当前位置： SCI文献检索 > BMC GENOMICS期刊下所有文献 > Identification of favorable SNP alleles and candidate genes for traits related to early maturity via GWAS in upland cotton.

Identification of favorable SNP alleles and candidate genes for traits related to early maturity via GWAS in upland cotton.

Abstract：

BACKGROUND:Early maturity is one of the most important and complex agronomic traits in upland cotton (Gossypium hirsutum L). To dissect the genetic architecture of this agronomically important trait, a population consisting of 355 upland cotton germplasm accessions was genotyped using the specific-locus amplified fragment sequencing (SLAF-seq) approach, of which a subset of 185 lines representative of the diversity among the accessions was phenotypically characterized for six early maturity traits in four environments. A genome-wide association study (GWAS) was conducted using the generalized linear model (GLM) and mixed linear model (MLM). RESULTS:A total of 81,675 SNPs in 355 upland cotton accessions were discovered using SLAF-seq and were subsequently used in GWAS. Thirteen significant associations between eight SNP loci and five early maturity traits were successfully identified using the GLM and MLM; two of the 13 associations were common between the models. By computing phenotypic effect values for the associations detected at each locus, 11 highly favorable SNP alleles were identified for five early maturity traits. Moreover, dosage pyramiding effects of the highly favorable SNP alleles and significant linear correlations between the numbers of highly favorable alleles and the phenotypic values of the target traits were identified. Most importantly, a major locus (rs13562854) on chromosome Dt3 and a potential candidate gene (CotAD_01947) for early maturity were detected. CONCLUSIONS:This study identified highly favorable SNP alleles and candidate genes associated with early maturity traits in upland cotton. The results demonstrate that GWAS is a powerful tool for dissecting complex traits and identifying candidate genes. The highly favorable SNP alleles and candidate genes for early maturity traits identified in this study should be show high potential for improvement of early maturity in future cotton breeding programs.

journal_name

BMC Genomics

journal_title

BMC genomics

authors

Su J,Pang C,Wei H,Li L,Liang B,Wang C,Song M,Wang H,Zhao S,Jia X,Mao G,Huang L,Geng D,Wang C,Fan S,Yu S

doi

10.1186/s12864-016-2875-z

subject

Has Abstract

pub_date

2016-08-30 00:00:00

pages

687

issn

1471-2164

pii

10.1186/s12864-016-2875-z

journal_volume

17

pub_type

杂志文章

相关文献

BMC GENOMICS文献大全
  • Positive correlation between gene coexpression and positional clustering in the zebrafish genome.

    abstract：BACKGROUND:Co-expressing genes tend to cluster in eukaryotic genomes. This paper analyzes correlation between the proximity of eukaryotic genes and their transcriptional expression pattern in the zebrafish (Danio rerio) genome using available microarray data and gene annotation. RESULTS:The analyses show that neighbou...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-10-42

    authors： Ng YK,Wu W,Zhang L

    更新日期：2009-01-22 00:00:00

  • Chips and tags suggest plant-environment interactions differ for two alpine Pachycladon species.

    abstract：BACKGROUND:Expression profiling has been proposed as a means for screening non-model organisms in their natural environments to identify genes potentially important in adaptive diversification. Tag profiling using high throughput sequencing is a relatively low cost means of expression profiling with deep coverage. Howe...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-13-322

    authors： Voelckel C,Gruenheit N,Biggs P,Deusch O,Lockhart P

    更新日期：2012-07-19 00:00:00

  • Comparative transcriptomics uncovers alternative splicing changes and signatures of selection from maize improvement.

    abstract：BACKGROUND:Alternative splicing (AS) is an important regulatory mechanism that greatly contributes to eukaryotic transcriptome diversity. A substantial amount of evidence has demonstrated that AS complexity is relevant to eukaryotic evolution, development, adaptation, and complexity. In this study, six teosinte and ten...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/s12864-015-1582-5

    authors： Huang J,Gao Y,Jia H,Liu L,Zhang D,Zhang Z

    更新日期：2015-05-08 00:00:00

  • Multi-species data integration and gene ranking enrich significant results in an alcoholism genome-wide association study.

    abstract：BACKGROUND:A variety of species and experimental designs have been used to study genetic influences on alcohol dependence, ethanol response, and related traits. Integration of these heterogeneous data can be used to produce a ranked target gene list for additional investigation. RESULTS:In this study, we performed a u...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-13-S8-S16

    authors： Zhao Z,Guo AY,van den Oord EJ,Aliev F,Jia P,Edenberg HJ,Riley BP,Dick DM,Bettinger JC,Davies AG,Grotewiel MS,Schuckit MA,Agrawal A,Kramer J,Nurnberger JI Jr,Kendler KS,Webb BT,Miles MF

