Plant microphenotype: from innovative imaging to computational analysis

The microphenotype plays a key role in bridging the gap between the genotype and the complex macro phenotype. In this article, we review the advances in data acquisition and the intelligent analysis of plant microphenotyping and present applications of microphenotyping in plant science over the past two decades. We then point out several challenges in this field and suggest that cross-scale image acquisition strategies, powerful artificial intelligence algorithms, advanced genetic analysis, and computational phenotyping need to be established and performed to better understand interactions among genotype, environment, and management. Microphenotyping has entered the era of Microphenotyping 3.0 and will largely advance functional genomics and plant science.

Exploring the Potential of Heterosis to Improve Nitrogen Use Efficiency in Popcorn Plants

Nitrogen is crucial for plant growth and development, and improving nitrogen use efficiency (NUE) is a viable strategy for reducing dependence on nitrogen inputs and promoting sustainability. While the benefits of heterosis in corn are well known, the physiological mechanisms underlying this phenomenon in popcorn are less understood. We aimed to investigate the effects of heterosis on growth and physiological traits in four popcorn lines and their hybrids under two contrasting nitrogen conditions. We evaluated morpho-agronomic and physiological traits such as leaf pigments, the maximum photochemical efficiency of PSII, and leaf gas exchange. Components associated with NUE were also evaluated. N deprivation caused reductions of up to 65% in terms of plant architecture, 37% in terms of leaf pigments, and 42% in terms of photosynthesis-related traits. Heterosis had significant effects on growth traits, NUE, and foliar pigments, particularly under low soil nitrogen conditions. N-utilization efficiency was found to be the mechanism favoring superior hybrid performance for NUE. Non-additive genetic effects were predominant in controlling the studied traits, indicating that exploring heterosis is the most effective strategy for obtaining superior hybrids to promote NUE. The findings are relevant and beneficial for agro farmers seeking sustainable agricultural practices and improved crop productivity through the optimization of nitrogen utilization.

Rapid and transient evolution of local adaptation to seasonal host fruits in an invasive pest fly

Both local adaptation and adaptive phenotypic plasticity can influence the match between phenotypic traits and local environmental conditions. Theory predicts that environments stable for multiple generations promote local adaptation, whereas highly heterogeneous environments favor adaptive phenotypic plasticity. However, when environments have periods of stability mixed with heterogeneity, the relative importance of local adaptation and adaptive phenotypic plasticity is unclear. Here, we used Drosophila suzukii as a model system to evaluate the relative influence of genetic and plastic effects on the match of populations to environments with periods of stability from three to four generations. This invasive pest insect can develop within different fruits, and persists throughout the year in a given location on a succession of distinct host fruits, each one being available for only a few generations. Using reciprocal common environment experiments of natural D. suzukii populations collected from cherry, strawberry, and blackberry, we found that both oviposition preference and offspring performance were higher on medium made with the fruit from which the population originated than on media made with alternative fruits. This pattern, which remained after two generations in the laboratory, was analyzed using a statistical method we developed to quantify the contributions of local adaptation and adaptive plasticity in determining fitness. Altogether, we found that genetic effects (local adaptation) dominate over plastic effects (adaptive phenotypic plasticity). Our study demonstrates that spatially and temporally variable selection does not prevent the rapid evolution of local adaptation in natural populations. The speed and strength of adaptation may be facilitated by several mechanisms including a large effective population size and strong selective pressures imposed by host plants.

Problem solving in fawn-footed mosaic-tailed rats Melomys cervinipes is not significantly influenced by maternal care or genetic effects

Innovative problem solving is thought to be a flexible trait that allows animals to adjust to changing or challenging environmental conditions. However, it is not known how problem solving develops during an animal's early life, or whether it may have a heritable component. We investigated whether maternal genetic and nongenetic effects influenced problem-solving ability in a native Australian rodent, the fawn-footed mosaic-tailed rat Melomys cervinipes. We measured direct (time spent grooming and huddling), indirect (time spent nesting), and total amount of maternal care received across pup development (postnatal Days 1-13). We measured problem solving in juveniles using matchbox tasks, and in mothers and adult offspring using six tasks of varying complexity (matchbox, cylinder, obstruction, pillar, tile, and lever tasks). We found no relationship between any maternal care measures and problem-solving abilities across multiple tests, suggesting limited (if any) maternal nongenetic effects. We also found that, as shown by low heritability estimates, problem solving only had a small heritable component in some tasks, but this was nonsignificant and requires further investigation. These results suggest that problem solving is unlikely to be constrained by maternal effects experienced during early development, and is, instead, more likely to be influenced by other factors (e.g., experience) later in an individual's lifetime.

Expression and Genetic Effects of GLI Pathogenesis-Related 1 Gene on Backfat Thickness in Pigs

Backfat thickness (BFT) is an important carcass composition trait and regarded as a breeding focus. Our initial transcriptome analysis of pig BFT identified GLI pathogenesis-related 1 (GLIPR1) as one of the promising candidate genes. This study was conducted to identify the expression profiles, polymorphisms, and genetic effects of the GLIPR1 gene on BFT in pigs. The expression of the GLIPR1 gene existed in every detected tissue, and there was a significantly higher expression in spleen and adipose tissue than others (p < 0.05). At the different ages of pig, the expression of the GLIPR1 gene was low at an early age, increased with growth, and reached the highest level at 180 days. Genetic polymorphism analysis was detected in 553 individuals of the Large White × Minzhu F2 population. Four SNPs in the promoter significantly associated with 6−7 rib BFT (p < 0.05) were predicted to alter the transcription factor binding sites (TFBS), and the mutations of g.38758089 T>G and g.38758114 G>C were predicted to change the TFs associated with the regulation of adipogenesis. Haplotypes were formed by the detected SNPs, and one block showed a strong association with BFT (p < 0.05). In summary, our results indicate that the expression profiles and genetic variants of GLIPR1 affected the BFT of pigs. To our knowledge, this study is the first to demonstrate the biological function and genetic effects of the GLIPR1 gene on the BFT of pig and provide genetic markers to optimize breeding for BFT in pigs.

