Constitutive and inducible oleoresin defenses share genetic architectures and mechanisms in Pinus taeda.

As organisms age the environment fluctuates, exerting differential selection across ontogeny. In particular, highly seasonal environments expose life stages to often drastically different thermal environments. This developmental variation is particularly striking in organisms with complex life cycles, wherein life history stages also exhibit distinct morphologies, physiologies, and behaviors. Genes acting pleiotropically on thermal responses may produce genetic correlations across ontogeny, constraining the independent evolution of each life stage to their respective thermal environments. To investigate whether developmental genetic correlations constrain the evolution thermal hardiness of the fly Drosophila melanogaster, we applied quantitative genetic analyses to cold hardiness measured in both larvae and adults from isogenic lines of the Drosophila Genetic Reference Panel (DGRP), using survival at stressful low temperatures as the phenotypic metric. Using full genome resequencing data for the DGRP, we also implemented genome-wide association (GWA) analysis using Bayesian Sparse Linear Mixed Models (BSLMMs) to estimate associations between naturally segregating variation and cold hardiness for both larvae and adults. Quantitative genetic analyses revealed no significant genetic correlation for cold hardiness between life stages, suggesting complete genetic decoupling of thermal hardiness across the metamorphic boundary. Both quantitative genetic and GWA analyses suggested that polygenic variation underlies cold hardiness in both stages, and that associated loci largely affected one stage or the other, but not both. However, reciprocal enrichment tests and correlations between BSLMM parameters for each life stage support some shared physiological mechanisms that may reflect common cellular thermal response pathways. Overall, these results suggest no developmental genetic constraints on cold hardiness across metamorphosis in D. melanogaster, an important consideration in evolutionary models of responses to changing climates. Genetic correlations for environmental sensitivity across ontogeny remains largely unexplored in other organisms, thus assessing the generality of genetic decoupling will require further quantitative or population genetic analysis in additional species.

Rapidly enhancing oleoresin production in conifer stems through genomic selection and genetic engineering may increase resistance to bark beetles and terpenoid yield for liquid biofuels. We integrated association genetic and genomic prediction analyses of oleoresin flow (g 24 h(-1)) using 4854 single nucleotide polymorphisms (SNPs) in expressed genes within a pedigreed population of loblolly pine (Pinus taeda) that was clonally replicated at three sites in the southeastern United States. Additive genetic variation in oleoresin flow (h(2) ≈ 0.12-0.30) was strongly correlated between years in which precipitation varied (r(a) ≈ 0.95), while the genetic correlation between sites declined from 0.8 to 0.37 with increasing differences in soil and climate among sites. A total of 231 SNPs were significantly associated with oleoresin flow, of which 81% were specific to individual sites. SNPs in sequences similar to ethylene signaling proteins, ABC transporters, and diterpenoid hydroxylases were associated with oleoresin flow across sites. Despite this complex genetic architecture, we developed a genomic prediction model to accelerate breeding for enhanced oleoresin flow that is robust to environmental variation. Results imply that breeding could increase oleoresin flow 1.5- to 2.4-fold in one generation.

Genetically improving constitutive resin canal development in Pinus stems may enhance the capacity to synthesize terpenes for bark beetle resistance, chemical feedstocks, and biofuels. To discover genes that potentially regulate axial resin canal number (RCN), single nucleotide polymorphisms (SNPs) in 4027 genes were tested for association with RCN in two growth rings and three environments in a complex pedigree of 520 Pinus taeda individuals (CCLONES). The map locations of associated genes were compared with RCN quantitative trait loci (QTLs) in a (P. taeda × Pinus elliottii) × P. elliottii pseudo-backcross of 345 full-sibs (BC1). Resin canal number was heritable (h(2) ˜ 0.12-0.21) and positively genetically correlated with xylem growth (rg ˜ 0.32-0.72) and oleoresin flow (rg ˜ 0.15-0.51). Sixteen well-supported candidate regulators of RCN were discovered in CCLONES, including genes associated across sites and ages, unidirectionally associated with oleoresin flow and xylem growth, and mapped to RCN QTLs in BC1. Breeding is predicted to increase RCN 11% in one generation and could be accelerated with genomic selection at accuracies of 0.45-0.52 across environments. There is significant genetic variation for RCN in loblolly pine, which can be exploited in breeding for elevated terpene content.

