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_005134UCD_Gh_M_005134genetic_marker
UCD_Gh_M_005135UCD_Gh_M_005135genetic_marker
UCD_Gh_M_005136UCD_Gh_M_005136genetic_marker
UCD_Gh_M_005137UCD_Gh_M_005137genetic_marker
UCD_Gh_M_005138UCD_Gh_M_005138genetic_marker
UCD_Gh_M_005139UCD_Gh_M_005139genetic_marker
UCD_Gh_M_005140UCD_Gh_M_005140genetic_marker
UCD_Gh_M_005141UCD_Gh_M_005141genetic_marker
UCD_Gh_M_005142UCD_Gh_M_005142genetic_marker
UCD_Gh_M_005143UCD_Gh_M_005143genetic_marker
UCD_Gh_M_005144UCD_Gh_M_005144genetic_marker
UCD_Gh_M_005145UCD_Gh_M_005145genetic_marker
UCD_Gh_M_005146UCD_Gh_M_005146genetic_marker
UCD_Gh_M_005147UCD_Gh_M_005147genetic_marker
UCD_Gh_M_005148UCD_Gh_M_005148genetic_marker
UCD_Gh_M_005149UCD_Gh_M_005149genetic_marker
UCD_Gh_M_005150UCD_Gh_M_005150genetic_marker
UCD_Gh_M_005151UCD_Gh_M_005151genetic_marker
UCD_Gh_M_005152UCD_Gh_M_005152genetic_marker
UCD_Gh_M_005153UCD_Gh_M_005153genetic_marker
UCD_Gh_M_005154UCD_Gh_M_005154genetic_marker
UCD_Gh_M_005155UCD_Gh_M_005155genetic_marker
UCD_Gh_M_005156UCD_Gh_M_005156genetic_marker
UCD_Gh_M_005157UCD_Gh_M_005157genetic_marker
UCD_Gh_M_005158UCD_Gh_M_005158genetic_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