贵州白香猪两品系微卫星座位的遗传分析

采用24个微卫星标记对贵州白香猪2个品系的遗传变异进行了检测.试验结果表明,2个品系在24个微卫星基因座的平均等位基因、平均期望杂合度、平均多态信息含量和平均近交系数分别为2.1667、2.0417,0.4074、0.4188,0.3436、0.3249和0.5377、0.5605.结果 提示贵州白香猪具有一定的遗传稳定性,已成为一个稳定的遗传群体,符合封闭群动物的遗传特征.     

Palynology and intergeneric relationships in subtribe Hyoseridinae (CompositaerLactuceae)

Ceratopteris pteridoides is an inbreeding species. Intralocus homozygosity is deduced from the almost total absence of genetic load (recessive deleterious and lethal genes) in sporophytes from natural populations, and from gametangial sequences which indicate intragametophytic selfing. This mating system and the profound capacity of the species for vegetative reproduction, coupled with the small size and geographical isolation of many populations, strongly support the hypothesis of individual homozygosity. However, polymorphism is exhibited both within and between populations in specific, genetically mediated, gametophytic characteristics. The population genetic structure of C. pteridoides is similar to other inbreeding species.     

Analysis of genetic variability in American Pit Bull Terrier breed of dogs with a high inbreeding level using microsatellite markers

The level of DNA polymorphism in 10 microsatellite loci of 27 American Pit Bull Terrier dogs with high percentage of blood and inbreeding coefficients of up to 43.8% was studied. The observed heterozygosity was higher than expected for this inbreeding level. The presence of a selection mechanism that prevents gametes from fusing to form a homozygosity genotype is suggested.     

Impact of habitat fragmentation on allelic diversity at microsatellite loci in Cunningham’s skink <Emphasis Type="Italic"> (Egernia cunninghami);</Emphasis> a preliminary study

Knowledge of processes that lead to genetic erosion for a range of species is important for conservation management. Relatively little work has assessed anthropogenic impacts on genetic variation in lizards. As part of our research program investigating effects of habitat fragmentation on Cunningham’s skink (Egernia cunninghami), allelic diversity at 10 microsatellite loci was assessed in deforested and adjacent naturally vegetated habitats at two locations on the Central tablelands of NSW, Australia. Previously we have shown that deforestation is associated with significantly reduced dispersal, but not increased levels of inbreeding and homozygosity, presumably owing to strong kin avoidance in mate choice. However, in this study, two measures of allelic diversity, allelic richness and the ratio of allele number to size range, indicate that local levels of variability are lower in deforested habitats. Levels of allelic diversity may be expected to decrease more rapidly than levels of heterozygosity, thereby flagging potential longer-term problems, such as inbreeding depression or reduced recruitment because of mate limitation through strong inbreeding avoidance.     

微卫星DNA监控大鼠近交系的培育

采用微卫星DNA技术来监控大鼠仔代基因状况,选择性地进行交配繁殖,使基因快速纯合,缩短培育新的近交系动物周期。利用PCR扩增30个微卫星DNA位点对封闭群SD和Wistar大鼠交配繁殖的仔代鼠进行微卫星DNA多态性分析,仔代中与母代SD大鼠相似系数高的与中的进行定向交配繁殖。F2代大鼠均为杂合多态的位点,没有纯合位点;到F9代时基因纯合位点达27个,纯合基因位点率为90%。每代相似系数具有不断上升的趋势,上升率为6-20%。采用皮肤移植方法验证了F9代大鼠间无排斥。建立了一种新的快速培育近交系动物的方法。     

Diurnal variability of gene arrangement frequencies in Drosophila subobscura populations from two habitats*

