SciELO - Scientific Electronic Library Online

 
vol.74 número3Identification and validation of novel EST-SSR markers in olivesSimulation of soil organic carbon changes in Vertisols under conservation tillage using the RothC model índice de autoresíndice de assuntospesquisa de artigos
Home Pagelista alfabética de periódicos  

Serviços Personalizados

Journal

Artigo

Indicadores

Links relacionados

Compartilhar


Scientia Agricola

versão impressa ISSN 0103-9016versão On-line ISSN 1678-992X

Sci. agric. (Piracicaba, Braz.) vol.74 no.3 Piracicaba mai./jun. 2017

http://dx.doi.org/10.1590/1678-992x-2016-0046 

Genetics and Plant Breeding

The genetic diversity among strawberry breeding resources based on SSRs

Soohwan Lim1 

Jeongyeo Lee1 

Hyun Joo Lee1 

Kun-Hyang Park1 

Dae-Soo Kim1 

Sung Ran Min1 

Won Seok Jang2 

Tae II Kim2 

HyeRan Kim1  3  * 

1Korea Research Institute of Bioscience and Biotechnology, 125 Gwahangno, Yuseong-gu - Daejeon – 305-806 - Republic of Korea

2Nonsan Strawberry Experiment Station/Chungcheong Nam- Do Agricultural Research and Extension Services - Nonsan - Chungnam – 320-862 - Republic of Korea

3University of Science and Technology/Systems and Bioengineering, 217 Gajeong-ro - Daejeon – 34113 - Republic of Korea

ABSTRACT:

Cultivated strawberry (Fragaria × ananassa Duch.) is a high value horticultural crop. In this study, the genetic diversity of 160 strawberry accessions was determined using five highly polymorphic simple sequence repeat (SSR) markers. Sixty different alleles were identified, with allele frequencies in the range of 0.006 to1. Similarity scores were in the range of 0.034 to 0.963 (average: 0.507). The accessions were categorized into five groups. Group 1 contained two diploid Fragaria vesca species and one unknown accession. Group 2 contained one accession (F x ananassa). Group 3 contained 20 F × ananassa accessions and six unknown accessions. Group 4 contained 48 F. × ananassa accessions, one octaploid Fragaria chiloensis species, and six unknown accessions while Group 5 contained 69 F. × ananassa accessions and six unknown accessions. Accessions within a pedigree were frequently grouped together. A total of 30 novel accessions were categorized alongside existing accessions. These results will allow breeders to develop strategies which incorporate more genetic diversity into new cultivars.

Keywords: Fragaria × ananassa; simple sequence repeat; cultivar identification

Introduction

Cultivated strawberry (Fragaria × ananassa Duch.) is an octoploid (2n = 8x = 56) generated by natural hybridization between two octoploid strawberry species, F. chiloensis and F. virginiana (Hancock et al., 2010). To date, 23 strawberry species have been reported, with various ploidy levels from diploid to decaploid (Nathewet et al., 2010; Rousseau-Gueutin et al., 2009).

Numerous strawberry breeding programs have been developed to generate new cultivars with improved taste and flavor or extended harvest period and shelf life (Capocasa et al., 2008; Faedi et al., 2000). Breeding success is associated with accessibility to breeding resources and genetic variations. Consequently, information regarding the genetic diversity and population structure of breeding resources is important for efficient development of new cultivars. Traditionally, the identification of strawberry cultivars was determined by the examination of differences in morphological or physiological characteristics such as leaf, flower, fruit parameters, and flowering habit (Dale, 1996; Nielsen and Lovell, 2000). However, such methods are unsuitable for cultivated strawberries as genetic and phenotypic variations between cultivars are minimal. As a consequence, DNA markers were developed to facilitate analysis of genetic diversity, linkage mapping, and identification of culti- vars (Chambers et al., 2013; Congiu et al., 2000; Degani et al., 2001; Garcia et al., 2002; Govan et al., 2008; Isobe et al., 2013; Kunihisa et al., 2003; Tyrka et al., 2002). SSR markers for strawberry were first developed using primer pairs that amplified characterized regions such as expressed sequence tags (ESTs) or genomic libraries, in contrast to other primer pairs that amplified anonymous DNA fragments (Ashley et al., 2003; Bassil et al., 2006; Gil-Ariza et al., 2006; James et al., 2003; Lewers et al., 2005; Monfort et al., 2006; Sargent et al., 2003). The completion of the genome sequence of diploid F. vesca (Shulaev et al., 2011) allowed robust SSRs to be developed and mapped on the Fragaria reference map (Rousseau-Gueutin et al., 2011; Sargent et al., 2011; Zorrilla-Fontanesi et al., 2011). In this study, we assessed the genetic diversity of 160 strawberry accessions used for breeding in Korea, including 34 newly collected accessions. The genotyping results will provide a molecular basis for future breeding programs and will facilitate the development of novel strawberry cultivars with increased genetic diversity.

Materials and Methods

Plant materials and DNA extraction

A total of 160 strawberry accessions (130 accessions from the Korea Rural Development Administration (RDA) Genebank Information Center, and 30 newly generated or collected accessions) were provided by the Nonsan Strawberry Experimental Station (Nonsan, Korea) (Table 1). Accessions were collected from Korea (26 accessions), Japan (46 accessions), the United States (45 accessions), Europe (13 accessions: four from the United Kingdom, three from the Netherlands, two each from Germany and Russia, and one each France and Spain), and other countries (nine accessions: three from each of Canada and Israel, two from China, and one from New Zealand). The countries of origin of 21 accessions were unknown. Genomic DNA was extracted from young leaves using a WizPrep Plant DNA Mini Kit (Wizbioso- lutions) according to the manufacturer's protocol. The final DNA concentration was adjusted to 10 ng per ul for use in a polymerase chain reaction (PCR).

