Development and application of the Faba_bean_130K targeted next-generation sequencing SNP genotyping platform based on transcriptome sequencing.

TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik
Chenyu WangTao Yang

Abstract

Large-scale faba bean transcriptome data are available, and the first genotyping platform based on liquid-phase probe targeted capture technology was developed for genetic and molecular breeding studies. Faba bean (Vicia faba L., 2n = 12) is an important food legume crop that is widely grown for multiple uses worldwide. However, no reference genome is currently available due to its very large genome size (approximately 13 Gb) and limited single nucleotide polymorphism (SNP) markers as well as highly efficient genotyping tools have been reported for faba bean. In this study, 16.7 billion clean reads were obtained from transcriptome libraries of flowers and leaves of 102 global faba bean accessions. A total of 243,120 unigenes were de novo assembled and functionally annotated. Moreover, a total of 1,579,411 SNPs were identified and further filtered according to a selection pipeline to develop a high-throughput, flexible, low-cost Faba_bean_130K targeted next-generation sequencing (TNGS) genotyping platform. A set of 69 Chinese faba bean accessions were genotyped with the TNGS genotyping platform, and the average mapping rate of captured reads to reference transcripts was 93.14%, of which 53.23% were located in the targeted region...Continue Reading

References

Jul 31, 2007·The Plant Journal : for Cell and Molecular Biology·W Brad BarbazukPatrick S Schnable
May 1, 2008·Nucleic Acids Research·Stefan GötzAna Conesa
Oct 15, 2008·PloS One·Nathan A BairdEric A Johnson
Nov 19, 2008·Nature Reviews. Genetics·Zhong WangMichael Snyder
Jan 27, 2009·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Xuxiao ZongRobert Redden
Jun 10, 2009·Bioinformatics·Heng LiUNKNOWN 1000 Genome Project Data Processing Subgroup
Aug 4, 2009·Genome Research·David H AlexanderKenneth Lange
Mar 13, 2010·PloS One·Morgan N PriceAdam P Arkin
Oct 26, 2010·Nature Genetics·Xuehui HuangBin Han
May 17, 2011·Nature Biotechnology·Manfred G GrabherrAviv Regev
May 17, 2011·PloS One·Robert J ElshireSharon E Mitchell
Jun 10, 2011·Bioinformatics·Petr DanecekUNKNOWN 1000 Genomes Project Analysis Group
Jun 18, 2011·Nature Reviews. Genetics·John W DaveyMark L Blaxter
Dec 29, 2011·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Hai-Fei WangRobert Redden
Feb 22, 2012·Briefings in Functional Genomics·Mahendar ThudiRajeev K Varshney
Mar 6, 2012·Nature Methods·Ben Langmead, Steven L Salzberg
Nov 1, 2012·Molecular Ecology·John W DaveyMark L Blaxter
Sep 17, 2013·Plant Biotechnology Journal·Huihui YuQifa Zhang
Oct 15, 2013·Molecular Plant·Haodong ChenQifa Zhang
Jan 21, 2014·Plant Cell Reports·Yuchun RaoQian Qian
Jan 29, 2014·Plant Science : an International Journal of Experimental Plant Biology·Sukhjiwan KaurJeffrey G Paull
Aug 15, 2014·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Allan F BrownEric W Jackson
Nov 18, 2014·Nature Methods·Benjamin BuchfinkDaniel H Huson
Jan 21, 2015·PloS One·Modhumita Ghosh DasguptaKonstantin V Krutovsky
Apr 14, 2015·Plant Biotechnology Journal·Anne WebbDonal M O'Sullivan
Jun 9, 2015·Scientific Reports·Charles CernayDavid Makowski
Aug 13, 2015·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·Peter G VosHerman J van Eck
Oct 16, 2015·Plant Biotechnology Journal·Mark O WinfieldKeith J Edwards
Jan 27, 2016·International Review of Cell and Molecular Biology·Reynante OrdonioMakoto Matsuoka
Jan 28, 2016·Genome Biology·Ana ConesaAli Mortazavi
Feb 22, 2017·Nature Plants·Christine H FoyerMichael J Considine
Apr 19, 2017·Journal of Experimental Botany·James W CooperChristine H Foyer
Jul 15, 2017·Frontiers in Plant Science·Matthew S RoddaSukhjiwan Kaur
Aug 10, 2017·TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik·S Ocaña-MoralE Madrid

❮ Previous
Next ❯

Related Concepts

Trending Feeds

COVID-19

Coronaviruses encompass a large family of viruses that cause the common cold as well as more serious diseases, such as the ongoing outbreak of coronavirus disease 2019 (COVID-19; formally known as 2019-nCoV). Coronaviruses can spread from animals to humans; symptoms include fever, cough, shortness of breath, and breathing difficulties; in more severe cases, infection can lead to death. This feed covers recent research on COVID-19.

Blastomycosis

Blastomycosis fungal infections spread through inhaling Blastomyces dermatitidis spores. Discover the latest research on blastomycosis fungal infections here.

Nuclear Pore Complex in ALS/FTD

Alterations in nucleocytoplasmic transport, controlled by the nuclear pore complex, may be involved in the pathomechanism underlying multiple neurodegenerative diseases including Amyotrophic Lateral Sclerosis and Frontotemporal Dementia. Here is the latest research on the nuclear pore complex in ALS and FTD.

Applications of Molecular Barcoding

The concept of molecular barcoding is that each original DNA or RNA molecule is attached to a unique sequence barcode. Sequence reads having different barcodes represent different original molecules, while sequence reads having the same barcode are results of PCR duplication from one original molecule. Discover the latest research on molecular barcoding here.

Chronic Fatigue Syndrome

Chronic fatigue syndrome is a disease characterized by unexplained disabling fatigue; the pathology of which is incompletely understood. Discover the latest research on chronic fatigue syndrome here.

Evolution of Pluripotency

Pluripotency refers to the ability of a cell to develop into three primary germ cell layers of the embryo. This feed focuses on the mechanisms that underlie the evolution of pluripotency. Here is the latest research.

Position Effect Variegation

Position Effect Variagation occurs when a gene is inactivated due to its positioning near heterochromatic regions within a chromosome. Discover the latest research on Position Effect Variagation here.

STING Receptor Agonists

Stimulator of IFN genes (STING) are a group of transmembrane proteins that are involved in the induction of type I interferon that is important in the innate immune response. The stimulation of STING has been an active area of research in the treatment of cancer and infectious diseases. Here is the latest research on STING receptor agonists.

Microbicide

Microbicides are products that can be applied to vaginal or rectal mucosal surfaces with the goal of preventing, or at least significantly reducing, the transmission of sexually transmitted infections. Here is the latest research on microbicides.