scholarly journals Using RNA-seq for genomic scaffold placement, correcting assemblies, and genetic map creation in a common Brassica rapa mapping population

2016 ◽  
Author(s):  
RJ Cody Markelz ◽  
Michael F Covington ◽  
Marcus T Brock ◽  
Upendra K Devisetty ◽  
Daniel J Kliebenstein ◽  
...  
Keyword(s):  
Genetic Map ◽  
Brassica Rapa ◽  
Mapping Population ◽  
High Density ◽  
Rna Seq ◽  
Model Species ◽  
Map Construction ◽  
Genomic Scaffold ◽  
Genome Annotations ◽  
Genomic Locations

AbstractBrassica rapa is a model species for agronomic, ecological, evolutionary and translational studies. Here we describe high-density SNP discovery and genetic map construction for a Brassica rapa recombinant inbred line (RIL) population derived from field collected RNA-seq data. This high-density genotype data enables the detection and correction of putative genome mis-assemblies and accurate assignment of scaffold sequences to their likely genomic locations. These assembly improvements represent 7.1-8.0% of the annotated Brassica rapa genome. We demonstrate how using this new resource leads to a significant improvement for QTL analysis over the current low-density genetic map. Improvements are achieved by the increased mapping resolution and by having known genomic coordinates to anchor the markers for candidate gene discovery. These new molecular resources and improvements in the genome annotation will benefit the Brassicaceae genomics community and may help guide other communities in finetuning genome annotations.

scholarly journals Using RNA-Seq for Genomic Scaffold Placement, Correcting Assemblies, and Genetic Map Creation in a Common Brassica rapa Mapping Population

2017 ◽  
Vol 7 (7) ◽  
pp. 2259-2270 ◽  
Author(s):  
R J Cody Markelz ◽  
Michael F Covington ◽  
Marcus T Brock ◽  
Upendra K Devisetty ◽  
Daniel J Kliebenstein ◽  
...  
Keyword(s):  
Genetic Map ◽  
Brassica Rapa ◽  
Mapping Population ◽  
High Density ◽  
Fine Tuning ◽  
Rna Seq ◽  
Map Construction ◽  
Genomic Scaffold ◽  
Genome Annotations ◽  
Genomic Locations

Abstract Brassica rapa is a model species for agronomic, ecological, evolutionary, and translational studies. Here, we describe high-density SNP discovery and genetic map construction for a B. rapa recombinant inbred line (RIL) population derived from field collected RNA sequencing (RNA-Seq) data. This high-density genotype data enables the detection and correction of putative genome misassemblies and accurate assignment of scaffold sequences to their likely genomic locations. These assembly improvements represent 7.1–8.0% of the annotated B. rapa genome. We demonstrate how using this new resource leads to a significant improvement for QTL analysis over the current low-density genetic map. Improvements are achieved by the increased mapping resolution and by having known genomic coordinates to anchor the markers for candidate gene discovery. These new molecular resources and improvements in the genome annotation will benefit the Brassicaceae genomics community and may help guide other communities in fine-tuning genome annotations.

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

2017 ◽  
Vol 8 ◽  
Author(s):  
Elise A. R. Serin ◽  
L. B. Snoek ◽  
Harm Nijveen ◽  
Leo A. J. Willems ◽  
Jose M. Jiménez-Gómez ◽  
...  
Keyword(s):  
Genetic Map ◽  
High Density ◽  
Rna Seq ◽  
Ril Population

scholarly journals High-Density Genetic Map Construction and QTL Mapping of Leaf and Needling Traits in Ziziphus jujuba Mill

2019 ◽  
Vol 10 ◽  
Author(s):  
Zhongtang Wang ◽  
Zhong Zhang ◽  
Haixia Tang ◽  
Qiong Zhang ◽  
Guangfang Zhou ◽  
...  
Keyword(s):  
Qtl Mapping ◽  
Genetic Map ◽  
High Density ◽  
Map Construction ◽  
Ziziphus Jujuba

scholarly journals Quantitative Trait Locus (QTLs) Mapping for Quality Traits of Wheat Based on High Density Genetic Map Combined With Bulked Segregant Analysis RNA-seq (BSR-Seq) Indicates That the Basic 7S Globulin Gene Is Related to Falling Number

