Rate Of Inbreeding Research Articles

Genetic Variability in the Italian Heavy Draught Horse from Pedigree Data and Genomic Information.

This study aimed to investigate the genetic diversity in the Italian Heavy Horse Breed from pedigree and genomic data. Pedigree information for 64,917 individuals were used to assess inbreeding level, effective population size (Ne), and effective numbers of founders and ancestors (fa/fe). Genotypic information from SNP markers were available for 267 individuals of both sexes, and it allowed estimating genomic inbreeding in two methods (observed versus expected homozygosity and from ROH) to study the breed genomic structure and possible selection signatures. Pedigree and genomic inbreeding were greatly correlated (0.65 on average). The inbreeding trend increased over time, apart from periods in which the base population enlarged, when Ne increased also. Recent bottlenecks did not occur in the genome, as fa/fe have shown. The observed homozygosity results were on average lower than expected, which was probably due to the use of French Breton stallions to support the breed genetic variability. High homozygous regions suggested that inbreeding increased in different periods. Two subpopulations were distinguished, which was probably due to the different inclusion of French animals by breeders. Few selection signatures were found at the population level, with possible associations to disease resistance. The almost low inbreeding rate suggested that despite the small breed size, conservation actions are not yet required.

Evidence for population genetic structure in two exploited Mekong River fishes across a natural riverine barrier.

Impacts of urban development on aquatic populations are often complex and difficult to ascertain, but population genetic analysis has allowed researchers to monitor and estimate gene flow in the context of existing and future hydroelectric projects. The Lower Mekong Basin is undergoing rapid hydroelectric development with around 50 completed and under-construction dams and 95 planned dams. The authors investigated the baseline genetic diversity of two exploited migratory fishes, the mud carp Henicorhynchus lobatus (five locations), and the rat-faced pangasiid catfish, Helicophagus leptorhynchus (two locations), in the Lower Mekong Basin using the genomic double digest restriction site-associated DNA (ddRAD) sequencing method. In both species, fish sampled upstream of Khone Falls were differentiated from those collected at other sites, and Ne estimates at the site above the falls were lower than those at other sites. This was the first study to utilize thousands of RAD-generated single nucleotide polymorphisms to indicate that the Mekong's Khone Falls are a potential barrier to gene flow for these two moderately migratory species. The recent completion of the Don Sahong dam across one of the only channels for migratory fishes through Khone Falls may further exacerbate signatures of isolation and continue to disrupt the migration patterns of regionally vital food fishes. In addition, H. lobatus populations downstream of Khone Falls, including the 3S Basin and Tonle Sap system, displayed robust connectivity. Potential obstruction of migration pathways between these river systems resulting from future dam construction may limit dispersal, which has led to elevated inbreeding rates and even local extirpation in other fragmented riverine species.

Genetic evaluation of growth and production performance and short term selection response for egg mass in Gramapriya female line chicken

A comprehensive study was carried out in Gramapriya female line (PD-3) with respect to growth, production, selection response and population structure utilizing the data generated for the last 7 generations at ICAR-Directorate of Poultry Research, Hyderabad, Telangana. The average fertility was 71.89% and hatchability was 80.52% on fertile egg set and 57.08% on total egg set. The least squares means (LSMs) for body weight at 4 and 6 weeks of age were 168.06±0.01 and 320.10±0.02 g, respectively. The heritability estimates from sire and dam components of variance were moderate to high for both body weight and shank length (0.27 to 0.35). The correlation coefficients (genetic and phenotypic) between body weights and shank length were positive and high in magnitude except with day old body weight. Age at sexual maturity (ASM) was 171.47±0.01 days in PD-3 population. The part period egg production (EP 40) at 40 weeks of age was 75.60±0.01 eggs with an egg mass (EM 40) of 4,157.19±0.99 g. The h2 estimates for ASM, EW 40, EP 40 and EM 40 were 0.16±0.07, 0.42±0.11, 0.18±0.07 and 0.15±0.06, respectively, which were moderate to high in magnitude. The egg production at 40 weeks of age was negatively associated with ASM, body weight and egg weight at different ages. Egg mass had significant positive association with egg production and egg weight at 40 weeks of age. The selection intensity (i) ranged from 0.32 to 0.85 while, rate of inbreeding ranged between 0.0031 and 0.0033 in PD-3 line. The direct selection response was 151.54 g on genetic scale and 79.75 on phenotypic scale for primary trait of selection, EM 40 over the last 7 generations. Realized and estimated heritability estimates were 0.29 and 0.15, respectively for EM 40. The study concluded that, PD-3 population was in ideal condition with respect to growth and production performance. Positive selection response for primary trait EM 40 was observed in the population maintaining both egg production and egg weight, the important traits for sustainable rural poultry farming.

