Understanding bovine embryo elongation: a transcriptomic study of trophoblastic vesicles.

Background: During the process of elongation, the embryo increases in size within the uterus, while the extra-embryonic tissues (EETs) develop and differentiate in preparation for implantation. As it grows, the ovoid embryo transforms into a tubular form first and then a filamentous form. This process is directed by numerous genes and pathways, the expression of which may be altered in the case of developmental irregularities such as when the conceptus is shorter than expected or when the embryo develops after splitting. In bovines, efforts to understand the molecular basis of elongation have employed trophoblastic vesicles (TVs)-short tubular EET pieces that lack an embryo-which also elongate in vivo. To date, however, we lack molecular analyses of TVs at the ovoid or filamentous stages that might shed light on the expression changes involved. Methods: Following in vivo development, we collected bovine conceptuses from the ovoid (D12) to filamentous stages (D18), sectioned them into small pieces with or without their embryonic disc (ED), and then, transferred them to a receptive bovine uterus to assess their elongation abilities. We also grew spherical blastocysts in vitro up to D8 and subjected them to the same treatment. Then, we assessed the differences in gene expression between different samples and fully elongating controls at different stages of elongation using a bovine array (10 K) and an extended qPCR array comprising 224 genes across 24 pathways. Results: In vivo, TVs elongated more or less depending on the stage at which they had been created and the time spent in utero. Their daily elongation rates differed from control EET, with the rates of TVs sometimes resembling those of earlier-stage EET. Overall, the molecular signatures of TVs followed a similar developmental trajectory as intact EET from D12-D18. However, within each stage, TVs and intact EET displayed distinct expression dynamics, some of which were shared with other short epithelial models. Conclusion: Differences between TVs and EET likely result from multiple factors, including a reduction in the length and signaling capabilities of TVs, delayed elongation from inadequate uterine signals, and modified crosstalk between the conceptus and the uterus. These findings confirm that close coordination between uterine, embryonic, and extra-embryonic tissues is required to orchestrate proper elongation and, based on the partial differentiation observed, raise questions about the presence/absence of certain developmental cues or even their asynchronies.

Cell specification and functional interactions in the pig blastocyst inferred from single-cell transcriptomics and uterine fluids proteomics.

The embryonic development of the pig comprises a long in utero pre- and peri-implantation development, which dramatically differs from mice and humans. During this peri-implantation period, a complex series of paracrine signals establishes an intimate dialogue between the embryo and the uterus. To better understand the biology of the pig blastocyst during this period, we generated a large dataset of single-cell RNAseq from early and hatched blastocysts, spheroid and ovoid conceptus and proteomic datasets from corresponding uterine fluids. Our results confirm the molecular specificity and functionality of the three main cell populations. We also discovered two previously unknown subpopulations of the trophectoderm, one characterised by the expression of LRP2, which could represent progenitor cells, and the other, expressing pro-apoptotic markers, which could correspond to the Rauber's layer. Our work provides new insights into the biology of these populations, their reciprocal functional interactions, and the molecular dialogue with the maternal uterine environment.

Specific Milk Composition of miR-30b Transgenic Mice Associated with Early Duodenum Maturation in Offspring with Lasting Consequences for Growth.

