Search

Abstract Background Since their domestication, recent inbreeding together with intensive artificial selection and population bottlenecks have allowed the prevalence of deleterious mutations and the increase of runs-of-homozygosity (ROH) in domestic pigs. This makes pigs a good model to understand the genetic underpinnings of inbreeding depression. Results Here we integrated a comprehensive dataset comprising 7239 domesticated pigs and wild boars genotyped by single nucleotide polymorphism (SNP) chips, along with phenotypic data encompassing growth, reproduction and disease-associated traits. Our study revealed differential ROH landscapes during domestication and artificial selection of Eurasian pigs. We observed associations between ROH burden and phenotypic traits such as body conformation and susceptibility to diseases like scrotal hernia. By examining associations of whole-genome and regional ROH burden with gene expression, we identified specific genes and pathways affected by inbreeding depression. Associations of regional ROH burden with gene expression also enabled the discovery of novel regulatory elements. Lastly, we inferred recessive lethal mutations by examining depletion of ROH in an inbred population with relatively small sample size, following by fine mapping with sequencing data. Conclusions These findings suggested that both phenotypic and genetic variations have been reshaped by inbreeding, and provided insights to the genetic mechanisms underlying inbreeding depression.

Abstract Genetic architecture of yield and yield contributing characters of five crosses in chickpea were performed by generation mean analysis. Non-significant χ2 values were noted for plant weight at harvest (PWH), number of pods per plant (NPd/P) and number of seeds per plant (NS/P) in cross-2; for number of secondary branches at first flower (NSBFF) and number of secondary branches at maximum flower (NSBMF) in cross-3 and for number of primary branches at maximum flower (NPBMF) in cross-4. Among these, PWH in cross-2; NSBFF and NSBMF in cross-3 and NPBMF in cross-4 were also non-significant regarding C and D scales. Non-significant scale coupled with non-significant χ2 values indicated only additive-dominance relationship for those characters and crosses that would likely be helpful in doing successful breeding plan easily for the development of potential lines in chickpea. Gene effects viz., additive [d], dominance [h], additive × additive [i] and dominance × dominance [l] were significant for different crosses and characters indicating involvement of additive, dominance, additive × additive and dominance × dominance gene interactions in the control of these traits. Most of the studied characters exhibited duplicate type of epistasis therefore, recurrent selection for these traits is suggested. Effective factor (K1) was less than one for all the characters and crosses indicating minimum one group of gene controlled the characters. Both broad (h2 b) and narrow (h2 n) sense heritability in majority cases were found to be high which indicates that selection for high heritability showing traits is likely to be effective. Mid-parent (MP) and better-parent (BP) heterosis found to be non-significant in maximum cases. All the characters and crosses showed non-significant inbreeding depression (ID) indicating a good sign for further genetic work.

Abstract Background Nelore cattle play a key role in tropical production systems due to their resilience to harsh conditions, such as heat stress and seasonally poor nutrition. Monitoring their genetic diversity is essential to manage the negative impacts of inbreeding. Traditionally, inbreeding and inbreeding depression are assessed by pedigree-based coefficients (F), but recently, genetic markers have been preferred for their precision in capturing the inbreeding level and identifying animals at risk of reduced productive and reproductive performance. Hence, we compared the inbreeding and inbreeding depression for productive and reproductive performance traits in Nelore cattle using different inbreeding coefficient estimation methods from pedigree information (FPed), the genomic relationship matrix (FGRM), runs of homozygosity (FROH) of different lengths (> 1 Mb (genome), between 1 and 2 Mb - FROH 1−2; 2–4 Mb FROH 2−4 or > 8 Mb FROH >8) and excess homozygosity (FSNP). Results The correlation between FPed and FROH was lower when the latter was based on shorter segments (r = 0.15 with FROH 1−2, r = 0.20 with FROH 2−4 and r = 0.28 with FROH 4−8). Meanwhile, the FPed had a moderate correlation with FSNP (r = 0.47) and high correlation with FROH >8 (r = 0.58) and FROH−genome (r = 0.60). The FROH−genome was highly correlated with inbreeding based on FROH>8 (r = 0.93) and FSNP (r = 0.88). The FGRM exhibited a high correlation with FROH−genome (r = 0.55) and FROH >8 (r = 0.51) and a lower correlation with other inbreeding estimators varying from 0.30 for FROH 2−4 to 0.37 for FROH 1−2. Increased levels of inbreeding had a negative impact on the productive and reproductive performance of Nelore cattle. The unfavorable inbreeding effect on productive and reproductive traits ranged from 0.12 to 0.51 for FPed, 0.19–0.59 for FGRM, 0.21–0.58 for FROH−genome, and 0.19–0.54 for FSNP per 1% of inbreeding scaled on the percentage of the mean. When scaling the linear regression coefficients on the standard deviation, the unfavorable inbreeding effect varied from 0.43 to 1.56% for FPed, 0.49–1.97% for FGRM, 0.34–2.2% for FROH−genome, and 0.50–1.62% for FSNP per 1% of inbreeding. The impact of the homozygous segments on reproductive and performance traits varied based on the chromosomes. This shows that specific homozygous chromosome segments can be signs of positive selection due to their beneficial effects on the traits. Conclusions The low correlation observed between FPed and genomic-based inbreeding estimates suggests that the presence of animals with one unknown parent (sire or dam) in the pedigree does not account for ancient inbreeding. The ROH hotspots surround genes related to reproduction, growth, meat quality, and adaptation to environmental stress. Inbreeding depression has adverse effects on productive and reproductive traits in Nelore cattle, particularly on age at puberty in young bulls and heifer calving at 30 months, as well as on scrotal circumference and body weight when scaled on the standard deviation of the trait.

Abstract Background Dairy cattle breeds are populations of limited effective size, subject to recurrent outbreaks of recessive defects that are commonly studied using positional cloning. However, this strategy, based on the observation of animals with characteristic features, may overlook a number of conditions, such as immune or metabolic genetic disorders, which may be confused with pathologies of environmental etiology. Results We present a data mining framework specifically designed to detect recessive defects in livestock that have been previously missed due to a lack of specific signs, incomplete penetrance, or incomplete linkage disequilibrium. This approach leverages the massive data generated by genomic selection. Its basic principle is to compare the observed and expected numbers of homozygotes for sliding haplotypes in animals with different life histories. Within three cattle breeds, we report 33 new loci responsible for increased risk of juvenile mortality and present a series of validations based on large-scale genotyping, clinical examination, and functional studies for candidate variants affecting the NOA1, RFC5, and ITGB7 genes. In particular, we describe disorders associated with NOA1 and RFC5 mutations for the first time in vertebrates. Conclusions The discovery of these many new defects will help to characterize the genetic basis of inbreeding depression, while their management will improve animal welfare and reduce losses to the industry.

ABSTRACT: In dairy cattle production, it is important to understand how inbreeding affects production, fertility, and health traits. However, there is still limited use of genomic information to estimate inbreeding, despite advancements in genotyping technologies. To address this gap, we investigated the effect of inbreeding on German Holstein dairy cattle using both pedigree-based and genomic-based inbreeding estimators. We employed one method based on pedigree information (Fped) together with 6 genomic-based methods, including 3 genome-wide complex trait analysis software estimators (Fhat1, Fhat2, Fhat3), VanRaden's first method (FVR1, with observed allele frequencies, and FVR0.5, when allele frequencies are set to 0.5), and one based on runs of homozygosity (Froh). Data from 24,489 cows with both phenotypes and genotypes were used, with a pedigree including 232,780 animals born between 1970 and 2018. We analyzed the effects of inbreeding depression on production, fertility, and health traits separately, using single-trait linear animal models as well as threshold models to account for the binary nature of the health traits. For the health traits, we transformed solutions from the liability scale to a probability scale for easier interpretation. Our results showed that the mean inbreeding coefficients from all estimators ranged from −0.003 to 0.243, with negative values observed for most genomic-based methods. We found out that a 1% increase in inbreeding caused a depression ranging from 25.94 kg (Fhat1) to 40.62 kg (Fhat3), 1.18 kg (Fhat2) to 1.70 kg (Fhat3), 0.90 kg (Fhat2) to 1.45 kg (Froh and Fhat3), 0.19 (Fped) to 0.34 d (Fhat3) for 305-d milk yield, fat, protein, and calving interval, respectively. The health traits showed very slight gradual changes when inbreeding was increased steadily from 0% to 50%, with digital dermatitis showing a rather contrasting trend to that of mastitis, which increased the more an animal was inbred. Overall, our study highlights the importance of considering both pedigree-based and genomic-based inbreeding estimators when assessing the impact on inbreeding, emphasizing that not all inbreeding is harmful.