Long-Term Evaluation of Breeding Scheme Alternatives for Endangered Honeybee Subspecies.

Modern breeding structures are emerging for European honeybee populations. However, while genetic evaluations of honeybees are becoming increasingly well understood, little is known about how selection decisions shape the populations’ genetic structures. We performed simulations evaluating 100 different selection schemes, defined by selection rates for dams and sires, in populations of 200, 500, or 1000 colonies per year and considering four different quantitative traits, reflecting different genetic parameters and numbers of influential loci. Focusing on sustainability, we evaluated genetic progress over 100 years and related it to inbreeding developments. While all populations allowed for sustainable breeding with generational inbreeding rates below 1% per generation, optimal selection rates differed and sustainable selection was harder to achieve in smaller populations and for stronger negative correlations of maternal and direct effects in the selection trait. In small populations, a third or a fourth of all candidate queens should be selected as dams, whereas this number declined to a sixth for larger population sizes. Furthermore, our simulations indicated that, particularly in small populations, as many sires as possible should be provided. We conclude that carefully applied breeding provides good prospects for currently endangered honeybee subspecies, since sustainable genetic progress improves their attractiveness to beekeepers.

Genetic variability and population structure based on pedigree information for Muzaffarnagari sheep in India

Abstract The objective of this study was to use pedigree analysis to evaluate the population structure and retention of genetic diversity in a flock of Muzaffarnagari sheep in India. Pedigrees of 5955 animals born between 1974 and 2003 was used to estimate the generation interval, pedigree completeness, and rate and level of inbreeding. Effective population size and parameters characterizing probabilities of gene origin were computed for lambs born between 2001 and 2003. The average numbers of equivalent complete generations were 3.41 and 5.00 for the whole and reference populations, respectively. The mean generation interval was 3.42 years. Average inbreeding coefficients for animals in the whole and reference populations were 1.79 and 1.23 %, respectively, and the rate of inbreeding was 0.68 % per generation. The average additive relationships for all animals and those in the reference population were 3.93 and 6.43 %, respectively. The realized effective population size, estimated from either the increase in coancestry between pairs of individuals or by regression of the average inbreeding coefficient on number of equivalent complete generations was approximately 76. Probabilities of gene origin were estimated by calculating effective numbers of founders (fe), ancestors (fa), founder genomes (fg), and non-founder genomes (fng) (33, 30, 15.4, and 28.9, respectively). The 10 most influential ancestors accounted for 50 % of the genetic variability, with a maximum individual contribution 6.53 %. The fe/fa ratio in the reference population was 1.10, indicating that occasional bottlenecks had occurred. Approximately 3.2 % of the initial heterozygosity had disappeared from the population. The results revealed that although there was some evidences of bottlenecks and genetic drift, considerable genetic variability remained in the population.