BACKGROUND: Milk composition is complex and includes numerous components essential for offspring growth and development. In addition to the high abundance of miR-30b microRNA, milk produced by the transgenic mouse model of miR-30b-mammary deregulation displays a significantly altered fatty acid profile. Moreover, wild-type adopted pups fed miR-30b milk present an early growth defect. OBJECTIVE: This study aimed to investigate the consequences of miR-30b milk feeding on the duodenal development of wild-type neonates, a prime target of suckled milk, along with comprehensive milk phenotyping. METHODS: The duodenums of wild-type pups fed miR-30b milk were extensively characterized at postnatal day (PND)-5, PND-6, and PND-15 using histological, transcriptomic, proteomic, and duodenal permeability analyses and compared with those of pups fed wild-type milk. Milk of miR-30b foster dams collected at mid-lactation was extensively analyzed using proteomic, metabolomic, and lipidomic approaches and hormonal immunoassays. RESULTS: At PND-5, wild-type pups fed miR-30b milk showed maturation of their duodenum with 1.5-fold (P < 0.05) and 1.3-fold (P < 0.10) increased expression of Claudin-3 and Claudin-4, respectively, and changes in 8 duodenal proteins (P < 0.10), with an earlier reduction in paracellular and transcellular permeability (183 ng/mL fluorescein sulfonic acid [FSA] and 12 ng/mL horseradish peroxidase [HRP], respectively, compared with 5700 ng/mL FSA and 90 ng/mL HRP in wild-type; P < 0.001). Compared with wild-type milk, miR-30b milk displayed an increase in total lipid (219 g/L compared with 151 g/L; P < 0.05), ceramide (17.6 µM compared with 6.9 µM; P < 0.05), and sphingomyelin concentrations (163.7 µM compared with 76.3 µM; P < 0.05); overexpression of 9 proteins involved in the gut barrier (P < 0.1); and higher insulin and leptin concentrations (1.88 ng/mL and 2.04 ng/mL, respectively, compared with 0.79 ng/mL and 1.06 ng/mL; P < 0.01). CONCLUSIONS: miR-30b milk displays significant changes in bioactive components associated with neonatal duodenal integrity and maturation, which could be involved in the earlier intestinal closure phenotype of the wild-type pups associated with a lower growth rate.

How Geography and Climate Shaped the Genomic Diversity of Italian Local Cattle and Sheep Breeds.

Understanding the relationships among geography, climate, and genetics is increasingly important for animal farming and breeding. In this study, we examine these inter-relationships in the context of local cattle and sheep breeds distributed along the Italian territory. To this aim, we used redundancy analysis on genomic data from previous projects combined with geographical coordinates and corresponding climatic data. The effect of geographic factors (latitude and longitude) was more important in sheep (26.4%) than that in cattle (13.8%). Once geography had been partialled out of analysis, 10.1% of cattle genomic diversity and 13.3% of that of sheep could be ascribed to climatic effects. Stronger geographic effects in sheep can be related to a combination of higher pre-domestication genetic variability together with biological and productive specificities. Climate alone seems to have had less impact on current genetic diversity in both species, even if climate and geography are greatly confounded. Results confirm that both species are the result of complex evolutionary histories triggered by interactions between human needs and environmental conditions.

Potential genetic robustness of Prnp and Sprn double knockout mouse embryos towards ShRNA-lentiviral inoculation.

The Shadoo and PrP prion protein family members are thought to be functionally related, but previous knockdown/knockout experiments in early mouse embryogenesis have provided seemingly contradictory results. In particular, Shadoo was found to be indispensable in the absence of PrP in knockdown analyses, but a double-knockout of the two had little phenotypic impact. We investigated this apparent discrepancy by comparing transcriptomes of WT, Prnp0/0 and Prnp0/0Sprn0/0 E6.5 mouse embryos following inoculation by Sprn- or Prnp-ShRNA lentiviral vectors. Our results suggest the possibility of genetic adaptation in Prnp0/0Sprn0/0 mice, thus providing a potential explanation for their previously observed resilience.

Individualized multi-omic pathway deviation scores using multiple factor analysis.

Malignant progression of normal tissue is typically driven by complex networks of somatic changes, including genetic mutations, copy number aberrations, epigenetic changes, and transcriptional reprogramming. To delineate aberrant multi-omic tumor features that correlate with clinical outcomes, we present a novel pathway-centric tool based on the multiple factor analysis framework called padma. Using a multi-omic consensus representation, padma quantifies and characterizes individualized pathway-specific multi-omic deviations and their underlying drivers, with respect to the sampled population. We demonstrate the utility of padma to correlate patient outcomes with complex genetic, epigenetic, and transcriptomic perturbations in clinically actionable pathways in breast and lung cancer.

