Carbon footprint based on lifetime productivity for future cows selected for resilience to climate-related disturbances.

Droughts, which can affect feed production, are projected to become more common under future climate conditions. In light of this, breeding cattle resilient to changes in feeding regimens is increasingly becoming an important topic. Body reserves can play a crucial role when feed resources are limited. We simulated populations of dairy cows selected with 2 different breeding goals: one reflecting the current breeding goal and the other placing weight on minimum level of body reserves in early lactation and change in body reserves during lactation. We considered this latter as a breeding goal for resilience. We used the 2 dynamic simulation programs ADAM and AQAL to predict performance of the cows after selection. In AQAL, we modeled moderate and severe drought by decreasing feed quality and quantity offered to cows during one year. We compared cows selected with the 2 breeding goals under 3 environments: without disturbances related to climate and with moderate and severe drought. In the environments without disturbances and the moderate drought, the cows selected with the current breeding goal had higher lifetime lactation efficiency (energy invested in milk/energy acquired from feed) and lower carbon footprint per kilogram of protein in milk and meat than cows selected for resilience. However, with severe drought, cows selected for resilience had higher lifetime lactation efficiency and lower carbon footprint per kilogram of protein in milk and meat than those selected with the current breeding goal. This suggests that cows selected for high productive performance do not perform well under very limiting conditions, leading to increased climate impact. The importance of inclusion of body reserves as a resilience trait in dairy cattle breeding depends on the future environment in which the cows will be used.

Emphasis on resilience in dairy cattle breeding: Possibilities and consequences.

This study aimed to investigate dairy cattle breeding goals with more emphasis on resilience. We simulated the consequences of increasing weight on resilience indicators and an assumed true resilience trait (TR). Two environments with different breeding goals were simulated to represent the variability of production systems across Europe. Ten different scenarios were stochastically simulated in a so-called pseudogenomic simulation approach. We showed that many modern dairy cattle breeding goals most likely have negative genetic gain for TR and promising resilience indicators such as the log-transformed, daily deviation from the lactation curve (LnVAR). In addition, there were many ways of improving TR by increasing the breeding goal weight of different resilience indicators. The results showed that adding breeding goal weight to resilience indicators, such as body condition score and LnVAR, could reverse the negative trend observed for resilience indicators. Loss in the aggregate genotype calculated with only current breeding goal traits was 12 to 76%. This loss was mainly due to a reduction in genetic gain in milk production. We observed higher genetic gain in beef production, fertility, and udder health when breeding for more resilience, but from an economical point of view, this was not high enough to compensate for the reduction in genetic gain in milk production. The highest genetic gain in TR was obtained when adding the highest breeding goal weight to LnVAR or TR, both with 0.29 genetic standard deviation units. The indicators we used, body condition score and LnVAR, can be measured on a large scale today with relatively cheap methods, which is crucial if we want to improve these traits through breeding. Economic values for resilience have to be estimated to find the most optimal breeding goal for a more resilient dairy cow in the future.

Combined mechanistic and genetic modelling to benchmark body reserve traits as proxies of dairy cows' lifetime efficiency in grass-based production systems.

Improving lifetime lactation efficiency of dairy cows by selection is difficult due to the complexity of this trait and the existence of genotype-by-environment interactions. This study aimed at assessing the relevance of traits derived from body reserves as lifetime efficiency indicators under contrasting nutritional environments. Given the absence of large-scale datasets covering a panel of feeding regimes, phenotypes were simulated for populations of 20 000 dairy cows using a mechanistic bioenergetic model. Ten phenotypes were computed for third-lactation cows. Analysed phenotypes comprised total milk production, lactation efficiency, BW at calving (BWcalv), DM intake (DMI) and interval between first insemination and conception. Five traits described levels and changes of body reserves at different periods during lactation. Lifetime lactation efficiency was computed for all cows (Life_Eff). Three nutritional environments were defined considering a grass-based production system with seasonal calving: a high non-limiting scenario (HS) mimicking ad libitum access to feed and two limiting environments with moderate (MS) and low (LS) feed offer. Variance components were estimated for all traits within and between environments using REML. Heritabilities estimated for milk production, lactation efficiency, BWcalv and DMI were moderate in the different environments (0.27-0.35 ± 0.04). The heritability of body reserve levels and dynamics were moderate in the HS and MS scenarios (0.23-0.30 ± 0.03) and lower in the LS scenario (0.14-0.25 ± 0.03). The heritability of Life_Eff was low in the HS environment (0.07 ± 0.01) and slightly increased in the limiting environments. All genetic correlations estimated between environments were moderate to high (≥0.66 ± 0.07), suggesting low to moderate genotype-by-environment interactions. Estimated genetic correlations were moderate between Life_Eff and body reserve levels (from 0.39 to 0.51 ± 0.08) and moderate but negative between Life_Eff and change in body reserves traits (-0.27 to -0.37 ± 0.09) in the HS environment. The genetic correlations between Life_Eff and body reserve levels increased to higher values in the limiting environments. In contrast, genetic correlations between Life_Eff and the changes in body reserves were closer to zero. In conclusion, this study showed that body reserve levels were relevant proxies of lifetime irrespective of the environment. In contrast, changes in body reserves that reflected energy mobilisation in early lactation were less informative about lifetime efficiency in environments with severe feed restrictions.