Table 1 List of 160 strawberry accessions used in this study including accession name, origin, IT number, parentage, scientific name, and status. 

No. Name Origin IT numbera Parentage Scientific name Status
1 Busan No.1101* Korea, South IT 232440 Unknown Fragaria × ananassa subsp. ananassa Cultivar
2 Chodong* Korea, South IT 232442 Harunoka × Yachio Fragaria × ananassa subsp. ananassa Cultivar
3 Daehak1* Korea, South IT 232439 Unknown Fragaria × ananassa subsp. ananassa Cultivar
4 Daeun* Korea, South IT 232453 Akihime × Redpearl Fragaria × ananassa subsp. ananassa Cultivar
5 Daewangb, * Korea, South IT 245989 Maehyang × Wonkyo3111 Fragaria × ananassa subsp. ananassa Cultivar
6 Daewangb, * Korea, South IT 245989 Maehyang × Wonkyo3111 Fragaria × ananassa subsp. ananassa Cultivar
7 Dahong* Korea, South IT 232450 Sachinoka × Maehyang Fragaria × ananassa subsp. ananassa Cultivar
8 Danmi* Korea, South IT 245379 Maehyang × Amaou Fragaria × ananassa subsp. ananassa Cultivar
9 Geumhyang* Korea, South IT 232448 Akihime × Tochiotome Fragaria × ananassa subsp. ananassa Cultivar
10 Johong* Korea, South IT 232446 Nyoho × Akihime Fragaria × ananassa subsp. ananassa Cultivar
11 Maehyang* Korea, South IT 232445 Tochinomine × Akihime Fragaria × ananassa subsp. ananassa Cultivar
12 Manhyang* Korea, South IT 245381 Nyoho × Akanekko Fragaria × ananassa subsp. ananassa Cultivar
13 Mihong* Korea, South IT 232444 Toyonoka × Reiko Fragaria × ananassa subsp. ananassa Cultivar
14 NS970524* Korea, South IT 245343 Unknown Fragaria × ananassa subsp. ananassa Line
15 Okmae* Korea, South IT 245987 Toyonoka × Maehyang Fragaria × ananassa subsp. ananassa Cultivar
16 Seolhyang* Korea, South IT 232447 Akihime × Redpearl Fragaria × ananassa subsp. ananassa Cultivar
17 Suhong* Korea, South IT 232441 Hokowase × Harunoka Fragaria × ananassa subsp. ananassa Cultivar
18 Sulhong* Korea, South IT 232443 Suhong × Toyonoka Fragaria × ananassa subsp. ananassa Cultivar
19 Wildstrawberry1* Korea, South IT 245312 Unknown Fragaria × ananassa subsp. ananassa Wild
20 Wildstrawberry2* Korea, South IT 245335 Unknown Fragaria × ananassa subsp. ananassa Wild
21 Wonkyo3111* Korea, South IT 245867 Open pollinated of Benihoppe Fragaria × ananassa subsp. ananassa Line
22 Aiberry* Japan IT 232465 Unknown Fragaria × ananassa subsp. ananassa Cultivar
23 Aihime* Japan IT 232463 Unknown Fragaria × ananassa subsp. ananassa Cultivar
24 Akanekko* Japan IT 232473 Aiberry × Hokowase Fragaria × ananassa subsp. ananassa Cultivar
25 Akasyanomitsuko Japan IT 245334 Nyoho × Kunowase Fragaria × ananassa subsp. ananassa Cultivar
26 Akihime Japan IT 245292 Kunowase × Nyoho Fragaria × ananassa subsp. ananassa Cultivar
27 Alps Japan IT 245363 Unknown Fragaria × ananassa subsp. ananassa Cultivar
28 Amaou Japan IT 232483 Fukuoka S6 Fragaria × ananassa subsp. ananassa Cultivar
29 Aska Japan IT 232470 Unknown Fragaria × ananassa subsp. ananassa Cultivar
30 Asuka Wave Japan IT 232480 [Uzushio × {(Kurume Sokusei-3 × Hokowase) × (Donner × Hokowase)}] × [(Kurume Sokusei-3 × Hokowase) × {Donner × (Kobe-1 × Hokowase)}] Fragaria × ananassa subsp. ananassa Cultivar
31 Bbiaberry Japan IT 245362 Unknown Fragaria × ananassa subsp. ananassa Cultivar
32 Benihoppe Japan IT 232482 Akihime × Sachinoka Fragaria × ananassa subsp. ananassa Cultivar
33 Chiduru Japan IT 232457 [(Donner-s)-s × (Harunoka-s)-s]-s × Harunoka-s Fragaria × ananassa subsp. ananassa Cultivar
34 Terunoka Japan IT 232461 Hokowase × Donner Fragaria × ananassa subsp. ananassa Cultivar
35 Everberry Japan IT 245337 Oishi-Sikinary × Haruyoi Fragaria × ananassa subsp. ananassa Cultivar
36 Goryeong Japan IT 245328 Takane Haikara × Donner Fragaria × ananassa subsp. ananassa Cultivar
37 Guardian Japan IT 245289 NC-1768 [Fairpeake × (Aberdeen × Redheart)] × Tennessee Beauty × Surecrop Fragaria × ananassa subsp. ananassa Cultivar
38 Harunoka Japan IT 232456 Kurume103 × Donner Fragaria × ananassa subsp. ananassa Cultivar
39 Haruyoi Japan IT 232460 Hokowase × Harunoka Fragaria × ananassa subsp. ananassa Cultivar
40 Hongbok Japan IT 245311 Kohuku Fragaria × ananassa subsp. ananassa Cultivar
41 Houkouwasec Japan IT 232455 Kogyoku (Fairfax salf seedling) × Tahoe Fragaria × ananassa subsp. ananassa Cultivar
42 Houkouwasec Japan IT 232455 Kogyoku (Fairfax salf seedling) × Tahoe Fragaria × ananassa subsp. ananassa Cultivar
43 Jumbo Japan IT 232484 Unknown Fragaria × ananassa subsp. ananassa Cultivar
44 Jumbo Pure Berry Japan IT 232486 Unknown Fragaria × ananassa subsp. ananassa Cultivar
45 Kunowase Japan IT 245308 Unknown Fragaria × ananassa subsp. ananassa Cultivar