Monitoring of genetic diversity in autochthonous Czech poultry breeds assessed by genealogical data

Czech local poultry breeds face high risks of extinction. Because these populations are closed, they are more likely to lose genetic diversity. The aim of this analysis was to determine the loss of genetic diversity in three Czech autochthonous poultry breeds. Pedigree data from a total of 1 932 Czech Gold Speckled Hens, 325 Czech White Geese and 111 Czech Crested Geese registered in studbooks between 2000 and 2018 were evaluated. Data were analysed to determine the major factors that affect the genetic variability of these breeds. The average numbers of equivalent complete generations ranged from 2.53 to 4.82. The effective numbers of founders were from 29 to 59, representing from 43% to 62% of the total number of founders. The effective number of ancestors was estimated in the range of 21 to 41. The average inbreeding coefficient and relatedness coefficient (in parentheses) for the reference populations were 2.0% (6.5%), 1.9% (4.9%) and 2.1% (9.3%), respectively. The results showed that the effective population size derived from the rate of inbreeding ranged from 46 to 108 and if derived from the rate of coancestry it ranged from 35 to 74. With regard to these results, the analysed breeds showed a high probability of allele loss and consequent loss of genetic diversity.

Genetic diversity evolution of a sheep breed reintroduced after extinction: Tracing back Christopher Columbus' first imported sheep

New World's hair sheep breeds may genetically stem from West African introgression into established ecotypes of Spanish descent presumably extinct in the XIX Century. However, present Canary non-wooled breeds have presumably regressively resulted from the absorption of primitive individuals through Venezuelan descendants. We studied genetic diversity, structure, and evolution of the Canary hair sheep since its reintroduction in the 1950s. Demographic and genetic variability were evaluated using ENDOG (v4.8). Effective population size based on individual inbreeding rate was around one third higher than when based on individual coancestry rate. Nei's distances and equivalent subpopulations number indicated a highly-structured population. Although genetic diversity loss since the founder generations could be considered small, narrower pedigree bottlenecks could result from intraflock breeding policies and excessive contribution of few ancestors. Long generation intervals could be considered when reducing inbreeding. Wright's fixation statistics indicated slight interflock inbreeding. Pedigree completeness suggested genetic parameters were reliable, hence controlling inbreeding negative effects, could indeed, be crucial preserving these animal resources, consolidating the population in the archipelago after reintroduction.

Variation in breeding practices and geographic isolation drive subpopulation differentiation, contributing to the loss of genetic diversity within dog breed lineages

BackgroundDiscrete breed ideals are not restricted to delimiting dog breeds from another, but also are key drivers of subpopulation differentiation. As genetic differentiation due to population fragmentation results in increased rates of inbreeding and loss of genetic diversity, detecting and alleviating the reasons of population fragmentation can provide effective tools for the maintenance of healthy dog breeds.ResultsUsing a genome-wide SNP array, we detected genetic differentiation to subpopulations in six breeds, Belgian Shepherd, English Greyhound, Finnish Lapphund, Italian Greyhound, Labrador Retriever and Shetland Sheepdog, either due to geographical isolation or as a result of differential breeding strategies. The subpopulation differentiation was strongest in show dog lineages.ConclusionsBesides geographical differentiation caused by founder effect and lack of gene flow, selection on champion looks or restricted pedigrees is a strong driver of population fragmentation. Artificial barriers for gene flow between the different subpopulations should be recognized, their necessity evaluated critically and perhaps abolished in order to maintain genetic diversity within a breed. Subpopulation differentiation might also result in false positive signals in genome-wide association studies of different traits.Lay summaryPurebred dogs are, by definition, reproductively isolated from other breeds. However, similar isolation can also occur within a breed due to conflicting breeder ideals and geographic distances between the dog populations. We show here that both of these examples can contribute to breed division, with subsequent loss of genetic variation in the resulting breed lineages. Breeders should avoid creating unnecessary boundaries between breed lineages and facilitate the exchange of dogs between countries.

