Rate Of Inbreeding Research Articles

Assessing the genetic vulnerability of Macaúba palm [Acrocomia aculeata (Jacq.) Lodd. ex Mart.] through the mating system and genetic diversity of open‐pollinated progenies

AbstractAt present, intelligent and sustainable agriculture presupposes a compromise between maximising crop yield and minimising its risk of genetic vulnerability. Breeding programmes should implement strategies that allow the development of superior genotypes and preserve genetic diversity, especially in perennial plants. The Macaúba palm (Acrocomia aculeata) is a species with the potential to produce oil at a level comparable to that of the oil palm, even in water‐deficient areas, which motivates its commercial interest and drives an increase in demand for seedlings from natural populations for commercial plantations. Therefore, to evaluate the impact of this selection procedure on the reduction of genetic diversity and, consequently, the genetic vulnerability of commercial planting, in the present study we analysed the population mating system and the genetic diversity of Open‐Pollinated Progenies (OPPs) from selected seed‐trees in relation to the genetic diversity of respective native populations (NPs). To achieve this, we evaluated the mating system and genetic diversity employing 14 microsatellite markers (SSR). The mating system indices estimated for A. aculeata palm indicated that the species present a mixed mating system () with a predominance of outcrossing. However, at the population level, the outcrossing rate ranged from . The biparental inbreeding rate was considered moderate (), with some variation between populations (from 0.0005 to 0.275). The multilocus correlated paternity was , ranging from 0 to 0.112 at population level, indicating that a significant portion of the progeny consisted of half‐sibs. The results demonstrate that there was no significant loss of genetic diversity of OPPs derived from artificial selection within NPs. In the OPPs the number of alleles (Na = 2.55) was similar to that of NP (Na = 2.56). Furthermore, the mean values of observed heterozygosity (HO) between NP and OPPs were similar, with a mean of 0.366 and 0.356, respectively. In conclusion, the procedure adopted to produce commercial seedlings in the present study should not represent a high risk of genetic vulnerability. In addition, our results will provide a guidance to breeders regarding selection intensity in both natural and improved populations, aiming to optimise the advancement of generations, thereby maximising future genetic gains while preserving genetic diversity. However, we recommend verifying the outcrossing rate and genetic diversity at the population level, as these factors could have significant effects on the vulnerability of the species and the macaúba crop.

Inbreeding Depression and Purging for Meat Performance Traits in German Sheep Breeds.

This study provides estimates on genetic parameters, inbreeding depression and purging for meat performance measures from 25 German sheep breeds. All German meat, merino sheep breeds and breeds of other breeding directions with a sufficient number of pedigree and performance data were included in this study. Phenotypic traits retrieved from the national database OviCap were evaluated: daily weight gain, meatiness score and ultrasound measurements for muscle and fat thickness. We employed animal models to estimate heritability, variance and covariance components for these meat performance traits as well as inbreeding depression and purging. The heritabilities, on average, reached estimates of 0.55, 0.34, 0.53 and 0.61 for daily weight gain, meatiness score and ultrasound measurements for muscle and fat thickness, respectively. We estimated the linear regression slopes for the individual rate of inbreeding, new and ancestral inbreeding, as well as the inbreeding coefficient and its interaction with the inbreeding coefficient of Ballou, employing animal models with non-genetic effects and the additive genetic effect of the animal. Across all breeds, inbreeding was only significant for daily weight gain, whereas for all other traits, estimates were not significant. Within sheep breeds, we found significant inbreeding depression for daily weight gain in German Mutton Merino and German Blackheaded Mutton as well as for the meatiness score in German Whiteheaded Mutton. Significant effects for purging, based on ancestral inbreeding and the interaction effect of the classical inbreeding coefficient with the inbreeding coefficient of Ballou, were not obvious either across or within any sheep breed. A 1% increase in inbreeding significantly decreased the phenotypic trait median of daily weight gain across all sheep breeds by 0.50% and 0.70% of phenotypic and genetic standard deviation, respectively. Purging effects due to ancestral inbreeding were not significant in any breed or across breeds. The results of this study may indicate that inbreeding depression may be more harmful in traits under stronger selection than in traits that exert low selection pressure. The results of this study demonstrate the different effects that result in meat performance traits due to inbreeding. With increasing rates of inbreeding and critical effective population sizes, selection intensity for breeding objectives has to be critically reviewed for each sheep breed. Inbreeding depression and purging should be evaluated in order to prevent a decrease in trait means due to inbreeding and to determine whether detrimental alleles are eliminated.

