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...
Main Authors: | , , , , , , |
---|---|
Format: | Article |
Language: | English |
Published: |
Frontiers Media S.A.
2017-12-01
|
Series: | Frontiers in Genetics |
Subjects: | |
Online Access: | http://journal.frontiersin.org/article/10.3389/fgene.2017.00201/full |
id |
doaj-9c57e09d67a94795b1a2b31a8d434a84 |
---|---|
record_format |
Article |
spelling |
doaj-9c57e09d67a94795b1a2b31a8d434a842020-11-24T22:43:26ZengFrontiers Media S.A.Frontiers in Genetics1664-80212017-12-01810.3389/fgene.2017.00201310192Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL PopulationElise A. R. Serin0L. B. Snoek1L. B. Snoek2Harm Nijveen3Harm Nijveen4Leo A. J. Willems5Jose M. Jiménez-Gómez6Jose M. Jiménez-Gómez7Henk W. M. Hilhorst8Wilco Ligterink9Wageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, NetherlandsLaboratory of Nematology, Wageningen University, Wageningen, NetherlandsTheoretical Biology and Bioinformatics, Utrecht University, Utrecht, NetherlandsWageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, NetherlandsLaboratory of Bioinformatics, Wageningen University, Wageningen, NetherlandsWageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, NetherlandsDepartment of Plant Breeding and Genetics, Max Planck Institute for Plant Breeding Research, Cologne, GermanyInstitut Jean-Pierre Bourgin, Institut National de la Recherche Agronomique, AgroParisTech, Centre National de la Recherche Scientifique, Université Paris-Saclay, Versailles Cedex, FranceWageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, NetherlandsWageningen Seed Lab, Laboratory of Plant Physiology, Wageningen University, Wageningen, NetherlandsHigh-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.http://journal.frontiersin.org/article/10.3389/fgene.2017.00201/fullArabidopsisgenetic mapgenotyping by sequencingQTL mappingRIL populationresolution |
collection |
DOAJ |
language |
English |
format |
Article |
sources |
DOAJ |
author |
Elise A. R. Serin L. B. Snoek L. B. Snoek Harm Nijveen Harm Nijveen Leo A. J. Willems Jose M. Jiménez-Gómez Jose M. Jiménez-Gómez Henk W. M. Hilhorst Wilco Ligterink |
spellingShingle |
Elise A. R. Serin L. B. Snoek L. B. Snoek Harm Nijveen Harm Nijveen Leo A. J. Willems Jose M. Jiménez-Gómez Jose M. Jiménez-Gómez Henk W. M. Hilhorst Wilco Ligterink Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population Frontiers in Genetics Arabidopsis genetic map genotyping by sequencing QTL mapping RIL population resolution |
author_facet |
Elise A. R. Serin L. B. Snoek L. B. Snoek Harm Nijveen Harm Nijveen Leo A. J. Willems Jose M. Jiménez-Gómez Jose M. Jiménez-Gómez Henk W. M. Hilhorst Wilco Ligterink |
author_sort |
Elise A. R. Serin |
title |
Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population |
title_short |
Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population |
title_full |
Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population |
title_fullStr |
Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population |
title_full_unstemmed |
Construction of a High-Density Genetic Map from RNA-Seq Data for an Arabidopsis Bay-0 × Shahdara RIL Population |
title_sort |
construction of a high-density genetic map from rna-seq data for an arabidopsis bay-0 × shahdara ril population |
publisher |
Frontiers Media S.A. |
series |
Frontiers in Genetics |
issn |
1664-8021 |
publishDate |
2017-12-01 |
description |
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. |
topic |
Arabidopsis genetic map genotyping by sequencing QTL mapping RIL population resolution |
url |
http://journal.frontiersin.org/article/10.3389/fgene.2017.00201/full |
work_keys_str_mv |
AT elisearserin constructionofahighdensitygeneticmapfromrnaseqdataforanarabidopsisbay0shahdararilpopulation AT lbsnoek constructionofahighdensitygeneticmapfromrnaseqdataforanarabidopsisbay0shahdararilpopulation AT lbsnoek constructionofahighdensitygeneticmapfromrnaseqdataforanarabidopsisbay0shahdararilpopulation AT harmnijveen constructionofahighdensitygeneticmapfromrnaseqdataforanarabidopsisbay0shahdararilpopulation AT harmnijveen constructionofahighdensitygeneticmapfromrnaseqdataforanarabidopsisbay0shahdararilpopulation AT leoajwillems constructionofahighdensitygeneticmapfromrnaseqdataforanarabidopsisbay0shahdararilpopulation AT josemjimenezgomez constructionofahighdensitygeneticmapfromrnaseqdataforanarabidopsisbay0shahdararilpopulation AT josemjimenezgomez constructionofahighdensitygeneticmapfromrnaseqdataforanarabidopsisbay0shahdararilpopulation AT henkwmhilhorst constructionofahighdensitygeneticmapfromrnaseqdataforanarabidopsisbay0shahdararilpopulation AT wilcoligterink constructionofahighdensitygeneticmapfromrnaseqdataforanarabidopsisbay0shahdararilpopulation |
_version_ |
1725695940475486208 |