Review: Opportunities and challenges for the genetic selection of dairy calf disease traits

Interest in dairy cow health continues to grow as we better understand health's relationship with production potential and animal welfare. Over the past decade, efforts have been made to incorporate health traits into national genetic evaluations. However, they have focused on the mature cow, with calf health largely being neglected. Diarrhoea and respiratory disease comprise the main illnesses with regard to calf health. Conventional methods to control calf disease involve early separation of calves from the dam and housing calves individually. However, public concern regarding these methods, and growing evidence that these methods may negatively impact calf development, mean the dairy industry may move away from these practices. Genetic selection may be a promising tool to address these major disease issues. In this review, we examined current literature for enhancing calf health through genetics and discussed alternative approaches to improve calf health via the use of epidemiological modelling approaches, and the potential of indirectly selecting for improved calf health through improving colostrum quality. Heritability estimates on the observed scale for diarrhoea ranged from 0.03 to 0.20, while for respiratory disease, estimates ranged from 0.02 to 0.24. The breadth in these ranges is due, at least in part, to differences in disease prevalence, population structure, data editing and models, as well as data collection practices, which should be all considered when comparing literature values. Incorporation of epidemiological theory into quantitative genetics provides an opportunity to better determine the level of genetic variation in disease traits, as it accounts for disease transmission among contemporaries. Colostrum intake is a major determinant of whether a calf develops either respiratory disease or diarrhoea. Colostrum traits have the advantage of being measured and reported on a continuous scale, which removes the issues classically associated with binary disease traits. Overall, genetic selection for improved calf health is feasible. However, to ensure the maximum response, first steps by any industry members should focus efforts on standardising recording practices and encouragement of uploading information to genetic evaluation centres through herd management software, as high-quality phenotypes are the backbone of any successful breeding programme.

SAS: Split antibiotic selection for identifying chaperones that improve protein solubility

Background

Heterologous expression of active, native-folded protein in Escherichia coli is critical in both academic research and biotechnology settings. When expressing non-native recombinant proteins in E. coli, obtaining soluble and active protein can be challenging. Numerous techniques can be used to enhance a proteins solubility, and largely focus on either altering the expression strain, plasmid vector features, growth conditions, or the protein coding sequence itself. However, there is no one-size-fits-all approach for addressing issues with protein solubility, and it can be both time and labor intensive to find a solution. An alternative approach is to use the co-expression of chaperones to assist with increasing protein solubility. By designing a genetic system where protein solubility is linked to viability, the appropriate protein folding factor can be selected for any given protein of interest. To this end, we developed a Split Antibiotic Selection (SAS) whereby an insoluble protein is inserted in-frame within the coding sequence of the hygromycin B resistance protein, aminoglycoside 7″-phosphotransferase-Ia (APH(7″)), to generate a tripartite fusion. By creating this tripartite fusion with APH(7″), the solubility of the inserted protein can be assessed by measuring the level of hygromycin B resistance of the cells.

Results

We demonstrate the functionality of this system using a known protein and co-chaperone pair, the human mitochondrial Hsp70 ATPase domain (ATPase70) and its co-chaperone human escort protein (Hep). Insertion of the insoluble ATPase70 within APH(7'') renders the tripartite fusion insoluble and results in sensitivity to hygromycin B. Antibiotic resistance can be rescued by expression of the co-chaperone Hep which assists in the folding of the APH(7'')-ATPase70-APH(7'') tripartite fusion and find that cellular hygromycin B resistance correlates with the total soluble fusion protein. Finally, using a diverse chaperone library, we find that SAS can be used in a pooled genetic selection to identify chaperones capable of improving client protein solubility.

Conclusions

The tripartite APH(7'') fusion links the in vivo solubility of the inserted protein of interest to hygromycin B resistance. This construct can be used in conjunction with a chaperone library to select for chaperones that increase the solubility of the inserted protein. This selection system can be applied to a variety of client proteins and eliminates the need to individually test chaperone-protein pairs to identify those that increase solubility.

Economic considerations of breeding for polledness versus disbudding in beef cattle

The domestication of animals has rendered horns less necessary for survival. Moreover, the use of polled and disbudded animals is interesting in order to avoid injuries of animals and handlers, among other advantages. We therefore conducted a comparative economic analysis of different traditional disbudding techniques versus selective breeding for polledness in Nelore cattle, the main beef breed of tropical systems in Brazil. The cost to obtain animals without horns was estimated in three different scenarios: disbudding with hot iron, disbudding with caustic paste, and phenotypic selection for polled animals. Price quotations of the materials were obtained in different states of the country and averaged. An initial frequency of horned animals of 92.16% was obtained based on the records of the Brazilian Association of Zebu Breeders. Selective breeding was found to be the best cost-effective scenario. This result differs from intensive production systems of dairy cattle in which traditional disbudding continues to be the best cost-effective scenario. The main explanation is the lack of difference in the price of Nelore semen from polled and horned bulls. Phenotypic selection for polled animals is the best cost-effective method, and it is in accordance with welfare practices. Care should be taken regarding the intensive use of few polled breeding animals in order to avoid inbreeding depression in other traits.

Estimating backfat depth, loin depth, and intramuscular fat percentage from ultrasound images in swine

Fast, accurate, and reliable estimates of backfat depth, loin depth, and intramuscular fat percentage in swine breeding stock are used to increase genetic improvement and farm profitability. The objective of this study was to develop an equation-based model for the estimation of swine backfat depth, loin depth, and intramuscular fat percentage estimates obtained from longitudinal ultrasound images. Images were collected from purebred Duroc (n = 230), purebred Large White (n = 154), and commercial (n = 190) pigs born in January 2021 at three farms located in North Carolina. An Exapad ultrasound machine captured longitudinal images across the 10th to 13th ribs at 182 (±12.8 SD) days of pig age. The total number of images processed for Duroc, Large White, and commercial pigs was 1 385, 928, and 1 168 images, respectively. To establish a standard measurement for model comparison, trained personnel following standard company procedures using the BioSoft Toolbox (v4.0.1.2; Biotronics Inc., Ames, IA) obtained backfat and loin depth measurements from the images. Longissimus muscle intramuscular fat percentage was predicted using near-infrared spectroscopy at approximately 22 h postmortem. Backfat and loin depth estimation were conducted only for commercial pigs (n = 190) while intramuscular fat estimation was conducted on all pigs (n = 574). Average backfat depth, loin depth, and intramuscular fat percentage were 14.6 (±2.6 SD) mm, 63.7 (±5.5 SD) mm, and 2.21 (±0.82 SD) %. Image analysis and estimation model development were conducted in MATLAB R2021a. Edge detection via the image gradient was applied to segment ultrasound images into backfat, loin, and rib regions. Segmented images were used to estimate backfat depth, loin depth, and loin intramuscular fat percentage. After image quality control and filtering, the image inclusion rate for each breed-trait combination ranged from 76 to 97%. All Duroc and commercial pigs and 97% of Large White pigs were represented by at least one image for trait estimation. Coefficient of determination of models for the estimation of backfat depth, loin depth, and intramuscular fat percentage were 0.58, 0.57, and 0.56, respectively. Root mean square error of backfat depth, loin depth, and intramuscular fat estimation were 1.65 mm, 3.58 mm, and 0.54%, respectively. Results demonstrate the feasibility of using ultrasound image gradient and an equation-based approach to estimate swine backfat and loin depth, and intramuscular fat percentage. This equation-based approach to estimate carcass traits in live swine can enhance genetic improvement.

Effect of selection for growth rate on the rabbit (Oryctolagus cuniculus) immune system and its response after experimental Staphylococcus aureus infection

The aim of the work was to evaluate if genetic selection for daily gain may affect the immune system. Two experiments were performed. The first one involved 80 rabbit females and their first two litters to explore the effect of selection on the ability of animals to maintain immune competence. Two generations from a line selected for average daily gain (ADG) were evaluated (VR19 generation 19th, n = 43; VR37 generation 37th, n = 37). In females, the effect of selection and its interaction with physiological state were not significant for any trait. In litters, the selection criterion increased the granulocyte to lymphocyte ratio. The second experiment involved 73 19-week-old females (VR19, n = 39; VR37, n = 34) to explore the effect of genetic selection on immune response after S. aureus infection. The VR37 rabbit females had lower counts for total lymphocytes, CD5+, CD4+, CD8+, CD25+, monocytes, the CD4+/CD8+ ratio and platelets than those of VR19 (-14, -21, -25, -15, -33, -18, -11 and -11%, respectively; P < 0.05). VR37 had less erythema (-8.4 percentage points; P < 0.05), fewer nodules (-6.5 percentage points; P < 0.05) and a smaller nodule size (-0.65 cm3 on 7 day post-inoculation; P < 0.05) compared to VR19. Our study suggests that genetic selection for average daily gain does not negatively affect the maintenance of a competent immune system or the ability to establish immune response. It seems that such selection may improve the response to S. aureus infections.

