Increase In Level Of Inbreeding Research Articles

Whole Genome Sequencing Provides Information on the Genomic Architecture and Diversity of Cultivated Gilthead Seabream (Sparus aurata) Broodstock Nuclei.

The gilthead seabream (Sparus aurata) is a species of relevance for the Mediterranean aquaculture industry. Despite the advancement of genetic tools for the species, breeding programs still do not often include genomics. In this study, we designed a genomic strategy to identify signatures of selection and genomic regions of high differentiation among populations of farmed fish stocks. A comparative DNA pooling sequencing approach was applied to identify signatures of selection in gilthead seabream from the same hatchery and from different nuclei that had not been subjected to genetic selection. Identified genomic regions were further investigated to detect SNPs with predicted high impact. The analyses underlined major genomic differences in the proportion of fixed alleles among the investigated nuclei. Some of these differences highlighted genomic regions, including genes involved in general metabolism and development already detected in QTL for growth, size, skeletal deformity, and adaptation to variation of oxygen levels in other teleosts. The obtained results pointed out the need to control the genetic effect of breeding programs in this species to avoid the reduction of genetic variability within populations and the increase in inbreeding level that, in turn, might lead to an increased frequency of alleles with deleterious effects.

Ефекти інбридингу на поширеність хромосомних порушень серед населення Слобожанщини

An increase in inbreeding level and advanced parental age are factors that increase the risk of having children with structural and numerical chromosomal abnormalities due to altered frequency of recombination and impaired behavior of chromosomes in meiosis. There is limited information on the effects of inbreeding on human chromosomal and genomic mutations. The purpose of the study was to assess the effect of inbreeding on the prevalence of chromosomal abnormalities in the districts of the Kharkiv region. Materials and methods. The study was conducted in four districts of the Kharkiv region – Balakliia, Vovchansk, Zmiiv, and Krasnograd (administrative and territorial structure is given as of July 1, 2020). Based on the data of analysis of 1,582 marriages between opposite-sex couples mean age at marriage, marital distance, and the random inbreeding coefficient (FST) were estimated. Of 654 children (aged 0–17 years) included in the study, 39 had chromosomal disorders that was the basis for the calculation of the prevalence of chromosomal abnormalities. Results and discussion. In four districts, the mean age at marriage for local residents was 27.8 ± 0.1 years. Men were 2.9 years older than women at marriage. The marital distance was 320.4 ± 28.4 km, varying from 263.17 ± 48.39 km in the Balakliia district to 400.12 ± 79.97 km in the Vovchansk district. The random inbreeding coefficient FST was 0.001292. In rural settlements, the random inbreeding coefficient FST was by 17.2 times higher than in urban settlements. The index rose by 80 percent over the last seven years. The prevalence of chromosomal pathology among children and adolescents was 0.08%, ranging from 0.05% in the Vovchansk district to 0.14% in the Krasnograd district. Among the cases included, there were patients with Down syndrome, Klinefelter syndrome, Turner syndrome, and Prader-Willi syndrome. The most common nosological entity was Down syndrome. The prevalence of chromosomal abnormalities in villages was by 2.6 times higher than in towns. A strong positive relationship was established between the random inbreeding coefficients FST and the prevalence of chromosomal disorders in the study area (r = 0.904). Conclusion. Almost two-fold increase in the inbreeding rate in the mentioned districts in just past seven years may contribute to accumulation of burden of chromosomal disorders of the population due to the presence of a positive correlation between the study population indicators

Genomic measures of inbreeding in the Norwegian\u2013Swedish Coldblooded Trotter and their associations with known QTL for reproduction and health traits

