Application of large-scale sequencing to marker discovery in plants

Henry, Robert J.; Edwards, Mark; Waters, Daniel Le; S, Gopala Krishnan; Bundock, Peter C; Sexton, Timothy; Masouleh, Ardashir Kharabian; Nock, Catherine J.; Pattemore, Julie

doi:10.1007/s12038-012-9253-z

Cited by 36 publications

(22 citation statements)

References 86 publications

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“…Gene-associated SNPs have been used to generate genetic maps [18] and determine genetic diversity [31], [67]. RNA-seq targets SNP discovery on coding sequences and enables discovery of gene-associated SNPs [68]. For species without a reference genome, using RNA-seq to identify SNPs can be a very efficient approach in identifying genetic markers [69].…”

Section: Discussionmentioning

confidence: 99%

De Novo Assembly of the Perennial Ryegrass Transcriptome Using an RNA-Seq Strategy

et al. 2014

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BackgroundPerennial ryegrass is a highly heterozygous outbreeding grass species used for turf and forage production. Heterozygosity can affect de-Bruijn graph assembly making de novo transcriptome assembly of species such as perennial ryegrass challenging. Creating a reference transcriptome from a homozygous perennial ryegrass genotype can circumvent the challenge of heterozygosity. The goals of this study were to perform RNA-sequencing on multiple tissues from a highly inbred genotype to develop a reference transcriptome. This was complemented with RNA-sequencing of a highly heterozygous genotype for SNP calling.Result De novo transcriptome assembly of the inbred genotype created 185,833 transcripts with an average length of 830 base pairs. Within the inbred reference transcriptome 78,560 predicted open reading frames were found of which 24,434 were predicted as complete. Functional annotation found 50,890 transcripts with a BLASTp hit from the Swiss-Prot non-redundant database, 58,941 transcripts with a Pfam protein domain and 1,151 transcripts encoding putative secreted peptides. To evaluate the reference transcriptome we targeted the high-affinity K+ transporter gene family and found multiple orthologs. Using the longest unique open reading frames as the reference sequence, 64,242 single nucleotide polymorphisms were found. One thousand sixty one open reading frames from the inbred genotype contained heterozygous sites, confirming the high degree of homozygosity.ConclusionOur study has developed an annotated, comprehensive transcriptome reference for perennial ryegrass that can aid in determining genetic variation, expression analysis, genome annotation, and gene mapping.

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Section: Discussionmentioning

confidence: 99%

De Novo Assembly of the Perennial Ryegrass Transcriptome Using an RNA-Seq Strategy

et al. 2014

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“…There are various advantages and limitations among the various NGS platforms, which vary in terms of sensitivity, accuracy, reproducibility and throughput. Among these platforms, Illumina sequencing technology, which generates large-scale reads (75–150 bp) at low costs with very high sequencing coverage, has been especially useful for de novo transcriptome studies [25]–[27].…”

Section: Introductionmentioning

confidence: 99%

SNP Discovery by Illumina-Based Transcriptome Sequencing of the Olive and the Genetic Characterization of Turkish Olive Genotypes Revealed by AFLP, SSR and SNP Markers

Kaya

Çetin²,

Kaya³

et al. 2013

PLoS ONE

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BackgroundThe olive tree (Olea europaea L.) is a diploid (2n = 2x = 46) outcrossing species mainly grown in the Mediterranean area, where it is the most important oil-producing crop. Because of its economic, cultural and ecological importance, various DNA markers have been used in the olive to characterize and elucidate homonyms, synonyms and unknown accessions. However, a comprehensive characterization and a full sequence of its transcriptome are unavailable, leading to the importance of an efficient large-scale single nucleotide polymorphism (SNP) discovery in olive. The objectives of this study were (1) to discover olive SNPs using next-generation sequencing and to identify SNP primers for cultivar identification and (2) to characterize 96 olive genotypes originating from different regions of Turkey.Methodology/Principal FindingsNext-generation sequencing technology was used with five distinct olive genotypes and generated cDNA, producing 126,542,413 reads using an Illumina Genome Analyzer IIx. Following quality and size trimming, the high-quality reads were assembled into 22,052 contigs with an average length of 1,321 bases and 45 singletons. The SNPs were filtered and 2,987 high-quality putative SNP primers were identified. The assembled sequences and singletons were subjected to BLAST similarity searches and annotated with a Gene Ontology identifier. To identify the 96 olive genotypes, these SNP primers were applied to the genotypes in combination with amplified fragment length polymorphism (AFLP) and simple sequence repeats (SSR) markers.Conclusions/SignificanceThis study marks the highest number of SNP markers discovered to date from olive genotypes using transcriptome sequencing. The developed SNP markers will provide a useful source for molecular genetic studies, such as genetic diversity and characterization, high density quantitative trait locus (QTL) analysis, association mapping and map-based gene cloning in the olive. High levels of genetic variation among Turkish olive genotypes revealed by SNPs, AFLPs and SSRs allowed us to characterize the Turkish olive genotype.

