivated and commonly grown for their thickened fl eshy has a unique oblong red root shading to white at the tip, whereas hypocotyle and the upper part of the root. They cross freely and giant radish type possesses a stronger, red-fl eshed root, wider in easily with related species, such as chinese small radish (Raphanus diameter and not prone to sponginess and glassiness. sativus var. sativus convar. sinensis Saz.) and R. raphanistrum Advanced practices in breeding major crops have demonstrated L. Radish is open-pollinated, self-incompatible, diploid species the superiority of inter-group over intra-group hybrids. For the with a chromosome number 2n = 18, small genome size, and optimum exploitation of heterosis, the parental lines should be DNA amount in the unreplicated gametic nucleus (referred to derived from genetically unrelated germplasm pools, commonly as C-value) ranging from 0.55 to 1.45 pg (Dolezel et al., 1992; referred to as heterotic groups (Melchinger and Gumber, 1998). Olszewska and Osiecka, 1983). Only few studies have so far been conducted to estimate phe- Radish breeding was practiced for centuries, by means of mass notypic (George and Evans, 1981) or genetic diversity of radish or pedigree selection. In the past two decades, the production of varieties (Demeke et al., 1992; Ellstrand and Marshall, 1985; F1 hybrids using cytoplasmatic male sterility has widely replaced Huh and Ohnishi, 2003; Rabbani et al., 1998; Thormann et al., simple breeding methods based on morphological traits (Banga, 1994). None of the currently available studies has focused on a 1976). Uniformity of varieties is becoming a high priority goal wider set of European radish varieties. Molecular markers, such in radish breeding. Over a third (35%) of currently grown radish as AFLP (Vos et al., 1995) and ISSR (Zietkiewitcz et al., 1994), were already successfully applied in genetic diversity analyses in various crops (Bohn et al., 1999; Simioniuc et al., 2002; Zhu et al., Received for publication 28 Apr. 2004. Accepted for publication 4 Aug. 2004. The 1998), and confi rmed the classifi cation of germplasm into known authors thank Andrea Schieder (radish breeder at the breeding company Juliwa- Enza) and the breeding company Nunhems for their generous cooperation in the heterotic groups (Lübberstedt et al., 2000; Pejic et al., 1998). study. The study was funded by the Bundesministerium für Verbraucherschutz, Our objectives were to establish the AFLP and ISSR protocols Ernährung und Landwirtschaft (BMVEL) and the Gemeinschaft zur Förderung for radish, and apply them to 1) investigate the genetic diversity der privaten deutschen Pfl anzenzüchtung e.V. (GFP), Germany. of a set of radish varieties that have currently been commercially 1To whom reprint requests should be addressed. E-mail address: Thomas. [email protected] produced in Europe, and 2) identify possible heterotic pools within J. AMER. SOC. HORT. SCI. 130(1):79–87. 2005. 79 JJanBookanBook 1.indb1.indb 7979 112/22/042/22/04 33:59:30:59:30 PPMM available cultivated radish germplasm. Furthermore, a method for check—an accession sown twice under coded numbers, and 2) an early detection of weed (chinese small radish and R. raphanis- laboratory duplicate—a randomly chosen accession duplicated trum) in cultivated radish can be derived from our study. after DNA extraction and re-duplicated in consecutive steps of the analyses. Materials and Methods Plants were grown either in the open fi eld or greenhouse, depending on their preferred growing conditions. Distinctive PLANT MATERIALS AND DNA EXTRACTION. Sixty-eight acces- morphological traits for giant radish, black radish, and french sions of cultivated radish grown in Europe were chosen for the breakfast radish were estimated according to the standard criteria study. The materials consisted of inbred lines, diploid and tet- of the International Union for the Protection of New Varieties raploid hybrid varieties, and open-pollinated varieties of garden of Plants (UPOV). radish and black radish. One accession of chinese small radish From a bulk of 20–30 plants per accession, 2–3 g of fresh and one accession of R. raphanistrum were added to the study leaf material were frozen in liquid nitrogen and ground to a fi ne (Table 1). Two control types were included to test the reliability powder. The extraction of genomic DNA was done following the and reproducibility of the AFLP and ISSR protocols: 1) blind modifi ed CTAB procedure (Hoisington et al., 1994). Table 1. Varieties of garden radish and black radishz, as well as the accessions of wild relatives of radish analyzed with amplifi ed fragment length polymorphism and inter-simple sequence repeat molecular markers. Variety Genetic Production Breeding Variety Genetic Production Breeding name (or code) constitutiony typex companyw name (or code) constitutiony typex companyw JW 6 Inbred line OF JE Duroz 4n Chr JW 9 Inbred line OF JE Fanal 4n N JW 14 Inbred line OF JE Cherry Belle OP NZ z z April Cross F1 hybrid JE Eiszapfen OP JE Cheriette F1 hybrid SS Eterna OP JE Content F1 hybrid UG EZ Falco OP OF JE Donar F1 hybrid UG Syn Flair OP UG/OF RZ Favorella F1 hybrid UG NZ Flamboyant OP JE z Florent F1 hybrid UG EZ Hilds Blauer Herbst OP N Fluo F1 hybrid Vil Hilmar OP UG N Hyronda F1 hybrid JE JW 30 OP JE Isar F1 hybrid OF Syn JW 31 OP JE JW 16 F1 hybrid OF JE Karissima OP UG N JW 17 F1 hybrid OF JE Marabelle OP OF/UG NZ JW 18 F1 hybrid OF JE Neckarperle OP OF N z JW 19 F1 hybrid OF JE Neckarruhm rot OP N z JW 20 F1 hybrid OF JE Neckarruhm weiss OP N Masterred F1 hybrid OF Sem Nelson OP GG Novella F1 hybrid UG NZ Parat OP JE Picard F1 hybrid OF RZ Patricia OP N Printo F1 hybrid OF NZ Raxe OP N Radius F1 hybrid UG EZ Red Silk OP HM Rondar F1 hybrid OF/UG Syn Ribella OP OF NZ R3 F1 hybrid OF JE Riesenbutter OP JE R6 F1 hybrid OF JE Rondeel OP RZ R16 F1 hybrid OF JE Rota OP RZ R49 F1 hybrid UG N Rudi OP OF JE z R50 F1 hybrid UG N Runder Schwarzer Winter OP N R51 F1 hybrid UG N Saxa – Rafi ne OP OF RZ Sunto F1 hybrid OF NZ Silva OP OF JE Tarzan F1 hybrid UG EZ Sirri OP OF RZ Trespa F1 hybrid UG EZ Sora OP N Vitella F1 hybrid UG NZ Topsi OP UG/OF N Wernar F1 hybrid OF Syn Chinese small radish (wild species) weed --- Boy 4n N R. raphanistrum (wild species) weed --- zBlack radish varieties. y4n and OP designate tetraploid variety and open-pollinated variety, respectively. xOF designates production in the open fi eld; UG designates the production under glass.