Genetic diversity and positive signatures of selection in indigenous cattle breeds of Iran.

Animal domestication, climate changes over time, and artificial selection have played significant roles in shaping the genome structure of various animal species, including cattle. These processes have led to the emergence of several indigenous cattle breeds with distinct genetic characteristics. This study focused on unraveling the genetic diversity and identifying candidate genomic regions in eight indigenous cattle breeds of Iran. The data consisted of ∼777 962 single nucleotide polymorphisms (SNPs) of 89 animals from Iranian indigenous cattle scattered throughout the country. We employed various methods, including integrated haplotype score, FST, and cross-population composite likelihood ratio, to conduct a genome scan for detecting selection signals within and between cattle populations. Average observed heterozygosity across the populations was 0.36, with a range of 0.32-0.40. In addition, negative and low rates of inbreeding (FIS) in the populations were observed. The genome-wide analysis revealed several genomic regions that harbored candidate genes associated with production traits (e.g., MFSD1, TYW5, ADRB2, BLK, and CRTC3), adaptation to local environmental constraints (CACNA2D1, CXCL3, and GRO1), and coat color (DYM). Finally, the study of the reported quantitative trait loci (QTL) regions in the cattle genome demonstrated that the identified regions were associated with QTL related to important traits such as milk composition, body weight, daily gain, feed conversion, and residual feed intake. Overall, this study contributes to a better understanding of the genetic diversity and potential candidate genes underlying important traits in Iranian indigenous cattle breeds, which can inform future breeding and conservation efforts.

Genetic Variability and Conservation Challenges in Lithuanian Dairy Cattle Populations.

The purpose of the study was to investigate the genetic variability of open Lithuanian Red and Red-and-White (LRWP) and Lithuanian Black-and-White (LBWP) dairy cattle populations and indicate the differences from the old genotypes of Lithuanian Black-and-White (LBW) and Lithuanian Red cattle (LR), which are currently under a conservation program. In order to gain a better understanding of the populations under conservation and to minimize the potential influence of other breeds, a distinct subgroup was formed that comprised animals whose father and mother belonged to the same breed (LR_pure and LBW_pure). The genetic variability was estimated using the number of founders, pedigree completeness, number of males and females in reproduction and age distribution, generation interval (GI), inbreeding coefficient (F) and effective population size (Ne). The highest average pedigree completeness values in the second generations of the old genotype LR and LBW were 100%. Higher ages of females in the populations under conservation were related to a higher GI and their longer life expectancy. In 2021, the reproductive age of bulls used for insemination within these populations ranged from 5.1 to 27.8 years. The proportions of males producing offspring in their older age indicate that the semen was used from the national gene bank of commercial artificial insemination companies. The GI (>5) in LR and LBW females was higher than that in LRWP and LBWP. The analysis of the data over the 15-year period showed that the GI of males in LRWP and LBWP decreased equally by 38%, while in LR_pure population, it increased by 80%. A high (9.24%) average inbreeding coefficient (F) was found in inbred animals of LR_pure population, while in LBW_pure, it was 5.35% in 2021. The coefficient of inbreeding varied within the different cattle populations. In the open LR population, it ranged from 1.48% to 2.7%, while in the LRWP population, it fell between 2.12% and 3.72%. The lowest effective population size (Ne) concerning the rate of inbreeding was observed in LBW_pure (23) and LR_pure (59), with the highest Ne identified in the LBWP population (462). When considering Ne based on the number of parents, LR_pure displayed the lowest Ne (42), while the highest Ne was found in LBWP (4449). An analysis of local cattle populations reveals that LR faces the most critical situation. This particular population has been steadily declining for a number of years, necessitating additional measures and efforts to safeguard the LR's ancestral genetic makeup. The results of the LBWP analysis also highlight a concerning trend. Even in very large populations with open breeding programs, the effective population size per generation can experience a significant decrease.

