Home > IX International Strawberry Symposium > Whole genome assembly in a Japanese strawberry cultivar, ‘Reikou’, and comparison with wild Fragaria genomes

Articles

Whole genome assembly in a Japanese strawberry cultivar, ‘Reikou’, and comparison with wild Fragaria genomes

Article number

1309_26

Pages

175 – 180

Language

English

Abstract

Cultivated strawberry (Fragaria × ananassa) is an allo-octoploid species, which chromosome number is 2n=8x=56. In this study, we report a chromosome-scale strawberry genome assembly of a Japanese cultivar.
Genomes of diploid Fragaria species were re-sequenced and compared with the most similar chromosome-scale scaffolds to investigate possible progenitor of each subgenomes.
The Illumina short reads derived from paired-end, mate pair and 10X Genomics libraries were obtained from a Japanese cultivar, ‘Reikou’. The scafffolds assembled using Denovo MAGIC 3.0 consisted of 32,715 sequences with a total length of 1.4 Gb and N50 length of 3.9 Mb.
The scaffolds were aligned onto the ‘Reikou’ S₁ linkage maps with IStraw90 Axiom SaNP array and ddRAD-Seq for pseudomolecule construction.

Publication

IX International Strawberry Symposium

Authors

K. Shirasawa, C. Chung, D. Boncan, H. Hirakawa, F. Maeda, T. Wada, T.F. Chan, S. Isobe

Keywords

strawberry, Fragaria species, whole genome, de novo assembly

Full text

https://doi.org/10.17660/ActaHortic.2021.1309.26

Groups involved

Online Articles (149)

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3. Improving strawberry cultivars for the future

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5. Efficiency of selecting strawberry genotypes resistant to fungal root and crown diseases while infecting germinating seeds

R.M. Puhachov | T.N. Kamedzko | I.G. Puhachova

6. High-throughput monoclonal antibody array generation and its application in metabolomics of cultivated strawberry

L. Guan | M. Zhao | T. Tian | H. Yu | Q. Wang

7. Botanical and phenological analysis of wild strawberry in JAAS

Fuhua Pang | Mizhen Zhao | Jing Wang | Huazhao Yuan | Weijian Cai

8. Investigation and classification of the five tetraploid Fragaria species native to China

9. Pollen observation of wild Fragaria species native to China using SEM

10. Cultivars developed in the strawberry breeding program of Fresas Nuevos Materiales S.A.

F. Pistón | J.M. Arenas | A. Refoyo

11. New strawberry breeding lines with low susceptibility to anthracnose in southwestern Spanish conditions

C. Borrero | A. Refoyo | F. Pistón | M. Avilés

12. New strawberry breeding lines with low susceptibility to Phytophthora crown and root rot in Huelva, Spain

C. Borrero | A. Refoyo | F. Pistón | M. Avilés

13. Silencing of strawberry pathogen defence related candidate genes by using specific strawberry fruit ripening-related promoters: an intragenic approach to improve fruit quality and resistance

14. Use of RAPD and SCAR markers for identification of strawberry genotypes with red stele resistance genes Rpf1 and fruit rot resistance genes Rca2 in the hybrid progenies

M. Sturzeanu | M. Ciuca | D. Cristina | A.G. Turcu

15. Genome-wide prediction of powdery mildew resistance in the octoploid strawberry

R. Tapia | L.F. Osorio | S. Verma | S. Lee | V.M. Whitaker

16. The origin and subgenome dynamics of the octoploid strawberries

A. Liston | T.-L. Ashman

17. Assessment of strawberry pre-breeding material for crown rot resistance and root traits by high-throughput screening

18. “Professor Staudt Collection”: fruit diversity in Fragaria virginiana Miller and Fragaria chiloensis Miller

19. Breeding potential of underutilized Fragaria species

20. Spider mite symptomatology in a segregating F₂ population in Fragaria ×ananassa Duch.

21. Resistance evaluation of two-spotted spider mite in the genus Fragaria L.

H. Wagner | A. Knorrn | K. Olbricht

22. ‘Rendezvous’: portrait of a new European strawberry cultivar

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23. ‘Malling™ Allure’ and ‘Malling™ Champion’: two new strawberry cultivars from NIAB EMR, United Kingdom

