TY  - JOUR
AU  - Kondić-Špika, Ankica
AU  - Mikić, Sanja
AU  - Mirosavljević, Milan
AU  - Trkulja, Dragana
AU  - Marjanović-Jeromela, Ana
AU  - Rajković, Dragana
AU  - Radanović, Aleksandra
AU  - Cvejić, Sandra
AU  - Glogovac, Svetlana
AU  - Dodig, Dejan
AU  - Božinović, Sofija
AU  - Šatović, Zlatko
AU  - Lazarević, Boris
AU  - Šimić, Domagoj
AU  - Novoselović, Dario
AU  - Vass, Imre
AU  - Pauk, Janos
AU  - Miladinović, Dragana
PY  - 2022
UR  - http://fiver.ifvcns.rs/handle/123456789/3447
AB  - The Pannonian Plain, as the most productive region of Southeast Europe, has a long tradition of agronomic production as well as agronomic research and plant breeding. Many research institutions from the agri-food sector of this region have a significant impact on agriculture. Their well-developed and fruitful breeding programmes resulted in productive crop varieties highly adapted to the specific regional environmental conditions. Rapid climatic changes that occurred during the last decades led to even more investigations of complex interactions between plants and their environments and the creation of climate-smart and resilient crops. Plant phenotyping is an essential part of botanical, biological, agronomic, physiological, biochemical, genetic, and other omics approaches. Phenotyping tools and applied methods differ among these disciplines, but all of them are used to evaluate and measure complex traits related to growth, yield, quality, and adaptation to different environmental stresses (biotic and abiotic). During almost a century-long period of plant breeding in the Pannonian region, plant phenotyping methods have changed, from simple measurements in the field to modern plant phenotyping and high-throughput non-invasive and digital technologies. In this review, we present a short historical background and the most recent developments in the field of plant phenotyping, as well as the results accomplished so far in Croatia, Hungary, and Serbia. Current status and perspectives for further simultaneous regional development and modernization of plant phenotyping are also discussed.
PB  - Oxford :  Society for Experimental Biology
T2  - Journal of Experimental Botany
T1  - Crop breeding for a changing climate in the Pannonian region: towards integration of modern phenotyping tools
EP  - 5110
IS  - 15
SP  - 5089
VL  - 73
DO  - 10.1093/jxb/erac181
ER  - 

@article{
author = "Kondić-Špika, Ankica and Mikić, Sanja and Mirosavljević, Milan and Trkulja, Dragana and Marjanović-Jeromela, Ana and Rajković, Dragana and Radanović, Aleksandra and Cvejić, Sandra and Glogovac, Svetlana and Dodig, Dejan and Božinović, Sofija and Šatović, Zlatko and Lazarević, Boris and Šimić, Domagoj and Novoselović, Dario and Vass, Imre and Pauk, Janos and Miladinović, Dragana",
year = "2022",
abstract = "The Pannonian Plain, as the most productive region of Southeast Europe, has a long tradition of agronomic production as well as agronomic research and plant breeding. Many research institutions from the agri-food sector of this region have a significant impact on agriculture. Their well-developed and fruitful breeding programmes resulted in productive crop varieties highly adapted to the specific regional environmental conditions. Rapid climatic changes that occurred during the last decades led to even more investigations of complex interactions between plants and their environments and the creation of climate-smart and resilient crops. Plant phenotyping is an essential part of botanical, biological, agronomic, physiological, biochemical, genetic, and other omics approaches. Phenotyping tools and applied methods differ among these disciplines, but all of them are used to evaluate and measure complex traits related to growth, yield, quality, and adaptation to different environmental stresses (biotic and abiotic). During almost a century-long period of plant breeding in the Pannonian region, plant phenotyping methods have changed, from simple measurements in the field to modern plant phenotyping and high-throughput non-invasive and digital technologies. In this review, we present a short historical background and the most recent developments in the field of plant phenotyping, as well as the results accomplished so far in Croatia, Hungary, and Serbia. Current status and perspectives for further simultaneous regional development and modernization of plant phenotyping are also discussed.",
publisher = "Oxford :  Society for Experimental Biology",
journal = "Journal of Experimental Botany",
title = "Crop breeding for a changing climate in the Pannonian region: towards integration of modern phenotyping tools",
pages = "5110-5089",
number = "15",
volume = "73",
doi = "10.1093/jxb/erac181"
}

