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Open access resources for genome-wide association mapping in rice.

S-McCouch PubMed Feed - Fri, 02/05/2016 - 06:18
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Open access resources for genome-wide association mapping in rice.

Nat Commun. 2016;7:10532

Authors: McCouch SR, Wright MH, Tung CW, Maron LG, McNally KL, Fitzgerald M, Singh N, DeClerck G, Agosto-Perez F, Korniliev P, Greenberg AJ, Naredo ME, Mercado SM, Harrington SE, Shi Y, Branchini DA, Kuser-Falcão PR, Leung H, Ebana K, Yano M, Eizenga G, McClung A, Mezey J

Abstract
Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement.

PMID: 26842267 [PubMed - in process]

Genome-wide association and high-resolution phenotyping link Oryza sativa panicle traits to numerous trait-specific QTL clusters.

S-McCouch PubMed Feed - Fri, 02/05/2016 - 06:18
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Genome-wide association and high-resolution phenotyping link Oryza sativa panicle traits to numerous trait-specific QTL clusters.

Nat Commun. 2016;7:10527

Authors: Crowell S, Korniliev P, Falcão A, Ismail A, Gregorio G, Mezey J, McCouch S

Abstract
Rice panicle architecture is a key target of selection when breeding for yield and grain quality. However, panicle phenotypes are difficult to measure and susceptible to confounding during genetic mapping due to correlation with flowering and subpopulation structure. Here we quantify 49 panicle phenotypes in 242 tropical rice accessions with the imaging platform PANorama. Using flowering as a covariate, we conduct a genome-wide association study (GWAS), detect numerous subpopulation-specific associations, and dissect multi-trait peaks using panicle phenotype covariates. Ten candidate genes in pathways known to regulate plant architecture fall under GWAS peaks, half of which overlap with quantitative trait loci identified in an experimental population. This is the first study to assess inflorescence phenotypes of field-grown material using a high-resolution phenotyping platform. Herein, we establish a panicle morphocline for domesticated rice, propose a genetic model underlying complex panicle traits, and demonstrate subtle links between panicle size and yield performance.

PMID: 26841834 [PubMed - in process]

Open access resources for genome-wide association mapping in rice.

GDeClerck_pubmed - Fri, 02/05/2016 - 06:18
Related Articles

Open access resources for genome-wide association mapping in rice.

Nat Commun. 2016;7:10532

Authors: McCouch SR, Wright MH, Tung CW, Maron LG, McNally KL, Fitzgerald M, Singh N, DeClerck G, Agosto-Perez F, Korniliev P, Greenberg AJ, Naredo ME, Mercado SM, Harrington SE, Shi Y, Branchini DA, Kuser-Falcão PR, Leung H, Ebana K, Yano M, Eizenga G, McClung A, Mezey J

Abstract
Increasing food production is essential to meet the demands of a growing human population, with its rising income levels and nutritional expectations. To address the demand, plant breeders seek new sources of genetic variation to enhance the productivity, sustainability and resilience of crop varieties. Here we launch a high-resolution, open-access research platform to facilitate genome-wide association mapping in rice, a staple food crop. The platform provides an immortal collection of diverse germplasm, a high-density single-nucleotide polymorphism data set tailored for gene discovery, well-documented analytical strategies, and a suite of bioinformatics resources to facilitate biological interpretation. Using grain length, we demonstrate the power and resolution of our new high-density rice array, the accompanying genotypic data set, and an expanded diversity panel for detecting major and minor effect QTLs and subpopulation-specific alleles, with immediate implications for rice improvement.

PMID: 26842267 [PubMed - in process]

Evolving technologies for growing, imaging, and analyzing 3D root system architecture of crop plants.

S-McCouch PubMed Feed - Sun, 12/20/2015 - 07:26

Evolving technologies for growing, imaging, and analyzing 3D root system architecture of crop plants.

