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You searched for: Journal name Genome biology Remove constraint Journal name: Genome biology Publication year rev 7987-2013 Remove constraint Publication year rev: 7987-2013 Source 2013 v.14 no.6 Remove constraint Source: 2013 v.14 no.6
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1. Comprehensive genotyping of the USA national maize inbred seed bank

Author:
Maria C Romay; Mark J Millard; Jeffrey C Glaubitz; Jason A Peiffer; Kelly L Swarts; Terry M Casstevens; Robert J Elshire; Charlotte B Acharya; Sharon E Mitchell; Sherry A Flint-Garcia; Michael D McMullen; James B Holland; Edward S Buckler; Candice A Gardner
Source:
Genome biology 2013 v.14 no.6 pp. R55
ISSN:
1474-760X
Subject:
alleles; corn; genetic distance; genetic variation; genotype; genotyping; germplasm; inbred lines; linkage disequilibrium; single nucleotide polymorphism; sweetcorn; United States
Abstract:
... BACKGROUND: Genotyping by sequencing, a new low-cost, high-throughput sequencing technology was used to genotype 2,815 maize inbred accessions, preserved mostly at the National Plant Germplasm System in the USA. The collection includes inbred lines from breeding programs all over the world. RESULTS: The method produced 681,257 single-nucleotide polymorphism (SNP) markers distributed across the ent ...
DOI:
10.1186/gb-2013-14-6-r55
PubMed:
23759205
PubMed Central:
PMC3707059

2. From pathogen genomes to host plant processes: the power of plant parasitic oomycetes

Author:
Marina Pais; Joe Win; Kentaro Yoshida; Graham J Etherington; Liliana M Cano; Sylvain Raffaele; Mark J Banfield; Alex Jones; Sophien Kamoun; Diane GO Saunders
Source:
Genome biology 2013 v.14 no.6 pp. 211
ISSN:
1474-760X
Subject:
Oomycetes; genome; host plants; nucleotide sequences; pathogens; plant pathology
Abstract:
... Recent pathogenomic research on plant parasitic oomycete effector function and plant host responses has resulted in major conceptual advances in plant pathology, which has been possible thanks to the availability of genome sequences. ...
DOI:
10.1186/gb-2013-14-6-211
PubMed:
23809564
PubMed Central:
PMC3706818

3. Gene regulatory networks in plants: learning causality from time and perturbation

Author:
Gabriel Krouk; Jesse Lingeman; Amy Marshall Colon; Gloria Coruzzi; Dennis Shasha
Source:
Genome biology 2013 v.14 no.6 pp. 123
ISSN:
1474-760X
Subject:
models; prediction; regulator genes
Abstract:
... The goal of systems biology is to generate models for predicting how a system will react under untested conditions or in response to genetic perturbations. This paper discusses experimental and analytical approaches to deriving causal relationships in gene regulatory networks. ...
DOI:
10.1186/gb-2013-14-6-123
PubMed:
23805876
PubMed Central:
PMC3707030

4. Genomics reveals new landscapes for crop improvement

Author:
Michael W Bevan; Cristobal Uauy
Source:
Genome biology 2013 v.14 no.6 pp. 206
ISSN:
1474-760X
Subject:
genetic variation; genome; genomics; translation (genetics)
Abstract:
... The sequencing of large and complex genomes of crop species, facilitated by new sequencing technologies and bioinformatic approaches, has provided new opportunities for crop improvement. Current challenges include understanding how genetic variation translates into phenotypic performance in the field. ...
DOI:
10.1186/gb-2013-14-6-206
PubMed:
23796126
PubMed Central:
PMC3706852

5. Identification of pathways directly regulated by SHORT VEGETATIVE PHASE during vegetative and reproductive development in Arabidopsis

Author:
Veronica Gregis; Fernando Andrés; Alice Sessa; Rosalinda F Guerra; Sara Simonini; Julieta L Mateos; Stefano Torti; Federico Zambelli; Gian Marco Prazzoli; Katrine N Bjerkan; Paul E Grini; Giulio Pavesi; Lucia Colombo; George Coupland; Martin M Kater
Source:
Genome biology 2013 v.14 no.6 pp. R56
ISSN:
1474-760X
Subject:
Arabidopsis; binding sites; flowering; genes; meristems; reverse transcriptase polymerase chain reaction; transcription factors; vegetative growth
Abstract:
... BACKGROUND: MADS-domain transcription factors play important roles during plant development. The Arabidopsis MADS-box gene SHORT VEGETATIVE PHASE (SVP) is a key regulator of two developmental phases. It functions as a repressor of the floral transition during the vegetative phase and later it contributes to the specification of floral meristems. How these distinct activities are conferred by a sin ...
DOI:
10.1186/gb-2013-14-6-r56
PubMed:
23759218
PubMed Central:
PMC3706845

