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_001426UCD_Gh_M_001426genetic_marker
UCD_Gh_M_001427UCD_Gh_M_001427genetic_marker
UCD_Gh_M_001428UCD_Gh_M_001428genetic_marker
UCD_Gh_M_001429UCD_Gh_M_001429genetic_marker
UCD_Gh_M_001430UCD_Gh_M_001430genetic_marker
UCD_Gh_M_001431UCD_Gh_M_001431genetic_marker
UCD_Gh_M_001432UCD_Gh_M_001432genetic_marker
UCD_Gh_M_001433UCD_Gh_M_001433genetic_marker
UCD_Gh_M_001434UCD_Gh_M_001434genetic_marker
UCD_Gh_M_001435UCD_Gh_M_001435genetic_marker
UCD_Gh_M_001436UCD_Gh_M_001436genetic_marker
UCD_Gh_M_001437UCD_Gh_M_001437genetic_marker
UCD_Gh_M_001438UCD_Gh_M_001438genetic_marker
UCD_Gh_M_001439UCD_Gh_M_001439genetic_marker
UCD_Gh_M_001440UCD_Gh_M_001440genetic_marker
UCD_Gh_M_001441UCD_Gh_M_001441genetic_marker
UCD_Gh_M_001442UCD_Gh_M_001442genetic_marker
UCD_Gh_M_001443UCD_Gh_M_001443genetic_marker
UCD_Gh_M_001444UCD_Gh_M_001444genetic_marker
UCD_Gh_M_001445UCD_Gh_M_001445genetic_marker
UCD_Gh_M_001446UCD_Gh_M_001446genetic_marker
UCD_Gh_M_001447UCD_Gh_M_001447genetic_marker
UCD_Gh_M_001448UCD_Gh_M_001448genetic_marker
UCD_Gh_M_001449UCD_Gh_M_001449genetic_marker
UCD_Gh_M_001450UCD_Gh_M_001450genetic_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