Optimization of selection for growth in Menz Sheep while minimizing inbreeding depression in fitness traits

The genetic trends in fitness (inbreeding, fertility and survival) of a closed nucleus flock of Menz sheep under selection during ten years for increased body weight were investigated to evaluate the consequences of selection for body weight on fitness. A mate selection tool was used to optimize in retrospect the actual selection and matings conducted over the project period to assess if the observed genetic gains in body weight could have been achieved with a reduced level of inbreeding. In the actual selection, the genetic trends for yearling weight, fertility of ewes and survival of lambs were 0.81 kg, –0.00026% and 0.016% per generation. The average inbreeding coefficient remained zero for the first few generations and then tended to increase over generations. The genetic gains achieved with the optimized retrospective selection and matings were highly comparable with the observed values, the correlation between the average breeding values of lambs born from the actual and optimized matings over the years being 0.99. However, the level of inbreeding with the optimized mate selections remained zero until late in the years of selection. Our results suggest that an optimal selection strategy that considers both genetic merits and coancestry of mates should be adopted to sustain the Menz sheep breeding program.     

Effects of population structures and selection strategies on the purging of inbreeding depression due to deleterious mutations

Stochastic simulations were run to compare the effects of nine breeding schemes, using full-sib mating, on the rate of purging of inbreeding depression due to mutations with equal deleterious effect on viability at unlinked loci in an outbred population. A number of full-sib mating lines were initiated from a large outbred population and maintained for 20 generations (if not extinct). Selection against deleterious mutations was allowed to occur within lines only, between lines or equal within and between lines, and surviving lines were either not crossed or crossed following every one or three generations of full-sib mating. The effectiveness of purging was indicated by the decreased number of lethal equivalents and the increased fitness of the purged population formed from crossing surviving lines after 20 generations under a given breeding scheme. The results show that the effectiveness of purging, the survival of the inbred lines and the inbreeding level attained are generally highest with between-line selection and lowest with within-line selection. Compared with no crossing, line crossing could lower the risk of extinction and the inbreeding coefficient of the purged population substantially with little loss of the effectiveness of purging. Compromising between the effectiveness of purging, and the risk of extinction and inbreeding coefficient, the breeding scheme with equal within- and between-line selection and crossing alternatively with full-sib mating is generally the most desirable scheme for purging deleterious mutations. Unless most deleterious mutations have relatively large effects on fitness in species with reproductive ability high enough to cope with the depressed fitness and thus increased risk of extinction with inbreeding, it is not justified to apply a breeding programme aimed at purging inbreeding depression by inbreeding and selection to a population of conservation concern.     

Severe inbreeding depression in a wild wolf (Canis lupus) population

The difficulty of obtaining pedigrees for wild populations has hampered the possibility of demonstrating inbreeding depression in nature. In a small, naturally restored, wild population of grey wolves in Scandinavia, founded in 1983, we constructed a pedigree for 24 of the 28 breeding pairs established in the period 1983-2002. Ancestry for the breeding animals was determined through a combination of field data (snow tracking and radio telemetry) and DNA microsatellite analysis. The population was founded by only three individuals. The inbreeding coefficient F varied between 0.00 and 0.41 for wolves born during the study period. The number of surviving pups per litter during their first winter after birth was strongly correlated with inbreeding coefficients of pups (R2=0.39, p<0.001). This inbreeding depression was recalculated to match standard estimates of lethal equivalents (2B), corresponding to 6.04 (2.58-9.48, 95% CI) litter-size-reducing equivalents in this wolf population.     

Inbreeding depression in small populations of self-incompatible plants.

Self-incompatibility (SI) is a widespread mechanism that prevents inbreeding in flowering plants. In many species, SI is controlled by a single locus (the S locus) where numerous alleles are maintained by negative frequency-dependent selection. Inbreeding depression, the decline in fitness of selfed individuals compared to outcrossed ones, is an essential factor in the evolution of SI systems. Conversely, breeding systems influence levels of inbreeding depression. Little is known about the joint effect of SI and drift on inbreeding depression. Here we studied, using a two-locus model, the effect of SI (frequency-dependent selection) on a locus subject to recurrent deleterious mutations causing inbreeding depression. Simulations were performed to assess the effect of population size and linkage between the two loci on the level of inbreeding depression and genetic load. We show that the sheltering of deleterious alleles linked to the S locus strengthens inbreeding depression in small populations. We discuss the implications of our results for the evolution of SI systems.     