The rich inversion polymorphism of chromosomes of Drosophila subobscura varies in association with environmental changes at spatial and temporal level. Due to random factors this might become less regular and this might be the reason that there is little evidence of altitudinal and seasonal, microgeographic and habitat‐related variability. The variability of gene arrangement frequencies over daytime period was investigated in populations of D. subobscura from two ecologically different habitats. According to gene arrangement frequencies and inversion polymorphism parameters populations fit into the existing patterns of regional polymorphism. Even though populations display daytime variability for the frequencies of arrangements of chromosomes U and J, the nonsignificant differences in other arrangement frequencies, as well as data obtained from genetic distances between samples from different times of day, rule out the existence of subpopulations distinguished from each other by diurnal activity within two habitats. Some particular arrangement frequencies vary according to temperature and humidity and some changes appear for different karyotypic combinations between beech and oak habitat, which suggests different adaptive advantages and selective mechanisms. Cluster analysis of gene arrangement frequencies indicates some importance of A chromosome arrangements for diurnal activity and show in dependence to other ecological data that internally fixed daily activity rhythm might exists in D. subobscura. Analysis of light, temperature and humidity factors in relation to the frequency data obtained indicate a choice of different ecological niche in a temporally structured habitat due to behavioural genetic information.     

Selection in heterogeneous environments maintains the gene arrangement polymorphism of Drosophila pseudoobscura

Chromosomal rearrangements may play an important role in how populations adapt to a local environment. The gene arrangement polymorphism on the third chromosome of Drosophila pseudoobscura is a model system to help determine the role that inversions play in the evolution of this species. The gene arrangements are the likely target of strong selection because they form classical clines across diverse geographic habitats, they cycle in frequency over seasons, and they form stable equilibria in population cages. A numerical approach was developed to estimate the fitness sets for 15 gene arrangement karyotypes in six niches based on a model of selection-migration balance. Gene arrangement frequencies in the six different niches were able to reach a stable meta-population equilibrium that matched the observed gene arrangement frequencies when recursions used the estimated fitnesses with a variety of initial inversion frequencies. These analyses show that a complex pattern of selection is operating in the six niches to maintain the D. pseudoobscura gene arrangement polymorphism. Models of local adaptation predict that the new inversion mutations were able to invade populations because they held combinations of two to 13 local adaptation loci together.     

Features of genetic variability in microsatellite DNA loci in the French Bulldog dog breed

Genetic variability in microsatellite markers PEZ1, PEZ3, PEZ6, PEZ8, FHC2010, and FHC2054 from a panel recommended by the International Society for Animal Genetics has been assessed for a micropopulation of dogs of the French Bulldog breed. The number and size of alleles, the number of alleles per locus, the effective number of alleles, the polymorphism index, expected and actual heterozygosity, and Wright’s fixation index have been determined to characterize each locus investigated. Deficit of heterozygous genotypes was observed in the micropopulation investigated, which is indicative of inbreeding. The relationship between the degree of homozygosity for six microsatellite loci and the degree of inbreeding has been analyzed. The results obtained point at a trend for increase of the relative abundance of homozygous loci upon an increase in the inbreeding coefficient of individuals.     

Local effects of inbreeding on embryo number and consequences for genetic diversity in Kerguelen mouflon

A classical paradigm in population genetics is that homozygosity or inbreeding affects individual fitness through increased disease susceptibility and mortality, and diminished breeding success. Using data from an insular population of mouflon (Ovis aries) founded by a single pair of individuals, we compare embryo number of ewes with different levels of inbreeding. Contrary to expectations, ewes with the highest levels of homozygosity showed the largest number of embryos. Using two different statistical approaches, we showed that this relationship is probably caused by heterozygosity at specific genes. The genetics of embryo number coupled with cyclic dynamics could play a central role in promoting genetic variation in this population.     

Red cell genetic abnormalities, beta-globin gene haplotypes, and APOB polymorphism in the Great Andamanese, a primitive Negrito tribe of Andaman and Nicobar Islands, India.