46 Kurume39 Japan IT 245327 Unknown Fragaria × ananassa subsp. ananassa Line
47 Kurume52 Japan IT 245332 Unknown Fragaria × ananassa subsp. ananassa Line
48 Myongbo Japan IT 245324 Meiho derived Fragaria × ananassa subsp. ananassa Cultivar
49 Nyoho Japan IT 232469 Kei210 × Reiko Fragaria × ananassa subsp. ananassa Cultivar
50 Pechikad Japan IT 245346 Unknown Fragaria × ananassa subsp. ananassa Cultivar
51 Pechikad Japan IT 245346 Unknown Fragaria × ananassa subsp. ananassa Cultivar
52 Red Pearl Japan IT 232475 Aiberry ×Toyonoka Fragaria × ananassa subsp. ananassa Cultivar
53 Regina Japan IT 245313 Amerikanischer Samling II (Geneva) × Deutsch Evern Fragaria × ananassa subsp. ananassa Cultivar
54 Reiko Japan IT 232468 Fukuba × Harunoka Fragaria × ananassa subsp. ananassa Cultivar
55 Reiyu Japan IT 232464 Unknown Fragaria × ananassa subsp. ananassa Cultivar
56 Rockyhara Japan IT 245329 Unknown Fragaria × ananassa subsp. ananassa Cultivar
57 Sachinoka Japan IT 232476 Toyonoka × Aiberry Fragaria × ananassa subsp. ananassa Cultivar
58 Sagahonoka Japan IT 232458 Unknown Fragaria × ananassa subsp. ananassa Cultivar
59 Shinyurbong Japan IT 245336 Unknown Fragaria × ananassa subsp. ananassa Cultivar
61 Sungkang17 Japan IT 245321 Morioka17 Fragaria × ananassa subsp. ananassa Line
62 Sungkang19 Japan IT 245322 Morioka19 Fragaria × ananassa subsp. ananassa Line
63 Syuko Japan IT 232477 Shizutakara × Haruyoi Fragaria × ananassa subsp. ananassa Cultivar
64 Tochinomine Japan IT 232479 (Florida69-266 × Reiko) × Nyoho Fragaria × ananassa subsp. ananassa Cultivar
65 Tochiotome Japan IT 232472 Kurume49 × Tochinomine Fragaria × ananassa subsp. ananassa Cultivar
66 Toyonoka Japan IT 232466 Himiko × Harunoka Fragaria × ananassa subsp. ananassa Cultivar
67 Wonyuk Japan IT 245325 Himiko derived Fragaria × ananassa subsp. ananassa Cultivar
68 Aiberry(ARS) United States IT 245365 Unknown Fragaria × ananassa subsp. ananassa Cultivar
69 Armore United States IT 232488 Blakemore × Aroma Fragaria × ananassa subsp. ananassa Cultivar
70 Berry Stare United States IT 232501 Unknown Fragaria × ananassa subsp. ananassa Cultivar
71 Berry Stare United States IT 232501 Unknown Fragaria × ananassa subsp. ananassa Cultivar
72 Blackmore United States IT 245298 Missionary × Howard 17 Fragaria × ananassa subsp. ananassa Cultivar
73 Camarosa United States IT 232510 Douglas × Cal 85.218-605 Fragaria × ananassa subsp. ananassa Cultivar
74 Cardinal United States IT 232487 Earlibelle × ARK 5063 Fragaria × ananassa subsp. ananassa Cultivar
75 Cascade United States IT 232503 Shasta × Northwest Fragaria × ananassa subsp. ananassa Cultivar
76 Catskill United States IT 232491 Unknown Fragaria × ananassa subsp. ananassa Cultivar
77 Columbia United States IT 232500 WA 157 × WA 175 Fragaria × ananassa subsp. ananassa Cultivar
78 Comet United States IT 232499 Earlibelle ×ARK 5063 Fragaria × ananassa subsp. ananassa Cultivar
79 Cyclone United States IT 232492 Unknown Fragaria × ananassa subsp. ananassa Cultivar
80 Dabreak United States IT 245299 Headliner × {Klonmore × [L-117-1-45-3 × (Suwannee × Konvoy)]} Fragaria × ananassa subsp. ananassa Cultivar
81 Diamante United States IT 245796 Cal. 87112-6 × Cal. 88270-1 Fragaria × ananassa subsp. ananassa Cultivar
82 Donner United States IT 245291 CAL 222 × CAL 145.52 Fragaria × ananassa subsp. ananassa Cultivar
83 Earlibritef United States IT 245382 Rosalinda × FL 90-38 Fragaria × ananassa subsp. ananassa Cultivar
84 Earlibritef United States IT 245382 Rosalinda × FL 90-38 Fragaria × ananassa subsp. ananassa Cultivar
85 Erie Star United States IT 245294 Unknown Fragaria × ananassa subsp. ananassa Cultivar
86 Flamenco United States IT 245349 Evita × EMR077 Fragaria × ananassa subsp. ananassa Cultivar
87 Floridabelle United States IT 232502 Sequioa × Earlibelle Fragaria × ananassa subsp. ananassa Cultivar
88 Huxley United States IT 232504 Unknown Fragaria × ananassa subsp. ananassa Cultivar
89 Juspa United States IT 245300 Unknown Fragaria × ananassa subsp. ananassa Cultivar
90 Klondike United States IT 245301 Unknown Fragaria × ananassa subsp. ananassa Cultivar
91 Lassen United States IT 232506 Blakemore × (Marshall × Fendalcinno) × Nich Ohmer × (Royal Sovereign × Howard 17) × (Mar-shall × Fendalcinno) Fragaria × ananassa subsp. ananassa Cultivar
92 Linn United States IT 232505 MDUS 3184 × ORUS 2414 Fragaria × ananassa subsp. ananassa Cultivar
93 Mingoi United States IT 245353 Unknown Fragaria × ananassa subsp. ananassa Cultivar
94 Missionary United States IT 245302 Unknown Fragaria × ananassa subsp. ananassa Cultivar
