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Next Generation Transcriptomic Sequencing and Polymorphism Detection in Pepper Varieties Saengryeg 211 and Saengryeg 213
Author(s) -
Ahn YulKyun,
Tripathi Swati,
Cho YoungIl,
Kim JeongHo,
Lee HyeEun,
Kim DoSun,
Woo JongGyu,
Yoon MooKyoung
Publication year - 2014
Publication title -
crop science
Language(s) - English
Resource type - Journals
SCImago Journal Rank - 0.76
H-Index - 147
eISSN - 1435-0653
pISSN - 0011-183X
DOI - 10.2135/cropsci2013.10.0673
Subject(s) - biology , genetics , pyrosequencing , single nucleotide polymorphism , pepper , locus (genetics) , functional genomics , computational biology , quantitative trait locus , genomics , transcriptome , gene , expressed sequence tag , indel , genome , dna sequencing , genotype , gene expression , horticulture
ABSTRACT Limited functional genomics resources and whole genome association studies could be substantially improved in pepper ( Capsicum annuum L., Solanaceae) through the application of a molecular approach for characterization of gene content and identification of molecular markers. We performed 454 GS‐FLX Titanium massive parallel pyrosequencing of polyA‐selected and normalized cDNA libraries generated from a single pool of transcripts obtained from two pepper varieties, the highly pungent Saengryeg 211 and the nonpungent Saengryeg 213, for de novo transcriptome assembly, functional annotation, and in silico discovery of potential molecular markers. A single 454 pyrosequencing run generated 361,671 and 274,269 reads totaling 164.49 and 124.60 Mb of sequence data, which assembled into 23,821 and 17,813 isotigs and 18,147 and 15,129 singletons for both varieties, respectively. These reads were organized into 20,352 and 15,781 ‘isogroups’ for both varieties. Assembled sequences were functionally annotated on the basis of homology to genes in multiple public databases and assigned with gene ontology (GO) terms. Analysis of sequence variants identified a total of 11,584 and 9641 potential single nucleotide polymorphisms (SNPs), which eventually resulted in 665 and 632 genotype‐specific SNPs for both the varieties, respectively, after examining SNP frequency distribution for each mapped unigenes. High‐throughput transcriptome profiling and large scale of polymorphic marker discovery using next generation sequencing (NGS) of two pepper varieties provides valuable information for functional genomics resources, which will help to further improve the pepper‐breeding efforts with respect to genetic linkage maps, quantitative trait locus (QTL) mapping, and marker‐assisted trait selection.