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“…Application of NGS in plant genomics studies has been extensively reviewed by a number of authors . NGS lowers the cost of sequencing and generates a large amount of data in a single sequencing run, making it feasible to study genetics at the whole genome level.…”

Section: Association Genomics Approach Using Next Generation Sequencimentioning

confidence: 99%

Advances in genomics for the improvement of quality in coffee

et al. 2016

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Coffee is an important crop that provides a livelihood to millions of people living in developing countries. Production of genotypes with improved coffee quality attributes is a primary target of coffee genetic improvement programs. Advances in genomics are providing new tools for analysis of coffee quality at the molecular level. The recent report of a genomic sequence for robusta coffee, Coffea canephora, is a major development. However, a reference genome sequence for the genetically more complex arabica coffee (C. arabica) will also be required to fully define the molecular determinants controlling quality in coffee produced from this high quality coffee species. Genes responsible for control of the levels of the major biochemical components in the coffee bean that are known to be important in determining coffee quality can now be identified by association analysis. However, the narrow genetic base of arabica coffee suggests that genomics analysis of the wild relatives of coffee (Coffea spp.) may be required to find the phenotypic diversity required for effective association genetic analysis. The genomic resources available for the study of coffee quality are described and the potential for the application of next generation sequencing and association genetic analysis to advance coffee quality research are explored.Key words: Coffee quality, genetics, genomics, biochemical compounds, next generation sequencing, association studies.This article is protected by copyright. All rights reserved. Accepted Article GENERAL INTRODUCTIONCoffee is an important crop and the second most traded commodity in the world (after petroleum) providing a living to more than 125 million people .Commercial coffee production is dominated by only two species belonging to the Coffea genus: C. arabica and C. canephora (the latter generally referred to as robusta coffee). All coffee species are diploid (2n=2x=22) and generally self-incompatible, except for C. arabica which is a self-fertile tetraploid (2n=4x=44) derived from a spontaneous hybridization between C. canephora (as paternal progenitor) and C.eugenioides (as maternal progenitor) 8 9.Although C. arabica is considered to have better cupping quality than C. canephora, improving the quality of both commercial species remains a target for most coffee improvement programs. With advances in genomic and sequencing technology, it is feasible to understand the coffee genome and the molecular inheritance underlying coffee quality, thereby helping improve the efficiency of breeding programs.This review will discuss current knowledge regarding the genetics of those biochemical compounds which are considered quality determinants, for use as a foundation for improving coffee quality by breeding. Available genomic resources for the study of the genetics of biochemical compounds that are likely to be playing a role in coffee flavour will also be discussed. In addition, the potential value of the study of genetics of coffee This article is protected by copyright. All rights reserved.Ac...

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Application of large-scale sequencing to marker discovery in plants

Cited by 36 publications

References 86 publications

De Novo Assembly of the Perennial Ryegrass Transcriptome Using an RNA-Seq Strategy

De Novo Assembly of the Perennial Ryegrass Transcriptome Using an RNA-Seq Strategy

SNP Discovery by Illumina-Based Transcriptome Sequencing of the Olive and the Genetic Characterization of Turkish Olive Genotypes Revealed by AFLP, SSR and SNP Markers

Advances in genomics for the improvement of quality in coffee

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