The genomics of exceptional longevity in rockfishes refine genetic foundations of human lifespan variation

Longevity is a defining, heritable trait that varies dramatically between species. To resolve the genetic regulation of this trait, we have mined genomic variation in rockfishes, ranging in longevity from 11 to over 205 years. Shifts in rockfish longevity occurred multiple times independently, and in a short evolutionary time frame, thus empowering convergence analyses. Our analyses reveal a common network of genes under convergent restricted evolution in long-lived lineages, encompassing established aging regulators such as insulin-signaling, yet also identify flavonoid (aryl-hydrocarbon) metabolism as a novel pathway modulating longevity. Further, these genes were used to refine human longevity GWAS, identifying the aryl-hydrocarbon metabolism pathway to be significantly associated with the 99th percentile of human longevity, independently validating its importance and conservation. This evolutionary intersection highlights a novel, conserved genetic architecture that associates with the evolution of longevity across vertebrates and provides actionable targets for research into lifespan and healthspan modulation.

Infants' attention to eyes is an independent, heritable trait predicting later verbal competence

From birth, infants orient preferentially to faces, and when looking at the face, they attend primarily to eyes and mouth — two areas that convey different types of information. Here, in a sample of 535 5-month-old infant twins, we assessed eye (relative to mouth) preference in early infancy. Eye preference was independent from all other concurrent traits measured, and had a moderate-to-high contribution from genetic influences (A = .57; 95% CI: .45, .66). Preference for eyes over mouth at 5 months predicted higher parent ratings of verbal competence in toddlerhood, but did not predict autistic traits. These results suggest that variation in eye looking reflects a type of biological niche picking emerging before infants can select their environments by other means (crawling or walking).

PSI-15 Embryo viability based upon energy

The objective of this study was to analyze embryo energy release and whether or not it is indicative of survivability upon successful implantation. In both bovine and equine reproduction, fertility is a lowly heritable trait that has an exceedingly large financial impact on the ability to grow genetic lines. In order to increase pregnancy rates, producers must have access to accurate decision-making tools. Nineteen (n = 19) fertilized bovine embryos collected via flushing by licensed veterinarian, Dr. Russell Killingsworth, DVM, in Shamrock, TX, were assessed for energy release using amplification of video with a Nikon Camera and Iolight Microscope. Once embryos were flushed, they were filmed for a thirty-five (35) second observation period. Embryo dimensions were then taken using Image J software. Embryo release of energy was humanly perceptible and measurable by changes in their morphological dimensions. Measurements of significance were taken on the embryo intercellular mass area (ICM), total embryo area, and on the vertical, diagonal, and horizontal axis of the sub-zonal distance, or the distance between the zona pellucida and outer edge of the ICM. All measurements were taken in microns. Once embryos were successfully measured, all were transferred into recipients. Significant findings presented that embryos with a greater ICM, total embryo area, and sub-zonal vertical, diagonal, and horizontal distance established pregnancies more frequently than embryos with less momentous differences in distance (P < 0.05). This research has shown the relationship between embryo energy and pregnancy had a significance of determining pregnancy viability. This has therefore resulted in enhanced prediction of embryo transfer techniques based on embryo quality making pregnancy rates for producers more predictable and consistent.

The effect of maternal smoking on offspring smoking is unrelated to heritable personality traits or initial subjective experiences

Introduction Maternal smoking is a risk factor for offspring smoking. Lifetime maternal smoking vs. prenatal tobacco exposure (PTE) appear to act through different mechanisms. This study tested the hypothesis that maternal smoking measures’ effects on offspring smoking could be attributable to hereditary mechanisms: personality traits (novelty-seeking, impulsivity, neuroticism, self-esteem) and initial subjective smoking experiences (pleasurable, unpleasurable, dizziness). Methods Data were drawn from the Social and Emotional Contexts of Adolescent Smoking Patterns (SECASP) study, an 8-year longitudinal study of 9 th or 10 th graders at baseline (≈age 15) who experiment with smoking (<100 lifetime cigarettes; N=594) at baseline. Young adult smoking frequency at the 8-year follow-up (≈age 23) was examined as a function of baseline characteristics (heritable trait, maternal smoking, PTE, sex) and baseline smoking frequency and nicotine dependence. Structural equation models determined whether inclusion of each heritable trait among offspring confounded the effects of maternal smoking (PTE or maternal smoking) on offspring smoking and nicotine dependence. Results Impulsiveness was associated with intermediate adolescent smoking frequency (B=0.135, SD=0.043 p=0.002) and nicotine dependence (B=0.012, SD=0.003, p<0.001). Unpleasurable first experience (B=0.886, SD=0.374, p=0.018) and dizziness (B=0.629, SD=0.293, p=0.032) showed a trend with intermediate smoking frequency that was non-significant after correcting for multiple comparisons. These traits did not confound maternal smoking’s effects. Conclusions None of the heritable traits examined in this model explained the effect of maternal smoking measures on adolescence or young adulthood offspring smoking. Further research is needed to elucidate the mechanism by which PTE and maternal smoking are linked to offspring smoking.

