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
SNP10SNP10genetic_marker
SNP100SNP100genetic_marker
SNP101SNP101genetic_marker
SNP102SNP102genetic_marker
SNP103SNP103genetic_marker
SNP104SNP104genetic_marker
SNP105SNP105genetic_marker
SNP106SNP106genetic_marker
SNP107SNP107genetic_marker
SNP108SNP108genetic_marker
SNP109SNP109genetic_marker
SNP11SNP11genetic_marker
SNP110SNP110genetic_marker
SNP112SNP112genetic_marker
SNP113SNP113genetic_marker
SNP114SNP114genetic_marker
SNP116SNP116genetic_marker
SNP117SNP117genetic_marker
SNP118SNP118genetic_marker
SNP12SNP12genetic_marker
SNP124SNP124genetic_marker
SNP125SNP125genetic_marker
SNP126SNP126genetic_marker
SNP127SNP127genetic_marker
SNP13SNP13genetic_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