Effect of rate of inbreeding on inbreeding depression in Drosophila melanogaster

Summary This experiment was designed to study the relationship between rate of inbreeding and observed inbreeding depression of larval viability, adult fecundity and cold shock mortality in Drosophila melanogaster. Rates of inbreeding used were full-sib mating and closed lines of N=4 and N=20. Eight generations of mating in the N=20 lines, three generations in the N=4 lines and one generation of full-sib mating were synchronised to simultaneously produce individuals with an expected level of inbreeding coefficient (F) of approximately 0.25. Inbreeding depression for the three traits was significant at F=0.25. N=20 lines showed significantly less inbreeding depression than full-sib mated lines for larval viability at approximately the same level of F. A similar trend was observed for fecundity. No effect of rate of inbreeding depression was found for cold shock mortality, but this trait was measured with less precision than the other two. Natural selection acting on loci influencing larval viability and fecundity during the process of inbreeding could explain these results. Selection is expected to be more effective with slow rates of inbreeding because there are more generations and greater opportunity for selection to act before F=0.25 is reached. Selection intensities seem to have been different in the three traits measured. Selection was most intense for larval viability, less intense for fecundity and, perhaps, negligible at loci influencing cold shock mortality.     

An effective rotational mating scheme for inbreeding reduction in captive populations illustrated by the rare sheep breed Kempisch Heideschaap

Within breeds and other captive populations, the risk of high inbreeding rates and loss of diversity can be high within (small) herds or subpopulations. When exchange of animals between different subpopulations is organised according to a rotational mating scheme, inbreeding rates can be restricted. Two such schemes, a breeding circle and a maximum avoidance of inbreeding scheme, are compared. In a breeding circle, flocks are organised in a circle where each flock serves as a donor flock for another flock, and the same donor-recipient combination is used in each breeding season. In the maximum inbreeding avoidance scheme, donor-recipient combinations change each year so that the use of the same combination is postponed as long as possible. Data from the Kempisch Heideschaap were used with computer simulations to determine the long-term effects of different breeding schemes. Without exchanging rams between flocks, high inbreeding rates (>1.5% per year) occurred. Both rotational mating schemes reduced inbreeding rates to on average 0.16% per year and variation across flocks in inbreeding rates, caused by differences in flock size, almost disappeared. Inbreeding rates with maximum inbreeding avoidance were more variable than with a breeding circle. Moreover, a breeding circle is easier to implement and operate. Breeding circles are thus efficient and flexible and can also be efficient for other captive populations, such as zoo populations of endangered wild species.     

Consequences of a One-male Harem Reproductive System and Inbreeding in a Captive Group of <Emphasis Type="BoldItalic">Cercopithecus solatus</Emphasis>

In closed captive populations, where dispersal is not possible, kin recognition and behavioral avoidance are the only mechanisms by which closely related individuals can avoid inbreeding. In the absence of avoidance, a loss of genetic diversity is inevitable in successive generations.In the 1980s, the CIRMF in Gabon established a small breeding group of sun-tailed monkeys (Cercopithecus solatus) with 4 individuals, and subsequently 17 births have been registered. We aimed to describe via microsatellite genotyping the reproductive system in the colony of Cercopithecus solatus, to evaluate the loss of genetic diversity with succeeding generations, and to evaluate consequences of inbreeding depression on a measure of the lifespan reproductive success of females giving birth to inbred vs. noninbred offspring. During the 11-yr period for which data are available, only alpha males sired offspring, confirming a one-male social organization. They reproduced only during their period of tenure. Two of the 3 alpha males were responsible for all the infants born. Genetic diversity decreased and inbreeding coefficients increased with successive generations. Interbirth interval was increased following the birth of an inbred infant, indicating possible increased maternal costs of rearing inbred infants. Loss of genetic variability in this captive group of sun-tailed monkeys has led to significant inbreeding depression and demonstrates the importance of male-mediated gene flow in restricted one-male harem breeding groups.     

