Abstract:
BACKGROUND:A genome-wide association study (GWAS) is the foremost strategy used for finding genes that control human diseases and agriculturally important traits, but it often reports false positives. In contrast, its complementary method, linkage analysis, provides direct genetic confirmation, but with limited resolution. A joint approach, using multiple linkage populations, dramatically improves resolution and statistical power. For example, this approach has been used to confirm that many complex traits, such as flowering time controlling adaptation in maize, are controlled by multiple genes with small effects. In addition, genotyping by sequencing (GBS) at low coverage not only produces genotyping errors, but also results in large datasets, making the use of high-throughput sequencing technologies computationally inefficient or unfeasible. RESULTS:In this study, we converted raw SNPs into effective recombination bins. The reduced bins not only retain the original information, but also correct sequencing errors from low-coverage genomic sequencing. To further increase the statistical power and resolution, we merged a new temperate maize nested association mapping (NAM) population derived in China (CN-NAM) with the existing maize NAM population developed in the US (US-NAM). Together, the two populations contain 36 families and 7,000 recombinant inbred lines (RILs). One million SNPs were generated for all the RILs with GBS at low coverage. We developed high-quality recombination maps for each NAM population to correct genotyping errors and improve the computational efficiency of the joint linkage analysis. The original one million SNPs were reduced to 4,932 and 5,296 recombination bins with average interval distances of 0.34 cM and 0.28 cM for CN-NAM and US-NAM, respectively. The quantitative trait locus (QTL) mapping for flowering time (days to tasseling) indicated that the high-density, recombination bin map improved resolution of QTL mapping by 50 % compared with that using a medium-density map. We also demonstrated that combining the CN-NAM and US-NAM populations improves the power to detect QTL by 50 % compared to single NAM population mapping. Among the QTLs mapped by joint usage of the US-NAM and CN-NAM maps, 25 % of the QTLs overlapped with known flowering-time genes in maize. CONCLUSION:This study provides directions and resources for the research community, especially maize researchers, for future studies using the recombination bin strategy for joint linkage analysis. Available resources include efficient usage of low-coverage genomic sequencing, detailed positions for genes controlling maize flowering, and recombination bin maps and flowering- time data for both CN and US NAMs. Maize researchers even have the opportunity to grow both CN and US NAM populations to study the traits of their interest, as the seeds of both NAM populations are available from the seed repository in China and the US.
journal_name
BMC Bioljournal_title
BMC biologyauthors
Li C,Li Y,Bradbury PJ,Wu X,Shi Y,Song Y,Zhang D,Rodgers-Melnick E,Buckler ES,Zhang Z,Li Y,Wang Tdoi
10.1186/s12915-015-0187-4subject
Has Abstractpub_date
2015-09-21 00:00:00pages
78issn
1741-7007pii
10.1186/s12915-015-0187-4journal_volume
13pub_type
杂志文章相关文献
BMC BIOLOGY文献大全abstract:BACKGROUND:Abnormalities in pyloric development or in contractile function of the pylorus cause reflux of duodenal contents into the stomach and increase the risk of gastric metaplasia and cancer. Abnormalities of the pyloric region are also linked to congenital defects such as the relatively common neonatal hypertroph...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/1741-7007-12-25
更新日期:2014-03-27 00:00:00
abstract::Ethylene gas is a major plant hormone that influences diverse processes in plant growth, development and stress responses throughout the plant life cycle. Responses to ethylene, such as fruit ripening, are significant to agriculture. The core molecular elements of the ethylene-signaling pathway have been uncovered, re...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-016-0230-0
更新日期:2016-01-27 00:00:00
abstract:BACKGROUND:Microarray analysis and 454 cDNA sequencing were used to investigate a centuries-old problem in regenerative biology: the basis of nerve-dependent limb regeneration in salamanders. Innervated (NR) and denervated (DL) forelimbs of Mexican axolotls were amputated and transcripts were sampled after 0, 5, and 14...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/1741-7007-7-1
更新日期:2009-01-13 00:00:00
abstract:BACKGROUND:Methods for assigning strains to bacterial species are cumbersome and no longer fit for purpose. The concatenated sequences of multiple house-keeping genes have been shown to be able to define and circumscribe bacterial species as sequence clusters. The advantage of this approach (multilocus sequence analysi...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/1741-7007-7-3
更新日期:2009-01-26 00:00:00
abstract::Rino Rappuoli is a graduate of Siena University, where he also earned his PhD before moving to the Sclavo Research Center, the Italian vaccine institute, also in Siena. He then spent two years in the USA, mostly at Harvard with John Murphy and Alwin Pappenheimer working on a new diphtheria vaccine based on a non-toxic...