Differences in branch hydraulic architecture related to the aridity of growing sites and seed sources of coastal Douglas-fir saplings

To better understand hydraulic adaptations of coastal Douglas-fir (Pseudotsuga menziesii var. menziesii (Mirb.) Franco) to local climate, we examined genetic (G) and environmental (E) responses of branch hydraulic architecture of 7-year-old saplings from dry and wet climates of origin grown at a relatively dry and a relatively wet common garden site in western Oregon. We sampled 2 years of branch growth from three dry-source and three wet-source families grown at both sites (72 branches, total). Overall, only 4 of the 11 traits had significant genetic (G) effects, whereas 9 traits had significant environmental (E) effects (P < 0.05). Both dry and wet sources had higher leaf-specific conductance (kl) at the dry than the wet site, but the values were achieved by different mechanisms and driven by G × E effects for leaf area/sapwood area (Al/As), shoot length (L), specific conductivity (Ks) and leaf-specific conductivity (Kl). Dry sources achieved higher kl in the dry site through higher Kl (via a lower Al/As and no change in Ks) with no difference in L. Wet sources achieved higher kl at the dry site through no difference in Kl (via no effect on Al/As, despite decreases in Al and As, and lower Ks) with lower L. Vulnerability to embolism (measured as percentage loss of conductivity at 4 MPa) had no G effect but an E effect, with slightly lower values at the dry site. Specific leaf area had G and E effects, with lower values for the dry sources and site. There were no G or E effects on wood density. The different responses of dry and wet sources to site aridity suggest that populations are differentially adapted to the aridity of growing sites. Population variation in response to aridity should be considered when selecting seed sources for establishing forests for future climates.

Increased Frequency of Copy Number Variations Revealed by Array Comparative Genomic Hybridization in the Offspring of Male Mice Exposed to Low Dose-Rate Ionizing Radiation

There is very little information on the transgenerational or genetic effects of low dose-rate ionizing radiation. We report the detection of the transgenerational effects of chronic low dose-rate irradiation in mice, at the molecular level in the whole genome, using array comparative genomic hybridization technology. We observed that the number of the mice with de novo copy number variations (specifically, deletions) was significantly increased in the offspring of C57BL/6J male mice exposed to 20 mGy/day gamma-rays for 400 days (total dose: 8000 mGy), as compared to non-irradiated controls. We did not detect any difference in the size of the de novo deletions between the irradiated and the non-irradiated groups. An analysis of the life span of the offspring suggested a possibility that de novo copy-number variations may be associated with shorter life spans.

Characterization of the Common Genetic Basis Underlying Seed Hilum Size, Yield, and Quality Traits in Soybean

Developing high yielding cultivars with outstanding quality traits are perpetual objectives throughout crop breeding operations. Confoundingly, both of these breeding objectives typically involve working with complex quantitative traits that can be affected by genetic and environmental factors. Establishing correlations of these complex traits with more easily identifiable and highly heritable traits can simplify breeding processes. In this study, two parental soybean genotypes contrasting in seed hilum size, yield, and seed quality, as well as 175 F₉ recombinant inbred lines (RILs) derived from these parents, were grown in 3 years. The h² _b of four hilum size, two quality and two yield traits, ranged from 0.72 to 0.87. The four observed hilum size traits exhibited significant correlation (P < 0.05) with most of seed yield and quality traits, as indicated by correlation coefficients varying from -0.35 to 0.42, which suggests that hilum size could be considered as a proxy trait for soybean yield and quality. Interestingly, among 53 significant quantitative trait loci (QTLs) with logarithm of odds (LOD) values ranging from 2.51 to 6.69 and accounting for 6.40-16.10% of genetic variation, three loci encoding hilum size, qSH6.2, qSH8, and qSH10, colocated with QTLs for seed yield and quality traits, demonstrating that genes impacting seed hilum size colocalize in part with genes acting on soybean yield and quality. As a result of the breeding efforts and field observations described in this work, it is reasonable to conclude that optimizing hilum size through selection focused on a few QTLs may be useful for breeding new high yielding soybean varieties with favorable quality characteristics.

