Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population

High-density genetic maps are essential for high resolution mapping of quantitative traits. Here, we present a new genetic map for an Arabidopsis Bayreuth × Shahdara recombinant inbred line (RIL) population, built on RNA-seq data. RNA-seq analysis on 160 RILs of this population identified 30,049 sin...

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Bibliographic Details
Published in:Frontiers in genetics 2017, Vol.8, p.201-201
Main Authors: Serin, Elise A R, Snoek, L B, Nijveen, Harm, Willems, Leo A J, Jiménez-Gómez, Jose M, Hilhorst, Henk W M, Ligterink, Wilco
Format: Article
Language:English
Subjects:
Arabidopsis
Chemical and Process Engineering
Engineering Sciences
Food engineering
Genetic map
Genetics
Genotyping by sequencing
Life Sciences
QTL mapping
Resolution
RIL population
RNA-seq
Vegetal Biology
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Summary:High-density genetic maps are essential for high resolution mapping of quantitative traits. Here, we present a new genetic map for an Arabidopsis Bayreuth × Shahdara recombinant inbred line (RIL) population, built on RNA-seq data. RNA-seq analysis on 160 RILs of this population identified 30,049 single-nucleotide polymorphisms (SNPs) covering the whole genome. Based on a 100-kbp window SNP binning method, 1059 bin-markers were identified, physically anchored on the genome. The total length of the RNA-seq genetic map spans 471.70 centimorgans (cM) with an average marker distance of 0.45 cM and a maximum marker distance of 4.81 cM. This high resolution genotyping revealed new recombination breakpoints in the population. To highlight the advantages of such high-density map, we compared it to two publicly available genetic maps for the same population, comprising 69 PCR-based markers and 497 gene expression markers derived from microarray data, respectively. In this study, we show that SNP markers can effectively be derived from RNA-seq data. The new RNA-seq map closes many existing gaps in marker coverage, saturating the previously available genetic maps. Quantitative trait locus (QTL) analysis for published phenotypes using the available genetic maps showed increased QTL mapping resolution and reduced QTL confidence interval using the RNA-seq map. The new high-density map is a valuable resource that facilitates the identification of candidate genes and map-based cloning approaches.
ISSN:1664-8021
1664-462X
1664-8021
1664-462X
DOI:10.3389/fgene.2017.00201