journal_title:BMC biology
pub_type: 面试
doi:10.1186/s12915-014-0100-6
更新日期:2014-11-29 00:00:00
abstract:BACKGROUND:Eukaryotic genome assembly remains a challenge in part due to the prevalence of complex DNA repeats. This is a particularly acute problem for holocentric nematodes because of the large number of satellite DNA sequences found throughout their genomes. These have been recalcitrant to most genome sequencing met...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-017-0473-4
更新日期:2018-01-11 00:00:00
abstract::Animal domestication has fascinated biologists since Charles Darwin first drew the parallel between evolution via natural selection and human-mediated breeding of livestock and companion animals. In this review we show how studies of ancient DNA from domestic animals and their wild progenitors and congeners have shed ...
journal_title:BMC biology
pub_type: 杂志文章,评审
doi:10.1186/s12915-019-0724-7
更新日期:2019-12-02 00:00:00
abstract:BACKGROUND:The green algae Chlamydomonas reinhardtii and Volvox carteri are important models for studying light perception and response, expressing many different photoreceptors. More than 10 opsins were reported in C. reinhardtii, yet only two-the channelrhodopsins-were functionally characterized. Characterization of ...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-018-0613-5
更新日期:2018-12-06 00:00:00
abstract::A recent paper in BMC Structural Biology reports the crystal structure of human prolylcarboxypeptidase (PRCP), one of the two members of the S28 peptidase family. Comparison of the substrate-binding site of PRCP with that of its family partner, dipeptidyl dipeptidase 7 (DPP7), helps to explain the different enzymatic ...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/1741-7007-8-87
更新日期:2010-06-28 00:00:00
abstract:BACKGROUND:mTOR signaling is an essential nutrient and energetic sensing pathway. Here we describe AIMTOR, a sensitive genetically encoded BRET (Bioluminescent Resonance Energy Transfer) biosensor to study mTOR activity in living cells. RESULTS:As a proof of principle, we show in both cell lines and primary cell cultu...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-020-00790-8
更新日期:2020-07-03 00:00:00
abstract:BACKGROUND:Parkinson's disease (PD) is a progressive neurodegenerative disorder characterized by both motor and non-motor symptoms. Gastrointestinal tract dysfunction is one of the non-motor features, where constipation is reported as the most common gastrointestinal symptom. Aromatic bacterial metabolites are attracti...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-020-00876-3
更新日期:2020-10-20 00:00:00
abstract:BACKGROUND:How tissue and organ sizes are specified is one of the great unsolved mysteries in biology. Experiments and mathematical modeling implicate feedback control of cell lineage progression, but a broad understanding of what lineage feedback accomplishes is lacking. RESULTS:By exploring the possible effects of v...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-015-0122-8
更新日期:2015-02-19 00:00:00
abstract:BACKGROUND:Astrocytes can mediate neurovascular coupling, modulate neuronal excitability, and promote synaptic maturation and remodeling. All these functions are likely to be modulated by the sleep/wake cycle, because brain metabolism, neuronal activity and synaptic turnover change as a function of behavioral state. Ye...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-015-0176-7
更新日期:2015-08-25 00:00:00
abstract::Cells are highly complex and orderly machines, with defined shapes and a startling variety of internal organizations. Complex geometry is a feature of both free-living unicellular organisms and cells inside multicellular animals. Where does the geometry of a cell come from? Many of the same questions that arise in dev...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/1741-7007-9-57
更新日期:2011-08-31 00:00:00
abstract:BACKGROUND:Kinases mTORC1 and AMPK act as energy sensors, controlling nutrient responses and cellular growth. Changes in nutrient levels affect diverse transcriptional networks, making it challenging to identify downstream paths that regulate cellular growth or a switch to development via nutrient variation. The life c...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-019-0673-1
更新日期:2019-07-18 00:00:00
abstract:BACKGROUND:The next big challenge in human genetics is understanding the 98% of the genome that comprises non-coding DNA. Hidden in this DNA are sequences critical for gene regulation, and new experimental strategies are needed to understand the functional role of gene-regulation sequences in health and disease. In thi...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/1741-7007-11-106
更新日期:2013-10-14 00:00:00
abstract:BACKGROUND:Metazoan lineages exhibit a wide range of regenerative capabilities that vary among developmental stage and tissue type. The most robust regenerative abilities are apparent in the phyla Cnidaria, Platyhelminthes, and Echinodermata, whose members are capable of whole-body regeneration (WBR). This phenomenon h...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-019-0633-9
更新日期:2019-02-22 00:00:00