Water scarcity can be a critical limitation for the poultry industry

Water is essential for various physiological functions and the productive performance of animals. However, with climatic uncertainties exacerbated by climatic changes, water could become a scarce nutrient shortly. This is already the case in one-third of the world's countries, which are under medium to high levels of water stress. Accordingly, with the growth of poultry production, the availability of water at ad libitum level may not be guaranteed, and birds can be under water restriction for variable periods. Thus, this article aims at attracting the attention of animal scientists to the freshwater shortage challenge, as well as shedding light on (1) the effects of climate change on the freshwater resources; (2) the effects of limited access to water, either by water restriction (WR) or water deprivation (WD), on the growth, feed efficiency, and meat quality of broilers; (3) the effects of different levels of WR or WD on egg production and egg quality traits; (4) the effects of limited access to water on the health, behavior, and welfare status of chickens; and (5) suggested solutions to overcome future water shortage challenges. In conclusion, severe water shortage/restriction might negatively influence the productivity, behavior, and welfare status of the chickens. Genetic background and environmental conditions may interact with the WR effects. The tolerance level of indigenous chicken breeds to limited water access could provide the knowhow to potential solutions to overcome water shortage problems. Selection of chicken strains with high tolerance capacity to thirst and limited water access regimens may be a sustainable solution for solving water scarcity problems.

Transgenerational endocrine disruptor effects of cadmium in zebrafish and contribution of standing epigenetic variation to adaptation

Evidence has emerged that environmentally-induced epigenetic changes can have long-lasting effects on gene transcription across generations. These recent findings highlight the need to investigate the transgenerational impacts of pollutants to assess their long term effects on populations. In this study, we investigated the transgenerational effect of cadmium on zebrafish across 4 generations. A first whole methylome approach carried out on fish of the first two generations led us to focus our investigations on the estradiol receptor alpha gene (esr1). We observed a sex-dependent transgenerational inheritance of Cd-induced DNA methylation changes up to the last generation. These changes were associated with single nucleotide polymorphisms (SNPs) that were themselves at the origin of the creation or deletion of methylation sites. Thus, Cd-induced genetic selection gave rise to DNA methylation changes. We also analyzed the transcription level of various sections of esr1 as well as estrogen responsive genes. While Cd triggered transgenerational disorders, Cd-induced epigenetic changes in esr1 contributed to the rapid transgenerational adaptation of fish to Cd. Our results provide insight into the processes underpinning rapid adaptation and highlight the need to maintain genetic diversity within natural populations to bolster the resilience of species faced with the global environmental changes.

Review: Use of assisted reproduction in seasonal-calving dairy herds

A unique aspect of seasonal-calving pasture-based systems of dairy production is the intense focus placed on achieving a concentrated herd-calving period in late winter and early spring. Hence, excellent reproductive performance is required during a short breeding period. A concentrated calving period also produces a problem in the form of a large number of male dairy calves being born at the same time; as these calves have little economic value due to poor beef merit, they present a potential welfare concern. A solution exists in the form of sex-sorted semen, but this is typically associated with poorer pregnancy per artificial insemination, and hence, the use of sex-sorted semen must be carefully considered. The logical strategy to use sex-sorted semen is to target the best genetic merit dams in the herd to generate replacement heifers, thereby accelerating herd genetic gain. On the other hand, if all dairy farmers adopt such a strategy, there will be a corresponding reduction in elite genetic merit male dairy calves being born, potentially reducing availability of the next generation of future bulls to be used for artificial insemination. Use of in vitro embryo production on elite dairy donors could avoid this problem by acting as a multiplier, potentially in tandem with Y-sorted semen to skew the offspring sex ratio towards more male calves. Use of sex-sorted semen on the best genetic merit dams can also facilitate a marked increase in the usage of beef semen on any dams that are deemed unsuitable for sex-sorted semen. The use of "beef on dairy" requires selection of beef bulls that generate offspring with traits that meet the key requirements of both the dairy farmer (e.g., gestation length and calving ease) and the beef farmer that must be motivated to purchase the calves (e.g., growth rate, age at slaughter, carcass value). Beef breed dams that have elite genetic merit for these traits could also be considered for in vitro embryo production, potentially in tandem with Y-sorted semen, to facilitate genetic gain for the growing "beef-on-dairy" market. It is possible to transfer a beef embryo (75-100% beef breed genetics) into dairy dams that are not required to generate replacements, but this is likely to remain a niche practice as there are many barriers to widespread adoption. Such combinations of assisted reproduction have the potential to improve the efficiency and sustainability metrics of seasonal-calving pasture-based dairy herds.

Characteristics of growth, carcass and meat quality of sheep with different feed efficiency phenotypes

The objective was to evaluate the performance, carcass and meat quality of 40 lambs classified by RFI (residual feed intake) and RIG (residual intake and gain). Dry matter intake (DMI) was recorded to calculate the RFI and RIG, classified as efficient, moderately or inefficient. After the confinement period, they were slaughtered and the carcass and meat quality were determined. The efficient animals had DMI scores of 0.700 RFI and 0.400 kg/d RIG, lower than the inefficient ones with similar weight gain. The RFI efficient animals showed greater shear force, without effect in the RIG classification. In general, the variables analyzed were not influenced by RFI or RIG. Efficiency measures do not affect the carcass and meat quality of sheep, but they do have the advantage of identifying animals with lower feed consumption, making the system more efficient. However, as the dataset is limited to fully assess the effects, this manuscript can be used as preliminary results for future studies.

Cytochrome P450 polymorphism: From evolution to clinical use

The cytochromes P450s can be divided in two groups, those of high importance for endogenous functions being evolutionary quite stable and those participating in detoxification of drugs and other xenobiotics having less important endogenous functions. In the latter group extensive genetic diversity has been allowed and in addition this is of high importance for survival in different environments. The genetic polymorphisms in these genes have evolved to some extent based on dietary restrictions and environmental factors and have not been subject of conservation due to less importance for survival. In cases of high dietary selection events, gene multiplication and amplification events have been seen. The different variants in genes encoding drug metabolizing enzymes can be used as genetic biomarkers (pharmacogenomic labels) for adjustment of drug treatment leading to less adverse drug reactions and better response. Indeed, this has improved the use of personalized medicine, although the missing heredity seen based on twin studies indicates that there are indeed many more genetic variants to be discovered before one can achieve a satisfactory relationship between genotype and phenotype with respect to drug metabolism and toxicity.

Targeting improved resilience in Merino sheep - Correlations between immune competence and health and fitness traits

Resilience can be defined as the ability of an animal to remain productive in the face of diverse environmental challenges. Several factors contribute to an animal's resilience including its ability to resist disease, cope with climatic extremes and respond to stressors. Immune competence, a proxy trait for general disease resistance, is expected to contribute to an animal's resilience. This research aimed to develop a practical method to assess immune competence in Merino sheep which would not restrict the future sale of tested animals, and to estimate genetic parameters associated with the novel trait. We also aimed to explore associations between immune competence and other industry-relevant disease resistance and fitness-related traits and to assess the ability of immune competence phenotypes to predict health outcomes. Here, the ability of Merino wethers (n = 1 339) to mount both an antibody-mediated and cell-mediated immune response was used to define their immune competence phenotype. For that purpose, antigens in a commercial vaccine were administered at the commencement of weaning and their responses were assessed. Univariate sire models were used to estimate variance components and heritabilities for immune competence and its component traits. Bivariate sire models were used to estimate genetic correlations between immune competence and a range of disease resistance and fitness-related traits. The heritability of immune competence and its component traits, antibody-mediated immune response and cell-mediated immune response were estimated at 0.49 ± 0.14, 0.52 ± 0.14 and 0.36 ± 0.11, respectively. Immune competence was favourably genetically correlated with breech flystrike incidence (-0.44 ± 0.39), worm egg count (-0.19 ± 0.23), dag score (-0.26 ± 0.31) and fitness compromise (-0.35 ± 0.24) but not fleece rot (0.17 ± 0.23). Results suggest that selection for immune competence has the potential to improve the resilience of Merino sheep; however, due to the large standard errors associated with correlation estimates reported here, further studies will be required in larger populations to validate associations between immune competence and disease resistance and fitness traits in Australian Merino sheep.