    更新日期：2012-01-01 00:00:00

  • Consistent levels of A-to-I RNA editing across individuals in coding sequences and non-conserved Alu repeats.

    abstract：BACKGROUND:Adenosine to inosine (A-to-I) RNA-editing is an essential post-transcriptional mechanism that occurs in numerous sites in the human transcriptome, mainly within Alu repeats. It has been shown to have consistent levels of editing across individuals in a few targets in the human brain and altered in several hu...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-11-608

    authors： Greenberger S,Levanon EY,Paz-Yaacov N,Barzilai A,Safran M,Osenberg S,Amariglio N,Rechavi G,Eisenberg E

    更新日期：2010-10-28 00:00:00

  • ATP-binding cassette systems in Burkholderia pseudomallei and Burkholderia mallei.

    abstract：BACKGROUND:ATP binding cassette (ABC) systems are responsible for the import and export of a wide variety of molecules across cell membranes and comprise one of largest protein superfamilies found in prokarya, eukarya and archea. ABC systems play important roles in bacterial lifestyle, virulence and survival. In this s...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-8-83

    authors： Harland DN,Dassa E,Titball RW,Brown KA,Atkins HS

    更新日期：2007-03-28 00:00:00

  • Characterization of genome-wide segmental duplications reveals a common genomic feature of association with immunity among domestic animals.

    abstract：BACKGROUND:Segmental duplications (SDs) commonly exist in plant and animal genomes, playing crucial roles in genomic rearrangement, gene innovation and the formation of copy number variants. However, they have received little attention in most livestock species. RESULTS:Aiming at characterizing SDs across the genomes ...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/s12864-017-3690-x

    authors： Feng X,Jiang J,Padhi A,Ning C,Fu J,Wang A,Mrode R,Liu JF

    更新日期：2017-04-12 00:00:00

  • Single nucleotide polymorphism discovery from expressed sequence tags in the waterflea Daphnia magna.

    abstract：BACKGROUND:Daphnia (Crustacea: Cladocera) plays a central role in standing aquatic ecosystems, has a well known ecology and is widely used in population studies and environmental risk assessments. Daphnia magna is, especially in Europe, intensively used to study stress responses of natural populations to pollutants, cl...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-12-309

    authors： Orsini L,Jansen M,Souche EL,Geldof S,De Meester L

    更新日期：2011-06-13 00:00:00

  • Identification and transcriptomic profiling of genes involved in increasing sugar content during salt stress in sweet sorghum leaves.

    abstract：BACKGROUND:Sweet sorghum is an annual C4 crop considered to be one of the most promising bio-energy crops due to its high sugar content in stem, yet it is poorly understood how this plant increases its sugar content in response to salt stress. In response to high NaCl, many of its major processes, such as photosynthesi...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/s12864-015-1760-5

    authors： Sui N,Yang Z,Liu M,Wang B

    更新日期：2015-07-19 00:00:00

  • Repeats and EST analysis for new organisms.

    abstract：BACKGROUND:Repeat masking is an important step in the EST analysis pipeline. For new species, genomic knowledge is scarce and good repeat libraries are typically unavailable. In these cases it is common practice to mask against known repeats from other species (i.e., model organisms). There are few studies that investi...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-9-23

    authors： Malde K,Jonassen I

    更新日期：2008-01-18 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

  • Host specialization of the blast fungus Magnaporthe oryzae is associated with dynamic gain and loss of genes linked to transposable elements.

    abstract：BACKGROUND:Magnaporthe oryzae (anamorph Pyricularia oryzae) is the causal agent of blast disease of Poaceae crops and their wild relatives. To understand the genetic mechanisms that drive host specialization of M. oryzae, we carried out whole genome resequencing of four M. oryzae isolates from rice (Oryza sativa), one ...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/s12864-016-2690-6

    authors： Yoshida K,Saunders DG,Mitsuoka C,Natsume S,Kosugi S,Saitoh H,Inoue Y,Chuma I,Tosa Y,Cano LM,Kamoun S,Terauchi R

    更新日期：2016-05-18 00:00:00

  • A novel method of transcriptome interpretation reveals a quantitative suppressive effect on tomato immune signaling by two domains in a single pathogen effector protein.

