IDEAS home Printed from https://ideas.repec.org/a/gam/jagris/v13y2023i1p193-d1033782.html
   My bibliography  Save this article

AgroGenome: Interactive Genomic-Based Web Server Developed Based on Data Collected for Accessions Stored in Polish Genebank

Author

Listed:
  • Jerzy H. Czembor

    (Plant Breeding and Acclimatization Institute—National Research Institute, Radzikow, 05-870 Blonie, Poland)

  • Elzbieta Czembor

    (Plant Breeding and Acclimatization Institute—National Research Institute, Radzikow, 05-870 Blonie, Poland)

  • Marcin Krystek

    (Poznan Supercomputing and Networking Center, ul. Jana Pawla II 10, 61-139 Poznan, Poland)

  • Juliusz Pukacki

    (Poznan Supercomputing and Networking Center, ul. Jana Pawla II 10, 61-139 Poznan, Poland)

Abstract

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.

Suggested Citation

  • Jerzy H. Czembor & Elzbieta Czembor & Marcin Krystek & Juliusz Pukacki, 2023. "AgroGenome: Interactive Genomic-Based Web Server Developed Based on Data Collected for Accessions Stored in Polish Genebank," Agriculture, MDPI, vol. 13(1), pages 1-16, January.
    • Handle: RePEc:gam:jagris:v:13:y:2023:i:1:p:193-:d:1033782
    as

    Download full text from publisher

    File URL: https://www.mdpi.com/2077-0472/13/1/193/pdf
    Download Restriction: no
    File URL: https://www.mdpi.com/2077-0472/13/1/193/
    Download Restriction: no
    ---><---

    References listed on IDEAS

    as
    1. Jeremy Schmutz & Steven B. Cannon & Jessica Schlueter & Jianxin Ma & Therese Mitros & William Nelson & David L. Hyten & Qijian Song & Jay J. Thelen & Jianlin Cheng & Dong Xu & Uffe Hellsten & Gregory , 2010. "Erratum: Genome sequence of the palaeopolyploid soybean," Nature, Nature, vol. 465(7294), pages 120-120, May.
    2. Julia Bailey-Serres & Jane E. Parker & Elizabeth A. Ainsworth & Giles E. D. Oldroyd & Julian I. Schroeder, 2019. "Genetic strategies for improving crop yields," Nature, Nature, vol. 575(7781), pages 109-118, November.
    3. Jeremy Schmutz & Steven B. Cannon & Jessica Schlueter & Jianxin Ma & Therese Mitros & William Nelson & David L. Hyten & Qijian Song & Jay J. Thelen & Jianlin Cheng & Dong Xu & Uffe Hellsten & Gregory , 2010. "Genome sequence of the palaeopolyploid soybean," Nature, Nature, vol. 463(7278), pages 178-183, January.
    4. Michael D. Purugganan & Dorian Q. Fuller, 2009. "The nature of selection during plant domestication," Nature, Nature, vol. 457(7231), pages 843-848, February.
    Full references (including those not matched with items on IDEAS)