Abstract Background The selection of individuals based on their predicted breeding values and mating of related individuals can increase the proportion of identical-by-descent alleles. In this context, the objectives of this study were to estimate inbreeding coefficients based on alternative metrics and data sources such as pedigree (FPED), hybrid genomic relationship matrix H (FH), and ROH of different length (FROH); and calculate Pearson correlations between the different metrics in a closed Nellore cattle population selected for body weight adjusted to 378 days of age (W378). In addition to total FROH (all classes) coefficients were also estimated based on the size class of the ROH segments: FROH1 (1–2 Mb), FROH2 (2–4 Mb), FROH3 (4–8 Mb), FROH4 (8–16 Mb), and FROH5 (> 16 Mb), and for each chromosome (FROH_CHR). Furthermore, we assessed the effect of each inbreeding metric on birth weight (BW), body weights adjusted to 210 (W210) and W378, scrotal circumference (SC), and residual feed intake (RFI). We also evaluated the chromosome-specific effects of inbreeding on growth traits. Results The correlation between FPED and FROH was 0.60 while between FH and FROH and FH and FPED were 0.69 and 0.61, respectively. The annual rate of inbreeding was 0.16% for FPED, 0.02% for FH, and 0.16% for FROH. A 1% increase in FROH5 resulted in a reduction of up to -1.327 ± 0.495 kg in W210 and W378. Four inbreeding coefficients (FPED, FH, FROH2, and FROH5) had a significant effect on W378, with reductions of up to -3.810 ± 1.753 kg per 1% increase in FROH2. There was an unfavorable effect of FPED on RFI (0.01 ± 0.0002 kg dry matter/day) and of FROH on SC (-0.056 ± 0.022 cm). The FROH_CHR coefficients calculated for BTA3, BTA5, and BTA8 significantly affected the growth traits. Conclusions Inbreeding depression was observed for all traits evaluated. However, these effects were greater for the criterion used for selection of the animals (i.e., W378). The increase in the genomic inbreeding was associated with a higher inbreeding depression on the traits evaluated when compared to pedigree-based inbreeding. Genomic information should be used as a tool during mating to optimize control of inbreeding and, consequently, minimize inbreeding depression in Nellore cattle.

Abstract Genetic rescue—an increase in population fitness following the introduction of new alleles—has been proven to ameliorate inbreeding depression in small, isolated populations, yet is rarely applied as a conservation tool. A lingering question regarding genetic rescue in wildlife conservation is how long beneficial effects persist in admixed populations. Using data collected over 40 years from 1192 endangered Florida panthers (Puma concolor coryi) across nine generations, we show that the experimental genetic rescue implemented in 1995—via the release of eight female pumas from Texas—alleviated morphological, genetic, and demographic correlates of inbreeding depression, subsequently preventing extirpation of the population. We present unequivocal evidence, for the first time in any terrestrial vertebrate, that genetic and phenotypic benefits of genetic rescue remain in this population after five generations of admixture, which helped increase panther abundance (> fivefold) and genetic effective population size (> 20-fold). Additionally, even with extensive admixture, microsatellite allele frequencies in the population continue to support the distinctness of Florida panthers from other North American puma populations, including Texas. Although threats including habitat loss, human-wildlife conflict, and infectious diseases are challenges to many imperiled populations, our results suggest genetic rescue can serve as an effective, multi-generational tool for conservation of small, isolated populations facing extinction from inbreeding.

Inbreeding depression, the reduced fitness of inbred relative to outbred individuals was described more than two centuries ago, long before the development of population genetics. Its impact is central to evolutionary ecology and the evolution of mating systems, in particular self-fertilization in hermaphrodites. In the first half of the 20th century, population genetics revealed a mechanism for inbreeding depression through homozygosity. Numerous theoretical studies have modeled inbreeding depression as a function of genetic architecture and analyzed how it varies with population selfing rates. A major concept in these models is purging, i.e., the purging of recessive deleterious mutations through inbreeding. Consequently, inbreeding depression is expected to decrease with increasing population selfing rates. Along with these theoretical studies, many experimental studies, particularly on plants, have measured inbreeding depression using experimental crosses or directly in the field. The results of these studies have revealed that the evolutionary ecology of inbreeding depression is difficult to capture and that empirical data do not exactly match model predictions, specifically purging efficacy. In addition, the lability of inbreeding depression in natural populations can qualitatively affect the selective role of inbreeding depression in the evolution of mating systems. Recently, several studies have demonstrated the role of epigenetics in shedding new light on the dynamics of inbreeding depression in natural populations. This review provides a general overview of the studies on inbreeding depression and how various angles can help capture its selective role in natural populations.

Inbreeding depression is a key factor regulating the evolution of self-fertilization in plants. Despite predictions that inbreeding depression should evolve with selfing rates as deleterious alleles are increasingly exposed and removed by selection, evidence of purging the genetic load in wild populations is equivocal at best. This discordance could be explained, in part, if the load underlying inbreeding depression is subject to soft selection, i.e., the fitness of selfed individuals depends on the frequency and density of selfed vs. outcrossed individuals in the population. Somewhat counterintuitively, this means that populations with contrasting mutation load can have similar fitness. Soft selection against selfed individuals may be expected when there is inbreeding depression for competitive ability in density-regulated populations. We tested population-level predictions of inbreeding depression in competitive ability by creating a density series of potted plants consisting of either purely outcrossed, purely selfed, or mixed (50% outcrossed, 50% selfed) seed of the mixed-mating biennial Sabatia angularis (Gentianaceae) representing ecological neighborhoods. Focusing on the growth and survival of juveniles, we show that mean plant size is independent of neighborhood composition when resources are limiting, but greatest in outcrossed neighborhoods at low densities. Across a range of densities, this manifests as stronger density-dependence in outcrossed populations compared to selfed or mixed ones. We also found significantly greater size inequalities among individuals in mixed neighborhoods, even at high densities where mean juvenile size converged, a key signature of asymmetric competition between outcrossed and selfed individuals. Our work illustrates how soft selection could shelter the genetic load underlying inbreeding depression and its demographic consequences.

ABSTRACT: This study leveraged a growing dataset of producer-recorded phenotypes for mastitis, reproductive diseases (metritis and retained placenta), and metabolic diseases (ketosis, milk fever, and displaced abomasum) to investigate the potential presence of inbreeding depression for these disease traits. Phenotypic, pedigree, and genomic information were obtained for 354,043 and 68,292 US Holstein and Jersey cows, respectively. Total inbreeding coefficients were calculated using both pedigree and genomic information; the latter included inbreeding estimates obtained using a genomic relationship matrix and runs of homozygosity. We also generated inbreeding coefficients based on the generational inbreeding for recent and old pedigree inbreeding, for different run-of-homozygosity length classes, and for recent and old homozygous-by-descent segment-based inbreeding. Estimates on the liability scale revealed significant evidence of inbreeding depression for reproductive-disease traits, with an increase in total pedigree and genomic inbreeding showing a notable effect for recent inbreeding. However, we found inconsistent evidence for inbreeding depression for mastitis or any metabolic diseases. Notably, in Holsteins, the probability of developing displaced abomasum decreased with inbreeding, particularly for older inbreeding. Estimates of disease probability for cows with low, average, and high inbreeding levels did not significantly differ across any inbreeding coefficient and trait combination, indicating that although inbreeding may affect disease incidence, it likely plays a smaller role compared with management and environmental factors.

Corn germplasm with different mesocotyl elongation was characterized for High Valleys in Mexico by estimating the general combinatory aptitude (GCA), specific combinatory aptitude (SCA), heterosis (H), inbreeding depression (ID) and principal component aptitude (PCA), with the purpose of directing the improvement for deep sowing. The hypothesis was that the parents and crosses of mesocotyl present variability in seedling and adult plant traits based on deep sowing. The 36 F1 and F2 crosses—derived from nine parents, three with short mesocotyl (S), three medium (M) and three long (L), obtained through Griffing diallel II—plus the parents were planted in sand beds and polyethylene bags in a greenhouse during the spring–summer cycles of 2021 and 2022. The following traits were measured: length of mesocotyl (LM), length of coleoptile, total seedling dry matter and 10 cob traits in addition to total dry matter. In 11 of the 14 traits, there was a positive and significant correlation (p ≤ 0.05) between the GCA of the parents and their LM. The highest SCA, H and ID (p ≤ 0.05) were for crosses L × L for all the traits measured. When comparing the GCA/SCA proportions, this relation varied from 0.76 to 0.97, which points to practically equal additive effects with those of dominance; however, in parents and L × L crosses, this relation was on average 0.94, 1.07 in M × M, 0.22 in S × S and 0.36 in L × S. In both F1 and F2, the variation was explained by two principal components: 89.5% for GCA and 73.4% for SCA. In both generations, the parents with higher GCA were H-48, HS-2 and Promesa, the three with long mesocotyl, while those with the highest GCA were crosses between these three hybrids.

