Dissection of the Octoploid Strawberry Genome by Deep Sequencing of the Genomes of Fragaria Species

Hirakawa, Hideki; Shirasawa, Kenta; Kosugi, Shunichi; Tashiro, Kosuke; Nakayama, Shinobu; Yamada, Manabu; Kohara, Mistuyo; Watanabe, Akïharu; Kishida, Yoshie; Fujishiro, Tsunakazu; Tsuruoka, Hisano; Minami, Chiharu; Sasamoto, Shigemi; Kato, Midori; Nanri, Keiko; Komaki, Akiko; Yanagi, Tetsuo; Guo-xin, Qin; Maeda, Fumi; Ishikawa, M.; Kuhara, Satoru; Sato, Shusei; Tabata, Satoshi; Isobe, Sachiko

doi:10.1093/dnares/dst049

Cited by 206 publications

(188 citation statements)

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“…The genome size of strawberry is estimated to be 692 Mb (Hirakawa et al 2013b). A wild diploid species, F. vesca , is one of the probable ancestral species, and 240 Mb of its genome has been sequenced (Shulaev et al 2011).…”

Section: Plant Species Registered In the Kazusa Marker Databasementioning

confidence: 99%

Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants

et al. 2014

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In order to provide useful genomic information for agronomical plants, we have established a database, the Kazusa Marker DataBase (http://marker.kazusa.or.jp). This database includes information on DNA markers, e.g., SSR and SNP markers, genetic linkage maps, and physical maps, that were developed at the Kazusa DNA Research Institute. Keyword searches for the markers, sequence data used for marker development, and experimental conditions are also available through this database. Currently, 10 plant species have been targeted: tomato (Solanum lycopersicum), pepper (Capsicum annuum), strawberry (Fragaria × ananassa), radish (Raphanus sativus), Lotus japonicus, soybean (Glycine max), peanut (Arachis hypogaea), red clover (Trifolium pratense), white clover (Trifolium repens), and eucalyptus (Eucalyptus camaldulensis). In addition, the number of plant species registered in this database will be increased as our research progresses. The Kazusa Marker DataBase will be a useful tool for both basic and applied sciences, such as genomics, genetics, and molecular breeding in crops.

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Section: Plant Species Registered In the Kazusa Marker Databasementioning

confidence: 99%

Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants

et al. 2014

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“…Garden strawberry (F. ananassa Duch.) is a commercial octoploid species which is thought to originate in part from diploid wild strawberry, F. vesca (Hirakawa et al, 2014). Strawberries have two modes of reproduction; vegetative through stolons (runners) and sexual through flowers and fruits.…”

Section: Introductionmentioning

confidence: 99%

PGPR Improves Yield of Strawberry Species under Less-Fertilized Conditions

Kurokura

Hiraide

Shimamura

et al. 2017

ecb

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Plant growth promoting rhizobacteria (PGPR) is applied as biofertilizer to expect better production potential on commercial crops while keeping sustainability, but their function is dependent on the combination of PGPR and target crops. It has been reported that the application of PGPR in the soil resulted in the increment of strawberry yield, but other reports argue that PGPR has no effect on the yield potential. In addition, it is not clear whether the application timing of PGPR affects in a forcing cultivation system which usually requires transplanting. In this study, responses of diploid wild strawberry (Fragaria vesca) and garden strawberry (F. ananassa Duch.) varieties to PGPR application were examined. Application of PGPR, Bacillus cereus KI-2, during the flower induction increased the total yield and number of fruits in F. vesca 'Hawaii-4', and in garden strawberry 'Hoko-wase'. The application resulted in earlier flowering in 'Hoko-wase' while no difference was observed in 'Tochi-otome'. Sucrose content was also altered in cultivar dependent manner so that it was increased in 'Hawaii-4', while it was decreased in 'Tochi-otome'. These results indicate that PGPR has a potential to improve the yield factors while keeping the quality of the fruits, but the effect is cultivar dependent.

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“…In some allopolyploid crops, the genomes of progenitors species were first sequenced and then were used to assemble the polyploid genomes of the domesticated forms. This strategy was used in cotton , Li et al 2015, strawberry (Hirakawa et al 2014) and peanut (Bertioli et al 2016). Several strategies to construct genomic libraries (collection of DNA that will be sequenced) have been developed.…”

Section: Current Approaches and Methods In Plant Domestication Studiesmentioning

confidence: 99%

Current approaches and methods in plant domestication studies

Guerra-García¹

2017

Bot. Sci.

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Background: The domestication process has left signatures in the genomes of domesticated species. Before the existence of molecular markers, only phenotypic traits could be used in domestication studies and breeding programs, but these approaches required long time and effort. In the last decades, the use of molecular markers dramatically increased, and the development of massive sequencing tools have enable to obtain thousands or even millions of molecular markers. Questions: The main goal of this review us to bring a general and an integrative perpective of the data, approaches and questions that can be answered using new sequencing tools. Species study and data description: This work focuses on domesticated plants, comparing genetic and genomic data. Results: The use of molecular markers in the last decades has increased the efficiency and accuracy of plant breeding, allowing to access information about domestication history and to identify genes affected by domestication. Some patterns have been identified in domesticated species: (1) genetic diversity reductions due to demographic bottlenecks and artificial selection; (2) frequently, mutations related with domestication syndrome preexisted at low frequency in natural populations; (3) accumulation of deleterious mutation; (4) gene flow between wild and cultivated populations; (5) phenotypic convergence usually do not result from molecular convergence. There are several approaches that can be used in massive sequencing tools: de novo genome sequencing, whole genome resequencing, reduction of genome complexity using restriction enzymes, transcriptome analysis and epigenetic studies. Conclusions: Despite the progress made, enormous challenges remain: storage of large databases; development of fast and accurate methods to evaluate phenotypes; identification of paralogous genes in polyploid species; and the analysis of large and highly diverse genomes. Keywords: artificial selection, genomics, plant breeding, molecular markers Métodos y enfoques modernos del estudio de la domesticación ResumenAntecedentes: La domesticación es un proceso que ha dejado huellas en los genomas de las especies domesticadas. Anterior al surgimiento de los marcadores moleculares, únicamente se utilizaban atributos fenotípicos para estudiar la domesticación y para seleccionar individuos para el mejoramiento de cultivos. En las últimas décadas, el uso de marcadores moleculares se ha incrementado dramáticamente, y las técnicas de secuenciación masiva han permitido obtener miles, e incluso millones de marcadores Preguntas: El objetivo de esta revisión es brindar una visión general e integrativa de los distintos tipos de datos, enfoques y preguntas que se pueden contestar usando nuevas herramientas de secuenciación. Especies de estudio y descripción de datos: Especies de plantas cultivadas, contrastando datos genéticos con datos genómicos. Resultados: El uso de marcadores moleculares ha incrementado la eficiencia del mejoramiento de cultivos y ha permitido hacer inferencias sobre la ...

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Dissection of the Octoploid Strawberry Genome by Deep Sequencing of the Genomes of Fragaria Species

Cited by 206 publications

References 50 publications

Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants

Kazusa Marker DataBase: a database for genomics, genetics, and molecular breeding in plants

PGPR Improves Yield of Strawberry Species under Less-Fertilized Conditions

Current approaches and methods in plant domestication studies

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