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Approaches in Characterizing Genetic Structure and Mapping in a Rice Multiparental Population1.18 MB
Published (Version of record)CC BY V4.0, Open Access
Published (Version of record)CC BY V4.0, Open
Journal article
Approaches in Characterizing Genetic Structure and Mapping in a Rice Multiparental Population
G3 : genes - genomes - genetics, Vol.7(6), pp.1721-1730
01/06/2017
PMCID: PMC5473752
PMID: 28592653
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Source: InCites
Abstract
Multi-parent Advanced Generation Intercross (MAGIC) populations are fast becoming mainstream tools for research and breeding, along with the technology and tools for analysis. This paper demonstrates the analysis of a rice MAGIC population from data filtering to imputation and processing of genetic data to characterizing genomic structure, and finally quantitative trait loci (QTL) mapping. In this study, 1316 S6:8 indica MAGIC (MI) lines and the eight founders were sequenced using Genotyping by Sequencing (GBS). As the GBS approach often includes missing data, the first step was to impute the missing SNPs. The observable number of recombinations in the population was then explored. Based on this case study, a general outline of procedures for a MAGIC analysis workflow is provided, as well as for QTL mapping of agronomic traits and biotic and abiotic stress, using the results from both association and interval mapping approaches. QTL for agronomic traits (yield, flowering time, and plant height), physical (grain length and grain width) and cooking properties (amylose content) of the rice grain, abiotic stress (submergence tolerance), and biotic stress (brown spot disease) were mapped. Through presenting this extensive analysis in the MI population in rice, we highlight important considerations when choosing analytical approaches. The methods and results reported in this paper will provide a guide to future genetic analysis methods applied to multi-parent populations.
Details
- Title
- Approaches in Characterizing Genetic Structure and Mapping in a Rice Multiparental Population
- Creators
- Chitra Raghavan - International Rice Research InstituteRamil Mauleon - International Rice Research InstituteVanica Lacorte - International Rice Research InstituteMonalisa Jubay - International Rice Research InstituteHein Zaw - International Rice Research InstituteJustine Bonifacio - International Rice Research InstituteRakesh Kumar Singh - International Rice Research InstituteB Emma Huang - Janssen Research & DevelopmentHei Leung - International Rice Research Institute (Phillipines)
- Publication Details
- G3 : genes - genomes - genetics, Vol.7(6), pp.1721-1730
- Publisher
- Oxford University Press
- Identifiers
- 991013099200502368
- Copyright
- © 2017 Raghavan et al. This is an open-access article distributed under the terms of the Creative Commons Attribution 4.0 International License (http://creativecommons.org/licenses/by/4.0/), which permits unrestricted use, distribution, and reproduction in any medium, provided the original work is properly cited.
- Academic Unit
- Faculty of Science and Engineering
- Language
- English
- Resource Type
- Journal article