Development of EST-based SNP and InDel markers and their utilization in tetraploid cotton genetic mapping.

Abstract:

BACKGROUND:Availability of molecular markers has proven to be an efficient tool in facilitating progress in plant breeding, which is particularly important in the case of less researched crops such as cotton. Considering the obvious advantages of single nucleotide polymorphisms (SNPs) and insertion-deletion polymorphisms (InDels), expressed sequence tags (ESTs) were analyzed in silico to identify SNPs and InDels in this study, aiming to develop more molecular markers in cotton. RESULTS:A total of 1,349 EST-based SNP and InDel markers were developed by comparing ESTs between Gossypium hirsutum and G. barbadense, mining G. hirsutum unigenes, and analyzing 3' untranslated region (3'UTR) sequences. The marker polymorphisms were investigated using the two parents of the mapping population based on the single-strand conformation polymorphism (SSCP) analysis. Of all the markers, 137 (10.16%) were polymorphic, and revealed 142 loci. Linkage analysis using a BC1 population mapped 133 loci on the 26 chromosomes. Statistical analysis of base variations in SNPs showed that base transitions accounted for 55.78% of the total base variations and gene ontology indicated that cotton genes varied greatly in harboring SNPs ranging from 1.00 to 24.00 SNPs per gene. Sanger sequencing of three randomly selected SNP markers revealed discrepancy between the in silico predicted sequences and the actual sequencing results. CONCLUSIONS:In silico analysis is a double-edged blade to develop EST-SNP/InDel markers. On the one hand, the designed markers can be well used in tetraploid cotton genetic mapping. And it plays a certain role in revealing transition preference and SNP frequency of cotton genes. On the other hand, the developmental efficiency of markers and polymorphism of designed primers are comparatively low.

journal_name

BMC Genomics

journal_title

BMC genomics

authors

Li X,Gao W,Guo H,Zhang X,Fang DD,Lin Z

doi

10.1186/1471-2164-15-1046

subject

Has Abstract

pub_date

2014-12-01 00:00:00

pages

1046

issn

1471-2164

pii

1471-2164-15-1046

journal_volume

15

pub_type

杂志文章
  • Massive parallel sequencing of mRNA in identification of unannotated salinity stress-inducible transcripts in rice (Oryza sativa L.).

    abstract:BACKGROUND:Microarray technology is limited to monitoring the expression of previously annotated genes that have corresponding probes on the array. Computationally annotated genes have not fully been validated, because ESTs and full-length cDNAs cannot cover entire transcribed regions. Here, mRNA-Seq (an Illumina cDNA ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-683

    authors: Mizuno H,Kawahara Y,Sakai H,Kanamori H,Wakimoto H,Yamagata H,Oono Y,Wu J,Ikawa H,Itoh T,Matsumoto T

    更新日期:2010-12-02 00:00:00

  • GaussianCpG: a Gaussian model for detection of CpG island in human genome sequences.

    abstract:BACKGROUND:As crucial markers in identifying biological elements and processes in mammalian genomes, CpG islands (CGI) play important roles in DNA methylation, gene regulation, epigenetic inheritance, gene mutation, chromosome inactivation and nuclesome retention. The generally accepted criteria of CGI rely on: (a) %G+...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-3731-5

    authors: Yu N,Guo X,Zelikovsky A,Pan Y

    更新日期:2017-05-24 00:00:00

  • A wing expressed sequence tag resource for Bicyclus anynana butterflies, an evo-devo model.

    abstract:BACKGROUND:Butterfly wing color patterns are a key model for integrating evolutionary developmental biology and the study of adaptive morphological evolution. Yet, despite the biological, economical and educational value of butterflies they are still relatively under-represented in terms of available genomic resources....