A unified framework for the integration of multiple hierarchical clusterings or networks from multi-source data.

BACKGROUND: Integrating data from different sources is a recurring question in computational biology. Much effort has been devoted to the integration of data sets of the same type, typically multiple numerical data tables. However, data types are generally heterogeneous: it is a common place to gather data in the form of trees, networks or factorial maps, as these representations all have an appealing visual interpretation that helps to study grouping patterns and interactions between entities. The question we aim to answer in this paper is that of the integration of such representations. RESULTS: To this end, we provide a simple procedure to compare data with various types, in particular trees or networks, that relies essentially on two steps: the first step projects the representations into a common coordinate system; the second step then uses a multi-table integration approach to compare the projected data. We rely on efficient and well-known methodologies for each step: the projection step is achieved by retrieving a distance matrix for each representation form and then applying multidimensional scaling to provide a new set of coordinates from all the pairwise distances. The integration step is then achieved by applying a multiple factor analysis to the multiple tables of the new coordinates. This procedure provides tools to integrate and compare data available, for instance, as tree or network structures. Our approach is complementary to kernel methods, traditionally used to answer the same question. CONCLUSION: Our approach is evaluated on simulation and used to analyze two real-world data sets: first, we compare several clusterings for different cell-types obtained from a transcriptomics single-cell data set in mouse embryos; second, we use our procedure to aggregate a multi-table data set from the TCGA breast cancer database, in order to compare several protein networks inferred for different breast cancer subtypes.

Assessment of trade-offs between feed efficiency, growth-related traits, and immune activity in experimental lines of layer chickens.

BACKGROUND: In all organisms, life-history traits are constrained by trade-offs, which may represent physiological limitations or be related to energy resource management. To detect trade-offs within a population, one promising approach is the use of artificial selection, because intensive selection on one trait can induce unplanned changes in others. In chickens, the breeding industry has achieved remarkable genetic progress in production and feed efficiency over the last 60 years. However, this may have been accomplished at the expense of other important biological functions, such as immunity. In the present study, we used three experimental lines of layer chicken-two that have been divergently selected for feed efficiency and one that has been selected for increased antibody response to inactivated Newcastle disease virus (ND3)-to explore the impact of improved feed efficiency on animals' immunocompetence and, vice versa, the impact of improved antibody response on animals' growth and feed efficiency. RESULTS: There were detectable differences between the low (R+) and high (R-) feed-efficiency lines with respect to vaccine-specific antibody responses and counts of monocytes, heterophils, and/or T cell population. The ND3 line presented reduced body weight and feed intake compared to the control line. ND3 chickens also demonstrated an improved antibody response against a set of commercial viral vaccines, but lower blood leucocyte counts. CONCLUSIONS: This study demonstrates the value of using experimental chicken lines that are divergently selected for RFI or for a high antibody production, to investigate the modulation of immune parameters in relation to growth and feed efficiency. Our results provide further evidence that long-term selection for the improvement of one trait may have consequences on other important biological functions. Hence, strategies to ensure optimal trade-offs among competing functions will ultimately be required in multi-trait selection programs in livestock.

Intensified Use of Reproductive Technologies and Reduced Dimensions of Breeding Schemes Put Genetic Diversity at Risk in Dairy Cattle Breeds.

In the management of dairy cattle breeds, two recent trends have arisen that pose potential threats to genetic diversity: the use of reproductive technologies (RT) and a reduction in the number of bulls in breeding schemes. The expected outcome of these changes, in terms of both genetic gain and genetic diversity, is not trivial to predict. Here, we simulated 15 breeding schemes similar to those carried out in large French dairy cattle breeds; breeding schemes differed with respect to their dimensions, the intensity of RT use, and the type of RT involved. We found that intensive use of RT resulted in improved genetic gain, but deteriorated genetic diversity. Specifically, a reduction in the interval between generations through the use of ovum pick-up and in vitro fertilization (OPU-IVF) resulted in a large increase in the inbreeding rate both per year and per generation, suggesting that OPU-IVF could have severe adverse effects on genetic diversity. To achieve a given level of genetic gain, the scenarios that best maintained genetic diversity were those with a higher number of sires/bulls and a medium intensity of RT use or those with a higher number of female donors to compensate for the increased intensity of RT.