J Integr Plant Biol. 2015 Dec 18;

Authors: Piñeros MA, Larson BG, Shaff JE, Schneider DJ, Falcão AX, Yuan L, Clark RT, Craft EJ, Davis TW, Pradier PL, Shaw NM, Assaranurak I, McCouch SR, Sturrock C, Bennett M, Kochian LV

Abstract
A plant's ability to maintain or improve its yield under limiting conditions, such as nutrient deficiency or drought, can be strongly influenced by root system architecture, the 3-dimensional distribution of the different root types in the soil. The ability to image, track and quantify these root system attributes in a dynamic fashion is a useful tool in assessing desirable genetic and physiological root traits. Recent advances in imaging technology and phenotyping software have resulted in substantive progress in describing and quantifying root system architecture. We have designed a hydroponic growth system which retains the 3-dimensional root system architecture (RSA) of the plant root system, while allowing for aeration, solution replenishment, and the imposition of nutrient treatments, as well as high quality imaging of the root system. The simplicity and flexibility of the system allows for modifications tailored the root system architecture of different crop species and improved throughput. This paper details the recent improvements and innovations in our root growth and imaging system which allows for greater image sensitivity (detection of fine roots and other root details), higher efficiency, and a broad array of growing conditions for plants that more closely mimic those found under field conditions.

PMID: 26683583 [PubMed - as supplied by publisher]

Dissection of the genetic architecture of rice resistance to the blast fungus Magnaporthe oryzae.

S-McCouch PubMed Feed - Wed, 11/18/2015 - 12:55
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Dissection of the genetic architecture of rice resistance to the blast fungus Magnaporthe oryzae.

Mol Plant Pathol. 2015 Nov 17;

Authors: Kang H, Wang Y, Peng S, Zhang Y, Xiao Y, Wang D, Qu S, Li Z, Yan S, Wang Z, Liu W, Ning Y, Korniliev P, Leung H, Mezey J, McCouch SR, Wang GL

Abstract
Resistance in rice cultivars to the rice blast fungus Magnaporthe oryzae is complex and is controlled by both major genes and quantitative trait loci (QTL). We undertook a genome-wide association study (GWAS) using the rice diversity panel 1 (RDP1) that was genotyped using a high-density (700,000 SNPs) array and inoculated with five diverse M. oryzae isolates. We identified 97 loci associated with blast resistance (LABRs). Among them, 82 were new regions and 15 co-localized with known blast resistance loci. The top 72 LABRs explained up to 98% of the phenotypic variation. The candidate genes in the LABRs encode NBS-LRR resistance proteins, receptor-like protein kinases, transcription factors, and defense-related proteins. Among them, LABR_64 was strongly associated with resistance to all five isolates. We analyzed the function of candidate genes underlying LABR_64 using RNAi technology and identified two new resistance alleles at the Pi5 locus. We demonstrate an efficient strategy for rapid allele discovery by leveraging the power of GWAS, coupled with RNAi technology for dissecting complex blast resistance in rice. This article is protected by copyright. All rights reserved.

PMID: 26574735 [PubMed - as supplied by publisher]

Erratum to: Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations.

S-McCouch PubMed Feed - Mon, 11/02/2015 - 09:36
Related Articles

Erratum to: Bridging the genotyping gap: using genotyping by sequencing (GBS) to add high-density SNP markers and new value to traditional bi-parental mapping and breeding populations.

Theor Appl Genet. 2015 Oct 31;

Authors: Spindel J, Wright M, Chen C, Cobb J, Gage J, Harrington S, Lorieux M, Ahmadi N, McCouch S

PMID: 26520113 [PubMed - as supplied by publisher]

How we remember what we can do.

GDeClerck_pubmed - Thu, 10/29/2015 - 06:20

How we remember what we can do.