95 NewYork884 United States IT 245297 Unknown Fragaria × ananassa subsp. ananassa Cultivar
96 North West United States IT 245303 Unknown Fragaria × ananassa subsp. ananassa Cultivar
97 NY1406 United States IT 245320 Unknown Fragaria × ananassa subsp. ananassa Line
98 Pink Panda United States IT 232511 Unknown Fragaria × ananassa subsp. ananassa Wild relatives
99 Premier United States IT 232509 Unknown Fragaria × ananassa subsp. ananassa Cultivar
100 Redgauntlet United States IT 245304 New Jersey 1051 × Auchincruive Climax Fragaria × ananassa subsp. ananassa Cultivar
101 Red Glow United States IT 232489 Fairland × Tennessee Shipper Fragaria × ananassa subsp. ananassa Cultivar
102 Red Rich United States IT 232497 Unknown Fragaria × ananassa subsp. ananassa Cultivar
103 Sari United States IT 245354 Unknown Fragaria × ananassa subsp. ananassa Cultivar
104 Shasta United States IT 232495 Marshall × Howard 17 Fragaria × ananassa subsp. ananassa Cultivar
105 Sweet Charlie United States IT 245345 FL 80-456 × Pajaro Fragaria × ananassa subsp. ananassa Cultivar
106 Dahoe United States IT 244919 Unknown Fragaria × ananassa subsp. ananassa Cultivar
107 Victoria United States IT 232508 Unknown Fragaria × ananassa subsp. ananassa Cultivar
108 Bolero United Kingdom IT 245348 LA0988 × Selva Fragaria × ananassa subsp. ananassa Cultivar
109 Dyd Babi United Kingdom IT 245318 Unknown Fragaria × ananassa subsp. ananassa Cultivar
110 Jonson's Early United Kingdom IT 245319 Unknown Fragaria × ananassa subsp. ananassa Cultivar
111 Jursey Belle United Kingdom IT 245296 (Lupton × Aberdeen) × Fairfax × (Pathfinder × Fairfax) Fragaria × ananassa subsp. ananassa Cultivar
112 Cavalier Canada IT 232515 Valentine (Howard 17 × Vanguard) × Sparkle Fragaria × ananassa subsp. ananassa Cultivar
113 Guards Man Canada IT 232496 Claribel × Sparkle Fragaria × ananassa subsp. ananassa Cultivar
114 Micmac Canada IT 232516 Tioga × Guardsman S1 Fragaria × ananassa subsp. ananassa Cultivar
115 Nowangg Israel IT 245351 Unknown Fragaria × ananassa subsp. ananassa Cultivar
116 Nowangg Israel IT 245351 Unknown Fragaria × ananassa subsp. ananassa Cultivar
117 Tamar Israel IT 232517 Osogrande × Dorit Fragaria × ananassa subsp. ananassa Cultivar
118 Chunseong China IT 245356 Unknown Fragaria × ananassa subsp. ananassa Cultivar
119 Gilgyung53 China IT 245307 Unknown Fragaria × ananassa subsp. ananassa Line
120 Senga Gigana Germany IT 232513 Unknown Fragaria × ananassa subsp. ananassa Cultivar
121 Senga Sengana Germany IT 232512 Markee × Sieger Fragaria × ananassa subsp. ananassa Cultivar
122 Elsanta Netherlands IT 245875 Gorella × Holiday Fragaria × ananassa subsp. ananassa Cultivar
123 Sarian Netherlands IT 245364 Unknown Fragaria × ananassa subsp. ananassa Cultivar
124 Bukaj Russia IT 245180 Unknown Fragaria × ananassa subsp. ananassa Cultivar
125 Kama Russia IT 245357 Sengasengana × Cavlier Fragaria × ananassa subsp. ananassa Cultivar
126 Favette France IT 245373 (Souvenir des Halles × Regina) × (Pocahontas × Aliso) Fragaria × ananassa subsp. ananassa Cultivar
127 Toteuklip Spain IT 245355 Unknown Fragaria × ananassa subsp. ananassa Cultivar
128 Chiloensis IT 245331 Unknown Fragaria chiloensis Cultivar
129 Fragaria Wild IT 245316 Unknown Fragaria × ananassa subsp. ananassa Wild
130 Jasan IT 232493 Unknown Fragaria × ananassa subsp. ananassa Cultivar
131 Crop Station Korea, South Unknown
132 Jirisan Wild Korea, South Unknown
133 Sakyejul Korea, South Shikisetzu Unpulished Fragaria × ananassa subsp. ananassa
134 Ssanta Korea, South Maehyang × Seolhyang Fragaria × ananassa subsp. ananassa
135 Sukhyang Korea, South Seolhyang × Maehyang Fragaria × ananassa subsp. ananassa
136 Elan Netherlands Fern × Rapella Fragaria × ananassa subsp. ananassa
137 New Zealand New Zealand Unknown
138 Caminoreal United States Cal 89.2307 × Cal 90.2533 Fragaria × ananassa subsp. ananassa
139 Festival United States Rosalinda × Osogrande Fragaria × ananassa subsp. ananassa
140 Florida United States Unknown
141 Fragaria Minnesota United States Unknown
142 Ventana United States Cal 93.170-606 × Cal 92.35-601 Fragaria × ananassa subsp. ananassa
143 Bious Unknown
144 EMC Unknown Fragaria vesca
145 Island Wild Unknown
146 Jepter Unknown
147 Naoami Unknown
148 Niigata Unknown
149 No0241 Unknown
150 No04113 Unknown
151 No06155 Unknown
152 No06172 Unknown
153 No06182 Unknown
154 No06183h Unknown
155 No06183h Unknown
156 No0636 Unknown
157 No0641 Unknown
158 No0643 Unknown
159 UC1 Unknown Fragaria vesca
160 Wild Strawberry3 Unknown