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-7-130

    authors: Beldade P,Rudd S,Gruber JD,Long AD

    更新日期:2006-05-31 00:00:00

  • Transcriptome profiling of aging Drosophila photoreceptors reveals gene expression trends that correlate with visual senescence.

    abstract:BACKGROUND:Aging is associated with functional decline of neurons and increased incidence of both neurodegenerative and ocular disease. Photoreceptor neurons in Drosophila melanogaster provide a powerful model for studying the molecular changes involved in functional senescence of neurons since decreased visual behavio...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-4304-3

    authors: Hall H,Medina P,Cooper DA,Escobedo SE,Rounds J,Brennan KJ,Vincent C,Miura P,Doerge R,Weake VM

    更新日期:2017-11-21 00:00:00

  • Investigation of transmembrane proteins using a computational approach.

    abstract:BACKGROUND:An important subfamily of membrane proteins are the transmembrane alpha-helical proteins, in which the membrane-spanning regions are made up of alpha-helices. Given the obvious biological and medical significance of these proteins, it is of tremendous practical importance to identify the location of transmem...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-9-S1-S7

    authors: Yang JY,Yang MQ,Dunker AK,Deng Y,Huang X

    更新日期:2008-01-01 00:00:00

  • Improving mammalian genome scaffolding using large insert mate-pair next-generation sequencing.

    abstract:BACKGROUND:Paired-tag sequencing approaches are commonly used for the analysis of genome structure. However, mammalian genomes have a complex organization with a variety of repetitive elements that complicate comprehensive genome-wide analyses. RESULTS:Here, we systematically assessed the utility of paired-end and mat...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-257

    authors: van Heesch S,Kloosterman WP,Lansu N,Ruzius FP,Levandowsky E,Lee CC,Zhou S,Goldstein S,Schwartz DC,Harkins TT,Guryev V,Cuppen E

    更新日期:2013-04-16 00:00:00

  • Sequencing of a QTL-rich region of the Theobroma cacao genome using pooled BACs and the identification of trait specific candidate genes.

    abstract:BACKGROUND:BAC-based physical maps provide for sequencing across an entire genome or a selected sub-genomic region of biological interest. Such a region can be approached with next-generation whole-genome sequencing and assembly as if it were an independent small genome. Using the minimum tiling path as a guide, specif...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-12-379

    authors: Feltus FA,Saski CA,Mockaitis K,Haiminen N,Parida L,Smith Z,Ford J,Staton ME,Ficklin SP,Blackmon BP,Cheng CH,Schnell RJ,Kuhn DN,Motamayor JC

    更新日期:2011-07-27 00:00:00

  • The phenylalanine ammonia lyase (PAL) gene family shows a gymnosperm-specific lineage.

    abstract:BACKGROUND:Phenylalanine ammonia lyase (PAL) is a key enzyme of the phenylpropanoid pathway that catalyzes the deamination of phenylalanine to trans-cinnamic acid, a precursor for the lignin and flavonoid biosynthetic pathways. To date, PAL genes have been less extensively studied in gymnosperms than in angiosperms. Ou...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-S3-S1

    authors: Bagal UR,Leebens-Mack JH,Lorenz WW,Dean JF

    更新日期:2012-06-11 00:00:00

  • Microarray analysis of ncRNA expression patterns in Caenorhabditis elegans after RNAi against snoRNA associated proteins.

    abstract:BACKGROUND:Short non-coding RNAs (ncRNAs) perform their cellular functions in ribonucleoprotein (RNP) complexes, which are also essential for maintaining the stability of the ncRNAs. Depletion of individual protein components of non-coding ribonucleoprotein (ncRNP) particles by RNA interference (RNAi) may therefore aff...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-9-278

    authors: Aftab MN,He H,Skogerbø G,Chen R

    更新日期:2008-06-11 00:00:00

  • Comparative transcriptomic analysis of bovine papillomatosis.

