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_009728UCD_Gh_M_009728genetic_marker
UCD_Gh_M_009729UCD_Gh_M_009729genetic_marker
UCD_Gh_M_009730UCD_Gh_M_009730genetic_marker
UCD_Gh_M_009731UCD_Gh_M_009731genetic_marker
UCD_Gh_M_009732UCD_Gh_M_009732genetic_marker
UCD_Gh_M_009733UCD_Gh_M_009733genetic_marker
UCD_Gh_M_009734UCD_Gh_M_009734genetic_marker
UCD_Gh_M_009735UCD_Gh_M_009735genetic_marker
UCD_Gh_M_009736UCD_Gh_M_009736genetic_marker
UCD_Gh_M_009737UCD_Gh_M_009737genetic_marker
UCD_Gh_M_009738UCD_Gh_M_009738genetic_marker
UCD_Gh_M_009739UCD_Gh_M_009739genetic_marker
UCD_Gh_M_009740UCD_Gh_M_009740genetic_marker
UCD_Gh_M_009741UCD_Gh_M_009741genetic_marker
UCD_Gh_M_009742UCD_Gh_M_009742genetic_marker
UCD_Gh_M_009743UCD_Gh_M_009743genetic_marker
UCD_Gh_M_009744UCD_Gh_M_009744genetic_marker
UCD_Gh_M_009745UCD_Gh_M_009745genetic_marker
UCD_Gh_M_009746UCD_Gh_M_009746genetic_marker
UCD_Gh_M_009747UCD_Gh_M_009747genetic_marker
UCD_Gh_M_009748UCD_Gh_M_009748genetic_marker
UCD_Gh_M_009749UCD_Gh_M_009749genetic_marker
UCD_Gh_M_009750UCD_Gh_M_009750genetic_marker
UCD_Gh_M_009751UCD_Gh_M_009751genetic_marker
UCD_Gh_M_009752UCD_Gh_M_009752genetic_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