aIT numbers were provided by the RDA-Genebank Information Center (http://www.genebank.go.kr);

b-hSame accessions collected from distant two pots;

*Accessions 1-24 were used to select the SSR markers.

SSR analysis

A subset of 24 strawberry accessions (accessions 1-24, Table 1) was used to select SSR markers that could discriminate effectively between the different accessions. Genotyping was performed using 16 SSR markers that were developed by three independent research groups (Chambers et al., 2013; Govan et al., 2008; Isobe et al., 2013). PCR products were analyzed using a MultiNA microchip electrophoresis system (MCE-202 MultiNA, Dongil Shimadzu). Peak sizes on electropherograms were automatically detected by MultiNA software (MultiNA Control Software and Data Analysis Software MultiNA Viewer, Dongil Shimadzu). Five SSR markers were selected from all the 160 strawberry accessions for analysis. Modified primer sequences for the markers are listed in Table 2. PCR reaction mixtures contained 1 ng of template DNA, 1 × PCR buffer, 0.25 mM of dNTP mixture, 2.5 μM of each primer, and 1 unit of i-Max II DNA polymerase (iNtRON) in a total volume of 20 μl. PCR conditions were as follows: initial denaturation at 94 °C for 5 min, followed by 36 cycles at 94 °C for 30 s, 50 °C for 30 s, and 72 °C for 30 s, and then a final extension at 72 °C for 5 min. PCR reactions were performed using a C1000 Touch Thermal Cycler (Bio Rad Laboratories).

Table 2 List of five SSR primer pairs used for genotyping 160 strawberry accessions. 

SSRa Primer sequencesb No. of alleles scored No. of rare allelesc Peak ranges observed (bp)
FG1a/b Forward : TGGTTTGCCGGTAGCAAATAGCAGCA
Reverse : TGACACACACTCTCTCTGTCTGATCCCT
12 5 123-167
FG2a/b Forward : TGAACTGGTCCATCGGTGCTGAAA
Reverse : TGATCACACAATACGCATTACCAAGCCT
8 1 298-362
FG7a/b Forward : GCAGTGCTACATCGACTCAGGTCCAA
Reverse : ACCAAGGAAGTGCCGAAGTGGGTTT
13 5 153-240
FG7c/d Forward : AGGTGTCCAAAGAGGGTTGCTGTAGA
Reverse : TCCCTCTCCCAATAACCCTTTGCTTC
19 7 236-396
FG7e/f Forward : ACGGTGCCGAGATGCCTGATTACT
Reverse : GCTGATCTCCACTTCCTCTCCTATCACCA
8 3 472-599

a Chambers et al., 2013, Mol Breeding;

bReverse primers were shorter than those of reference due to deletion of M13 sequence;

cAlleles with frequency lower than 0.1.

Genetic diversity analysis

The genetic diversity of 160 strawberry accessions was analyzed using five selected SSR markers. First, SSR marker peaks were scored as 1 (presence of peak) or 0 (absence of peak) for each accession. Rare alleles and accession-specific alleles were applied in this study to distinguish strawberry accessions (Cho et al., 2007; Govan et al., 2008; Yoon et al., 2012). The binary data set for all strawberry accessions was then assembled in a single matrix and analyzed using the unweighted pair group method with an arithmetic mean (UPGMA, http://genomes.urv.cat/UPGMA/) algorithm (using the Jaccard coefficient) to calculate genetic similarities and distances between the accessions. Output data in the Newick format were used with MEGA version 6 to produce a dendrogram (Tamura et al., 2013).

Results and Discussion

Evaluation of diversity markers and genotyping of 160 strawberry accessions

In this study, we strengthened strawberry breeding resources in Korea by analyzing 160 previously collected or newly generated strawberry germplasms. To determine the optimal markers for genotyping, 16 previously developed SSRs (nine from Govan et al. (2008), six from Chambers et al. (2013), and one from Isobe et al. (2013)) were used to test 24 of the 160 strawberry accessions (accession 1-24) (Table 1). Of the sixteen markers, eight yielded dim or difficult to interpret fingerprints, and three were insufficiently polymorphic (Figure 1). The remaining five markers, which were developed by Chambers et al. (2013), revealed clear fragments that were highly polymorphic between accessions (Figure 1). These five markers were chosen for genotyping from all 160 accessions. A total of 60 alleles (19 from FG7c/d, 13 from FG7a/b, 12 from FG1a/b, and 8 from each of FG2a/b and FG7e/f) were obtained from the five markers across all accessions (Table 2). All the markers were highly polymorphic: individual markers separated the 160 accessions into 17 (FG7e/f) to 54 (FG2a/b) allelic patterns. Allele sizes among the 160 accessions were in the range of 123 bp (FG1a/b) to 599 bp (FG7e/f) (Table 2), which differed slightly from those observed previously (Chambers et al., 2013). These differences may be attributable to the different strawberry accessions tested, slight modifications to primers (see Table 2), different PCR conditions, and different genotyping equipment.