Subtle sexual plumage color dimorphism and size dimorphism in a South American colonial breeder, the Monk Parakeet (Myiopsitta monachus)

BackgroundParrots (Psittacidae Family) are one of the most colorful groups of birds in the world, their colors produced both structurally and via unusual pigments (psittacofulvins). Most species are considered to be monogamous, and many have been viewed historically as sexually monomorphic and monochromatic. However, studies using morphometric analysis and spectrophotometric techniques have revealed sexual size dimorphism and also sexual plumage color dimorphism among some species. The Monk Parakeet (Myiopsitta monachus), a native parrot of South America, is an interesting species for the study of plumage coloration and size since it is considered sexually monochromatic and monomorphic. Furthermore, recent studies show that the Monk Parakeet has extra-bond paternity behavior and even breeding trios, which suggests that sexual selection may play an important role in this species, and that it might have sexually dimorphic plumage (albeit imperceptible by humans) and be dimorphic in size.MethodsFor the determination of plumage color we used spectrophotometry in the range of avian vision (300‒700 nm) and performed a morphological analysis.ResultsOur spectrophotometric results indicate that the Monk Parakeet shows subtle sexual plumage color dimorphism in three (crown, nape and wing) out of twelve body regions. Similarly, our morphometric analysis showed that there are subtle sex differences in body size (bill and weight).ConclusionsAlthough the Monk Parakeet shows extra-bond paternity and breeding trio behaviors which could increase sexual dimorphism, these behaviors occur among highly related individuals; perhaps the high rate of inbreeding is responsible for the attenuation of sexual plumage color dimorphism and sex differences in body size observed.

Genetic Parameters and Inbreeding Effect of Morphological Traits in Sardinian Anglo Arab Horse.

Simple SummaryCannon bone circumference, chest girth, shoulder length, and withers height are important biometric measures that are useful to describe the horse’s body conformation correctly. It is interesting to observe how these traits are connected to each other and how they are used to improve the genetic progress of the breed. The percentages of Thoroughbred and Arabian blood were also estimated for each horse in the pedigree population, to evaluate how the conformation might be modified thanks to different breeding purposes such as: racing, jumping, and other equestrian disciplines. The results show that the improvement of the Arabian blood determined a depressive effect on the studied traits; on the contrary, when the Thoroughbred blood percentage increases, the measures of the studied traits increase too. The trait most affected by the variation of the two blood percentages was withers height. It has been demonstrated that the conformation is related to sporting results, soundness, and durability and that body and legs shape are highly heritable. At this purpose, it might be useful, to restart the body measurements collection and to match them with the horse’s performance at races.The purpose of this study was to estimate the heritability and genetic correlations of four biometric measurements and an overall score (OS) in the Sardinian Anglo-Arab horse (SAA); moreover, the effect of inbreeding on these traits was investigated. A dataset with 43,624 horses (27,052 females and 16,572 males) was provided by the Agricultural Research Agency of Sardinia (AGRIS). Cannon bone circumference (BC), chest girth (CG), shoulder length (SL), and withers height (WH) were measured on 6033 SAA horses born in Sardinia between 1967 and 2005; beside the measurements, an overall score (OS) was taken comparing the morphology of each horse to an “ideal type” that is scored out of 100. The mean value is 20.5 cm for BC, 185.9 cm for CG, 67.6 cm for SL, 160.8 cm for WH, and 73.2 for the OS. The heritability estimates ranged from 0.78 to 0.23. The results allow to foresee high genetic progress through the breeding programs. The most affected trait by the inbreeding rate seems to only be the withers height.

Review: Understanding Rare Genetic Diseases in Low Resource Regions Like Jammu and Kashmir - India.

Rare diseases (RDs) are the clinical conditions affecting a few percentage of individuals in a general population compared to other diseases. Limited clinical information and a lack of reliable epidemiological data make their timely diagnosis and therapeutic management difficult. Emerging Next-Generation DNA Sequencing technologies have enhanced our horizons on patho-physiological understanding of many of the RDs and ushered us into an era of diagnostic and therapeutic research related to this ignored health challenge. Unfortunately, relevant research is meager in developing countries which lack a reliable estimate of the exact burden of most of the RDs. India is to be considered as the “Pandora’s Box of genetic disorders.” Owing to its huge population heterogeneity and high inbreeding or endogamy rates, a higher burden of rare recessive genetic diseases is expected and supported by the literature findings that endogamy is highly detrimental to health as it enhances the degree of homozygosity of recessive alleles in the general population. The population of a low resource region Jammu and Kashmir (J&K) – India, is highly inbred. Some of its population groups variably practice consanguinity. In context with the region’s typical geographical topography, highly inbred population structure and unique but heterogeneous gene pool, a huge burden of known and uncharacterized genetic disorders is expected. Unfortunately, many suspected cases of genetic disorders remain undiagnosed or misdiagnosed due to lack of appropriate clinical as well as diagnostic resources in the region, causing patients to face a huge psycho-socio-economic crisis and many a time suffer life-long with their ailment. In this review, the major challenges associated with RDs are highlighted in general and an account on the methods that can be adopted for conducting fruitful molecular genetic studies in genetically vulnerable and low resource regions is also provided, with an example of a region like J&K – India.

