Identification of SNP and SSR markers in eggplant using RAD tag sequencing
Lorenzo Barchi,Sergio Lanteri,Ezio Portis,Alberto Acquadro,Giampiero Valè,Laura Toppino,Giuseppe Leonardo Rotino +6 more
Reads0
Chats0
TLDR
The high throughput sequencing of the RAD tags allowed the discovery of a large number of DNA markers, which will prove useful for extending the current knowledge of the genome organization of eggplant, for assisting in marker-aided selection and for carrying out comparative genomic analyses within the Solanaceae family.Abstract:
Background: The eggplant (Solanum melongena L.) genome is relatively unexplored, especially compared to those of the other major Solanaceae crops tomato and potato. In particular, no SNP markers are publicly available; on the other hand, over 1,000 SSR markers were developed and publicly available. We have combined the recently developed Restriction-site Associated DNA (RAD) approach with Illumina DNA sequencing for rapid and mass discovery of both SNP and SSR markers for eggplant. Results: RAD tags were generated from the genomic DNA of a pair of eggplant mapping parents, and sequenced to produce ~17.5 Mb of sequences arrangeable into ~78,000 contigs. The resulting non-redundant genomic sequence dataset consisted of ~45,000 sequences, of which ~29% were putative coding sequences and ~70% were in common between the mapping parents. The shared sequences allowed the discovery of ~10,000 SNPs and nearly 1,000 indels, equivalent to a SNP frequency of 0.8 per Kb and an indel frequency of 0.07 per Kb. Over 2,000 of the SNPs are likely to be mappable via the Illumina GoldenGate assay. A subset of 384 SNPs was used to successfully fingerprint a panel of eggplant germplasm, producing a set of informative diversity data. The RAD sequences also included nearly 2,000 putative SSRs, and primer pairs were designed to amplify 1,155 loci. Conclusion: The high throughput sequencing of the RAD tags allowed the discovery of a large number of DNA markers, which will prove useful for extending our current knowledge of the genome organization of eggplant, for assisting in marker-aided selection and for carrying out comparative genomic analyses within the Solanaceae family.read more
Citations
More filters
Journal ArticleDOI
Stacks: an analysis tool set for population genomics
Julian M. Catchen,Paul A. Hohenlohe,Paul A. Hohenlohe,Susan Bassham,Angel Amores,William A. Cresko +5 more
TL;DR: The expanded population genomics functions in Stacks will make it a useful tool to harness the newest generation of massively parallel genotyping data for ecological and evolutionary genetics.
Journal ArticleDOI
Special features of RAD Sequencing data: implications for genotyping.
John W. Davey,Timothee Cezard,Pablo Fuentes-Utrilla,Cathlene Eland,Karim Gharbi,Mark Blaxter +5 more
TL;DR: It is shown that there are several sources of bias specific to RAD‐Seq that are not explicitly addressed by current genotyping tools, namely restriction fragment bias, restriction site heterozygosity and PCR GC content bias, and that most RAD loci will be accurately genotyped by existing tools.
Journal ArticleDOI
SNP Discovery through Next-Generation Sequencing and Its Applications.
TL;DR: Various aspects of SNP discovery are touched upon, highlighting key points in availability and selection of appropriate sequencing platforms, bioinformatics pipelines, SNP filtering criteria, and applications of SNPs in genetic analyses.
Journal ArticleDOI
Genotyping-by-Sequencing in Plants
TL;DR: The current state of GBS in plants is summarized and the promises it holds as a genome-wide genotyping application are summarized.
Journal ArticleDOI
Draft Genome Sequence of Eggplant (Solanum melongena L.): the Representative Solanum Species Indigenous to the Old World
Hideki Hirakawa,Kenta Shirasawa,Koji Miyatake,Tsukasa Nunome,Satomi Negoro,Akio Ohyama,Hirotaka Yamaguchi,Shusei Sato,Sachiko Isobe,Satoshi Tabata,Hiroyuki Fukuoka +10 more
TL;DR: The detailed comparative analysis of the eggplant and tomato genomes will facilitate the understanding of the genomic architecture of solanaceous plants, which will contribute to cultivation and further utilization of these crops.
References
More filters
Book ChapterDOI
Primer3 on the WWW for general users and for biologist programmers.
Steve Rozen,Helen Skaletsky +1 more
TL;DR: This chapter assumes acquaintance with the principles and practice of PCR, as outlined in, for example, refs.
Journal ArticleDOI
A general method applicable to the search for similarities in the amino acid sequence of two proteins
TL;DR: A computer adaptable method for finding similarities in the amino acid sequences of two proteins has been developed and it is possible to determine whether significant homology exists between the proteins to trace their possible evolutionary development.
NTSYS-pc Numerical Taxonomy and Multivariate Analysis System, version 2.1: Owner manual
F.J. Rohlf,F Rohlf +1 more
Journal ArticleDOI
Velvet: Algorithms for de novo short read assembly using de Bruijn graphs
Daniel R. Zerbino,Ewan Birney +1 more
TL;DR: Velvet represents a new approach to assembly that can leverage very short reads in combination with read pairs to produce useful assemblies and is in close agreement with simulated results without read-pair information.