Socioaffect Neurosci Psychol. 2015;5:24807

Authors: Declerck G

Abstract
According to the motor simulation theory, the knowledge we possess of what we can do is based on simulation mechanisms triggered by an off-line activation of the brain areas involved in motor control. Action capabilities memory does not work by storing some content, but consists in the capacity, rooted in sensory-motor systems, to reenact off-line action sequences exhibiting the range of our powers. In this paper, I present several arguments from cognitive neuropsychology, but also first-person analysis of experience, against this hypothesis. The claim that perceptual access to affordances is mediated by motor simulation processes rests on a misunderstanding of what affordances are, and comes up against a computational reality principle. Motor simulation cannot provide access to affordances because (i) the affordances we are aware of at each moment are too many for their realization to be simulated by the brain and (ii) affordances are not equivalent to currently or personally feasible actions. The explanatory significance of the simulation theory must then be revised downwards compared to what is claimed by most of its advocates. One additional challenge is to determine the prerequisite, in terms of cognitive processing, for the motor simulation mechanisms to work. To overcome the limitations of the simulation theory, I propose a new approach: the direct content specification hypothesis. This hypothesis states that, at least for the most basic actions of our behavioral repertoire, the action possibilities we are aware of through perception are directly specified by perceptual variables characterizing the content of our experience. The cognitive system responsible for the perception of action possibilities is consequently far more direct, in terms of cognitive processing, than what is stated by the simulation theory. To support this hypothesis I review evidence from current neuropsychological research, in particular data suggesting a phenomenon of 'fossilization' of affordances. Fossilization can be defined as a gap between the capacities that are treated as available by the cognitive system and the capacities this system really has at its disposal. These considerations do not mean that motor simulation cannot contribute to explain how we gain perceptual knowledge of what we can do based on the memory of our past performances. However, when precisely motor simulation plays a role and what it is for exactly currently remain largely unknown.

PMID: 26507953 [PubMed]

Convergent Loss of Awn in Two Cultivated Rice Species Oryza sativa and Oryza glaberrima Is Caused by Mutations in Different Loci.

S-McCouch PubMed Feed - Sat, 09/05/2015 - 08:05
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Convergent Loss of Awn in Two Cultivated Rice Species Oryza sativa and Oryza glaberrima Is Caused by Mutations in Different Loci.

G3 (Bethesda). 2015 Sep 2;

Authors: Furuta T, Komeda N, Asano K, Uehara K, Gamuyao R, Shim-Angeles RB, Nagai K, Doi K, Wang DR, Yasui H, Yoshimura A, Wu J, McCouch SR, Ashikari M

Abstract
A long awn is one of the distinct morphological features of wild rice species. This organ is thought to aid in seed dispersal and prevent predation by animals. Most cultivated varieties of Oryza sativa and Oryza glaberrima, however, have lost the ability to form long awns. The causal genetic factors responsible for the loss of awn in these two rice species remain largely unknown. Here, we evaluated three sets of chromosome segment substitution lines (CSSLs) in a common O. sativa genetic background (cv. Koshihikari) that harbor genomic fragments from O. nivara, O. rufipogon and O. glaberrima donors. Phenotypic analyses of these libraries revealed the existence of three genes, Regulator of Awn Elongation 1 (RAE1), RAE2, and RAE3 involved in the loss of long awns in cultivated rice. Donor segments at two of these genes, RAE1 and RAE2, induced long awn formation in the CSSLs whereas an O. sativa segment at RAE3 induced long awn formation in O. glaberrima. These results suggest that the two cultivated rice species, O. sativa and O. glaberrima, have taken independent paths to become awnless.

PMID: 26338659 [PubMed - as supplied by publisher]

De Novo Transcriptome Assembly and Identification of Gene Candidates for Rapid Evolution of Soil Al Tolerance in Anthoxanthum odoratum at the Long-Term Park Grass Experiment.

S-McCouch PubMed Feed - Tue, 07/07/2015 - 07:25

De Novo Transcriptome Assembly and Identification of Gene Candidates for Rapid Evolution of Soil Al Tolerance in Anthoxanthum odoratum at the Long-Term Park Grass Experiment.

PLoS One. 2015;10(7):e0124424

Authors: Gould B, McCouch S, Geber M

Abstract
Studies of adaptation in the wild grass Anthoxanthum odoratum at the Park Grass Experiment (PGE) provided one of the earliest examples of rapid evolution in plants. Anthoxanthum has become locally adapted to differences in soil Al toxicity, which have developed there due to soil acidification from long-term experimental fertilizer treatments. In this study, we used transcriptome sequencing to identify Al stress responsive genes in Anthoxanhum and identify candidates among them for further molecular study of rapid Al tolerance evolution at the PGE. We examined the Al content of Anthoxanthum tissues and conducted RNA-sequencing of root tips, the primary site of Al induced damage. We found that despite its high tolerance Anthoxanthum is not an Al accumulating species. Genes similar to those involved in organic acid exudation (TaALMT1, ZmMATE), cell wall modification (OsSTAR1), and internal Al detoxification (OsNRAT1) in cultivated grasses were responsive to Al exposure. Expression of a large suite of novel loci was also triggered by early exposure to Al stress in roots. Three-hundred forty five transcripts were significantly more up- or down-regulated in tolerant vs. sensitive Anthoxanthum genotypes, providing important targets for future study of rapid evolution at the PGE.