Kondić-Špika, A., Mikić, S., Mirosavljević, M., Trkulja, D., Marjanović-Jeromela, A., Rajković, D., Radanović, A., Cvejić, S., Glogovac, S., Dodig, D., Božinović, S., Šatović, Z., Lazarević, B., Šimić, D., Novoselović, D., Vass, I., Pauk, J.,& Miladinović, D.. (2022). Crop breeding for a changing climate in the Pannonian region: towards integration of modern phenotyping tools. in Journal of Experimental Botany
Oxford :  Society for Experimental Biology., 73(15), 5089-5110.
https://doi.org/10.1093/jxb/erac181

Kondić-Špika A, Mikić S, Mirosavljević M, Trkulja D, Marjanović-Jeromela A, Rajković D, Radanović A, Cvejić S, Glogovac S, Dodig D, Božinović S, Šatović Z, Lazarević B, Šimić D, Novoselović D, Vass I, Pauk J, Miladinović D. Crop breeding for a changing climate in the Pannonian region: towards integration of modern phenotyping tools. in Journal of Experimental Botany. 2022;73(15):5089-5110.
doi:10.1093/jxb/erac181 .

Kondić-Špika, Ankica, Mikić, Sanja, Mirosavljević, Milan, Trkulja, Dragana, Marjanović-Jeromela, Ana, Rajković, Dragana, Radanović, Aleksandra, Cvejić, Sandra, Glogovac, Svetlana, Dodig, Dejan, Božinović, Sofija, Šatović, Zlatko, Lazarević, Boris, Šimić, Domagoj, Novoselović, Dario, Vass, Imre, Pauk, Janos, Miladinović, Dragana, "Crop breeding for a changing climate in the Pannonian region: towards integration of modern phenotyping tools" in Journal of Experimental Botany, 73, no. 15 (2022):5089-5110,
https://doi.org/10.1093/jxb/erac181 . .

TY  - JOUR
AU  - Adams, Thomas M.
AU  - Olsson, Tjelvar S. G.
AU  - Ramirez-Gonzalez, Ricardo H.
AU  - Bryant, Ruth
AU  - Bryson, Rosie
AU  - Campos, Pablo Eduardo
AU  - Fenwick, Paul
AU  - Feuerhelm, David
AU  - Hayes, Charlotte
AU  - Henriksson, Tina
AU  - Hubbard, Amelia
AU  - Jevtić, Radivoje
AU  - Judge, Christopher
AU  - Kerton, Matthew
AU  - Lage, Jacob
AU  - Lewis, Clare M.
AU  - Lilly, Christine
AU  - Meidan, Udi
AU  - Novoselović, Dario
AU  - Patrick, Colin
AU  - Wanyera, Ruth
AU  - Saunders, Diane G. O.
PY  - 2021
UR  - http://fiver.ifvcns.rs/handle/123456789/2077
AB  - BackgroundTranscriptomics is being increasingly applied to generate new insight into the interactions between plants and their pathogens. For the wheat yellow (stripe) rust pathogen (Puccinia striiformis f. sp. tritici, Pst) RNA-based sequencing (RNA-Seq) has proved particularly valuable, overcoming the barriers associated with its obligate biotrophic nature. This includes the application of RNA-Seq approaches to study Pst and wheat gene expression dynamics over time and the Pst population composition through the use of a novel RNA-Seq based surveillance approach called "field pathogenomics". As a dual RNA-Seq approach, the field pathogenomics technique also provides gene expression data from the host, giving new insight into host responses. However, this has created a wealth of data for interrogation.ResultsHere, we used the field pathogenomics approach to generate 538 new RNA-Seq datasets from Pst-infected field wheat samples, doubling the amount of transcriptomics data available for this important pathosystem. We then analysed these datasets alongside 66 RNA-Seq datasets from four Pst infection time-courses and 420 Pst-infected plant field and laboratory samples that were publicly available. A database of gene expression values for Pst and wheat was generated for each of these 1024 RNA-Seq datasets and incorporated into the development of the rust expression browser (http://www.rust-expression.com). This enables for the first time simultaneous 'point-and-click' access to gene expression profiles for Pst and its wheat host and represents the largest database of processed RNA-Seq datasets available for any of the three Puccinia wheat rust pathogens. We also demonstrated the utility of the browser through investigation of expression of putative Pst virulence genes over time and examined the host plants response to Pst infection.ConclusionsThe rust expression browser offers immense value to the wider community, facilitating data sharing and transparency and the underlying database can be continually expanded as more datasets become publicly available.
PB  - BMC, London
T2  - BMC Genomics
T1  - Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP
IS  - 1
VL  - 22
DO  - 10.1186/s12864-021-07488-3
ER  - 

