A Long-Read Transcriptome Assembly of Cotton (Gossypium hirsutum L.) and Intraspecific Single Nucleotide Polymorphism Discovery.

Publication Overview
TitleA Long-Read Transcriptome Assembly of Cotton (Gossypium hirsutum L.) and Intraspecific Single Nucleotide Polymorphism Discovery.
AuthorsAshrafi H, Hulse-Kemp AM, Wang F, Yang SS, Guan X, Jones DC, Matvienko M, Mockaitis K, Chen ZJ, Stelly DM, Van Deynze A
TypeJournal Article
Journal NameThe Plant Genome
Volume8
Issue2
Year2015
Page(s)1-14
CitationAshrafi H, Hulse-Kemp AM, Wang F, Yang SS, Guan X, Jones DC, Matvienko M, Mockaitis K, Chen ZJ, Stelly DM, Van Deynze A. A Long-Read Transcriptome Assembly of Cotton (Gossypium hirsutum L.) and Intraspecific Single Nucleotide Polymorphism Discovery. 2015; 8(2):1-14.

Abstract

Upland cotton (Gossypium hirsutum L.) has a narrow germplasm base, which constrains marker development and hampers intraspecific breeding. A pressing need exists for high-throughput single nucleotide polymorphism (SNP) markers that can be readily applied to germplasm in breeding and breeding-related research programs. Despite progress made in developing new sequencing technologies during the past decade, the cost of sequencing remains substantial when one is dealing with numerous samples and large genomes. Several strategies have been proposed to lower the cost of sequencing for multiple genotypes of large-genome species like cotton, such as transcriptome sequencing and reduced-representation DNA sequencing. This paper reports the development of a transcriptome assembly of the inbred line Texas Marker-1 (TM-1), a genetic standard for cotton, its usefulness as a reference for RNA sequencing (RNA-seq)-based SNP identification, and the availability of transcriptome sequences of four other cotton cultivars. An assembly of TM-1 was made using Roche 454 transcriptome reads combined with an assembly of all available public expressed sequence tag (EST) sequences of TM-1. The TM-1 assembly consists of 72,450 contigs with a total of 70 million bp. Functional predictions of the transcripts were estimated by alignment to selected protein databases. Transcriptome sequences of the five lines, including TM-1, were obtained using an Illumina Genome Analyzer-II, and the short reads were mapped to the TM-1 assembly to discover SNPs among the five lines. We identified >14,000 unfiltered allelic SNPs, of which ∼3,700 SNPs were retained for assay development after applying several rigorous filters. This paper reports availability of the reference transcriptome assembly and shows its utility in developing intraspecific SNP markers in upland cotton.
Features
This publication contains information about 14,613 features:
Feature NameUniquenameType
UCD_Gh_M_009177UCD_Gh_M_009177genetic_marker
UCD_Gh_M_009178UCD_Gh_M_009178genetic_marker
UCD_Gh_M_009179UCD_Gh_M_009179genetic_marker
UCD_Gh_M_009180UCD_Gh_M_009180genetic_marker
UCD_Gh_M_009181UCD_Gh_M_009181genetic_marker
UCD_Gh_M_009182UCD_Gh_M_009182genetic_marker
UCD_Gh_M_009183UCD_Gh_M_009183genetic_marker
UCD_Gh_M_009184UCD_Gh_M_009184genetic_marker
UCD_Gh_M_009185UCD_Gh_M_009185genetic_marker
UCD_Gh_M_009186UCD_Gh_M_009186genetic_marker
UCD_Gh_M_009187UCD_Gh_M_009187genetic_marker
UCD_Gh_M_009188UCD_Gh_M_009188genetic_marker
UCD_Gh_M_009189UCD_Gh_M_009189genetic_marker
UCD_Gh_M_009190UCD_Gh_M_009190genetic_marker
UCD_Gh_M_009191UCD_Gh_M_009191genetic_marker
UCD_Gh_M_009192UCD_Gh_M_009192genetic_marker
UCD_Gh_M_009193UCD_Gh_M_009193genetic_marker
UCD_Gh_M_009194UCD_Gh_M_009194genetic_marker
UCD_Gh_M_009195UCD_Gh_M_009195genetic_marker
UCD_Gh_M_009196UCD_Gh_M_009196genetic_marker
UCD_Gh_M_009197UCD_Gh_M_009197genetic_marker
UCD_Gh_M_009198UCD_Gh_M_009198genetic_marker
UCD_Gh_M_009199UCD_Gh_M_009199genetic_marker
UCD_Gh_M_009200UCD_Gh_M_009200genetic_marker
UCD_Gh_M_009201UCD_Gh_M_009201genetic_marker

Pages

Libraries
This publication contains information about 1 libraries:
Library NameUnique NameOrganism
TAMU_CottonSNP63KTAMU_CottonSNP63KGossypium spp.
Properties
Additional details for this publication include:
Property NameValue
URLhttps://dl.sciencesocieties.org/publications/tpg/articles/8/2/plantgenome2014.10.0068