6. Mapping gene activity of Arabidopsis root hairs

Author:
Ping Lan; Wenfeng Li; Wen-Dar Lin; Simonetta Santi; Wolfgang Schmidt
Source:
Genome biology 2013 v.14 no.6 pp. R67
ISSN:
1474-760X
Subject:
protoplasts; proteins; messenger RNA; Arabidopsis; alternative splicing; protein synthesis; proteome; morphogenesis; models; gene expression; root hairs; chromosome mapping; introns
Abstract:
... BACKGROUND: Quantitative information on gene activity at single cell-type resolution is essential for the understanding of how cells work and interact. Root hairs, or trichoblasts, tubular-shaped outgrowths of specialized cells in the epidermis, represent an ideal model for cell fate acquisition and differentiation in plants. RESULTS: Here, we provide an atlas of gene and protein expression in Ara ...
DOI:
10.1186/gb-2013-14-6-r67
PubMed:
23800126
PubMed Central:
PMC3707065

7. Phytophthora capsici-tomato interaction features dramatic shifts in gene expression associated with a hemi-biotrophic lifestyle

Author:
Julietta Jupe; Remco Stam; Andrew JM Howden; Jenny A Morris; Runxuan Zhang; Pete E Hedley; Edgar Huitema
Source:
Genome biology 2013 v.14 no.6 pp. R63
ISSN:
1474-760X
Subject:
Phytophthora capsici; disease outbreaks; ecosystems; gene expression; genes; host range; hosts; immunity; microarray technology; microorganisms; nucleotide sequences; plant pathogens; tomatoes; transcription (genetics); transcriptome
Abstract:
... BACKGROUND: Plant-microbe interactions feature complex signal interplay between pathogens and their hosts. Phytophthora species comprise a destructive group of fungus-like plant pathogens, collectively affecting a wide range of plants important to agriculture and natural ecosystems. Despite the availability of genome sequences of both hosts and microbes, little is known about the signal interplay ...
DOI:
10.1186/gb-2013-14-6-r63
PubMed:
23799990
PubMed Central:
PMC4054836

8. Plastic, fantastic! Phenotypic variance in the transcriptional landscape of the grape berry

Author:
Alisdair R Fernie; Takayuki Tohge
Source:
Genome biology 2013 v.14 no.6 pp. 3062
ISSN:
1474-760X
Subject:
Vitis vinifera; grapes; phenotypic variation
Abstract:
... Evaluation of the common grapevine Vitis vinifera across multiple harvests and field locations provides important insights into crop transcriptional plasticity under diverse agricultural regimes.Please see related Research: http://genomebiology.com/2013/14/6/R54 ...
DOI:
10.1186/gb-2013-14-6-119
PubMed:
23742251
PubMed Central:
PMC3706855

9. Reference genomes and transcriptomes of Nicotiana sylvestris and Nicotiana tomentosiformis

Author:
Nicolas Sierro; James ND Battey; Sonia Ouadi; Lucien Bovet; Simon Goepfert; Nicolas Bakaher; Manuel C Peitsch; Nikolai V Ivanov
Source:
Genome biology 2013 v.14 no.6 pp. R60
ISSN:
1474-760X
Subject:
Nicotiana sylvestris; Nicotiana tabacum; Nicotiana tomentosiformis; abiotic stress; diploidy; diterpenoids; evolution; flowers; gene expression regulation; genes; heavy metals; interspecific hybridization; leaves; metabolism; retrotransposons; roots; terminal repeat sequences; transcriptome; South America
Abstract:
... BACKGROUND: Nicotiana sylvestris and Nicotiana tomentosiformis are members of the Solanaceae family that includes tomato, potato, eggplant and pepper. These two Nicotiana species originate from South America and exhibit different alkaloid and diterpenoid production. N. sylvestris is cultivated largely as an ornamental plant and it has been used as a diploid model system for studies of terpenoid pr ...
DOI:
10.1186/gb-2013-14-6-r60
PubMed:
23773524
PubMed Central:
PMC3707018

10. User guide for mapping-by-sequencing in Arabidopsis

Author:
Geo Velikkakam James; Vipul Patel; Karl JV Nordström; Jonas R Klasen; Patrice A Salomé; Detlef Weigel; Korbinian Schneeberger
Source:
Genome biology 2013 v.14 no.6 pp. R61
ISSN:
1474-760X
Subject:
Arabidopsis; chromosome mapping; experimental design; mutants; sequence analysis
Abstract:
... Mapping-by-sequencing combines genetic mapping with whole-genome sequencing in order to accelerate mutant identification. However, application of mapping-by-sequencing requires decisions on various practical settings on the experimental design that are not intuitively answered. Following an experimentally determined recombination landscape of Arabidopsis and next generation sequencing-specific bia ...
DOI:
10.1186/gb-2013-14-6-r61
PubMed:
23773572
PubMed Central:
PMC3706810

