Single nucleotide polymorphism discovery through Illumina-based transcriptome sequencing and mapping in lentil

Publication Overview
TitleSingle nucleotide polymorphism discovery through Illumina-based transcriptome sequencing and mapping in lentil
AuthorsYilmaz Temel H, Gol D, Kaya Akkale HB, Kahriman A, Tanyolac MB
TypeJournal Article
Journal NameTurkish Journal of Agriculture and Forestry
Volume39
Year2015
Page(s)470-488
CitationYilmaz Temel H, Gol D, Kaya Akkale HB, Kahriman A, Tanyolac MB. Single nucleotide polymorphism discovery through Illumina-based transcriptome sequencing and mapping in lentil. Turkish Journal of Agriculture and Forestry. 2015; 39:470-488.

Abstract

Lentil, which belongs to the family Leguminosae (Fabaceae), is a diploid (2n = 2x = 14 chromosomes) self-pollinating crop with a genome size of 4063 Mbp. Because of its nutritional importance and role in the fixation of nitrogen from the atmosphere, lentil is a widely used crop species in molecular genetic studies. By using DNA markers, to date, a limited number of polymorphic bands have been generated. Therefore, it is necessary to develop additional markers to saturate the genome at high density. Single nucleotide polymorphism (SNP) markers are promising for this purpose because of their abundance, stability, and heredity; they can be used to generate a large number of markers over a short distance that are distributed in both intragenic and intergenic regions. Transcriptome sequencing technology was applied to 2 lentil genotypes, and cDNAs were sequenced using the Illumina platform. A total of 111,105,153 sequence reads were generated after trimming. The high-quality reads were assembled, producing 97,528 contigs with an N50 of 1996 bp. The Genome Analysis Tool Kit Unified Genotyper algorithm detected 50,960 putative SNP primers. A genetic linkage map was constructed by using JoinMap4.0 and the map consists of 7 major linkage groups that could be represented as 7 chromosomes of lentil. The extensive sequence information and large number of SNPs obtained in this study could potentially be used for future highdensity linkage map construction and association mapping. The large number of contigs obtained in this study could be used for the identification of orthologous transcripts from cDNA data on other organisms.
Features
This publication contains information about 361 features:
Feature NameUniquenameType
SNP199SNP199genetic_marker
SNP200SNP200genetic_marker
SNP201SNP201genetic_marker
SNP202SNP202genetic_marker
SNP203SNP203genetic_marker
SNP204SNP204genetic_marker
SNP21SNP21genetic_marker
SNP211SNP211genetic_marker
SNP212SNP212genetic_marker
SNP213SNP213genetic_marker
SNP214SNP214genetic_marker
SNP215SNP215genetic_marker
SNP216SNP216genetic_marker
SNP217SNP217genetic_marker
SNP218SNP218genetic_marker
SNP22SNP22genetic_marker
SNP221SNP221genetic_marker
SNP223SNP223genetic_marker
SNP224SNP224genetic_marker
SNP225SNP225genetic_marker
SNP227SNP227genetic_marker
SNP228SNP228genetic_marker
SNP229SNP229genetic_marker
SNP23SNP23genetic_marker
SNP230SNP230genetic_marker

Pages

Featuremaps
This publication contains information about 1 maps:
Map Name
lentil-PrecozxWA8649041-F7-2015
Properties
Additional details for this publication include:
Property NameValue
URLhttp://journals.tubitak.gov.tr/agriculture/abstract.htm?id=16381