The present investigation on heterosis and inbreeding depression in wheat was carried out at the Crop Research Farm of CSAUA&T, Nawabganj, Kanpur, U.P., India, during the Rabi crop season 2019-20. A ten parental half-diallel cross comprising of 45 F1s and 45 F2s together with parents was grown in three replications. The outcome of better parent heterosis revealed that the cross combinations, namely, HD3086 x HD-2733, HD3086 x K0307, HD3086 x HD2967, HD3086 x K1601, and HD2967 x K0402 exhibited positive and high heterosis for grain yield. In the case of economic heterosis over the check (HD2967), the cross combination viz. HD3086 x K0307, HD3086 x HD2967, HD-967 x K0402, HD2967 x K1601, and HD2967 x K1314 exhibited significant and positive heterosis for grain yield. Inbreeding depression for grain yield ranged from 1.51 (DH 29767 x K 8962) to 8.95 (DBW 88 x K 8962) percent. For grain yield, out of the 45 crosses, all combinations exhibited significant and positive inbreeding depression in F2. The cross combinations may be used to increase grain yield and to produce better transgressive segregants for future breeding programs to maintain the specific gene pool of bread wheat.

Inbreeding depression is likely to play an important role during biological invasion. But relatively few studies have investigated the fitness of selfed and outcrossed offspring in self-incompatible invasive plants in natural environments in their introduced range. Moreover, the majority of studies on inbreeding depression have investigated self-compatible species with mixed mating, and less is known about the intensity of inbreeding depression in outcrossing self-incompatible species. Here, we address these questions experimentally by comparing selfed and outcrossed progeny of purple loosestrife (Lythrum salicaria) over four growing seasons, including three under field conditions in a freshwater marsh in southern Ontario, Canada, a region where L. salicaria is highly invasive. The tristylous mating system of L. salicaria involves disassortative mating among floral morphs enforced by trimorphic incompatibility. However, owing to partial incompatibility, self-fertilized seed can be obtained by manual self-pollination thus facilitating comparisons of selfed and outcrossed progeny. We compared progeny with and without intraspecific competition from selfed or outcrossed neighbours and examined the influence of breeding treatment and competition on fitness correlates by measuring a range of life-history traits including: proportion of seeds germinating, days to germination, survival, proportion of plants flowering, time to flowering, vegetative mass, and inflorescence number and mass. We analysed data for each trait using functions from time series estimates of growth and two multiplicative estimates of fitness. We detected varying intensities of inbreeding depression for several traits in three of the four years of the experiment, including inflorescence mass and reproductive output. Cumulative inbreeding depression over four years averaged δ = 0.48 and 0.68, depending on the method used to estimate multiplicative fitness. The competition treatments did not significantly affect plant performance and the magnitude of inbreeding depression. Given the primarily outcrossing mating system of L. salicaria populations, the detection of inbreeding depression for several key life-history traits was as predicted by theory. Our results suggests that biparental inbreeding and low selfing in colonizing populations may have significant effects on demographic parameters such as population growth.

Inbreeding depression (ID) is a major selective force during mating system evolution primarily contributed by highly to partially recessive deleterious mutations. Theories suggest that transient genetic association with fitness alleles can be important in affecting the evolution of alleles that modify the selfing rate during its sweep. Nevertheless, empirical tests often focus on the pre-existing genetic association between selfing rate and ID maintained under mutation–selection balance. Therefore, how this standing genetic association is affected by key factors and its impacts on the evolution of selfing remain unclear. I show that as the selection coefficient of deleterious mutations increases, the association between selfing rate and ID declines from positive to negative. These results predict that association between selfing and ID tends to be negative in populations with low selfing rates, while positive in highly selfing populations. Using population genetic and quantitative genetic models, I show that standing genetic associations between selfing rate and fitness alleles can significantly impact the evolution of the mean selfing rate of a population. I present better metrics of population-level ID, which can be calculated based on the correlation coefficient between individual selfing rate and the fitness of selfed and outcrossed offspring.

Only approximately 356 North Atlantic right whales (Eubalaena glacialis) remain. With extremely low levels of genetic diversity, limited options for mates, and variation in reproductive success across females, there is concern regarding the potential for genetic limitations of population growth from inbreeding depression. In this study, we quantified reproductive success of female North Atlantic right whales with a modified de-lifing approach using reproductive history information collected over decades of field observations. We used double-digest restriction site-associated sequencing to sequence approximately 2% of the genome of 105 female North Atlantic right whales and combined genomic inbreeding estimates with individual fecundity values to assess evidence of inbreeding depression. Inbreeding depression could not explain the variance in reproductive success of females, however we present evidence that inbreeding depression may be affecting the viability of inbred fetuses—potentially lowering the reproductive success of the species as a whole. Combined, these results allay some concerns that genetic factors are impacting species survival as genetic diversity is being retained through selection against inbred fetuses. While still far fewer calves are being born each year than expected, the small role of genetics underlying variance in female fecundity suggests that variance may be explained by external factors that can potentially be mitigated through protection measures designed to reduce serious injury and mortality from human activities.

The biofortification of pearl millet, a prime staple crop around the world with increased grain iron (Fe) and zinc (Zn) concentrations is part of continuing attempts to fight micronutrient deficiency. The goal of the current study was to examine heterosis, heritability, genetic advancement and inbreeding depression (ID) for yield, and associated features in pearl millet or bajra [Pennisetum glaucum (L.) R. Br.]. The majority of crosses with days to 50% flowering, maturity, and plant height showed negligible inbreeding depression and significant heterosis in the desired direction. Yield and other associated characteristics demonstrated significant average heterosis and heterobeltiosis, along with severe inbreeding depression. The presence of additive gene effects for grain Fe and Zn content was shown by the lower value of better parent and relative heterosis in F1s and the absence of inbreeding depression in F2. Majority of the characteristics had moderate to high heritability and low to average genetic advance. Crosses, 30127 x J 2556 for maturity; 30725 x ICMB 05333, J 2454 x 30348 and 30843 x ICMB 98222 for height of plants; 30727 x J 2523, ICMB 99222 x ICMB 08222, 30127 x J 2556, and 30843 x ICMB 98222 for panicle diameter; 30727 x J 2523 and 30725 x ICMB 05333 for seed yield/plant; J 2372 x 30610, ICMB 99222 x ICMB 08222, and 30843 x ICMB 98222 for test weight/1000 grain weight; 30843 x ICMB 98222 and ICMB 99222 x ICMB 08222 for Fe content; 30727 x J 2523, J 2372 x 30610, J 2454 x 30348, 30127 x J 2556, 30843 x ICMB 98222, ICMB 99222 x ICMB 08222, and ICMB 10444 x ICMB 97222 for Zn content showed average to high heritability (broad sense) associated with high to medium genetic advance (GA) that can be improved through selection.

Abstract Conservation is prioritized based on accepted taxa. As a consequence, a conservation incentive exists to emphasize inter‐population differences to define taxa, potentially leading to taxonomic inflation. But stressing the uniqueness of threatened populations has the side effect of hindering conservation actions that promote inter‐population gene flow, such as genetic rescue. These actions may be of critical importance for severely inbred populations involved in extinction vortices, for which an inflated taxonomy can become a conservation trap. Here, we exemplify this scenario with the western capercaillie (Tetrao urogallus, Phasianidae) population in the Cantabrian Mountains, described and legally listed as a subspecies not supported by recent molecular data. The Cantabrian capercaillie population is Critically Endangered after a long‐lasting decline and a recent demographic collapse. It shows clear signs of inbreeding depression, including striking clutch size decreases as well as reduced hatchability and chick survival. This critical situation could be alleviated through a genetic rescue, but this possibility is hindered by inertias rooted in the putative uniqueness of the Cantabrian capercaillie. It had been previously argued that poor taxonomy could hamper conservation, through the oblivion of populations deserving, but not having, a taxonomic status. We show that taxonomic inflation can also become an obstacle for effective conservation.