Genetic effects of non-ionizing electromagnetic fields

This is a review of the research on the genetic effects of non-ionizing electromagnetic field (EMF), mainly on radiofrequency radiation (RFR) and static and extremely low frequency EMF (ELF-EMF). The majority of the studies are on genotoxicity (e.g., DNA damage, chromatin conformation changes, etc.) and gene expression. Genetic effects of EMF depend on various factors, including field parameters and characteristics (frequency, intensity, wave-shape), cell type, and exposure duration. The types of gene expression affected (e.g., genes involved in cell cycle arrest, apoptosis and stress responses, heat-shock proteins) are consistent with the findings that EMF causes genetic damages. Many studies reported effects in cells and animals after exposure to EMF at intensities similar to those in the public and occupational environments. The mechanisms by which effects are induced by EMF are basically unknown. Involvement of free radicals is a likely possibility. EMF also interacts synergistically with different entities on genetic functions. Interactions, particularly with chemotherapeutic compounds, raise the possibility of using EMF as an adjuvant for cancer treatment to increase the efficacy and decrease side effects of traditional chemotherapeutic drugs. Other data, such as adaptive effects and mitotic spindle aberrations after EMF exposure, further support the notion that EMF causes genetic effects in living organisms.

Genes, geology and germs: gut microbiota across a primate hybrid zone are explained by site soil properties, not host species

Gut microbiota in geographically isolated host populations are often distinct. These differences have been attributed to between-population differences in host behaviours, environments, genetics and geographical distance. However, which factors are most important remains unknown. Here, we fill this gap for baboons by leveraging information on 13 environmental variables from 14 baboon populations spanning a natural hybrid zone. Sampling across a hybrid zone allowed us to additionally test whether phylosymbiosis (codiversification between hosts and their microbiota) is detectable in admixed, closely related primates. We found little evidence of genetic effects: none of host genetic ancestry, host genetic relatedness nor genetic distance between host populations were strong predictors of baboon gut microbiota. Instead, gut microbiota were best explained by the baboons' environments, especially the soil's geologic history and exchangeable sodium. Indeed, soil effects were 15 times stronger than those of host-population F_ST, perhaps because soil predicts which foods are present, or because baboons are terrestrial and consume soil microbes incidentally with their food. Our results support an emerging picture in which environmental variation is the dominant predictor of host-associated microbiomes. We are the first to show that such effects overshadow host species identity among members of the same primate genus.

Crossbreeding effects on growth and efficiency in beef cow-calf systems: evaluation of Angus, Caracu, Hereford and Nelore breed direct, maternal and heterosis effects

The objective of this study was to determine breed additive and heterosis effects on growth curves, total milk yield (TMY), calf weaning weight (WW), predicted energy intake (EI), and cow efficiency (CE) of purebred and crossbred beef cows raised in Southern Brazil. The data were from 175 purebred and crossbred cows representing eight genetic groups: Angus (A), Hereford (H), Nelore (N), A × H (AH), H × A (HA), A × N (AN), N × A (NA), and Caracu (C) × A (CA). Growth of the cows was modeled using the nonlinear Brody function and machine milking was used to assess TMY. WW was linearly adjusted to 210 d. EI was predicted with an equation in which the independent variables were estimates of parameters of the Brody function and TMY. The ratio of WW to EI estimated CE. Taurine–indicine heterosis effects were significant for all traits, and greater than those for taurine breed crosses. In general, crossbred cows were heavier at maturity, matured earlier, produced more milk, weaned heavier calves, and were predicted to consume more energy. Thus, they were more efficient than purebred cows, despite their greater predicted feed intake. Among the purebreds, A cows matured most rapidly, weighed the least at maturity, produced the most milk, weaned the heaviest calves, were predicted to consume the least energy; and were therefore most efficient among the breeds that were evaluated. These results are useful as inputs to bioeconomic models that can be used to predict productive and economic outcomes from crossbreeding and to facilitate recommendations for beef producers of southern Brazil and other similar subtropical climatic regions.

Identification of genetic associations of ECHS1 gene with milk fatty acid traits in dairy cattle

Our previous genome-wide association study identified 83 genome-wide significant SNPs and 20 novel promising candidate genes for milk fatty acids in Chinese Holstein. Among them, the enoyl-CoA hydratase, short chain 1 (ECHS1) and enoyl-CoA hydratase and 3-hydroxyacyl CoA dehydrogenase (EHHADH) genes were located near two SNPs and one SNP respectively, and they play important roles in fatty acid metabolism pathways. We herein validated whether the two genes have genetic effects on milk fatty acid traits in dairy cattle. By re-sequencing the full-length coding region, partially adjacent introns and 3000 bp up/downstream flanking sequences, we identified 12 SNPs in ECHS1: two in exons, four in the 3' flanking region and six in introns. The g.25858322C>T SNP results in an amino acid replacement from leucine to phenylalanine and changes the secondary structure of the ECHS1 protein, and single-locus association analysis showed that it was significantly associated with three milk fatty acids (P = 0.0002-0.0013). The remaining 11 SNPs were found to be significantly associated with at least one milk fatty acid (P = <0.0001-0.0040). Also, we found that two haplotype blocks, consisting of nine and two SNPs respectively, were significantly associated with eight milk fatty acids (P = <0.0001-0.0125). However, none of polymorphisms was observed in the EHHADH gene. In conclusion, our findings are the first to indicate that the ECHS1 gene has a significant genetic impact on long-chain unsaturated and medium-chain saturated fatty acid traits in dairy cattle, although the biological mechanism is still undetermined and requires further in-depth validation.