119 Pedigree and Population-Based Genomic Inbreeding Trends Over Time in Five Commercial Swine Breeding Populations

Abstract Controlling inbreeding within a population is critical to maintain additive genetic variance and reduce negative consequences such as inbreeding depression in small, closed herds. Some breeding programs may utilize subjective standard operating procedures (SOPs) such as setting the minimum number of boars, limiting the number of matings per boar, and limiting the relationships among active boars. Software programs such as Matesel can control inbreeding within a population more precisely using evolutionary algorithms by optimizing the mating and selection process to constrain inbreeding at a given target degree or other metric specified (e.g., coancestry). The main problem has been the choice of what relationship matrix to use in constraining inbreeding in these programs. Furthermore, there are many different genomic inbreeding metrics that can be used to quantify inbreeding rates over time. The objective of the current research was to investigate the trends in the pedigree [PED, (A diagonal – 1) * 100] and two population-based genomic inbreeding metrics. One based on expected homozygosity (2pq, Ghom) and one based on drift (squared allele frequency changes, Gdrift). Data included nucleus animals born from 2017 through 2022 from five different genetic lines (lines A-E). Most parents and male selection candidates were genotyped using the commercial 50k SNP panel from GeneSeek. Pedigree was traced back at least 3 generations. A total of 80k animals were sampled from the total number of genotyped animals for computational reasons across line and birth year. Results show that in general, the maternal lines (A and B) showed the least rate of inbreeding over time (0.30 and 0.43% / year for A and B, respectively), while terminal lines were greater, especially line D (0.36 to 0.76% / year). Pedigree inbreeding in 2022 was between 1.48% (line A) to 3.80% (line D) after subtracting the average pedigree inbreeding in 2017. Population-based genomic measures of inbreeding showed a very small difference in line A (0.09%), larger Gdrift than Ghom in line B (1.37%), and larger Ghom than Gdrift in lines C, D, and E (2.87% to 4.38%). In general, the trend for PED and Gdrift was very similar for all lines, while Ghom tended to increase rapidly out of control in the three terminal lines (C-E) in later years. Future research will focus on integrating results from the diagonals of a variety of G matrices on an individual basis (e.g., VanRaden 1 and 2, runs-of-homozygosity, and a linkage-analysis matrix). Results showed the pedigree and genomic drift trends over time were similar, however, the genomic homozygosity trend was much greater in terminal lines.

121 Quantifying Genetic Relationships to Maintain Genetic Diversity in the Canadian Dairy Population

Abstract Intensive selection pressure coupled with the use of a limited number of high genetic merit sires has resulted in reduced effective population size and increased levels of inbreeding in dairy cattle populations. The increased rate of inbreeding amplifies the frequency of recessive deleterious alleles, possibly leading to inbreeding depression in economically important traits, such as disease resistance, fertility and production. To better understand the relationship of available and active breeding sires to Canadian herds, quantifying genetic relationships between these groups could prove insightful. The genetic relationship value (R-value) represents the average number of alleles identical by descent shared between an animal and a reference population and is currently estimated based on pedigree information. Furthermore, the average R-value indicates the relationship of a sire to the rest of the population. Estimating the R-value between sires and individual herds may offer a more refined tool for producers to select sires that are less related to their specific herds. The aim of this study was to quantify and characterize R-values between individual sires and individual herds within the Canadian Holstein population. To quantify R-values, a dataset comprised of 11,914 sires born between 1953 and 2020 and 584,740 active cows born between 1997 and 2022 from 5,592 herds was considered. Active cows were defined as those currently alive, on milk recording, and actively contributing to the national milk inventory. Active sires were considered those used to breed the active cows. All data were provided by Lactanet Canada and analyses were carried out on PEDIG using the par2 program for relationship estimation. Results indicate that herd-level R-values (i.e., R-values estimated using individual sires and individual herds) showed variation. The R-value of individual sires to individual herds containing active cows ranged from 0.43% to 32.38. This result indicates that outbred sires are available to individual farmers when the population is considered at the herd level, and that the development of herd-level R-values may provide a selection tool which promotes the use of less related sires. Next steps include developing and estimating genomic R-values and comparing them with the pedigree-based R-values for the genotyped Canadian Holstein population. By better understanding of the relationship of available breeding sires to individual Canadian herds, a simple tool for producers to identify sires which are less related to their herds can be developed.