@article{
author = "Adams, Thomas M. and Olsson, Tjelvar S. G. and Ramirez-Gonzalez, Ricardo H. and Bryant, Ruth and Bryson, Rosie and Campos, Pablo Eduardo and Fenwick, Paul and Feuerhelm, David and Hayes, Charlotte and Henriksson, Tina and Hubbard, Amelia and Jevtić, Radivoje and Judge, Christopher and Kerton, Matthew and Lage, Jacob and Lewis, Clare M. and Lilly, Christine and Meidan, Udi and Novoselović, Dario and Patrick, Colin and Wanyera, Ruth and Saunders, Diane G. O.",
year = "2021",
abstract = "BackgroundTranscriptomics is being increasingly applied to generate new insight into the interactions between plants and their pathogens. For the wheat yellow (stripe) rust pathogen (Puccinia striiformis f. sp. tritici, Pst) RNA-based sequencing (RNA-Seq) has proved particularly valuable, overcoming the barriers associated with its obligate biotrophic nature. This includes the application of RNA-Seq approaches to study Pst and wheat gene expression dynamics over time and the Pst population composition through the use of a novel RNA-Seq based surveillance approach called "field pathogenomics". As a dual RNA-Seq approach, the field pathogenomics technique also provides gene expression data from the host, giving new insight into host responses. However, this has created a wealth of data for interrogation.ResultsHere, we used the field pathogenomics approach to generate 538 new RNA-Seq datasets from Pst-infected field wheat samples, doubling the amount of transcriptomics data available for this important pathosystem. We then analysed these datasets alongside 66 RNA-Seq datasets from four Pst infection time-courses and 420 Pst-infected plant field and laboratory samples that were publicly available. A database of gene expression values for Pst and wheat was generated for each of these 1024 RNA-Seq datasets and incorporated into the development of the rust expression browser (http://www.rust-expression.com). This enables for the first time simultaneous 'point-and-click' access to gene expression profiles for Pst and its wheat host and represents the largest database of processed RNA-Seq datasets available for any of the three Puccinia wheat rust pathogens. We also demonstrated the utility of the browser through investigation of expression of putative Pst virulence genes over time and examined the host plants response to Pst infection.ConclusionsThe rust expression browser offers immense value to the wider community, facilitating data sharing and transparency and the underlying database can be continually expanded as more datasets become publicly available.",
publisher = "BMC, London",
journal = "BMC Genomics",
title = "Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP",
number = "1",
volume = "22",
doi = "10.1186/s12864-021-07488-3"
}