PiQSARS: A pipeline for quantitative and statistical analyses of ratiometric fluorescent biosensors.

Genetically encoded ratiometric fluorescent probes are cutting-edge tools in biology. They allow precise and dynamic measurement of various physiological parameters within cell compartments. Because data extraction and analysis are time consuming and may lead to inconsistencies between results, we describe here a standardized pipeline for•Semi-automated treatment of time-lapse fluorescence microscopy images.•Quantification of individual cell signal.•Statistical analysis of the data.First, a dedicated macro was developed using the FIJI software to reproducibly quantify the fluorescence ratio as a function of time. Raw data are then exported and analyzed using R and MATLAB softwares. Calculation and statistical analysis of selected graphic parameters are performed. In addition, a functional principal component analysis allows summarizing the dataset. Finally, a principal component analysis is performed to check consistency and final analysis is presented as a visual diagram. The method is adapted to any ratiometric fluorescent probe. As an example, the analysis of the cytoplasmic HyPer probe in response to an acute cell treatment with increasing amounts of hydrogen peroxide is shown. In conclusion, the pipeline allows to save time and analyze a larger amount of samples while reducing manual interventions and consequently increasing the robustness of the analysis.

Molecular signatures of muscle growth and composition deciphered by the meta-analysis of age-related public transcriptomics data.

The lean-to-fat ratio is a major issue in the beef meat industry from both carcass and meat production perspectives. This industrial perspective has motivated meat physiologists to use transcriptomics technologies to decipher mechanisms behind fat deposition within muscle during the time course of muscle growth. However, synthetic biological information from this volume of data remains to be produced to identify mechanisms found in various breeds and rearing practices. We conducted a meta-analysis on 10 transcriptomic data sets stored in public databases, from the longissimus thoracis of five different bovine breeds divergent by age. We updated gene identifiers on the last version of the bovine genome (UCD1.2), and the 715 genes common to the 10 studies were subjected to the meta-analysis. Of the 238 genes differentially expressed (DEG), we identified a transcriptional signature of the dynamic regulation of glycolytic and oxidative metabolisms that agrees with a known shift between those two pathways from the animal puberty. We proposed some master genes of the myogenesis, namely MYOG and MAPK14, as probable regulators of the glycolytic and oxidative metabolisms. We also identified overexpressed genes related to lipid metabolism (APOE, LDLR, MXRA8, and HSP90AA1) that may contribute to the expected enhanced marbling as age increases. Lastly, we proposed a transcriptional signature related to the induction (YBX1) or repression (MAPK14, YWAH, ERBB2) of the commitment of myogenic progenitors into the adipogenic lineage. The relationships between the abundance of the identified mRNA and marbling values remain to be analyzed in a marbling biomarkers discovery perspectives.

The Prion-like protein Shadoo is involved in mouse embryonic and mammary development and differentiation.

Shadoo belongs to the prion protein family, an evolutionary conserved and extensively studied family due to the implication of PrP in Transmissible Spongiform Encephalopathies. However, the biological function of these genes remains poorly understood. While Sprn-knockdown experiments suggested an involvement of Shadoo during mouse embryonic development, Sprn-knockout experiments in 129Pas/C57BL/6J or 129Pas/FVB/NCr mice did not confirm it. In the present study, we analyzed the impact of Sprn gene invalidation in a pure FVB/NJ genetic background, using a zinc finger nuclease approach. The in-depth analysis of the derived knockout transgenic mice revealed a significant increase in embryonic lethality at early post-implantation stages, a growth retardation of young Sprn-knockout pups fed by wild type mice and a lactation defect of Sprn-knockout females. Histological and transcriptional analyses of knockout E7.5 embryos, E14.5 placentas and G7.5 mammary glands revealed specific roles of the Shadoo protein in mouse early embryogenesis, tissue development and differentiation with a potential antagonist action between PrP and Shadoo. This study thus highlights the entanglement between the proteins of the prion family.