Figure 1 Gel images of 24 strawberry accessions examined by 16 SSR markers. (A) Clear and highly polymorphic markers. (B) Dim or difficult to interpret markers. (C) Few polymorphic markers. 

Allele frequencies were in the 0.006-1 range (Figure 2). Of the 60 alleles identified in the 160 accessions, 21 alleles (35 %) occurred with low frequency (< 0.1). These 'rare alleles' were detected by all five markers: one rare allele was identified using FG2a/b, three alleles from FG7e/f, five alleles from FG1a/b and FG7a/b, and seven alleles from FG7c/d (Table 2). One allele detected with FG7c/d (291 bp) was detected only in a single accession, accession 80 (from United States), which was suggestive of an accession-specific allele. Of the 160 strawberry accessions, 53 % (84 accessions) possessed 1-8 rare alleles, indicating the value of the rare alleles in discerning the different accessions. Of these 84 accessions, the largest number (32) was collected from the United States, followed by Japan (19), unknown origin (12), Korea (10), Europe (8), Canada (1), China (1), and New Zealand (1). One of the two Chinese accessions (accession 119) possessed five rare alleles, whereas the other Chinese accession (accession 118) showed no rare allele. This result indicated that the origin of the germplasm and the genetic relationship did not always correlated in strawberry resources.

Figure 2 A histogram of allele frequencies for 60 alleles in 160 strawberry accessions. 

Genetic diversity and classification of strawberry accessions

The genetic relationships between 160 strawberry accessions were analyzed using the 60 polymorphic alleles generated from the five SSR markers (Figure 3). Together, the five SSR markers distinguished 155 of the accessions. The remaining accessions consisted of five pairs of duplicates (accession 83 (including its duplicate, accession 84), accession 115 (including its duplicate, accession 116), accession 70 (including its duplicate, accession 71), accession 5 (including its duplicate, accession 6), and accession 154 (including its duplicate, accession 155)) that appeared to have the same allelic patterns for the five SSR markers (Figure 3). These results supported the effectiveness of our genotyping approach. However, two additional duplicates (accession 41 (including its duplicate, accession 42) and accession 50 (including its duplicate, accession 51)), which were collected separately, appeared to be of different genotypes. The two accessions 41 and 42 were similar but not identical (Figure 3), and both belonged to group 4. One allele (302 bp from FG7c/d) was present in accession 41 but was absent in accession 42. The two accessions 50 and 51 were genetically distant and belonged to groups 3 and 5, respectively (Figure 3). These two accessions differed by 10 alleles, suggesting that they were from different strawberry lines.

Figure 3 Classification of 160 strawberry accessions based on their molecular diversity. Genetic similarities were calculated by UPGMA and the dendrogram was constructed using MEGA V.6. 

Excluding the five duplicate pairs, the genetic similarities of the strawberry accessions were in the range 0.034-0.963, with an average value of 0.507. The highest similarity value (0.963) was between accession 148 (unknown origin) and accession 43 (from Japan), and between accession 125 (from Russia) and accession 120 (from Germany). The lowest similarity value (0.034) was between accession 159 (unknown origin) and accession 119 (from China).

The 160 strawberry accessions were divided into five groups according to genetic distance (Figure 3). Group 1 contained two diploid F. vesca species (accession 159 and accession 144) and one new accession, accession 160. These accessions were dissimilar to other accessions and were genetically distant showing the lower genetic similarities with other accessions (0.1, 0.19, 0.16 for accession 159, accession 144, and accession 160, respectively) compared to the average genetic similarities among the 160 accessions (0.509). These three accessions possessed relatively few SSR alleles (5 in accession 159, 11 in accession 144, and 9 in accession 160), compared to the average from all accessions (21.9). This was consistent with the simpler genetic structure found in diploid species such as F. vesca compared to octoploid species (F chiloensis and F × ananassa). These data suggested that accession 160 belonged to F. vesca or another diploid species. Group 2 contained only one accession, accession 80, which was collected from the United States (Figure 3). One accession-specific allele (291 bp at FG7c/d) was detected in accession 80, alongside a further 16 SSR alleles.

Group 3 contained 20 F. × ananassa accessions (8 from the United States, 5 from Japan, 3 each from Korea and Europe, and 1 from China) and six unknown origin accessions (Figure 3). In this group, several accessions were closely grouped in line with their geographical origins. For example, three accessions from the United States (accession 94, accession 107, and accession 90) and three from Japan (accession 49, accession 56, and accession 50 (including its duplicate, accession 51)) were closely grouped. Four of the six unknown origin accessions (accession 154 (including its duplicate, accession 155), accession 152, and accession 151) were also closely grouped, allowing for speculation that these may have originated in the same country. Of the 26 accessions in group 3, 16 (62 %) possessed at least one rare allele, which distinguishes the F. x ananassa accessions in this group from those in other groups.

The remaining 130 accessions were clustered into Groups 4 and 5, indicating minimal variability among these accessions within groups. Group 4 contained 48 F × ananassa accessions (17 from United States, 13 from Japan, 11 from Korea, 4 from Europe, and 1 each from Canada, China, and New Zealand), one octoploid species (F. chiloensis), and six unknown origin accessions (Figure 3). F. chiloensis, which is one of the parents of F. × ananassa cultivars, was located in a subcluster with three wild strawberry accessions (accession 19, accession 20, and accession 129) and three new accessions (accession 131, accession 132, and accession 145).

