Genome-wide association mapping to candidate polymorphism resolution in the unsequenced barley genome

Although commonplace in human disease genetics, genome-wide association (GWA) studies have only relatively recently been applied to plants. Using 32 phenotypes in the inbreeding crop barley, we report GWA mapping of 15 morphological traits across ∼500 cultivars genotyped with 1,536 SNPs. In contrast to the majority of human GWA studies, we observe high levels of linkage disequilibrium within and between chromosomes. Despite this, GWA analysis readily detected common alleles of high penetrance. To investigate the potential of combining GWA mapping with comparative analysis to resolve traits to candidate polymorphism level in unsequenced genomes, we fine-mapped a selected phenotype (anthocyanin pigmentation) within a 140-kb interval containing three genes. Of these, resequencing the putative anthocyanin pathway gene HvbHLH1 identified a deletion resulting in a premature stop codon upstream of the basic helix-loop-helix domain, which was diagnostic for lack of anthocyanin in our association and biparental mapping populations. The methodology described here is transferable to species with limited genomic resources, providing a paradigm for reducing the threshold of map-based cloning in unsequenced crops.

Tackling regional climate change by leaf albedo bio-geoengineering

The likelihood that continuing greenhouse-gas emissions will lead to an unmanageable degree of climate change [1] has stimulated the search for planetary-scale technological solutions for reducing global warming [2] (“geoengineering”), typically characterized by the necessity for costly new infrastructures and industries [3]. We suggest that the existing global infrastructure associated with arable agriculture can help, given that crop plants exert an important influence over the climatic energy budget 4 and 5 because of differences in their albedo (solar reflectivity) compared to soils and to natural vegetation [6]. Specifically, we propose a “bio-geoengineering” approach to mitigate surface warming, in which crop varieties having specific leaf glossiness and/or canopy morphological traits are specifically chosen to maximize solar reflectivity. We quantify this by modifying the canopy albedo of vegetation in prescribed cropland areas in a global-climate model, and thereby estimate the near-term potential for bio-geoengineering to be a summertime cooling of more than 1°C throughout much of central North America and midlatitude Eurasia, equivalent to seasonally offsetting approximately one-fifth of regional warming due to doubling of atmospheric CO2[7]. Ultimately, genetic modification of plant leaf waxes or canopy structure could achieve greater temperature reductions, although better characterization of existing intraspecies variability is needed first.

Analysis of DNA polymorphism in ancient barley herbarium material: validation of the KASP SNP genotyping platform

The availability of crop specimens archived in herbaria and old seed collections represent valuable resources for the analysis of plant genetic diversity and crop domestication. The ability to extract ancient DNA (aDNA) from such samples has recently allowed molecular genetic investigations to be undertaken in ancient materials. While analyses of aDNA initially focused on the use of markers which occur in multiple copies such as the internal transcribed spacer region (ITS) within ribosomal DNA and those requiring amplification of short DNA regions of variable length such as simple sequence repeats (SSRs), emphasis is now moving towards the genotyping of single nucleotide polymorphisms (SNPs), traditionally undertaken in aDNA by Sanger sequencing. Here, using a panel of barley aDNA samples previously surveyed by Sanger sequencing for putative causative SNPs within the flowering-time gene PPD-H1, we assess the utility of the Kompetitive Allele Specific PCR (KASP) genotyping platform for aDNA analysis. We find KASP to out-perform Sanger sequencing in the genotyping of aDNA samples (78% versus 61% success, respectively), as well as being robust to contamination. The small template size (≥46 bp) and one-step, closed-tube amplification/genotyping process make this platform ideally suited to the genotypic analysis of aDNA, a process which is often hampered by template DNA degradation and sample cross-contamination. Such attributes, as well as its flexibility of use and relatively low cost, make KASP particularly relevant to the genetic analysis of aDNA samples. Furthermore, KASP provides a common platform for the genotyping and analysis of corresponding SNPs in ancient, landrace and modern plant materials. The extended haplotype analysis of PPD-H1 undertaken here (allelic variation at which is thought to be important for the spread of domestication and local adaptation) provides further resolution to the previously identified geographic cline of flowering-time allele distribution, illustrating how KASP can be used to aid genetic analyses of aDNA from plant species. We further demonstrate the utility of KASP by genotyping ten additional genetic markers diagnostic for morphological traits in barley, shedding light on the phenotypic traits, alleles and allele combinations present in these unviable ancient specimens, as well as their geographic distributions.