A.B. Whitehouse | A.W. Johnson | K.J. Hopson | A.J. Passey | D. Sargent

24. Recent progress in strawberry breeding and genetics at NIAB EMR, East Malling, UK

25. Whole genome assembly in a Japanese strawberry cultivar, ‘Reikou’, and comparison with wild Fragaria genomes

26. Coordination of genebank activities between different national collections of berry genetic resources in Europe in the frame of ECPGR

M. Höfer

27. Improvement of strawberry for potential anthocyanin content and bioactive compound producing cultivars through breeding program

M. Sirijan | P. Chaiprasart

28. Generating novel strawberry pre-breeding material from a Fragaria × ananassa backcrossing program with F. virginiana subsp. glauca inter-specific hybrids

29. ‘Francesca’, ‘Lauretta’, ‘Silvia’ and ‘Dina’: four new strawberry cultivars for northern and southern European cultivation conditions from the Marche Polytechnic University breeding programme

30. RNAi-based approaches to induce resistance against grey mould disease in strawberry

31. Isolation and phenotypical characterization of the FT-like genes in strawberry (Fragaria × ananassa)

32. The sugar transporter system of strawberry: genome-wide identification and expression correlation with fruit soluble sugar-related traits in Fragaria × ananassa Duchesne germplasms collection

33. Evaluation of strawberry (Fragaria × ananassa) cultivars in Estonia

A. Kikas | M. Vinogradov | L. Arus | P. Laurson | A.-V. Libek

34. Advances in F₁ hybrid day-neutral strawberry breeding at ABZ Seeds, Andijk, The Netherlands

G. Bentvelsen | A. van der Vange

35. Influence of TiO₂ foliar spray application on photosynthesis and chlorophyll fluorescence of strawberry during low light intensity season in a greenhouse

H.G. Choi

36. Drought tolerance of strawberries as related to reaction type and water content and redistribution in leaves

D.B. Shokaeva

37. Profitable day-neutral strawberry cultivar and planting date combination for year-round strawberry fruit production in the Southern Cape, South Africa

P. Parehwa | G.C. Linsley-Noakes | J. Jordaan | J. Pauw

38. Low tunnels for season extension of day-neutral strawberries in the US Pacific Northwest

J. Fernandez-Salvador | E. Chernoh | A. Pheil | B. Renne

39. Productivity and fruit quality of ‘Clery’ strawberry affected by planting density in a soilless growing system

40. The influence of stolon harvest frequency and nitrate: ammonium ratio on asexual reproduction of day-neutral strawberries (Fragaria ×ananassa ‘Albion’)

X. Shi | R. Hernández | M. Hoffmann

41. Performance of wood fibre as a substrate in hydroponic strawberry production under different fertigation strategies

T. Woznicki | K. Kusnierek | A. Sønsteby

42. Effect of summer planting time on strawberry productivity and quality

43. Strawberry production (Fragaria × ananassa Duchesne ex Rozier) in coconut fiber slabs under greenhouse, a teaching tool

E. Cedillo | L.P. Martínez | P. Castro | F.D. Contreras

44. Use of containerized transplants to increase growth and production of day neutral strawberries under organic management

J. Fernandez-Salvador | T. Barker | E. Chernoh | K. Poblador | S. Tao

45. Chilling requirement of strawberry June-bearer ‘Opera’

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46. Reuse of drain water with a first-flush-system on strawberry trayfields drastically reduces the use of groundwater

D. Baets | P. Melis | S. Laurijssen | T. Van Delm

47. Winter manipulation of photoperiod and chill to enhance the perpetual flowering nature of ‘Soprano’

N. Gallace | P. Lieten

48. Autonomous UV-C application to deal with low and high powdery mildew disease pressure in strawberry

S. Laurijssen | P. Melis | D. Baets | T. Van Delm

49. Current status of strawberry industry in China

50. Cultivation performance and flowering behavior of day-neutral ‘Portola’ strawberry in solar greenhouse

51. The effect of light intensity and duration on yield and quality of everbearer and June-bearer strawberry cultivars in a LED lit multi-tiered vertical growing system