Analysis of inbreeding depression in the first litter size of mice in a long-term selection experiment with respect to the age of the inbreeding

An understanding of inbreeding and inbreeding depression are important in evolutionary biology, conservation genetics, and animal breeding. A new method was developed to detect departures from the classical model of inbreeding; in particular, it investigated differences between the effects of inbreeding in recent generations from that in the more distant past. The method was applied in a long-term selection experiment on first-litter size in mice. The total pedigree included 74,630 animals with approximately 30,000 phenotypic records. The experiment comprised several different lines. The highest inbreeding coefficients (F) within a line ranged from 0.22 to 0.64, and the average effective population size (N(e)) was 58.1. The analysis divided F into two parts, corresponding to the inbreeding occurring in recent generations ('new') and that which preceded it ('old'). The analysis was repeated for different definitions of 'old' and 'new', depending on length of the 'new' period. In 15 of these tests, 'new' inbreeding was estimated to cause greater depression than 'old'. The estimated depression ranged from -11.53 to -0.79 for the 'new' inbreeding and from -5.22 to 15.51 for 'old'. The difference was significant, the 'new' period included at least 25 generations of inbreeding. Since there were only small differences in N(e) between lines, and near constant N(e) within lines, the effect of 'new' and 'old' cannot be attributed to the effects of 'fast' versus 'slow' inbreeding. It was concluded that this departure from the classical model, which predicts no distinction between this 'old and 'new' inbreeding, must implicate natural selection and purging in influencing the magnitude of depression.     

Differential inbreeding tolerance in two geographically distinct strains of root voles Microtus oeconomus

Two geographically distinct strains of Microtus oeconomus, each consisting of an inbred (sibling mating) and an outbred treatment group, were bred in the laboratory over three generations to determine the effects of inbreeding on reproductive parameters, growth rates of young and paternal behavior The southern strain (orginating from southern Norway) suffered from depressed reproductive rate (litter size and pregnancy rates) most likely due to inbreeding, while no effects of inbreeding were detected m the northern strain (originating from northern Norway) This result questions previous generalizations about inbreeding tolerance at the species level for Microtus Growth rates and paternal behavior did not differ significantly between inbred and outbred voles in either strain Inbreeding depression rather than inbreeding avoidance is the most likely mechanism behind the depression in reproductive parameters of inbred southern voles This is suggested by the decrease in the proportion of breeding pairs with the number of generations of inbreeding, and by the reduced litter size of inbred compared with outbred pairs Field and laboratory studies have shown that behavioral and demographic traits, possibly related to the degree of inbreeding, differ between the two strains which suggests that inbreeding tolerance might be a life history adaptation     

而今迈步从头越: 马铃薯育种跨入“有种”时代

现代栽培马铃薯(Solanum tuberosum)是同源四倍体, 基因组高度杂合, 遗传组成复杂, 存在严重的自交衰退, 优异性状难以聚合, 使得育种周期漫长, 造成基于种子传代的马铃薯杂交育种难以突破。与此同时, 块茎无性繁殖导致马铃薯繁殖系数低、储运成本高和易携带病虫害等痼疾, 且种薯脱毒成本高, 限制其产业化发展。近期, 中国农业科学院深圳农业基因组研究所黄三文团队运用基因组设计理论和方法体系培育杂交马铃薯, 用二倍体育种替代四倍体育种, 实现了用杂交种子繁殖替代薯块繁殖, 创制了第1代高纯度的二倍体自交系和杂种优势明显的杂交马铃薯品系。该研究是马铃薯育种领域里程碑式的重大成果, 开启了基于基因组设计和种子迭代的马铃薯生物育种新纪元。     

Temporal change in inbreeding depression in life‐history traits in captive populations of guppy (Poecilia reticulata): evidence for purging?