Effect of Individual Rate of Inbreeding, Recent and Ancestral Inbreeding on Wool Quality, Muscling Conformation and Exterior in German Sheep Breeds.

This study provides comprehensive results on the current status of inbreeding depression for traits upon which sheep are selected for the herdbook in Germany. A total of 30 sheep breeds from the OviCap national database met the inclusion criteria for the present analysis regarding the depth and completeness of pedigrees and the number of animals with phenotypic data. We analyzed heritabilities and inbreeding depression for the three breeding objective traits of wool quality, muscling conformation and exterior. Heritabilities were across all breeds of moderate size, with estimates of 0.18 for wool quality and muscling conformation and of 0.14 for exterior. The models employed to estimate linear regression slopes for individual and ancestral inbreeding rates also account for non-genetic effects and the additive genetic effect of the animal. Inbreeding depression was obvious for all three traits when we averaged the estimates across all 30 sheep breeds. Inbreeding depression was significant for wool quality for only a few breeds, whereas for muscling conformation, 14/30 breeds achieved significant estimates. A 1% increase in inbreeding decreased the mean of all three traits across all sheep breeds by 0.33% of their standard deviation. Positive effects due to ancestral inbreeding were only significant in very few breeds in the different traits. Across all 30 sheep breeds, there were indications that purging effects (a reduction in negative effects of inbreeding depression due to selection for heterozygotes) may play a role for the exterior. The results of this study should help for reviewing breeding programs, particularly for sheep breeds with critical effective population sizes and increasing rates of inbreeding, with regard to the selection policy and selection intensity applied.

Tidal gradients, fine-scale homing and a potential cryptic ecotype of wild spawning pink salmon (Oncorhynchus gorbuscha).

The homing behaviour of salmon is a remarkable natural phenomenon, critical for shaping the ecology and evolution of populations yet the spatial scale at which it occurs is poorly understood. This study investigated the spatial scale and mechanisms driving homing as depicted by spawning site-choice behaviour in pink salmon (Oncorhynchus gorbuscha) in Prince William Sound, Alaska. Molecular pedigree analyses of over 30,000 adult spawners in four streams revealed that pink salmon exhibit fine-scale site fidelity within a stream, returning to within <100 m of their parents. Homing behaviours were driven in part by a salinity gradient between intertidal and freshwater environments, with individuals incubated in freshwater environments more than twice as likely to spawn upstream of tidal influence than those incubated in the intertidal. Our findings challenge the traditional view that pink salmon populations are genetically and phenotypically homogenous due to their short freshwater residency as juveniles and high rates of dispersal as returning adults (i.e. straying). This study has important implications for rates of inbreeding, local adaptation and gene flow within populations, and is particularly relevant to the management of salmon hatcheries, given the high incidence of hatchery-origin pink salmon, reared in freshwater hatchery environments, that stray into wild populations of Prince William Sound.