abstract:BACKGROUND:Autophagy mediates lysosomal degradation of cytosolic components. Recent work has associated autophagic dysfunction with pathologies, including cancer and cardiovascular disease. To date, the identification of clinically-applicable drugs that modulate autophagy has been hampered by the lack of standardized a...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/1741-7007-9-38
更新日期:2011-06-02 00:00:00
abstract:BACKGROUND:The International Mouse Phenotyping Consortium is generating null allele mice for every protein-coding gene in the genome and characterizing these mice to identify gene-phenotype associations. While CRISPR/Cas9-mediated null allele production in mice is highly efficient, generation of conditional alleles has...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-018-0529-0
更新日期:2018-06-21 00:00:00
abstract:BACKGROUND:Annotation of cell identity is an essential process in neuroscience that allows comparison of cells, including that of neural activities across different animals. In Caenorhabditis elegans, although unique identities have been assigned to all neurons, the number of annotatable neurons in an intact animal has...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-020-0745-2
更新日期:2020-03-19 00:00:00
abstract:BACKGROUND:A key event in plant morphogenesis is the establishment of a division plane. A plant-specific microtubular preprophase band (PPB) accurately predicts the line of cell division, whereas the phragmoplast, another plant-specific array, executes cell division by maintaining this predicted line. Although establis...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/1741-7007-3-11
更新日期:2005-04-14 00:00:00
abstract:BACKGROUND:Gq is a heterotrimeric G protein that plays an important role in numerous physiological processes. To delineate the molecular mechanisms and kinetics of signalling through this protein, its activation should be measurable in single living cells. Recently, fluorescence resonance energy transfer (FRET) sensors...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/1741-7007-9-32
更新日期:2011-05-27 00:00:00
abstract::The vertebrate nervous system is deeply divided into 'somatic' and 'visceral' subsystems that respond to external and internal stimuli, respectively. Molecular characterization of neurons in different groups of mollusks by Nomaksteinsky and colleagues, published in this issue of BMC Biology, reveals that the viscero-s...
journal_title:BMC biology
pub_type: 评论,杂志文章
doi:10.1186/1741-7007-11-54
更新日期:2013-04-30 00:00:00
abstract:BACKGROUND:TPA Induced Sequence 7 acts as a transcriptional co-regulator controlling the expression of genes involved in differentiation of various cell types, including skeletal myoblasts. We and others have shown that TIS7 regulates adult myogenesis through MyoD, one of the essential myogenic regulatory factors. RES...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-016-0318-6
更新日期:2016-10-25 00:00:00
abstract:BACKGROUND:Collective neural crest cell migration is critical to the form and function of the vertebrate face and neck, distributing bone, cartilage, and nerve cells into peripheral targets that are intimately linked with head vasculature. The vasculature and neural crest structures are ultimately linked, but when and ...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-016-0323-9
更新日期:2016-12-15 00:00:00
abstract:BACKGROUND:The study of microbial communities has been revolutionised in recent years by the widespread adoption of culture independent analytical techniques such as 16S rRNA gene sequencing and metagenomics. One potential confounder of these sequence-based approaches is the presence of contamination in DNA extraction ...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-014-0087-z
更新日期:2014-11-12 00:00:00
abstract:BACKGROUND:The red algae (Rhodophyta) diverged from the green algae and plants (Viridiplantae) over one billion years ago within the kingdom Archaeplastida. These photosynthetic lineages provide an ideal model to study plastid genome reduction in deep time. To this end, we assembled a large dataset of the plastid genom...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-016-0299-5
更新日期:2016-09-02 00:00:00
abstract:BACKGROUND:Parkinson's disease (PD)-associated E3 ubiquitin ligase Parkin is enriched at glutamatergic synapses, where it ubiquitinates multiple substrates, suggesting that its mutation/loss-of-function could contribute to the etiology of PD by disrupting excitatory neurotransmission. Here, we evaluate the impact of fo...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-018-0567-7
更新日期:2018-09-10 00:00:00
abstract:BACKGROUND:Because "laws of nature" do not exist in ecology, much of the foundations of community ecology rely on broad statistical generalisations. One of the strongest generalisations is the positive relationship between density and distribution within a given taxonomic assemblage; that is, locally abundant species a...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/1741-7007-3-5
更新日期:2005-03-01 00:00:00
abstract:BACKGROUND:The western flower thrips, Frankliniella occidentalis (Pergande), is a globally invasive pest and plant virus vector on a wide array of food, fiber, and ornamental crops. The underlying genetic mechanisms of the processes governing thrips pest and vector biology, feeding behaviors, ecology, and insecticide r...
journal_title:BMC biology
pub_type: 杂志文章
doi:10.1186/s12915-020-00862-9
更新日期:2020-10-19 00:00:00