Analytical and decision support tools for Genomics-Assisted Breeding

R.K. Varshney; V.K. Singh; J.M. Hickey; X. Xun; D.F. Marshall; J. Wang; D. Edwards; J-M Ribaut

doi:10.1016/j.tplants.2015.10.018

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Analytical and decision support tools for Genomics-Assisted Breeding

Journal article

Open access

Peer reviewed

Analytical and decision support tools for Genomics-Assisted Breeding

R.K. Varshney, V.K. Singh, J.M. Hickey, X. Xun, D.F. Marshall, J. Wang, D. Edwards and J-M Ribaut

Trends in Plant Science, Vol.21(4), pp.354-363

2016

DOI: https://doi.org/10.1016/j.tplants.2015.10.018

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Abstract

To successfully implement genomics-assisted breeding (GAB) in crop improvement programs, efficient and effective analytical and decision support tools (ADSTs) are ‘must haves’ to evaluate and select plants for developing next-generation crops. Here we review the applications and deployment of appropriate ADSTs for GAB, in the context of next-generation sequencing (NGS), an emerging source of massive genomic information. We discuss suitable software tools and pipelines for marker-based approaches (markers/haplotypes), including large-scale genotypic and phenotypic, data management, and molecular breeding approaches. Although phenotyping remains expensive and time consuming, prediction of allelic effects on phenotypes opens new doors to enhance genetic gain across crop cycles, building on reliable phenotyping approaches and good crop information systems, including pedigree information and target haplotypes.

Details

Title: Analytical and decision support tools for Genomics-Assisted Breeding
Authors/Creators: R.K. Varshney (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
V.K. Singh (Author/Creator) - International Crops Research Institute for the Semi-Arid Tropics
J.M. Hickey (Author/Creator) - Roslin Institute
X. Xun (Author/Creator) - BGI Group (China)
D.F. Marshall (Author/Creator) - James Hutton Institute
J. Wang (Author/Creator) - BGI Group (China)
D. Edwards (Author/Creator) - The University of Western Australia
J-M Ribaut (Author/Creator) - Centro Internacional de Mejoramiento de Maíz Y Trigo
Publication Details: Trends in Plant Science, Vol.21(4), pp.354-363
Publisher: Elsevier BV
Identifiers: 991005543475207891
Copyright: © 2015 The Authors.
Murdoch Affiliation: Murdoch University
Language: English
Resource Type: Journal article

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Collaboration types: Domestic collaboration; International collaboration
Citation topics: 3 Agriculture, Environment & Ecology; 3.4 Crop Science; 3.4.96 QTL
Web Of Science research areas: Plant Sciences
ESI research areas: Plant & Animal Science