2020 ◽  
Vol 11 ◽  
Author(s):  
Qiao Li ◽  
Zhifen Pan ◽  
Yuan Gao ◽  
Tao Li ◽  
Junjun Liang ◽  
...  
Keyword(s):  
Genetic Map ◽  
Quantitative Trait ◽  
Recombinant Inbred Lines ◽  
High Density ◽  
Genetic Maps ◽  
Phenotypic Variance ◽  
Quality Traits ◽  
Rna Seq ◽  
Falling Number ◽  
7S Globulin

Numerous quantitative trait loci (QTLs) have been identified for wheat quality; however, most are confined to low-density genetic maps. In this study, based on specific-locus amplified fragment sequencing (SLAF-seq), a high-density genetic map was constructed with 193 recombinant inbred lines derived from Chuanmai 42 and Chuanmai 39. In total, 30 QTLs with phenotypic variance explained (PVE) up to 47.99% were identified for falling number (FN), grain protein content (GPC), grain hardness (GH), and starch pasting properties across three environments. Five NAM genes closely adjacent to QGPC.cib-4A probably have effects on GPC. QGH.cib-5D was the only one detected for GH with high PVE of 33.31–47.99% across the three environments and was assumed to be related to the nearest pina-D1 and pinb-D1genes. Three QTLs were identified for FN in at least two environments, of which QFN.cib-3D had relatively higher PVE of 16.58–25.74%. The positive effect of QFN.cib-3D for high FN was verified in a double-haploid population derived from Chuanmai 42 × Kechengmai 4. The combination of these QTLs has a considerable effect on increasing FN. The transcript levels of Basic 7S globulin and Basic 7S globulin 2 in QFN.cib-3D were significantly different between low FN and high FN bulks, as observed through bulk segregant RNA-seq (BSR). These QTLs and candidate genes based on the high-density genetic map would be beneficial for further understanding of the genetic mechanism of quality traits and molecular breeding of wheat.

scholarly journals polymapR – linkage analysis and genetic map construction from F1 populations of outcrossing polyploids

2017 ◽  
Author(s):  
Peter M. Bourke ◽  
Geert van Geest ◽  
Roeland E. Voorrips ◽  
Johannes Jansen ◽  
Twan Kranenburg ◽  
...  
Keyword(s):  
Linkage Analysis ◽  
Genetic Map ◽  
Genetic Research ◽  
Diploid Species ◽  
R Package ◽  
High Density ◽  
Genetic Linkage Analysis ◽  
Map Construction ◽  
Preferential Chromosome Pairing ◽  
Polyploid Crops

AbstractMotivationPolyploid species carry more than two copies of each chromosome, a condition found in many of the world’s most important crops. Genetic mapping in polyploids is more complex than in diploid species, resulting in a lack of available software tools. These are needed if we are to realise all the opportunities offered by modern genotyping platforms for genetic research and breeding in polyploid crops.ResultspolymapR is an R package for genetic linkage analysis and integrated genetic map construction from bi-parental populations of outcrossing autopolyploids. It can currently analyse triploid, tetraploid and hexaploid marker datasets and is applicable to various crops including potato, leek, alfalfa, blueberry, chrysanthemum, sweet potato or kiwifruit. It can detect, estimate and correct for preferential chromosome pairing, and has been tested on high-density marker datasets from potato, rose and chrysanthemum, generating high-density integrated linkage maps in all of these crops.Availability and ImplementationpolymapR is freely available under the general public license from the Comprehensive R Archive Network (CRAN) at http://cran.r-project.org/packages=polymapR.ContactChris Maliepaard [email protected] or Roeland E. Voorrips [email protected]

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