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1.
The influence of selection and epistasis on inbreeding depression estimates   总被引：1，自引：0，他引：1  
Inbreeding depression estimates obtained by regression of the individual performance on the inbreeding were studied by stochastic simulation under various genetic models (solely additive, partial dominance, overdominance and epistasis), and mating strategies (random mating versus selection). In all models, inbreeding depression estimates based on the individual pedigree inbreeding coefficients were compared with estimates based on the true level of autozygosity. For the model with partial dominance and selection, the estimates of inbreeding depression from pedigree information were more negative (lower) than those based on true inbreeding coefficients whereas, in contrast, they were less negative (higher) for the models with overdominance and selection. The difference in the variation of true and pedigree individual inbreeding coefficient indicated that biased estimates might occur even in random mating populations. The estimation of inbreeding depression was further complicated when epistatic effects were present. The sign and the magnitude of the inbreeding effect (depression) estimates might be rather heterogeneous if additive by dominance effects are present because they are strongly dependent on the gene frequency. It was also shown that inbreeding depression is possible in models with negative additive by dominance effects. In models with dominance by dominance inheritance it was difficult to assess the non-linear relationship between performance and inbreeding, while at the same time, non-linear estimates based on pedigree information were extremely biased. The results obtained indicate that new or additional methodologies are required if reliable conclusions about consequences of inbreeding depression are needed.  相似文献   

2.
不同来源大白猪总产仔数近交衰退评估   总被引：2，自引：2，他引：0  
旨在评估两个不同来源大白猪群体经过近8个世代的选育后总产仔数（total number of piglets born，TNB）近交衰退的程度。本研究对1 937头大白猪使用GeneSeek GGP Porcine HD芯片进行分型，其中1 039头来自加系大白猪和898头来自法系大白猪，且两品系均有表型记录和系谱记录，系谱共由3 086头大白猪组成。分别使用系谱、SNP和ROH进行个体近交系数估计，并将近交系数作为协变量利用动物模型对总产仔数进行近交衰退评估。为了精准定位导致总产仔数衰退的基因组片段，又进一步对每条染色体以及显著染色体分段计算近交系数并估计其效应，检测是否能引起总产仔数发生近交衰退现象。对于加系群体，FROH、FGRM和FPED估计的近交系数均值分别为0.124、0.042和0.013，其中FROH和FPED相关最高，相关系数为0.358；对于法系群体，FROH、FGRM和FPED均值分别为0.123、0.052和0.007，其中FROH和FGRM相关最高，相关系数为0.371。利用3种不同计算方法所得近交系数用于估计近交衰退时，加系群体的总产仔数均检测到显著的近交衰退，而且当FROH、FGRM和FPED每增加10%时，总产仔数分别减少0.571、0.341和0.823头；但法系群体仅有FROH估计的总产仔数检测到显著近交衰退，FROH每增加10%时，总产仔数减少0.690头。为了锁定相关的染色体和基因组区段，首先利用ROH估计每条染色体近交系数并进行近交衰退分析发现，加系群体中检测到第6、7、8和13号染色体产生了显著近的总产仔数交衰退，而法系群体未检测到与近交衰退相关的染色体。然后，又将与加系总产仔数近交衰退显著相关的4条染色体平均分为2、4、6、8个片段进行近交衰退检测，其中平均分成8段后的染色片段的长度范围为15.1~25.8 Mb。在第6、7和8号染色体分别检测到1、2和3个与总产仔数相关的近交衰退染色体片段。这些区域注释到了CUL7、MAPK14和PPARD基因与胎盘发育相关，AREG和EREG基因与卵母细胞成熟有关。本研究利用3种近交系数计算方法对两个不同来源的大白猪总产仔数进行近交衰退评估，在加系大白猪中3种估计方法都能检测到近交衰退的现象，而法系群体中只有FROH才能检测到。而且通过ROH方法进一步确定了能引起加系大白猪总产仔数衰退的4条染色体和6个特定的染色体区段，还注释到了与繁殖相关的候选基因。这为揭示近交衰退的遗传机制提供了新的研究手段，也为基因组选种选配提供了参考依据。  相似文献   