Multi-tissue RNAseq reveals genetic and temporal differences in acute response to viral (IHNV) infection among three selected lines of rainbow trout with varying resistance

Utilizing RNA-seq, this study compared the transcriptomic responses of three improved strains (VSel, PSel, and CSel) of rainbow trout fry during acute stages of challenge with infectious hematopoietic necrosis virus (IHNV). The VSel strain has been selected for resistance against the specific strain of IHNV used in our challenge, PSel has undergone selection for utilization of plant-protein based feeds and previously has shown elevated non-specific disease resistance despite no disease related selection pressures, and the final strain, CSel, is a commercial strain that has been domesticated for several years but has not been selected for specific viral disease resistance. Following a 21-day IHNV challenge, Kaplan-Meier survival estimator curves and cumulative percent mortality (CPM) showed significant differences in IHNV resistance across strains: VSel - 19.3 ± 5.0%, PSel - 67. ± 3.03%, CSel - 94.6 ± 4.1% CPM. To evaluate acute responses to IHNV infection, whole blood, as well as samples from the kidney, liver, and intestine, were collected at 0, 4, 12, 24, and 48 h post infection (hpi). Serum lysozyme activity, a marker of non-specific innate immunity, showed strain and temporal effects during the acute infection phase with PSel showing the highest activity at 0 and 48 hpi. Differential gene expression responses were detected, with varying degrees, in all tissues, both between strains, as well as across acute timepoints within strains. The VSel strain showed upregulation for a particular subset of viral recognition genes during early infection timepoints and rather limited upregulation of immune genes later, while maintaining and reactivating metabolic pathways. The CSel strain showed a downregulation of metabolic related genes and a limited upregulation of immune genes, while the PSel strain showed similar downregulation of metabolic genes during acute infection, yet when compared to the CSel strain, showed a more robust innate immune response. Evaluation of upregulated immune response genes, as well as interferon-related genes showed the PSel strain to have the greatest number of uniquely upregulated immune genes in both the kidney and intestine, with CSel and PSel showing a similar number of such genes upregulated in liver. A moderate number of immune response genes were shared between PSel and CSel in all tissues, though both PSel and VSel showed a high number of uniquely overexpressed immune response genes in the kidney, and PSel showed the highest number of uniquely upregulated interferon related genes in the intestine. Overall, the VSel response was unique from the CSel with very little overlap in activated immune responses. Findings from this study highlight the disparity in IHNV resistance among genetic strains of rainbow trout, while identifying molecular mechanisms underlying differences in disease phenotypes. Furthermore, our results on trout strains with distinct selection backgrounds yields comparative insights into the adaptive gains brought about by selection programs for pathogen-specific disease resistance, as well as the non-specific immune enhancement associated with selection for utilization of plant-based diets.

Ocean Acidification Alters Developmental Timing and Gene Expression of Ion Transport Proteins During Larval Development in Resilient and Susceptible Lineages of the Pacific Oyster (Crassostrea gigas)

Ocean acidification (OA) adversely impacts initial shell formation of bivalve larvae. Despite many studies observing large differences in developmental success between distinct genetic populations of bivalves exposed to OA, few studies have investigated the molecular mechanisms that enable resilient larvae to build their initial shell in aragonite-undersaturated conditions. This knowledge is key to their ecological and economical conservation. Herein, we used a genetic-selection program for Crassostrea gigas to produce a resilient and susceptible larval lineage to OA. The resilient and susceptible larvae were sampled every 3 h over a 24-h period in aragonite-undersaturated and control conditions. The susceptible lineage failed to develop a larval shell in aragonite-undersaturated conditions, whereas 52% of the resilient lineage developed to D-larvae by 24 h post fertilisation. We measured the expression of 23 genes involved in initial shell formation by RT-qPCR, which revealed significant genotype-by-time and environment-by-time interactions for the transcription of these genes. Aragonite-undersaturated conditions upregulated a single gene encoding a protein involved in ion transport, Na⁺ K⁺ ATPase, in both the resilient and susceptible lineage. These results were corroborated by a second experiment involving 25 pair-mated C. gigas families exposed to aragonite-undersaturated and control conditions. Our findings indicate C. gigas have a fixed capacity to modulate expression of genes involved in initial shell formation in response to OA. Thus, phenotypic differences to OA between the resilient and susceptible lineage are likely explained by other cellular processes, such as bioenergetics or protein translation.

Dual genetic selection of the theophylline riboswitch with altered aptamer specificity for caffeine

The aptamer domain of the theophylline riboswitch was randomized to generate a library containing millions of different variants. Dual genetic selection utilizing the cat-upp fusion gene was performed for the library, which successfully led to the identification of a caffeine-specific synthetic riboswitch. When a chloramphenicol-resistance gene was expressed under control of this riboswitch, E. coli cells showed chloramphenicol resistance only in the presence of caffeine. When inserted upstream of the gfpuv or lacZ gene, the caffeine riboswitch induced the expression of green fluorescent protein or β-galactosidase in the presence of caffeine, respectively. When tested with various concentrations of caffeine, the β-galactosidase activity was proportional to the amount of caffeine, clearly indicating the caffeine-dependent gene regulation by the caffeine riboswitch.

Dynamics of Verticillium dahliae race 1 population under managed agricultural ecosystems

BACKGROUND

Plant pathogens and their hosts undergo adaptive changes in managed agricultural ecosystems, by overcoming host resistance, but the underlying genetic adaptations are difficult to determine in natural settings. Verticillium dahliae is a fungal pathogen that causes Verticillium wilt on many economically important crops including lettuce. We assessed the dynamics of changes in the V. dahliae genome under selection in a long-term field experiment.

RESULTS

In this study, a field was fumigated before the Verticillium dahliae race 1 strain (VdLs.16) was introduced. A derivative 145-strain population was collected over a 6-year period from this field in which a seggregating population of lettuce derived from Vr1/vr1 parents were evaluated. We de novo sequenced the parental genome of VdLs.16 strain and resequenced the derivative strains to analyze the genetic variations that accumulate over time in the field cropped with lettuce. Population genomics analyses identified 2769 single-nucleotide polymorphisms (SNPs) and 750 insertion/deletions (In-Dels) in the 145 isolates compared with the parental genome. Sequence divergence was identified in the coding sequence regions of 378 genes and in the putative promoter regions of 604 genes. Five-hundred and nine SNPs/In-Dels were identified as fixed. The SNPs and In-Dels were significantly enriched in the transposon-rich, gene-sparse regions, and in those genes with functional roles in signaling and transcriptional regulation.

CONCLUSIONS

Under the managed ecosystem continuously cropped to lettuce, the local adaptation of V. dahliae evolves at a whole genome scale to accumulate SNPs/In-Dels nonrandomly in hypervariable regions that encode components of signal transduction and transcriptional regulation.

Transcriptomic responses of saline-adapted Nile tilapia (Oreochromis niloticus) to rearing in both saline and freshwater

The Nile tilapia, Oreochromis niloticus, is an important species for global aquaculture. Recently, a single genetic line of Nile tilapia was developed using estimated breeding values (EBVs) for body weight under moderately saline water that showed significant improvement in growth performance. To explore the molecular mechanisms underlying this enhanced growth capacity, RNA-Seq was used to profile differences in gene expression in the liver and pituitary gland of high- and low-growth performance families of male Nile tilapia progeny, reared in either saline or freshwater environments. Comparisons of tissues from high- and low-EBV families, and also between fish reared in either saline or freshwater, revealed 142 and 2208 differentially expressed genes (DEGs), respectively. DEGs identified between the EBV groups comprised a number of genes involved in the regulation of growth and reproduction. We found an overexpression of hormone genes involved in growth-inhibition in the pituitary of Low-EBV tilapia including 2 somatostatin genes (GHIH), corticoliberin (CRH) and tachykinin-3-like protein. Furthermore, several genes associated with the cAMP pathway were underexpressed in low-EBV tilapia pituitary together with several early response genes. This study provides insight into the transcriptomic factors associated with growth performance in saline-adapted Nile tilapia reared in environments with high and low salinity levels and provides valuable knowledge for the future development of selection strategies to improve growth performance in this species.