Group 5 contained 69 F. × ananassa accessions (27 from Japan, 19 from the United States, 12 from Korea, 6 from Europe, 3 from Israel, and 2 from Canada) and six unknown origin accessions (Figure 3 and Table 1). Our five SSR markers confirmed the pedigree of some accessions such as accession 17 (the offspring of accession 41 and accession 42) and accession 38, and accession 54 (the grandparent of accession 12) (Figure 3 and Table 1). In addition. as shown in Figure 3 and Table 1, accession 134 was the offspring of accession 16, accession 26, and accession 52 were parents of accession 135, and accession 45 was one of the parents of accession 26. Certain accessions that shared at least one parent were also closely clustered. For example, accession 74 and accession 78 were both offspring of 'Earlibelle' and 'ARK5063'. Accession 139 and accessions 83 (including its duplicate, accession 84) shared the parent 'Rosalinda', and accession 139 and accession 117 shared the parent 'Osogrande' (Figure 3 and Table 1). By contrast, some accessions were in different groups despite sharing parents. For example, accession 39 (group 3) and accession 17 (group 4) were both offspring of accession 38 and 'Hokowase' (Figure 3 and Table 1). This result confirmed the previous observations of these accessions that clustered into the different group (Cho et al., 2007). Similarly, accession 16 (group 4) and accession 4 (group 5) were in different groups despite sharing parents (accession 26 and accession 52). This latter result was unexpected, as previous research had placed accession 16 and accession 4 in the same group (Hong et al., 2014) which might be due to the use of different batches of strawberry accessions or the number of accessions compared in two studies.

To date, most reports classifying Korean strawberry resources have examined only small numbers of accessions, such as those registered in the RDA-Genebank Information Center (http://www.genebank.go.kr). In this study, we presented an expanded dendrogram classifying 160 Korea strawberry breeding accessions, including 30 new, unregistered accessions. These new accessions were distributed throughout the dendrogram: three accessions in group 1, five in group 3, twelve in group 4, and ten in group 5. Further phenotypic classification of the new accessions, coupled with our marker-associated analysis, will enhance their value in breeding programs. Many of the accessions characterized in this study were generated by preexisting breeding programs, and consequently exhibited minimal genetic variation. The characterization of 160 strawberry accessions in the study will allow breeders to design new breeding strategies to incorporate more genetic diversity into new cultivars.

Acknowledgments

This work was supported by grants from the export promotion technology development research programs (315047-3) funded by the Ministry of Agriculture, Food and Rural Affairs, Republic of Korea, and a grant from the KRIBB Research Initiative Program.

References

Ashley, M.; Wilk, J.; Styan, S.; Craft, K.; Jones, K.; Feldheim, K.; Lewers, K.; Ashman, T. 2003. High variability and disomic segregation of micro satellites in the octoploid Fragaria virginiana Mill.(Rosaceae). Theoretical and Applied Genetics 107: 1201-1207. [ Links ]

Bassil, N.; Gunn, M.; Folta, K.; Lewers, K. 2006. Microsatellite markers for Fragaria from 'Strawberry Festival' expressed sequence tags. Molecular Ecology Notes 6: 473-476. [ Links ]

Capocasa, F.; Diamanti, J.; Tulipani, S.; Battino, M.; Mezzetti, B. 2008. Breeding strawberry (Fragaria × ananassa Duch) to increase fruit nutritional quality. Biofactors 34: 67. [ Links ]

Chambers, A.; Carle, S.; Njuguna, W.; Chamala, S.; Bassil, N.; Whitaker, V.M.; Barbazuk, W. B.; Folta, K.M. 2013. A genome- enabled, high-throughput, and multiplexed fingerprinting platform for strawberry (Fragaria L.). Molecular Breeding 31: 615-629. [ Links ]

Cho, K.; Rho, I.; Cho, Y.; Park, P 2007. Identification of Korean strawberry cultivars using DNA markers. Korean Journal of Breeding Science 40: 401-407. [ Links ]

Congiu, L.; Chicca, M.; Cella, R.; Rossi, R.; Bernacchia, G. 2000. The use of random amplified polymorphic DNA (RAPD) markers to identify strawberry varieties: a forensic application. Molecular Ecology 9: 229-232. [ Links ]

Dale, A. 1996. A key and vegetative descriptions of thirty-two common strawberry varieties grown in North America. Advanced Strawberry Research 15: 1-12. [ Links ]

Degani, C.; Rowland, L.J.; Saunders, J.A.; Hokanson, S.C.; Ogden, E.L.; Golan-Goldhirsh, A.; Galletta, G.J. 2001. A comparison of genetic relationship measures in strawberry (Fragaria × ananassa Duch.) based on AFLPs, RAPDs, and pedigree data. Euphytica 117: 1-12. [ Links ]

Faedi, W.; Mourgues, F.; Rosati, C. 2000. Strawberry breeding and varieties: situation and perspectives. Acta Horticulturae 567: 51-59. [ Links ]

Garcia, M.; Ontivero, M.; Diaz Ricci, J.; Castagnaro, A. 2002. Morphological traits and high resolution RAPD markers for the identification of the main strawberry varieties cultivated in Argentina. Plant Breeding 121: 76-80. [ Links ]

Gil-Ariza, D.; Amaya, I.; Botella, M.; Blanco, J.M.; Caballero, J.; López-Aranda, J.; Valpuesta, V.; Sánchez-Sevilla, J. 2006. EST-derived polymorphic microsatellites from cultivated strawberry (Fragaria × ananassa) are useful for diversity studies and varietal identification among Fragaria species. Molecular Ecology Notes 6: 1195-1197. [ Links ]

Govan, C.; Simpson, D.; Johnson, A.; Tobutt, K.; Sargent, D. 2008. A reliable multiplexed microsatellite set for genotyping Fragaria and its use in a survey of 60 F. × ananassa cultivars. Molecular Breeding 22: 649-661. [ Links ]