3.
Although epistatic effects are well defined and, in principle, can be exploited in quantitative-genetic selection theory, they often are ignored or even treated as nuisance parameters in practical applications. Traditionally, epistasis is considered as an interaction between genes at unspecified loci. Inspired by the observation that functional genes are often organised in physical clusters, we developed a model to combine additive effects and additive × additive interactions in linked gene clusters of defined length. Malécot's kinship concept is extended to identity by descent probabilities for chromosome segments of a given length in Morgan units, called epistatic kinship. Using the analogy of Malécot's kinship and Wright's relationship and inbreeding coefficients, epistatic relationship coefficients and epistatic inbreeding coefficients are defined. Simple rules are given to set up the epistatic numerator relationship matrix and its inverse directly from a pedigree list. The well-known single locus parameters and algorithms to set up the additive numerator relationship matrix and its inverse are a special case of the suggested methodology for a chromosome segment length of null Morgan. A proof of concept of the suggested method is given with a small simulation study. Assuming additive, linked epistatic and residual variance components, 100 replicated data sets for 1000 individuals are generated. From these data, residual maximum likelihood estimates of the variance components and of the chromosome segment size are obtained. Potential applications of the methodology are discussed. Given that a substantial variance component is attributed to this effect, the expected genetic gain can be increased on the short term if selection is on additive and epistatic effects, the latter comprising additive × additive interaction effect of loci in linkage disequilibrium. This extra benefit, however, will diminish through crossing over in subsequent generations. Despite some practical problems yet to be solved, the suggested model and algorithms open new perspectives to use a higher proportion of genetic variability in selection and breeding.  相似文献   

4.
Genetic variation at 59 protein coding loci (16 polymorphic) and 25 microsatellite loci was analysed for 11 indigenous south-east Asian goat populations, and the Australian feral population, to determine the magnitude of genetic differentiation and the genetic relationships among the populations. Significant deviations from Hardy–Weinberg equilibrium were detected in one or more populations for eight of the nine protein loci with codominant alleles, and for microsatellites for all except the two Sri Lankan populations and for all but four loci. For both marker types, average inbreeding coefficients ( F IS) were exceptionally high. Heterogeneity of deviations from Hardy–Weinberg equilibrium for the microsatellites showed no differences for among loci within populations as compared with among populations within loci. For protein loci, however, the former was higher, indicating selection affecting allele frequencies at some loci. The variance among protein loci was significantly higher than among microsatellite loci, further indicating selection at some protein loci. There was significant differentiation among populations for both protein and microsatellite loci, most likely reflecting the geography of south-east Asia, and the presumed spread of goats throughout the region. Phylogenies derived from pair-wise genetic distance estimates show some similar clustering for the microsatellite and protein based trees, but bootstrap support was generally low for both. A phylogeny based on the combined set of 38 protein and microsatellite loci showed better consistency with geography and higher bootstrap values. The genetic distance phylogeny and the Weitzman diversity tree derived from microsatellite data showed some identical clusters, and both identified the Ujung Pandang and Australia populations as contributing most to overall genetic diversity.  相似文献   