Abstract: The breeding of Physalis peruviana is incipient in Brazil and is shown to be the most promising alternative for the development of productive genotypes with fruit quality. Therefore, the objective was to evaluate the combining ability between inbred lines of P. peruviana, thus indicating the selection of hybrids with fruit quality. Therefore, four populations from different origins were selfed for three generations and crossed in controlled hybridizations, resulting in 28 P. peruviana populations. The hybrid in relation to the parent performance, based on the effects of general and specific combining ability, was compared in a full diallel mating design (Griffing Method 1). In the analysis of variance, the factor genotype was partitioned into the following causes of variation: i) parents and F1 hybrids, ii) selfed generations and iii) Genotype × environment (GE) interaction. There were significant differences between Parents and F1 hybrids for the trait fruit polar diameter. Still, the interaction between specific combining ability x environment and, reciprocal effect x environment, was significant. However, for the Xanxerê environment, there was a reduction of approximately 3.0 mm in the polar diameter of the fruit in the hybrid Colombia x Peru and a reduction of 4.5 mm for the reciprocal (Peru x Colombia). In the comparison of the selfed generations S0 with S1, the fruit weight of the Lages population decreased by 0.380 g. There was also a reduction of 974.5 kg.ha-1 in the fruit yield of the Peruvian population. Thus, the performance of the P. peruviana populations in hybrid combinations is unpromising, indicating the existence of only one P. peruviana gene pool, with a restricted genetic basis.

Abstract Augmenting depleted genetic diversity can improve the fitness and evolutionary potential of wildlife populations, but developing effective management approaches requires genetically monitored test cases. One such case is the small, isolated and inbred Cotter River population of an endangered Australian freshwater fish, the Macquarie perch Macquaria australasica, which over 3 years (2017–2019) received 71 translocated migrants from a closely related, genetically more diverse population. We used genetic monitoring to test whether immigrants bred, interbred with local fish and augmented population genetic diversity. We also investigated whether levels of river flow affected recruitment, inbreeding depression and juvenile dispersal. Fish length was used to estimate the age, birth year cohort and growth of 524 individuals born between 2016 and 2020 under variable flow conditions. DArT genome‐wide genotypes were used to assess individual ancestry, heterozygosity, short‐term effective population size and identify parent‐offspring and full‐sibling families. Of 442 individuals born after translocations commenced, only two (0.45%) were of mixed ancestry; these were half‐sibs with one translocated parent in common. Numbers of breeders and genetic diversity for five birth year cohorts of the Cotter River fish were low, especially in low‐flow years. Additionally, individuals born in the year of lowest flow evidently suffered from inbreeding depression for juvenile growth. The year of highest flow was associated with the largest number of breeders, lowest inbreeding in the offspring and greatest juvenile dispersal distances. Genetic diversity decreased in the upstream direction, flagging restricted access of breeders to the most upstream breeding sites, exacerbated by low river flow. Our results suggest that the effectiveness of translocations could be increased by focussing on upstream sites and moving more individuals per year; using riverine sources should be considered. Our results indicate that river flow sufficient to facilitate fish movement through the system would increase the number of breeders, promote individuals' growth, reduce inbreeding depression and promote genetic rescue.

IntroductionInbreeding depression (ID) in food-deceptive plants have been reported previously, however, it has not been often proven that selfed seeds germinate better than outbred ones or that selfing affects ID. To resolved these issues, food-deceptive related Dactylorhiza majalis, D. incarnata var. incarnata and D. fuchsii orchids were investigated.MethodsHand pollination treatments and control pollination were conducted. Fruit set, number of seeds per fruit, seed length, number of well-developed seeds per fruit, and proportion of in vitro asymbiotic germination seeds, were analyzed in relation to inflorescence levels and used as fitness indicators for these orchids. The ID and pollen limitation were measured.ResultsThe lowest ID (δ = −1.000) was in D. majalis, and present in combination with a high pollen limitation in its populations. D. fuchsii showed higher ID (δ = 0.366), and D. incarnata var. incarnata weak ID (δ = 0.065), although ID varied between its fitness components. The seed number per fruit differed significantly between the treatments and the inflorescence levels in treatments.DiscussionThis study emphasizes that the breeding system rather than the flower position on the inflorescence shaped the quality and quantity of reproductive output. The ID and its effect on germination of food-deceptive orchid seeds undoubtedly played an important role.

Abstract The male genitals of internal fertilisers evolve rapidly and divergently, and sexual selection is generally responsible for this. Many sexually selected traits are condition‐dependent—with their expression dependent upon the resources available to be allocated to them—as revealed by genetic or environmental manipulations of condition. However, it is not clear whether male genitals are also condition‐dependent. Here we manipulate condition in two ways (via inbreeding and diet) to test the condition‐dependence of the genital arch of Drosophila simulans. We found that genital size but not genital shape suffered from inbreeding depression, whereas genital size and shape were affected by dietary manipulation of condition. The differential effects of these treatments likely reflect underlying genetic architecture that has been shaped by past selection: inbreeding depression is only expected when traits have a history of directional selection, while diet impacts traits regardless of historical selection. Nonetheless, our results suggest genitals can be condition‐dependent like other sexually selected traits.

Aim of study: We aimed at identifying differences in the response to water shortage between Eucalyptus globulus clones. Area of study: Field trials were established in SW Spain. Material and methods: Potted plants from six clones were grown in a greenhouse for 35 days under two watering regimes. Two clones were F0 genotypes and the other four were F1 (hybrid) genotypes, including one inbred clone. Differences in stomatal conductance, hydraulic traits, growth and specific leaf area (SLA) were analyzed. Main results: Water shortage decreased SLA, growth in height and leaf area and leaf-specific hydraulic conductivity (KLmax). We measured the highest growth in F1 genotypes and the lowest in the clone in which SLA was lowest. The inbred clone showed the highest growth reduction under water shortage. There was substantial hysteresis between leaf water potential (Y) and native embolism, most probably a result of combined cavitation and refilling. High losses of hydraulic conductance were compatible with high stomatal conductances. Maximum values of stomatal conductance decreased with the soil water content estimated from predawn Y and were lowest in the inbred clone, showing less plasticity and a diminished ability to cope with high temperatures, which could explain its poor development under field conditions. Research highlights: Soil water content and predawn Y appeared as critical factors controlling stomata closure, while stomatal conductance and SLA could be useful to predict differences in growth and survival from early trials.

Abstract Rapid environmental change presents a significant challenge to the persistence of natural populations. Rapid adaptation that increases population growth, enabling populations that declined following severe environmental change to grow and avoid extinction, is called evolutionary rescue. Numerous studies have shown that evolutionary rescue can indeed prevent extinction. Here, we extend those results by considering the demographic history of populations. To evaluate how demographic history influences evolutionary rescue, we created 80 populations of red flour beetle, Tribolium castaneum, with three classes of demographic history: diverse populations that did not experience a bottleneck, and populations that experienced either an intermediate or a strong bottleneck. We subjected these populations to a new and challenging environment for six discrete generations and tracked extinction and population size. Populations that did not experience a bottleneck in their demographic history avoided extinction entirely, while more than 20% of populations that experienced an intermediate or strong bottleneck went extinct. Similarly, among the extant populations at the end of the experiment, adaptation increased the growth rate in the novel environment the most for populations that had not experienced a bottleneck in their history. Taken together, these results highlight the importance of considering the demographic history of populations to make useful and effective conservation decisions and management strategies for populations experiencing environmental change that pushes them toward extinction.