    Most related items

    These are the items that most often cite the same works as this one and are cited by the same works as this one.
    1. Wolfgang Goettel & Hengyou Zhang & Ying Li & Zhenzhen Qiao & He Jiang & Dianyun Hou & Qijian Song & Vincent R. Pantalone & Bao-Hua Song & Deyue Yu & Yong-qiang Charles An, 2022. "POWR1 is a domestication gene pleiotropically regulating seed quality and yield in soybean," Nature Communications, Nature, vol. 13(1), pages 1-11, December.
    2. Hai Anh Tran & Hyun Jo & Thi Cuc Nguyen & Jeong-Dong Lee & Hak Soo Seo & Jong Tae Song, 2024. "Genome-Wide Association Analysis for Submergence Tolerance at the Early Vegetative and Germination Stages in Wild Soybean ( Glycine soja )," Agriculture, MDPI, vol. 14(9), pages 1-17, September.
    3. Yukari Nagatoshi & Kenta Ikazaki & Yasufumi Kobayashi & Nobuyuki Mizuno & Ryohei Sugita & Yumiko Takebayashi & Mikiko Kojima & Hitoshi Sakakibara & Natsuko I. Kobayashi & Keitaro Tanoi & Kenichiro Fuj, 2023. "Phosphate starvation response precedes abscisic acid response under progressive mild drought in plants," Nature Communications, Nature, vol. 14(1), pages 1-16, December.
    4. Octavio R. Salazar & Ke Chen & Vanessa J. Melino & Muppala P. Reddy & Eva Hřibová & Jana Čížková & Denisa Beránková & Juan Pablo Arciniegas Vega & Lina María Cáceres Leal & Manuel Aranda & Lukasz Jare, 2024. "SOS1 tonoplast neo-localization and the RGG protein SALTY are important in the extreme salinity tolerance of Salicornia bigelovii," Nature Communications, Nature, vol. 15(1), pages 1-21, December.
    5. Shichen Li & Zhihui Sun & Qing Sang & Chao Qin & Lingping Kong & Xin Huang & Huan Liu & Tong Su & Haiyang Li & Milan He & Chao Fang & Lingshuang Wang & Shuangrong Liu & Bin Liu & Baohui Liu & Xiangdon, 2023. "Soybean reduced internode 1 determines internode length and improves grain yield at dense planting," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    6. Isaac Njaci & Bernice Waweru & Nadia Kamal & Meki Shehabu Muktar & David Fisher & Heidrun Gundlach & Collins Muli & Lucy Muthui & Mary Maranga & Davies Kiambi & Brigitte L. Maass & Peter M. F. Emmrich, 2023. "Chromosome-level genome assembly and population genomic resource to accelerate orphan crop lablab breeding," Nature Communications, Nature, vol. 14(1), pages 1-13, December.
    7. Weidong Wang & Liyang Chen & Kevin Fengler & Joy Bolar & Victor Llaca & Xutong Wang & Chancelor B. Clark & Tomara J. Fleury & Jon Myrvold & David Oneal & Maria Magdalena Dyk & Ashley Hudson & Jesse Mu, 2021. "A giant NLR gene confers broad-spectrum resistance to Phytophthora sojae in soybean," Nature Communications, Nature, vol. 12(1), pages 1-8, December.
    8. Jiaqi Sun & Shiyu Huang & Qing Lu & Shuo Li & Shizhen Zhao & Xiaojian Zheng & Qian Zhou & Wenxiao Zhang & Jie Li & Lili Wang & Ke Zhang & Wenyu Zheng & Xianzhong Feng & Baohui Liu & Fanjiang Kong & Fe, 2023. "UV-B irradiation-activated E3 ligase GmILPA1 modulates gibberellin catabolism to increase plant height in soybean," Nature Communications, Nature, vol. 14(1), pages 1-17, December.
    9. Xiao Feng & Qipian Chen & Weihong Wu & Jiexin Wang & Guohong Li & Shaohua Xu & Shao Shao & Min Liu & Cairong Zhong & Chung-I Wu & Suhua Shi & Ziwen He, 2024. "Genomic evidence for rediploidization and adaptive evolution following the whole-genome triplication," Nature Communications, Nature, vol. 15(1), pages 1-15, December.
    10. Jessen V. Bredeson & Jessica B. Lyons & Ibukun O. Oniyinde & Nneka R. Okereke & Olufisayo Kolade & Ikenna Nnabue & Christian O. Nwadili & Eva Hřibová & Matthew Parker & Jeremiah Nwogha & Shengqiang Sh, 2022. "Chromosome evolution and the genetic basis of agronomically important traits in greater yam," Nature Communications, Nature, vol. 13(1), pages 1-16, December.
    11. Aron Park & Se-Hee Kang & Byeong-Hee Kang & Sreeparna Chowdhury & Seo-Young Shin & Won-Ho Lee & Jeong-Dong Lee & Sungwoo Lee & Yu-Mi Choi & Bo-Keun Ha, 2023. "Identification of a Novel KTi-1 Allele Associated with Reduced Trypsin Inhibitor Activity in Soybean Accessions," Agriculture, MDPI, vol. 13(11), pages 1-14, October.
