eprintid: 9161
rev_number: 12
eprint_status: archive
userid: 1305
dir: disk0/00/00/91/61
datestamp: 2015-12-08 05:00:11
lastmod: 2016-08-19 04:06:32
status_changed: 2015-12-08 05:00:11
type: article
metadata_visibility: show
creators_name: Varshney, R K
creators_name: Singh, V K
creators_name: Hickey, J M
creators_name: Xun, X
creators_name: Marshall, D F
creators_name: Wang, J
creators_name: Edwards, D
creators_name: Ribaut, J M
icrisatcreators_name: Varshney, R K
icrisatcreators_name: Singh, V K
affiliation: ICRISAT (Patancheru)
affiliation: School of Plant Biology, University of Western Australia (Crawley)
affiliation: The Roslin Institute and Royal(Dick) School of Veterinary Studies,The University of Edinburgh (Easter Bush)
affiliation: Beijing Genomics Institute(BGI) (Shenzhen)
affiliation: Information and Computational Sciences, The James Hutton Institute (Dundee)
affiliation: Generation Challenge Program/Integrated Breeding Platform (Mexico)
country: India
country: Australia
country: UK
country: China
country: Mexico
title: Analytical and Decision Support Tools for Genomics-Assisted Breeding
ispublished: inpress
subjects: s2.13
divisions: D3
crps: crp1.5
full_text_status: public
keywords: Data management, Decision support tools, Genetic mapping, Genomic selection, Genomics-assisted breeding, Marker assisted selection
note: Open access funded by the Author(s)
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.
date: 2015-12
date_type: published
publication: Trends in Plant Science
publisher: Elsevier
pagerange: 01-10
id_number: 10.1016/j.tplants.2015.10.018
refereed: TRUE
issn: 1360-1385
official_url: http://dx.doi.org/10.1016/j.tplants.2015.10.018
related_url_url: https://scholar.google.co.in/scholar?hl=en&q=Analytical+and+Decision+Support+Tools+for+Genomics-Assisted+Breeding&btnG=
related_url_type: pub
citation:   Varshney, R K and Singh, V K and Hickey, J M and Xun, X and Marshall, D F and Wang, J and Edwards, D and Ribaut, J M  (2015) Analytical and Decision Support Tools for Genomics-Assisted Breeding.  Trends in Plant Science.  01-10.  ISSN 1360-1385    (In Press)  
document_url: http://oar.icrisat.org/9161/1/PIIS1360138515002770.pdf