Pangenomic Classification of Pituitary Neuroendocrine Tumors.

Pituitary neuroendocrine tumors (PitNETs) are common, with five main histological subtypes: lactotroph, somatotroph, and thyrotroph (POU1F1/PIT1 lineage); corticotroph (TBX19/TPIT lineage); and gonadotroph (NR5A1/SF1 lineage). We report a comprehensive pangenomic classification of PitNETs. PitNETs from POU1F1/PIT1 lineage showed an epigenetic signature of diffuse DNA hypomethylation, with transposable elements expression and chromosomal instability (except for GNAS-mutated somatotrophs). In TPIT lineage, corticotrophs were divided into three classes: the USP8-mutated with overt secretion, the USP8-wild-type with increased invasiveness and increased epithelial-mesenchymal transition, and the large silent tumors with gonadotroph transdifferentiation. Unexpected expression of gonadotroph markers was also found in GNAS-wild-type somatotrophs (SF1 expression), challenging the current definition of SF1/gonadotroph lineage. This classification improves our understanding and affects the clinical stratification of patients with PitNETs.

The impact of genomic selection on genetic diversity and genetic gain in three French dairy cattle breeds.

BACKGROUND: In France, implementation of genomic evaluations in dairy cattle breeds started in 2009 and this has modified the breeding schemes drastically. In this context, the goal of our study was to understand the impact of genomic selection on the genetic diversity of bulls from three French dairy cattle breeds born between 2005 and 2015 (Montbéliarde, Normande and Holstein) and the factors that are involved. METHODS: We compared annual genetic gains, inbreeding rates based on runs of homozygosity (ROH) and pedigree data, and mean ROH length within breeds, before and after the implementation of genomic selection. RESULTS: Genomic selection induced an increase in mean annual genetic gains of 50, 71 and 33% for Montbéliarde, Normande and Holstein bulls, respectively, and in parallel, the generation intervals were reduced by a factor of 1.7, 1.9 and 2, respectively. We found no significant change in inbreeding rate for the two national breeds, Montbéliarde and Normande, and a significant increase in inbreeding rate for the Holstein international breed, which is now as high as 0.55% per year based on ROH and 0.49% per year based on pedigree data (equivalent to a rate of 1.36 and 1.39% per generation, respectively). The mean ROH length was longer for bulls from the Holstein breed than for those from the other two breeds. CONCLUSIONS: With the implementation of genomic selection, the annual genetic gain increased for bulls from the three major French dairy cattle breeds. At the same time, the annual loss of genetic diversity increased for Holstein bulls, possibly because of the massive use of a few elite bulls in this breed, but not for Montbéliarde and Normande bulls. The increase in mean ROH length in Holstein may reflect the occurrence of recent inbreeding. New strategies in breeding schemes, such as female donor stations and embryo transfer, and recent implementation of genomic evaluations in small regional breeds should be studied carefully in order to ensure the sustainability of breeding schemes in the future.

Fine-tuned adaptation of embryo-endometrium pairs at implantation revealed by transcriptome analyses in Bos taurus.