5.
The most common goal of animal conservation programmes is to maintain genetic diversity. Various measures for genetic variability based on pedigree information can be used, but most of them are very sensitive to completeness of pedigree information. Different criteria based on probability of identity-by-descent (effective population size via increase in inbreeding Ne) or probability of gene origin (effective number of founders fe, ancestors fa and founder genomes Ng) were used to describe the genetic variability of three Austrian cattle breeds [Original Pinzgau (PI), Tux-Zillertal (TZ), Carinthian Blond (CB)]. Reference populations for PI were defined by animals born between 1993 and 1997 and for TZ and CB by all living animals, irrespective of birth year. The numbers of animals in the reference populations were 9706, 471 and 230 for PI, TZ and CB, respectively. The average complete generation equivalent showed the different quality of pedigree information: 5.33 for PI, 2.52 for TZ and 1.73 for CB. The following Nes were calculated: 76 for PI and CB and 43 for TZ. For PI, TZ and CB a fe-value of 65.4, 21.0 and 29.9, a fa-value of 32.1, 14.2 and 29.0 and a Ng-value of 19.5, 9.7 and 22.6, respectively, were calculated. In particular, the results for TZ demonstrate the urgent need for a well-planned conservation programme.  相似文献   

6.
In closed rabbit lines selected for prolificacy at the Polytechnic University of Valencia, genetic responses are predicted using BLUP. With a standard additive BLUP model and year‐season (YS) effects fitted as fixed, genetic trends were overestimated compared to responses estimated using control populations obtained from frozen embryos. In these lines, there is a confounding between genetic trend, YS effects and inbreeding, and the role of dominance is uncertain. This is a common situation in data from reproductively closed selection lines. This paper fits different genetic evaluation models to data of these lines, aiming to identify the source of these biases: dominance, inbreeding depression and/or an ill‐conditioned model due to the strong collinearity between YS, inbreeding and genetic trend. The study involved three maternal lines (A, V and H) and analysed two traits, total born (TB) and the number of kits at weaning (NW). Models fitting YS effect as fixed or random were implemented, in addition to additive genetic, permanent environment effects and non‐inbred dominance deviations effects. When YS was fitted as a fixed effect, the genetic trends were overestimated compared to control populations, inbreeding had an apparent positive effect on litter size and the environmental trends were negative. When YS was fitted as random, the genetic trends were compatible with control populations results, inbreeding had a negative effect (lower prolificacy) and environmental trends were flat. The model fitting random YS, inbreeding and non‐inbred dominance deviations yielded the following ratios of additive and dominance variances to total variance for NW: 0.06 and 0.01 for line A, 0.06 and 0.00 for line V and 0.01 and 0.08 for line H. Except for line H, dominance deviations seem to be of low relevance. When it is confounded with inbreeding as in these lines, fitting YS effect as random allows correct estimation of genetic trends.  相似文献   

7.
Multilocus homozygosity, measured as the proportion of the autosomal genome in homozygous genotypes or in runs of homozygosity, was compared with the respective pedigree inbreeding coefficients in 64 Iberian pigs genotyped using the Porcine SNP60 Beadchip. Pigs were sampled from a set of experimental animals with a large inbreeding variation born in a closed strain with a completely recorded multi‐generation genealogy. Individual inbreeding coefficients calculated from pedigree were strongly correlated with the different SNP‐derived metrics of homozygosity (r = 0.814–0.919). However, unequal correlations between molecular and pedigree inbreeding were observed at chromosomal level being mainly dependent on the number of SNPs and on the correlation between heterozygosities measured across different loci. A panel of 192 SNPs of intermediate frequencies was selected for genotyping 322 piglets to test inbreeding depression on postweaning growth performance (daily gain and weight at 90 days). The negative effects on these traits of homozygosities calculated from the genotypes of 168 quality‐checked SNPs were similar to those of inbreeding coefficients. The results support that few hundreds of SNPs may be useful for measuring inbreeding and inbreeding depression, when the population structure or the mating system causes a large variance of inbreeding.  相似文献   