PMID: 26148203 [PubMed - as supplied by publisher]

Correction: Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice...

S-McCouch PubMed Feed - Wed, 07/01/2015 - 09:01
Related Articles

Correction: Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines.

PLoS Genet. 2015 Jun;11(6):e1005350

Authors: Spindel J, Begum H, Akdemir D, Virk P, Collard B, Redoña E, Atlin G, Jannink JL, McCouch SR

Abstract
[This corrects the article DOI: 10.1371/journal.pgen.1004982.].

PMID: 26125618 [PubMed - as supplied by publisher]

LABA1, a Domestication Gene Associated with Long, Barbed Awns in Wild Rice.

S-McCouch PubMed Feed - Thu, 06/18/2015 - 07:23

LABA1, a Domestication Gene Associated with Long, Barbed Awns in Wild Rice.

Plant Cell. 2015 Jun 16;

Authors: Hua L, Wang DR, Tan L, Fu Y, Liu F, Xiao L, Zhu Z, Fu Q, Sun X, Gu P, Cai H, McCouch SR, Sun C

Abstract
Common wild rice (Oryza rufipogon), the wild relative of Asian cultivated rice (Oryza sativa), flaunts long, barbed awns, which are necessary for efficient propagation and dissemination of seeds. By contrast, O. sativa cultivars have been selected to be awnless or to harbor short, barbless awns, which facilitate seed processing and storage. The transition from long, barbed awns to short, barbless awns was a crucial event in rice domestication. Here, we show that the presence of long, barbed awns in wild rice is controlled by a major gene on chromosome 4, LONG AND BARBED AWN1 (LABA1), which encodes a cytokinin-activating enzyme. A frame-shift deletion in LABA1 of cultivated rice reduces the cytokinin concentration in awn primordia, disrupting barb formation and awn elongation. Sequencing analysis demonstrated low nucleotide diversity and a selective sweep encompassing an ∼800-kb region around the derived laba1 allele in cultivated rice. Haplotype analysis revealed that the laba1 allele originated in the japonica subspecies and moved into the indica gene pool via introgression, suggesting that humans selected for this locus in early rice domestication. Identification of LABA1 provides new insights into rice domestication and also sheds light on the molecular mechanism underlying awn development.

PMID: 26082172 [PubMed - as supplied by publisher]

The Tyrosine Aminomutase TAM1 Is Required for β-Tyrosine Biosynthesis in Rice.

S-McCouch PubMed Feed - Thu, 04/23/2015 - 06:56

The Tyrosine Aminomutase TAM1 Is Required for β-Tyrosine Biosynthesis in Rice.

Plant Cell. 2015 Apr 21;

Authors: Yan J, Aboshi T, Teraishi M, Strickler SR, Spindel JE, Tung CW, Takata R, Matsumoto F, Maesaka Y, McCouch SR, Okumoto Y, Mori N, Jander G