Recurrent genomic selection for wheat grain fructans

AbstractFructans are carbohydrates found in many plants, including wheat (Triticum aestivum L.), and they serve physiological roles in both plants and humans. Genomic selection (GS) could facilitate the rapid development of climate‐resilient, nutritionally improved wheat cultivars, such as high‐fructan cultivars, while decreasing resource‐intensive phenotyping requirements. However, few empirical studies have examined GS for nutritional quality breeding. Although GS can accelerate gain from selection, loss of genetic variation and inbreeding may limit the potential for long‐term gain. The objectives of this study were (a) to determine realized gain from GS for wheat grain fructan content with simple truncated selection (TS) and optimized contribution selection (OCS) methods, (b) to determine if gains agree with theoretical expectations, and (c) to compare impacts of selection on inbreeding, genetic variance, and indirect selection on agronomic characteristics. Over 2 yr, two cycles of GS were performed with equal contribution TS and inbreeding‐constrained OCS selection. Genomic selection with TS and OCS led to a 25 ± 12% and 34 ± 6.4% increase in wheat grain fructan content, respectively. Although positive gains from selection were observed for both populations, OCS populations exhibited these gains while simultaneously retaining greater genetic variance and lower inbreeding levels relative to TS populations. Selection for wheat grain fructan content did not change plant height but significantly decreased days to heading in OCS populations. In this study, GS effectively improved the nutritional quality of wheat, and OCS controlled the rate of inbreeding.

Estimation of inbreeding and identification of regions under heavy selection based on runs of homozygosity in a Large White pig population

BackgroundRuns of homozygosity (ROHs) are homozygous segments of the genome where the two haplotypes inherited from the parents are identical. The current availability of genotypes for a very large number of single nucleotide polymorphisms (SNPs) is leading to more accurate characterization of ROHs in the whole genome. Here, we investigated the occurrence and distribution of ROHs in 3,692 Large White pigs and compared estimates of inbreeding coefficients calculated based on ROHs (FROH), homozygosity (FHOM), genomic relationship matrix (FGRM) and pedigree (FPED). Furthermore, we identified genomic regions with high ROH frequencies and annotated their candidate genes.ResultsIn total, 176,182 ROHs were identified from 3,569 animals, and all individuals displayed at least one ROH longer than 1 Mb. The ROHs identified were unevenly distributed on the autosomes. The highest and lowest coverages of Sus scrofa chromosomes (SSC) by ROH were on SSC14 and SSC13, respectively. The highest pairwise correlation among the different inbreeding coefficient estimates was 0.95 between FROH_total and FHOM, while the lowest was − 0.083 between FGRM and FPED. The correlations between FPED and FROH using four classes of ROH lengths ranged from 0.18 to 0.37 and increased with increasing ROH length, except for ROH > 10 Mb. Twelve ROH islands were located on four chromosomes (SSC1, 4, 6 and 14). These ROH islands harboured genes associated with reproduction, muscular development, fat deposition and adaptation, such as SIRT1, MYPN, SETDB1 and PSMD4.ConclusionFROH can be used to accurately assess individual inbreeding levels compared to other inbreeding coefficient estimators. In the absence of pedigree records, FROH can provide an alternative to inbreeding estimates. Our findings can be used not only to effectively increase the response to selection by appropriately managing the rate of inbreeding and minimizing the negative effects of inbreeding depression but also to help detect genomic regions with an effect on traits under selection.