Intraspecific trait variation is correlated with establishment success of alien mammals

Many studies have aimed to identify common predictors of successful introductions of alien species, but the search has had limited success, particularly for animals. Past research focused primarily on mean trait values, even though genetic and phenotypic variation has been shown to play a role in establishment success in plants and some animals (mostly invertebrates). Using a global database describing 511 introduction events representing 97 mammalian species, we show that intraspecific variation in morphological traits is associated with establishment success, even when controlling for the positive effect of propagule pressure. In particular, greater establishment success is associated with more variation in adult body size but, surprisingly, less variation in neonate body size, potentially reflecting distinct trade-offs and constraints that influence population dynamics differently. We find no mean trait descriptors associated with establishment success, although species occupying wider native distribution ranges (which likely have larger niches) are more successful. Our results emphasize the importance of explicitly considering intraspecific variation to predict establishment success in animal species and generally to understand population dynamics. This understanding might improve management of alien species and increase the success of intentional releases, for example, for biocontrol or reintroductions.

Small mammals of the mid-Araguaia River in central Brazil, with the description of a new species of climbing rat

The mid-Araguaia River basin in central Brazil is considered a priority area for biodiversity conservation, and Parque Estadual do Cantao (PEC) is one of the most important protected areas in this ecotone between Cerrado and Amazonia. This area suffers an intensive human pressure with high rates of deforestation, and still remains poorly studied in terms of biodiversity. From June 2007 to November 2008 we sampled small mammals from both banks of the mid-Araguaia River, in the states of Tocantins and Para. Data are given about morphological traits, geographic distribution and natural history of 22 species of small non-volant mammals (eight marsupials and 14 rodents) surveyed at PEC and its surroundings. We also present mitochondrial phylogenetic analyses that allow species identification within the genera: Oecomys, Oligoryzomys and Rhipidomys, and delineate an undescribed species of Thrichomys. Based on morphologic and molecular data, we describe a new species of Rhipidomys previously assigned to R. nitela, which is apparently endemic to the Araguaia-Tocantins basin in the Cerrado. Additionally, our phylogenetic analyses provide support for the role played by the Araguaia River as an important geographic barrier for two sister species of Rhipidomys.

Craniometric Similarities Within and Between Human Populations in Comparison with Neutral Genetic Data

The statement that pairs of individuals from different populations are often more genetically similar than pairs from the same population is a widespread idea inside and outside the scientific community. Witherspoon et al. [""Genetic similarities within and between human populations,"" Genetics 176:351-359 (2007)] proposed an index called the dissimilarity fraction (omega) to access in a quantitative way the validity of this statement for genetic systems. Witherspoon demonstrated that, as the number of loci increases, omega decreases to a point where, when enough sampling is available, the statement is false. In this study, we applied the dissimilarity fraction to Howells`s craniometric database to establish whether or not similar results are obtained for cranial morphological traits. Although in genetic studies thousands of loci are available, Howells`s database provides no more than 55 metric traits, making the contribution of each variable important. To cope with this limitation, we developed a routine that takes this effect into consideration when calculating. omega Contrary to what was observed for the genetic data, our results show that cranial morphology asymptotically approaches a mean omega of 0.3 and therefore supports the initial statement-that is, that individuals from the same geographic region do not form clear and discrete clusters-further questioning the idea of the existence of discrete biological clusters in the human species. Finally, by assuming that cranial morphology is under an additive polygenetic model, we can say that the population history signal of human craniometric traits presents the same resolution as a neutral genetic system dependent on no more than 20 loci.

Ontogeny of body size and shape of Antarctic and subantarctic fur seals

Pre- and post-weaning functional demands on body size and shape of mammals are often in conflict, especially in species where weaning involves a change of habitat. Compared with long lactations, brief lactations are expected to be associated with fast rates of development and attainment of adult traits. We describe allometry and growth for several morphological traits in two closely related fur seal species with large differences in lactation duration at a sympatric site. Longitudinal data were collected from Antarctic (Arctocephalus gazella (Peters, 1875); 120 d lactation) and subantarctic (Arctocephalus tropicalis (Gray, 1872); 300 d lactation) fur seals. Body mass was similar in neonates of both species, but A. gazella neonates were longer, less voluminous, and had larger foreflippers. The species were similar in rate of preweaning growth in body mass, but growth rates of linear variables were faster for A. gazella pups. Consequently, neonatal differences in body shape increased over lactation, and A. gazella pups approached adult body shape faster than did A. tropicalis pups. Our results indicate that preweaning growth is associated with significant changes in body shape, involving the acquisition of a longer, more slender body with larger foreflippers in A. gazella. These differences suggest that A. gazella pups are physically more mature at approximately 100 d of age (close to weaning age) than A. tropicalis pups of the same age

