PANOMICS meets germplasm

Weckwerth, W and Ghatak, A and Bellaire, A and Chaturvedi, P and Varshney, R K (2020) PANOMICS meets germplasm. Plant Biotechnology Journal (TSI), 18 (7). pp. 1507-1525. ISSN 1467-7644

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Abstract

Genotyping-by-sequencing has enabled approaches for genomic selection to improve yield, stress resistance and nutritional value. More and more resource studies are emerging providing 1000 and more genotypes and millions of SNPs for one species covering a hitherto inaccessible intraspecific genetic variation. The larger the databases are growing, the better statistical approaches for genomic selection will be available. However, there are clear limitations on the statistical but also on the biological part. Intraspecific genetic variation is able to explain a high proportion of the phenotypes, but a large part of phenotypic plasticity also stems from environmentally driven transcriptional, post-transcriptional, ranslational, post-translational, epigenetic and metabolic regulation. Moreover, regulation of the same gene can have different phenotypic outputs in different environments. Consequently, to explain and understand environment-dependent phenotypic plasticity based on the available genotype variation we have to integrate the analysis of further molecular levels reflecting the complete information flow from the gene to metabolism to phenotype. Interestingly, metabolomics platforms are already more cost-effective than NGS platforms and are decisive for the prediction of nutritional value or stress resistance. Here, we propose three fundamental pillars for future breeding strategies in the framework of Green Systems Biology: (i) combining genome selection with environment dependent PANOMICS analysis and deep learning to improve prediction accuracy for marker dependent trait performance; (ii) PANOMICS resolution at subtissue, cellular and subcellular level provides information about fundamental functions of selected markers; (iii) combining PANOMICS with genome editing and speed breeding tools to accelerate and enhance large-scale functional validation of trait-specific precision breeding.

Item Type:	Article
Divisions:	Research Program : Genetic Gains
CRP:	CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC)
Uncontrolled Keywords:	Green systems biology, PANOMICS, Plant systems biology, Multi-omics, Phenotyping, Crop improvement, Germplasm, Genome editing, GWAS.
Subjects:	Others > Genetics and Genomics Others > Germplasm
Depositing User:	Mr Arun S
Date Deposited:	14 Aug 2020 11:39
Last Modified:	14 Aug 2020 11:40
URI:	http://oar.icrisat.org/id/eprint/11557
Official URL:	https://doi.org/10.1111/pbi.13372
Projects:	UNSPECIFIED
Funders:	UNSPECIFIED
Acknowledgement:	We thank Austrian Science Fund (FWF, DerWissenschaftsfonds), Grant agreement number W1257-820 for the financial support of Arindam Ghatak. Rajeev K Varshney is thankful to Science & Engineering Research Board (SERB) of Department of Science & Technology (DST), Government of India for providing the J.C.Bose National Fellowship (SB/S9/Z-13/2019) and CGIAR Research Program on Grain Legumes and Dryland Cereals (GLDC) for Funding Research at Center of Excellence in Genomics & Systems Biology (CEGSB), ICRISAT, Patancheru, Hyderabad, India. ICRISAT is a member of CGIAR Consortium.
Links:	Google Scholar

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