The epiallelic potential of transposable elements and its evolutionary significance in plants

DNA provides the fundamental framework for heritability, yet heritable trait variation need not be completely ‘hard-wired’ into the DNA sequence. In plants, the epigenetic machinery that controls transposable element (TE) activity, and which includes DNA methylation, underpins most known cases of inherited trait variants that are independent of DNA sequence changes. Here, we review our current knowledge of the extent, mechanisms and potential adaptive contribution of epiallelic variation at TE-containing alleles in this group of species. For the purpose of this review, we focus mainly on DNA methylation, as it provides an easily quantifiable readout of such variation. The picture that emerges is complex. On the one hand, pronounced differences in DNA methylation at TE sequences can either occur spontaneously or be induced experimentally en masse across the genome through genetic means. Many of these epivariants are stably inherited over multiple sexual generations, thus leading to transgenerational epigenetic inheritance. Functional consequences can be significant, yet they are typically of limited magnitude and although the same epivariants can be found in nature, the factors involved in their generation in this setting remain to be determined. On the other hand, moderate DNA methylation variation at TE-containing alleles can be reproducibly induced by the environment, again usually with mild effects, and most of this variation tends to be lost across generations. Based on these considerations, we argue that TE-containing alleles, rather than their inherited epiallelic variants, are the main targets of natural selection. Thus, we propose that the adaptive contribution of TE-associated epivariation, whether stable or not, lies predominantly in its capacity to modulate TE mobilization in response to the environment, hence providing hard-wired opportunities for the flexible exploration of the phenotypic space. This article is part of the theme issue ‘How does epigenetics influence the course of evolution?’

A study of the heterochronic sense/antisense RNA representation in florets of sexual and apomictic Paspalum notatum

Background Apomixis, an asexual mode of plant reproduction, is a genetically heritable trait evolutionarily related to sexuality, which enables the fixation of heterozygous genetic combinations through the development of maternal seeds. Recently, reference floral transcriptomes were generated from sexual and apomictic biotypes of Paspalum notatum, one of the most well-known plant models for the study of apomixis. However, the transcriptome dynamics, the occurrence of apomixis vs. sexual expression heterochronicity across consecutive developmental steps and the orientation of transcription (sense/antisense) remain unexplored. Results We produced 24 Illumina TruSeq®/ Hiseq 1500 sense/antisense floral transcriptome libraries covering four developmental stages (premeiosis, meiosis, postmeiosis, and anthesis) in biological triplicates, from an obligate apomictic and a full sexual genotype. De novo assemblies with Trinity yielded 103,699 and 100,114 transcripts for the apomictic and sexual samples respectively. A global comparative analysis involving reads from all developmental stages revealed 19,352 differentially expressed sense transcripts, of which 13,205 (68%) and 6147 (32%) were up- and down-regulated in apomictic samples with respect to the sexual ones. Interestingly, 100 differentially expressed antisense transcripts were detected, 55 (55%) of them up- and 45 (45%) down-regulated in apomictic libraries. A stage-by-stage comparative analysis showed a higher number of differentially expressed candidates due to heterochronicity discrimination: the highest number of differential sense transcripts was detected at premeiosis (23,651), followed by meiosis (22,830), postmeiosis (19,100), and anthesis (17,962), while the highest number of differential antisense transcripts were detected at anthesis (495), followed by postmeiosis (164), meiosis (120) and premeiosis (115). Members of the AP2, ARF, MYB and WRKY transcription factor families, as well as the auxin, jasmonate and cytokinin plant hormone families appeared broadly deregulated. Moreover, the chronological expression profile of several well-characterized apomixis controllers was examined in detail. Conclusions This work provides a quantitative sense/antisense gene expression catalogue covering several subsequent reproductive developmental stages from premeiosis to anthesis for apomictic and sexual P. notatum, with potential to reveal heterochronic expression between reproductive types and discover sense/antisense mediated regulation. We detected a contrasting transcriptional and hormonal control in apomixis and sexuality as well as specific sense/antisense modulation occurring at the onset of parthenogenesis.