An essential stage in the establishment of seed orchards is the formation of an optimal composition, avoiding inbreeding depression in the produced seed material, which develops as a result of crossbreeding between closely related plus trees. The negative effect can be reduced by ensuring the genetic heterogeneity of the seeds. The purpose of this study is to give a relative evaluation of the plus trees of Scots pine (Pinus sylvestris L.) as one of the most economically significant tree species on the European continent according to their physiological conditions. The formation and lignification of the xylem of the plus trees were investigated in the Nizhny Novgorod region of Russia. A histochemical examination was performed using the reaction of phloroglucinol to lignin. Phenotypic differences in the physiological conditions of plus trees appeared on a uniform ecological background that indicates their genotypic determinism. This fact was confirmed by ANOVA. The share of the influence of differences between the proper plus trees was between 25.16±8.91 % and 53.98±5.48 %. According to the results of the factor and cluster analysis, the association of plus trees was generated by the similarity of the multidimensional estimates of the xylem conditions. The objects that were statistically most distant from the others were determined. The hereditary conditionality of the identified differences among plus trees allows us to consider their grouping into clusters as genotypically determined. This information provides a reasonable approach to the formation of an assortment of Scots pine clonal seed orchards. For citation: Besschetnova N.N., Besschetnov V.P., Babich N.A., Bryntsev V.A. Differentiation of Plus Trees of Scots Pine by Xylem Conditions. Lesnoy Zhurnal = Russian Forestry Journal, 2023, no. 4, pp. 9–25. (In Russ.). https://doi.org/10.37482/0536-1036-2023-4-9-25

Abstract Background Pedigree-based inbreeding coefficients have been generally included in statistical models for genetic evaluation of Japanese Black cattle. The use of genomic data is expected to provide precise assessment of inbreeding level and depression. Recently, many measures have been used for genome-based inbreeding coefficients; however, with no consensus on which is the most appropriate. Therefore, we compared the pedigree- ( $${F}_{PED}$$ F PED ) and multiple genome-based inbreeding coefficients, which were calculated from the genomic relationship matrix with observed allele frequencies ( $${F}_{GRM}$$ F GRM ), correlation between uniting gametes ( $${F}_{UNI}$$ F UNI ), the observed vs expected number of homozygous genotypes ( $${F}_{HOM}$$ F HOM ), runs of homozygosity (ROH) segments ( $${F}_{ROH}$$ F ROH ) and heterozygosity by descent segments ( $${F}_{HBD}$$ F HBD ). We quantified inbreeding depression from estimating regression coefficients of inbreeding coefficients on three reproductive traits: age at first calving (AFC), calving difficulty (CD) and gestation length (GL) in Japanese Black cattle. Results The highest correlations with $${F}_{PED}$$ F PED were for $${F}_{ROH}$$ F ROH (0.86) and $${F}_{HBD}$$ F HBD (0.85) whereas $${F}_{GRM}$$ F GRM and $${F}_{UNI}$$ F UNI provided weak correlations with $${F}_{PED}$$ F PED , with range 0.33–0.55. Except for $${F}_{GRM}$$ F GRM and $${F}_{UNI}$$ F UNI , there were strong correlations among genome-based inbreeding coefficients ( $$\ge$$ ≥ 0.94). The estimates of regression coefficients of inbreeding depression for $${F}_{PED}$$ F PED was 2.1 for AFC, 0.63 for CD and -1.21 for GL, respectively, but $${F}_{PED}$$ F PED had no significant effects on all traits. Genome-based inbreeding coefficients provided larger effects on all reproductive traits than $${F}_{PED}$$ F PED . In particular, for CD, all estimated regression coefficients for genome-based inbreeding coefficients were significant, and for GL, that for $${F}_{UNI}$$ F UNI had a significant.. Although there were no significant effects when using overall genome-level inbreeding coefficients for AFC and GL, $${F}_{ROH}$$ F ROH provided significant effects at chromosomal level in four chromosomes for AFC, three chromosomes for CD, and two chromosomes for GL. In addition, similar results were obtained for $${F}_{HBD}$$ F HBD . Conclusions Genome-based inbreeding coefficients can capture more phenotypic variation than $${F}_{PED}$$ F PED . In particular, $${F}_{ROH}$$ F ROH and $${F}_{HBD}$$ F HBD can be considered good estimators for quantifying inbreeding level and identifying inbreeding depression at the chromosome level. These findings might improve the quantification of inbreeding and breeding programs using genome-based inbreeding coefficients.

Inbreeding is unavoidable in small populations. However, the deleterious effects of inbreeding on fitness-related traits (inbreeding depression) may not be an inevitable phenomenon, since deleterious recessive alleles causing inbreeding depression might be purged from populations through inbreeding and selection. Inbreeding purging has been of great interest in conservation biology and animal breeding, because populations manifesting lower inbreeding depression could be created even with a small number of breeding animals, if inbreeding purging exists. To date, many studies intending to detect inbreeding purging in captive and domesticated animal populations have been carried out using pedigree analysis. Ballou’s ancestral inbreeding coefficient (FBAL−ANC) is one of the most widely used measurements to detect inbreeding purging, but the theoretical basis for FBAL−ANC has not been fully established. In most of the published works, estimates from stochastic simulation (gene-dropping simulation) have been used. In this report, the author provides a mathematical basis for FBAL−ANC and proposes a new estimate by hybridizing stochastic and deterministic computation processes. A stochastic simulation suggests that the proposed method could considerably reduce the variance of estimates, compared to ordinary gene-dropping simulation, in which whole gene transmissions in a pedigree are stochastically determined. The favorable property of the proposed method results from the bypass of a part of the stochastic process in the ordinary gene-dropping simulation. Using the proposed method, the reliability of the estimates of FBAL−ANC could be remarkably enhanced. The relationship between FBAL−ANC and other pedigree-based parameters is also discussed.

Abstract Plant reproductive ecology is one of the research hotspots in ecology. With the increasing attention paid to the conservation of plant diversity, the research on reproductive characteristics and flowering biological characteristics of more species has attracted more attention. However, plant reproduction is affected by multiple interacting factors such as pollen limitation and resource availability. Vitex negundo var. heterophylla (Franch.) Rehder (Lamiaceae) is a significant species for water and soil conservation. Previous studies have revealed its mating system by the biological characteristics of flowering and SSR markers, but its reproductive strategies remain to be further studied. We evaluated reproductive success through artificial pollination to explore the reproductive characteristics of V. negundo var. heterophylla for the first time. From the results of fruit set, there is a mixed mating system dominated by outcrossing in V. negundo var. heterophylla accompanied by self‐compatibility, and it cannot carry out autonomous selfing. Our data show the pollinator‐mediated interaction in the success of reproduction, whereas the effect of anemophily is very weak. And the seed germination rate of inbred line progenies was lower than that of hybrid progenies, which is suspected to be caused by inbreeding depression. The research will provide scientific information for the protection and conservation of V. negundo var. heterophylla from the point of view of reproduction. In sum, the results are necessary to protect animal vectors in the background of insect decline.

Abstract Background The reduction in phenotypic performance of a population due to mating between close relatives is called inbreeding depression. The genetic background of inbreeding depression for semen traits is poorly understood. Thus, the objectives were to estimate the effect of inbreeding and to identify genomic regions underlying inbreeding depression of semen traits including ejaculate volume (EV), sperm concentration (SC), and sperm motility (SM). The dataset comprised ~ 330 K semen records from ~ 1.5 K Holstein bulls genotyped with 50 K single nucleotide polymorphism (SNP) BeadChip. Genomic inbreeding coefficients were estimated using runs of homozygosity (i.e., F ROH > 1 Mb) and excess of SNP homozygosity (F SNP). The effect of inbreeding was estimated by regressing phenotypes of semen traits on inbreeding coefficients. Associated variants with inbreeding depression were also detected by regressing phenotypes on ROH state of the variants. Results Significant inbreeding depression was observed for SC and SM (p

Abstract Quantifying relationships between genetic variation and population viability is important from both basic biological and applied conservation perspectives, yet few populations have been monitored with both long‐term demographic and population genetics approaches. To empirically test whether and how genetic variation and population dynamics are related, we present one such paired approach. First, we use eight years of historical demographic data from five populations of Boechera fecunda (Brassicaceae), a rare, self‐compatible perennial plant endemic to Montana, USA, and use integral projection models to estimate the stochastic population growth rate (λS) and extinction risk of each population. We then combine these demographic estimates with previously published metrics of genetic variation in the same populations to test whether genetic diversity within populations is linked to demographic performance. Our results show that in this predominantly inbred species, standing genetic variation and demography are weakly positively correlated. However, the inbreeding coefficient was not strongly correlated with demographic performance, suggesting that more inbred populations are not necessarily less viable or at higher extinction risk than less inbred populations. A contemporary re‐census of these populations revealed that neither genetic nor demographic parameters were consistently strong predictors of current population density, although populations showing lower probabilities of extinction in demographic models had larger population sizes at present. In the absence of evidence for inbreeding depression decreasing population viability in this species, we recommend conservation of distinct, potentially locally adapted populations of B. fecunda rather than alternatives such as translocations or reintroductions.