    12. Rahul Kumar & Prashant Swapnil & Mukesh Meena & Shweta Selpair & Bal Govind Yadav, 2022. "Plant Growth-Promoting Rhizobacteria (PGPR): Approaches to Alleviate Abiotic Stresses for Enhancement of Growth and Development of Medicinal Plants," Sustainability, MDPI, vol. 14(23), pages 1-16, November.
    13. David Wickell & Li-Yaung Kuo & Hsiao-Pei Yang & Amra Dhabalia Ashok & Iker Irisarri & Armin Dadras & Sophie de Vries & Jan de Vries & Yao-Moan Huang & Zheng Li & Michael S. Barker & Nolan T. Hartwick , 2021. "Underwater CAM photosynthesis elucidated by Isoetes genome," Nature Communications, Nature, vol. 12(1), pages 1-13, December.
    14. Zilong Guo & Hongrui Cao & Jing Zhao & Shuang Bai & Wenting Peng & Jian Li & Lili Sun & Liyu Chen & Zhihao Lin & Chen Shi & Qing Yang & Yongqing Yang & Xiurong Wang & Jiang Tian & Zhichang Chen & Hong, 2022. "A natural uORF variant confers phosphorus acquisition diversity in soybean," Nature Communications, Nature, vol. 13(1), pages 1-14, December.
    15. Wu, Lihong & Quan, Hao & Wu, Lina & Zhang, Xi & Feng, Hao & Ding, Dianyuan & Siddique, Kadambot H.M., 2023. "Responses of winter wheat yield and water productivity to sowing time and plastic mulching in the Loess Plateau," Agricultural Water Management, Elsevier, vol. 289(C).
    16. repec:idb:brikps:64718 is not listed on IDEAS
    17. Serge Svizzero, 2018. "Plant domestication more rapid under optimizing behavior," Post-Print hal-02145462, HAL.
    18. Mu, Qing & Cai, Huanjie & Sun, Shikun & Wen, Shanshan & Xu, Jiatun & Dong, Mengqi & Saddique, Qaisar, 2021. "The physiological response of winter wheat under short-term drought conditions and the sensitivity of different indices to soil water changes," Agricultural Water Management, Elsevier, vol. 243(C).
    19. Ru Fang, Yan & Zhang, Silu & Zhou, Ziqiao & Shi, Wenjun & Hui Xie, Guang, 2022. "Sustainable development in China: Valuation of bioenergy potential and CO2 reduction from crop straw," Applied Energy, Elsevier, vol. 322(C).
    20. Douglas Gollin, 2020. "Conserving genetic resources for agriculture: economic implications of emerging science," Food Security: The Science, Sociology and Economics of Food Production and Access to Food, Springer;The International Society for Plant Pathology, vol. 12(5), pages 919-927, October.
    21. Yongming Liu & Gengxin Xie & Qichang Yang & Maozhi Ren, 2021. "Biotechnological development of plants for space agriculture," Nature Communications, Nature, vol. 12(1), pages 1-3, December.

    Corrections

    All material on this site has been provided by the respective publishers and authors. You can help correct errors and omissions. When requesting a correction, please mention this item's handle: RePEc:gam:jagris:v:13:y:2023:i:1:p:193-:d:1033782. See general information about how to correct material in RePEc.

    If you have authored this item and are not yet registered with RePEc, we encourage you to do it here. This allows to link your profile to this item. It also allows you to accept potential citations to this item that we are uncertain about.

    If CitEc recognized a bibliographic reference but did not link an item in RePEc to it, you can help with this form .

    If you know of missing items citing this one, you can help us creating those links by adding the relevant references in the same way as above, for each refering item. If you are a registered author of this item, you may also want to check the "citations" tab in your RePEc Author Service profile, as there may be some citations waiting for confirmation.

    For technical questions regarding this item, or to correct its authors, title, abstract, bibliographic or download information, contact: MDPI Indexing Manager (email available below). General contact details of provider: https://www.mdpi.com .

    Please note that corrections may take a couple of weeks to filter through the various RePEc services.

    IDEAS is a RePEc service. RePEc uses bibliographic data supplied by the respective publishers.