Using SNP/INDEL diversity patterns to identify a core group of genotypes from FVC11, a superior hybrid family of Fragaria virginiana Miller and F. chiloensis (L.) Miller

Ranaweera, L. T.; Perera, H. A. C. R.; Weebadde, Cholani; Finn, Chad E.; Bassil, Nahla V.; Hancock, James F.

doi:10.1007/s10722-019-00819-0

Cited by 4 publications

(3 citation statements)

References 20 publications

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“…However, simple spreadsheets or manually prepared note pages cannot be used to visualize the essential information and complex pedigrees. Breeding programs often suffer a lot when the breeder gets retired or moved to a different position [44–46]. The newly hired breeder cannot practically go through the individual records of the existing breeding germplasm.…”

Section: Resultsmentioning

confidence: 99%

Application of Pedimap — a pedigree visualization tool — to facilitate the decisioning of rice breeding in Sri Lanka

Rathnayake

Sahibdeen

Udawela³

et al. 2020

Preprint

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17The development of rice cultivars with desirable traits is essential. The decision-making is a 18 crucial step in rice breeding programs. The breeders can make efficient and pragmatic decisions 19 if an organized pedigree visualization platform is available for the material of the rice breeding 20 germplasm. The staple food in Sri Lanka is rice, and there is a great demand for improved 21 varieties with high yield and other promising traits. In the present study, the available data of 22 all the rice varieties released by Rice Research and Development Institute, Sri Lanka, and the 23 related landraces and genotypes were arranged in Pedimap, a pedigree visualization tool. 24 Pedimap can showcase pedigree relationships, phenotypic, and molecular data. The Identity by 25 Descent (IBD) probabilities were calculated using FlexQTL software and included in the 26 Pedimap database. The parentage selection based on the variations of phenotypic traits, 27 selection of marker alleles for molecular breeding, and detection of the founders of genetic 28 effects can be swiftly conducted using Pedimap. However, the power of harnessing the value 29of Pedimap for making breeding decisions relies on the availability of data for the traits, 30 markers, and genomic sequences. Thus, it is imperative to characterize the breeding 31 germplasms using standard phenomic and genomic characterization procedures before 32 organized into Pedimap. Thereby, the worldwide breeding programs can benefit from each 33 other to produce improved varieties to meet global challenges. 34 35

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Section: Resultsmentioning

confidence: 99%

Application of Pedimap — a pedigree visualization tool — to facilitate the decisioning of rice breeding in Sri Lanka

Rathnayake

Sahibdeen

Udawela³

et al. 2020

Preprint

View full text Add to dashboard Cite

show abstract

“…However, simple spreadsheets or manually prepared note pages cannot be used to visualize the essential information and complex pedigrees. Breeding programs often suffer a lot when the breeder gets retired or moved to a different position 49 – 51 . The newly hired breeder cannot practically go through the individual records of the existing breeding germplasm.…”

Section: Discussionmentioning

confidence: 99%

Application of Pedimap: a pedigree visualization tool to facilitate the decisioning of rice breeding in Sri Lanka