Abstract Background Allegheny woodrats (Neotoma magister) are found in metapopulations distributed throughout the Interior Highlands and Appalachia. Historically these metapopulations persisted as relatively fluid networks, enabling gene flow between subpopulations and recolonization of formerly extirpated regions. However, over the past 45 years, the abundance of Allegheny woodrats has declined throughout the species’ range due to a combination of habitat destruction, declining hard mast availability, and roundworm parasitism. In an effort to initiate genetic rescue of a small, genetically depauperate subpopulation in New Jersey, woodrats were translocated from a genetically robust population in Pennsylvania (PA) in 2015, 2016 and 2017. Herein, we assess the efficacy of these translocations to restore genetic diversity within the recipient population. Results We designed a novel 134 single nucleotide polymorphism panel, which was used to genotype the six woodrats translocated from PA and 82 individuals from the NJ population captured before and after the translocation events. These data indicated that a minimum of two translocated individuals successfully produced at least 13 offspring, who reproduced as well. Further, population-wide observed heterozygosity rose substantially following the first set of translocations, reached levels comparable to that of populations in Indiana and Ohio, and remained elevated over the subsequent years. Abundance also increased during the monitoring period, suggesting Pennsylvania translocations initiated genetic rescue of the New Jersey population. Conclusions Our results indicate, encouragingly, that very small numbers of translocated individuals can successfully restore the genetic diversity of a threatened population. Our work also highlights the challenges of managing very small populations, such as when translocated individuals have greater reproductive success relative to residents. Finally, we note that ongoing work with Allegheny woodrats may broadly shape our understanding of genetic rescue within metapopulations and across heterogeneous landscapes.

The use of open-pollinated seeds from seed orchards is a common strategy for the deployment of genetically improved eucalypts, including Eucalyptus globulus, an important pulpwood tree in many temperate climate areas. However, seed quality can be affected by the rate of selfing and to a lesser extent by contamination from pollen outside the orchard. Inbreeding between related parents and especially from self-crosses is known to cause diminished growth and developmental abnormalities in the resulting progeny. This study looks at the magnitude and variation in selfing and the impact in inbreeding depression across several E. globulus families collected over the years in a seed orchard. The effects on growth and development of outcrossed and selfed progeny were studied across five progeny trials, after pedigree reconstruction of the open pollinated progeny based on SSR genotyping. An additive genetic mixed linear model was fitted to the data to evaluate the impact of inbreeding on height growth. The results showed a significant inbreeding depression, with a height growth reduction of 15% in selfed progeny, when compared with crosses from unrelated parents. These inbreeding depression values varied among families, ranging between 7% and 24%, evidencing the importance of genetic background. Contamination rates were on average 10% suggesting long distance pollen dispersal was present. A small number of abnormal phenotypes (less than 10%) was observed in the field. This was associated with specific, unrelated, crosses and not to high inbreeding rates such as found among selfed progeny. The relevance of these results for orchard management and parent selection is discussed.

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 572 K 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

Abstract Females and males often have markedly different mortality rates and life spans, but it is unclear why these forms of sexual dimorphism evolve. The unguarded X hypothesis contends that dimorphic life spans arise from sex differences in X or Z chromosome copy number (i.e., one copy in the “heterogametic” sex; two copies in the “homogametic” sex), which leads to a disproportionate expression of deleterious mutations by the heterogametic sex (e.g., mammalian males; avian females). Although data on adult sex ratios and sex‐specific longevity are consistent with predictions of the unguarded X hypothesis, direct experimental evidence remains scant, and alternative explanations are difficult to rule out. Using a simple population genetic model, we show that the unguarded X effect on sex differential mortality is a function of several reasonably well‐studied evolutionary parameters, including the proportion of the genome that is sex linked, the genomic deleterious mutation rate, the mean dominance of deleterious mutations, the relative rates of mutation and strengths of selection in each sex, and the average effect of mutations on survival and longevity relative to their effects on fitness. We review published estimates of these parameters, parameterize our model with them, and show that unguarded X effects are too small to explain observed sex differences in life span across species. For example, sex differences in mean life span are known to often exceed 20% (e.g., in mammals), whereas our parameterized models predict unguarded X effects of a few percent (e.g., 1–3% in Drosophila and mammals). Indeed, these predicted unguarded X effects fall below statistical thresholds of detectability in most experiments, potentially explaining why direct tests of the hypothesis have generated little support for it. Our results suggest that evolution of sexually dimorphic life spans is predominantly attributable to other mechanisms, potentially including “toxic Y” effects and sexual dimorphism for optimal investment in survival versus reproduction.

Abstract Recent studies have shown that current levels of inbreeding, estimated by runs of homozygosity (ROH), are moderate to high in farmed rainbow trout lines. Based on ROH metrics, the aims of our study were to (i) quantify inbreeding effects on female size (postspawning body weight, fork length) and reproduction traits (spawning date, coelomic fluid weight, spawn weight, egg number, average egg weight) in rainbow trout, and (ii) identify both the genomic regions and inbreeding events affecting performance. We analysed the performance of 1346 females under linear animal models including random additive and dominance genetics effects, with fixed covariates accounting for inbreeding effects at different temporal and genomic scales. A significant effect of genome‐wide inbreeding (F) was only observed for spawning date and egg weight, with performance variations of +12.3% and −3.8%, respectively, for 0.1 unit increase in F level. At different local genomic scales, we observed highly variable inbreeding effects on the seven traits under study, ranging from increasing to decreasing trait values. As widely reported in the literature, the main scenario observed during this study was a negative impact of recent inbreeding. However, other scenarios such as positive effects of recent inbreeding or negative impacts of old inbreeding were also observed. Although partial dominance appeared to be the main hypothesis explaining inbreeding depression for all the traits studied, the overdominance hypothesis might also play a significant role in inbreeding depression affecting fecundity (egg number and mass) traits in rainbow trout. These findings suggest that region‐specific inbreeding can strongly impact performance without necessarily observing genome‐wide inbreeding effects. They shed light on the genetic architecture of inbreeding depression and its evolution along the genome over time. The use of region‐specific metrics may enable breeders to more accurately manage the trade‐off between genetic merit and the undesirable side effects associated with inbreeding.

The relationship between inbreeding and traits of disease resistance in shrimp has not been studied comprehensively. To explore the effect of inbreeding on white spot syndrome virus (WSSV) resistance in Fenneropenaeus chinensis, we established F. chinensis “Huanghai No. 5” populations with different inbreeding coefficients. We infected F. chinensis individuals with WSSV to compare WSSV-resistance between five inbred groups and a control group. Survival time, survival rate, distribution of deaths, and cumulative mortality rate were analyzed. A mixed linear model was established based on the acquired data. The viral load in muscle tissue of F. chinensis of 12 families from the five inbred groups and the control group was determined at different time points via real-time PCR. The average survival and longest survival time of the inbred groups were lower than those of the control group, and the coefficient of variation was universally greater than that of the control group. The least squares means of survival time of the five inbred groups (F0.1325, F0.25, F0.3125, F0.375, F0.5) were 118.96 115.14, 124.58, 123.97, and 101.34 h, respectively, which were 10.28%, 13.16%, 6.04%, 6.5%, and 23.57% lower than that of the control group. Further, when the inbreeding coefficient increased by 10%, WSSV infection survival time was changed by − 7.76%, − 5.26%, − 1.93%, − 1.73%, and − 4.71% for the five inbred groups, respectively. Thus, the results indicated that inbreeding enhanced the susceptibility of F. chinensis to WSSV infection, and the resistance of F. chinensis to WSSV declined as the inbreeding coefficient values increased, consequently, resulting in greater population dispersion, intensified differentiation, and instability of resistant phenotypes. In conclusion, we elucidated the effect of inbreeding on F. chinensis resistance to WSSV infection and established a theoretical basis to conduct further research in the future.

Abstract Genetic rescue has emerged as an important tool to prevent extinction and improve fitness of declining populations. In principle, genetic rescue increases genetic variation in a population through translocation of unrelated individuals from an outside source population. Genetic rescue remains uncommon in conservation management due to concerns about the risk of outbreeding depression. Lack of data evaluating success of genetic rescue interventions has hampered willingness to use this technique to improve the genetic viability of inbred, bottlenecked populations. Here, we evaluate the success of a genetic rescue intervention within the endangered Central California Coast Coho Salmon Evolutionarily Significant Unit using ∼17 years of genetic and demographic data, including pre‐ and postoutcrossing with fish from a nearby watershed. We assessed fitness of outcrossed F1 and F2 progeny in a captive setting, and then used mark–recapture to estimate survival of juveniles released into streams. We found that outcrossing decreased relatedness among adults, and their hybrid progeny had higher fitness in both captive and stream settings relative to nonhybrids. Importantly, we did not observe evidence of outbreeding depression in either the F1 or F2 generations. This study highlights that genetic rescue can be a useful tool in the conservation of imperiled salmonids.