Controlling Coancestry and Thereby Future Inbreeding by Optimum-Contribution Selection Using Alternative Genomic-Relationship Matrices.

We tested the consequences of using alternative genomic relationship matrices to predict genomic breeding values (GEBVs) and control of coancestry in optimum contribution selection, where the relationship matrix used to calculate GEBVs was not necessarily the same as that used to control coancestry. A stochastic simulation study was carried out to investigate genetic gain and true genomic inbreeding in breeding schemes that applied genomic optimum contribution selection (GOCS) with different genomic relationship matrices. Three genomic-relationship matrices were used to predict the GEBVs based on three information sources: markers (GM), QTL (GQ), and markers and QTL (GA). Strictly, GQ is not possible to implement in practice since we do not know the quantitative trait loci (QTL) positions, but more and more information is becoming available especially about the largest QTL. Two genomic-relationship matrices were used to control coancestry: GM and GA. Three genetic architectures were simulated: with 7702, 1000, and 500 QTLs together with 54,218 markers. Selection was for a single trait with heritability 0.2. All selection candidates were phenotyped and genotyped before selection. With 7702 QTL, there were no significant differences in rates of genetic gain at the same rate of true inbreeding using different genomic relationship matrices in GOCS. However, as the number of QTLs was reduced to 1000, prediction of GEBVs using a genomic relationship matrix constructed based on GQ and control of coancestry using GM realized 29.7% higher genetic gain than using GM for both prediction and control of coancestry. Forty-three percent of this increased rate of genetic gain was due to increased accuracies of GEBVs. These findings indicate that with large numbers of QTL, it is not critical what information, i.e., markers or QTL, is used to construct genomic-relationship matrices. However, it becomes critical with small numbers of QTL. This highlights the importance of using genomic-relationship matrices that focus on QTL regions for GEBV estimation when the number of QTL is small in GOCS. Relationships used to control coancestry are preferably based on marker data.

Genomic Breeding Programs Realize Larger Benefits by Cooperation in the Presence of Genotype × Environment Interaction Than Conventional Breeding Programs.

Genotype × environment interaction (G × E) is of increasing importance for dairy cattle breeders due to international multiple-environment selection of animals as well as the differentiation of production environments within countries. This theoretical simulation study tested the hypothesis that genomic selection (GS) breeding programs realize larger genetic benefits by cooperation in the presence of G × E than conventional pedigree-based selection (PS) breeding programs. We simulated two breeding programs each with their own cattle population and environment. Two populations had either equal or unequal population sizes. Selection of sires was done either across environments (cooperative) or within their own environment (independent). Four scenarios, (GS/PS) × (cooperative/independent), were performed. The genetic correlation (rg) between the single breeding goal trait expressed in two environments was varied between 0.5 and 0.9. We compared scenarios for genetic gain, rate of inbreeding, proportion of selected external sires, and the split-point rg that is the lowest value of rg for long-term cooperation. Between two equal-sized populations, cooperative GS breeding programs achieved a maximum increase of 19.3% in genetic gain and a maximum reduction of 24.4% in rate of inbreeding compared to independent GS breeding programs. The increase in genetic gain and the reduction in rate of inbreeding realized by GS breeding programs with cooperation were respectively at maximum 9.7% and 24.7% higher than those realized by PS breeding programs with cooperation. Secondly, cooperative GS breeding programs allowed a slightly lower split-point rg than cooperative PS breeding programs (0.85∼0.875 vs ≥ 0.9). Between two unequal-sized populations, cooperative GS breeding programs realized higher increase in genetic gain and showed greater probability for long-term cooperation than cooperative PS breeding programs. Secondly, cooperation using GS were more beneficial to the small population while also beneficial but much less to the large population. In summary, by cooperation in the presence of G × E, GS breeding programs realize larger improvements in terms of the genetic gain and rate of inbreeding, and have greater possibility of long-term cooperation than conventional PS breeding programs. Therefore, we recommend cooperative GS breeding programs in situations with mild to moderate G × E, depending on the sizes of two populations.