Inbreeding depression, which generally affects the fitness of small populations, may be diminished by purging recessive deleterious alleles when inbreeding persists over several generations. Evidence of purging remains rare, especially because of the difficulties of separating the effects of various factors affecting fitness in small populations. We compared the expression of life-history traits in inbred populations of guppy (Poecilia reticulata) with contemporary control populations over 10 generations in captivity. We estimated inbreeding depression as the difference between the two types of populations at each generation. After 10 generations, the inbreeding coefficient reached a maximum value of 0.56 and 0.16 in the inbred and control populations, respectively. Analysing changes in the life-history traits across generations showed that inbreeding depression in clutch size and offspring survival increased during the first four to six generations in the populations from the inbred treatment and subsequently decreased as expected if purging occurred. Inbreeding depression in two other traits was weaker but showed similar changes across generations. The loss of six populations in the inbred treatment indicates that removal of deleterious alleles also occurred by extinction of populations that presumably harboured high genetic load.     

Long-term exhaustion of the inbreeding load in Drosophila melanogaster

Inbreeding depression, the decline in fitness of inbred individuals, is a ubiquitous phenomenon of great relevance in evolutionary biology and in the fields of animal and plant breeding and conservation. Inbreeding depression is due to the expression of recessive deleterious alleles that are concealed in heterozygous state in noninbred individuals, the so-called inbreeding load. Genetic purging reduces inbreeding depression by removing these alleles when expressed in homozygosis due to inbreeding. It is generally thought that fast inbreeding (such as that generated by full-sib mating lines) removes only highly deleterious recessive alleles, while slow inbreeding can also remove mildly deleterious ones. However, a question remains regarding which proportion of the inbreeding load can be removed by purging under slow inbreeding in moderately large populations. We report results of two long-term slow inbreeding Drosophila experiments (125–234 generations), each using a large population and a number of derived lines with effective sizes about 1000 and 50, respectively. The inbreeding load was virtually exhausted after more than one hundred generations in large populations and between a few tens and over one hundred generations in the lines. This result is not expected from genetic drift alone, and is in agreement with the theoretical purging predictions. Computer simulations suggest that these results are consistent with a model of relatively few deleterious mutations of large homozygous effects and partially recessive gene action.Subject terms: Quantitative trait, Inbreeding     

Photosynthetic responses of seven tropical seagrasses to elevated seawater temperature

This study uses chlorophyll a fluorescence to examine the effect of environmentally relevant (1–4 h) exposures of thermal stress (35–45 °C) on seagrass photosynthetic yield in seven tropical species of seagrasses. Acute response of each tropical seagrass species to thermal stress was characterised, and the capacity of each species to tolerate and recover from thermal stress was assessed. Two fundamental characteristics of heat stress were observed. The first effect was a decrease in photosynthetic yield (F_v / F_m) characterised by reductions in F and F_m′. The dramatic decline in F_v / F_m ratio, due to chronic inhibition of photosynthesis, indicates an intolerance of Halophila ovalis, Zostera capricorni and Syringodium isoetifolium to ecologically relevant exposures of thermal stress and structural alterations to the PhotoSystem II (PSII) reaction centres. The decline in F_m′ represents heat-induced photoinhibition related to closure of PSII reaction centres and chloroplast dysfunction. The key finding was that Cymodocea rotundata, Cymodocea serrulata, Halodule uninervis and Thalassia hemprichii were more tolerant to thermal stress than H. ovalis, Z. capricorni and S. isoetifolium. After 3 days of 4 h temperature treatments ranging from 25 to 40 °C, C. rotundata, C. serrulata and H. uninervis demonstrated a wide tolerance to temperature with no detrimental effect on F_v / F_m′ qN or qP responses. These three species are restricted to subtropical and tropical waters and their tolerance to seawater temperatures up to 40 °C is likely to be an adaptive response to high temperatures commonly occurring at low tides and peak solar irradiance. The results of temperature experiments suggest that the photosynthetic condition of all seagrass species tested are likely to suffer irreparable effects from short-term or episodic changes in seawater temperatures as high as 40–45 °C. Acute stress responses of seagrasses to elevated seawater temperatures are consistent with observed reductions in above-ground biomass during a recent El Niño event.     

Effective size and F-statistics of subdivided populations for sex-linked loci.