8.
The purpose of this study is to use demographic and litter size data on four Spanish maternal lines of rabbits (A, V, H and LP), as a case study, in order to: (i) estimate the effective population size of the lines, as a measure of the rate of increase of inbreeding, and (ii) study whether the inbreeding effect on litter size traits depends on the pattern of its accumulation over time. The lines are being selected for litter size at weaning and are kept closed at the same selection nucleus under the same selection and management programme. The study considered 47 794 l and a pedigree of 14 622 animals. Some practices in mating and selection management allow an increase of the inbreeding coefficient lower than 0.01 per generation in these lines of around 25 males and 125 females. Their effective population size (Ne) was around 57.3, showing that the effect of selection, increasing the inbreeding, was counterbalanced by the management practices, intended to reduce the rate of inbreeding increase. The inbreeding of each individual was broken down into three components: old, intermediate and new inbreeding. The coefficients of regression of the old, intermediate and new inbreeding on total born (TB), number born alive (NBA) and number weaned (NW) per litter showed a decreasing trend from positive to negative values. Regression coefficients significantly different from zero were those for the old inbreeding on TB (6.79 ± 2.37) and NBA (5.92 ± 2.37). The contrast between the coefficients of regression between the old and new inbreeding were significant for the three litter size traits: 7.57 ± 1.72 for TB; 6.66 ± 1.73 for NBA and 5.13 ± 1.67 for NW. These results have been interpreted as the combined action of purging unfavourable genes and artificial selection favoured by the inbreeding throughout the generations of selection.  相似文献   

9.
Recent publications indicate that single‐step models are suitable to estimate breeding values, dominance deviations and total genetic values with acceptable quality. Additive single‐step methods implicitly extend known number of allele information from genotyped to non‐genotyped animals. This theory is well derived in an additive setting. It was recently shown, at least empirically, that this basic strategy can be extended to dominance with reasonable prediction quality. Our study addressed two additional issues. It illustrated the theoretical basis for extension and validated genomic predictions to dominance based on single‐step genomic best linear unbiased prediction theory. This development was then extended to include inbreeding into dominance relationships, which is a currently not yet solved issue. Different parametrizations of dominance relationship matrices were proposed. Five dominance single‐step inverse matrices were tested and described as C1 , C2 , C3 , C4 and C5 . Genotypes were simulated for a real pig population (n = 11,943 animals). In order to avoid any confounding issues with additive effects, pseudo‐records including only dominance deviations and residuals were simulated. SNP effects of heterozygous genotypes were summed up to generate true dominance deviations. We added random noise to those values and used them as phenotypes. Accuracy was defined as correlation between true and predicted dominance deviations. We conducted five replicates and estimated accuracies in three sets: between all ( S1 ), non‐genotyped ( S2 ) and inbred non‐genotyped ( S3 ) animals. Potential bias was assessed by regressing true dominance deviations on predicted values. Matrices accounting for inbreeding ( C3 , C4 and C5 ) best fit. Accuracies were on average 0.77, 0.40 and 0.46 in S1 , S2 and S3 , respectively. In addition, C3 , C4 and C5 scenarios have shown better accuracies than C1 and C2 , and dominance deviations were less biased. Better matrix compatibility (accuracy and bias) was observed by re‐scaling diagonal elements to 1 minus the inbreeding coefficient ( C5 ).  相似文献   

10.
Since purebred dog populations represent closed gene pools, a relatively high level of consanguinity between individuals, and hence of inbreeding, is common. This case control study was conducted to establish the possible connection between the actual level of homozygosity due to inbreeding and specific diseases (flea allergy, osteochondrosis, laryngeal paralysis, neoplasm, autoimmune disease, hypoplastic trachea, and food allergy) occurring in the Bouvier Belge des Flandres breed. One hundred and sixty-eight animals referred to the Utrecht University Clinic formed the patient group. Each of the seven diseases was chosen because of the demonstrability of the diagnosis. Each animal was chosen because one of the selected diseases was established in that individual, and because its pedigree was complete. All dogs of the patient group were born between 1 January 1980 and 31 December 1985. A control group (n = 123) was randomly chosen from the total population of registered Bouviers born in the Netherlands in the same period. pedigree data were obtained from the Dutch Kennel Club. The extent of inbreeding was determined for all animals using Wright's inbreeding coefficient. The distribution of inbreeding coefficients in each patient group was compared with the distribution in controls. Inbreeding coefficients in the control group ranged from 0.0 to 0.406. Animals in which osteochondrosis, food allergy, autoimmune disease, neoplasm, or hypoplastic trachea was diagnosed had higher inbreeding coefficients than controls. It was concluded that in the Bouvier Belge des Flandres dog population examined, the level of homozygosity was positively correlated with occurrence of these diseases.  相似文献   