Adams, T. M., Olsson, T. S. G., Ramirez-Gonzalez, R. H., Bryant, R., Bryson, R., Campos, P. E., Fenwick, P., Feuerhelm, D., Hayes, C., Henriksson, T., Hubbard, A., Jevtić, R., Judge, C., Kerton, M., Lage, J., Lewis, C. M., Lilly, C., Meidan, U., Novoselović, D., Patrick, C., Wanyera, R.,& Saunders, D. G. O.. (2021). Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP. in BMC Genomics
BMC, London., 22(1).
https://doi.org/10.1186/s12864-021-07488-3

Adams TM, Olsson TSG, Ramirez-Gonzalez RH, Bryant R, Bryson R, Campos PE, Fenwick P, Feuerhelm D, Hayes C, Henriksson T, Hubbard A, Jevtić R, Judge C, Kerton M, Lage J, Lewis CM, Lilly C, Meidan U, Novoselović D, Patrick C, Wanyera R, Saunders DGO. Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP. in BMC Genomics. 2021;22(1).
doi:10.1186/s12864-021-07488-3 .

Adams, Thomas M., Olsson, Tjelvar S. G., Ramirez-Gonzalez, Ricardo H., Bryant, Ruth, Bryson, Rosie, Campos, Pablo Eduardo, Fenwick, Paul, Feuerhelm, David, Hayes, Charlotte, Henriksson, Tina, Hubbard, Amelia, Jevtić, Radivoje, Judge, Christopher, Kerton, Matthew, Lage, Jacob, Lewis, Clare M., Lilly, Christine, Meidan, Udi, Novoselović, Dario, Patrick, Colin, Wanyera, Ruth, Saunders, Diane G. O., "Rust expression browser: an open source database for simultaneous analysis of host and pathogen gene expression profiles with expVIP" in BMC Genomics, 22, no. 1 (2021),
https://doi.org/10.1186/s12864-021-07488-3 . .

TY  - JOUR
AU  - Jones, H.
AU  - Gosman, N.
AU  - Horsnell, R.
AU  - Rose, G. A.
AU  - Everest, L. A.
AU  - Bentley, A. R.
AU  - Tha, S.
AU  - Uauy, C.
AU  - Kowalski, A.
AU  - Novoselović, Dario
AU  - Simek, R.
AU  - Kobiljski, Borislav
AU  - Kondić-Špika, Ankica
AU  - Brbaklić, Ljiljana
AU  - Mitrofanova, O.
AU  - Chesnokov, Y.
AU  - Bonnett, D.
AU  - Greenland, A.
PY  - 2013
UR  - http://fiver.ifvcns.rs/handle/123456789/1255
AB  - Hexaploid bread wheat evolved from a rare hybridisation, which resulted in a loss of genetic diversity in the wheat D-genome with respect to the ancestral donor, Aegilops tauschii. Novel genetic variation can be introduced into modern wheat by recreating the above hybridisation; however, the information associated with the Ae. tauschii accessions in germplasm collections is limited, making rational selection of accessions into a re-synthesis programme difficult. We describe methodologies to identify novel diversity from Ae. tauschii accessions that combines Bayesian analysis of genotypic data, sub-species diversity and geographic information that summarises variation in climate and habitat at the collection point for each accession. Comparisons were made between diversity discovered amongst a panel of Ae. tauschii accessions, bread wheat varieties and lines from the CIMMYT synthetic hexaploid wheat programme. The selection of Ae. tauschii accessions based on differing approaches had significant effect on diversity within each set. Our results suggest that a strategy that combines several criteria will be most effective in maximising the sampled variation across multiple parameters. The analysis of multiple layers of variation in ex situ Ae. tauschii collections allows for an informed and rational approach to the inclusion of wild relatives into crop breeding programmes.
PB  - Springer, New York
T2  - Theoretical & Applied Genetics
T1  - Strategy for exploiting exotic germplasm using genetic, morphological, and environmental diversity: the Aegilops tauschii Coss. example
EP  - 1808
IS  - 7
SP  - 1793
VL  - 126
DO  - 10.1007/s00122-013-2093-x
ER  - 