Abstract
Non-protein amino acids, often isomers of the standard 20 protein amino acids, have defense-related functions in many plant species. A targeted search for jasmonate-induced metabolites in cultivated rice (Oryza sativa) identified (R)-β-tyrosine, an isomer of the common amino acid (S)-α-tyrosine in the seeds, leaves, roots, and root exudates of the Nipponbare cultivar. Assays with 119 diverse cultivars showed a distinct presence/absence polymorphism, with β-tyrosine being most prevalent in temperate japonica cultivars. Genetic mapping identified a candidate gene on chromosome 12, which was confirmed to encode a tyrosine aminomutase (TAM1) by transient expression in Nicotiana benthamiana and in vitro enzyme assays. A point mutation in TAM1 eliminated β-tyrosine production in Nipponbare. Rice cultivars that do not produce β-tyrosine have a chromosome 12 deletion that encompasses TAM1. Although β-tyrosine accumulation was induced by the plant defense signaling molecule jasmonic acid, bioassays with hemipteran and lepidopteran herbivores showed no negative effects at physiologically relevant β-tyrosine concentrations. In contrast, root growth of Arabidopsis thaliana and other tested dicot plants was inhibited by concentrations as low as 1 μM. As β-tyrosine is exuded into hydroponic medium at higher concentrations, it may contribute to the allelopathic potential of rice.

PMID: 25901084 [PubMed - as supplied by publisher]

Genome-Wide Association Mapping for Yield and Other Agronomic Traits in an Elite Breeding Population of Tropical Rice (Oryza sativa).

S-McCouch PubMed Feed - Thu, 03/19/2015 - 07:43

Genome-Wide Association Mapping for Yield and Other Agronomic Traits in an Elite Breeding Population of Tropical Rice (Oryza sativa).

PLoS One. 2015;10(3):e0119873

Authors: Begum H, Spindel JE, Lalusin A, Borromeo T, Gregorio G, Hernandez J, Virk P, Collard B, McCouch SR

Abstract
Genome-wide association mapping studies (GWAS) are frequently used to detect QTL in diverse collections of crop germplasm, based on historic recombination events and linkage disequilibrium across the genome. Generally, diversity panels genotyped with high density SNP panels are utilized in order to assay a wide range of alleles and haplotypes and to monitor recombination breakpoints across the genome. By contrast, GWAS have not generally been performed in breeding populations. In this study we performed association mapping for 19 agronomic traits including yield and yield components in a breeding population of elite irrigated tropical rice breeding lines so that the results would be more directly applicable to breeding than those from a diversity panel. The population was genotyped with 71,710 SNPs using genotyping-by-sequencing (GBS), and GWAS performed with the explicit goal of expediting selection in the breeding program. Using this breeding panel we identified 52 QTL for 11 agronomic traits, including large effect QTLs for flowering time and grain length/grain width/grain-length-breadth ratio. We also identified haplotypes that can be used to select plants in our population for short stature (plant height), early flowering time, and high yield, and thus demonstrate the utility of association mapping in breeding populations for informing breeding decisions. We conclude by exploring how the newly identified significant SNPs and insights into the genetic architecture of these quantitative traits can be leveraged to build genomic-assisted selection models.

PMID: 25785447 [PubMed - as supplied by publisher]

Development and GBS-genotyping of introgression lines (ILs) using two wild species of rice, O. meridionalis and O. rufipogon, in a common recurrent parent, O. sativa cv. Curinga.

S-McCouch PubMed Feed - Tue, 02/24/2015 - 08:04

Development and GBS-genotyping of introgression lines (ILs) using two wild species of rice, O. meridionalis and O. rufipogon, in a common recurrent parent, O. sativa cv. Curinga.

Mol Breed. 2015;35(2):81

Authors: Arbelaez JD, Moreno LT, Singh N, Tung CW, Maron LG, Ospina Y, Martinez CP, Grenier C, Lorieux M, McCouch S

Abstract
Two populations of interspecific introgression lines (ILs) in a common recurrent parent were developed for use in pre-breeding and QTL mapping. The ILs were derived from crosses between cv Curinga, a tropical japonica upland cultivar, and two different wild donors, Oryza meridionalis Ng. accession (W2112) and Oryza rufipogon Griff. accession (IRGC 105491). The lines were genotyped using genotyping-by-sequencing (GBS) and SSRs. The 32 Curinga/O. meridionalis ILs contain 76.73 % of the donor genome in individual introgressed segments, and each line has an average of 94.9 % recurrent parent genome. The 48 Curinga/O. rufipogon ILs collectively contain 97.6 % of the donor genome with an average of 89.9 % recurrent parent genome per line. To confirm that these populations were segregating for traits of interest, they were phenotyped for pericarp color in the greenhouse and for four agronomic traits-days to flowering, plant height, number of tillers, and number of panicles-in an upland field environment. Seeds from these IL libraries and the accompanying GBS datasets are publicly available and represent valuable genetic resources for exploring the genetics and breeding potential of rice wild relatives.