Matriline effects on metamorphic traits in a natural system in the European common frog (Rana temporaria)

Successful reproduction is an important determinant of the fitness of an individual and of the dynamics of populations. Offspring of the European common frog (Rana temporaria) exhibit a high degree of variability in metamorphic traits. However, environmental factors alone cannot explain this phenotypic variability, and the influence of genetic factors remains to be determined. Here, we tested whether the maternal genotype influences developmental time, body size, and body condition of offspring in a forest pond in Germany. We collected fertilized eggs from all 57 clutches deposited in the pond. We used multilocus genotypes based on seven microsatellite loci to assign metamorphosed offspring to mothers and to determine the number of fathers for a single matriline. We tested the influence of genetic effects in the same environment by comparing variability of metamorphic traits within and between full-sib offspring grouped to matrilines and tested whether multiple paternity increases the variability of metamorphic traits in a single matriline. The variability in size and body condition was higher within matrilines than between them, which indicates that these traits are more strongly influenced by environmental effects, which are counteracting underlying genetic effects. The developmental time varied considerably between matrilines and variability increased with the effective number of fathers, suggesting an additive genetic effect of multiple paternity. Our results show that metamorphic traits are shaped by environmental as well as genetic effects.

Epidemiological studies of atomic bomb radiation at the Radiation Effects Research Foundation

Epidemiological studies of people who were exposed to atomic bomb radiation and their children who were conceived after parental exposure to radiation (F₁) have investigated late health effects of atomic bomb radiation and its transgenerational effects. Those studies were initiated by the Atomic Bomb Casualty Commission (ABCC) in the 1950s. ABCC was reorganized to the Radiation Effects Research Foundation (RERF) in 1975, which continued the work of the ABCC. Follow-up of vital status and cause of death is performed for all RERF cohorts, including the atomic bomb survivors (the Life Span Study: LSS), in utero survivors, and the children of the survivors (F₁). Cancer incidence is investigated for accessible subpopulations of the cohorts. Health examinations for subcohorts of the LSS and in utero survivors are conducted as the Adult Health Study (AHS); a program of health examinations for a subcohort of the F₁ study is called the F₁ Offspring Clinical Study (FOCS). Participants of all clinical programs are asked to donate their blood and urine for storage and future biomedical investigations. Epidemiological studies have observed increased radiation risks for malignant diseases among survivors including those exposed in utero, and possible risks for some noncancer diseases. No increased risks due to parental exposure to radiation have been observed for malignancies or other diseases in F₁, but continuing investigations are required.

Determination of Genetic Effects of LIPK and LIPJ Genes on Milk Fatty Acids in Dairy Cattle

In our previous genome-wide association study (GWAS) on milk fatty acids (FAs) in Chinese Holstein, we discovered 83 genome-wide significant single nucleotide polymorphisms (SNPs) associated with milk FAs. Two of them were close to lipase family member K (LIPK) and lipase family member J (LIPJ), respectively. Hence, this study is a follow-up to verify whether the LIPK and LIPJ have significant genetic effects on milk FAs in dairy cattle. By re-sequencing the entire exons, and 3 kb of 5′ and 3′ flanking regions, two and seven SNPs were identified in LIPK and LIPJ, respectively, including a novel SNP, ss158213049726. With the Haploview 4.1 software, we found that five of the SNPs in LIPJ formed a haplotype block (D′ = 0.96 ~ 1.00). Single-locus association analyses revealed that each SNP in LIPK and LIPJ was significantly associated with at least one milk FA (p = < 1.00 × 10⁻⁴ ~ 4.88 × 10⁻²), and the haplotype-based association analyses showed significant genetic effects on nine milk FAs (p = < 1.00 × 10⁻⁴ ~ 3.98 × 10⁻²). Out of these SNPs, the missense mutation in LIPK gene, rs42774527, could change the protein secondary structure and function predicted by SOPMA, SIFT, and PROVEAN softwares. With the Genomatix software, we predicted that two SNPs, rs110322221 in LIPK and rs211373799 in LIPJ, altered the transcription factors binding sites (TFBSs), indicating their potential regulation on promoter activity of the genes. Furthermore, we found that both LIPK and LIPJ had relatively high expressions in the mammary gland. In conclusion, our research is the first to demonstrate that LIPK and LIPJ genes have significant associations with milk FAs, and the identified SNPs might be served as genetic markers to optimize breeding programs for milk FAs in dairy cattle. This research deserves in-depth verification.

Heritability of telomere variation: it is all about the environment!

Individual differences in telomere length have been linked to survival and senescence. Understanding the heritability of telomere length can provide important insight into individual differences and facilitate our understanding of the evolution of telomeres. However, to gain accurate and meaningful estimates of telomere heritability it is vital that the impact of the environment, and how this may vary, is understood and accounted for. The aim of this review is to raise awareness of this important, but much under-appreciated point. We outline the factors known to impact telomere length and discuss the fact that telomere length is a trait that changes with age. We highlight statistical methods that can separate genetic from environmental effects and control for confounding variables. We then review how well previous studies in vertebrate populations including humans have taken these factors into account. We argue that studies to date either use methodological techniques that confound environmental and genetic effects, or use appropriate methods but lack sufficient power to fully separate these components. We discuss potential solutions. We conclude that we need larger studies, which also span longer time periods, to account for changing environmental effects, if we are to determine meaningful estimates of the genetic component of telomere length.

This article is part of the theme issue ‘Understanding diversity in telomere dynamics'.

