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Analytical and Decision Support Tools for Genomics-Assisted Breeding

Research output: Contribution to journalLiterature review

  • Rajeev K Varshney
  • Vikas K Singh
  • John M Hickey
  • Xu Xun
  • David F Marshall
  • Jun Wang
  • David Edwards
  • Jean-Marcel Ribaut

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    Rights statement: © 2015 The Authors. Published by Elsevier Ltd. This is an open access article under the CC BY license (http://creativecommons.org/licenses/by/4.0/).

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    Licence: Creative Commons: Attribution (CC-BY)

Original languageEnglish
Pages (from-to)354-363
JournalTrends in plant science
Volume21
Issue number4
Early online date1 Dec 2015
DOIs
Publication statusPublished - Apr 2016

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.

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