Paradox lost: variable colour-pattern geometry is associated with differences in movement in aposematic frogs

Aposematic signal variation is a paradox: predators are better at learning and retaining the association between conspicuousness and unprofitability when signal variation is low. Movement patterns and variable colour patterns are linked in non-aposematic species: striped patterns generate illusions of altered speed and direction when moving linearly, affecting predators' tracking ability; blotched patterns benefit instead from unpredictable pauses and random movement. We tested whether the extensive colour-pattern variation in an aposematic frog is linked to movement, and found that individuals moving directionally and faster have more elongated patterns than individuals moving randomly and slowly. This may help explain the paradox of polymorphic aposematism: variable warning signals may reduce protection, but predator defence might still be effective if specific behaviours are tuned to specific signals. The interacting effects of behavioural and morphological traits may be a key to the evolution of warning signals. © 2014 The Author(s) Published by the Royal Society. All rights reserved.

Sex, androgens, and whole-organism performance in an Australian lizard

Understanding underlying physiological differences between the sexes in circulating androgens and how hormonal variation affects morphology-performance relationships may help clarify the evolution of sexual dimorphism in diverse taxa. Using a widely distributed Australian lizard (Eulamprus quoyii) with weak sexual dimorphism and no dichromatism, we tested whether circulating androgens differed between the sexes and whether they covaried with morphological and performance traits (bite force, sprint speed, endurance). Males had larger head dimensions, stronger bite force, faster sprint speed, and longer endurance compared to females. We found that the sexes did not differ in androgen concentrations and that androgens were weakly associated with both morphological and performance traits. Interestingly, high circulating androgens showed a nonlinear relationship with bite force in males and not females, with this relationship possibly being related to alternative male reproductive tactics. Our results suggest that androgens are not strongly correlated with most performance and morphological traits, although they may play an important organizational role during the development of morphological traits, which could explain the differences in morphology and thus performance between the sexes. Differences in performance between the sexes suggest differential selection on these functional traits between males and females. © 2014 The Linnean Society of London.

Modos de aplicação de zinco na nutricão e na produção de massa seca de plantas de trigo

Zinc application methods can affect the nutrition and the initial development of the wheat. Thus, the aim of this work was to analyze the different ways of Zn application in the soil, on nutrition and on dry matter production. A completely randomized experimental design with four replications was used. The experiment was composed by the following Zn application treatments: control (no zinc application); soil incorporation, furrow located, seeds treatment and leaf pulverization. The experimental unit was composed of a pot filled with 7 L of soil. Morphological traits for each plant were determined on 52 days after emergence by the evaluations of plant height, internodes number, tillers number and aerial part dry matter. Still, the soil and plant chemical analysis was accomplished. The furrow located method provided larger concentrations of the micronutrient available. The zinc application methods did not influence the initial growth of the wheat plants. The zinc concentration in leaves was influenced by the different application methods, being the leaf pulverization the one that was caused the largest zinc accumulation on aerial part dry matter.

Bayesian inference in genetic parameter estimation of visual scores in Nellore beef-cattle

The aim of this study was to estimate the components of variance and genetic parameters for the visual scores which constitute the Morphological Evaluation System (MES), such as body structure (S), precocity (P) and musculature (M) in Nellore beef-cattle at the weaning and yearling stages, by using threshold Bayesian models. The information used for this was gleaned from visual scores of 5,407 animals evaluated at the weaning and 2,649 at the yearling stages. The genetic parameters for visual score traits were estimated through two-trait analysis, using the threshold animal model, with Bayesian statistics methodology and MTGSAM (Multiple Trait Gibbs Sampler for Animal Models) threshold software. Heritability estimates for S, P and M were 0.68, 0.65 and 0.62 (at weaning) and 0.44, 0.38 and 0.32 (at the yearling stage), respectively. Heritability estimates for S, P and M were found to be high, and so it is expected that these traits should respond favorably to direct selection. The visual scores evaluated at the weaning and yearling stages might be used in the composition of new selection indexes, as they presented sufficient genetic variability to promote genetic progress in such morphological traits.