Genetic evaluation of growth and reproductive performances of crossbred pigs reared under intensive system in tropical humid coastal climate

Pig farming is one of the most economically viable options for the rural backward and resource-poor farmers in Asian countries. Growth rate and litter size are the most important traits based on which the crossbreeding programs are typically planned in commercial pig farming. The modern system of farming with high yielding improved pig germplasm helps in economic growth in piggery enterprises. The present study was undertaken to evaluate the influence of various genetic and non-genetic factors on growth and reproductive performances of 75% crossbred progenies of Large White Yorkshire and indigenous Agonda Goan pigs. Body weights were recorded at birth, weaning, and at monthly intervals up to 10 months of age. Reproductive performances were also recorded for litter size and weights at birth and weaning stages, age at first farrowing, number of services per conception, farrowing interval, and pre-weaning mortality. The general linear model was used to estimate overall least square means of body weights at different ages considering the effects of different factors at certain levels viz., generation (i = first, second, third, fourth), sex (j = male, female), litter size at birth (k = 1-3, 4-6, 7-9, ≥10), parity (l = 1, 2, ≥3), season (m = summer, rainy, spring), and period of birth (n = 2012-2015, 2016-2019). The heritability and genetic correlations for different traits were estimated by restricted maximum likelihood (REML) method using WOMBAT software. The re(production) parameters were analyzed to assess the genetic improvement in successive generations. There was significant difference (p < 0.01) in body weights among different generations where animals belonging to latest generation showed maximum body weights indicating ideal selective breeding in the herd. Other fixed effects also had significant effects on growth performance which clearly signifies to the crucial influence of rearing environment and animal factors like parity of dams as well as litter size at birth. The overall birth weight, weaning weight, and weight at 10 months of age were 1.00 ± 0.01 kg, 7.57 ± 0.07 kg, and 81.58 ± 1.96 kg, respectively. Nevertheless, weaning weight and weight at marketing age (8 months) were 8.04 ± 0.27 kg and 75.48 ± 1.40 kg, respectively, in fourth generation, indicating higher post-weaning growth rate of 337.20 g/day. During this fourth generation, mean litter size at birth was 8.35 ± 0.43 and litter size at weaning was 7.79 ± 0.39 with lowest percentage of pre-weaning mortality (4.11 ± 1.51). The average age at first farrowing and farrowing interval was 293 ± 17.24 and 195 ± 4.78 days, respectively. There was apparently greater genetic gain in each generation except for the second generation which might be due to the environment and managemental issues that hindered reproductive performance traits and body growth. The heritability estimate for weaning weight was 0.45 and higher heritability values were observed for all the body weights except weight at third month. Genetic as well as phenotypic correlations were moderate to high among the growth traits. The heritability and genetic correlations at birth and weaning indicate the reliability of selection at an early age. The findings indicated that there is scope for improvement through genetic selection in later generations and the 75% crossbred pigs thrived well in the prevailing hot and humid tropical coastal climate. The improved germplasm could satisfy the farmers' need in a commercial venture with high economic return.

Genetically selected alcohol-preferring msP rats to study alcohol use disorder: Anything lost in translation?

For several decades, genetically selected alcohol-preferring rats have been successfully used to mimic and study alcohol use disorders (AUD). These rat lines have been instrumental in advancing our understanding of the neurobiology of alcoholism and enabling pharmacological studies to evaluate drug efficacy on alcohol drinking and relapse. Moreover, the results of these studies have identified genetic variables that are linked to AUD vulnerability. This is an up-to-date review that focuses on genetically selected Marchigian Sardinian alcohol-preferring (msP) rats. To support the translational relevance of the findings that are obtained from msP rats and highlight important similarities to AUD patients, we also discuss the results of recent brain imaging studies. Finally, to demonstrate the importance of studying sex differences in animal models of AUD, we present original data that highlight behavioral differences in the response to alcohol in male and female rats. Female msP rats exhibited higher alcohol consumption compared with males. Furthermore, msP rats of both sexes exhibit higher anxiety- and depressive-like behaviors in the elevated plus maze and forced swim test, respectively, compared with unselected Wistar controls. Notably, voluntary alcohol drinking decreases foot-shock stress and depressive-like behavior in both sexes, whereas anxiety-like behavior in the elevated plus maze is attenuated only in males. These findings suggest that male and female msP rats both drink high amounts of alcohol to self-medicate negative affective symptoms. For females, this behavior may be driven by an attempt to treat stress and depressive-like conditions. For males, generalized anxiety appears to be an important additional factor in the motivation to drink alcohol. This article is part of the special issue on 'Vulnerabilities to Substance Abuse.'

Genetic parameters for performance, feed efficiency, and carcass traits in Senepol heifers

Improving feed efficiency is a key breeding goal in the beef cattle industry. In this study, we estimated the genetic parameters for feed efficiency and carcass traits in Senepol cattle raised in tropical regions. Various indicators of feed efficiency [gain to feed ratio (G:F), feed conversion ratio (FCR), residual weight gain (RG), residual intake and body weight gain (RIG), and residual feed intake (RFI)] as well as growth [final BW, average daily gain (ADG), and DM intake (DMI)], and carcass [rib-eye area (REA), backfat thickness (BF), intramuscular fat score, and carcass conformation score] traits were included in the study. After data editing, records from 1 393 heifers obtained between 2009 and 2018 were used for the analyses. We fitted an animal model that included contemporary group (animals from the same farm that were evaluated in the same test season) as the fixed effect, and a linear effect of animal age at the beginning of the test as a covariate; in addition to random direct additive genetic and residual effects. The (co)variance components were estimated by Bayesian inference in uni- and bivariate analyses. Our results showed that feed efficiency indicators derived from residual variables such as RG, RIG, and RFI can be improved through genetic selection (h² = 0.14 ± 0.06, 0.13 ± 0.06, and 0.20 ± 0.08, respectively). Variables calculated as ratios such as G:F and FCR were more influenced by environmental factors (h² = 0.08 ± 0.05 and 0.09 ± 0.05), and were, therefore, less suitable for use in breeding programs. The traits with the greatest and impact on genetic progress in feed efficiency were ADG, REA, and BF. The traits with the greatest and least impact on growth and carcass traits were RG and RFI, respectively. Selection for feed efficiency will result in distinct overall effects on the growth and carcass traits of Senepol heifers. Direct selection for lower RFI may reduce DMI and increase carcass fatness at the finishing stage, but it might also result in reduced growth and muscle deposition. Residual BW gain is associated with the highest weight gain and zero impact on REA and BF, however, it is linked to higher feed consumption. Thus, the most suitable feed efficiency indicator was RIG, as it promoted the greatest decrease in feed intake concomitant with faster growth, with a similar impact on carcass traits when compared to the other feed efficiency indicators.

Recent genetic advances on boar taint reduction as an alternative to castration: a review

Boar taint is an unpleasant odor in male pig meat, mainly caused by androstenone, skatole, and indole, which are deposited in the fat tissue. Piglet castration is the most common practice to prevent boar taint. However, castration is likely to be banished in a few years due to animal welfare concerns. Alternatives to castration, such as genetic selection, have been assessed. Androstenone and skatole have moderate to high heritability, which makes it feasible to select against these compounds. This review presents the latest results obtained on genetic selection against boar taint, on correlation with other traits, on differences in breeds, and on candidate genes related to boar taint. QTLs for androstenone and skatole have been reported mainly on chromosomes 6, 7, and 14. These chromosomes were reported to contain genes responsible for synthesis and degradation of androstenone and skatole. A myriad of work has been done to find markers or genes that can be used to select animals with lower boar taint. The selection against boar taint could decrease performance of some reproduction traits. However, a favorable response on production traits has been observed by selecting against boar taint. Selection results have shown that it is possible to reduce boar taint in few generations. In addition, modifications in diet and environment conditions could be associated with genetic selection to reduce boar taint. Nevertheless, costs to measure and select against boar taint should be rewarded with incentives from the market; otherwise, it would be difficult to implement genetic selection.

Relationship between sire predicted transmitting ability for daughter pregnancy rate and daughter's reproductive performance and milk production in Japanese dairy herds

Modern genetic improvement in dairy cattle is directed towards improvement of fertility; however, reproduction traits generally exhibit a genetic antagonism with milk yield. Herein, we aimed to clarify the effects of sire predicted transmitting ability (PTA) for daughter pregnancy rate (DPR) on the reproductive performance and milk yield of daughters in Japanese dairy herds. We conducted a retrospective cohort study on four dairy herds in eastern Hokkaido, Japan, using 1,612 records from 1,018 cows with first, second, or third calvings between March 2015 and September 2018. First, we classified sires into three groups based on the tertile value of their DPR estimate: ≤ −2.2 (low), −2.1 to −0.4 (intermediate), and ≥ −0.3 (high). Subsequently, we compared the sire PTA estimates, reproductive performance, and milk production among DPR groups for each parity of the daughters. In the first and second parity, the hazard of pregnancy by 200 days postpartum was highest in cows from the high-DPR group (P < 0.05); in the third parity, it was unaffected by DPR group. Although sire PTA for milk production in cows from the low-DPR group was highest, actual milk production was unaffected by DPR group regardless of parity. Our findings demonstrate that using sires with PTA for high fertility can enable farmers to improve reproductive performance without decreasing milk yield in Japanese dairy herds. However, it should be noted that sires with PTA for high fertility are at risk for reducing the genetic merit for milk production.

