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

Fundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)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.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 subpopulatio710527FAPESP - FUNDAÇÃO DE AMPARO À PESQUISA DO ESTADO DE SÃO PAULOFundação de Amparo à Pesquisa do Estado de São Paulo (FAPESP)2011/03110-

The effects of resource availability and environmental conditions on genetic rankings for carbon isotope discrimination during growth in tomato and rice

Carbon isotope discrimination (Δ) is frequently used as an index of leaf intercellular CO2 concentration (ci) and variation in photosynthetic water use efficiency. In this study, the stability of Δ was evaluated in greenhouse grown tomato and rice with respect to variable growth conditions including temperature, nutrient availability, soil flooding (in rice), irradiance, and root constriction in small soil volumes. Δ exhibited several characteristics indicative of contrasting set-point behavior among genotypes of both crops. These included generally small main environmental effects and lower observed levels of G x E interaction across the diverse treatments than observed in associated measures of relative growth rate, photosynthetic rate, biomass allocation pattern, or specific leaf area. Growth irradiance stood out among environmental parameters tested as having consistently large main affects on Δ for all genotypes screened in both crops. We suggest that this may be related to contrasting mechanisms of stomatal aperture modulation associated with the different environmental variables. For temperature and nutrient availability, feedback processes directly linked to ci and/or metabolite pools associated with ci may have played the primary role in coordinating stomatal conductance and photosynthetic capacity. In contrast, light has a direct effect on stomatal aperture in addition to feedback mediated through ci

International agreements and the plant genetics research community: A guide to practice

Plant genetic resources (PGR), including collections held in national and international gene banks, provide access to a wide array of genetic diversity and are critical to genomics research, conservation efforts, and applied breeding. Yet, there is a general lack of awareness in the research community about the rules and treaties that govern the use of PGR, about access and benefit sharing obligations contained in international treaties and/or national laws, and about how best to comply with potentially applicable requirements. This article provides a brief history and overview of three key international agreements, namely the Convention on Biological Diversity, the Nagoya Protocol, and the International Treaty on Plant Genetic Resources for Food and Agriculture, which collectively address responsibilities and obligations related to the use of much of the world’s PGR. By highlighting the coverage and key considerations of each agreement, the article provides a guide for those who use PGR in plant genetics research to better understand when and how international agreements apply, and—where the rules are unclear—to suggest best practices for compliance with existing agreements

A history of concussions is associated with symptoms of common mental disorders in former male professional athletes across a range of sports

Objective: Recent reports suggest that exposure to repetitive concussions in sports is associated with an increased risk of symptoms of distress, anxiety and depression, sleep disturbance or substance abuse/dependence (typically referred as symptoms of common mental disorders[CMD]) and of later development of neurodegenerative disease, in particular chronic traumatic encephalopathy (CTE). The primary aim of this study was to explore the relationship between sports career-related concussions and the subsequent occurrence of symptoms of CMD among former male professional athletes retired from football (soccer), ice hockey and rugby (union). Methods: Cross-sectional analyses were performed on baseline electronic questionnaires from three prospective cohort studies among former male professional athletes retired from football (soccer), ice hockey and rugby (union). The number of confirmed concussions was examined through a single question, while symptoms of distress, anxiety and depression, sleep disturbance and adverse alcohol use were assessed using validated questionnaires. Results: From 1,957 former professional athletes contacted, a total of 576 (29%) completed the questionnaire. Of these, 23% had not incurred a concussion during their career, 34% had two or three, 18% four or five, and 11% six or more concussions. The number of sports career-related concussions was a predictor for all outcome measures (β = 0.072–0.109; P ≤ 0.040). Specifically, former professional athletes who reported a history of four or five concussions were approximately 1.5 times more likely to report symptoms of CMD, rising to a two- to five-fold increase in those reporting a history of six or more sports career-related concussions. Conclusions: These data demonstrate an association between exposure to sports concussion and subsequent risk of symptoms of CMD in former professional athletes across a range of contact sports. Further work to explore the association between sports concussion and symptoms of CMD is required; in the meanwhile, strategies for effective risk reduction and improved management appear indicated

New horizons for plant translational research

In this issue, we launch a new article collection "The Promise of Plant Translational Research," featuring articles from leading plant researchers and call for additional plant translational research to be submitted to PLOS Biology for inclusion in this collection. We also discuss in this Editorial why this field has a vital role to play in meeting the challenges of sustainably feeding a growing world population

The Gramene Genetic Diversity Module: a resource for genotype-phenotype association analysis in grass species

The Genetic Diversity module of the Gramene database ("http://www.gramene.org/diversity":http://www.gramene.org/diversity) is specifically designed to handle data from high-throughput sequencing and array-based genotyping plateforms. Empowered by the Genomic Diversity and Phenotype Data Model, Gramene Genetic Diversity module provides live database connectivities of RFLP, SSR and SNP allele data, information about QTL, passport data for wild and cultivated germplasm from rice, maize, wheat, and _Arabidopsis_, and quantitative phenotypic data for some of these accessions. Large datasets of SNP variation are searchable via genomic positions of interest by SNP Query tool on a sequenced genome; and, trait associations, patterns of linkage disequilibrium and diversity can be evaluated using TASSEL. The Gramene database is updated twice a year, with the most recent release (Build #31) completed in May 2010

Segregation analysis of molecular markers in a population derived from coffea liberica hiern x c. eugenioides l

Coffee is a very important crop for the world economy. The commercial coffee production is based on two species, Coffea arabica L. (70%) and C. canephora Pierre (30%). C. arabica is the only allotetraploid (2n=4x=44) species, which has its primary center of diversity in the southwestern Ethiopia highlands. C. arabica is the only species cultivated in Colombia and represents a very important economic and social value. However, C. arabica has a very narrow genetic diversity and therefore, the use of diploid species on coffee breeding is very important because they allow to broad its diversity. In this work, the genetic segregation patterns were evaluated on a population of 101 F1 hybrid plants from a cross between the diploid species C. liberica and C. eugenioides using 618 molecular markers, of which 168 SSRs and 2 ESTs exhibited polymorphic patterns that allowed segregation analysis. Approximately 24% of the loci were null alleles, and the segregation distortion reached 23.5% at 0.01. A total of four segregant types were observed, from up to seven possibilities. The origins of null alleles, possible causes of segregation distortion, different segregation patterns obtained and recombination frequencies are discussed. The knowledge derived from this study allowed to better understand the genetic segregation behavior of these markers with the aim of developing genetic maps that have important applications for coffee breeding programs as well as other commercial crops.El café es un cultivo importante para la economía mundial. La producción comercial de café se basa en dos especies, Coffea arabica L. (70%) y C. canephora Pierre (30%). La primera es la única alotetraploide (2n = 4x = 44) que tiene su centro primario de diversidad en las tierras altas del suroeste de Etiola segunda es la única cultivada en Colombia y representa un importante valor económico y social. Sin embargo, C. arabica tiene una base genética muy estrecha y por ello es importante el uso de especies diploides en el mejora-miento del café para ampliar su diversidad. En este trabajo fueron evaluados los patrones de segregación genética en una población consistente en 101 plantas híbridas F1 de un cruce entre la especie diploide C. liberica y C. eugenioides utilizando 618 marcadores moleculares, de las cuales 168 SSR y 2 EST exhibieron patrones polimórficos que permitieron el análisis de segregación. Aproximadamente 24% de los loci fueron alelos nulos y la distorsión de la segregación alcanzó 23.5% (