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_009076UCD_Gh_M_009076genetic_marker
UCD_Gh_M_009077UCD_Gh_M_009077genetic_marker
UCD_Gh_M_009078UCD_Gh_M_009078genetic_marker
UCD_Gh_M_009079UCD_Gh_M_009079genetic_marker
UCD_Gh_M_009080UCD_Gh_M_009080genetic_marker
UCD_Gh_M_009081UCD_Gh_M_009081genetic_marker
UCD_Gh_M_009082UCD_Gh_M_009082genetic_marker
UCD_Gh_M_009083UCD_Gh_M_009083genetic_marker
UCD_Gh_M_009084UCD_Gh_M_009084genetic_marker
UCD_Gh_M_009085UCD_Gh_M_009085genetic_marker
UCD_Gh_M_009086UCD_Gh_M_009086genetic_marker
UCD_Gh_M_009087UCD_Gh_M_009087genetic_marker
UCD_Gh_M_009088UCD_Gh_M_009088genetic_marker
UCD_Gh_M_009089UCD_Gh_M_009089genetic_marker
UCD_Gh_M_009090UCD_Gh_M_009090genetic_marker
UCD_Gh_M_009091UCD_Gh_M_009091genetic_marker
UCD_Gh_M_009092UCD_Gh_M_009092genetic_marker
UCD_Gh_M_009093UCD_Gh_M_009093genetic_marker
UCD_Gh_M_009094UCD_Gh_M_009094genetic_marker
UCD_Gh_M_009095UCD_Gh_M_009095genetic_marker
UCD_Gh_M_009096UCD_Gh_M_009096genetic_marker
UCD_Gh_M_009097UCD_Gh_M_009097genetic_marker
UCD_Gh_M_009098UCD_Gh_M_009098genetic_marker
UCD_Gh_M_009099UCD_Gh_M_009099genetic_marker
UCD_Gh_M_009100UCD_Gh_M_009100genetic_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