The Implications of Vitamin D Status During Pregnancy on Mother and her Developing Child

Pregnancy is a time of tremendous growth and physiological changes for mother and her developing fetus with lifelong implications for the child. The concert of actions that must occur so mother does not reject the foreign tissue of the fetus is substantial. There must be exquisite balance between maternal tolerance to these foreign proteins of paternal origin but also immune surveillance and function such that the mother is not immunocompromised. When this process goes awry, the mother may experience such pregnancy complications as preeclampsia and infections. Vitamin D deficiency affects these processes. Controversy continues with regard to the optimal daily intake of vitamin D, when sunlight exposure should be taken into account, and how to define sufficiency during such vulnerable and critical periods of development. The importance of vitamin D supplementation during pregnancy in preventing some of the health risks to the mother and fetus appears linked to achieving 25(OH)D concentrations >40 ng/mL, the beginning point of the plateau where conversion of the vitamin D metabolite 25(OH)D, the pre-hormone, to 1,25(OH)2D, the active hormone, is optimized. Throughout pregnancy, the delivery of adequate vitamin D substrate-through sunlight or supplement-is required to protect both mother and fetus, and when in sufficient supply, favorably impacts the epigenome of the fetus, and in turn, long term health. There is a growing need for future research endeavors to focus not only on critical period(s) from pre-conception through pregnancy, but throughout life to prevent certain epigenetic changes that adversely affect health. There is urgency based on emerging research to correct deficiency and maintain optimal vitamin D status. The impact of vitamin D and its metabolites on genetic signaling during pregnancy in both mother and fetus is an area of great activity and still in its early stages. While vitamin D repletion during pregnancy minimizes the risk of certain adverse outcomes (e.g., preterm birth, asthma, preeclampsia, and gestational diabetes), the mechanisms of how these processes occur are not fully understood. As we intensify our research efforts in these areas. it is only a matter of time that such mechanisms will be defined.

Genetic association of the ACACB gene with milk yield and composition traits in dairy cattle

Previously, we re-sequenced the whole genomes of eight Holstein bulls with high or low milk protein and fat percentage, and we detected two indels in the ACACB (acetyl-CoA carboxylase beta) gene that were polymorphic between the two groups. Thus, we considered ACACB as a promising candidate gene potentially affecting milk composition traits. Herein, we verified the genetic effects of ACACB on five milk traits in a Chinese Holstein population. We identified six SNPs in the 5'-promoter region, five in the 5'- untranslated region (UTR), 11 in exons, four in the 3'-UTR and three in the 3'-flanking region by re-sequencing the entire coding and regulatory regions of ACACB. One of these SNPs (ss1987461005) is reported here for the first time, and three of the SNPs (rs109482081, rs110819816 and rs109281947) were predicted to result in amino acid replacements. Genotype-phenotype association analyses showed that all the identified SNPs, except for ss1987461005, rs208919019 and rs134447911, were significantly associated with milk yield, fat yield, fat percentage, protein yield or protein percentage (P < 0.0001 to 0.0484). Linkage disequilibrium analyses were conducted among the identified SNPs to confirm the genetic associations. Two SNPs-rs135874354 (g.66218726T>C) and rs210928430 (g.66218117G>A)-were predicted to alter transcription factor binding sites in the 5'-promoter region of ACACB. A luciferase activity assay showed that the promoter activity of haplotype TG was significantly higher than that of CG (P = 0.0002) and that the promoter activity of haplotype TA was remarkably higher than that of CA (P = 7.4285E-09), showing that the T allele of rs135874354 increased promoter activity. Thus, rs135874354 was considered to be a potentially functional mutation. Our findings have, for the first time, profiled the genetic effect of ACACB on milk production traits in dairy cattle and revealed a potentially causal mutation that requires further the in-depth validation.

Genetic effects of released swimming crab (Portunus trituberculatus) on wild populations inferred from mitochondrial control region sequences

Along the coast of Shandong Province in China, an extensive hatchery-release programme has been conducted for more than 10 years. However, no information has been reported concerning the long-term effects on the wild population resulting from the release of large numbers of juveniles in Portunus trituberculatus. In this study, sequence variation of swimming crab P. trituberculatus based on the mitochondrial control region was investigated for 946 swimming crabs at the releasing sites from 2012 to 2014. The result showed that the wild P. trituberculatus was characterized by high genetic diversity indices, and not significantly different from the previous study. Low F_ST values were estimated among the groups of different years and different sites, which suggested no genetic differentiation found in the wild population after the stock enhancement programme. Hence, the long-term extensive hatchery release programme has not affected the genetic structure of wild P. trituberculatus populations along the coast of Shandong Province.

Heritability of white matter microstructure in late middle age: A twin study of tract-based fractional anisotropy and absolute diffusivity indices

There is evidence that differences among individuals in white matter microstructure, as measured with diffusion tensor imaging (DTI), are under genetic control. However, little is known about the relative contribution of genetic and environmental effects on different diffusivity indices among late middle-aged adults. Here, we examined the magnitude of genetic influences for fractional anisotropy (FA), and mean (MD), axial (AD), and radial (RD) diffusivities in male twins aged 56-66 years old. Using an atlas-based registration approach to delineate individual white matter tracts, we investigated mean DTI-based indices within the corpus callosum, 12 bilateral tracts and all these regions of interest combined. All four diffusivity indices had high heritability at the global level (72%-80%). The magnitude of genetic effects in individual tracts varied from 0% to 82% for FA, 0% to 81% for MD, 8% to 77% for AD, and 0% to 80% for RD with most of the tracts showing significant heritability estimates. Despite the narrow age range of this community-based sample, age was correlated with all four diffusivity indices at the global level. In sum, all diffusion indices proved to have substantial heritability for most of the tracts and the heritability estimates were similar in magnitude for different diffusivity measures. Future studies could aim to discover the particular set of genes that underlie the significant heritability of white matter microstructure. Hum Brain Mapp 38:2026-2036, 2017. © 2017 Wiley Periodicals, Inc.