Runaway fathers? Limited pollen dispersal and mating system in Rhizophora racemosa populations of a disturbed mangrove estuary

The contribution of pollen mediated gene flow in demographic stability is largely dependent on how far pollen can be dispersed, as well as how this dispersal affects the mating in breeding individuals. In this study patterns of pollen dispersal and mating systems in Rhizophora racemosa populations of the Cameroon Estuary complex (CEC) were assessed from 29 adult trees with their progeny seedlings (i.e., 483 propagules), sampled from three plots. Using progeny arrays constructed from eight microsatellite markers, we employed two-generational analyses to assess pollen pool structure, pollen dispersal distances, and mating systems. We found mean number of sires contributing to the pollen pool of a mother tree was low (2–3) and pollen dispersal distances were short (<12 m). Male gametic divergence among siblings was moderate (0.158 ≤ Φft ≤ 0.277). Low biparental inbreeding rates and moderate multi-locus outcrossing rates (0.559–0.650), suggest a mixed mating system comprising of spontaneous selfing (geitonogamy) and outcrossing. Our results show that pollen dispersal does not contribute to among patch genetic connectivity since the spatial scales of the patches far exceeds estimated pollen dispersal distances; indicating high gene flow previously reported within the CEC is predominantly mediated by propagule dispersal.

Mate selection provides similar genetic progress and average inbreeding than optimum contribution selection in the long-term

Optimum contribution selection (OCS) and mate selection (MS) are alternative strategies to maximize genetic gain under controlled rates of inbreeding. There is evidence in the literature that MS outperforms OCS in controlling inbreeding under the same expected genetic gain in the short-term. It is unclear, however, if the same would occur in the long-term. This study aimed to compare OCS and MS regarding short- and long-term genetic progress and inbreeding, using simulated data. The structure of the simulated population aimed to mimic an aquaculture breeding program. Twenty discrete generations were simulated, considering 50 families and 2000 offspring per generation, and a trait with a heritability of 0.3. OCS and MS were applied using a differential evolution (DE) algorithm, under an objective function that accounted for genetic merit, coancestry among selection candidates and inbreeding of the future progeny. For OCS, the optimization process consisted of selection based on optimum contribution followed by minimum inbreeding mating. Objective functions using different weights on coancestry were tested. For each application, 20 replicates were simulated and the results were compared based on their average. Both strategies, OCS and MS, were very effective in controlling inbreeding over the generations. In the short-term, MS was more efficient than OCS in controlling inbreeding under the same genetic gain. In the long-term, OCS and MS resulted in similar genetic progress and average inbreeding, under the same penalty on coancestry.

Effect of genomic selection on rate of inbreeding and coancestry and effective population size of Holstein and Jersey cattle populations