Hancock, J.F.; Finn, C.E.; Luby, J.J.; Dale, A.; Callow, P.W.; Serçe, S. 2010. Reconstruction of the strawberry, Fragaria × ananassa, using genotypes of F. virginiana and F. chiloensis. HortScience 45: 1006-1013. [ Links ]

Hong, J.; Cho, K.; Kwon, Y. 2014. Construction of DNA profile data base of strawberry cultivars using microsatellite markers. Korean Journal of Horticultural Science 32: 853-863. [ Links ]

Isobe, S.N.; Hirakawa, H.; Sato, S.; Maeda, F.; Ishikawa, M.; Mori, T.; Yamamoto, Y.; Shirasawa, K.; Kimura, M.; Fukami, M. 2013. Construction of an integrated high density simple sequence repeat linkage map in cultivated strawberry (Fragaria × ananassa) and its applicability. DNA Research 20: 79-92. [ Links ]

James, C.; Wilson, F.; Hadonou, A.; Tobutt, K. 2003. Isolation and characterization of polymorphic microsatellites in diploid strawberry (Fragaria vesca L.) for mapping, diversity studies and clone identification. Molecular Ecology Notes 3: 171-173. [ Links ]

Kunihisa, M.; Fukino, N.; Matsumoto, S. 2003. Development of cleavage amplified polymorphic sequence (CAPS) markers for identification of strawberry cultivars. Euphytica 134: 209-215. [ Links ]

Lewers, K.; Styan, S.; Hokanson, S.; Bassil, N. 2005. Strawberry GenBank-derived and genomic simple sequence repeat (SSR) markers and their utility with strawberry, blackberry, and red and black raspberry. Journal of the American Society for Horticultural Science 130: 102-115. [ Links ]

Monfort, A.; Vilanova, S.; Davis, T.; Arús, P. 2006. A new set of polymorphic simple sequence repeat (SSR) markers from a wild strawberry (Fragaria vesca) are transferable to other diploid Fragaria species and to Fragaria × ananassa. Molecular Ecology Notes 6: 197-200. [ Links ]

Nathewet, P; Hummer, K.E.; Yanagi, T.; Iwatsubo, Y.; Sone, K. 2010. Karyotype analysis in octoploid and decaploid wild strawberries in Fragaria (Rosaceae). Cytologia 75: 277-288. [ Links ]

Nielsen, J.; Lovell, P. 2000. Value of morphological characters for cultivar identification in strawberry (Fragaria × ananassa). New Zealand Journal of Crop and Horticultural Science 28: 89-96. [ Links ]

Rousseau-Gueutin, M.; Gaston, A.; Ainouche, A.; Ainouche, M.L.; Olbricht, K.; Staudt, G.; Richard, L.; Denoyes-Rothan, B. 2009. Tracking the evolutionary history of polyploidy in Fragaria L. (strawberry): new insights from phylogenetic analyses of low-copy nuclear genes. Molecular Phylogenetics and Evolution 51: 515-530. [ Links ]

Rousseau-Gueutin, M.; Richard, L.; Le Dantec, L.; Caron, H.; Denoyes-Rothan, B. 2011. Development, mapping and transferability of Fragaria EST-SSRs within the Rosodae supertribe. Plant Breeding 130: 248-255. [ Links ]

Sargent, D.; Hadonou, A.; Simpson, D. 2003. Development and characterization of polymorphic microsatellite markers from Fragaria viridis, a wild diploid strawberry. Molecular Ecology Notes 3: 550-552. [ Links ]

Sargent, D.J.; Kuchta, P; Girona, E.L.; Zhang, H.; Davis, T.M.; Celton, J.-M.; Marchese, A.; Korbin, M.; Folta, K.M.; Shulaev, V. 2011. Simple sequence repeat marker development and mapping targeted to previously unmapped regions of the strawberry genome sequence. The Plant Genome 4: 165-177. [ Links ]

Shulaev, V.; Sargent, D.J.; Crowhurst, R.N.; Mockler, T.C.; Folkerts, O.; Delcher, A.L.; Jaiswal, P; Mockaitis, K.; Liston, A.; Mane, S.P. 2011. The genome of woodland strawberry (Fragaria vesca). Nature Genetics 43: 109-116. [ Links ]

Tamura, K.; Stecher, G.; Peterson, D.; Filipski, A.; Kumar, S. 2013. MEGA6: molecular evolutionary genetics analysis version 6.0. Molecular Biology and Evolution 30: 2725-2729. [ Links ]

Tyrka, M.; Dziadczyk, P; Hortynski, J.A. 2002. Simplified AFLP procedure as a tool for identification of strawberry cultivars and advanced breeding lines. Euphytica 125: 273-280. [ Links ]

Yoon, M.-Y.; Moe, K.T.; Kim, D.-Y.; Rho, I.-R.; Kim, S.; Kim, K.-T.; Won, M.-K.; Chung, J.-W.; Park, Y.-J. 2012. Genetic diversity and population structure analysis of strawberry (Fragaria × ananassa Duch.) using SSR markers. Electronic Journal of Biotechnology 15: 6-6. [ Links ]

Zorrilla-Fontanesi, Y.; Cabeza, A.; Torres, A.M.; Botella, M.A.; Valpuesta, V.; Monfort, A.; Sánchez-Sevilla, J.F.; Amaya, I. 2011. Development and bin mapping of strawberry genic- SSRs in diploid Fragaria and their transferability across the subfamily. Molecular Breeding 27: 137-156. [ Links ]

Received: February 16, 2016; Accepted: June 21, 2016

*Corresponding author <kimhr@kribb.re.kr>

Edited by: Roberto Fritsche Neto

Creative Commons License This is an Open Access article distributed under the terms of the Creative Commons Attribution License, which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.