POPULATION DOCUMENTATION OF PELUNG CHICKEN IN FIVE SUB DISTRICTS IN GARUT REGENCY

Pelung chicken is a local Indonesian chicken originating from Cianjur. The Pelung population data is still not known with certainty. This study aims to obtain the total and structure of population, determine the effective population size (Ne), and the rate of inbreeding (∆F) in Pelung chickens in five districts in Garut Regency. This research was conducted from May to June 2022 in Cikajang, Pasirwangi, Bayongbong, Samarang, and Cigedug Districts. The study used, quantitative descriptive methods and data were obtained by direct interview techniques in which a total of respondents were interviewed. The results of the study showed that the total population of Pelung chickens at the research location was 1,867 Pelung chickens with 452 birds in district of Cikajang, 316 of Pasirwangi, 555 of Bayongbong, 194 of Samarang, and 350 of Cigedug. The total number of effective population sizes at the study site was 465 individuals. The inbreeding rate per generation in five sub-districts was 0.1%, with the highest inbreeding rates in Samarang 0.82%, followed by Cigedug 0.78%, Pasirwangi 0.54%, Cikajang 0.42%, and Bayongbong 0.39%.

Analysis of inbreeding of the Latvian local goat breed

The objective of this study was to perform an analysis of the pedigree of the Latvian Old-Type Local Goat (LVKVT) breed to estimate the levels of inbreeding and effective population size using pedigree data. The study was based on the pedigree data of 1596 goats that were alive at the time of data selection in 2019. During the last ten years, the average generation interval for male goats was 4.40 ± 0.20 years, for female goats – 4.34 ± 0.16 years. Pedigree information on the LVKVT goats from the 1st to the 6th generation was available from 1989. For animals born in 2006 and later, the completeness of the pedigree for the first generation was from 83.9 % and in 2019 reached 100 %. Starting from 2014, the completeness of the second and third generations of pedigree exceeded 80 %. During the last decade, the average inbreeding level in population varied from 3.05 % in 2012 to 2.30 % in 2019. However, the number of inbred animals in the LVKVT population has increased and in 2019 the number of inbred animals was 109 with an average rate of inbreeding of 5.94 %. The rate of inbreeding is increased and in 2019 was 0.56. The effective population size based on the rate of inbreeding is decreased and 2019 was 89, and it is not below of recommended FAO effective population size – 50 animals. However, the breeding organization of goats must be monitored the effective population size of LVKVT breed every year to provide the development of strategies for breeding programs which would promote preserve genetic diversity.

The Potential of Instrumental Insemination for Sustainable Honeybee Breeding.

Mating control is crucial in honeybee breeding and commonly guaranteed by bringing virgin queens to isolated mating stations (IMS) for their nuptial flights. However, most breeding programs struggle to provide sufficiently many IMS. Research institutions routinely perform instrumental insemination of honeybees, but its potential to substitute IMS in breeding programs has not been sufficiently studied. We performed stochastic simulations to compare instrumental insemination strategies and mating on IMS in terms of genetic progress and inbreeding development. We focused on the role of paternal generation intervals, which can be shortened to two years with instrumental insemination in comparison to three years when using IMS. After 70 years, instrumental insemination yielded up to 42% higher genetic gain than IMS strategies-particularly with few available mating sites. Inbreeding rates with instrumental insemination and IMS were comparable. When the paternal generation interval in instrumental insemination was stretched to three years, the number of drone producers required for sustainable breeding was reduced substantially. In contrast, when shortening the interval to two years, it yielded the highest generational inbreeding rates (up to 2.28%). Overall, instrumental insemination with drones from a single colony appears as a viable strategy for honeybee breeding and a promising alternative to IMS.

Estimation of Cumulative Inbreeding Rate in Indian Major Carps of Maharashtra State Hatcheries

The hatcheries of Maharashtra state, India breed mainly the species of catla, rohu and mrigal, and are the main suppliers of fish seed in the region. These hatcheries function as isolated and genetically closed units raising their own broodstock within the hatcheries, which leads to the accumulation of inbreeding at a faster rate. In the present study effective population size and cumulative inbreeding rates were estimated. The cumulative inbreeding rates ranged from 0.71-19.09%, 0.05-5.23% and 0.11- 4.24% for catla, mrigal and rohu, respectively.

