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 Genomicsjournal_title
BMC genomicsauthors
Li X,Gao W,Guo H,Zhang X,Fang DD,Lin Zdoi
10.1186/1471-2164-15-1046subject
Has Abstractpub_date
2014-12-01 00:00:00pages
1046issn
1471-2164pii
1471-2164-15-1046journal_volume
15pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Chemical bioavailability is an important dose metric in environmental risk assessment. Although many approaches have been used to evaluate bioavailability, not a single approach is free from limitations. Previously, we developed a new genomics-based approach that integrated microarray technology and regressi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2541-5
更新日期:2016-03-08 00:00:00
abstract:BACKGROUND:CRISPR is a microbial immune system likely to be involved in host-parasite coevolution. It functions using target sequences encoded by the bacterial genome, which interfere with invading nucleic acids using a homology-dependent system. The system also requires protospacer associated motifs (PAMs), short moti...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-663
更新日期:2014-08-08 00:00:00
abstract:BACKGROUND:CCCH type zinc finger proteins are RNA binding proteins with regulatory functions at all stages of mRNA metabolism. The best-characterized member, tritetraproline (TTP), binds to AU rich elements in 3' UTRs of unstable mRNAs, mediating their degradation. In kinetoplastids, CCCH type zinc finger proteins have...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-11-283
更新日期:2010-05-05 00:00:00
abstract:BACKGROUND:The response of the trout, O. mykiss, head kidney to bacterial lipopolysaccharide (LPS) or active and attenuated infectious hematopoietic necrosis virus (IHNV and attINHV respectively) intraperitoneal challenge, 24 and 72 hours post-injection, was investigated using a salmonid-specific cDNA microarray. RESU...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-141
更新日期:2008-03-26 00:00:00
abstract:BACKGROUND:There is strong but mostly circumstantial evidence that genetic factors modulate the severity of influenza infection in humans. Using genetically diverse but fully inbred strains of mice it has been shown that host sequence variants have a strong influence on the severity of influenza A disease progression. ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-411
更新日期:2012-08-20 00:00:00
abstract:BACKGROUND:Cold tolerance is a key determinant of the geographical distribution range of a plant species and crop production. Cold acclimation can enhance freezing-tolerance of plant species through a period of exposure to low nonfreezing temperatures. As a subtropical evergreen broadleaf plant, oil-tea camellia demons...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3570-4
更新日期:2017-02-28 00:00:00
abstract:BACKGROUND:The σ(54) subunit controls a unique class of promoters in bacteria. Such promoters, without exception, require enhancer binding proteins (EBPs) for transcription initiation. Desulfovibrio vulgaris Hildenborough, a model bacterium for sulfate reduction studies, has a high number of EBPs, more than most sequen...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2176-y
更新日期:2015-11-10 00:00:00
abstract:BACKGROUND:Mycosphaerella fijiensis is a ascomycete that causes Black Sigatoka in bananas. Recently, the M. fijiensis genome was sequenced. Repetitive sequences are ubiquitous components of fungal genomes. In most genomic analyses, repetitive sequences are associated with transposable elements (TEs). TEs are dispersed ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-720
更新日期:2012-12-22 00:00:00
abstract:BACKGROUND:Bifidobacterial genome analysis has provided insights as to how these gut commensals adapt to and persist in the human GIT, while also revealing genetic diversity among members of a given bifidobacterial (sub)species. Bifidobacteria are notoriously recalcitrant to genetic modification, which prevents explora...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1968-4
更新日期:2015-10-21 00:00:00
abstract:BACKGROUND:Adjuvant Radiotherapy (RT) after surgical removal of tumors proved beneficial in long-term tumor control and treatment planning. For many years, it has been well concluded that radio-sensitivities of tumors upon radiotherapy decrease according to the sizes of tumors and RT models based on Poisson statistics ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-S2-S9
更新日期:2008-09-16 00:00:00
abstract:BACKGROUND:Cotton is an important fiber crop but has serious heterosis effects, and cytoplasmic male sterility (CMS) is the major cause of heterosis in plants. However, to the best of our knowledge, no studies have investigated CMS Yamian A in cotton with the genetic background of Australian wild Gossypium bickii. Conj...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07261-y
更新日期:2020-12-02 00:00:00
abstract:BACKGROUND:The Bacillus cereus sensu lato group consists of six species (B. anthracis, B. cereus, B. mycoides, B. pseudomycoides, B. thuringiensis, and B. weihenstephanensis). While classical microbial taxonomy proposed these organisms as distinct species, newer molecular phylogenies and comparative genome sequencing s...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-430
更新日期:2011-08-24 00:00:00
abstract:BACKGROUND:The ballan wrasse (Labrus bergylta) belongs to a large teleost family containing more than 600 species showing several unique evolutionary traits such as lack of stomach and hermaphroditism. Agastric fish are found throughout the teleost phylogeny, in quite diverse and unrelated lineages, indicating stomach ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4570-8
更新日期:2018-03-06 00:00:00
abstract:BACKGROUND:Although profiling of RNA in single cells has broadened our understanding of development, cancer biology and mechanisms of disease dissemination, it requires the development of reliable and flexible methods. Here we demonstrate that the EpiStem RNA-Amp™ methodology reproducibly generates microgram amounts of...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1129
更新日期:2014-12-17 00:00:00
abstract:BACKGROUND:Alternative splicing (AS) regulation is extensive and shapes the functional complexity of higher organisms. However, the contribution of alternative splicing to fungal biology is not well studied. RESULTS:This study provides sequences of the transcriptomes of the plant wilt pathogen Verticillium dahliae, us...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3507-y