11. The advantages of SMRT sequencing [Erratum: December 2017, v.18(1); p.156]

Author:
Richard J Roberts; Mauricio O Carneiro; Michael C Schatz
Source:
Genome biology 2013 v.14 no.6 pp. 405
ISSN:
1474-760X
Subject:
genome; nucleotide sequences; sequence analysis
Abstract:
... Of the current next-generation sequencing technologies, SMRT sequencing is sometimes overlooked. However, attributes such as long reads, modified base detection and high accuracy make SMRT a useful technology and an ideal approach to the complete sequencing of small genomes. ...
DOI:
10.1186/gb-2013-14-6-405
PubMed:
23822731
PubMed Central:
PMC3953343

12. The circadian clock goes genomic

Author:
Dorothee Staiger; Jieun Shin; Mikael Johansson; Seth J Davis
Source:
Genome biology 2013 v.14 no.6 pp. 208
ISSN:
1474-760X
Subject:
circadian rhythm; genome; genomics; plant genetics; plants (botany)
Abstract:
... Large-scale biology among plant species, as well as comparative genomics of circadian clock architecture and clock-regulated output processes, have greatly advanced our understanding of the endogenous timing system in plants. ...
DOI:
10.1186/gb-2013-14-6-208
PubMed:
23796230
PubMed Central:
PMC3706883

13. A conifer genome spruces up plant phylogenomics

Author:
Pamela S Soltis; Douglas E Soltis
Source:
Genome biology 2013 v.14 no.6 pp. 122
ISSN:
1474-760X
Subject:
Picea abies; conifers; evolution; genome
Abstract:
... The Norway spruce genome provides key insights into the evolution of plant genomes, leading to testable new hypotheses about conifer, gymnosperm, and vascular plant evolution. ...
DOI:
10.1186/gb-2013-14-6-122
PubMed:
23805854
PubMed Central:
PMC3706884

14. The genome sequence of the most widely cultivated cacao type and its use to identify candidate genes regulating pod color

Author:
Juan C Motamayor; Keithanne Mockaitis; Jeremy Schmutz; Niina Haiminen; Donald Livingstone III; Omar Cornejo; Seth D Findley; Ping Zheng; Filippo Utro; Stefan Royaert; Christopher Saski; Jerry Jenkins; Ram Podicheti; Meixia Zhao; Brian E Scheffler; Joseph C Stack; Frank A Feltus; Guiliana M Mustiga; Freddy Amores; Wilbert Phillips; Jean Philippe Marelli; Gregory D May; Howard Shapiro; Jianxin Ma; Carlos D Bustamante; Raymond J Schnell; Dorrie Main; Don Gilbert; Laxmi Parida; David N Kuhn
Source:
Genome biology 2013 v.14 no.6 pp. r53
ISSN:
1474-760X
Subject:
Brassicaceae; Rosaceae; Solanaceae; Theobroma cacao; chromosome mapping; color; cultivars; gene expression; genes; haplotypes; loci; nucleotide sequences; pigmentation; researchers; single nucleotide polymorphism; small interfering RNA; transcription factors
Abstract:
... BACKGROUND: Theobroma cacao L. cultivar Matina 1-6 belongs to the most cultivated cacao type. The availability of its genome sequence and methods for identifying genes responsible for important cacao traits will aid cacao researchers and breeders. RESULTS: We describe the sequencing and assembly of the genome of Theobroma cacao L. cultivar Matina 1-6. The genome of the Matina 1-6 cultivar is 445 M ...
DOI:
10.1186/gb-2013-14-6-r53
PubMed:
23731509
PubMed Central:
PMC4053823

15. A high density physical map of chromosome 1BL supports evolutionary studies, map-based cloning and sequencing in wheat

Author:
Romain Philippe; Etienne Paux; Isabelle Bertin; Pierre Sourdille; Fréderic Choulet; Christel Laugier; Hana Šimková; Jan Šafář; Arnaud Bellec; Sonia Vautrin; Zeev Frenkel; Federica Cattonaro; Federica Magni; Simone Scalabrin; Mihaela M Martis; Klaus FX Mayer; Abraham Korol; Hélène Bergès; Jaroslav Doležel; Catherine Feuillet
Source:
Genome biology 2013 v.14 no.6 pp. R64
ISSN:
1474-760X
Subject:
breeding; chromosome mapping; crops; cultivars; evolution; genes; genomics; grasses; hexaploidy; molecular cloning; nucleotide sequences; quantitative trait loci; telomeres; wheat
Abstract:
... BACKGROUND: As for other major crops, achieving a complete wheat genome sequence is essential for the application of genomics to breeding new and improved varieties. To overcome the complexities of the large, highly repetitive and hexaploid wheat genome, the International Wheat Genome Sequencing Consortium established a chromosome-based strategy that was validated by the construction of the physic ...
DOI:
10.1186/gb-2013-14-6-r64
PubMed:
23800011
PubMed Central:
PMC4054855