An inbred strain limits the segregating variance and provides more power and requires fewer experimental animals to produce good reproducibility. This study was undertaken with the aim to assess the impact of sex of offsprings and sex specific microsatellite variants on performance and fitness traits in F4 inbred Swiss albino mice. The phenomics of different performance and fitness traits were estimated on 506 F4 inbred mice population. Two ‘X’ chromosome specific microsatellite loci (DXMit187 and DxMit172) were used for PCR-Microsatellite genotyping of 102 F4 inbred population. PIC estimates showed that both the loci were informative for the population. In the current population, with the increasing level of “F” a declining trend was observed for Body weight at birth (BWB), Body weight at weaning (BWW), Litter size at weaning (LSW) and Litter weight at weaning (LWW). In F4 inbred population, BWW and ABW for males (17.32±0.32g and 30.81±0.31g) were significantly (p

Introduction: Consanguinity is associated with increase in the likelihood of receiving two copies of deleterious gene from parents, which brings the hidden recessive disorders. This further increases the risk of neonatal and post neonatal mortality. Some of which may also have negative effect on metrical traits of the children, thereby affecting their development and reducing their cognitive abilities. Aim: To examine the effect of parental consanguinity on various metrical traits like linear, circumferential and weight measurements among the Muslim males. Materials and Methods: A cross-sectional study was conducted amongst the Muslim males living in the different river islands of Barpeta district in Assam. The study consisted 1438 males (587 inbred and 851 non-inbred). A total of 936 boys (3 years to 18 years) were measured at an interval of one year. The rest (502 adult men) from 19 to 60 years were in age cohorts of five-years age interval. They were measured for stature, sitting height, lower extremity length, body weight, waist circumference, abdominal circumference and hip circumference. Inbreeding depression on trait was calculated using average coefficient of inbreeding and % of depression in a trait. Wright’s path coefficient method was used for the calculation of inbreeding coefficient. Results: The average coefficient of inbreeding was found to be 0.01637931154. A significant increase in the difference of mean values in all the linear, circumferential and weight measurements has been observed at many ages with the increase in the inbreeding coefficient during childhood and adolescence phase of life. But the difference in mean variance in the adult body parameters between the inbred and non-inbred was statistically insignificant at almost all ages (p>0.05). Conclusion: Consanguinity has not affected any of the adult body measurements. A significant positive association between consanguinity and diminution of body measurements found during the growing period needs to be correlated with the other socio demographic variables because the growing period is always more dependent on environmental variables.

Understanding inbreeding depressions (IBDs), the effect on the phenotypic performance of inbreeding, is of major importance for evolution and conservation genetics. Inbreeding depressions in aquatic animals were well documented in a domestic or captive population, while there is less evidence of inbreeding depression in natural populations. Chinese shrimp, Fenneropenaeus chinensis, is an important species in both aquaculture and fishery activities in China. To investigate inbreeding depression in natural populations, four Fenneropenaeus chinensis natural populations (Huanghua, Qinhuangdao, Qingdao, and Haiyang) were collected from the Bohai and Yellow seas. Microsatellite markers were used to evaluate individual inbreeding coefficients (F) of all samples. Furthermore, the effects of inbreeding on growth traits were investigated. The results showed marker-based F was continuous and ranged from 0 to 0.585, with an average of 0.191 ± 0.127, and there was no significant difference among the average F of the four populations. Regression analysis using the four populations showed inbreeding had a very significant (p < 0.01) effect on body weight. When analyzing a single population, regression coefficients were also all negative and those in Huanghua and in Qingdao were significant at the level of p < 0.05 and < 0.01, respectively. Inbreeding depressions, expressed as the percent change in body weight per 10% increase in F, were 2.75% in Huanghua, 2.22% in Qingdao, and 3.69% in all samples. This study provided a piece of rare evidence of inbreeding depression in natural populations and also guidance toward the conservation of wild Fenneropenaeus chinensis resources.

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.

Although mixed mating systems involving both selfing and outcrossing are fairly common in hermaphrodites, the mechanisms maintaining mixed mating are still unknown in many cases. In some species, individuals that have not yet found a mating partner delay self-fertilization for some time. This “waiting time” to selfing (WT) can exhibit heritable variation between individuals and is subject to two opposing selection pressures: waiting longer increases the density-dependent probability to encounter a mate within that time and thereby the chance to avoid inbreeding depression (ID) in offspring, but also increases the risk of dying before reproduction. It has long been hypothesized that fluctuations in population density and thus mate availability can lead to stable intermediate WTs, but to our knowledge there are so far no quantitative models that also take into account the joint evolutionary dynamics of ID. We use an individual-based model and a mathematical approximation to explore how delayed selfing evolves in response to density and density fluctuations. We find that at high density, when individuals meet often, WT evolution is dominated by genetic drift; at intermediate densities, strong ID causes WT to increase; and at low densities, ID is purged and WT approaches zero. Positive feedback loops drive the system to either complete selfing or complete outcrossing. Fluctuating density can slow down convergence to these alternative stable states. However, mixed mating, in the sense of either a stable polymorphism in WT, or stable intermediate waiting times, was never observed. Thus, additional factors need to be explored to explain the persistence of delayed selfing.

Abstract Background Although inbreeding caused by the mating of animals related through a recent common ancestor is expected to have more harmful effects on phenotypes than ancient inbreeding (old inbreeding), estimating these effects requires a clear definition of recent (new) and ancient (old) inbreeding. Several methods have been proposed to classify inbreeding using pedigree and genomic data. Unfortunately, these methods are largely based on heuristic criteria such as the number of generations from a common ancestor or length of runs of homozygosity (ROH) segments. To mitigate these deficiencies, this study aimed to develop a method to classify pedigree and genomic inbreeding into recent and ancient classes based on a grid search algorithm driven by the assumption that new inbreeding tends to have a more pronounced detrimental effect on traits. The proposed method was tested using a cattle population characterized by a deep pedigree. Results Effects of recent and ancient inbreeding were assessed on four growth traits (birth, weaning and yearling weights and average daily gain). Thresholds to classify inbreeding into recent and ancient classes were trait-specific and varied across traits and sources of information. Using pedigree information, inbreeding generated in the last 10 to 11 generations was considered as recent. When genomic information (ROH) was used, thresholds ranged between four to seven generations, indicating, in part, the ability of ROH segments to characterize the harmful effects of inbreeding in shorter periods of time. Nevertheless, using the proposed classification method, the discrimination between new and old inbreeding was less robust when ROH segments were used compared to pedigree. Using several model comparison criteria, the proposed approach was generally better than existing methods. Recent inbreeding appeared to be more harmful across the growth traits analyzed. However, both new and old inbreeding were found to be associated with decreased yearling weight and average daily gain. Conclusions The proposed method provided a more objective quantitative approach for the classification of inbreeding. The proposed method detected a clear divergence in the effects of old and recent inbreeding using pedigree data and it was superior to existing methods for all analyzed traits. Using ROH data, the discrimination between old and recent inbreeding was less clear and the proposed method was superior to existing approaches for two out of the four analyzed traits. Deleterious effects of recent inbreeding were detected sooner (fewer generations) using genomic information than pedigree. Difference in the results using genomic and pedigree information could be due to the dissimilarity in the number of generations to a common ancestor. Additionally, the uncertainty associated with the identification of ROH segments and associated inbreeding could have an effect on the results. Potential biases in the estimation of inbreeding effects may occur when new and old inbreeding are discriminated based on arbitrary thresholds. To minimize the impact of inbreeding, mating designs should take the different inbreeding origins into consideration.