For a population subdivided into an arbitrary number (s) of subpopulations, each consisting of different numbers of separate sexes, with arbitrary distributions of family size and variable migration rates by males (dm) and females (df), the recurrence equations for inbreeding coefficient and coancestry between individuals within and among subpopulations for a sex-linked locus are derived and the corresponding expressions for asymptotic effective size are obtained by solving the recurrence equations. The usual assumptions are made which are stable population size and structure, discrete generations, the island migration model, and without mutation and selection. The results show that population structure has an important effect on the inbreeding coefficients in any generation, asymptotic effective size, and F-statistics. Gene exchange among subpopulations inhibits inbreeding in initial generations but increases inbreeding in later generations. The larger the migration rate, the greater the final inbreeding coefficients and the smaller the effective size. Thus if the inbreeding coefficient is to be restricted to a specific value within a given number of generations, the appropriate population structure (the values of s, dm, and df) can be obtained by using the recurrence equations. It is shown that the greater the extent of subdivision (large s, small dm and df), the larger the effective size. For a given subdivided population, the effective size for a sex-linked locus may be larger or smaller than that for an autosomal locus, depending on the sex ratio, variance and covariance of family size, and the extend of subdivision. For the special case of a single unsubdivided population, our recurrence equations for inbreeding coefficient and coancestry and formulas for effective size reduce to the simple expressions derived by previous authors.     

INBREEDING IN DARWIN'S MEDIUM GROUND FINCHES (GEOSPIZA FORTIS)

We studied the frequency and causes of inbreeding and its effect on reproductive success in a population of Darwin's Medium Ground Finches (Geospiza fortis) on Isla Daphne Major, Galápagos, during four breeding seasons (1981, 1983, 1984, and 1987). Pedigree analysis showed that levels of inbreeding were low but comparable with those observed in other passerine birds. For pairs with at least half of their grandparents known, approximately 20% of all pairings were between detectably related birds. The frequency of pairings between closely related birds (coefficient of kinship [φ] ≥ 0.250) among all pairs was 0.6%. We detected no effect of inbreeding on reproductive success, although sample sizes were small. The observed reproductive output of related pairs was not significantly different from the output of unrelated pairs, and there was no correlation between a pair's kinship coefficient and an estimate of the potential magnitude of inbreeding depression. Comparisons with a study of Great Tits (Parus major) by van Noordwijk and Scharloo (1981) suggest that, even if present, the fitness costs of inbreeding in this population of G. fortis would be low. Observed levels of inbreeding in each breeding episode were accurately predicted by simulations of random mating in which relatedness had no influence on pairing between individuals. This result suggests that levels of inbreeding in this population are determined more by demographic factors than by behavioral avoidance of mating with kin.     

Estimation of the time of divergence between Japanese Mishima Island cattle and other cattle populations using microsatellite DNA markers

We applied the theory of random genetic drift to determine the divergence history of a closed cattle population over the relatively short timescale of several hundred years. The divergence history of the closed population of Mishima Island cattle, a national natural treasure of Japan, was examined, and the results were compared with historical documents. Inbreeding depression in the isolated population was investigated for body size and fertility. Twenty-one DNA microsatellite markers in Mishima Island cattle and 3 major breeds from the mainland were genotyped. For the mainland breeds, all 21 or 20 markers were segregating. However, nearly half the number of loci (9 of 21) was fixed in the Island cattle. The average number of alleles per locus of Island cattle was markedly lower than that in the mainland breeds. These results support the theory that Island cattle have been isolated for a considerable period of time. The number of generations of isolation was estimated as 14.1-22.6, and the year of divergence was calculated as 1778-1846. In view of these findings, we propose that Island cattle diverged from the mainland population at around 1800 and were isolated for about 200 years. These estimates are in agreement with historical documents showing that divergence occurred between 1672 and 1880. The total inbreeding coefficient of the present population was predicted to be in the range of 0.51-0.60. However, historical reports dated over 100 years do not support changes in fertility, so that there is no evidence for inbreeding depression.     

Genetic variation (protein markers and microsatellites) in endangered Catalonian donkeys

Genetic variation of the endangered Catalonian donkey breed (Equus asinus) has been analysed at 19 loci including seven protein loci and 12 microsatellite loci isolated from the domestic horse, in 98 individuals of both sexes. Only four protein markers and three microsatellites were polymorphic. Allele frequencies of the analysed loci showed close agreement with Hardy–Weinberg proportions, with the exception of the MPZ002 locus (P<0.01). The within-population inbreeding estimate was not significantly different from zero (as measured by F_IS-statistic). The cumulative-exclusion probability for all polymorphic loci was 82.9%, this value still being very low so that these markers could efficiently be utilised for verification of parentage.     