The Great Andamanese are a primitive Negrito tribe of the Andaman and Nicobar Islands, India, with a total population of 37. We studied 29 individuals from eight families from this population for abnormal hemoglobins, G6PD deficiency, DNA haplotypes, and apolipoprotein B (APOB, gene) polymorphism. Hb E was detected in five individuals, the prevalence of Hb E heterozygotes being 14.3%. One individual had beta-thalassemia trait. One female was G6PD deficient and showed the G6PD Orissa mutation. Haplotype analysis of the beta-globin gene cluster showed that the betaE chromosomes were linked to two haplotypes (- - - - - + + and + + - + + + +) representing the framework 1 gene, whereas the betaA chromosomes showed eight different haplotypic patterns corresponding to framework 1 and 3 genes. APOB polymorphism analysis showed that the 631-base-pair (bp) allele was the predominant one with a high homozygosity rate, which could be due to the higher rate of inbreeding in this isolated group. The presence of Hb E and our findings on haplotype analysis supports the hypothesis that the Great Andamanese are reasonably believed to be the surviving representatives of the Negrito race that once flourished in the entire Southeast Asian region in ancient times.     

A Systematic Approach to Mapping Recessive Disease Genes in Individuals from Outbred Populations

The identification of recessive disease-causing genes by homozygosity mapping is often restricted by lack of suitable consanguineous families. To overcome these limitations, we apply homozygosity mapping to single affected individuals from outbred populations. In 72 individuals of 54 kindred ascertained worldwide with known homozygous mutations in 13 different recessive disease genes, we performed total genome homozygosity mapping using 250,000 SNP arrays. Likelihood ratio Z-scores (ZLR) were plotted across the genome to detect ZLR peaks that reflect segments of homozygosity by descent, which may harbor the mutated gene. In 93% of cases, the causative gene was positioned within a consistent ZLR peak of homozygosity. The number of peaks reflected the degree of inbreeding. We demonstrate that disease-causing homozygous mutations can be detected in single cases from outbred populations within a single ZLR peak of homozygosity as short as 2 Mb, containing an average of only 16 candidate genes. As many specialty clinics have access to cohorts of individuals from outbred populations, and as our approach will result in smaller genetic candidate regions, the new strategy of homozygosity mapping in single outbred individuals will strongly accelerate the discovery of novel recessive disease genes.     

Telomere length reveals cumulative individual and transgenerational inbreeding effects in a passerine bird

Inbreeding results in more homozygous offspring that should suffer reduced fitness, but it can be difficult to quantify these costs for several reasons. First, inbreeding depression may vary with ecological or physiological stress and only be detectable over long time periods. Second, parental homozygosity may indirectly affect offspring fitness, thus confounding analyses that consider offspring homozygosity alone. Finally, measurement of inbreeding coefficients, survival and reproductive success may often be too crude to detect inbreeding costs in wild populations. Telomere length provides a more precise measure of somatic costs, predicts survival in many species and should reflect differences in somatic condition that result from varying ability to cope with environmental stressors. We studied relative telomere length in a wild population of Seychelles warblers (Acrocephalus sechellensis) to assess the lifelong relationship between individual homozygosity, which reflects genome‐wide inbreeding in this species, and telomere length. In juveniles, individual homozygosity was negatively associated with telomere length in poor seasons. In adults, individual homozygosity was consistently negatively related to telomere length, suggesting the accumulation of inbreeding depression during life. Maternal homozygosity also negatively predicted offspring telomere length. Our results show that somatic inbreeding costs are environmentally dependent at certain life stages but may accumulate throughout life.     

Detecting inbreeding depression for reproductive traits in Iberian pigs using genome-wide data

Background

The current availability of genotypes for very large numbers of single nucleotide polymorphisms (SNPs) is leading to more accurate estimates of inbreeding coefficients and more detailed approaches for detecting inbreeding depression. In the present study, genome-wide information was used to detect inbreeding depression for two reproductive traits (total number of piglets born and number of piglets born alive) in an ancient strain of Iberian pigs (the Guadyerbas strain) that is currently under serious danger of extinction.