BackgroundSince the 1950s, the Norwegian–Swedish Coldblooded trotter (NSCT) has been intensively selected for harness racing performance. As a result, the racing performance of the NSCT has improved remarkably; however, this improved racing performance has also been accompanied by a gradual increase in inbreeding level. Inbreeding in NSCT has historically been monitored by using traditional methods that are based on pedigree analysis, but with recent advancements in genomics, the NSCT industry has shown interest in adopting molecular approaches for the selection and maintenance of this breed. Consequently, the aims of the current study were to estimate genomic-based inbreeding coefficients, i.e. the proportion of runs of homozygosity (ROH), for a sample of NSCT individuals using high-density genotyping array data, and subsequently to compare the resulting rate of genomic-based F (FROH) to that of pedigree-based F (FPED) coefficients within the breed.ResultsA total of 566 raced NSCT were available for analyses. Average FROH ranged from 1.78 to 13.95%. Correlations between FROH and FPED were significant (P < 0.001) and ranged from 0.27 to 0.56, with FPED and FROH from 2000 to 2009 increasing by 1.48 and 3.15%, respectively. Comparisons of ROH between individuals yielded 1403 regions that were present in at least 95% of the sampled horses. The average percentage of a single chromosome covered in ROH ranged from 9.84 to 18.82% with chromosome 31 and 18 showing, respectively, the largest and smallest amount of homozygosity.ConclusionsGenomic inbreeding coefficients were higher than pedigree inbreeding coefficients with both methods showing a gradual increase in inbreeding level in the NSCT breed between 2000 and 2009. Opportunities exist for the NSCT industry to develop programs that provide breeders with easily interpretable feedback on regions of the genome that are suboptimal from the perspective of genetic merit or that are sensitive to inbreeding within the population. The use of molecular data to identify genomic regions that may contribute to inbreeding depression in the NSCT will likely prove to be a valuable tool for the preservation of its genetic diversity in the long term.

Inbreeding and Mortality Risk in a Captive Population of Mhorr Gazelle (Nanger dama mhorr)

This study aimed to evaluate the genetic variation and examine the association of inbreeding level on mortality risk (at days 7, 30 and 180 – weaning age) of Mhorr gazelle in captivity for the year 1969–2000 as recorded in the studbook record kept by Australasian Regional Association of Zoological Parks and Aquaria (ARAZPA). The effective number of founders, ancestors and founder genomes was found to be 3.42, 3, and 1.44 for the studied reference population. The reference population is composed of animals which are alive, with known parents and known sex. Animals that are less than 10 years old (based on birth dates up to 2008) with no remarks on its death are considered alive. The population may not have experienced a severe bottleneck, as the values on the effective number of founders and ancestors are almost equal. However, the effective number of founder genomes is low, which demonstrates gene loss due to genetic drift. The mean inbreeding coefficients of the individual, sire and dam were found to be 0.2971 ± 0.1043, 0.2300 ± 0.1141 0.2339 ± 0.1070, respectively. The maximum inbreeding level of the population is 0.5247 (52.47%). This means that parent–offspring or full-sib mating must have happened. The increase in inbreeding level of an individual was found to be significantly associated (p&lt;0.10) with an increase in p mortality risk at day 180 or weaning age. Increasing inbreeding level of sires was found to be significantly associated with increasing risk in mortality at day 30, which indicates that inbred parents also can influence the survival of an offspring. Efficient breeding programs are as important for decreasing mortality in captive populations, as the provision of optimum zoo management practices.