Fisher's sons' effect in sexual selection: absent, intermittent or just low experimental power?

The Fisherian sexual selection paradigm has been called the null model of sexual selection. At its heart is the expectation of a genetic correlation (r_G ) between female preference and male trait. However, recent meta-analysis has shown estimated correlations are often extremely weak and not statistically significant. We show here that systematic failure of studies to reject the null hypothesis that r_G  = 0 is almost certainly due to the low power of most experimental designs used. We provide an easy way to assess experimental power a priori and suggest that current data make it difficult to definitively test a key component of the Fisher effect.

Self-organizing dominance hierarchies in a wild primate population

Linear dominance hierarchies, which are common in social animals, can profoundly influence access to limited resources, reproductive opportunities and health. In spite of their importance, the mechanisms that govern the dynamics of such hierarchies remain unclear. Two hypotheses explain how linear hierarchies might emerge and change over time. The 'prior attributes hypothesis' posits that individual differences in fighting ability directly determine dominance ranks. By contrast, the 'social dynamics hypothesis' posits that dominance ranks emerge from social self-organization dynamics such as winner and loser effects. While the prior attributes hypothesis is well supported in the literature, current support for the social dynamics hypothesis is limited to experimental studies that artificially eliminate or minimize individual differences in fighting abilities. Here, we present the first evidence supporting the social dynamics hypothesis in a wild population. Specifically, we test for winner and loser effects on male hierarchy dynamics in wild baboons, using a novel statistical approach based on the Elo rating method for cardinal rank assignment, which enables the detection of winner and loser effects in uncontrolled group settings. Our results demonstrate (i) the presence of winner and loser effects, and (ii) that individual susceptibility to such effects may have a genetic basis. Taken together, our results show that both social self-organization dynamics and prior attributes can combine to influence hierarchy dynamics even when agonistic interactions are strongly influenced by differences in individual attributes. We hypothesize that, despite variation in individual attributes, winner and loser effects exist (i) because these effects could be particularly beneficial when fighting abilities in other group members change over time, and (ii) because the coevolution of prior attributes and winner and loser effects maintains a balance of both effects.

Transcriptome Alterations In X-Irradiated Human Gingiva Fibroblasts

Ionizing radiation is known to induce genomic lesions, such as DNA double strand breaks, whose repair can lead to mutations that can modulate cellular and organismal fate. Soon after radiation exposure, cells induce transcriptional changes and alterations of cell cycle programs to respond to the received DNA damage. Radiation-induced mutations occur through misrepair in a stochastic manner and increase the risk of developing cancers years after the incident, especially after high dose radiation exposures. Here, the authors analyzed the transcriptomic response of primary human gingival fibroblasts exposed to increasing doses of acute high dose-rate x rays. In the dataset obtained after 0.5 and 5 Gy x-ray exposures and two different repair intervals (0.5 h and 16 h), the authors discovered several radiation-induced fusion transcripts in conjunction with dose-dependent gene expression changes involving a total of 3,383 genes. Principal component analysis of repeated experiments revealed that the duration of the post-exposure repair intervals had a stronger impact than irradiation dose. Subsequent overrepresentation analyses showed a number of KEGG gene sets and WikiPathways, including pathways known to relate to radioresistance in fibroblasts (Wnt, integrin signaling). Moreover, a significant radiation-induced modulation of microRNA targets was detected. The data sets on IR-induced transcriptomic alterations in primary gingival fibroblasts will facilitate genomic comparisons in various genotoxic exposure scenarios.

A post-GWAS confirming the SCD gene associated with milk medium- and long-chain unsaturated fatty acids in Chinese Holstein population

The stearoyl-CoA desaturase (delta-9-desaturase) gene encodes a key enzyme in the cellular biosynthesis of monounsaturated fatty acids. In our initial genome-wide association study (GWAS) of Chinese Holstein cows, 19 SNPs fell in a 1.8-Mb region (20.3-22.1 Mb) on chromosome 26 underlying the SCD gene and were highly significantly associated with C14:1 or C14 index. The aims of this study were to verify whether the SCD gene has significant genetic effects on milk fatty acid composition in dairy cattle. By resequencing the entire coding region of the bovine SCD gene, a total of six variations were identified, including three coding variations (g.10153G>A, g.10213T>C and g.10329C>T) and three intronic variations (g.6926A>G, g.8646G>A and g.16158G>C). The SNP in exon 3, g.10329C>T, was predicted to result in an amino acid replacement from alanine (GCG) to valine (GTG) in the SCD protein. An association study for 16 milk fatty acids using 346 Chinese Holstein cows with accurate phenotypes and genotypes was performed using the mixed animal model with the proc mixed procedure in sas 9.2. All six detected SNPs were revealed to be associated with six medium- and long-chain unsaturated fatty acids (P = 0.0457 to P < 0.0001), specifically for C14:1 and C14 index (P = 0.0005 to P < 0.0001). Subsequently, strong linkage disequilibrium (D' = 0.88-1.00) was observed among all six SNPs in SCD and the five SNPs (rs41623887, rs109923480, rs42090224, rs42092174 and rs42091426) within the 1.8-Mb region identified in our previous GWAS, indicating that the significant association of the SCD gene with milk fatty acid content traits reduced the observed significant 1.8-Mb chromosome region in GWAS. Haplotype-based analysis revealed significant associations of the haplotypes encompassing the six SCD SNPs and one SNP (rs109923480) in a GWAS with C14:1, C14 index, C16:1 and C16 index (P = 0.0011 to P < 0.0001). In summary, our findings provide replicate evidence for our previous GWAS and demonstrate that variants in the SCD gene are significantly associated with milk fatty acid composition in dairy cattle, which provides clear evidence for an increased understanding of milk fatty acid synthesis and enhances opportunities to improve milk-fat composition in dairy cattle.