Inbreeding depression due to mildly deleterious mutations in finite populations: size does matter

We studied the effects of population size on the inbreeding depression and genetic load caused by deleterious mutations at a single locus. Analysis shows how the inbreeding depression decreases as population size becomes smaller and/or the rate of inbreeding increases. This pattern contrasts with that for the load, which increases as population size becomes smaller but decreases as inbreeding rate goes up. The depression and load both approach asymptotic limits when the population size becomes very large or very small. Numerical results show that the transition between the small and the large population regimes is quite rapid, and occurs largely over a range of population sizes that vary by a factor of 10. The effects of drift on inbreeding depression may bias some estimates of the genomic rate of deleterious mutation. These effects could also be important in the evolution of breeding systems in hermaphroditic organisms and in the conservation of endangered populations.     

THE EFFECTS OF FIVE GENERATIONS OF ENFORCED SELFING ON POTENTIAL MALE AND FEMALE FUNCTION IN MIMULUS GUTTATUS

In prior work we detected no significant inbreeding depression for pollen and ovule production in the highly selfing Mimulus micranthus, but both characters showed high inbreeding depression in the mixed-mating M. guttatus. The goal of this study was to determine if the genetic load for these traits in M. guttatus could be purged in a program of enforced selfing. These characters should have been under much stronger selection in our artificial breeding program than previously reported characters such as biomass and total flower production because, for example, plants unable to produce viable pollen could not contribute to future generations. Purging of genetic load was investigated at the level of both the population and the individual maternal line within two populations of M. guttatus. Mean ovule number, pollen number, and pollen viability declined significantly as plants became more inbred. The mean performance of outcross progeny generated from crosses between pairs of maternal inbred lines always exceeded that of self progeny and was fairly constant for each trait through all five generations. The consistent performance of outcross progeny and the universally negative relationships between performance and degree of inbreeding are interpreted as evidence for the weakness of selection relative to the quick fixation of deleterious alleles due to drift during the inbreeding process. The selective removal (purging) of deleterious alleles from our population would have been revealed by an increase in performance of outcross progeny or an attenuation of the effects of increasing homozygosity. The relationships between the mean of each of these traits and the expected inbreeding coefficient were linear, but one population displayed a significant negative curvilinear relationship between the log of male fertility (a function of pollen number and viability) and the inbreeding coefficient. The generally linear form of the responses to inbreeding were taken as evidence consistent with an additive model of gene action, but the negative curvilinear relationship between male fertility and the inbreeding coefficient suggested reinforcing epistasis. Within both populations there was significant genetic variation among maternal lineages for the response to inbreeding in all traits. Although all inbred lineages declined at least somewhat in performance, several maternal lines maintained levels of performance just below outcross means even after four or five generations of selfing. We suggest that selection among maternal lines will have a greater effect than selecting within lines in lowering the genetic load of populations.     

INBREEDING DEPRESSION IN FOUR POPULATIONS OF COLLINSIA HETEROPHYLLA NUTT (SCROPHULARIACEAE)

The effects of one and two generations of inbreeding were studied in plants from four natural populations of the annual plant, Collinsia heterophylla, using inbred and outcrossed plants generated by hand pollinations to create expected inbreeding coefficients ranging from 0–0.75. The selfing rates of the populations were estimated using allozyme markers to range from 0.37–0.69. Inbreeding depression was mild, ranging from 5–40%, but significant effects were detected for characters measured at all stages of the life cycle. Fitness components declined significantly with the inbreeding coefficient, and regression of fitness characters on inbreeding coefficients gave no evidence of any strongly synergistic effects attributable to the different genetic factors that contribute to decline in fitness under inbreeding. The magnitude of inbreeding depression did not clearly decrease with the populations' levels of inbreeding. This is not surprising because the selfing rates are similar enough that it is unlikely that the populations have been characterized for long periods of time by these different inbreeding levels.