Genealogical structure of the Colombian Romosinuano Creole cattle

The Romosinuano cattle breed is one of the most important Creole genetic resources in Colombia, and interesting traits like adaptation or reproductive efficiency have promoted its use in different countries in America. To consolidate the genealogical historical records, the review of very first yield records in this population was used to reconstruct the genealogy of the breed since the first animals incorporated to the in vivo germplasm bank and estimate different demographic parameters. The complete genealogy comprises 17,136 animals with 5.8 years of generation interval for two pathways. The estimated average inbreeding for the population and inbred animals was 2.53% and 6.32% respectively, with a progressive increase of inbred animals across the generations. Almost 48% of the total animals presented some level of consanguinity. Effective population size (Ne) based on the inbreeding rate estimated by regression in all generations was 120 animals whereas Ne estimated by equivalent generations was 69 animals. Effective number of founders (Fe), effective number of ancestors (Fa), and ancestors explaining 50% of variability were 75, 48, and 22, respectively. The relation between Fa/Fe of 64% indicates a genetic bottleneck effect in the population studied.

Difficulties in maintaining small horse breed populations, possible ways of decreasing the growth rate of inbreeding

Nowadays, the need for the survival and preservation of endangered breeds, including strains, genealogical lines, female families, has gained social acceptance. The primary objective within breeding conversation is to prevent genetic loss of the breed and to maintain genetic and phenotypic diversity. In simple terms: to avoid inbreeding. One of the conditions for the long-term maintenance of small breeds is to increase the population. The protection of mare families and genealogical lines is also an extremely important professional starting point. . The possibility of extending the persistence of the breed over time is helped by increasing the generation interval. In the case of endangered breeds, it is usually justified to deviate from the species-specific sex ratio when maintaining the breed, because a narrow sex ratio is beneficial for maintaining genetic diversity.

Investigating the benefits and perils of importing genetic material in small cattle breeding programs via simulation

Small breeding programs are limited in achieving competitive genetic gain and prone to high rates of inbreeding. Thus, they often import genetic material to increase genetic gain and to limit the loss of genetic variability. However, the benefit of import depends on the strength of genotype-by-environment interaction. Import also diminishes the relevance of domestic selection and the use of domestic breeding animals. Introduction of genomic selection has potentially exacerbated this issue, but is also opening the potential for smaller breeding programs. The aim of this paper was to determine when and to what extent small breeding programs benefit from importing genetic material by quantifying the genetic gain as well as the sources of genetic gain. We simulated 2 cattle breeding programs of the same breed that represented a large foreign and a small domestic breeding program. The programs differed in selection parameters of sire selection, and in the initial genetic mean and annual genetic gain. We evaluated a control scenario without the use of foreign sires in the domestic breeding program and 24 scenarios that varied the percentage of domestic dams mated with foreign sires, the genetic correlation between the breeding programs (0.8 or 0.9), and the time of implementing genomic selection in the domestic compared with the foreign breeding program (concurrently or with a 10-yr delay). We compared the scenarios based on the genetic gain and genic standard deviation. Finally, we partitioned breeding values and genetic trends of the scenarios to quantify the contribution of domestic selection and import to the domestic genetic gain. The simulation revealed that when both breeding programs implemented genomic selection simultaneously, the use of foreign sires increased domestic genetic gain only when genetic correlation was 0.9 (10%-18% increase). In contrast, when the domestic breeding program implemented genomic selection with a 10-yr delay, import increased genetic gain at both tested correlations, 0.8 (5%-23% increase) and 0.9 (15%-53% increase). The increase was significant when we mated at least 10% or 25% domestic females with foreign sires and increased with the increasing use of foreign sires, but with a diminishing return. The partitioning analysis revealed that the contribution of import expectedly increased with the increased use of foreign sires. However, the increase did not depend on the genetic correlation and was not proportional to the increase in domestic genetic gain. This represents a peril for small breeding programs because they could be overly relying on import with diminishing returns for the genetic gain, marginal benefit for the genetic variability, and large loss of the domestic germplasm. The benefit and peril of import depends on an interplay of genetic correlation, extent of using foreign sires, and a breeding scheme. It is therefore crucial that small breeding programs assess the possible benefits of import beyond domestic selection. The benefit of import should be weighed against the perils of decreased use of domestic sires and decreased contribution and value of domestic selection.