Digestive efficiency traits in growing pigs are genetically correlated with sow litter traits in the Large White breed.

Digestive efficiency traits are promising selection criteria to improve feed efficiency in pigs. However, the genetic relationships between digestive efficiency and sow reproductive traits are mostly unknown and need to be estimated. In this study, reproductive traits were available for 61 601 litters recorded on 21 719 Large White purebred sows. The traits were comprised of the number of born alive (NBA) and the number of weaned piglets (NWP), the number of stillbirths (NSB) and piglet mortality during suckling (PM). For a subset of 32518 litters, the mean (MBW) and CV of piglet birth weights (CVBW) were deduced from individual piglet weights as well as the proportion of piglets weighing less than 1 kg (PPL1K). Growth and feed efficiency traits were available for 4 643 Large White male pigs related to sows with reproductive performances. They comprised average daily gain (ADG), daily feed intake (DFI) and feed conversion ratio (FCR). A subset of 1 391 pigs had predictions for digestibility coefficients (DC) of energy, organic matter and nitrogen obtained by analysing faecal samples with near-infrared spectrometry. Estimated heritabilities were low for NBA, NSB, NWP and PM (0.08 ± 0.01 to 0.11 ± 0.01) and low to moderate for litter weight characteristics (0.14 ± 0.02 to 0.38 ± 0.01). Heritability estimates were moderate to high for ADG, DFI and FCR (0.37 ± 0.04 to 0.54 ± 0.05) and moderate for DC traits (0.26 ± 0.06 to 0.38 ± 0.07). Genetic correlations were low between ADG, or alternatively FCR, and reproductive traits. They were significantly different from zero with MBW (0.19 ± 0.06 with ADG and -0.15 ± 0.06 with FCR) and PPL1K (-0.19 ± 0.07 with ADG and 0.18 ± 0.07 with FCR). All genetic correlations between DFI and reproductive traits were low and not significantly different from zero. Genetic correlations between DC traits and NBA were significantly different from zero for DC of organic matter and energy (<-0.25 ± 0.11). DC traits were moderately correlated with MBW (>0.30 ± 0.11), CVBW (<-0.36 ± 0.11) and PPL1K (<-0.37 ± 0.11) at the genetic level. Genetic correlations between DC traits and PM were significantly negative and hence favourable (<-0.38 ± 0.12). Finally, genetic correlations between DC traits and NWP were close to zero. These results suggested that sows closely related to growing pigs with the best digestive efficiency would produce heavier and more homogeneous piglets, with slightly smaller litter sizes at birth but better survival. Hence, there is usable genetic variation in DC that could be exploited to define new selection strategies in maternal lines aiming at improving not only feed efficiency but also piglet survival.

Genetic relationships between efficiency traits and gut microbiota traits in growing pigs being fed with a conventional or a high-fiber diet.

