Abstract:
BACKGROUND:Rapid acquisition of accurate genotyping information is essential for all genetic marker-based studies. For species with relatively small genomes, complete genome resequencing is a feasible approach for genotyping; however, for species with large and highly repetitive genomes, the acquisition of whole genome sequences for the purpose of genotyping is still relatively inefficient and too expensive to be carried out on a high-throughput basis. Sorghum bicolor is a C4 grass with a sequenced genome size of ~730 Mb, of which ~80% is highly repetitive. We have developed a restriction enzyme targeted genome resequencing method for genetic analysis, termed Digital Genotyping (DG), to be applied to sorghum and other grass species with large repeat-rich genomes. RESULTS:DG templates are generated using one of three methylation sensitive restriction enzymes that recognize a nested set of 4, 6 or 8 bp GC-rich sequences, enabling varying depth of analysis and integration of results among assays. Variation in sequencing efficiency among DG markers was correlated with template GC-content and length. The expected DG allele sequence was obtained 97.3% of the time with a ratio of expected to alternative allele sequence acquisition of >20:1. A genetic map aligned to the sorghum genome sequence with an average resolution of 1.47 cM was constructed using 1,772 DG markers from 137 recombinant inbred lines. The DG map enhanced the detection of QTL for variation in plant height and precisely aligned QTL such as Dw3 to underlying genes/alleles. Higher-resolution NgoMIV-based DG haplotypes were used to trace the origin of DNA on SBI-06, spanning Ma1 and Dw2 from progenitors to BTx623 and IS3620C. DG marker analysis identified the correct location of two miss-assembled regions and located seven super contigs in the sorghum reference genome sequence. CONCLUSION:DG technology provides a cost-effective approach to rapidly generate accurate genotyping data in sorghum. Currently, data derived from DG are used for many marker-based analyses, including marker-assisted breeding, pedigree and QTL analysis, genetic map construction, map-based gene cloning and association studies. DG in combination with whole genome resequencing is dramatically accelerating all aspects of genetic analysis of sorghum, an important genetic reference for C4 grass species.
journal_name
BMC Genomicsjournal_title
BMC genomicsauthors
Morishige DT,Klein PE,Hilley JL,Sahraeian SM,Sharma A,Mullet JEdoi
10.1186/1471-2164-14-448subject
Has Abstractpub_date
2013-07-05 00:00:00pages
448issn
1471-2164pii
1471-2164-14-448journal_volume
14pub_type
杂志文章相关文献
BMC GENOMICS文献大全abstract:BACKGROUND:Yellow-feathered chickens (YFCs) have a long history in China. They are well-known for the nutritional and commercial importance attributable to their yellow color phenotype. Currently, there is a huge paucity in knowledge of the genetic determinants responsible for phenotypic and biochemical properties of t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-6736-4
更新日期:2020-04-20 00:00:00
abstract:BACKGROUND:Escherichia coli infections known as colibacillosis constitute a considerable challenge to poultry farmers worldwide, in terms of decreased animal welfare and production economy. Colibacillosis is caused by avian pathogenic E. coli (APEC). APEC strains are extraintestinal pathogenic E. coli and have in gener...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3415-6
更新日期:2017-01-03 00:00:00
abstract:BACKGROUND:Brain-derived neurotrophic factor (BDNF) is a major signaling molecule that the brain uses to control a vast network of intracellular cascades fundamental to properties of learning and memory, and cognition. While much is known about BDNF signaling in the healthy nervous system where it controls the mitogen ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6033-2
更新日期:2019-08-28 00:00:00
abstract:BACKGROUND:We performed large-scale bacterial artificial chromosome (BAC) end-sequencing of two BAC libraries (an EcoRI- and a BamHI-digested library) and conducted an in silico analysis to characterize the obtained sequence data, to make them a useful resource for genomic research on the silkworm (Bombyx mori). RESUL...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-8-314
更新日期:2007-09-07 00:00:00
abstract:BACKGROUND:Genomes store information for building and maintaining organisms. Complete sequencing of many genomes provides the opportunity to study and compare global information properties of those genomes. RESULTS:We have analyzed aspects of the information content of Homo sapiens, Mus musculus, Drosophila melanogast...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-509
更新日期:2008-10-30 00:00:00
abstract:BACKGROUND:The autism spectrum encompasses a set of complex multigenic developmental disorders that severely impact the development of language, non-verbal communication, and social skills, and are associated with odd, stereotyped, repetitive behavior and restricted interests. To date, diagnosis of these neurologically...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-7-118