Acute hepatopancreatic necrosis disease (VPAHPND), a chronic disease in shrimp (Penaeus vannamei) population raised in latin America

In Latin American shrimp farming, acute hepatopancreatic necrosis disease (AHPND) does not cause the acute mortalities observed in SE Asia. Herein we report for the first time a new phase of infection of AHPND, a chronic phase based on two experimental AHPND-challenge trials using shrimp lines from Latin America. Three shrimp lines of Penaeus vannamei were challenged with a highly pathogenic strain of Vibrio parahaemolyticus causing AHPND (VP_AHPND). PCR and histopathology assays were used for confirmation of AHPND in the trials. The first study was to compare survival between the lines. A follow-up trial was conducted to document hepatopancreas heterotrophic bacterial count and to measure the expression of VP_AHPND binary toxin genes (pirAB genes) at 24 h.p.i. One of the Latin American shrimp lines, APE1, had significantly higher survival than recorded for the other two lines (APE2 & APE3) and the specific-pathogen-free positive control line. Histopathology showed typical AHPND acute and terminal phase lesions in VP_AHPND challenged groups, although destructive cellular changes were more pronounced in the SPF line. Histopathology of animals surviving AHPND revealed a unique chronic phase of infection that resembles septic hepatopancreatic necrosis (SHPN), recognized as diagnostic of digestive tract vibriosis. Data to support our finding, including a quantitative RT-PCR assay, confirmed the expression of pirAB genes and the differential hepatopancreas heterotrophic plate count (HPC) among the different lines challenged. The results explain in part why the shrimp industry in some Latin American countries continues to grow despite the presence of AHPND. In addition, the biology and pathology of AHPND resistant/tolerant shrimp appear to be quite unique in this Latin American shrimp population.

Evolution in crop improvement approaches and future prospects of molecular markers to CRISPR/Cas9 system

The advent of genetic selection and genome modification method assure about a real novel reformation in biotechnology and genetic engineering. With the extensive capabilities of molecular markers of them being stable, cost-effective and easy to use, they ultimately become a potent tool for variety of applications such a gene targeting, selection, editing, functional genomics; mainly for the improvisation of commercially important crops. Three main benefits of molecular marker in the field of agriculture and crop improvement programmes first, reduction of the duration of breeding programmes, second, they allow creation of new genetic variation and genetic diversity of plants and third most promising benefit is help in production of engineered plant for disease resistance, or resistance from pathogen and herbicides. This review is anticipated to present an outline how the techniques have been evolved from the simple conventional applications of DNA based molecular markers to highly throughput CRISPR technology and geared the crop yield. Techniques like using Zinc Finger Nucleases (ZFNs), Transcription Activator-Like Effector Nucleases (TALENs) and Clustered Regularly Interspaced Short Palindromic Repeats (CRISPR/Cas9) systems have revolutionised in the field of genome editing. These have been promptly accepted in both the research and commercial industry. On the whole, the widespread use of molecular markers with their types, their appliance in plant breeding along with the advances in genetic selection and genome editing together being a novel strategy to boost crop yield has been reviewed.

The relationships among sire's predicted transmitting ability for daughter pregnancy rate and cow conception rate and daughter's reproductive performance in Canadian Holstein cows

The objectives of this study were to (1) characterize the variability for sire's predicted transmitting ability (PTA) for daughter's pregnancy rate (DPR) and cow conception rate (CCR), (2) determine the relationships among sire's PTA for DPR, sire's PTA for CCR, daughter's parity, and daughter's 305-d mature-equivalent (ME) milk production, and (3) evaluate the associations among sire's PTA for DPR and CCR and daughter's reproductive performance [pregnancy to first artificial insemination (P/AI), pregnancy by 150 d in milk (PR150) and pregnancy loss (PL) after first AI] in Canadian Holstein cows. The data were obtained from 822 lactating Holstein cows from 10 commercial dairy herds located in Alberta. Overall mean (range) for sire's PTA for DPR and CCR was -0.09 (-9.6 to 8.2) and -0.05 (-9.9 to 7.4), respectively. Sire's PTA for DPR was strongly and positively associated with sire's PTA for CCR (r = 0.89; P < 0.01). Sire's PTA for DPR and CCR were weakly and negatively associated with parity (r = -0.15 and -0.17, respectively; P < 0.01); however, the amount of phenotypic variation in sire's PTA for DPR and CCR explainable by parity was small (coefficient of determination; R² = 0.02). The daughter's 305-d ME milk production tended to be weakly but positively associated with sire's PTA for DPR (r = 0.06; P = 0.07) and CCR (r = 0.06; P = 0.10); however, the amount of phenotypic variation in daughter's 305-d ME milk production explainable by changes in sire's PTA for DPR or CCR was small (R² = 0.004 and 0.003, respectively). Overall P/AI, PR150 and PL were 38, 65 and 12%, respectively. Sire's PTA for DPR tended to be associated with P/AI (P = 0.08) but was significantly associated with PR150 (P = 0.03). For every unit increase in sire's PTA for DPR, the estimated probabilities for P/AI and PR150 increased by 6.2 and 7.5%, respectively. Sire's PTA for CCR was not associated with P/AI or PR150. Neither sire's PTA for DPR nor CCR were associated with PL. In summary, sire's PTA for DPR and CCR were highly variable and positively correlated. Sire's PTA for DPR was associated with daughter's P/AI and PR150, but sire's PTA for CCR was not associated with any of the measured reproductive outcomes. Therefore, selecting sires with high PTA for DPR has the potential to improve the reproductive efficiency of Canadian dairy herds.

Genetic consequences of pond production of a pikeperch (Sander lucioperca L.) stock with natural origin: the effects of changed selection pressure and reduced population size

The pikeperch (Sander lucioperca L.) possesses great potential for diversifying European aquaculture. However, studies on the genetic risk of stocking natural waters with farmed individuals of this species have been limited. Even the effect of pond culture on the genetic composition of stocks with natural-origin has not yet been determined. Our study aimed to compare the genetic variability of a wild living pikeperch population, a pond cultured broodstock (originating from the wild population) and its offspring generation. We also aimed to detect the potential signs of selection using three different methods. By analyzing the molecular data with 14 microsatellite markers, we illustrated that the impact of pond culture on the genetic diversity of fish stocks is similar to hatchery rearing due to its diversity reducing effect caused by using lower effective population sizes. Although the heterozygosity was similar in all populations (H_o = 0.68–0.71), the average number of alleles and allelic richness were significantly lower in the pond cultured stocks (NA = 7.5 and 6; AR = 7.5 and 5.9) compared to the wild population (NA = 11.00, AR = 10.47). Despite the semi-natural conditions of the present study, we detected changing selection pressure in one of the 14 microsatellite markers.

In vivo model to study the impact of genetic variation on clinical outcome of mastitis in uniparous dairy cows

Background

In dairy herds, mastitis causes detrimental economic losses. Genetic selection offers a sustainable tool to select animals with reduced susceptibility towards postpartum diseases. Studying underlying mechanisms is important to assess the physiological processes that cause differences between selected haplotypes. Therefore, the objective of this study was to establish an in vivo infection model to study the impact of selecting for alternative paternal haplotypes in a particular genomic region on cattle chromosome 18 for mastitis susceptibility under defined conditions in uniparous dairy cows.

Results

At the start of pathogen challenge, no significant differences between the favorable (Q) and unfavorable (q) haplotypes were detected. Intramammary infection (IMI) with Staphylococcus aureus 1027 (S. aureus, n = 24, 96 h) or Escherichia coli 1303 (E. coli, n = 12, 24 h) was successfully induced in all uniparous cows. This finding was confirmed by clinical signs of mastitis and repeated recovery of the respective pathogen from milk samples of challenged quarters in each animal. After S. aureus challenge, Q-uniparous cows showed lower somatic cell counts 24 h and 36 h after challenge (P < 0.05), lower bacterial shedding in milk 12 h after challenge (P < 0.01) and a minor decrease in total milk yield 12 h and 24 h after challenge (P < 0.01) compared to q-uniparous cows.

Conclusion

An in vivo infection model to study the impact of genetic selection for mastitis susceptibility under defined conditions in uniparous dairy cows was successfully established and revealed significant differences between the two genetically selected haplotype groups. This result might explain their differences in susceptibility towards IMI. These clinical findings form the basis for further in-depth molecular analysis to clarify the underlying genetic mechanisms for mastitis resistance.