In pigs, the gut microbiota composition plays a major role in the process of digestion, but is influenced by many external factors, especially diet. To be used in breeding applications, genotype by diet interactions on microbiota composition have to be quantified, as well as their impact on genetic covariances with feed efficiency (FE) and digestive efficiency (DE) traits. This study aimed at determining the impact of an alternative diet on variance components of microbiota traits (genera and alpha diversity indices) and estimating genetic correlations between microbiota and efficiency traits for pigs fed a conventional (CO) or a high-fiber (HF) diet. Fecal microbes of 812 full-siblings fed a CO diet and 752 pigs fed the HF diet were characterized at 16 weeks of age by sequencing the V3-V4 region of the 16S rRNA gene. A total of 231 genera were identified. Digestibility coefficients of nitrogen, organic matter, and energy were predicted analyzing the same fecal samples with near infrared spectrometry. Daily feed intake, feed conversion ratio, residual feed intake and average daily gain (ADG) were also recorded. The 71 genera present in more than 20% of individuals were retained for genetic analyses. Heritability (h²) of microbiota traits were similar between diets (from null to 0.38 ±â€…0.12 in the CO diet and to 0.39 ±â€…0.12 in the HF diet). Only three out of the 24 genera and two alpha diversity indices with significant h² in both diets had genetic correlations across diets significantly different from 0.99 (P < 0.05), indicating limited genetic by diet interactions for these traits. When both diets were analyzed jointly, 59 genera had h² significantly different from zero. Based on the genetic correlations between these genera and ADG, FE, and DE traits, three groups of genera could be identified. A group of 29 genera had abundances favorably correlated with DE and FE traits, 14 genera were unfavorably correlated with DE traits, and the last group of 16 genera had abundances with correlations close to zero with production traits. However, genera abundances favorably correlated with DE and FE traits were unfavorably correlated with ADG, and vice versa. Alpha diversity indices had correlation patterns similar to the first group. In the end, genetic by diet interactions on gut microbiota composition of growing pigs were limited in this study. Based on this study, microbiota-based traits could be used as proxies to improve FE and DE in growing pigs.

The link between the composition of the gut microbiota, i.e the composition of microorganisms in the gut, in pigs and their feed efficiency, i.e. their ability to utilize nutrients, as well as their ability to digest were studied from a genetic point of view. A family structure of 1,564 pigs were studied and fed with two different diets. One of the full-sib was fed a conventional diet used in breeding farms and the other one an alternative diet containing raw materials, less expensive but with a higher content of dietary fibers more difficult to digest. This study has shown that some microbiota microorganisms were genetically correlated with feed and digestive efficiency performances, positively or negatively, depending on the microorganisms. In addition, the diversity of microorganisms in the animal's gut was favorably correlated with the feed and digestive performances studied. Therefore, there is a genetic link between these performances and the composition of the animal's gut microbiota. Thus, a potential genetic selection on some intestinal microorganisms or diversity of microorganisms would allow to improve these performances, and in particular when pigs are fed with diet more difficult to digest.

Exogenic origin for the volatiles sampled by the Lunar CRater Observation and Sensing Satellite impact.

Returning humans to the Moon presents an unprecedented opportunity to determine the origin of volatiles stored in the permanently shaded regions (PSRs), which trace the history of lunar volcanic activity, solar wind surface chemistry, and volatile delivery to the Earth and Moon through impacts of comets, asteroids, and micrometeoroids. So far, the source of the volatiles sampled by the Lunar Crater Observation and Sensing Satellite (LCROSS) plume has remained undetermined. We show here that the source could not be volcanic outgassing and the composition is best explained by cometary impacts. Ruling out a volcanic source means that volatiles in the top 1-3 meters of the Cabeus PSR regolith may be younger than the latest volcanic outgassing event (~1 billion years ago; Gya).

Impact of a high-fibre diet on genetic parameters of production traits in growing pigs.