更新日期:2006-05-18 00:00:00
abstract:BACKGROUND:Antimicrobial resistance is one of our most serious health threats. Antimicrobial peptides (AMPs), effecter molecules of innate immune system, can defend host organisms against microbes and most have shown a lowered likelihood for bacteria to form resistance compared to many conventional drugs. Thus, AMPs ar...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06978-0
更新日期:2020-08-28 00:00:00
abstract:BACKGROUND:One member of the W family of human endogenous retroviruses (HERV) appears to have been functionally adopted by the human host. Nevertheless, a highly diversified and regulated transcription from a range of HERV-W elements has been observed in human tissues and cells. Aberrant expression of members of this f...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-22
更新日期:2011-01-12 00:00:00
abstract:BACKGROUND:Ensifer alkalisoli YIC4027, a recently characterized nitrogen-fixing bacterium of the genus Ensifer, has been isolated from root nodules of the host plant Sesbania cannabina. This plant is widely used as green manure and for soil remediation. E. alkalisoli YIC4027 can grow in saline-alkaline soils and is a n...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6004-7
更新日期:2019-08-12 00:00:00
abstract:BACKGROUND:Mitochondrial genomes of flowering plants (angiosperms) are highly dynamic in genome structure. The mitogenome of the earliest angiosperm Amborella is remarkable in carrying rampant foreign DNAs, in contrast to Liriodendron, the other only known early angiosperm mitogenome that is described as 'fossilized'. ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-4991-4
更新日期:2018-08-14 00:00:00
abstract:BACKGROUND:Aquaporins are a large family of transmembrane channel proteins that are present throughout all domains of life and are implicated in human disorders. These channels, allow the passive but selective movement of water and other small neutral solutes across cell membranes. Aquaporins have been classified into ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-12-S4-S8
更新日期:2011-12-22 00:00:00
abstract:BACKGROUND:Even before having its genome sequence published in 2004, Kluyveromyces lactis had long been considered a model organism for studies in genetics and physiology. Research on Kluyveromyces lactis is quite advanced and this yeast species is one of the few with which it is possible to perform formal genetic anal...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-517
更新日期:2012-10-01 00:00:00
abstract:BACKGROUND:Leishmania (L) are intracellular protozoan parasites that are able to survive and replicate within the harsh and potentially hostile phagolysosomal environment of mammalian mononuclear phagocytes. A complex interplay then takes place between the macrophage (MPhi) striving to eliminate the pathogen and the pa...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-9-238
更新日期:2008-05-21 00:00:00
abstract:BACKGROUND:One of the most common and recurrent vaginal infections is bacterial vaginosis (BV). The diagnosis is based on changes to the "normal" vaginal microbiome; however, the normal microbiome appears to differ according to reproductive status and ethnicity, and even among individuals within these groups. The Amsel...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5284-7
更新日期:2018-12-31 00:00:00
abstract:BACKGROUND:The expanding number and global distributions of herbicide resistant weedy species threaten food, fuel, fiber and bioproduct sustainability and agroecosystem longevity. Amongst the most competitive weeds, Amaranthus palmeri S. Wats has rapidly evolved resistance to glyphosate primarily through massive amplif...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-3336-4
更新日期:2017-01-17 00:00:00
abstract:BACKGROUND:Fungal pathogens of plants produce diverse repertoires of secondary metabolites, which have functions ranging from iron acquisition, defense against immune perturbation, to toxic assaults on the host. The wheat pathogen Zymoseptoria tritici causes Septoria tritici blotch, a foliar disease which is a signific...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-3969-y
更新日期:2017-08-17 00:00:00
abstract:BACKGROUND:Poxviruses constitute one of the largest and most complex animal virus families known. The notorious smallpox disease has been eradicated and the virus contained, but its simian sister, monkeypox is an emerging, untreatable infectious disease, killing 1 to 10 % of its human victims. In the case of poxviruses...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-016-2826-8
更新日期:2016-08-31 00:00:00
abstract:BACKGROUND:Precision medicine is a medical approach that takes into account individual genetic variability and often requires Next Generation Sequencing data in order to predict new treatments. Here we present GMIEC, Genomic Modules Identification et Characterization for genomics medicine, an application that is able t...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-020-06996-y