Linking Gamma-H2AX Foci and Cancer in Rat Skin Exposed to Heavy Ions and Electron Radiation

This study uses acute doses of three test radiations, [Ar ions (L = 125 keVμ), Ne ions (L = 25 keVμ) and electron radiation] to examine a potential quantitative link between rat skin cancer induction and gamma-H2AX foci in rat keratinocytes exposed in vitro to radiations with comparable L values. Theory provided a testable link between cancer yield and gamma-H2AX foci yields: YCa(D,L)rat = (NF)2YAX(D,L)keratinocyte (eqn 1), where YCa(D,L) is cancers(rat) at 1.0 y, YAX(D,L) is in vitro gamma-H2AX foci(keratinocyte) , D is radiation dose, L is linear energy transfer, N is irradiated keratinocytes in vivo, and F is the error rate of end joining. An explicit expression for cancer yield was derived based on cancers arising in the ion track region in proportion to D and L (first term) and independently in proportion to D in the delta ray region in between the ion tracks (second term): YCa(D,L) = CCaLD + BCaD (eqn 1a). Parameters quantified include: CCa = 0.000589 ± 0.000150 cancers-micron[rat(kev)Gy]; BCa = 0.0088 ± 0.0035 cancers(ratGy), F = (8.18 ± 0.91) × 10; N = (8.8 ± 1.2) × 10 and (NF)2 = 0.036 ± 0.006 cancer keratinocyte(rat H2AX foci). Verification of eqns (1) and (1a) and the constancy of F support the hypothesis that end-rejoining errors play a major role in radiation carcinogenesis in rat skin. Cancer yields per rat were consistently predictable based on gamma-H2AX foci yields in keratinocytes in vitro such that 27.8 H2AXfoci(keratinocyte) predicted 1.0 cancer(rat) at 1 y.

Intersubject variability of and genetic effects on the brain's functional connectivity during infancy

Infancy is a period featuring a high level of intersubject variability but the brain basis for such variability and the potential genetic/environmental contributions remain largely unexplored. The assessment of the brain's functional connectivity during infancy by the resting state functional magnetic resonance imaging (rsfMRI) technique (Biswal et al., 1995) provides a unique means to probe the brain basis of intersubject variability during infancy. In this study, an unusually large typically developing human infant sample including 58 singletons, 132 dizygotic twins, and 98 monozygotic twins with rsfMRI scans during the first 2 years of life was recruited to delineate the spatial and temporal developmental patterns of both the intersubject variability of and genetic effects on the brain's functional connectivity. Through systematic voxelwise functional connectivity analyses, our results revealed that the intersubject variability at birth features lower variability in primary functional areas but higher values in association areas. Although the relative pattern remains largely consistent, the magnitude of intersubject variability undergoes an interesting U-shaped growth during the first 2 years of life. Overall, the intersubject variability patterns during infancy show both adult-like and infant-specific characteristics (Mueller et al., 2013). On the other hand, age-dependent genetic effects were observed showing significant but bidirectional relationships with intersubject variability. The temporal and spatial patterns of the intersubject variability of and genetic contributions to the brain's functional connectivity documented in this study shed light on the largely uncharted functional development of the brain during infancy.

Estimating directional epistasis

Epistasis, i.e., the fact that gene effects depend on the genetic background, is a direct consequence of the complexity of genetic architectures. Despite this, most of the models used in evolutionary and quantitative genetics pay scant attention to genetic interactions. For instance, the traditional decomposition of genetic effects models epistasis as noise around the evolutionarily-relevant additive effects. Such an approach is only valid if it is assumed that there is no general pattern among interactions—a highly speculative scenario. Systematic interactions generate directional epistasis, which has major evolutionary consequences. In spite of its importance, directional epistasis is rarely measured or reported by quantitative geneticists, not only because its relevance is generally ignored, but also due to the lack of simple, operational, and accessible methods for its estimation. This paper describes conceptual and statistical tools that can be used to estimate directional epistasis from various kinds of data, including QTL mapping results, phenotype measurements in mutants, and artificial selection responses. As an illustration, I measured directional epistasis from a real-life example. I then discuss the interpretation of the estimates, showing how they can be used to draw meaningful biological inferences.