The use of diets with increased fibre content from alternative feedstuffs less digestible for pigs is a solution considered to limit the impact of increased feed costs on pig production. This study aimed at determining the impact of an alternative diet on genetic parameters for growth, feed efficiency, carcass composition and meat quality traits. A total of 783 Large White pigs were fed a high-fibre (HF) diet and 880 of their sibs were fed a conventional (CO) cereal-based diet. Individual daily feed intake, average daily gain, feed conversion ratio and residual feed intake were recorded as well as lean meat percentage (LMP), carcass yield (CY) and meat quality traits. Pigs fed the CO diet had better performances for growth and feed efficiency than pigs fed the HF diet. They also had lower LMP and higher CY. In addition, pigs fed the CO diet had lower loin percentage and ham percentage and higher backfat percentage. No differences were observed in meat quality traits between diets, except for a* and b* values. For all traits, the genetic variances and heritability were not different between diets. Genetic correlations for traits between diets ranged between 0.80 ± 0.13 and 0.99 ± not estimable, and none were significantly different from 0.99, except for LMP. Thus, traits in both diets were considered as mainly affected by similar sets of genes in the two diets. A genetic correlation lower than 0.80 would justify redesigning the breeding scheme; however, some genetic correlations did not differ significantly from 0.80 either. Therefore, larger populations are needed for a more definitive answer regarding the design of the breeding scheme. To further evaluate selection strategies, a production index was computed within diets for the 29 sires with estimated breeding value reliability higher than 0.35. The rank correlation between indices estimated in the CO and in the HF diet was 0.72. Altogether, we concluded that limited interaction between feed and genetics could be evidenced, and based on these results there is no need to change pig selection schemes to adapt to the future increased use of alternative feedstuffs in production farms.

[Salmonella meningitis in an infant due to a pet turtle]. / Méningite à Salmonelle chez un nourrisson due à une tortue domestique.

In humans, Salmonella most often causes self-limiting gastroenteritis, but more severe symptoms such as sepsis and meningitis can also occur and can sometimes have a fatal outcome. Even if the meningitis is not fatal, sequelae such as epilepsy, cranial nerve palsies, and hydrocephalus can occur. In the United States, it has been estimated that approximately 6% of the human cases of salmonellosis can be attributed to contact with reptiles or amphibians. The infection may take place by direct contact between reptile and human or indirectly via contact with an environment contaminated with Salmonella from a reptile. Salmonella enterica subsp. enterica serotype Vitkin is a common gut inhabitant of reptiles. Though human cases due to this organism are exceedingly rare, it may infect young infants and immunocompromised individuals with a history of intimate associations with reptiles. Gastroenteritis is the most common presentation ; others include peritonitis, meningitis and bacteremia. We report a case of meningitis caused by S. enterica subsp. enterica serotype Vitkin in a 1-month-old child due to a pet turtle.

Genetic mapping of grapevine ( Vitis vinifera L.) applied to the detection of QTLs for seedlessness and berry weight.

Parental and consensus genetic maps of Vitis vinifera L. (2n = 38) were constructed using a F(1) progeny of 139 individuals from a cross between two partially seedless genotypes. The consensus map contained 301 markers [250 amplification fragment length polymorphisms (AFLPs), 44 simple sequence repeats (SSRs), three isozymes, two random amplified polymorphic DNAs (RAPDs), one sequence-characterized amplified region (SCAR), and one phenotypic marker, berry color] mapped onto 20 linkage groups, and covered 1,002 cM. The maternal map consisted of 157 markers covering 767 cM (22 groups). The paternal map consisted of 144 markers covering 816 cM (23 groups). Differences in recombination rates between these maps and another unpublished map are discussed. The major gene for berry color was mapped on both the paternal and consensus maps. Quantitative trait loci (QTLs) for several quantitative subtraits of seedlessness in 3 successive years were searched for, based on parental maps: berry weight, seed number, seed total fresh and dry weights, seed percent dry matter, and seed mean fresh and dry weights. QTLs with large effects (R(2) up to 51%) were detected for all traits and years at the same location on one linkage group, with some evidence for the existence of a second linked major QTL for some of them. For these major QTLs, differences in relative parental effects were observed between traits. Three QTLs with small effects (R(2) from 6% to 11%) were also found on three other linkage groups, for berry weight and seed number in a single year, and for seed dry matter in 2 different years.

Identification of resistance gene analogs linked to a powdery mildew resistance locus in grapevine.

Oligonucleotide primers, designed to conserved regions of nucleotide binding site (NBS) motifs within previously cloned pathogen resistance genes, were used to amplify resistance gene analogs (RGAs) from grapevine. Twenty eight unique grapevine RGA sequences were identified and subdivided into 22 groups on the basis of nucleic acid sequence-identity of approximately 70% or greater. Representatives from each group were used in a bulked segregant analysis strategy to screen for restriction fragment length polymorphisms linked to the powdery mildew resistance locus, Run1, introgressed into Vitis vinifera L. from the wild grape species Muscadinia rotundifolia. Three RGA markers were found to be tightly linked to the Run1 locus. Of these markers, two (GLP1-12 and MHD145) cosegregated with the resistance phenotype in 167 progeny tested, whereas the third marker (MHD98) was mapped to a position 2.4 cM from the Run1 locus. The results demonstrate the usefulness of RGA sequences, when used in combination with bulked segregant analysis, to rapidly generate markers tightly linked to resistance loci in crop species.