If you work with phenology, you work with bud cold hardiness dynamics

<p>Budbreak is one of the most observed and studied phenological phases in perennial plants. Historically, two effects of temperature are used to model budbreak: the accumulation of heat units (forcing); and the accumulation of time spent at low temperatures (chilling). These two effects have a well-established negative correlation: the more chilling, the less forcing is required to reach budbreak. However, prediction of budbreak remains a challenge, as even artificial warming experiments do not match changes in observed budbreak timing during the past few decades of climate warming. The cold hardiness of buds is, however, largely ignored in estimations of timing to budbreak. Cold hardiness level fluctuates throughout the winter as temperatures change, constantly altering the initiation point of deacclimation. During budbreak assays, cold hardiness loss is extremely slow (low deacclimation rate) at low chill accumulation, and increases to a maximum at high chill accumulation. By standardizing deacclimation rates for each species based on the maximum observed, a deacclimation potential describes dormancy fulfillment. Our studies show that deacclimation rates vary at different temperatures demonstrating the effect of forcing is non-linear. We show that the concept of variable chilling requirements for satisfying dormancy (high chill vs. low chill) is largely erroneous and instead these phenotypes reflect previously unmeasured differences between species or genotypes regarding the interaction between cold hardiness state and deacclimation potential. Our studies show that forcing responses (maximum rates of deacclimation) are normally distributed within a species, and are a heritable trait. Three effects of temperature are thus necessary to describe contemporary phenology patterns as well as predict future impacts of climate change: the accumulation of chill, the forcing temperature response, and the cold hardiness of buds.</p>

PSXI-20 Milking collar activity data is associated with health events and feed intake in lactating Holstein cattle

Feed is the largest expense for dairy farms, thus feed efficiency is essential to the sustainability and future of the industry. Our objective was to evaluate the association of milking collar activity with feed intake and health status in lactating cows. Health status was classified for impact of three durations of time (overall, current, or post diagnosis) and as: healthy, mastitis, lame, multiple, or other. Activity data for 155 lactating cows with feed intake records were averaged across two-hour windows to obtain a daily two-hour average. A larger population (n > 1,600) was used to filter out sensor failures and normalize data. Sensor data were adjusted for parity and contemporary group creating adjusted sensor measure (ASM). Dry matter intake (DMI) was adjusted (aDMI) for metabolic body weight, days in milk, and energy sinks used to calculate residual feed intake. Associations between ASM and aDMI, DMI, or health were conducted in SAS9.4. An association of ASM with aDMI was identified (estimate = 0.1635 kg/log count of average activity in a 2-hour period; P < 0.0029). ASM was also associated with DMI (0.2329 kg/log count of average activity, P < 0.0007). ASM was associated with current and overall health timeframes (P < 0.0008 and P < 0.0001, respectively). When health, ASM, and their interaction were included in a model with the response variable aDMI, significant associations were found in the models, including current and overall health (current health: ASM and health: P < 0.0001, interaction: P < 0.0009; overall health: ASM, health, and interaction: P < 0.0001). These results indicate that milking collar data may be useful as a predictor of feed intake either directly or indirectly through detection of health events. Additional studies are needed to determine the predictive ability of collar activity data and the relationship between collar data and health, and to assess if collar activity is an environmental proxy or heritable trait.

PSI-10 Genetic parameters for soybean allergy response in divergently-selected pigs

Genetically selecting for improved animal resilience has become of great interest in modern livestock breeding. In this context, piglets experience a transitory allergic response to soybean proteins that has a negative impact on their growth and welfare. The main objective of this study was to determine whether soybean allergy response is a heritable trait, using divergently selected pig lines. The base generation pigs were generated from nine sire lines (primarily Yorkshire and Landrace) and two dam sources (Yorkshire × Chester White F1 and Landrace × Yorkshire F1). Soybean allergic response was measured, following a skin test protocol, on pigs that received a diet containing 28% soybean meal for 21 consecutive days post-weaning. The skin test was performed with an intradermal injection of soybean protein. Wheel and flare scores (ranging from 0 to 3) were assigned approximately 60 minutes post-injection. Based on the skin test total scores (i.e., the sum of the wheal and flair scores, ranging from 0 to 6), animals were selected to create two (a high and a low) soybean protein reacting lines, and bred within lines for nine generations. Phenotypes used in this study were measured on a total of 5,505 animals born from generations one to nine, in both high and low reacting lines. Significant systematic effects (P < 0.05) included in the statistical model were birth year, birth season, sex, and weaning weight (as a covariate). Genetic parameters for the skin test were estimated using a pedigree-based relationship matrix containing 9,201 animals, and a threshold animal mixed model. The genetic variance estimated for soybean allergy was 0.091, indicating that there is genetic variability in this trait. The heritability estimated for soybean allergy response was 0.139, which indicates that food allergy response is a heritable trait and can be improved through selective breeding.