Objective Inbreeding depression of reproduction is a major concern in the conservation of native chicken genetic resources. Here, based on the successful development of strongly inbred (Sinb) and weakly inbred (Winb) Langshan chickens, we aimed to evaluate inbreeding effects on reproductive traits and identify candidate genes involved in inbreeding depression of reproduction in Langshan chickens. Methods A two-sample t-test was performed to estimate the differences in phenotypic values of reproductive traits between Sinb and Winb chicken groups. Three healthy chickens with reproductive trait values around the group mean values were selected from each of the groups. Differences in ovarian and hypothalamus transcriptomes between the two groups of chickens were analyzed by RNA sequencing (RNA-Seq). Results The Sinb chicken group showed an obvious inbreeding depression in reproduction, especially for traits of age at the first egg and egg number at 300 days (p

Abstract Runs of homozygosity (ROH) are pervasive in diploid genomes and expose the effects of deleterious recessive mutations, but how exactly these regions contribute to variation in fitness remains unclear. Here, we combined empirical analyses and simulations to explore the deleterious effects of ROH with varying genetic map lengths in wild Soay sheep. Using a long‐term dataset of 4879 individuals genotyped at 417K SNPs, we found that inbreeding depression increases with ROH length. A 1% genomic increase in long ROH (>12.5 cM) reduced the odds of first‐year survival by 12.4% compared to only 7.7% for medium ROH (1.56–12.5 cM), whereas short ROH (

A recent study on the population structure of the German Brown population found increasing levels of classical and ancestral inbreeding coefficients. Thus, the aim of this study was to determine the effects of inbreeding depression and purging on longevity traits using classical and ancestral inbreeding coefficients according to Kalinowski (2002) (Fa_Kal, FNew), Ballou (1997) (Fa_Bal), and Baumung (2015) (Ahc). For this purpose, uncensored data of 480,440 cows born between 1990 and 2001 were available. We analyzed 17 longevity traits, including herd life, length of productive life, number of calvings, lifetime and effective lifetime production for milk, fat, and protein yield, the survival to the 2nd, 4th, 6th, 8th, and 10th lactation number, and the culling frequencies due to infertility, or udder and foot and leg problems. Inbreeding depression was significant and negative for all traits but for culling due to udder and to foot and leg problems. When expressed in percentages of genetic standard deviations, inbreeding depression per 1% increase in inbreeding was −3.61 to −10.98%, −2.42 to −2.99%, −2.21 to −4.58%, and 5.13% for lifetime production traits, lifetime traits, survival rates, and culling due to infertility, respectively. Heterosis and recombination effects due to US Brown Swiss genes were positive and counteracted inbreeding depression. The effects of FNew were not significantly different from zero, while Fa_Kal had negative effects on lifetime and lifetime production traits. Similarly, the interaction of F with Fa_Bal was significantly negative. Thus, purging effects could not be shown for longevity traits in German Brown. A possible explanation may be seen in the breed history of the German Brown, that through the introgression of US Brown Swiss bulls ancestral inbreeding increased and longevity decreased. Our results show, that reducing a further increase in inbreeding in mating plans is advisable to prevent a further decline in longevity due to inbreeding depression, as purging effects were very unlikely in this population.

Among the extant populations of the critically endangered Aeolian wall lizard, the most vulnerable is the one surviving on La Canna, a columnar volcanic stack off the Filicudi Island. Here, I report the results of the first climbing expedition by a biologist on La Canna, that contributed direct observations and updated information on the size, morphology, and genetic variability of this population. Lizard density at the sampling site (a small terrace at 50 m of elevation) was 1.7 m−2, twice of a previous estimate. Standard methods for estimating population size are unsuitable for La Canna. An educated guess of about a hundred individuals can be drawn, considering the extent of habitat available on the stack and the number of observed lizards. Lizards on La Canna were not fearless, despite what was reported by alpinists, possibly because of aggressive intraspecific interactions or high environmental temperatures during sampling. Biometric data significantly extend the body size of La Canna’s lizards and indicate that it is not smaller than other P. raffonei populations. A complete lack of genetic diversity was found at the mitochondrial nd4 gene, in line with previous allozyme data and with estimates on other microinsular Podarcis populations. The small size of the La Canna population implies severe genetic drift and an extremely high level of inbreeding, as supported by low heterozygosity found across the genome. Detrimental effects of inbreeding depression are evident as cephalic malformations observed in all captured lizards of La Canna and might represent the more immediate threat to the persistence of this population.

Background: Argemone ochroleuca is a worldwide invasive weed but is also highly valuable for their chemical compounds. Knowledge about its reproduction will help create plans for its control or its propagation. Questions: Does A. ochroleuca has an incompatibility system like other Papaveraceae species? Which are the reproductive strategies that favor the seed formation in A. ochroleuca? Studied species: A. ochroleuca is an annual species with bisexual flowers. Study site and dates: Mexico City, Mexico. The fieldwork was performed from February to May in 2013, 2014, and 2017. Methods: Direct observations were made to describe the flower cycle of A. ochroleuca. We used self-pollinated flowers to analyze if this species is self-incompatible by following the pollen tube growth through gynoecium. Controlled pollinations were made to quantify and compare the number of seeds produced per treatment to know the mating system and explore if the species presents a mechanism of reproductive assurance through autogamy, or exhibits inbreeding depression. Results: A. ochroleuca is self-compatible and exhibits a mixed mating system. Although outcrossing is how more seeds are produced, both autogamy and pseudocleistogamy are present as reproductive assurance mechanisms. Naturally pollinated flowers produce the maximum number of seeds, but inbreeding depression is present in the population. Thus, the number of seeds will be affected by continuous selfing. Conclusions: This study highlights the mixed mating system and reproductive assurance mechanisms as successful strategies for A. ochroleuca, a common pattern in invasive weeds.

The intensive breeding work of Holstein-Friesian cattle has led to the decrease in the diversity within the population and to inbreeding depression, which may impair its functional traits. In addition, as shown by the research, production traits are negatively correlated with functional traits such as reproduction, health, and longevity, which have a very strong impact on the profit of dairy farms. The aim of this study was to compare milk yield traits of hybrids obtained by crossbreeding of Polish Holstein Friesian (PHF) cows and Swedish Red (SRB) bulls with values obtained for pure PHF cows. For the study, 100 primiparous cows were selected and divided into two groups. The experimental group consisted of 50 crossbreds (PHF×SRB), while the control group consisted of 50 purebred PHF cows. The study showed a higher content of milk components (fat by 11.78%, protein by 9.06%, dry matter by 5.75%) in PHF×SRB, as compared to PHF. A lower level of SCC (by 38.94%) has also been shown in hybrids, which indicates their higher resistance to udder diseases. The experiment demonstrated a highly significant impact of heterosis on performance parameters and technological quality of milk in F1 generation obtained as a result of crossbreeding between PHF cows and SRB bulls.

The intensive breeding work of Holstein-Friesian cattle has led to the decrease in the diversity within the population and to inbreeding depression, which may impair its functional traits. In addition, as shown by the research, production traits are negatively correlated with functional traits such as reproduction, health, and longevity, which have a very strong impact on the profit of dairy farms. The aim of this study was to compare milk yield traits of hybrids obtained by crossbreeding of Polish Holstein Friesian (PHF) cows and Swedish Red (SRB) bulls with values obtained for pure PHF cows. For the study, 100 primiparous cows were selected and divided into two groups. The experimental group consisted of 50 crossbreds (PHF×SRB), while the control group consisted of 50 purebred PHF cows. The study showed a higher content of milk components (fat by 11.78%, protein by 9.06%, dry matter by 5.75%) in PHF×SRB, as compared to PHF. A lower level of SCC (by 38.94%) has also been shown in hybrids, which indicates their higher resistance to udder diseases. The experiment demonstrated a highly significant impact of heterosis on performance parameters and technological quality of milk in F1 generation obtained as a result of crossbreeding between PHF cows and SRB bulls.

Abstract Environmental stress can have a profound effect on inbreeding depression. Quantifying this effect is of particular importance in threatened populations, which are often simultaneously subject to both inbreeding and environmental stress. But while the prevalence of inbreeding–stress interactions is well known, the importance and broader applicability of such interactions in conservation are not clearly understood. We used seed beetles, Callosobruchus maculatus, as a model system to quantify how environmental stressors (here host quality and temperature stress) interact with inbreeding as measured by changes in the magnitude of inbreeding depression, δ, as well as the relative importance of inbreeding–stress interactions to overall fitness. We found that while both environmental stressors caused substantial inbreeding–stress interactions as measured by change in δ, the relative importance of these interactions to overall survival was modest. This suggests that assessing inbreeding–stress interactions within the framework of δ alone may give an inaccurate representation of the relevance of interactions to population persistence. Furthermore, we found that the effect of environmental stress on fitness, but not inbreeding depression, varied strongly among populations. These results suggest that the outcomes of inbreeding–stress interactions are not easily generalized, an important consideration in conservation settings.