Rathnayake

Sahibdeen

Udawela³

et al. 2020

Sci Rep

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the development of rice cultivars with desirable traits is essential. the decision-making is a crucial step in rice breeding programs. Breeders can make efficient and pragmatic decisions if an organized pedigree visualization platform is available for the accessions and cultivars in rice breeding germplasm. in the present study, the available data of all the rice varieties released by Rice Research and Development institute, Sri Lanka, and the related landraces and genotypes were arranged in pedimap, a pedigree visualization tool. pedimap can showcase pedigree relationships, phenotypic, and molecular data. the identity by descent probabilities were calculated using flexQtL software and included in the pedimap database. the parentage selection based on the variations of phenotypic traits, selection of marker alleles for molecular breeding, and detection of the founders of genetic effects can be swiftly conducted using Pedimap. However, the power of harnessing the value of pedimap for making breeding decisions relies on the availability of data for the traits, markers, and genomic sequences. thus, it is imperative to characterize the breeding germplasms using standard phenomic and genomic characterization procedures such as the assessment of before organized into Pedimap. Thereby, the worldwide breeding programs can benefit from each other to produce improved varieties to meet global challenges. Rice is one of the major crops in the world, with an annual production over 700 million metric tons 1. Half of the world population consumes rice as the staple food 2. Currently, the demand for rice is rapidly increasing due to the growth of the human population 3. However, the current rice production cannot meet the increasing demand causing severe food security issues. The biotic and abiotic stresses also exert a negative influence on rice production 4. The rice farming is also a way of living for many people, especially in numerous Asian countries 5. At present, 1.8 million Sri Lankan families engage in rice farming over 870,000 hectares 6. The annual rice production in Sri Lanka is approximately 2.3 million metric tons (MT), which is insufficient to fulfill the domestic rice demand of 3.0 million 7. Hence, the Sri Lankan government spends about USD 400 million to import rice annually 7,8. The rice production is mainly affected by drought and irregular rainfall patterns caused by climate change 9-11 , adverse soil conditions such as salinity 6,12 , and pest and disease attacks 13. The biotic and abiotic stresses in rice farming can be controlled using numerous agronomic practices such as irrigation, drainage, fertilization, and the application of pesticides. However, the rate of success of the controlling methods is limited 13 due to the unpredictable nature of climate change, soil degradation, variations in pest dynamics, and development of pest resistance 14. Therefore, breeding is considered as the most successful strategy to produce high yielding and stress-resilient rice varieties 15. The improved rice genotypes can...

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“…× ananassa cultivars ( Monfort et al, 2006 ; Shimomura and Hirashima, 2006 ; Honjo et al, 2011 ). The IStraw90 Axiom array is a genotyping platform for Fragaria able to identify SNPs, indels, and also is used for mapping ( Mahoney et al, 2016 ; Nagano et al, 2017 ; Sooriyapathirana et al, 2019 ; Oh et al, 2020 ). In the case of F. chiloensis subsp.…”

Section: The Chilean Strawberrymentioning

confidence: 99%

Southern Species From the Biodiversity Hotspot of Central Chile: A Source of Color, Aroma, and Metabolites for Global Agriculture and Food Industry in a Scenario of Climate Change

et al. 2020

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Two interesting plants within the Chilean flora (wild and crop species) can be found with a history related to modern fruticulture: Fragaria chiloensis subsp. chiloensis (Rosaceae) and Vasconcellea pubescens (Caricaceae). Both species have a wide natural distribution, which goes from the Andes mountains to the sea (East-West), and from the Atacama desert to the South of Chile (North-South). The growing locations are included within the Chilean Winter Rainfall-Valdivian Forest hotspot. Global warming is of great concern as it increases the risk of losing wild plant species, but at the same time, gives a chance for usually longer term genetic improvement using naturally adapted material and the source for generating healthy foods. Modern agriculture intensifies the attractiveness of native undomesticated species as a way to provide compounds like antioxidants or tolerant plants for climate change scenario. F. chiloensis subsp. chiloensis as the mother of commercial strawberry (Fragaria × ananassa) is an interesting genetic source for the improvement of fruit flavor and stress tolerance. On the other hand, V. pubescens produces fruit with high level of antioxidants and proteolytic enzymes of interest to the food industry. The current review compiles the botanical, physiological and phytochemical description of F. chiloensis subsp. chiloensis and V. pubescens, highlighting their potential as functional foods and as source of compounds with several applications in the pharmaceutical, biotechnological, and food science. The impact of global warming scenario on the distribution of the species is also discussed.

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Using SNP/INDEL diversity patterns to identify a core group of genotypes from FVC11, a superior hybrid family of Fragaria virginiana Miller and F. chiloensis (L.) Miller

Cited by 4 publications

References 20 publications

Application of Pedimap — a pedigree visualization tool — to facilitate the decisioning of rice breeding in Sri Lanka

Application of Pedimap — a pedigree visualization tool — to facilitate the decisioning of rice breeding in Sri Lanka

Application of Pedimap: a pedigree visualization tool to facilitate the decisioning of rice breeding in Sri Lanka

Southern Species From the Biodiversity Hotspot of Central Chile: A Source of Color, Aroma, and Metabolites for Global Agriculture and Food Industry in a Scenario of Climate Change

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