Integrating genomic selection into dairy cattle breeding programmes: a review.

Extensive genetic progress has been achieved in dairy cattle populations on many traits of economic importance because of efficient breeding programmes. Success of these programmes has relied on progeny testing of the best young males to accurately assess their genetic merit and hence their potential for breeding. Over the last few years, the integration of dense genomic information into statistical tools used to make selection decisions, commonly referred to as genomic selection, has enabled gains in predicting accuracy of breeding values for young animals without own performance. The possibility to select animals at an early stage allows defining new breeding strategies aimed at boosting genetic progress while reducing costs. The first objective of this article was to review methods used to model and optimize breeding schemes integrating genomic selection and to discuss their relative advantages and limitations. The second objective was to summarize the main results and perspectives on the use of genomic selection in practical breeding schemes, on the basis of the example of dairy cattle populations. Two main designs of breeding programmes integrating genomic selection were studied in dairy cattle. Genomic selection can be used either for pre-selecting males to be progeny tested or for selecting males to be used as active sires in the population. The first option produces moderate genetic gains without changing the structure of breeding programmes. The second option leads to large genetic gains, up to double those of conventional schemes because of a major reduction in the mean generation interval, but it requires greater changes in breeding programme structure. The literature suggests that genomic selection becomes more attractive when it is coupled with embryo transfer technologies to further increase selection intensity on the dam-to-sire pathway. The use of genomic information also offers new opportunities to improve preservation of genetic variation. However, recent simulation studies have shown that putting constraints on genomic inbreeding rates for defining optimal contributions of breeding animals could significantly reduce achievable genetic gain. Finally, the article summarizes the potential of genomic selection to include new traits in the breeding goal to meet societal demands regarding animal health and environmental efficiency in animal production.

A definition of unknown parent groups based on bull usage patterns across herds.

In genetic evaluations, the definition of unknown parent groups (UPG) is usually based on time periods, selection path and flows of foreign founders. The definition of UPG may be more complex for populations presenting genetic heterogeneity due to both, large national expansion and coexistence of artificial insemination (AI) and natural service (NS). A UPG definition method accounting for beef bull flows was proposed and applied to the French Charolais cattle population. It assumed that, at a given time period, unknown parents belonged to the same UPG when their progeny were bred in herds that used bulls with similar origins (birth region and reproduction way). Thus, the birth period, region and AI rate of a herd were pointed out to be the three criteria reflecting genetic disparities at the national level in a beef cattle population. To deal with regional genetic disparities, 14 regions were identified using a factorial approach combining principal component analysis and Ward clustering. The selection nucleus of the French cattle population was dispersed over three main breeding areas. Flows of NS bulls were mainly carried out within each breeding area. On the contrary, the use and the selection of AI bulls were based on a national pool of candidates. Within a time period, herds of different regions were clustered together when they used bulls coming from the same origin and with an estimated difference of genetic level lower than 20% of genetic standard deviation (σg) for calf muscle and skeleton scores (SS) at weaning. This led to the definition of 16 UPG of sires, which were validated as robust and relevant in a sire model, meaning numerically stable and corresponding to distinct genetic subpopulations. The UPG genetic levels were estimated for muscle and SS under sire and animal models. Whatever the trait, differences between bull UPG estimates within a time period could reach 0.5 σg across regions. For a given time period, bull UPG estimates for muscle and SS were generally larger by 0.30 to 0.75 σg than those of cows. Including genetic groups in the evaluation model increased the estimated genetic trends by 20% to 30%. It also provoked re-ranking in favor of bulls and cows without pedigree.

Genetic structure of the European Charolais and Limousin cattle metapopulations using pedigree analyses.