更新日期:2020-09-10 00:00:00
abstract:BACKGROUND:Rapeseed (Brassica napus) is an important oil seed crop in the Brassicaceae family. Chemical induced male sterility (CIMS) is one of the widely used method to produce the hybrids in B. napus. Identification of the key genes and pathways that involved in CIMS were important to understand the underlying molecu...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-018-5203-y
更新日期:2018-11-07 00:00:00
abstract:BACKGROUND:Most studies on the paper mulberry are mainly focused on the medicated and pharmacology, fiber quality, leaves feed development, little is known about its mechanism of adaptability to abiotic stress. Physiological measurement, transcriptomics and proteomic analysis were employed to understand its response to...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-2047-6
更新日期:2015-11-05 00:00:00
abstract:BACKGROUND:Infectious laryngotracheitis virus (ILTV; gallid herpesvirus 1) infection causes high mortality and huge economic losses in the poultry industry. To protect chickens against ILTV infection, chicken-embryo origin (CEO) and tissue-culture origin (TCO) vaccines have been used. However, the transmission of vacci...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-143
更新日期:2012-04-24 00:00:00
abstract:BACKGROUND:Aphid (Macrosiphoniella sanbourni) stress drastically influences the yield and quality of chrysanthemum, and grafting has been widely used to improve tolerance to biotic and abiotic stresses. However, the effect of grafting on the resistance of chrysanthemum to aphids remains unclear. Therefore, we used the ...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6158-3
更新日期:2019-10-25 00:00:00
abstract:BACKGROUND:Intramuscular fat (IMF) is one of the most important factors positively associated with meat quality. Triglycerides (TGs), as the main component of IMF, play an essential role in muscle lipid metabolism. This transcriptome analysis of pectoralis muscle tissue aimed to identify functional genes and biological...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-019-6221-0
更新日期:2019-11-15 00:00:00
abstract::Following the publication of this article [1], the authors reported that the original shading in columns 3 and 4 of Table 3, which indicated the presence or absence of viruses in each library, had been removed during typesetting. ...
journal_title:BMC genomics
pub_type: 杂志文章,已发布勘误
doi:10.1186/s12864-019-6067-5
更新日期:2019-09-05 00:00:00
abstract:BACKGROUND:Osteoporosis is a common and debilitating bone disease that is characterised by a low bone mineral density (BMD), a highly heritable trait. Genome-wide association studies (GWAS) have proven to be very successful in identifying common genetic variants associated with BMD adjusted for age, gender and weight, ...
journal_title:BMC genomics
pub_type: 杂志文章,meta分析
doi:10.1186/s12864-016-2481-0
更新日期:2016-02-25 00:00:00
abstract:BACKGROUND:Actinobacillus pleuropneumoniae causes pleuropneumonia in pigs, a disease which is associated with high morbidity and mortality, as well as impaired animal welfare. To obtain in-depth understanding of this infection, the interplay between virulence factors of the pathogen and defense mechanisms of the porcin...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-015-1557-6
更新日期:2015-05-28 00:00:00
abstract:BACKGROUND:Next generation sequencing provides a powerful tool to study genome structure in species whose genomes are far from being completely sequenced. In this work we describe and compare different computational approaches to evaluate the repetitive component of the genome of sunflower, by using medium/low coverage...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-14-686
更新日期:2013-10-06 00:00:00
abstract:BACKGROUND:Research using the model system Xenopus laevis has provided critical insights into the mechanisms of early vertebrate development and cell biology. Large scale sequencing efforts have provided an increasingly important resource for researchers. To provide full advantage of the available sequence, we have ana...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-6-123
更新日期:2005-09-14 00:00:00
abstract:BACKGROUND:Thoroughbred horses are the most expensive domestic animals, and their running ability and knowledge about their muscle-related diseases are important in animal genetics. While the horse reference genome is available, there has been no large-scale functional annotation of the genome using expressed genes der...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/1471-2164-13-473
更新日期:2012-09-12 00:00:00
abstract:BACKGROUND:Complete mitochondrial genomes are much better suited for the taxonomic identification and phylogenetic studies of nematodes than morphology or traditionally-used molecular markers, but they remain unavailable for the entire Camallanidae family (Chromadorea). As the only published mitogenome in the Camallani...
journal_title:BMC genomics
pub_type: 杂志文章
doi:10.1186/s12864-017-4237-x
更新日期:2017-11-02 00:00:00