Characterization of functional traits with focus on udder health in heifers with divergent paternally inherited haplotypes on BTA18

Background

A major challenge in modern medicine and animal husbandry is the issue of antimicrobial resistance. One approach to solving this potential medical hazard is the selection of farm animals with less susceptibility to infectious diseases. Recent advances in functional genome analysis and quantitative genetics have opened the horizon to apply genetic marker information for efficiently identifying animals with preferential predisposition regarding health traits. The current study characterizes functional traits with a focus on udder health in dairy heifers. The animals were selected for having inherited alternative paternal haplotypes for a genomic region on Bos taurus chromosome (BTA) 18 genetically associated with divergent susceptibility to longevity and animal health, particularly mastitis.

Results

In the first weeks of lactation, the q heifers which had inherited the unfavorable (q) paternal haplotype displayed a significantly higher number of udder quarters with very low somatic cell count (< 10,000 cells / ml) compared to their paternal half-sib sisters with the favorable (Q) paternal haplotype. This might result in impaired mammary gland sentinel function towards invading pathogens. Furthermore, across the course of the first lactation, there was indication that q half-sib heifers showed higher somatic cell counts, a surrogate trait for udder health, in whole milkings compared to their paternal half-sib sisters with the favorable (Q) paternal haplotype. Moreover, heifers with the haplotype Q had a higher feed intake and higher milk yield compared to those with the q haplotype. Results of this study indicate that differences in milk production and calculated energy balance per se are not the main drivers of the genetically determined differences between the BTA18 Q and q groups of heifers.

Conclusions

The paternally inherited haplotype from a targeted BTA18 genomic region affect somatic cell count in udder quarters during the early postpartum period and might also contribute to further aspects of animal’s health and performance traits due to indirect effects on feed intake and metabolism.

Electronic supplementary material

The online version of this article (10.1186/s12917-019-1988-4) contains supplementary material, which is available to authorized users.

Spectroscopic determination of leaf chlorophyll content and color for genetic selection on Sassafras tzumu

BACKGROUND

Reflectance spectroscopy, like IR, VIS-NIR, combined with chemometric, has been widely used in plant leaf chemical analysis. But less studies have been made on the application of NIR reflectance spectroscopy to plant leaf color and pigments analysis and the possibility of using it for genetic breeding selection. Here, we examine the ability of NIR reflectance spectroscopy to determine the plant leaf color and chlorophyll content in Sassafras tzumu leaves and use the prediction results for genetic selection. Fresh and living tree leaves were used for NIR spectra collection, leaf color parameters (a*, b* and L*) and chlorophyll content were measured with standard analytical methods, partial least squares regression (PLSR) were used for model construction, the coefficient of determination (R²) [cross-validation ( R CV 2 ) and validation ( R V 2 )] and root mean square error (RMSE) [cross-validation (RMSE_CV) and validation (RMSE_V)] were used for model performance evaluation, significant Multivariate Correlation algorithm was applied for model improvement, to find out the most important region related to the leaf color parameters and chlorophyll model, which have been simulated 100 times for accuracy estimation.

RESULTS

Leaf color parameters (a*, b* and L*) and chlorophyll content were well predicted by NIR reflectance spectroscopy on fresh leaves in vivo. The mean R CV 2 and RMSE_CV of a*, b*, L* and chlorophyll content were (0.82, 4.43), (0.63, 3.72), (0.61, 2.35) and (0.86, 0.13%) respectively. Three most important NIR regions, including 1087, 1215 and 2219 nm, which were highly related to a*, b*, L* and chlorophyll content were found. NIR reflectance spectra technology can be successfully used for genetic breeding program. High heritability of a*, b*, L* and chlorophyll content (h ² = 0.77, 0.89, 0.78, 0.81 respectively) were estimated. Several families with bright red color or bright yellow color were selected.

CONCLUSIONS

NIR spectroscopy is promising for the rapid prediction of leaf color and chlorophyll content of living fresh leaves. It has the ability to simultaneously measure multiple plant leaf traits, potentially allowing for quick and economic prediction in situ.

Genome changes due to artificial selection in U.S. Holstein cattle

Background

The availability of a unique unselected Holstein line since 1964 provided a direct comparison between selected and unselected Holstein genomes whereas large Holstein samples provided unprecedented statistical power for identifying high-confidence SNP effects. Utilizing these unique resources, we aimed to identify genome changes affected by selection since 1964.

Results

Direct comparison of genome-wide SNP markers between a Holstein line unselected since 1964 and contemporary Holsteins showed that the 40 years of artificial selection since 1964 resulted in genome landscape changes. Among the regions affected by selection, the regions containing 198 genes with fertility functions had a larger negative correlation than that of all SNPs between the SNP effects on milk yield and daughter pregnancy rate. These results supported the hypothesis that hitchhiking of genetic selection for milk production by negative effects of fertility genes contributed to the unintended declines in fertility since 1964. The genome regions subjected to selection also contained 67 immunity genes, the bovine MHC region of Chr23 with significantly decreased heterozygosity in contemporary Holsteins, and large gene clusters including T-cell receptor and immunoglobulin genes.

Conclusions

This study for the first time provided direct evidence that genetic selection for milk production affected fertility and immunity genes and that the hitchhiking of genetic selection for milk production by negative fertility effects contributed to the fertility declines since 1964, and identified a large number of candidate fertility and immunity genes affected by selection. The results provided novel understanding about genome changes due to artificial selection and their impact on fertility and immunity genes and could facilitate developing genetic methods to reverse the declines in fertility and immunity in Holstein cattle.

Electronic supplementary material

The online version of this article (10.1186/s12864-019-5459-x) contains supplementary material, which is available to authorized users.

Genetic Selection for Mastitis Resistance

Mastitis is a prevalent and costly disease on dairy farms. Improved management and hygiene can reduce the risk of infection by contagious or environmental pathogens, and genetic selection can confer permanent improvement in mastitis resistance. National veterinary recording systems in the Nordic countries have allowed direct selection for sire families with low incidence of clinical mastitis for 3 decades, whereas other countries have practiced indirect selection for lower somatic cell count. Recently, pooling of producer-recorded data from on-farm herd management software programs has enabled selection for reduced incidence of clinical mastitis in the United States and other leading dairy countries.

Should We Genetically Select for the Beauty Norm of Fair Skin?

Fair skin is often regarded as a beauty ideal in many parts of the world. Genetic selection for non-disease traits may allow reproducers to select fair skin for the purposes of beauty, and may be justified under various procreative principles. In this paper I assess the ethics of genetic selection for fair skin as a beauty feature. In particular, I explore the discriminatory aspects and demands of such selection. Using race and colour hierarchies that many would find objectionable, I argue that selection for beauty that is underpinned by such hierarchies is not a trivial selection. Given this, I claim that we should not make such selections.

FASTBAC-Seq: Functional Analysis of Toxin-Antitoxin Systems in Bacteria by Deep Sequencing

As the number of bacterial genomes and transcriptomes increases, so does the number of newly identified toxin-antitoxin (TA) systems. However, their functional characterization remains challenging, often requiring the use of overexpression vectors that can lead to misinterpretations of in vivo results. To fill this gap, we developed a systematic approach called FASTBAC-Seq (Functional AnalysiS of Toxin-Antitoxin Systems in BACteria by Deep Sequencing). Combining life/death phenotypic selection with next-generation sequencing, FASTBAC-Seq allows the rapid identification of loss-of-function (toxicity) mutations in toxin-encoding genes belonging to TA loci with nucleotide resolution. Here, we present the setup used on the first-time application of FASBACT-Seq to characterize a member of the aapA/IsoA family of type I TA systems hosted on the chromosome of the major human gastric pathogen Helicobacter pylori. We propose FASBACT-Seq as a powerful tool for the functional characterization of TA systems that can in addition uncover key elements for the understanding of gene expression regulation in bacteria.

Does selection for growth rate in broilers affect their resistance and tolerance to Eimeria maxima?

Chickens exhibit varied responses to infection with Eimeria parasites. We hypothesise that broilers selected for increased growth rate will show lower resistance and tolerance to a coccidian challenge. 288 chickens of fast (F) or slow (S) growing lines were inoculated with 0 (control), 2500 (low-dose), or 7000 (high-dose) sporulated E. maxima oocysts at 13 days of age in two consecutive rounds. Gain and Intake were measured daily and their values relative to BW at the point of infection were calculated over the pre-patent (days 1-4 post-infection), acute (d5-8 pi), and recovery (d9-12 pi) phases of infection to assess the impact of infection. Levels of plasma carotenoids, vitamins E and A, long bone mineralisation, caecal microbiota diversity indices, and histological measurements were assessed at the acute (d6 pi) and recovery stage (d13 pi). In addition, we measured the levels of nitric oxide metabolites and the number of parasite genome copies in the jejunumat d6pi. In absolute terms F birds grew 1.42 times faster than S birds when not infected. Infection significantly reduced relative daily gain and intake (P < 0.001), with the effects being most pronounced during the acute phase (P < 0.001). Levels of all metabolites were significantly decreased, apart from NO which increased (P < 0.001) in response to infection on d6pi, and were accompanied by changes in histomorphometric features and the presence of E. maxima genome copies in infected birds, which persisted to d13pi. Furthermore, infection reduced tibia and femur mineralisation, which also persisted to d13pi. Reductions in measured variables were mostly independent of dose size, as was the level of parasite replication. The impact of infection was similar for S and F-line birds for all measured parameters, and there were no significant interactions between line x dose size on any of these parameters. In conclusion, our results suggest that line differences in productive performance do not influence host responses to coccidiosis when offered nutrient adequate diets.