Genetic diversity in livestock populations is a significant contributor to the sustainability of animal production. Also, genetic diversity allows animal production to become more responsive to environmental changes and market demands. The loss of genetic diversity can result in a plateau in production and may also result in loss of fitness or viability in animal production. In this study, we investigated the rate of inbreeding (ΔF), rate of coancestry (Δf), and effective population size (Ne) as important quantitative indicators of genetic diversity and evaluated the effect of the recent implementation of genomic selection on the loss of genetic diversity in North American Holstein and Jersey dairy cattle. To estimate the rate of inbreeding and coancestry, inbreeding and coancestry coefficients were calculated using the traditional pedigree method and genomic methods estimated from segment- and marker-based approaches. Furthermore, we estimated Ne from the rate of inbreeding and coancestry and extent of linkage disequilibrium. A total of 205,755 and 89,238 pedigreed and genotyped animals born between 1990 and 2018 inclusively were available for Holsteins and Jerseys, respectively. The estimated average pedigree inbreeding coefficients were 7.74 and 7.20% for Holsteins and Jerseys, respectively. The corresponding values for the segment and marker-by-marker genomic inbreeding coefficients were 13.61, 15.64, and 31.40% for Holsteins and 21.16, 22.54, and 42.62% for Jerseys, respectively. The average coancestry coefficients were 8.33 and 15.84% for Holsteins and 9.23 and 23.46% for Jerseys with pedigree and genomic measures, respectively. Generation interval for the whole 29-yr time period averaged approximately 5 yr for all selection pathways combined. The ΔF per generation based on pedigree, segment, and marker-by-marker genomic measures for the entire 29-yr period was estimated to be 0.75, 1.10, 1.16, and 1.02% for Holstein animals and 0.67, 0.62, 0.63, and 0.59% for Jersey animals, respectively. The Δf was estimated to be 0.98 and 0.98% for Holsteins and 0.73 and 0.78% for Jerseys with pedigree and genomic measures, respectively. These ΔF and Δf translated to an Ne that ranged from 43 to 66 animals for Holsteins and 64 to 85 animals for Jerseys. In addition, the Ne based on linkage disequilibrium was 58 and 120 for Holsteins and Jerseys, respectively. The 10-yr period that involved the application of genomic selection resulted in an increased ΔF per generation with ranges from 1.19 to 2.06% for pedigree and genomic measures in Holsteins. Given the rate at which inbreeding is increasing after the implementation of genomic selection, there is a need to implement measures and means for controlling the rate of inbreeding per year, which will help to manage and maintain farm animal genetic resources.

Inbreeding, effective population size, and coancestry in the Latxa dairy sheep breed

Traditionally, breeding programs have estimated and managed inbreeding based on pedigree information. The availability of genomic marker panels has made possible new alternatives to achieve more precise estimates, for example in case of missing pedigree. The objective of the present study was to assess and compare, different estimation methods (pedigree-based methodologies, single SNP-based approach (homozygosity) and runs of homozygosity-based method) to analyze the evolution of genetic diversity measured as inbreeding or as coancestry of 3 selected populations of Latxa dairy sheep (Latxa Cara Rubia and Latxa Cara Negra from Euskadi and Navarre). Genomic data came from 972 artificial insemination rams genotyped with the Illumina OvineSNP50 BeadChip (Illumina Inc., San Diego, CA) whose genealogy consisted of 4,484 animals. Inbreeding estimates based on molecular data were more similar between them than compared with those based on pedigree information. However, the SNP-based approach estimations of effective population size differed more, reflecting the sensitivity of effective population size to small changes in the evolution of inbreeding. The 2 Latxa Cara Negra populations showed increases of inbreeding rates with time and effective population sizes between 64 and 103 animals, depending on breed and methodology used. The Latxa Cara Rubia population did not show an increase in inbreeding rate, mainly due to semen importation from the related French population of Manech Tête Rousse. The effective size estimates based on coancestry increase show a higher variability and they are more sensitive to the source of information and the data structure considered. Realized effective population size based on individual increase in inbreeding were in agreement with the previous estimates. Coancestry evolution analysis based on DNA information showed an increase on coancestry during the last 10 yr in all breeds, as a consequence of the selection process. Moreover, the increase on coancestry between Latxa Cara Rubia and Manech Tête Rousse was more noticeable between than within each of those breeds.

Genomic selection strategies to improve maternal traits in Norwegian White Sheep.

This study tested and compared different implementation strategies for genomic selection for Norwegian White Sheep, aiming to increase genetic gain for maternal traits. These strategies were evaluated for their genetic gain ingrowth, carcass and maternal traits, total genetic gain, a weighted sum of the gain in each trait and rates of inbreeding through a full-scale stochastic simulation. Results showed genomic selection schemes to increase genetic gain for maternal traits but reduced genetic gain for other traits. This could also be obtained by selecting rams for artificial selection at a higher age. Implementation of genomic selection in the current breeding structure increased genetic gain for maternal traits up to 57%, outcompeted by reducing the generation interval for artificial insemination rams from current 3 to 2years. Then, total genetic gain for maternal traits increased by 65%-77% and total genetic gain by18%-20%, but at increased rates of inbreeding.