11.
Reference populations for genomic selection usually involve selected individuals, which may result in biased prediction of estimated genomic breeding values (GEBV). In a simulation study, bias and accuracy of GEBV were explored for various genetic models with individuals selectively genotyped in a typical nucleus breeding program. We compared the performance of three existing methods, that is, Best Linear Unbiased Prediction of breeding values using pedigree‐based relationships (PBLUP), genomic relationships for genotyped animals only (GBLUP) and a Single‐Step approach (SSGBLUP) using both. For a scenario with no‐selection and random mating (RR), prediction was unbiased. However, lower accuracy and bias were observed for scenarios with selection and random mating (SR) or selection and positive assortative mating (SA). As expected, bias disappeared when all individuals were genotyped and used in GBLUP. SSGBLUP showed higher accuracy compared to GBLUP, and bias of prediction was negligible with SR. However, PBLUP and SSGBLUP still showed bias in SA due to high inbreeding. SSGBLUP and PBLUP were unbiased provided that inbreeding was accounted for in the relationship matrices. Selective genotyping based on extreme phenotypic contrasts increased the prediction accuracy, but prediction was biased when using GBLUP. SSGBLUP could correct the biasedness while gaining higher accuracy than GBLUP. In a typical animal breeding program, where it is too expensive to genotype all animals, it would be appropriate to genotype phenotypically contrasting selection candidates and use a Single‐Step approach to obtain accurate and unbiased prediction of GEBV.  相似文献   

12.
The genetic relationship among individuals at one locus is characterized by nine coefficients of identity. The coefficients of inbreeding, coancestry and dominance (or fraternity) are just linear functions of them. Here, it is shown how they can be estimated using biallelic and triallelic markers using the method of moments, and comparisons are made with other methods based on molecular coancestry or molecular covariance. It is concluded that in the general case of dominance and inbreeding with biallelic markers, only the coefficients of inbreeding and coancestry can be estimated, but neither the single coefficients of identity nor the coefficient of dominance can be estimated. More than two alleles are required for a full estimation as illustrated with the triallelic situation.  相似文献   

13.
Two strains of rabbits (strains 1077 and 2066) have been selected since 1974 for increased litter size. Each strain is split into a fixed number of reproduction groups. The mating scheme is similar to random non-sib herd mating. The number of animals per generation is higher in strain 1077 (28 mated bucks and 104 mated does) than in strain 2066 (17 and 59, respectively). The increase of the inbreeding coefficient is higher in strain 2066 than in strain 1077 (27 and 21%, respectively, at generation 20). The mean standard deviation of the individual inbreeding coefficients per generation is low (less than 4%) in both strains. Short-term inbreeding is stable over generations. The observed inbreeding effective size Ne f and the observed familial structure effective size Ne h converge to the same value. The number of founder genomes still present in the genetic pool of the generation decreases regularly: from 5.6 to 2.4 between G6 and G20 for strain 1077. It is a bit lower over time for strain 2066 (from 5.7 to 1.9 between G6 and G20). The effective number of founders is nearly twice as small as the total number: 30 for strain 1077 and 15 for strain 2066. The effective number of major ancestors decreases slightly in strain 1077 (13.6 in G6 and 12.9 in G20) and regularly in strain 2066 (13.8 in G6 and 9.4 in G20).  相似文献   