Global analysis of Plasmodium falciparum histidine-rich protein-2 (pfhrp2) and pfhrp3 gene deletions using whole-genome sequencing data and meta-analysis

Many rapid diagnostic tests (RDT) used on suspected malaria cases are based on the detection of the protein encoded by the Plasmodium falciparum histidine-rich protein-2 (pfhrp2) gene, which shares a high sequence homology with pfhrp3 in the 3D7 reference genome. Parasite isolates showing pfhrp2 and pfhrp3 gene deletions have been emerging over the years, but a comprehensive genetic analysis of these variants is still lacking. With this purpose, genomic data from experimental P. falciparum genetic crosses between different laboratory lines (3D7, HB3, DD2, 7G8 and GB4) were first analysed (n = 98). The frequency of pfhrp2 deletions was consistent with a Mendelian prediction in HB3 × DD2 (56.7%; 95%CI = (39.5%-72.9%)). Moreover, the pfhrp2 and pfhrp3 deletions segregated independently of each other in the same genetic cross. Analysis of 3D7 × HB3 and 7G8 × GB4 estimated the probability of spontaneously generating a pfhrp2 deletion during sexual recombination to be up to 6.2%. Next, whole genome sequence data from 1970 P. falciparum isolates collected globally were analysed. Nine samples displayed depth of coverage consistent with pfhrp2 deletions (0.5%), but the corresponding split-read analysis could not confirm deletions in seven of these samples. Twenty-eight isolates had evidence of pfhrp3 deletions (1.4%), which are widespread in Southeast Asia. Finally, a meta-analysis of published data revealed a positive mean association between the frequencies of pfhrp2 and pfhrp3 deletions in Africa and South America. This result suggested a shared selective pressure acting on these genetic variants. In conclusion, evidence of genetic selection on both pfhrp2 and pfhrp3 deletions was presented, but experimental crosses do not provide evidence of a fitness cost of these variants. Further work is urgently needed to accurately determine the prevalence and the degree of association between these genetic variants, and the respective impact on diagnostic accuracy of many in-use RDT.

Systems biology analysis of mitogen activated protein kinase inhibitor resistance in malignant melanoma

BACKGROUND

Kinase inhibition in the mitogen activated protein kinase (MAPK) pathway is a standard therapy for cancer patients with activating BRAF mutations. However, the anti-tumorigenic effect and clinical benefit are only transient, and tumors are prone to treatment resistance and relapse. To elucidate mechanistic insights into drug resistance, we have established an in vitro cellular model of MAPK inhibitor resistance in malignant melanoma.

METHODS

The cellular model evolved in response to clinical dosage of the BRAF inhibitor, vemurafenib, PLX4032. We conducted transcriptomic expression profiling using RNA-Seq and RT-qPCR arrays. Pathways of melanogenesis, MAPK signaling, cell cycle, and metabolism were significantly enriched among the set of differentially expressed genes of vemurafenib-resistant cells vs control. The underlying mechanism of treatment resistance and pathway rewiring was uncovered to be based on non-genomic adaptation and validated in two distinct melanoma models, SK-MEL-28 and A375. Both cell lines have activating BRAF mutations and display metastatic potential.

RESULTS

Downregulation of dual specific phosphatases, tumor suppressors, and negative MAPK regulators reengages mitogenic signaling. Upregulation of growth factors, cytokines, and cognate receptors triggers signaling pathways circumventing BRAF blockage. Further, changes in amino acid and one-carbon metabolism support cellular proliferation despite MAPK inhibitor treatment. In addition, treatment-resistant cells upregulate pigmentation and melanogenesis, pathways which partially overlap with MAPK signaling. Upstream regulator analysis discovered significant perturbation in oncogenic forkhead box and hypoxia inducible factor family transcription factors.

CONCLUSIONS

The established cellular models offer mechanistic insight into cellular changes and therapeutic targets under inhibitor resistance in malignant melanoma. At a systems biology level, the MAPK pathway undergoes major rewiring while acquiring inhibitor resistance. The outcome of this transcriptional plasticity is selection for a set of transcriptional master regulators, which circumvent upstream targeted kinases and provide alternative routes of mitogenic activation. A fine-woven network of redundant signals maintains similar effector genes allowing for tumor cell survival and malignant progression in therapy-resistant cancer.

A review on breeding and genetic strategies in Iranian buffaloes (Bubalus bubalis)

The aim of current study was to review breeding progress and update information on genetic strategies in Iranian buffaloes. Iranian buffalo is one of the vital domestic animals throughout north, north-west, south and south-west of Iran with measurable characteristics both in milk and meat production. The species plays an important role in rural economy of the country due to its unique characteristics such as resistance to diseases and parasites, having long productive lifespan and showing higher capability of consuming low-quality forage. In Iran, total production of milk and meat devoted to buffaloes are 293,000 and 24,700 tons, respectively. Selection activities and milk yield recording are carrying out by the central government through the Animal Breeding Centre of Iran. The main breeding activities of Iranian buffaloes included the estimation of genetic parameters and genetic trends for performance traits using different models and methods, estimation of economic values and selection criteria and analysis of population structure. Incorporating different aspects of dairy buffalo management together with improved housing, nutrition, breeding and milking, is known to produce significant improvements in buffalo production. Therefore, identifying genetic potential of Iranian buffaloes, selection of superior breeds, improving nutritional management and reproduction and developing the education and increasing the skills of practical breeders can be useful in order to enhance the performance and profitability of Iranian buffaloes.

Directed Evolution of Orthogonal Pyrrolysyl-tRNA Synthetases in Escherichia coli for the Genetic Encoding of Noncanonical Amino Acids

The directed evolution of orthogonal aminoacyl-tRNA synthetases (aaRS) for the genetic encoding of noncanonical amino acids (ncAA) has paved the way for the site-specific incorporation of >170 functionally diverse ncAAs into proteins in a large number of organisms [1, 2]. Here, we describe the directed evolution of orthogonal pyrrolysyl-tRNA synthetase (PylRS) mutants with new amino acid selectivities from libraries using a two-step selection protocol based on chloramphenicol and barnase reporter systems. Although this protocol focuses on the evolution of PylRS variants, this procedure can be universally employed to evolve orthogonal aaRS.

Detection and Differentiation of Multiple Viral RNAs Using Branched DNA FISH Coupled to Confocal Microscopy and Flow Cytometry

Due to the exceptionally high mutation rates of RNA-dependent RNA polymerases, infectious RNA viruses generate extensive sequence diversity, leading to some of the lowest barriers to the development of antiviral drug resistance in the microbial world. We have previously discovered that higher barriers to the development of drug resistance can be achieved through dominant suppression of drug-resistant viruses by their drug-susceptible parents. We have explored the existence of dominant drug targets in poliovirus, dengue virus and hepatitis C virus (HCV). The low replication capacity of HCV required the development of novel strategies for identifying cells co-infected with drug-susceptible and drug-resistant strains. To monitor co-infected cell populations, we generated codon-altered versions of the JFH1 strain of HCV. Then, we could differentiate the codon-altered and wild-type strains using a novel type of RNA fluorescent in situ hybridization (FISH) coupled with flow cytometry or confocal microscopy. Both of these techniques can be used in conjunction with standard antibody-protein detection methods. Here, we describe a detailed protocol for both RNA FISH flow cytometry and confocal microscopy.

