title: Analytical and Decision Support Tools for Genomics-Assisted Breeding.
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.
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India; School of Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, Australia. Electronic address: r.k.varshney@cgiar.org.
authors.forename: Rajeev K
authors.initials: RK
authors.lastname: Varshney
authors.affiliation: International Crops Research Institute for the Semi-Arid Tropics (ICRISAT), Patancheru, India.
authors.forename: Vikas K
authors.initials: VK
authors.lastname: Singh
authors.affiliation: The Roslin Institute and Royal (Dick) School of Veterinary Studies, The University of Edinburgh, Easter Bush, UK.
authors.forename: John M
authors.initials: JM
authors.lastname: Hickey
authors.affiliation: Beijing Genomics Institute (BGI) Shenzhen, Shenzhen, China.
authors.forename: Xu
authors.initials: X
authors.lastname: Xun
authors.affiliation: Information and Computational Sciences, The James Hutton Institute, Invergowrie, Dundee, UK.
authors.forename: David F
authors.initials: DF
authors.lastname: Marshall
authors.affiliation: Beijing Genomics Institute (BGI) Shenzhen, Shenzhen, China.
authors.forename: Jun
authors.initials: J
authors.lastname: Wang
authors.affiliation: School of Plant Biology, University of Western Australia, 35 Stirling Highway, Crawley, Australia.
authors.forename: David
authors.initials: D
authors.lastname: Edwards
authors.affiliation: Generation Challenge Program/Integrated Breeding Platform, c/o CIMMYT, Apdo. Postal 6-641, DF Mexico, Mexico.
authors.forename: Jean-Marcel
authors.initials: JM
authors.lastname: Ribaut
keywords: data management; decision support tools; genetic mapping; genomic selection; genomics-assisted breeding; marker assisted selection