BACKGROUND: Genetic diversity is a necessary condition for populations to evolve under natural adaptation, artificial selection, or both. However, genetic diversity is often threatened, in particular in domestic animal populations where artificial selection, genetic drift and inbreeding are strong. In this context, cryopreserved genetic resources are a promising option to reintroduce lost variants and to limit inbreeding. However, while the use of ancient genetic resources is more common in plant breeding, it is less documented in animals due to a longer generation interval, making it difficult to fill the gap in performance due to continuous selection. This study investigates one of the only concrete cases available in animals, for which cryopreserved semen from a bull born in 1977 in a lost lineage was introduced into the breeding scheme of a French local dairy cattle breed, the Abondance breed, more than 20 years later.
RESULTS: We found that this re-introduced bull was genetically distinct with respect to the current population and thus allowed part of the genetic diversity lost over time to be restored. The expected negative gap in milk production due to continuous selection was absorbed in a few years by preferential mating with elite cows. Moreover, the re-use of this bull more than two decades later did not increase the level of inbreeding, and even tended to reduce it by avoiding mating with relatives. Finally, the reintroduction of a bull from a lost lineage in the breeding scheme allowed for improved performance for reproductive abilities, a trait that was less subject to selection in the past.
CONCLUSIONS: The use of cryopreserved material is an efficient way to manage the genetic diversity of an animal population, by mitigating the effects of both inbreeding and strong selection. However, attention should be paid to mating of animals to limit the disadvantages associated with incorporating original genetic material, notably a discrepancy in the breeding values for selected traits or an increase in inbreeding. Therefore, careful characterization of the genetic resources available in cryobanks could help to ensure the sustainable management of populations, in particular local or small populations. These results could also be transferred to the conservation of wild threatened populations.

Additive genetic variance, VA, is the key parameter for predicting adaptive and neutral phenotypic evolution. Changes in demography (e.g. increased close-relative inbreeding) can alter VA, but how they do so depends on the (typically unknown) gene action and allele frequencies across many loci. For example, VA increases proportionally with the inbreeding coefficient when allelic effects are additive, but smaller (or larger) increases can occur when allele frequencies are unequal at causal loci with dominance effects. Here, we describe an experimental approach to assess the potential for dominance effects to deflate VA under inbreeding. Applying a powerful paired pedigree design in Drosophila serrata, we measured 11 wing traits on half-sibling families bred via either random or sibling mating, differing only in homozygosity (not allele frequency). Despite close inbreeding and substantial power to detect small VA, we detected no deviation from the expected additive effect of inbreeding on genetic (co)variances. Our results suggest the average dominance coefficient is very small relative to the additive effect, or that allele frequencies are relatively equal at loci affecting wing traits. We outline the further opportunities for this paired pedigree approach to reveal the characteristics of VA, providing insight into historical selection and future evolutionary potential.

Developing sound breeding programs for aquaculture species may be challenging when matings cannot be controlled due to communal spawning. We developed a genotyping-by-sequencing marker panel of 300 SNPs for parentage testing and sex determination by using data from an in-house reference genome as well as a 90 K SNP genotyping array based on different populations of yellowtail kingfish (Seriola lalandi). The minimum and maximum distance between adjacent marker pairs were 0.7 Mb and 13 Mb, respectively, with an average marker spacing of 2 Mb. Weak evidence of the linkage disequilibrium between adjacent marker pairs was found. The results showed high panel performance for parental assignment, with probability exclusion values equaling 1. The rate of false positives when using cross-population data was null. A skewed distribution of genetic contributions by dominant females was observed, thus increasing the risk of higher rates of inbreeding in subsequent captive generations when no parentage data are used. All these results are discussed in the context of breeding program design, using this marker panel to increase the sustainability of this aquaculture resource.