Plant cuticular wax compounds perform functions that are essential for the survival of terrestrial plants. Despite their importance, the genetic control of these compounds is poorly understood outside of model taxa. Here we investigate the genetic basis of variation in cuticular compounds in Eucalyptus globulus using quantitative genetic and quantitative trait loci (QTL) analyses. Quantitative genetic analysis was conducted using 246 open-pollinated progeny from 13 native sub-races throughout the geographic range. QTL analysis was conducted using 112 clonally replicated progeny from an outcross F2 population. Nine compounds exhibited significant genetic variation among sub-races with three exhibiting signals of diversifying selection. Fifty-two QTL were found with co-location of QTL for related compounds commonly observed. Notable among these was the QTL for five wax esters, which co-located with a gene from the KCS family, previously implicated in the biosynthesis of cuticular waxes in Arabidopsis. In combination, the QTL and quantitative genetic analyses suggest the variation and differentiation in cuticular wax compounds within E.globulus has a complex genetic origin. Sub-races exhibited independent latitudinal and longitudinal differentiation in cuticular wax compounds, likely reflecting processes such as historic gene flow and diversifying selection acting upon genes that have diverse functions in distinct biochemical pathways.

BackgroundGenetic selection for host resistance offers a desirable complement to chemical treatment to control infectious disease in livestock. Quantitative genetics disease data frequently originate from field studies and are often binary. However, current methods to analyse binary disease data fail to take infection dynamics into account. Moreover, genetic analyses tend to focus on host susceptibility, ignoring potential variation in infectiousness, i.e. the ability of a host to transmit the infection. This stands in contrast to epidemiological studies, which reveal that variation in infectiousness plays an important role in the progression and severity of epidemics. In this study, we aim at filling this gap by deriving an expression for the probability of becoming infected that incorporates infection dynamics and is an explicit function of both host susceptibility and infectiousness. We then validate this expression according to epidemiological theory and by simulating epidemiological scenarios, and explore implications of integrating this expression into genetic analyses.ResultsOur simulations show that the derived expression is valid for a range of stochastic genetic-epidemiological scenarios. In the particular case of variation in susceptibility only, the expression can be incorporated into conventional quantitative genetic analyses using a complementary log-log link function (rather than probit or logit). Similarly, if there is moderate variation in both susceptibility and infectiousness, it is possible to use a logarithmic link function, combined with an indirect genetic effects model. However, in the presence of highly infectious individuals, i.e. super-spreaders, the use of any model that is linear in susceptibility and infectiousness causes biased estimates. Thus, in order to identify super-spreaders, novel analytical methods using our derived expression are required.ConclusionsWe have derived a genetic-epidemiological function for quantitative genetic analyses of binary infectious disease data, which, unlike current approaches, takes infection dynamics into account and allows for variation in host susceptibility and infectiousness.

Summary Resin canals produce and transport oleoresins that are important for tree defenses within the Pinaceae family. Rapid measurement techniques are needed to better understand how resin canal characteristics vary due to genetic and environmental effects. Here we describe a semi-automated microscopy imaging system that was built for quantifying longitudinal resin canals. Tree increment cores from 210 loblolly pine ( Pinus taeda L.) trees were prepared into radial strips and the transverse surface of the samples polished with 400 and then 600 grit sandpaper. Each sample was imaged along its entire length (pith to bark) with the images collected from a monochrome camera connected to a Plan Fluorite 4× objective lens. The samples were imaged on the transverse surface via transmitted 850 nm near-infrared light directed at the radial surfaces of the samples. A total of 24 153 images were collected and then processed offline in Python using the Open Computer Vision Library (OpenCV) using a series of algorithms including contrast correction, noise removal, thresholding, contour identification, erosion, and dilation. A total of 24 491 resin canals were identified and their size quantified. The resin canals were assigned into annual rings and positioned within the earlywood or latewood of a ring using cross-correlation whereby a pseudo-density value was derived from the images and matched with density values measured by X-ray densitometry. Of the total resin canals identified, 51.5% were in the earlywood and 48.5% in the latewood, with the majority being detected in the earlywood in the first six years and the latewood in years 7 and above. This study represents the most information collected on the resin canals of loblolly pine. The detailed description of the hardware and image analysis methods should serve as a useful guide to others interested in imaging resin canals as well as other anatomical features.