Análise genética de escores de avaliação visual de bovinos com modelos bayesianos de limiar e linear

O objetivo deste trabalho foi comparar as estimativas de parâmetros genéticos obtidas em análises bayesianas uni-característica e bi-característica, em modelo animal linear e de limiar, considerando-se as características categóricas morfológicas de bovinos da raça Nelore. Os dados de musculosidade, estrutura física e conformação foram obtidos entre 2000 e 2005, em 3.864 animais de 13 fazendas participantes do Programa Nelore Brasil. Foram realizadas análises bayesianas uni e bi-características, em modelos de limiar e linear. de modo geral, os modelos de limiar e linear foram eficientes na estimação dos parâmetros genéticos para escores visuais em análises bayesianas uni-características. Nas análises bi-características, observou-se que: com utilização de dados contínuos e categóricos, o modelo de limiar proporcionou estimativas de correlação genética de maior magnitude do que aquelas do modelo linear; e com o uso de dados categóricos, as estimativas de herdabilidade foram semelhantes. A vantagem do modelo linear foi o menor tempo gasto no processamento das análises. Na avaliação genética de animais para escores visuais, o uso do modelo de limiar ou linear não influenciou a classificação dos animais, quanto aos valores genéticos preditos, o que indica que ambos os modelos podem ser utilizados em programas de melhoramento genético.

Estimativas de correlações genéticas entre escores visuais e características de carcaça medidas por ultrassonografia em bovinos Nelore utilizando modelos bayesianos linear-limiar

O objetivo neste estudo foi estimar as correlações genéticas entre escores visuais e características de carcaça medidas por ultrassonografia em bovinos da raça Nelore utilizando a estatística bayesiana por meio da Amostragem de Gibbs, sob modelo animal linear-limiar. Foram estudadas as características categóricas morfológicas de musculosidade, estrutura física, conformação e sacro, avaliadas aos 15 e 22 meses de idade. Para as características de carcaça, foram avaliadas as características área de olho-de-lombo, espessura de gordura subcutânea, espessura de gordura subcutânea na garupa e altura na garupa. Os escores visuais devem ser empregados como critérios de seleção para aumentar o progresso genético para a característica área de olhode-lombo e, consequentemente, melhorar o rendimento de carcaça. As estimativas de correlação genética obtidas para musculosidade com espessura de gordura subcutânea e espessura de gordura subcutânea na garupa indicaram que a seleção para musculosidade pode levar a animais com melhor acabamento de carcaça. A seleção para a estrutura física e conformação aos 15 e 22 meses de idade pode promover resposta correlacionada para o aumento da altura na garupa.

Avaliação genética de características de escores visuais de bovinos da raça Nelore da desmama até a maturidade

Os objetivos neste estudo foram estimar parâmetros genéticos das características categóricas musculosidade, estrutura física, aspectos raciais, conformação, ônfalo, pigmentação e sacro e predizer os valores genéticos utilizando-se a estatística bayesiana sob modelo animal de limiar, considerando diferentes idades de bovinos da raça Nelore. As informações de escores visuais foram obtidas nos anos de 2000 a 2005 de bovinos provenientes de 13 fazendas participantes do Programa Nelore Brasil. Nas análises bicaracterísticas, foram utilizados 500.000 até 1.100.000 ciclos para alcançar a convergência da cadeia de Gibbs. O descarte inicial e o intervalo amostral foram de 100.000 e 1.000 ciclos, respectivamente. As características de escores visuais avaliadas aos 8 e 22 meses de idade apresentaram estimativas de herdabilidades moderadas, indicando resposta rápida à seleção direta. Os escores visuais indicaram possibilidade de resposta rápida à seleção direta e, portanto, devem ser incorporados em programas de melhoramento genético como critérios de seleção. As estimativas de correlações genéticas entre musculosidade, estrutura física e conformação também indicam que a seleção direta para uma destas características trará progresso genético às outras. Recomenda-se utilizar os escores visuais como critérios de seleção em pelo menos duas fases de vida do animal, na desmama e ao sobreano.

Análise bayesiana na estimação de correlações genéticas entre escores visuais e características reprodutivas de bovinos Nelore utilizando modelos linear-limiar

Estimaram-se as correlações genéticas entre os escores visuais e as características reprodutivas, utilizando a estatística bayesiana sob modelo animal linear-limiar, em bovinos da raça Nelore. Foram estudadas características categóricas morfológicas, avaliadas visualmente aos oito, 15 e 22 meses de idade; e características contínuas de perímetro escrotal padronizado aos 365 e 450 dias de idade, além da idade ao primeiro parto. As estimativas de correlações genéticas foram de sentido favorável à seleção, apresentando magnitudes moderadas, sugerindo que a seleção de animais para um biótipo desejável pode levar a animais com maior fertilidade e precocidade sexual. As estimativas de correlação genética para o perímetro escrotal padronizado aos 450 dias e a idade ao primeiro parto com as características morfológicas avaliadas aos 22 meses de idade foram maiores do que as obtidas entre as características de escores visuais avaliadas aos oito e 15 meses de idade. A utilização de escores visuais como critério de seleção trará progresso genético também para as características reprodutivas.