The genetic variation of the European population at a macro-geographic scale follows genetic gradients which reflect main migration events. However, less is known about factors affecting mating patterns at a micro-geographic scale. In this study we have analyzed 726,718 autosomal single nucleotide variants in 435 individuals from the catalan Pyrenees covering around 200 km of a vast and abrupt region in the north of the Iberian Peninsula, for which we have information about the geographic origin of all grand-parents and parents. At a macro-geographic scale, our analyses recapitulate the genetic gradient observed in Spain. However, we also identified the presence of micro-population substructure among the sampled individuals. Such micro-population substructure does not correlate with geographic barriers such as the expected by the orography of the considered region, but by the bishoprics present in the covered geographic area. These results support that, on top of main human migrations, long ongoing socio-cultural factors have also shaped the genetic diversity observed at rural populations.

BACKGROUND: On-going climate change will drastically modify agriculture in the future, with a need for more sustainable systems, in particular regarding animal production. In this context, genetic diversity is a key factor for adaptation to new conditions: local breeds likely harbor unique adaptive features and represent a key component of diversity to reach resilience. However, local breeds often suffer from small population sizes, which puts these valuable resources at risk of extinction. In chickens, population management programs were initiated a few decades ago in France, relying on a particular niche market that aims at promoting and protecting local breeds. We conducted a unique comprehensive study of 22 French local breeds, along with four commercial lines, to evaluate their genetic conservation status and the efficiency of the population management programs.
RESULTS: Using a 57K single nucleotide polymorphism (SNP) chip, we demonstrated that both the between- and within-breed genetic diversity levels are high in the French local chicken populations. Diversity is mainly structured according to the breeds\' selection and history. Nevertheless, we observed a prominent sub-structuring of breeds according to farmers\' practices in terms of exchange, leading to more or less isolated flocks. By analysing demographic parameters and molecular information, we showed that consistent management programs are efficient in conserving genetic diversity, since breeds that integrated such programs earlier had older inbreeding.
CONCLUSIONS: Management programs of French local chicken breeds have maintained their genetic diversity at a good level. We recommend that future programs sample as many individuals as possible, with emphasis on both males and females from the start, and focus on a quick and strong increase of population size while conserving as many families as possible. We also stress the usefulness of molecular tools to monitor small populations for which pedigrees are not always available. Finally, the breed appears to be an appropriate operational unit for the conservation of genetic diversity, even for local breeds, for which varieties, if present, could also be taken into account.

BACKGROUND: Genetics driven interventions if adopted in conservation breeding projects may enhance the overall success by prioritizing breeding among genetically most competent individuals and delaying or completely diminishing the ill effects of inbreeding.
RESULTS: In the present study, we investigated genetic make-up of 15 tigers housed at five different captive facilities of West Bengal in India and report the moderate level of genetic variation. We identified five tigers based on individual genetic attributes that may be prioritized for future breeding or animal exchange programmes. The occurrence of first and second order related individuals in captivity require management attention and they should be paired considering their immediate genetic background.
CONCLUSIONS: Considering tiger as a case study, we highlight the use of genetic assessment and necessity to validate the studbook records in formulating adaptive management strategies for long-term conservation and management of species of interest.

BACKGROUND: To understand which reproductive barriers initiate speciation is a major question in evolutionary research. Despite their high species numbers and specific biology, there are only few studies on speciation in Hymenoptera. This study aims to identify very early reproductive barriers in a local, sympatric population of Nasonia vitripennis (Walker 1836), a hymenopterous parasitoid of fly pupae. We studied ecological barriers, sexual barriers, and the reduction in F1-female offspring as a postmating barrier, as well as the population structure using microsatellites.
RESULTS: We found considerable inbreeding within female strains and a population structure with either three or five subpopulation clusters defined by microsatellites. In addition, there are two ecotypes, one parasitizing fly pupae in bird nests and the other on carrion. The nest ecotype is mainly formed from one of the microsatellite clusters, the two or four remaining microsatellite clusters form the carrion ecotype. There was slight sexual isolation and a reduction in F1-female offspring between inbreeding strains from the same microsatellite clusters and the same ecotypes. Strains from different microsatellite clusters are separated by a reduction in F1-female offspring. Ecotypes are separated only by ecological barriers.
CONCLUSIONS: This is the first demonstration of very early reproductive barriers within a sympatric population of Hymenoptera. It demonstrates that sexual and premating barriers can precede ecological separation. This indicates the complexity of ecotype formation and highlights the general need for more studies within homogenous populations for the identification of the earliest barriers in the speciation process.