Impact of kinship matrices on genetic gain and inbreeding with optimum contribution selection in a genomic dairy cattle breeding program

BackgroundGenomic selection has increased genetic gain in dairy cattle, but in some cases it has resulted in higher inbreeding rates. Therefore, there is need for research on efficient management of inbreeding in genomically-selected dairy cattle populations, especially for local breeds with a small population size. Optimum contribution selection (OCS) minimizes the increase in average kinship while it maximizes genetic gain. However, there is no consensus on how to construct the kinship matrix used for OCS and whether it should be based on pedigree or genomic information. VanRaden’s method 1 (VR1) is a genomic relationship matrix in which centered genotype scores are scaled with the sum of 2p(1-p) where p is the reference allele frequency at each locus, and VanRaden’s method 2 (VR2) scales each locus with 2p(1-p), thereby giving greater weight to loci with a low minor allele frequency. We compared the effects of nine kinship matrices on genetic gain, kinship, inbreeding, genetic diversity, and minor allele frequency when applying OCS in a simulated small dairy cattle population. We used VR1 and VR2, each using base animals, all genotyped animals, and the current generation of animals to compute reference allele frequencies. We also set the reference allele frequencies to 0.5 for VR1 and the pedigree-based relationship matrix. We constrained OCS to select a fixed number of sires per generation for all scenarios. Efficiency of the different matrices were compared by calculating the rate of genetic gain for a given rate of increase in average kinship.ResultsWe found that: (i) genomic relationships were more efficient than pedigree-based relationships at managing inbreeding, (ii) reference allele frequencies computed from base animals were more efficient compared to reference allele frequencies computed from recent animals, and (iii) VR1 was slightly more efficient than VR2, but the difference was not statistically significant.ConclusionsUsing genomic relationships for OCS realizes more genetic gain for a given amount of kinship and inbreeding than using pedigree relationships when the number of sires is fixed. For a small genomic dairy cattle breeding program, we recommend that the implementation of OCS uses VR1 with reference allele frequencies estimated either from base animals or old genotyped animals.

Identification of runs of homozygosity associated with male fertility in Italian Brown Swiss cattle.

Intensive selection for improved productivity has been accompanied by an increase in inbreeding rates and a reduction in genetic diversity. The increase in inbreeding tends to impact performance, especially fitness-related traits such as male fertility. Inbreeding can be monitored using runs of homozygosity (ROH), defined as contiguous lengths of homozygous genotypes observed in an individual's chromosome. The goal of this study was to evaluate the presence of ROH in Italian Brown Swiss cattle and assess its association with bull fertility. First, we evaluated the association between ROH and male fertility using 1,102 Italian Brown Swiss bulls with sire conception rate records and 572K SNPs spanning the entire genome. Second, we split the entire population into 100 high-fertility and 100 low-fertility bulls to investigate the potential enrichment of ROH segments in the low-fertility group. Finally, we mapped the significant ROH regions to the bovine genome to identify candidate genes associated with sperm biology and male fertility. Notably, there was a negative association between bull fertility and the amount of homozygosity. Four different ROH regions located in chromosomes 6, 10, 11, and 24 were significantly overrepresented in low-fertility bulls (Fisher's exact test, p-value <0.01). Remarkably, these four genomic regions harbor many genes such as WDR19, RPL9, LIAS, UBE2K, DPF3, 5S-rRNA, 7SK, U6, and WDR7 that are related to sperm biology and male fertility. Overall, our findings suggest that inbreeding and increased homozygosity have a negative impact on male fertility in Italian Brown Swiss cattle. The quantification of ROH can contribute to minimizing the inbreeding rate and avoid its negative effect on fitness-related traits, such as male fertility.