52. Behaviour of everbearers ‘Portola’ and ‘Verity’ in response to treatment with Prohexadione-Calcium

N. Gallace | P. Lieten

53. Nitrogen fertilization in the nursery: effect on strawberry tray plant yield and performance

P. Lieten | N. Gallace

54. Effects of temperature and photoperiod on photosynthesis in everbearing strawberry

R. Rivero | A. Sønsteby | K.A. Solhaug | O.M. Heide | S.F. Remberg

55. Evaluating the state of the Oregon strawberry industry in 2019

J. Fernandez-Salvador | E. Chernoh | C. Bobo-Shisler

56. Current status and future prospect of strawberry production in East Asia and Southeast Asia

T. Nishizawa

57. Comparison of flower bud differentiation in strawberry in different latitudes and altitudes

58. Current strawberry research in Belarus, review

N.V. Klakotskaya | R.M. Puhachov

59. Benefits of using silicon as a nutrient in sustainable strawberry production

B. Liu | C. Asiana | H. Wileman | X. Jin | A.M. Hall

60. Effect of different slit numbers of plug tray cells on growth parameters in strawberry transplants

J.N. Ndikumana | Y.H. Lee | N.I. Park | S.J. Hong | Y.R. Yeoung

61. The evaluation of some Italian strawberry genotypes in Romania

M. Sturzeanu | G. Baruzzi | P. Sbrighi | M. Calinescu

62. Development of strawberry flower initials: timing and response to nitrogen application and temperature conditions at northern latitudes

M. Rantanen | M. Pohjola | S. Karhu

63. Growth, yield and fruit quality of organic day-neutral strawberry in field and low tunnel settings in the southeastern United States

S. Gu | T.S. Rana

64. Low tunnels increased early-season yield of organic June-bearing strawberries in southeastern United States

S. Gu | A. Ballard

65. Application of eco-friendly practices alternative to soil chemical fumigation: preliminary results on strawberry

66. Good experiences with everbearing strawberries cultivated in running tunnels

S. Schrey | L. Linnemannstöns

67. Design of a new planting system to produce strawberry out of season in central Mexico

P.A. Dávalos-González | A.E. Jofre-Garfías | R. Aguilar-García

68. Strawberry iron-manganese chlorosis: a mathematic model to understand the phenomenon

R. Aguilar-García | P.A. Dávalos-González | A.E. Jofre-Garfías

69. Strawberry cultivar response to plant density using tray plant in macrotunnel

P.A. Dávalos-González | R. Aguilar-García | A.E. Jofre-Garfías

70. Optimisation of the micropropagation protocol of cultivated strawberry (Fragaria × ananassa Duch.)

L. Barat | J. Perrotte

71. Rotation length, crop rotation, anaerobic soil disinfestation and mustard seed meal affect organic strawberry yield and soil-borne disease incidence in California

M. Zavatta | J. Muramoto | M. Mazzola | C. Shennan

72. Circular use of nutrients in soilless strawberry cultivation: spent growing media as key element

B. Vandecasteele | F. Amery | L. Blindeman | R. Visser

73. Yield and dry matter allocation in soilless strawberry with sheep manure compost

H.E. Alvarado-Raya | R. López-García | G. Calderón-Zavala

74. Yield quality of vertically grown strawberries in greenhouse and open area

K. Kampuss | I. Sivicka | D. Sergejeva | S. Kampuse

75. Ultraviolet-C (UV-C) for disease and pest management and automating UV-C delivery technology for strawberry

F. Takeda | W. Janisiewicz | B. Short | T. Leskey | A. Stager

76. Between-row treatments for weed management in day-neutral strawberry plantings in the northern United States

77. Research on the influence of temperature on the strawberry blossom weevil – Anthonomus rubi (Herbst)

L.B. Neagu Frăsin

78. Strawberry crop in extreme climatic zones of Chilean Patagonia

M. Gambardella | E. Contreras | C. Gomà | J. Grez

79. Physiological process related to low flowering in Chilean white strawberry (Fragaria chiloensis (L.) Mill. subsp. chiloensis f. chiloensis)

J. Grez | E. Contreras | S. Sanchez | M. Gambardella

80. The effect of temperature, photoperiod and cultivar on strawberry growth, development and yield in out-of-season glasshouse production