PMID: 25705117 [PubMed - as supplied by publisher]

Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines.

S-McCouch PubMed Feed - Wed, 02/18/2015 - 08:48
Related Articles

Genomic Selection and Association Mapping in Rice (Oryza sativa): Effect of Trait Genetic Architecture, Training Population Composition, Marker Number and Statistical Model on Accuracy of Rice Genomic Selection in Elite, Tropical Rice Breeding Lines.

PLoS Genet. 2015 Feb;11(2):e1004982

Authors: Spindel J, Begum H, Akdemir D, Virk P, Collard B, Redoña E, Atlin G, Jannink JL, McCouch SR

Abstract
Genomic Selection (GS) is a new breeding method in which genome-wide markers are used to predict the breeding value of individuals in a breeding population. GS has been shown to improve breeding efficiency in dairy cattle and several crop plant species, and here we evaluate for the first time its efficacy for breeding inbred lines of rice. We performed a genome-wide association study (GWAS) in conjunction with five-fold GS cross-validation on a population of 363 elite breeding lines from the International Rice Research Institute's (IRRI) irrigated rice breeding program and herein report the GS results. The population was genotyped with 73,147 markers using genotyping-by-sequencing. The training population, statistical method used to build the GS model, number of markers, and trait were varied to determine their effect on prediction accuracy. For all three traits, genomic prediction models outperformed prediction based on pedigree records alone. Prediction accuracies ranged from 0.31 and 0.34 for grain yield and plant height to 0.63 for flowering time. Analyses using subsets of the full marker set suggest that using one marker every 0.2 cM is sufficient for genomic selection in this collection of rice breeding materials. RR-BLUP was the best performing statistical method for grain yield where no large effect QTL were detected by GWAS, while for flowering time, where a single very large effect QTL was detected, the non-GS multiple linear regression method outperformed GS models. For plant height, in which four mid-sized QTL were identified by GWAS, random forest produced the most consistently accurate GS models. Our results suggest that GS, informed by GWAS interpretations of genetic architecture and population structure, could become an effective tool for increasing the efficiency of rice breeding as the costs of genotyping continue to decline.

PMID: 25689273 [PubMed - as supplied by publisher]

Bridging Data Models and Terminologies to Support Adverse Drug Event Reporting Using EHR Data.

GDeClerck_pubmed - Wed, 12/10/2014 - 08:25
Related Articles

Bridging Data Models and Terminologies to Support Adverse Drug Event Reporting Using EHR Data.

Methods Inf Med. 2014 Dec 9;54(1)

Authors: Declerck G, Hussain S, Daniel C, Yuksel M, Laleci GB, Twagirumukiza M, Jaulent MC

PMID: 25487120 [PubMed - as supplied by publisher]

Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa , document novel gene space of aus and indica.

S-McCouch PubMed Feed - Thu, 12/04/2014 - 06:51

Whole genome de novo assemblies of three divergent strains of rice, Oryza sativa , document novel gene space of aus and indica.

Genome Biol. 2014 Dec 3;15(11):506

Authors: Schatz MC, Maron LG, Stein JC, Wences A, Gurtowski J, Biggers E, Lee H, Kramer M, Antoniou E, Ghiban E, Wright MH, Chia JM, Ware D, McCouch SR, McCombie W

Abstract
BackgroundThe use of high throughput genome-sequencing technologies has uncovered a large extent of structural variation in eukaryotic genomes that makes important contributions to genomic diversity and phenotypic variation. When the genomes of different strains of a given organism are compared, whole genome resequencing data are typically aligned to an established reference sequence. However, when the reference differs in significant structural ways from the individuals under study, the analysis is often incomplete or inaccurate.ResultsHere, we use rice as a model to demonstrate how improvements in sequencing and assembly technology allow rapid and inexpensive de novo assembly of next generation sequence data into high-quality assemblies that can be directly compared using whole genome alignment to provide an unbiased assessment. Using this approach, we are able to accurately assess the `pan-genome¿ of three divergent rice varieties and document several megabases of each genome absent in the other two.ConclusionsMany of the genome-specific loci are annotated to contain genes, reflecting the potential for new biological properties that would be missed by standard reference-mapping approaches. We further provide a detailed analysis of several loci associated with agriculturally important traits, including the S5 hybrid sterility locus, the Sub1 submergence tolerance locus, the LRK gene cluster associated with improved yield, and the Pup1 cluster associated with phosphorus deficiency, illustrating the utility of our approach for biological discovery. All of the data and software are openly available to support further breeding and functional studies of rice and other species.