Pathway optimization and key enzyme evolution of N-acetylneuraminate biosynthesis using an in vivo aptazyme-based biosensor

N-acetylneuraminate (NeuAc) biosynthesis has drawn much attention owing to its wide applications in many aspects. Previously, we engineered for the first time an artificial NeuAc biosynthetic pathway in Escherichia coli using glucose as sole substrate. However, rigorous requirements for the flux and cofactor balance make subsequent strain improvement rather difficult. In this study, an in vivo NeuAc biosensor was designed and applied for genetic screening the mutant library of NeuAc producer. Its NeuAc responsive manner was demonstrated using sfgfp as a reporter and a Ni²⁺-based selection system was developed to couple the cell growth with in vivo NeuAc concentration. Employing this selection system, the NeuAc biosynthesis pathway was optimized and the key enzyme NeuAc synthase was evolved, which improved the titer by 34% and 23%, respectively. The final strain produced up to 8.31g/L NeuAc in minimal medium using glucose as sole carbon source. This work demonstrated the effectiveness of NeuAc biosensor in genetic screening and great potential in metabolic engineering of other organisms.

On the catalytic mechanism of bacteriophage HK97 capsid crosslinking

During maturation of the phage HK97 capsid, each of the 415 capsid subunits forms covalent bonds to neighboring subunits, stabilizing the capsid. Crosslinking is catalyzed not by a separate enzyme but by subunits of the assembled capsid in response to conformational rearrangements during maturation. This report investigates the catalytic mechanism. Earlier work established that the crosslinks are isopeptide (amide) bonds between side chains of a lysine on one subunit and an asparagine on another subunit, aided by a catalytic glutamate on a third subunit. The mature capsid structure suggests that the reaction may be facilitated by the arrival of a valine with the lysine to complete a hydrophobic pocket surrounding the glutamate, lysine and asparagine. We show that this valine has an essential role for efficient crosslinking, and that any of six other amino acids can successfully substitute for valine. Evidently none of the remaining 13 amino acids will work.

Post-translocational adaptation drives evolution through genetic selection and transcriptional shift in Saccharomyces cerevisiae

Adaptation by natural selection might improve the fitness of an organism and its probability to survive in unfavorable environmental conditions. Decoding the genetic basis of adaptive evolution is one of the great challenges to deal with. To this purpose, Saccharomyces cerevisiae has been largely investigated because of its short division time, excellent aneuploidy tolerance and the availability of the complete sequence of its genome with a thorough genome database. In the past, we developed a system, named bridge-induced translocation, to trigger specific, non-reciprocal translocations, exploiting the endogenous recombination system of budding yeast. This technique allows users to generate a heterogeneous population of cells with different aneuploidies and increased phenotypic variation. In this work, we demonstrate that ad hoc chromosomal translocations might induce adaptation, fostering selection of thermo-tolerant yeast strains with improved phenotypic fitness. This "yeast eugenomics" correlates with a shift to enhanced expression of genes involved in stress response, heat shock as well as carbohydrate metabolism. We propose that the bridge-induced translocation is a suitable approach to generate adapted, physiologically boosted strains for biotechnological applications.

Periparturient immunosuppression and strategies to improve dairy cow health during the periparturient period

Common health problems observed during peripartum include milk fever, mastitis, fatty liver disease, ketosis, dystocia, retained placenta, metritis, hypomagnesaemia and abomasal displacements. The increased incidence of health problems observed during the periparturient period can be partly attributed to suboptimal immune responses. Factors contributing to decreased periparturient immunity include the act of parturition itself, impaired leukocytic activity, effects of colostrogenesis and lactogenesis, and associated hypocalcemia and negative energy balance. Nutritional and other management strategies represent a relevant short-term strategy aimed at improving the health and welfare of the transitioning cow. Additionally, it is important to consider improving the health of dairy herds through the genetic selection of animals with enhanced robustness by identifying those with superior disease resistance or resilience in the face of infection. As a consequence these animals are better able to cope with the production and environmental stresses. These may provide long-term selection strategies for improving the health and welfare of the transitioning cow particularly when combined with sound management practices, allowing dairy cattle to reach their full genetic potential.

Mytilus hybridisation and impact on aquaculture: A minireview

The three species in the blue mussel complex (Mytilus edulis, Mytilus galloprovincialis and Mytilus trossulus) show varying levels of hybridisation wherever they occur sympatrically. The spatial variation in hybridisation patterns is potentially governed by environmental conditions, larval dispersal and aquaculture practices. Commercial mussel cultivation has been shown to increase hybridisation through introduction of non-native species or spat transfer. There is evidence that mussel cultivation may promote commercially less desirable phenotypes (e.g. fragile shells), however, to what extent hybridisation impacts aquaculture is currently not clear. The aim of this review is to summarize the available information on Mytilus hybridisation patterns in Europe and their promotion through aquaculture practices in order to shed light on the overall implications for the aquaculture industry.

Evaluating the impact of a fluoropolymer plant on a river macrobenthic community by a combined chemical, ecological and genetic approach

Effect-based monitoring is a recommended approach suggested in European Guidelines to assess the response of ecosystem affected by a pollution source, considering the effects at community, population, individual but also at suborganism level. A combined chemical, ecological and genetic approach was applied in order to assess the impact of a fluoropolymer plant on the macrobenthic community of the Northern Italian river Bormida (Piedmont region). The macrobenthic community living downstream of the industrial discharge was chronically exposed to a mixture of perfluoroalkyl substances (PFAS), with perfluorooctanoic acid as the main compound, at concentrations up to several μgL(-1). Ecological assessment proved that the downstream community was not substantially different from that living upstream of the pollution source. The impact on community is not quantifiable with the traditional monitoring methods used for ecological classification under European regulation because macrobenthic communities showed only slight differences in their structure. In order to highlight effects on genetic variability of the native population, a subcellular analysis by using the AFLP (Amplified Fragment Length Polymorphism) genetic technique was applied to genotype of individuals of a selected species (Hydropsyche modesta, Trichoptera) collected in the two sampling sites. Percentage of variation between the two populations was 6.8%, a threshold compatible with a genetic drift induced in the downstream population. The genetic study carried out in field identified a significant divergence between exposed and non-exposed populations, but at present it is not possible to associate this divergence to a specific effect induced by PFAS.

Directed evolution of the substrate specificity of dialkylglycine decarboxylase

Dialkylglycine decarboxylase (DGD) is an unusual pyridoxal phosphate dependent enzyme that catalyzes decarboxylation in the first and transamination in the second half-reaction of its ping-pong catalytic cycle. Directed evolution was employed to alter the substrate specificity of DGD from 2-aminoisobutyrate (AIB) to 1-aminocyclohexane-1-carboxylate (AC6C). Four rounds of directed evolution led to the identification of several mutants, with clones in the final rounds containing five persistent mutations. The best clones show ~2.5-fold decrease in KM and ~2-fold increase in kcat, giving a modest ~5-fold increase in catalytic efficiency for AC6C. Additional rounds of directed evolution did not improve catalytic activity toward AC6C. Only one (S306F) of the five persistent mutations is close to the active site. S306F was observed in all 33 clones except one, and the mutation is shown to stabilize the enzyme toward denaturation. The other four persistent mutations are near the surface of the enzyme. The S306F mutation and the distal mutations all have significant effects on the kinetic parameters for AIB and AC6C. Molecular dynamics simulations suggest that the mutations alter the conformational landscape of the enzyme, favoring a more open active site conformation that facilitates the reactivity of the larger substrate. We speculate that the small increases in kcat/KM for AC6C are due to two constraints. The first is the mechanistic requirement for catalyzing oxidative decarboxylation via a concerted decarboxylation/proton transfer transition state. The second is that DGD must catalyze transamination at the same active site in the second half-reaction of the ping-pong catalytic cycle.

Serotonin release in the caudal nidopallium of adult laying hens genetically selected for high and low feather pecking behavior: an in vivo microdialysis study

Severe feather pecking (FP) is a detrimental behavior causing welfare problems in laying hens. Divergent genetic selection for FP in White Leghorns resulted in strong differences in FP incidences between lines. More recently, it was shown that the high FP (HFP) birds have increased locomotor activity as compared to hens of the low FP (LFP) line, but whether these lines differ in central serotonin (5-hydroxytryptamine, 5-HT) release is unknown. We compared baseline release levels of central 5-HT, and the metabolite 5-HIAA in the limbic and prefrontal subcomponents of the caudal nidopallium by in vivo microdialysis in adult HFP and LFP laying hens from the ninth generation of selection. A single subcutaneous d-fenfluramine injection (0.5 mg/kg) was given to release neuronal serotonin in order to investigate presynaptic storage capacity. The present study shows that HFP hens had higher baseline levels of 5-HT in the caudal nidopallium as compared to LFP laying hens. Remarkably, no differences in plasma tryptophan levels (precursor of 5-HT) between the lines were observed. d-fenfluramine increased 5-HT levels in both lines similarly indirectly suggesting that presynaptic storage capacity was the same. The present study shows that HFP hens release more 5-HT under baseline conditions in the caudal nidopallium as compared to the LFP birds. This suggests that HFP hens are characterized by a higher tonic 5-HT release.