16. The plant microbiome

Author:
Thomas R Turner; Euan K James; Philip S Poole
Source:
Genome biology 2013 v.14 no.6 pp. 209
ISSN:
1474-760X
Subject:
genome; hosts; plant health
Abstract:
... Plant genomes contribute to the structure and function of the plant microbiome, a key determinant of plant health and productivity. High-throughput technologies are revealing interactions between these complex communities and their hosts in unprecedented detail. ...
DOI:
10.1186/gb-2013-14-6-209
PubMed:
23805896
PubMed Central:
PMC3706808

17. The plasticity of the grapevine berry transcriptome

Author:
Silvia Dal Santo; Giovanni Battista Tornielli; Sara Zenoni; Marianna Fasoli; Lorenzo Farina; Andrea Anesi; Flavia Guzzo; Massimo Delledonne; Mario Pezzotti
Source:
Genome biology 2013 v.14 no.6 pp. r54
ISSN:
1474-760X
Subject:
Vitis vinifera; environmental factors; gene expression; genes; genotype; metabolism; phenotype; phenotypic plasticity; small fruits; transcription factors; transcriptome; translation (genetics); vineyards; viticulture; weather; Italy
Abstract:
... BACKGROUND: Phenotypic plasticity refers to the range of phenotypes a single genotype can express as a function of its environment. These phenotypic variations are attributable to the effect of the environment on the expression and function of genes influencing plastic traits. We investigated phenotypic plasticity in grapevine by comparing the berry transcriptome in a single clone of the vegetativ ...
DOI:
10.1186/gb-2013-14-6-r54
PubMed:
23759170
PubMed Central:
PMC3706941

18. The promise of genomics in the study of plant-pollinator interactions

Author:
Elizabeth L Clare; Florian P Schiestl; Andrew R Leitch; Lars Chittka
Source:
Genome biology 2013 v.14 no.6 pp. 207
ISSN:
1474-760X
Subject:
evolution; flowering; flowers; genomics; herbivores; landscapes; plant tissues; pollinators
Abstract:
... Flowers exist in exceedingly complex fitness landscapes, in which subtle variation in each trait can affect the pollinators, herbivores and pleiotropically linked traits in other plant tissues. A whole-genome approach to flower evolution will help our understanding of plant-pollinator interactions. ...
DOI:
10.1186/gb-2013-14-6-207
PubMed:
23796166
PubMed Central:
PMC3707021

19. Analyzing the soybean transcriptome during autoregulation of mycorrhization identifies the transcription factors GmNF-YA1a/b as positive regulators of arbuscular mycorrhization

Author:
Sara Schaarschmidt; Peter M Gresshoff; Bettina Hause
Source:
Genome biology 2013 v.14 no.6 pp. R62
ISSN:
1474-760X
Subject:
Glycine max; Rhizophagus irregularis; autoregulation; gene expression regulation; genes; mutants; mycorrhizal fungi; plant organs; roots; shoots; soybeans; transcription factors; transcriptome; vesicular arbuscular mycorrhizae
Abstract:
... BACKGROUND: Similarly to the legume-rhizobia symbiosis, the arbuscular mycorrhiza interaction is controlled by autoregulation representing a feedback inhibition involving the CLAVATA1-like receptor kinase NARK in shoots. However, little is known about signals and targets down-stream of NARK. To find NARK-related transcriptional changes in mycorrhizal soybean (Glycine max) plants, we analyzed wild- ...
DOI:
10.1186/gb-2013-14-6-r62
PubMed:
23777981
PubMed Central:
PMC3706930

20. Biofuel and energy crops: high-yield Saccharinae take center stage in the post-genomics era

Author:
Savio de Siqueira Ferreira; Milton Yutaka Nishiyama Jr; Andrew H Paterson; Glaucia Mendes Souza
Source:
Genome biology 2013 v.14 no.6 pp. 210
ISSN:
1474-760X
Subject:
Miscanthus; biofuels; biotechnology; energy crops; feedstocks; sugarcane
Abstract:
... The Saccharinae, especially sugarcane, Miscanthus and sorghum, present remarkable characteristics for bioenergy production. Biotechnology of these plants will be important for a sustainable feedstock supply. Herein, we review knowledge useful for their improvement and synergies gained by their parallel study. ...
DOI:
10.1186/gb-2013-14-6-210
PubMed:
23805917
PubMed Central:
PMC3707038