Interactions between embryo and endometrium at implantation are critical for the progression of pregnancy. These reciprocal actions involve exchange of paracrine signals that govern implantation and placentation. However, it remains unknown how these interactions between the conceptus and the endometrium are coordinated at the level of an individual pregnancy. Under the hypothesis that gene expression in endometrium is dependent on gene expression of extraembryonic tissues and genes expressed in extraembryonic tissues are dependent of genes expressed in the endometrium, we performed an integrative analysis of transcriptome profiles of paired extraembryonic tissue and endometria obtained from cattle (Bos taurus) pregnancies initiated by artificial insemination. We quantified strong dependence (|r| > 0.95, empirical false discovery rate [eFDR] < 0.01) in transcript abundance of genes expressed in the extraembryonic tissues and genes expressed in the endometrium. The profiles of connectivity revealed distinct coexpression patterns of extraembryonic tissues with caruncular and intercaruncular areas of the endometrium. Notably, a subset of highly coexpressed genes between extraembryonic tissue (n = 229) and caruncular areas of the endometrium (n = 218, r > 0.9999, eFDR < 0.001) revealed a blueprint of gene expression specific to each pregnancy. Gene ontology analyses of genes coexpressed between extraembryonic tissue and endometrium revealed significantly enriched modules with critical contribution for implantation and placentation, including "in utero embryonic development," "placenta development," and "regulation of transcription." Coexpressing modules were remarkably specific to caruncular or intercaruncular areas of the endometrium. The quantitative association between genes expressed in extraembryonic tissue and endometrium emphasize a coordinated communication between these two entities in mammals. We provide evidence that implantation in mammalian pregnancy relies on the ability of the extraembryonic tissue and the endometrium to develop a fine-tuned adaptive response characteristic of each pregnancy.

A genomic map of climate adaptation in Mediterranean cattle breeds.

Domestic species such as cattle (Bos taurus taurus and B. t. indicus) represent attractive biological models to characterize the genetic basis of short-term evolutionary response to climate pressure induced by their post-domestication history. Here, using newly generated dense SNP genotyping data, we assessed the structuring of genetic diversity of 21 autochtonous cattle breeds from the whole Mediterranean basin and performed genome-wide association analyses with covariables discriminating the different Mediterranean climate subtypes. This provided insights into both the demographic and adaptive histories of Mediterranean cattle. In particular, a detailed functional annotation of genes surrounding variants associated with climate variations highlighted several biological functions involved in Mediterranean climate adaptation such as thermotolerance, UV protection, pathogen resistance or metabolism with strong candidate genes identified (e.g., NDUFB3, FBN1, METTL3, LEF1, ANTXR2 and TCF7). Accordingly, our results suggest that main selective pressures affecting cattle in Mediterranean area may have been related to variation in heat and UV exposure, in food resources availability and in exposure to pathogens, such as anthrax bacteria (Bacillus anthracis). Furthermore, the observed contribution of the three main bovine ancestries (indicine, European and African taurine) in these different populations suggested that adaptation to local climate conditions may have either relied on standing genomic variation of taurine origin, or adaptive introgression from indicine origin, depending on the local breed origins. Taken together, our results highlight the genetic uniqueness of local Mediterranean cattle breeds and strongly support conservation of these populations.

Different pre-implantation phenotypes of bovine blastocysts produced in vitro.

Embryo transfer in cattle is performed with blastocysts produced in vivo or in vitro using defined media. However, outdated systems such as those that use serum and co-culture remain of interest for research purposes. Here, we investigated the effect of additional culture time on in vitro-produced embryos. Specifically, we compared embryos that formed a blastocoel at different times after fertilisation to those that stayed in culture for up to two additional days with respect to their development in vivo after temporary transfer to oestrus-synchronised recipients. A pre-transfer set (D6, D6+1, D6+2, D7, D7+1, D8) was examined using microarray analyses and correlated with a post-transfer set that included two different days of transfer (D6-T6, D6+2-T8, D7+1-T8, D8-T8). All surviving conceptuses reached primitive-streak stages and filamentous sizes similarly to in vivo (D18) or in vitro controls (D7/T7). The recovery rate differed between D6 and D8 embryos that were immediately transferred (58 vs 25%). With an intermediate survival rate (33%), the D6 embryos with two additional days in culture produced nine times more IFN-tau (IFNT) at D18 than the D6 embryos that were immediately transferred. At the end of culture, D6 and D6+2 embryos displayed the highest number of gene expression differences. Despite a mortality of 40­60%, no signature was detectable in any of the transferred groups that would account for the embryos' fates. Initially reputed to be beneficial in producing more blastocysts, our culture system of B2 medium plus serum and co-culture generated blastocysts that were distinct from those developed in vivo (D7).