    abstract：BACKGROUND:Effector proteins are translocated into host cells by plant-pathogens to undermine pattern-triggered immunity (PTI), the plant response to microbe-associated molecular patterns that interferes with the infection process. Individual effectors are found in variable repertoires where some constituents target th...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/s12864-016-2534-4

    authors： Worley JN,Pombo MA,Zheng Y,Dunham DM,Myers CR,Fei Z,Martin GB

    更新日期：2016-03-14 00:00:00

  • Global assessment of organ specific basal gene expression over a diurnal cycle with analyses of gene copies exhibiting cyclic expression patterns.

    abstract：BACKGROUND:Studying functional divergences between paralogs that originated from genome duplication is a significant topic in investigating molecular evolution. Genes that exhibit basal level cyclic expression patterns including circadian and light responsive genes are important physiological regulators. Temporal shift...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/s12864-020-07202-9

    authors： Lu Y,Boswell M,Boswell W,Salinas RY,Savage M,Reyes J,Walter S,Marks R,Gonzalez T,Medrano G,Warren WC,Schartl M,Walter RB

    更新日期：2020-11-11 00:00:00

  • A novel analytical method, Birth Date Selection Mapping, detects response of the Angus (Bos taurus) genome to selection on complex traits.

    abstract：BACKGROUND:Several methods have recently been developed to identify regions of the genome that have been exposed to strong selection. However, recent theoretical and empirical work suggests that polygenic models are required to identify the genomic regions that are more moderately responding to ongoing selection on com...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-13-606

    authors： Decker JE,Vasco DA,McKay SD,McClure MC,Rolf MM,Kim J,Northcutt SL,Bauck S,Woodward BW,Schnabel RD,Taylor JF

    更新日期：2012-11-09 00:00:00

  • Inference of high resolution HLA types using genome-wide RNA or DNA sequencing reads.

    abstract：BACKGROUND:Accurate HLA typing at amino acid level (four-digit resolution) is critical in hematopoietic and organ transplantations, pathogenesis studies of autoimmune and infectious diseases, as well as the development of immunoncology therapies. With the rapid adoption of genome-wide sequencing in biomedical research,...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-15-325

    authors： Bai Y,Ni M,Cooper B,Wei Y,Fury W

    更新日期：2014-05-01 00:00:00

  • Prioritizing disease candidate genes by a gene interconnectedness-based approach.

    abstract：BACKGROUND:Genome-wide disease-gene finding approaches may sometimes provide us with a long list of candidate genes. Since using pure experimental approaches to verify all candidates could be expensive, a number of network-based methods have been developed to prioritize candidates. Such tools usually have a set of para...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-12-S3-S25

    authors： Hsu CL,Huang YH,Hsu CT,Yang UC

    更新日期：2011-11-30 00:00:00

  • Transcriptional responses of PBMC in psychosocially stressed animals indicate an alerting of the immune system in female but not in castrated male pigs.

    abstract：BACKGROUND:Brain and immune system are linked in a bi-directional manner. To date, it remained largely unknown why immune components become suppressed, enhanced, or remain unaffected in relation to psychosocial stress. Therefore, we mixed unfamiliar pigs with different levels of aggressiveness. We separated castrated m...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-15-967

    authors： Oster M,Muráni E,Ponsuksili S,D'Eath RB,Turner SP,Evans G,Thölking L,Kurt E,Klont R,Foury A,Mormède P,Wimmers K

    更新日期：2014-11-08 00:00:00

  • Methods for high-throughput MethylCap-Seq data analysis.

    abstract：BACKGROUND:Advances in whole genome profiling have revolutionized the cancer research field, but at the same time have raised new bioinformatics challenges. For next generation sequencing (NGS), these include data storage, computational costs, sequence processing and alignment, delineating appropriate statistical measu...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-13-S6-S14

    authors： Rodriguez BA,Frankhouser D,Murphy M,Trimarchi M,Tam HH,Curfman J,Huang R,Chan MW,Lai HC,Parikh D,Ball B,Schwind S,Blum W,Marcucci G,Yan P,Bundschuh R

    更新日期：2012-01-01 00:00:00

  • The metabolome as a link in the genotype-phenotype map for peroxide resistance in the fruit fly, Drosophila melanogaster.

    abstract：BACKGROUND:Genetic association studies that seek to explain the inheritance of complex traits typically fail to explain a majority of the heritability of the trait under study. Thus, we are left with a gap in the map from genotype to phenotype. Several approaches have been used to fill this gap, including those that at...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/s12864-020-6739-1

    authors： Harrison BR,Wang L,Gajda E,Hoffman EV,Chung BY,Pletcher SD,Raftery D,Promislow DEL

    更新日期：2020-05-04 00:00:00

  • Divergence in function and expression of the NOD26-like intrinsic proteins in plants.