The polymorphism of prescutellar bristles (＂prsc＂) in melon fly, ＂Bactrocera cucurbitae＂ (Coquillett), was investigated by artificial selection of phenotypes and quantitative genetic analysis. In the wild strain, generally more than 95% population have 2 ＂prsc＂ while some may have 4 ＂prsc＂. By selection, however, a group of phenotypes was appeared with the number of ＂prsc＂ reach up to 14 and more. All multiplied bristles were randomly arranged in a region of posterior half of ＂scutum＂ and between the lateral ＂vita＂. The quantitative genetic analysis was conducted by crossing two strains of different phenotypes, one from each strain. In each cross only one virgin male and one virgin female were paired, with a total of 6 pairs in each experiment, and 200-500 offsprings from each experiment were examined for their phenotypes. For each cross, only one 2-＂prsc＂ individuals (the major component of the wild population) and one 12-＂prsc＂ or 14-＂prsc＂ individuals from the selected strains were interbred, and then inbred F_1 for the F_2 progeny. The results showed that for 2-＂prsc＂ × 12-＂prsc＂, the F_1 progeny constituted a group of phenotypes with different ＂prsc＂ numbers, and the mean was 4.7 ± 0.9 which was in-between two parental phenotypes. The mean of ＂prsc＂ in F_2 is 4.7 ± 1.9. The difference between the means of F_1 and F_2 is insignificant in the t-test (P ＞ 0.05). For 2-＂prsc＂ × 14-＂prsc＂, the F_1 progeny constituted a group of phenotypes, with the mean of 5.0 ± 1.0 which was in-between their parental phenotypes. The F_2 offsprings had their mean at 5.1 ± 2.3. The t-test indicated no significant difference between the means of F_1 and F_2 (P ＞ 0.05). Moreover, as the coefficients of variation of F_2 were higher than those of F_1 (40.1% ＞ 19.5% versus 45.9% ＞ 21.7%), it suggests that more variability around the mean of F_2 than that of F_1. The extreme values in ＂prsc＂ for F_2 were extended to the range of their parental values (2-15 ＂prsc＂ and 1-17 ＂prsc＂, respectively) than did the extreme values of F_1. Results of this study were similar to that reported by Emerson & East (1913), indicating that the ＂prsc＂ of melon fly is a continuous and quantitative trait in inheritance.

BackgroundIdentification of genes or even nucleotides that are responsible for quantitative and adaptive trait variation is a difficult task due to the complex interdependence between a large number of genetic and environmental factors. The polymorphism of the mitogenome is one of the factors that can contribute to quantitative trait variation. However, the effects of the mitogenome have not been comprehensively studied, since large numbers of mitogenome sequences and recorded phenotypes are required to reach the adequate power of analysis. Current research in our group focuses on acquiring the necessary mitochondria sequence information and analysing its influence on the phenotype of a quantitative trait. To facilitate these tasks we have produced software for processing pedigrees that is optimised for maternal lineage analysis.ResultsWe present MaGelLAn 1.0 (maternal genealogy lineage analyser), a suite of four Python scripts (modules) that is designed to facilitate the analysis of the impact of mitogenome polymorphism on quantitative trait variation by combining molecular and pedigree information. MaGelLAn 1.0 is primarily used to: (1) optimise the sampling strategy for molecular analyses; (2) identify and correct pedigree inconsistencies; and (3) identify maternal lineages and assign the corresponding mitogenome sequences to all individuals in the pedigree, this information being used as input to any of the standard software for quantitative genetic (association) analysis. In addition, MaGelLAn 1.0 allows computing the mitogenome (maternal) effective population sizes and probability of mitogenome (maternal) identity that are useful for conservation management of small populations.ConclusionsMaGelLAn is the first tool for pedigree analysis that focuses on quantitative genetic analyses of mitogenome data. It is conceived with the purpose to significantly reduce the effort in handling and preparing large pedigrees for processing the information linked to maternal lines. The software source code, along with the manual and the example files can be downloaded at http://lissp.irb.hr/software/magellan-1-0/ and https://github.com/sristov/magellan.Electronic supplementary materialThe online version of this article (doi:10.1186/s12711-016-0242-9) contains supplementary material, which is available to authorized users.

With the recent introduction of Verticillium wilt (VW), caused by Verticillium albo‐atrum Reinke & Berth., on alfalfa (Medicago sativa L.), many North American alfalfa breeders have been using European cultivars as sources of resistance. The objective of this research was to compare the inheritance of VW resistance in plants selected from the European cultivars ‘Vertus’ and ‘Maris Kabul,’ each deriving at least some of its resistance from different origins. Qualitative genetic analyses complemented by quantitative genetic analyses were done on four sets of complete diallels (S1's, F1's, and reciprocals) within each cultivar and two sets of Design II matings between Vertus and Maris Kabul for valid comparisons, parents were chosen so that each set was represented by one parent for each of five disease severity classes based on topgrowth symptoms. Disease evaluations were done on about 12‐week old seedlings in growth chambers, 6 weeks after inoculation. Many of the Maris Kabul S1's and moderately to highly resistant ✕ susceptible crosses had definite bimodal distributions, suggestive of a dominant gene conditioning moderate to high resistance. However, inheritance apparently was more complex than any single gene model according to qualitative analyses. Although inheritance in Vertus progenies also appeared to he complex, the absence of definite bimodal distributions suggested that the inheritance differed from that in the Maris Kabul progenies. The hypothesis of different inheritance in these plants from the two cultivars was supported by progeny distributions in Vertus ✕ Maris Kabul crosses. Furthermore, quantitative genetic analyses indicated thai nonadditive genetic effects were about four‐fold larger in these Maris Kabul progenies than in these Vertus progenies. Both sources of resistance appear useful for developing highly resistant cultivars. More stable resistance might be possible from the combination of genes from the two cultivars.