S. Read | M.A. Else | P. Hadley | C. Twitchen

81. Establishing micropropagation protocols for new strawberry (Fragaria × ananassa) breeding lines

S. Sabbadini | M. Marcellini | B. Mezzetti | F. Capocasa

82. Preliminary results of different strawberry cultivars in multi-cropping soilless cultivation

83. Evaluation of strawberry genotypes response to reduced water irrigation trial in southern Spain

B. Mezzetti | A.C. Galvez | T. Cera | M. Marcellini | F. Capocasa

84. Preliminary results of soilless cultivated strawberry cultivars in the autumn-spring cycle in the mid-Adriatic area

85. Micropropagated strawberry mother plants for high quality frigo and plug plants nursery production

86. Life cycle assessment of strawberry soilless cultivation and packaging: an Italian case study

87. Effects of arbuscular mycorrhizae Glomus iranicum var. tenuihypharum on strawberry fruit yield and quality

88. Quantitative analysis of cultivation environment effects on growth and yield during summer and autumn everbearing strawberry production (cultivar ‘Suzuakane’)

89. Effect of organic fertilizer on growth of strawberry cultivar ‘Sonata’

90. Collaborative development of a national strawberry research and outreach project for underserved growers

91. The effect of temperature and light intensity on rate of strawberry fruit ripening

C. Twitchen | M.A. Else | P. Hadley

92. Open and protected cultivation of strawberry in Armenia

S.S. Hovsepyan

93. The effect of LED illumination on flower differentiation of strawberry short-day cultivars in winter production season

94. Grower acceptance of new end-of-life management strategies for plastic mulch in strawberry systems

L.W. DeVetter | J.R. Goldberger | C. Miles | J. Gomez

95. Four layer strawberry cultivation

M. Hofkens | P. Melis | S. Laurijssen | D. Baets | T. Van Delm

96. Effect of irrigation regime on yield and plant growth of ‘Sonsation’ strawberry grown in an open field in Estonia

97. Overcoming dormancy of achenes and physiology of strawberry treated with plant regulators

98. Sustainability of strawberry nurseries and fruit production in relation to fumigation practices in Europe

99. Soil pest management in current California strawberry production: a review

100. The inhibition of Colletotrichum acutatum by monochromic pulsed and non-pulsed radiation at different time durations

N. Rasiukevičiūtė | A. Brazaitytė | A. Valiuškaitė | V. Vaštakaitė-Kairienė

101. Essential oils as bio-fungicide against strawberry Colletotrichum acutatum

N. Rasiukevičiūtė | A. Valiuškaitė | A. Morkeliūnė | N. Uselis

102. Soil-borne diseases increasing in Finnish strawberry production

P. Parikka | S. Latvala

103. Comparison of defence responses of detached leaves of local strawberry cultivars against grey mould disease

Ö.F. Bilgin | Ş.H. Attar | H. Günaçtı | S. Kafkas | N.E. Kafkas

104. Scouting of pests and beneficials is essential in application of IPM strategy in strawberry

J. Smessaert | D. Baets | P. Melis | T. Van Delm

105. Selecting tolerant strawberry germplasm to the fungus Macrophomina phaseolina

106. Basamid effectivity against strawberry soil-borne pests in Europe

107. The impact of planting material and soil fumigants on charcoal rot of strawberry in Australia

D.J. McFarlane | S.W. Mattner | A.O. Gomez | D.R. Oag

108. ‘Red Leaf’: a new disorder in Australian strawberry plants

109. Induction and suppression of the defense response mediated by two fungal derived molecules in strawberry plants

110. Systematic grid-based detection and quantification of six major strawberry pathogens for nursery fields

Thien Ho | J. Buhler | M. Meyer-Jertberg | J.C. Broome

111. In vitro evaluation of fungicides against Cylindrocarpon destructans, Rhizoctonia fragariae and Pestalotiopsis spp. in strawberries