更新日期:2017-02-06 00:00:00
abstract:BACKGROUND:Dense single nucleotide polymorphism (SNP) genotyping arrays provide extensive information on polymorphic variation across the genome of species of interest. Such information can be used in studies of the genetic architecture of quantitative traits and to improve the accuracy of selection in breeding program...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-90
更新日期:2014-02-06 00:00:00
abstract:BACKGROUND:The Engrailed Homology 1 (EH1) motif is a small region, believed to have evolved convergently in homeobox and forkhead containing proteins, that interacts with the Drosophila protein groucho (C. elegans unc-37, Human Transducin-like Enhancers of Split). The small size of the motif makes its reliable identifi...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-6-169
更新日期:2005-11-27 00:00:00
abstract:BACKGROUND:Selenium (Se) is a trace element that occurs in proteins in the form of selenocysteine (Sec) and in tRNAs in the form of selenouridine (SeU). Selenophosphate synthetase (SelD) is required for both utilization traits. However, previous research also revealed SelDs in two organisms lacking Sec and SeU, suggest...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-251
更新日期:2008-05-29 00:00:00
abstract:BACKGROUND:Understanding the evolution of the vertebrate pancreas is key to understanding its functions. The chondrichthyes (cartilaginous fish such as sharks and rays) have often been suggested to possess the most ancient example of a distinct pancreas with both hormonal (endocrine) and digestive (exocrine) roles. The...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-15-1074
更新日期:2014-12-06 00:00:00
abstract:BACKGROUND:An underlying tenet of the epigenetic code hypothesis is the existence of protein domains that can recognize various chromatin structures. To date, two major candidates have emerged: (i) the bromodomain, which can recognize certain acetylation marks and (ii) the chromodomain, which can recognize certain meth...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-6
更新日期:2006-01-16 00:00:00
abstract:BACKGROUND:Avian infectious bronchitis virus (IBV) is a gamma coronavirus that severely affects the poultry industry worldwide. Long non-coding RNAs (lncRNAs), a subset of non-coding RNAs with a length of more than 200 nucleotides, have been recently recognized as pivotal factors in the pathogenesis of viral infections...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-07359-3
更新日期:2021-01-20 00:00:00
abstract:BACKGROUND:Betula platyphylla is a common tree species in northern China that has high economic and medicinal value. Our laboratory has been devoted to genome research on B. platyphylla for approximately 10 years. As primary organelle genomes, the complete genome sequences of chloroplasts are important to study the div...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5346-x
更新日期:2018-12-20 00:00:00
abstract:BACKGROUND:RNA amplification is necessary for profiling gene expression from small tissue samples. Previous studies have shown that the T7 based amplification techniques are reproducible but may distort the true abundance of targets. However, the consequences of such distortions on the ability to detect biological vari...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-252
更新日期:2006-10-09 00:00:00
abstract:BACKGROUND:Embryonic and fetal exposure to maternal obesity causes several maladaptive morphological and epigenetic changes in exposed offspring. The timing of these events is unclear, but changes can be observed even after a short exposure to maternal obesity around the time of conception. The hypothesis of this work ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5120-0
更新日期:2018-10-11 00:00:00
abstract:BACKGROUND:Plants contain significant quantities of small RNAs (sRNAs) derived from various sRNA biogenesis pathways. Many of these sRNAs play regulatory roles in plants. Previous analysis revealed that numerous sRNAs in corn, rice and soybean seeds have high sequence similarity to animal genes. However, exogenous RNA ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-381
更新日期:2012-08-08 00:00:00
abstract:BACKGROUND:Soybean seed weight is not only a yield component, but also a critical trait for various soybean food products such as sprouts, edamame, soy nuts, natto and miso. Linkage analysis and genome-wide association study (GWAS) are two complementary and powerful tools to connect phenotypic differences to the underl...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3922-0
更新日期:2017-07-12 00:00:00
abstract:BACKGROUND:Human leucocyte antigen (HLA) genes play an important role in determining the outcome of organ transplantation and are linked to many human diseases. Because of the diversity and polymorphisms of HLA loci, HLA typing at high resolution is challenging even with whole-genome sequencing data. RESULTS:We have d...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-16-S2-S7
更新日期:2015-01-01 00:00:00
abstract:BACKGROUND:Our previous study had proved that nigericin could reduce colorectal cancer cell proliferation in dose- and time-dependent manners by targeting Wnt/β-catenin signaling. To better elucidate its potential anti-cancer mechanism, two pancreatic cancer (PC) cell lines were exposed to increasing concentrations of ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6032-3
更新日期:2019-09-18 00:00:00
abstract:BACKGROUND:Microsatellites are widely used for many genetic studies. In contrast to single nucleotide polymorphism (SNP) and genotyping-by-sequencing methods, they are readily typed in samples of low DNA quality/concentration (e.g. museum/non-invasive samples), and enable the quick, cheap identification of species, hyb...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-176
更新日期:2013-03-15 00:00:00
abstract:BACKGROUND:Next-generation sequencing is providing researchers with a relatively fast and affordable option for developing genomic resources for organisms that are not among the traditional genetic models. Here we present a de novo assembly of the guppy (Poecilia reticulata) transcriptome using 454 sequence reads, and ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-202
更新日期:2011-04-20 00:00:00