PMID: 25468217 [PubMed - as supplied by publisher]

Describing Localized Diseases in Medical Ontology: An FMA-based Algorithm.

GDeClerck_pubmed - Thu, 08/28/2014 - 08:48
Related Articles

Describing Localized Diseases in Medical Ontology: An FMA-based Algorithm.

Stud Health Technol Inform. 2014;205:1023-1027

Authors: Charlet J, Mazuel L, Declerck G, Miroux P, Gayet P

Abstract
ONTOLURGENCES is a termino-ontological resource developed to index and retrieve information in electronic Emergency Medical Record. In this project, we improved the ontology coverage to accommodate both anatomical and pathophysiological concepts in emergency medicine. This work lead to the automatic addition of 3,470 concepts and their underlying semantic formalization. In our method, we reuse and select the anatomical concepts relevant to emergency from FMA: To capture the anatomical specific concepts, (i) we involved Emergency practitioners and identified the key concepts from this domain; (ii) we applied an automatic algorithm to define the semantic relationships and integrated the result in the existing ontology.

PMID: 25160343 [PubMed - as supplied by publisher]

Automatic annotation of ICD-to-MedDRA mappings with SKOS predicates.

GDeClerck_pubmed - Thu, 08/28/2014 - 08:48
Related Articles

Automatic annotation of ICD-to-MedDRA mappings with SKOS predicates.

Stud Health Technol Inform. 2014;205:1013-1017

Authors: Declerck G, Souvignet J, Rodrigues JM, Jaulent MC

Abstract
Robust alignments between ICD and MedDRA are essential to enable the secondary use of clinical data for pharmacovigilance research. UMLS makes available ICD-to-MedDRA mappings, but they are only poorly specified, which introduces difficulties when exploited in an automatic way. SKOS vocabulary can help achieve quality and machine-processable mappings. We have developed an algorithm based on several simple rules which annotates automatically ICD-to-MedDRA mappings with SKOS predicates. The method was tested and evaluated on a sample of ICD-10-to MedDRA mappings extracted from UMLS. The algorithm demonstrated satisfying performances, especially for skos:exactMatch properties, which suggests that automatic methods can be used to improve the quality of terminology mappings.

PMID: 25160341 [PubMed - as supplied by publisher]

Ci4SeR - Curation Interface for Semantic Resources - Evaluation with Adverse Drug Reactions.

GDeClerck_pubmed - Thu, 08/28/2014 - 08:48
Related Articles

Ci4SeR - Curation Interface for Semantic Resources - Evaluation with Adverse Drug Reactions.

Stud Health Technol Inform. 2014;205:116-120

Authors: Souvignet J, Asfari H, Declerck G, Lardon J, Trombert-Paviot B, Jaulent MC, Bousquet C

Abstract
Evaluation and validation have become a crucial problem for the development of semantic resources. We developed Ci4SeR, a Graphical User Interface to optimize the curation work (not taking into account structural aspects), suitable for any type of resource with lightweight description logic. We tested it on OntoADR, an ontology of adverse drug reactions. A single curator has reviewed 326 terms (1020 axioms) in an estimated time of 120 hours (2.71 concepts and 8.5 axioms reviewed per hour) and added 1874 new axioms (15.6 axioms per hour). Compared with previous manual endeavours, the interface allows increasing the speed-rate of reviewed concepts by 68% and axiom addition by 486%. A wider use of Ci4SeR would help semantic resources curation and improve completeness of knowledge modelling.

PMID: 25160157 [PubMed - as supplied by publisher]

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