Loblolly, Pinustaeda L., and shortleaf, Pinusechinata Mill., pines respond to attack by the southern pine beetle (SPB), Dendroctonusfrontalis Zimmermann, or invasion by the SPB fungal associate, Ceratocystisminor (Hedgecock) Hunt, by forming a necrotic lesion around the wound site. This response was compared between trees that had no known prior experience with SPB or C. minor (naive trees) and trees that had been exposed to SPB or C. minor the previous year (experienced trees). No significant differences were observed in the average length of the lesions between experienced and naive trees in either pine species. However, the experienced loblolly pines had higher concentrations of inner bark monoterpenes than did the naive loblolly pines and the experienced shortleaf pines had a significantly different inner bark monoterpene composition compared with naive shortleaf pines during the June sample period. The monoterpene composition in unwounded tissue of experienced shortleaf pine closely resembled the observed monoterpene composition of lesion tissue at this time. The observed differences in inner bark monoterpenes following fungal or beetle exposure could render the trees less susceptible to later bark beetle attack for a period of time following the initial exposure.

José M. Álvarez-Castro has been supported by the Autonomous Administration Xunta de Galicia through project EM2014/024 to edit this Research Topic Issue

Causal Genomic and Epigenomic Network Analysis emerges as a New Generation of Genetic Studies of Complex Diseases.

Comprehensive Clinical and Genetic Analyses of Circulating Bile Acids and Their Associations With Diabetes and Its Indices.

<p dir="ltr">Bile acids (BAs) are cholesterol-derived compounds that regulate glucose, lipid, and energy metabolism. Despite their significance in glucose homeostasis, the association between specific BA molecular species and their synthetic pathways with diabetes mellitus (DM) is unclear. Here, we used a recently validated stable-isotope dilution high-performance liquid chromatography with tandem mass spectrometry (LC-MS/MS) method to quantify a panel of BAs in fasting plasma from subjects (n=2,145) and explored structural and genetic determinants of BAs linked to DM, insulin resistance and obesity. Multiple 12α-hydroxylated BAs were associated with DM [adjusted odds ratios (aORs):1.3-1.9 (all P<0.05)] and insulin resistance [aORs:1.3-2.2 (all P<0.05)]. Conversely, multiple 6α-hydroxylated BAs and isolithocholic acid (Iso-LCA) were inversely associated with DM and obesity [aORs:0.3-0.9 (all P<0.05)]. Genome-wide association studies (GWAS) revealed multiple genome-wide significant loci linked with nine of the 14 DM-associated BAs, including a locus for Iso-LCA (rs11866815). Mendelian randomization analyses showed genetically elevated DCA levels were causally associated with higher BMI, and Iso-LCA levels were causally associated with reduced BMI and DM risk. In conclusion, comprehensive large-scale quantitative mass spectrometry and genetics analyses show circulating levels of multiple structurally specific BAs, especially DCA and Iso-LCA, are clinically associated with and genetically linked to obesity and DM.</p>

<p dir="ltr">Bile acids (BAs) are cholesterol-derived compounds that regulate glucose, lipid, and energy metabolism. Despite their significance in glucose homeostasis, the association between specific BA molecular species and their synthetic pathways with diabetes mellitus (DM) is unclear. Here, we used a recently validated stable-isotope dilution high-performance liquid chromatography with tandem mass spectrometry (LC-MS/MS) method to quantify a panel of BAs in fasting plasma from subjects (n=2,145) and explored structural and genetic determinants of BAs linked to DM, insulin resistance and obesity. Multiple 12α-hydroxylated BAs were associated with DM [adjusted odds ratios (aORs):1.3-1.9 (all P<0.05)] and insulin resistance [aORs:1.3-2.2 (all P<0.05)]. Conversely, multiple 6α-hydroxylated BAs and isolithocholic acid (Iso-LCA) were inversely associated with DM and obesity [aORs:0.3-0.9 (all P<0.05)]. Genome-wide association studies (GWAS) revealed multiple genome-wide significant loci linked with nine of the 14 DM-associated BAs, including a locus for Iso-LCA (rs11866815). Mendelian randomization analyses showed genetically elevated DCA levels were causally associated with higher BMI, and Iso-LCA levels were causally associated with reduced BMI and DM risk. In conclusion, comprehensive large-scale quantitative mass spectrometry and genetics analyses show circulating levels of multiple structurally specific BAs, especially DCA and Iso-LCA, are clinically associated with and genetically linked to obesity and DM.</p>