P. Lieten | S. Van Kerckhove | W. Van Hemelrijck

112. Modern substrate cultivation offers possibilities for a minimum of residues in strawberry

P. Melis | S. Laurijssen | D. Baets | M. Hofkens | T. Van Delm

113. Warning system for the strawberry moth, Aphelia viburniana Fabr., in Romania

L.B. Neagu Frăsin

114. Postharvest hexanal vapor applications on strawberry fruit

A.T. Öz | N.E. Kafkas

115. Effect of sudangrass biosolarization on Verticillium dahliae populations in coastal California

T. Jacobs | A. Tubeileh | S. Steinmaus

116. Influence of forced air cooling regimes on postharvest quality of strawberries during the marketing period

117. Comparison of two strawberry postharvest handling strategies: rapidly cooled or non-cooled fruit to the distributor

D.A. Neuwald | M. Grötzinger | R. Wood | D. Kittemann | J. Wünsche

118. A comparison of major taste- and health-related compounds among newly released Italian strawberry cultivars

D. Milosavljević | V. Maksimović | J. Milivojević | J. Dragišić Maksimović

119. Is multivarietal brand a viable solution to valorize and extend marketing of strawberries?

T. Mendes da Silva | C. Peano | N.R. Giuggioli

120. Role of strawberry cultivars on some quality parameters

M.A. Sarıdaş | S. Paydaş Kargı | E. Ağçam

121. Health-promoting properties as a target for selecting strawberry cultivars in breeding programmes

122. Strawberry postharvest shelf life is related to total acid content and fruit firmness

F. Pistón | A.G. Pérez | C. Sanz | A. Refoyo

123. Identification of volatile compounds of Turkish local strawberry genotypes using various extraction techniques by GC/MS

G. Nogay | İ. Ürün | Ş.H. Attar | S. Kafkas | N.E. Kafkas

124. Organoleptic and functional characteristics of some local Turkish strawberry cultivars

125. Storage of halved strawberry fruits affects aroma, phytochemical content and gene expression

126. Correlation analysis between plant phenotype and fruit soluble sugar content of different strawberry cultivars

127. Antioxidant effects of strawberry extract on HepG2 stressed with an oxidant agent

128. Characterization of the nutritional and phytochemical content of ‘Romina’ strawberry (Fragaria × ananassa) and evaluation of its cytotoxic effects on ovarian cancer cells

129. The preventive effect of strawberries against the onset of common human diseases induced by oxidative stress

D. Cianciosi | J. Ansary | L. Regolo | F. Giampieri | T.Y. Forbes-Hernandez

130. The anticancer activity of strawberry

J. Ansary | T.Y. Forbes-Hernandez | L. Regolo | D. Cianciosi | F. Giampieri

131. Specialized metabolites profile of strawberry fruit during flash-freezing

J. Šic Žlabur | B. Duralija | Z. Emanović | N. Mikulec | S. Voća

132. Comparison of five essential oils on postharvest strawberry fruit quality

133. Phenylalanine ammonialyase and invertase activities in strawberry fruit during ripening progress

134. Quality assessment of strawberry cultivars grown in western Serbia

135. NIRS as a fast screening technique for total nutrients in strawberry leaves and in spent growing media

B. Vandecasteele | C. Van Waes

136. Development of a new phenotypic roadmap to improve strawberry aroma based on direct injection mass spectrometry

137. Effects of plant type and calcium cyanamide dosage on yield, nutritional and nutraceutical traits of strawberry in Sicily

L. Sabatino | G. Caracciolo | B.B. Consentino | C. Prinzivalli | F. D¿Anna

138. What can we learn from consumers’ perception of strawberry quality?

S. Predieri | N. Lippi | G.M. Daniele

139. Strawberry phenolic extract increases lifespan in C. elegans

140. Changes in the content of metals of strawberry after preparation of phenolic-rich and anthocyanin-rich extracts for use in biomedicine and nutrition

141. Investigating the composition and the anti-proliferative mechanism of a strawberry (Fragaria × ananassa) methanolic extract on in vitro murine breast cancer cells

L. Mazzoni | T.Y. Forbes-Hernandez | F. Capocasa

142. Variation of polyphenol and vitamin C fruit content induced by strawberry breeding

L. Mazzoni | R. Qaderi | M. Marcellini | B. Mezzetti | F. Capocasa

143. The effect of storage conditions on the quality of everbearing strawberry cultivar ‘Capri’

N. Cvelbar Weber | J. Jakopic | D. Koron

144. Strawberry fruit quality with the increased iron application

145. Volatile components in three strawberry cultivars with white flesh

146. The hunt for the purple strawberry: change in anthocyanin profile leads to a colour change from red to burgundy

T.J. O¿Hare | H.T. Hong

147. Understanding consumer preferences for new market entry: a study of strawberry consumption in Jakarta

R.E. Roberts | B. Eslick | D. KC

148. Anthocyanins in wild relatives of strawberry (Fragaria L.)

K.E. Hummer | T.T. Hoai | R.W. Durst

149. Updates on Italian strawberry breeding programs coordinated by CREA