Genetic gain and inbreeding from simulation of different genomic mating schemes for pig improvement

BackgroundGenomic selection involves choosing as parents those elite individuals with the higher genomic estimated breeding values (GEBV) to accelerate the speed of genetic improvement in domestic animals. But after multi-generation selection, the rate of inbreeding and the occurrence of homozygous harmful alleles might increase, which would reduce performance and genetic diversity. To mitigate the above problems, we can utilize genomic mating (GM) based upon optimal mate allocation to construct the best genotypic combinations in the next generation. In this study, we used stochastic simulation to investigate the impact of various factors on the efficiencies of GM to optimize pairing combinations after genomic selection of candidates in a pig population. These factors included: the algorithm used to derive inbreeding coefficients; the trait heritability (0.1, 0.3 or 0.5); the kind of GM scheme (focused average GEBV or inbreeding); the approach for computing the genomic relationship matrix (by SNP or runs of homozygosity (ROH)). The outcomes were compared to three traditional mating schemes (random, positive assortative or negative assortative matings). In addition, the performance of the GM approach was tested on real datasets obtained from a Large White pig breeding population.ResultsGenomic mating outperforms other approaches in limiting the inbreeding accumulation for the same expected genetic gain. The use of ROH-based genealogical relatedness in GM achieved faster genetic gains than using relatedness based on individual SNPs. The GROH-based GM schemes with the maximum genetic gain resulted in 0.9%–2.6% higher rates of genetic gain ΔG, and 13%–83.3% lower ΔF than positive assortative mating regardless of heritability. The rates of inbreeding were always the fastest with positive assortative mating. Results from a purebred Large White pig population, confirmed that GM with ROH-based GRM was more efficient than traditional mating schemes.ConclusionCompared with traditional mating schemes, genomic mating can not only achieve sustainable genetic progress but also effectively control the rates of inbreeding accumulation in the population. Our findings demonstrated that breeders should consider using genomic mating for genetic improvement of pigs.

Clonal diploid and autopolyploid breeding strategies to harness heterosis: insights from stochastic simulation

Key messageReciprocal recurrent selection sometimes increases genetic gain per unit cost in clonal diploids with heterosis due to dominance, but it typically does not benefit autopolyploids.Breeding can change the dominance as well as additive genetic value of populations, thus utilizing heterosis. A common hybrid breeding strategy is reciprocal recurrent selection (RRS), in which parents of hybrids are typically recycled within pools based on general combining ability. However, the relative performances of RRS and other breeding strategies have not been thoroughly compared. RRS can have relatively increased costs and longer cycle lengths, but these are sometimes outweighed by its ability to harness heterosis due to dominance. Here, we used stochastic simulation to compare genetic gain per unit cost of RRS, terminal crossing, recurrent selection on breeding value, and recurrent selection on cross performance considering different amounts of population heterosis due to dominance, relative cycle lengths, time horizons, estimation methods, selection intensities, and ploidy levels. In diploids with phenotypic selection at high intensity, whether RRS was the optimal breeding strategy depended on the initial population heterosis. However, in diploids with rapid-cycling genomic selection at high intensity, RRS was the optimal breeding strategy after 50 years over almost all amounts of initial population heterosis under the study assumptions. Diploid RRS required more population heterosis to outperform other strategies as its relative cycle length increased and as selection intensity and time horizon decreased. The optimal strategy depended on selection intensity, a proxy for inbreeding rate. Use of diploid fully inbred parents vs. outbred parents with RRS typically did not affect genetic gain. In autopolyploids, RRS typically did not outperform one-pool strategies regardless of the initial population heterosis.

Outlining inbreeding in the Brazilian higher education system

AbstractThis study describes characteristics of academic inbreeding in the Brazilian higher education system. Results show the rate of inbreeding significantly differs among distinct types of institutions, fields of knowledge, states and university ranking tiers. According to this study, inbreeding is most likely to be found in established elite research institutions, concentrated in the Southeast of Brazil, in the STEM fields. These also happen to be the main providers and most prestigious consumers of the well‐trained local academic workforce, supporting the conclusion that both internal and external factors could be influencing the high concentration of inbred scholars at prominent alma maters. It contributes to international literature by evaluating the role of individual characteristics and by showing how the expansion of higher education to more geographically distant areas may establish different patterns of inbreeding.