AgroGenome: Interactive Genomic-Based Web Server Developed Based on Data Collected for Accessions Stored in Polish Genebank
New intensive farming systems have resulted in a narrowing of the genetic diversity used in breeding programs. Breeders are looking for new sources of variation of specific traits to make genetic progress in adaptation to changing environmental conditions. Genomics-based plant germplasm research see...
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| Format: | Article |
| Language: | English |
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MDPI AG
2023-01-01
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| Series: | Agriculture |
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| Online Access: | https://www.mdpi.com/2077-0472/13/1/193 |
| _version_ | 1797447240980103168 |
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| author | Jerzy H. Czembor Elzbieta Czembor Marcin Krystek Juliusz Pukacki |
| author_facet | Jerzy H. Czembor Elzbieta Czembor Marcin Krystek Juliusz Pukacki |
| author_sort | Jerzy H. Czembor |
| collection | DOAJ |
| description | New intensive farming systems have resulted in a narrowing of the genetic diversity used in breeding programs. Breeders are looking for new sources of variation of specific traits to make genetic progress in adaptation to changing environmental conditions. Genomics-based plant germplasm research seeks to apply the techniques of genomics to germplasm characterization. Using these new methods and obtained data, plant breeders can increase the rate of genetic gains in specific breeding programs. Due to the complexity of heterogeneous sources of information, it is necessary to collect large quantities of referenced data. Molecular platforms are becoming increasingly important for the development of strategic germplasm resources for more effective molecular breeding of new cultivars. Following this trend in plant breeding, the AgroGenome portal for precise breeding programs was developed based on data collected for accessions stored in the Polish Genebank. It combines passport data of genotypes, phenotypic characteristics and interactive GWAS analysis visualization on the Manhattan plots based on GWAS results and on JBrowse interface. The AgroGenome portal can be utilized by breeders or researchers to explore diversity among investigated genomes. It is especially important to identify markers for tracking specific traits and identify QTL. The AgroGenome portal facilitates the exploitation and use of plant genetic resources stored in the Polish Genebank. |
| first_indexed | 2024-03-09T13:53:00Z |
| format | Article |
| id | doaj.art-5e88d982ce664031a33ef2a85fb66629 |
| institution | Directory Open Access Journal |
| issn | 2077-0472 |
| language | English |
| last_indexed | 2024-03-09T13:53:00Z |
| publishDate | 2023-01-01 |
| publisher | MDPI AG |
| record_format | Article |
| series | Agriculture |
| spelling | doaj.art-5e88d982ce664031a33ef2a85fb666292023-11-30T20:47:05ZengMDPI AGAgriculture2077-04722023-01-0113119310.3390/agriculture13010193AgroGenome: Interactive Genomic-Based Web Server Developed Based on Data Collected for Accessions Stored in Polish GenebankJerzy H. Czembor0Elzbieta Czembor1Marcin Krystek2Juliusz Pukacki3Plant Breeding and Acclimatization Institute—National Research Institute, Radzikow, 05-870 Blonie, PolandPlant Breeding and Acclimatization Institute—National Research Institute, Radzikow, 05-870 Blonie, PolandPoznan Supercomputing and Networking Center, ul. Jana Pawla II 10, 61-139 Poznan, PolandPoznan Supercomputing and Networking Center, ul. Jana Pawla II 10, 61-139 Poznan, PolandNew intensive farming systems have resulted in a narrowing of the genetic diversity used in breeding programs. Breeders are looking for new sources of variation of specific traits to make genetic progress in adaptation to changing environmental conditions. Genomics-based plant germplasm research seeks to apply the techniques of genomics to germplasm characterization. Using these new methods and obtained data, plant breeders can increase the rate of genetic gains in specific breeding programs. Due to the complexity of heterogeneous sources of information, it is necessary to collect large quantities of referenced data. Molecular platforms are becoming increasingly important for the development of strategic germplasm resources for more effective molecular breeding of new cultivars. Following this trend in plant breeding, the AgroGenome portal for precise breeding programs was developed based on data collected for accessions stored in the Polish Genebank. It combines passport data of genotypes, phenotypic characteristics and interactive GWAS analysis visualization on the Manhattan plots based on GWAS results and on JBrowse interface. The AgroGenome portal can be utilized by breeders or researchers to explore diversity among investigated genomes. It is especially important to identify markers for tracking specific traits and identify QTL. The AgroGenome portal facilitates the exploitation and use of plant genetic resources stored in the Polish Genebank.https://www.mdpi.com/2077-0472/13/1/193AgroGenome portalbiodiversitycrop designbig datagenomic selectiongenomics |
| spellingShingle | Jerzy H. Czembor Elzbieta Czembor Marcin Krystek Juliusz Pukacki AgroGenome: Interactive Genomic-Based Web Server Developed Based on Data Collected for Accessions Stored in Polish Genebank Agriculture AgroGenome portal biodiversity crop design big data genomic selection genomics |
| title | AgroGenome: Interactive Genomic-Based Web Server Developed Based on Data Collected for Accessions Stored in Polish Genebank |
| title_full | AgroGenome: Interactive Genomic-Based Web Server Developed Based on Data Collected for Accessions Stored in Polish Genebank |
| title_fullStr | AgroGenome: Interactive Genomic-Based Web Server Developed Based on Data Collected for Accessions Stored in Polish Genebank |
| title_full_unstemmed | AgroGenome: Interactive Genomic-Based Web Server Developed Based on Data Collected for Accessions Stored in Polish Genebank |
| title_short | AgroGenome: Interactive Genomic-Based Web Server Developed Based on Data Collected for Accessions Stored in Polish Genebank |
| title_sort | agrogenome interactive genomic based web server developed based on data collected for accessions stored in polish genebank |
| topic | AgroGenome portal biodiversity crop design big data genomic selection genomics |
| url | https://www.mdpi.com/2077-0472/13/1/193 |
| work_keys_str_mv | AT jerzyhczembor agrogenomeinteractivegenomicbasedwebserverdevelopedbasedondatacollectedforaccessionsstoredinpolishgenebank AT elzbietaczembor agrogenomeinteractivegenomicbasedwebserverdevelopedbasedondatacollectedforaccessionsstoredinpolishgenebank AT marcinkrystek agrogenomeinteractivegenomicbasedwebserverdevelopedbasedondatacollectedforaccessionsstoredinpolishgenebank AT juliuszpukacki agrogenomeinteractivegenomicbasedwebserverdevelopedbasedondatacollectedforaccessionsstoredinpolishgenebank |