Pedigree analysis of a highly fragmented population, the Lidia cattle breed

The aim of the study was to analyze the pedigree information of the Lidia bovine breed based on animals registered in the Herdbook and belonging to those lineages recognized as conforming to the official breed standard. Pedigree records of 272,574 animals belonging to 83 herds classified in 30 lineages were used. The average number of equivalent generations known was 4.5 (varying among lineages from 4 in Braganza to 5.2 in Baltasar Iban). The generation interval (7.5 years) was longer than that estimated in other cattle breeds. The effective size was less than 50 and consequently the estimated increase in inbreeding per generation was greater than 1% in all the lineages analyzed. The increase in inbreeding level expected for the next 50 years varied from 7.4% in Braganza to 31.3% in Diego Garrido. The ratios among the effective number of founders, the effective number of ancestors and the effective number of founder genomes was considered evidence that genetic drift explained most of the loss of genetic variability in the Lidia bovine breed due to the reduced effective population sizes of the lineages, more than bottlenecks did, as they have been less dramatic. The lineage allele loss due to the genetic drift and the effect of inbreeding are the major concerns in managing the genetic diversity of the Lidia bovine breed. The analysis of pedigree information still remains as the main useful resource to establish genetic diversity conservation guidelines in the Lidia bovine breed. Minimizing inbreeding increase within lineages in the sub-divided Lidia breed must be the major concern in managing the genetic diversity of this breed.

Effects of Inbreeding on Production and Survival in Jerseys

Responses of registered Jersey cows to various levels of inbreeding were examined with pedigree data supplied by the American Jersey Cattle Association and test-day production data from 1970 through 1998 obtained from the Animal Breeding Center at Cornell University. Rate of increase in level of inbreeding is accelerating with time, making it more difficult for producers to make matings that avoid the potentially deleterious effects of inbreeding. Production losses caused by inbreeding were significant and curvilinear for all traits studied except somatic cell linear score, with the greatest losses at higher levels of inbreeding. Inbreeding was found to have the greatest effect on production at early ages and early in lactation. Early onset of the deleterious effects of inbreeding resulted in larger net present value losses than if effects of inbreeding occurred later in the life of an animal. Losses were probably enhanced because of the need to freshen animals as early as possible to maximize net present value returns. Survival decreased as level of inbreeding increased and was likely to have a greater negative impact on the financial health of the dairy enterprise than production losses.

Effects of Inbreeding on Production and Survival in Holsteins

Responses of registered Holstein cows to various levels of inbreeding were examined with pedigree data supplied by the Holstein Association USA and test-day production data from 1970 through 1998 obtained from the Animal Breeding Center at Cornell University. Rate of increase in level of inbreeding has been accelerating over time, making it more difficult for producers to make matings that avoid the potentially deleterious effects of inbreeding. Milk production losses per lactation caused by inbreeding were generally 35kg per percentage inbreeding level >0.01 but increased to 55kg per percentage inbreeding level from 0.07 to 0.10. Somatic cell score was not affected by level of inbreeding. Inbreeding had the greatest effect on production at ages <22 mo and early in lactation. Early onset of the deleterious effects of inbreeding resulted in larger net present value losses than when effects of inbreeding occurred later. Losses were likely enhanced due to the need to freshen animals as early as possible to maximize net present value returns. Survival decreased as level of inbreeding increased and was likely to have a greater negative impact on the financial health of the dairy enterprise than production losses.

Calculation and Use of Inbreeding Coefficients for Genetic Evaluation of United States Dairy Cattle

Inbreeding coefficients are calculated routinely for all animals included in national genetic evaluations for yield traits. The base population for inbreeding is defined as animals born during 1960. Animals with unknown parents are assumed to have inbreeding coefficients that are equal to the mean of coefficients for animals with known parents born during the same year. Mean inbreeding coefficients reached .03 to .04 for recent years, and coefficients for some animals exceeded .50. The annual increase in level of inbreeding was highest for Milking Shorthorns, but the rate of change of that increase was greatest for Holsteins. Accounting for inbreeding in calculation of the inverse of the relationship matrix had only a small effect on evaluations. For Jerseys, the maximum change in breeding value was 73kg of milk for cows and 40kg of milk for bulls with ≥10 daughters. Estimates of inbreeding depression were similar across breeds for production traits and were −29.6kg of milk, −1.08kg of fat, and −.97kg of protein per 1% of inbreeding for Holsteins. In January 1994, the USDA began considering the percentage of inbreeding when calculating inverses of relationship matrices, the largest matrix representing over 20million Holsteins; this inbreeding percentage was released to the dairy industry for bulls.