The Istrian sheep breed has been subjected to selection for dairy traits for more than two decades. However, a detailed study of some important population-specific parameters such as effective population size (Ne) and connectedness between flocks has never been carried out. The aim of the study was to examine the above parameters in dairy Istrian sheep subjected to a national selection program. The Ne was estimated as the mean rate of increase in coancestry, and connectedness was determined using four different statistics. The Ne was estimated at 73 animals with pedigree constraints imposed on 4 equivalent generations and 3 full generations. Analysis of ΔNe (\"sliding window approach\") revealed a negative ΔNe indicating a progressive loss of genetic variability (ΔNeNEG≥4 = -6.6, p < 0.01; ΔNeNFG≥3 = -4.9, p > 0.05). The overall connectedness (r¯ ~ 0.0001) was below the acceptable level for unbiased ranking of the animals belonging to different flocks (ri,j  = 0.05). OCS appears to be the best option for the long-term survival (self-sufficiency) of the breed, but genetic links between flocks need to be strengthened to allow unbiased ranking of the animals based on the estimated breeding values.

The mating system is a central parameter of plant biology because it shapes their ecological and evolutionary properties. Therefore, determining ecological variables that influence the mating system is important for a deeper understanding of the functioning of plant populations. Here, using old concepts and recent statistical developments, we propose a new statistical tool to make inferences about ecological determinants of outcrossing in natural plant populations. The method requires codominant genotypes of seeds collected from maternal plants within different locations. Using extensive computer simulations, we demonstrated that the method is robust to the issues expected for real-world data, including the Wahlund effect, inbreeding and genotyping errors such as allele dropout and allele misclassification. Furthermore, we showed that the estimates of ecological effects and outcrossing rates can be severely biased if genotyping errors and genetic differentiation are not treated explicitly. Application of the new method to the case study of a dioecious tree (Taxus baccata) allowed revealing that female trees that grow in lower local densities have a greater tendency towards mating with relatives. Moreover, we also demonstrated that biparental inbreeding is higher in populations that are characterized by a longer mean distance between trees and a smaller mean trunk perimeter. We found these results to agree with both the theoretical predictions and the history of English yew.

The Pura Raza Español (PRE) is an autochthonous Spanish horse population distributed in 65 countries and managed by a single association. Since 1960s, breeding animals have been steadily exported to other countries to establish local subpopulations. We analysed the genetic structure of a PRE horse meta-population (MP) of 215,500 animals from countries with at least 80 active animals (27 countries comprising 77% of the total animals in the complete pedigree). Genotypes from active animals (59% of the total animals in the complete pedigree) were also studied. Genetic analysis of the MP was performed using classical parameters such as inbreeding (F), coancestry, founder contribution, effective number of founders/ancestors (fe/fa) and gene flow between countries. Results showed that the MPF coefficient decreased in the last two decades (1990-2013), indicating an explicit management against F. Founder contribution to genetic variability across countries mainly came from females (73.6%). In general, unbalanced contributions of founders reflected the high loss of genetic diversity along generations (fe/fa as low as 32/19 for the whole MP). Despite this differential contribution, the proportional contribution to the global diversity of each country was similar. The highest within-country coancestry value corresponded to Cuba (0.1509), being the only country with highly inbred individuals (over 12%), and the lowest value corresponded to Spain (0.0574). These results should help to avoid further declines in genetic variability and increases in F levels, especially in small countries like Cuba. In parallel, only nine countries presented descendants in a single population, suggesting a common origin for all countries and/or a substantial exchange of genetic material between populations. Spain and the US showed the highest gene flow rates. These results support the need of a coordinated management strategy, especially promoting the exchange of genetic material to increase the effective population size and maintain the levels of genetic diversity in the PRE horse population.