    abstract:BACKGROUND:Bovine papillomavirus (BPV) belongs to the Papillomaviridae family and infects epithelial cells of bovines and closely related animals, causing hyperproliferative lesions known as warts or papillomas, which may regress or progress to form benign or malignant tumors. The virus enters the host cell and interac...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-5361-y

    authors: Barreto DM,Barros GS,Santos LABO,Soares RC,Batista MVA

    更新日期:2018-12-19 00:00:00

  • Comparative transcriptomics reveals suppressed expression of genes related to auxin and the cell cycle contributes to the resistance of cucumber against Meloidogyne incognita.

    abstract:BACKGROUND:Meloidogyne incognita is a devastating nematode that causes significant losses in cucumber production worldwide. Although numerous studies have emphasized on the susceptible response of plants after nematode infection, the exact regulation mechanism of M. incognita-resistance in cucumber remains elusive. Ver...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-4979-0

    authors: Wang X,Cheng C,Zhang K,Tian Z,Xu J,Yang S,Lou Q,Li J,Chen JF

    更新日期:2018-08-03 00:00:00

  • A microarray platform and novel SNP calling algorithm to evaluate Plasmodium falciparum field samples of low DNA quantity.

    abstract:BACKGROUND:Analysis of single nucleotide polymorphisms (SNPs) derived from whole-genome studies allows for rapid evaluation of genome-wide diversity, and genomic epidemiology studies of Plasmodium falciparum provide insights into parasite population structure, gene flow, drug resistance and vaccine development. In area...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-719

    authors: Jacob CG,Tan JC,Miller BA,Tan A,Takala-Harrison S,Ferdig MT,Plowe CV

    更新日期:2014-08-26 00:00:00

  • Analysis of microRNAs, phased small interfering RNAs and their potential targets in Rosarugosa Thunb.

    abstract:BACKGROUND:MicroRNAs (miRNAs) are small non-coding RNAs that play important roles by regulating other genes. Rosa rugosa Thunb. is an important ornamental and edible plant, yet there are only a few studies on the miRNAs and their functions in R. rugosa. RESULTS:We sequenced 10 samll RNA profiles from the roots, petals...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-5325-2

    authors: Guo J,Wang Q,Liu L,Ren S,Li S,Liao P,Zhao Z,Lu C,Jiang B,Sunkar R,Zheng Y

    更新日期:2019-04-18 00:00:00

  • Database of exact tandem repeats in the Zebrafish genome.

    abstract:BACKGROUND:Sequencing of the approximately 1.7 billion bases of the zebrafish genome is currently underway. To date, few high resolution genetic maps exist for the zebrafish genome, based mainly on single nucleotide polymorphisms (SNPs) and short microsatellite repeats. The desire to construct a higher resolution genet...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-347

    authors: Rouchka EC

    更新日期:2010-06-01 00:00:00

  • Developing the anemone Aiptasia as a tractable model for cnidarian-dinoflagellate symbiosis: the transcriptome of aposymbiotic A. pallida.

    abstract:BACKGROUND:Coral reefs are hotspots of oceanic biodiversity, forming the foundation of ecosystems that are important both ecologically and for their direct practical impacts on humans. Corals are declining globally due to a number of stressors, including rising sea-surface temperatures and pollution; such stresses can ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-13-271

    authors: Lehnert EM,Burriesci MS,Pringle JR

    更新日期:2012-06-22 00:00:00

  • In silico identification and comparative analysis of differentially expressed genes in human and mouse tissues.

    abstract:BACKGROUND:Screening for differentially expressed genes on the genomic scale and comparative analysis of the expression profiles of orthologous genes between species to study gene function and regulation are becoming increasingly feasible. Expressed sequence tags (ESTs) are an excellent source of data for such studies ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-7-86

    authors: Pao SY,Lin WL,Hwang MJ

    更新日期:2006-04-21 00:00:00

  • Transcription analysis of the porcine alveolar macrophage response to porcine circovirus type 2.