Methods

A total of 109 sows with phenotypic records were genotyped with the PorcineSNP60 BeadChip v1. Inbreeding depression was estimated using a bivariate animal model in which the inbreeding coefficient was included as a covariate. We used two different measures of genomic inbreeding to perform the analyses: inbreeding estimated on a SNP-by-SNP basis and inbreeding estimated from runs of homozygosity. We also performed the analyses using pedigree-based inbreeding.

Results

Significant inbreeding depression was detected for both traits using all three measures of inbreeding. Genome-wide information allowed us to identify one region on chromosome 13 associated with inbreeding depression. This region spans from 27 to 54 Mb and overlaps with a previously detected quantitative trait locus and includes the inter-alpha-trypsin inhibitor gene cluster that is involved with embryo implantation.

Conclusions

Our results highlight the value of high-density SNP genotyping for providing new insights on where genes causing inbreeding depression are located in the genome. Genomic measures of inbreeding obtained on a SNP-by-SNP basis or those based on the presence/absence of runs of homozygosity represent a suitable alternative to pedigree-based measures to detect inbreeding depression, and a useful tool for mapping studies. To our knowledge, this is the first study in domesticated animals using the SNP-by-SNP inbreeding coefficient to map specific regions within chromosomes associated with inbreeding depression.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-014-0081-5) contains supplementary material, which is available to authorized users.     

A study of some genetic characteristics of the Fur and Baggara tribes of the Sudan

The average inbreeding coefficients of the highly consanguineous Fur and Baggara tribes of Western Sudan were 0.04167 and 0.04450, respectively. Two hundred ninety-eight subjects from the two tribes were tested for polymorphism of hemoglobins, seven red cell enzymes, and four serum proteins. The Baggara showed a higher gene frequency of HbS and TfD and lower gene frequency of GdA and PC compared to the Fur. Both tribes showed a low gene frequency of PGM1 and high frequency of G6PD deficiency when compared to other Sudanese tribes. In spite of the high degree of inbreeding, no significant deviation from the Hardy-Weinburg equilibrium was observed in either tribe. The effects of inbreeding seem to be offset by mixing between the two tribes on Gabal Marra Plateau. The flow of the sickle gene from the Baggara into the Fur and other Sudanese tribes is discussed.     

What should we weigh to estimate heterozygosity,alleles or loci?

The interest to study the effects of inbreeding in natural populations has increased in the last years. Several microsatellite-derived metrics have recently been developed to infer inbreeding from multilocus heterozygosity data without requiring detailed pedigrees that are difficult to obtain in open populations. Internal relatedness (IR) is currently the most widespread used index and its main attribute is that allele frequency is incorporated into the measure. However, IR underestimates heterozygosity of individuals carrying rare alleles. For example, descendants of immigrants paired with natives (normally more outbred) bearing novel or rare alleles would be considered more homozygous than descendants of native parents. Thus, the analogy between homozygosity and inbreeding that generally is carried out would have no logic in those cases. We propose an alternative index, homozygosity by loci (HL) that avoids such problems by weighing the contribution of each locus to the homozygosity index depending on their allelic variability. Under a wide range of simulated scenarios, we found that our index (HL) correlated better than both IR and uncorrected homozygosity (H(O)), measured as proportion of homozygous loci) with genome-wide homozygosity and inbreeding coefficients in open populations. In these populations, which are likely to prevail in nature, the use of HL instead of IR reduced considerably the sample sizes required to achieve a given statistical power. This is likely to have important consequences on the ability to detect heterozygosity fitness correlations assuming the relationship between genome-wide heterozygosity and fitness traits.     