Pedigree collected by the Interbeef service allowed genetic diversity to be assessed by using pedigree analyses for the European Charolais (CHA) and Limousin (LIM) cattle populations registered in national herdbooks in Denmark (DNK), France (FRA), Ireland (IRL), Sweden (SWE), and, solely for the LIM breed, the United Kingdom (UK). The CHA data set included 2,563,189 calves with weaning performance, of which 96.1% were recorded in FRA, 3.0% in SWE, 0.5% in IRL, and 0.4% in DNK. The LIM data set included 1,652,734 calves with weaning performance, of which 91.9% were recorded in FRA, 4.9% in UK, 1.8% in DNK, 0.9% SWE, and 0.5% in IRL. Pedigree files included 3,191,132 CHA and 2,409,659 LIM animals. Gene flows were rather limited between populations, except from FRA toward other countries. Pedigree completeness was good in all subpopulations for both breeds and allowed the pedigree to be traced back to the French population. A relatively high level of genetic diversity was assessed in each CHA and LIM subpopulation by estimating either effective population sizes (N(e) >244 and N(e) >345 in the CHA and LIM subpopulations, respectively), relationship coefficients within subpopulations (<1.3% in both breeds), or probability of gene origins. However, in each subpopulation, it was shown that founders and also ancestors had unbalanced genetic contributions, leading to a moderate but continuous reduction in genetic diversity. Analyses between populations suggested that all European CHA and LIM populations were differentiated very little. The Swedish CHA population was assessed as genetically more distant from the other CHA populations because of fewer gene flows from other countries and because of the use of North American sires to introgress the polled phenotype. In each European subpopulation, most of the main ancestors, which explained 50% of gene origin, were born in FRA. However, those main ancestors were different between countries. Moreover, in both breeds, the main ancestors, which explained 50% of the gene origin in DNK, IRL, SWE, and UK for the LIM breed, were found to be infrequently used in FRA. Those results were consistent with the low relationship coefficients estimated between subpopulations (<0.6% in both the CHA and LIM breeds). Therefore, in both breeds, each subpopulation may constitute a reservoir of genetic diversity for the other ones.

Somatic chimerism, genetic inheritance, and mapping of the fleshless berry (flb) mutation in grapevine (Vitis vinifera L.).

The fleshless berry (flb) mutation of grapevine (Vitis vinifera L. 'Ugni Blanc') impairs the differentiation and division of inner mesocarp cells responsible for flesh in grapevine berries. In order to study the inheritance of the mutation and to map the flb locus, 5 segregating populations were created. Progeny plants were classified as mutant or wild type by scoring for the presence of an ovary phenotype associated with the Flb- phenotype at anthesis. Phenotypic segregation revealed the involvement of a single dominant allele that was heterozygous in the original mutant. Through bulk segregant analysis, microsatellite (simple sequence repeat (SSR)) markers linked to the mutation were identified, and the flb locus was assigned to linkage group 18. The locus position was then refined by analyzing individual progeny and the segregation of SSR markers in the target region with the closest marker 5.6 cM distant from the flb locus. All progeny with the Flb- ovary phenotype differed from the original fleshless berry mutant in that no berries formed after anthesis. Our data suggest that the original mutant plant was a chimera with the mutated allele present in only 1 cell layer (L2 layer) of the ovary and berry.

Genetic and physical mapping of the grapevine powdery mildew resistance gene, Run1, using a bacterial artificial chromosome library.

Resistance to grapevine powdery mildew is controlled by Run1, a single dominant gene present in the wild grapevine species, Muscadinia rotundifolia, but absent from the cultivated species, Vitis vinifera. Run1 has been introgressed into V. vinifera using a pseudo-backcross strategy, and genetic markers have previously been identified that are linked to the resistance locus. Here we describe the construction of comprehensive genetic and physical maps spanning the resistance locus that will enable future positional cloning of the resistance gene. Physical mapping was performed using a bacterial artificial chromosome (BAC) library constructed using genomic DNA extracted from a resistant V. vinifera individual carrying Run1 within an introgression. BAC contig assembly has enabled 20 new genetic markers to be identified that are closely linked to Run1, and the position of the resistance locus has been refined, locating the gene between the simple sequence repeat (SSR) marker, VMC4f3.1, and the BAC end sequence-derived marker, CB292.294. This region contains two multigene families of resistance gene analogues (RGA). A comparison of physical and genetic mapping data indicates that recombination is severely repressed in the vicinity of Run1, possibly due to divergent sequence contained within the introgressed fragment from M. rotundifolia that carries the Run1 gene.