    abstract:BACKGROUND:Porcine circovirus type 2 (PCV2) is the causal agent of postweaning multisystemic wasting syndrome (PMWS), which has severely impacted the swine industry worldwide. PCV2 triggers a weak and atypical innate immune response, but the key genes and mechanisms by which the virus interferes with host innate immuni...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-353

    authors: Li W,Liu S,Wang Y,Deng F,Yan W,Yang K,Chen H,He Q,Charreyre C,Audoneet JC

    更新日期:2013-05-27 00:00:00

  • Accurate single nucleotide variant detection in viral populations by combining probabilistic clustering with a statistical test of strand bias.

    abstract:BACKGROUND:Deep sequencing is a powerful tool for assessing viral genetic diversity. Such experiments harness the high coverage afforded by next generation sequencing protocols by treating sequencing reads as a population sample. Distinguishing true single nucleotide variants (SNVs) from sequencing errors remains chall...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-501

    authors: McElroy K,Zagordi O,Bull R,Luciani F,Beerenwinkel N

    更新日期:2013-07-24 00:00:00

  • Widespread promoter methylation of synaptic plasticity genes in long-term potentiation in the adult brain in vivo.

    abstract:BACKGROUND:DNA methylation is a key modulator of gene expression in mammalian development and cellular differentiation, including neurons. To date, the role of DNA modifications in long-term potentiation (LTP) has not been explored. RESULTS:To investigate the occurrence of DNA methylation changes in LTP, we undertook ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-3621-x

    authors: Maag JL,Kaczorowski DC,Panja D,Peters TJ,Bramham CR,Wibrand K,Dinger ME

    更新日期:2017-03-23 00:00:00

  • Changes in H3K27ac following lipopolysaccharide stimulation of nasopharyngeal epithelial cells.

    abstract:BACKGROUND:The epithelium is the first line of defense against pathogens. Notably the epithelial cells lining the respiratory track are crucial in sensing airborne microbes and mounting an effective immune response via the expression of target genes such as cytokines and chemokines. Gene expression regulation following...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-5295-4

    authors: Borghini L,Hibberd M,Davila S

    更新日期:2018-12-27 00:00:00

  • Functional annotation of novel lineage-specific genes using co-expression and promoter analysis.

    abstract:BACKGROUND:The diversity of placental architectures within and among mammalian orders is believed to be the result of adaptive evolution. Although, the genetic basis for these differences is unknown, some may arise from rapidly diverging and lineage-specific genes. Previously, we identified 91 novel lineage-specific tr...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-161

    authors: Kumar CG,Everts RE,Loor JJ,Lewin HA

    更新日期:2010-03-09 00:00:00

  • Transcriptomics analysis revealing candidate genes and networks for sex differentiation of yesso scallop (Patinopecten yessoensis).

    abstract:BACKGROUND:The Yesso scallop, Patinopecten (Mizuhopecten) yessoensis, is a commercially important bivalve in the coastal countries of Northeast Asia. It has complex modes of sex differentiation, but knowledge of the mechanisms underlying this sex determination and differentiation is limited. RESULTS:In this study, the...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-019-6021-6

    authors: Zhou L,Liu Z,Dong Y,Sun X,Wu B,Yu T,Zheng Y,Yang A,Zhao Q,Zhao D

    更新日期:2019-08-23 00:00:00

  • Global proteomic analysis of the oocyst/sporozoite of Toxoplasma gondii reveals commitment to a host-independent lifestyle.

    abstract:BACKGROUND:Toxoplasmosis is caused by the apicomplexan parasite Toxoplasma gondii and can be acquired either congenitally or via the oral route. In the latter case, transmission is mediated by two distinct invasive stages, i.e., bradyzoites residing in tissue cysts or sporozoites contained in environmentally resistant ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-14-183

    authors: Possenti A,Fratini F,Fantozzi L,Pozio E,Dubey JP,Ponzi M,Pizzi E,Spano F

    更新日期:2013-03-15 00:00:00

  • A deconvolution method and its application in analyzing the cellular fractions in acute myeloid leukemia samples.