14.
Using pedigree data, the inbreeding coefficients of 715 Austrian dual‐purpose Simmental (Fleckvieh) bulls stationed in two artificial insemination (AI) centres in Upper and Lower Austria were calculated and incorporated in statistical models for the analysis of semen quality. Five semen quality parameters (volume, concentration, motility, number of spermatozoa per ejaculate and percentage of viable spermatozoa) of approximately 30 000 ejaculates, used in two separate data sets, were investigated. The mixed model included the fixed effects age class of the bull, bull handler, semen collector, month and year of collection, number of collection per bull and day, time interval since last collection, the linear continuous effect of the inbreeding coefficient of the bull, interactions between age class and month, and age class and interval since last collection, respectively, as well as the random effect of the bull and the random residual effect. Non‐linear effects of inbreeding were significant for motility only. Despite the quite low inbreeding coefficients (mean 1.3%), all semen quality traits showed inbreeding depression, in four of the five traits significantly in at least one of the data sets. The magnitude of inbreeding depression was small, which might partly be caused by the low inbreeding levels and a potential pre‐selection of the bulls in the AI centres. However, monitoring of inbreeding depression on fertility traits is recommended to avoid unrecognized deterioration of such traits.  相似文献   

15.
Polish Arabian horses are a good example of a small population derived from a finite number of founders. Pedigree analysis showed significant reduction in the genetic diversity of the population. However, taking into account some circumstances suggesting the presence of balancing selection favouring heterozygotes in Polish breeding, it seems that this referred to pedigree uniformity rather than to a real decrease in genetic variability. The aim of the current study was to verify the hypothesis that balancing selection affects the population. The mare selection process was examined in detail regarding the polymorphism of 10 protein markers. The findings confirmed the tendency to favour the more heterozygous mares with regard to average heterozygosity in total and in relation to particular loci, studs, fathers and inbreeding ranges. The results were discussed in consideration of selection criteria, inbreeding level of Polish Arabs and heterozygosity in other populations.  相似文献   

16.
Non-additive genetic effects are usually ignored in animal breeding programs due to data structure (e.g., incomplete pedigree), computational limitations and over-parameterization of the models. However, non-additive genetic effects may play an important role in the expression of complex traits in livestock species, such as fertility and reproduction traits. In this study, components of genetic variance for additive and non-additive genetic effects were estimated for a variety of fertility and reproduction traits in Holstein cattle using pedigree and genomic relationship matrices. Four linear models were used: (a) an additive genetic model; (b) a model including both additive and epistatic (additive by additive) genetic effects; (c) a model including both additive and dominance effects; and (d) a full model including additive, epistatic and dominance genetic effects. Nine fertility and reproduction traits were analysed, and models were run separately for heifers (N = 5,825) and cows (N = 6,090). For some traits, a larger proportion of phenotypic variance was explained by non-additive genetic effects compared with additive effects, indicating that epistasis, dominance or a combination thereof is of great importance. Epistatic genetic effects contributed more to the total phenotypic variance than dominance genetic effects. Although these models varied considerably in the partitioning of the components of genetic variance, the models including a non-additive genetic effect did not show a clear advantage over the additive model based on the Akaike information criterion. The partitioning of variance components resulted in a re-ranking of cows based solely on the cows’ additive genetic effects between models, indicating that adjusting for non-additive genetic effects could affect selection decisions made in dairy cattle breeding programs. These results suggest that non-additive genetic effects play an important role in some fertility and reproduction traits in Holstein cattle.  相似文献   