    abstract：BACKGROUND:NOD26-like intrinsic proteins (NIPs) that belong to the aquaporin superfamily are plant-specific and exhibit a similar three-dimensional structure. Experimental evidences however revealed that functional divergence should have extensively occurred among NIP genes. It is therefore intriguing to further invest...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-10-313

    authors： Liu Q,Wang H,Zhang Z,Wu J,Feng Y,Zhu Z

    更新日期：2009-07-15 00:00:00

  • Changes in activity of metabolic and regulatory pathways during germination of S. coelicolor.

    abstract：BACKGROUND:Bacterial spore germination is a developmental process during which all required metabolic pathways are restored to transfer cells from their dormant state into vegetative growth. Streptomyces are soil dwelling filamentous bacteria with complex life cycle, studied mostly for they ability to synthesize second...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-15-1173

    authors： Bobek J,Strakova E,Zikova A,Vohradsky J

    更新日期：2014-12-23 00:00:00

  • Cell population-specific expression analysis of human cerebellum.

    abstract：BACKGROUND:Interpreting gene expression profiles obtained from heterogeneous samples can be difficult because bulk gene expression measures are not resolved to individual cell populations. We have recently devised Population-Specific Expression Analysis (PSEA), a statistical method that identifies individual cell types...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-13-610

    authors： Kuhn A,Kumar A,Beilina A,Dillman A,Cookson MR,Singleton AB

    更新日期：2012-11-12 00:00:00

  • Generation of SNP datasets for orangutan population genomics using improved reduced-representation sequencing and direct comparisons of SNP calling algorithms.

    abstract：BACKGROUND:High-throughput sequencing has opened up exciting possibilities in population and conservation genetics by enabling the assessment of genetic variation at genome-wide scales. One approach to reduce genome complexity, i.e. investigating only parts of the genome, is reduced-representation library (RRL) sequenc...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-15-16

    authors： Greminger MP,Stölting KN,Nater A,Goossens B,Arora N,Bruggmann R,Patrignani A,Nussberger B,Sharma R,Kraus RH,Ambu LN,Singleton I,Chikhi L,van Schaik CP,Krützen M

    更新日期：2014-01-10 00:00:00

  • Dual species transcript profiling during the interaction between banana (Musa acuminata) and the fungal pathogen Fusarium oxysporum f. sp. cubense.

    abstract：BACKGROUND:Banana wilt disease, caused by Fusarium oxysporum f. sp. cubense Tropical Race 4 (Foc TR4), is one of the most devastating diseases in banana (Musa spp.). Foc is a soil borne pathogen that causes rot of the roots or wilt of leaves by colonizing the xylem vessels. The dual RNA sequencing is used to simultaneo...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/s12864-019-5902-z

    authors： Li W,Wang X,Li C,Sun J,Li S,Peng M

    更新日期：2019-06-24 00:00:00

  • ICPD-a new peak detection algorithm for LC/MS.

    abstract：BACKGROUND:The identification and quantification of proteins using label-free Liquid Chromatography/Mass Spectrometry (LC/MS) play crucial roles in biological and biomedical research. Increasing evidence has shown that biomarkers are often low abundance proteins. However, LC/MS systems are subject to considerable noise...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-11-S3-S8

    authors： Zhang J,Haskins W

    更新日期：2010-12-01 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

  • Stenotrophomonas comparative genomics reveals genes and functions that differentiate beneficial and pathogenic bacteria.

    abstract：BACKGROUND:In recent years, the number of human infections caused by opportunistic pathogens has increased dramatically. Plant rhizospheres are one of the most typical natural reservoirs for these pathogens but they also represent a great source for beneficial microbes with potential for biotechnological applications. ...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-15-482

    authors： Alavi P,Starcher MR,Thallinger GG,Zachow C,Müller H,Berg G

    更新日期：2014-06-18 00:00:00

  • Analyzing adjuvant radiotherapy suggests a non monotonic radio-sensitivity over tumor volumes.

    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

    authors： Yang JY,Niemierko A,Yang MQ,Deng Y

    更新日期：2008-09-16 00:00:00

  • Evaluation and optimisation of indel detection workflows for ion torrent sequencing of the BRCA1 and BRCA2 genes.

    abstract：BACKGROUND:The Ion Torrent PGM is a popular benchtop sequencer that shows promise in replacing conventional Sanger sequencing as the gold standard for mutation detection. Despite the PGM's reported high accuracy in calling single nucleotide variations, it tends to generate many false positive calls in detecting inserti...

    journal_title：BMC genomics

    pub_type： 杂志文章

    doi：10.1186/1471-2164-15-516

    authors： Yeo ZX,Wong JC,Rozen SG,Lee AS

    更新日期：2014-06-24 00:00:00