Genetic variation in alkaloid accumulation in leaves of Nicotiana

Alkaloids are plant secondary metabolites that are widely distributed in Nicotiana species and contribute greatly to the quality of tobacco leaves. Some alkaloids, such as nornicotine and myosmine, have adverse effects on human health. To reduce the content of harmful alkaloids in tobacco leaves through conventional breeding, a genetic study of the alkaloid variation among different genotypes is required. In this study, alkaloid profiles in leaves of five Nicotiana tabacum cultivars and Nicotiana tomentosiformis were investigated. Six alkaloids were identified from all six genotypes via gas chromatograph-mass spectrometry (GC-MS). Significant differences in alkaloid content were observed both among different leaf positions and among cultivars. The contents of nornicotine and myosmine were positively and significantly correlated (R(2)=0.881), and were also separated from those of other alkaloids by clustering. Thus, the genotype plays a major role in alkaloid accumulation, indicating a high potential for manipulation of alkaloid content through traditional breeding.

Genetic analysis of reaction time variability: room for improvement?

BACKGROUND

Increased reaction time variability (RTV) on cognitive tasks requiring a speeded response is characteristic of several psychiatric disorders. In attention deficit hyperactivity disorder (ADHD), the association with RTV is strong phenotypically and genetically, yet high RTV is not a stable impairment but shows ADHD-sensitive improvement under certain conditions, such as those with rewards. The state regulation theory proposed that the RTV difference score, which captures change from baseline to a rewarded or fast condition, specifically measures 'state regulation'. By contrast, the interpretation of RTV baseline (slow, unrewarded) scores is debated. We aimed to investigate directly the degree of phenotypic and etiological overlap between RTV baseline and RTV difference scores. Method We conducted genetic model fitting analyses on go/no-go and fast task RTV data, across task conditions manipulating rewards and event rate, from a population-based twin sample (n=1314) and an ADHD and control sibling-pair sample (n=1265).

RESULTS

Phenotypic and genetic/familial correlations were consistently high (0.72-0.98) between RTV baseline and difference scores, across tasks, manipulations and samples. By contrast, correlations were low between RTV in the manipulated condition and difference scores. A comparison across two different go/no-go task RTV difference scores (slow-fast/slow-incentive) showed high phenotypic and genetic/familial overlap (r = 0.75-0.83).

CONCLUSIONS

Our finding that RTV difference scores measure largely the same etiological process as RTV under baseline condition supports theories emphasizing the malleability of the observed high RTV. Given the statistical shortcomings of difference scores, we recommend the use of RTV baseline scores for most analyses, including genetic analyses.

Serotonin transporter gene variation, infant abuse, and responsiveness to stress in rhesus macaque mothers and infants

A functional polymorphism in the promoter region of the serotonin transporter (5-HTTLPR) gene has been associated with variation in anxiety and hypothalamus-pituitary-adrenal (HPA) axis function in humans and rhesus macaques. Individuals carrying the short allele are at a higher risk for developmental psychopathology, and this risk is magnified in short allele carriers who have experienced early life stress. This study investigated the relationship between 5-HTTLPR allelic variation, infant abuse, and behavioral and hormonal responses to stress in rhesus macaques. Subjects were 10 abusive mothers and their infants, and 10 nonabusive mother-infant pairs. Mothers and infants were genotyped for the rh5-HTTLPR, and studied in the first 6 months of infant life. For mothers and infants, we measured social group behavior, behavioral responses to handling procedures, and plasma concentrations of ACTH and cortisol under basal conditions and in response to stress tests. The proportion of individuals carrying the short rh5-HTTLPR allele was significantly higher among abusive mothers than controls. Among mothers and infants, the short allele was associated with higher basal cortisol levels and greater hormonal stress responses in the infants. In addition, infants who carried the short rh5-HTTLPR allele had higher anxiety scores than infants homozygous for the long allele. The rh5-HTTLPR genotype also interacted with early adverse experience to impact HPA axis function in the infants. These results are consistent with those of previous studies which demonstrate associations between serotonergic activity and anxiety and stress reactivity, and add additional evidence suggesting that genetic variation in serotonergic function may contribute to the occurrence of abusive parenting in rhesus macaques and modulate emotional behavior and HPA axis function.

A developmental twin study of symptoms of anxiety and depression: evidence for genetic innovation and attenuation

BACKGROUND

Little is known about the pattern of genetic and environmental influences on symptoms of anxiety and depression (SxAnxDep) from childhood to early adulthood.MethodParental- and self-reported levels of SxAnxDep were assessed at ages 8-9, 13-14, 16-17 and 19-20 years in 2508 twins from the Swedish Twin Study of Child and Adolescent Development (TCHAD). Analysis conducted using the Mx program included SxAnxDep by parental and self-report.

RESULTS

The best-fit model revealed one genetic risk factor for SxAnxDep acting at ages 8-9, 13-14, 16-17 and 19-20, and new sets of genetic risk factors 'coming on line' in early adolescence, late adolescence and early adulthood. Together, these genetic factors were very strong influences on the levels of SxAnxDep reported in common by parents and twins with heritability estimates, correcting for rater- and time-specific effects, ranging from 72% to 89%. The first genetic factor, which accounted for 72% of the variance in SxAnxDep at ages 8-9, attenuated sharply in influence, accounting for only 12% of the variance by ages 19-20. No evidence was found for shared environmental influences. Although not statistically significant, the correlation between genetic risk factors for SxAnxDep in males and females declined with advancing age.

CONCLUSIONS

Genetic effects on SxAnxDep are developmentally dynamic from middle childhood to young adulthood, demonstrating both genetic innovation and genetic attenuation. The attenuation might explain the low levels of continuity observed for anxiety and depressive disorders from childhood to adulthood. Differences in genetic risk factors for SxAnxDep in males and females may increase during development.