Domestic Fowl Breed Variation in Egg White Protein Expression: Application of Proteomics and Transcriptomics.

Avian egg white is essential for protecting and nourishing bird embryos during their development. Being produced in the female magnum, variability in hen oviduct gene expression may affect egg white composition in domestic chickens. Since traditional poultry breeds may represent a source of variation, in the present study we describe the egg white proteome (mass spectrometry) and corresponding magnum transcriptome (high-throughput sequencing) for 20 hens from five domestic fowl breeds (large breeds: Araucana, Czech golden pencilled, Minorca; and small breeds: Booted bantam, Rosecomb bantam). In total, we identified 189 egg white proteins and 16391 magnum-expressed genes. The majority of egg white protein content comprised proteins with an antimicrobial function. Despite general similarity, Between-class Principal Component Analysis revealed significant breed-specific variability in protein abundances, differentiating especially small and large breeds. Though we found strong association between magnum mRNA expression and egg white protein abundance across genes, coinertia analysis revealed no transcriptome/proteome costructure at the individual level. Our study is the first to show variation in protein abundances in egg white across chicken breeds with potential effects on egg quality, biosafety, and chick development. The observed interindividual variation probably results from post-transcriptional regulation creating a discrepancy between proteomic and transcriptomic data.

Detection of new pathways involved in the acceptance and the utilisation of a plant-based diet in isogenic lines of rainbow trout fry.

To meet the growing demand of fish feed for aquaculture, an increasing proportion of marine ingredients are being replaced by blends of plant products. However, the total replacement of marine ingredients in salmonid diets impairs fish performance. This is particularly true during the early fry stage and this stage is therefore considered of particular importance. In rainbow trout (RBT), the existence of a genetic variability to survive and grow with plant-based diets devoid of marine ingredients has now been proved, but the mechanisms behind are little studied especially at early stage. To investigate these, we analysed the whole transcriptome of three isogenic lines of RBT fry, which have similar growth when fed a marine resources-based diet (M diet) but which highly differ in their responses to a plant-based diet (V diet). Analysis of transcriptomes profiles revealed 1740, 1834 and 246 probes differentially expressed among the three genotypes when fed the V diet. The use of these lines led to the discovery of potential molecular markers linked to plant-based diet utilisation, some of them belonging to new pathways, never described before. An important number of genes was related to immunity, but further investigations are needed to better understand the difference between the genotypes in their immune status response to V diet exposure. Finally, differences in expression of genes related to feed intake and sensory perception among genotypes suggested that the mechanisms underlying the differences in growth on plant-based diet are closely linked to diet acceptance. Research on plants components affecting feed intake should be thus further explored.

Genomics for Ruminants in Developing Countries: From Principles to Practice.

Using genomic information, local ruminant populations can be better characterized and compared to selected ones. Genetic relationships between animals can be established even without systematic pedigree recording, provided a budget is available for genotyping. Genomic selection (GS) can rely on a subset of the total population and does not require a costly national infrastructure, e.g., based on progeny testing. Yet, the use of genomic tools for animal breeding in developing countries is still limited. We identify three main reasons for this: (i) the instruments for cheap recording of phenotypes and data management are still limiting. (ii) many developing countries are recurrently exposed to unfavorable conditions (heat, diseases, poor nutrition) requiring special attention to fitness traits, (iii) a high level of expertise in quantitative genetics, modeling, and data manipulation is needed to perform genomic analyses. Yet, the potential outcomes go much beyond genetic improvements and can improve the resilience of the whole farming system. They include a better management of genetic diversity of local populations, a more balanced genetic progress and the possibility to unravel the genetic basis of adaptation of local breeds through whole genome approaches. A GS program being developed by BAIF, a large Indian NGO, is analyzed as a pilot case. It relies on the creation of a female reference population of Bos indicus and crossbreds, recorded with modern technology (e.g., smartphones) to collect performances at low cost in tiny herds on production and fertility. Finally, recommendations for the implementation of GS in developing countries are proposed.