A Multiparent Advanced Generation Inter-Cross to Fine-Map Quantitative Traits in Arabidopsis thaliana

By P. Kover, W. Valdar, J. Trakalo, N. Scarcelli, Ian M. Ehrenreich, M. Purugganan, Caroline Durrant, Richard Mott. PLoS Genetics, 2009

595 citations recorded by the source corpus.

Identifying natural allelic variation that underlies quantitative trait variation remains a fundamental problem in genetics. Most studies have employed either simple synthetic populations with restricted allelic variation or performed association mapping on a sample of naturally occurring haplotypes. Both of these approaches have some limitations, therefore alternative resources for the genetic dissection of complex traits continue to be sought. Here we describe one such alternative, the Multiparent Advanced Generation Inter-Cross (MAGIC). This approach is expected to improve the precision with which QTL can be mapped, improving the outlook for QTL cloning. Here, we present the first panel of MAGIC lines developed: a set of 527 recombinant inbred lines (RILs) descended from a heterogeneous stock of 19 intermated accessions of the plant Arabidopsis thaliana. These lines and the 19 founders were genotyped with 1,260 single nucleotide polymorphisms and phenotyped for development-related traits. Analytical methods were developed to fine-map quantitative trait loci (QTL) in the MAGIC lines by reconstructing the genome of each line as a mosaic of the founders. We show by simulation that QTL explaining 10% of the phenotypic variance will be detected in most situations with an average mapping error of about 300 kb, and that if the number of lines were doubled the mapping error would be under 200 kb. We also show how the power to detect a QTL and the mapping accuracy vary, depending on QTL location. We demonstrate the utility of this new mapping population by mapping several known QTL with high precision and by finding novel QTL for germination data and bolting time. Our results provide strong support for similar ongoing efforts to produce MAGIC lines in other organisms.

Subfields: Genetics, Plant Science

View Paper: https://www.semanticscholar.org/paper/17d7b11eae9c5f5830697ff0c1319e3b983545a6

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Citations in the corpus

The advantages and limitations of trait analysis with GWAS: a review (2013, background): “the Multi-parent Advanced Generation Inter-Cross (MAGIC) and Arabidopsis multi-parent RIL (AMPRIL) [7,8].”
Genetic mapping of quantitative trait loci in crops (2017, methodology): “[21] first developed a MAGIC population in A.”
Natural variations and genome-wide association studies in crop plants. (2014, background): “In the model plant Arabidopsis, the Multiparent Advanced Generation Inter-Cross (MAGIC) population was generated, including hundreds of RILs descended from a heterogeneous stock of 19 intermated Arabidopsis accessions (57).”
Multiple reference genomes and transcriptomes for Arabidopsis thaliana (2011, background): “In total, 75% (20,550) of protein-coding genes (and 21% of non-coding RNAs and 21% of pseudogenes) were expressed in at least one accession (false discovery rate (FDR) 5%), and 46% (9,360) of expressed protein-coding genes were differentially expressed between at least one pair of accessions(27) (Fi”
Genome‐wide Association for Plant Height and Flowering Time across 15 Tropical Maize Populations under Managed Drought Stress and Well‐Watered Conditions in Sub‐Saharan Africa (2016, methodology): “Unlike structured populations such as nested association mapping (NAM; McMullen et al. 2009) or Multiparent Advanced Generation Inter-Cross (MAGIC; Kover et al. 2009) populations, the WEMA populations were not designed to be analyzed together.”
Association Mapping for Enhancing Maize (Zea mays L.) Genetic Improvement (2011, background): “The NAM and MAGIC populations provide an ideal resource for gene identifi cation and validation in maize including the identifi cation of numerous small-eff ect QTL contributing to a target agronomic trait (Buckler et al., 2009; Kover et al., 2009).”
Marker-Assisted Plant Breeding: Principles and Practices (2015, background): “The confidence interval would decline to about 200 kb if the number of MILs used for analysis was doubled (Kover et al. 2009).”
R/qtl2: Software for Mapping Quantitative Trait Loci with High-Dimensional Data and Multiparent Populations (2018, unknown): “…recombinant inbred lines by sel ﬁ ng; 3-way advanced inter-cross populations, Diversity Outbred mice, heterogeneous stocks, 19-way MAGIC lines like the Kover et al. (2009) Arabidopsis lines, and 6-way doubled haploids following a design of maize MAGIC lines being developed at the University of…”