@article{
author = "Jones, H. and Gosman, N. and Horsnell, R. and Rose, G. A. and Everest, L. A. and Bentley, A. R. and Tha, S. and Uauy, C. and Kowalski, A. and Novoselović, Dario and Simek, R. and Kobiljski, Borislav and Kondić-Špika, Ankica and Brbaklić, Ljiljana and Mitrofanova, O. and Chesnokov, Y. and Bonnett, D. and Greenland, A.",
year = "2013",
abstract = "Hexaploid bread wheat evolved from a rare hybridisation, which resulted in a loss of genetic diversity in the wheat D-genome with respect to the ancestral donor, Aegilops tauschii. Novel genetic variation can be introduced into modern wheat by recreating the above hybridisation; however, the information associated with the Ae. tauschii accessions in germplasm collections is limited, making rational selection of accessions into a re-synthesis programme difficult. We describe methodologies to identify novel diversity from Ae. tauschii accessions that combines Bayesian analysis of genotypic data, sub-species diversity and geographic information that summarises variation in climate and habitat at the collection point for each accession. Comparisons were made between diversity discovered amongst a panel of Ae. tauschii accessions, bread wheat varieties and lines from the CIMMYT synthetic hexaploid wheat programme. The selection of Ae. tauschii accessions based on differing approaches had significant effect on diversity within each set. Our results suggest that a strategy that combines several criteria will be most effective in maximising the sampled variation across multiple parameters. The analysis of multiple layers of variation in ex situ Ae. tauschii collections allows for an informed and rational approach to the inclusion of wild relatives into crop breeding programmes.",
publisher = "Springer, New York",
journal = "Theoretical & Applied Genetics",
title = "Strategy for exploiting exotic germplasm using genetic, morphological, and environmental diversity: the Aegilops tauschii Coss. example",
pages = "1808-1793",
number = "7",
volume = "126",
doi = "10.1007/s00122-013-2093-x"
}

Jones, H., Gosman, N., Horsnell, R., Rose, G. A., Everest, L. A., Bentley, A. R., Tha, S., Uauy, C., Kowalski, A., Novoselović, D., Simek, R., Kobiljski, B., Kondić-Špika, A., Brbaklić, L., Mitrofanova, O., Chesnokov, Y., Bonnett, D.,& Greenland, A.. (2013). Strategy for exploiting exotic germplasm using genetic, morphological, and environmental diversity: the Aegilops tauschii Coss. example. in Theoretical & Applied Genetics
Springer, New York., 126(7), 1793-1808.
https://doi.org/10.1007/s00122-013-2093-x

Jones H, Gosman N, Horsnell R, Rose GA, Everest LA, Bentley AR, Tha S, Uauy C, Kowalski A, Novoselović D, Simek R, Kobiljski B, Kondić-Špika A, Brbaklić L, Mitrofanova O, Chesnokov Y, Bonnett D, Greenland A. Strategy for exploiting exotic germplasm using genetic, morphological, and environmental diversity: the Aegilops tauschii Coss. example. in Theoretical & Applied Genetics. 2013;126(7):1793-1808.
doi:10.1007/s00122-013-2093-x .

Jones, H., Gosman, N., Horsnell, R., Rose, G. A., Everest, L. A., Bentley, A. R., Tha, S., Uauy, C., Kowalski, A., Novoselović, Dario, Simek, R., Kobiljski, Borislav, Kondić-Špika, Ankica, Brbaklić, Ljiljana, Mitrofanova, O., Chesnokov, Y., Bonnett, D., Greenland, A., "Strategy for exploiting exotic germplasm using genetic, morphological, and environmental diversity: the Aegilops tauschii Coss. example" in Theoretical & Applied Genetics, 126, no. 7 (2013):1793-1808,
https://doi.org/10.1007/s00122-013-2093-x . .