    abstract:BACKGROUND:The identification of cell type-specific genes (markers) is an essential step for the deconvolution of the cellular fractions, primarily, from the gene expression data of a bulk sample. However, the genes with significant changes identified by pair-wise comparisons cannot indeed represent the specificity of ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-020-06888-1

    authors: Li H,Sharma A,Ming W,Sun X,Liu H

    更新日期:2020-09-23 00:00:00

  • Does replication groups scoring reduce false positive rate in SNP interaction discovery?

    abstract:BACKGROUND:Computational methods that infer single nucleotide polymorphism (SNP) interactions from phenotype data may uncover new biological mechanisms in non-Mendelian diseases. However, practical aspects of such analysis face many problems. Present experimental studies typically use SNP arrays with hundreds of thousa...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-11-58

    authors: Toplak M,Curk T,Demsar J,Zupan B

    更新日期:2010-01-22 00:00:00

  • Genome-wide association study reveals novel loci associated with body size and carcass yields in Pekin ducks.

    abstract:BACKGROUND:Pekin duck products have become popular in Asia over recent decades and account for an increasing market share. However, the genetic mechanisms affecting carcass growth in Pekin ducks remain unknown. This study aimed to identify quantitative trait loci affecting body size and carcass yields in Pekin ducks. ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-018-5379-1

    authors: Deng MT,Zhu F,Yang YZ,Yang FX,Hao JP,Chen SR,Hou ZC

    更新日期:2019-01-03 00:00:00

  • Integrative phenotyping framework (iPF): integrative clustering of multiple omics data identifies novel lung disease subphenotypes.

    abstract:BACKGROUND:The increased multi-omics information on carefully phenotyped patients in studies of complex diseases requires novel methods for data integration. Unlike continuous intensity measurements from most omics data sets, phenome data contain clinical variables that are binary, ordinal and categorical. RESULTS:In ...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-015-2170-4

    authors: Kim S,Herazo-Maya JD,Kang DD,Juan-Guardela BM,Tedrow J,Martinez FJ,Sciurba FC,Tseng GC,Kaminski N

    更新日期:2015-11-11 00:00:00

  • Autocorrelation analysis reveals widespread spatial biases in microarray experiments.

    abstract:BACKGROUND:DNA microarrays provide the ability to interrogate multiple genes in a single experiment and have revolutionized genomic research. However, the microarray technology suffers from various forms of biases and relatively low reproducibility. A particular source of false data has been described, in which non-ran...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-8-164

    authors: Koren A,Tirosh I,Barkai N

    更新日期:2007-06-12 00:00:00

  • Biological networks in Parkinson's disease: an insight into the epigenetic mechanisms associated with this disease.

    abstract:BACKGROUND:Parkinson's disease (PD) is the second most prevalent neurodegenerative disorders in the world. Studying PD from systems biology perspective involving genes and their regulators might provide deeper insights into the complex molecular interactions associated with this disease. RESULT:We have studied gene co...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/s12864-017-4098-3

    authors: Chatterjee P,Roy D,Bhattacharyya M,Bandyopadhyay S

    更新日期:2017-09-12 00:00:00

  • Unique aspects of fiber degradation by the ruminal ethanologen Ruminococcus albus 7 revealed by physiological and transcriptomic analysis.

    abstract:BACKGROUND:Bacteria in the genus Ruminococcus are ubiquitous members of the mammalian gastrointestinal tract. In particular, they are important in ruminants where they digest a wide range of plant cell wall polysaccharides. For example, Ruminococcus albus 7 is a primary cellulose degrader that produces acetate usable b...

    journal_title:BMC genomics

    pub_type: 杂志文章

    doi:10.1186/1471-2164-15-1066

    authors: Christopherson MR,Dawson JA,Stevenson DM,Cunningham AC,Bramhacharya S,Weimer PJ,Kendziorski C,Suen G

    更新日期:2014-12-04 00:00:00