No inbreeding depression but increased sexual investment in highly inbred ant colonies

Inbreeding can lead to the expression of deleterious recessive alleles and to a subsequent fitness reduction. In Hymenoptera, deleterious alleles are purged in haploid males moderating inbreeding costs. However, in these haplodiploid species, inbreeding can result in the production of sterile diploid males. We investigated the effects of inbreeding on the individual and colony level in field colonies of the highly inbred ant Hypoponera opacior. In this species, outbreeding winged sexuals and nest‐mating wingless sexuals mate during two separate reproductive periods. We show that regular sib‐matings lead to high levels of homozygosity and the occasional production of diploid males, which sporadically sire triploid offspring. On the individual level, inbreeding was associated with an increased body size in workers. On the colony level, we found no evidence for inbreeding depression as productivity was unaffected by the level of homozygosity. Instead, inbred colonies altered their allocation strategies by investing more resources into sexuals than into workers. This shift towards sexual production was due to an increased investment in both males and queens, which was particularly pronounced in the dispersive generation. The absence of inbreeding depression combined with increased reproductive investment, especially in outbreeding sexuals, suggests that these ants have evolved active strategies to regulate the extent and effects of frequent inbreeding.     

Fitness and the level of homozygosity in a social insect

To date very few studies have addressed the effects of inbreeding in social Hymenoptera, perhaps because the costs of inbreeding are generally considered marginal owing to male haploidy whereby recessive deleterious alleles are strongly exposed to selection in males. Here, we present one of the first studies on the effects of queen and worker homozygosity on colony performance. In a wild population of the ant Formica exsecta, the relative investment of single‐queen colonies in sexual production decreased with increased worker homozygosity. This may either stem from increased homozygosity decreasing the likelihood of diploid brood to develop into queens or a lower efficiency of more homozygous workers at feeding larvae and thus a lower proportion of the female brood developing into queens. There was also a significant negative association between colony age and the level of queen but not worker homozygosity. This association may stem from inbreeding affecting queen lifespan and/or their fecundity, and thus colony survival. However, there was no association between queen homozygosity and colony size, suggesting that inbreeding affects colony survival as a result of inbred queens having a shorter lifespan rather than a lower fecundity. Finally, there was no significant association between either worker or queen homozygosity and the probability of successful colony founding, colony size and colony productivity, the three other traits studied. Overall, these results indicate that inbreeding depression may have important effects on colony fitness by affecting both the parental (queen) and offspring (worker) generations cohabiting within an ant colony.     

Genomic and phenotypic effects of inbreeding across two different hatchery management regimes in Chinook salmon

Genomic approaches permit direct estimation of inbreeding and its effect on fitness. We used genomic‐based estimates of inbreeding to investigate their relationship with eight adult traits in a captive‐reared Pacific salmonid that is released into the wild. Estimates were also used to determine whether alternative broodstock management approaches reduced risks of inbreeding. Specifically, 1,100 unlinked restriction‐site associated (RAD) loci were used to compare pairwise relatedness, derived from a relationship matrix, and individual inbreeding, estimated by comparing observed and expected homozygosity, across four generations in two hatchery lines of Chinook salmon that were derived from the same source. The lines are managed as “integrated” with the founding wild stock, with ongoing gene flow, and as “segregated” with no gene flow. While relatedness and inbreeding increased in the first generation of both lines, possibly due to population subdivision caused by hatchery initiation, the integrated line had significantly lower levels in some subsequent generations (relatedness: F₂–F₄; inbreeding F₂). Generally, inbreeding was similar between the lines despite large differences in effective numbers of breeders. Inbreeding did not affect fecundity, reproductive effort, return timing, fork length, weight, condition factor, and daily growth coefficient. However, it delayed spawn timing by 1.75 days per one standard deviation increase in F (~0.16). The results indicate that integrated management may reduce inbreeding but also suggest that it is relatively low in a small, segregated hatchery population that maximized number of breeders. Our findings demonstrate the utility of genomics to monitor inbreeding under alternative management strategies in captive breeding programs.