17.
Abstract

To examine the genetic variation in two endangered Norwegian horse breeds, the pedigree structures were investigated, and key parameters such as inbreeding coefficients, effective population size, effective number of founders, effective number of ancestors and effective number of founder genomes were calculated. The data consisted of 31,142 individuals of the D?le horse and 1973 individuals of the Nordland/Lyngen horse, for which the complete generation equivalent was 10.5 and 7.2, respectively. In both breeds, the pedigree data were more than 98.5% complete in the fourth generation, allowing the rate of inbreeding and the effective population size to be precisely estimated, actually measuring the fractional loss of heterozygosity, comparable across generations (not so for the other measures). The level of inbreeding was about 12% in both breeds, with a rather wavy pattern during the past 50 years in the D?le. Considering the last generations only, the effective population size was found to be 152 in the D?le and 42 in the Nordland/Lyngen. For both populations selection in the future should be based on optimal contribution.  相似文献   

18.
Inbreeding depression in closed populations impairs animal fitness, health, and productivity. However, not all inbreeding is expected to be equally damaging. Recent inbreeding is thought to be more harmful than ancient inbreeding because selection decreases the frequency of unfavourable alleles with time. Accordingly, selection efficiency is improved by inbreeding in a process called purging. This research aimed to quantify inbreeding depression on growth and prolificacy traits in two lines of rabbits selected for just one growth (Caldes line) or prolificacy (Prat line) trait, and also to find some evidence of purging of deleterious alleles by selection. Caldes line comprised 51 generations and 124,371 animals in the pedigree. Prat line comprised 34 generations and 161,039 animals in the pedigree. The effects of old, intermediate, and new inbreeding (Fold, Fint, and Fnew), as well as total cumulated classical inbreeding (F) and 3 measurements of ancestral inbreeding (AHC, Fa.K, and Fa.B) were estimated for average daily gain (ADG), slaughter weight (SW), weaning weight (WW), born alive (BA), the total number of kits (NT), and the number of weaned kits (NW). There was a clear inbreeding depression for all growth and prolificacy traits in the Caldes line (−7.19 g/d, −0.45 kg, −0.25 kg, −6 kits, −4 kits, and −4 kits per unit of increase in F for ADG, SW, WW, BA, NT, and NW, respectively) and also in Prat line (−7.48 g/d, −0.31 kg, −0.11 kg, −4 kits, −5 kits, and −4 kits per unit of increase in F for ADG, SW, WW, BA, NT, and NW, respectively). The inbreeding partition appears to be a reliable alternative for assessing inbreeding depression and purging. Thus, for example, in the Caldes line and for ADG the regression coefficients were −7.61, −5.41, and 7.76 g/d per unit of increase in Fnew, Fint, and Fold, respectively. In addition, AHC and Fa.B may provide more accurate evidence of purging than Fa.K. This study confirms the existence of inbreeding depression for growth and prolificacy traits in both lines of rabbits and shows evidence of purging of deleterious recessive alleles involved both in growth and prolificacy, independently of the selection criteria established in the line.  相似文献   

19.
The purpose of this study was to develop and investigate selection strategies that aim at maximizing long-term genetic response while conserving gene diversity and controlling inbreeding in populations of limited effective size, assuming complete knowledge of all genes affecting a quantitative trait. Three selection strategies were proposed to select on 100 quantitative trait loci (QTL) and compared with truncation selection on breeding value. Alternative selection strategies aimed at maximizing the average breeding value of parents with a penalty on (1) the number of unfavourable QTL genotypes among parents (OS-I), (2) the negative of the logarithm of the frequency of the favourable allele at each QTL among parents (OS-II), and (3) the average pedigree relationship among parents (OS-III). When all QTL and their effects were known, the strategies examined were able to obtain extra long-term responses, conserve QTL diversity and reduce inbreeding, compared with truncation selection. Strategy OS-II was the most effective in conserving QTL diversity and OS-III in reducing inbreeding. By changing the magnitude of the penalties applied, the impact on long-term response, inbreeding and diversity can be controlled. Extra long-term responses over truncation selection of OS-I and OS-II were even greater when effects of QTL were estimated rather than assumed known, indicating the applicability of results to practical strategies for marker-assisted selection. Extra responses are expected to be reduced for larger population sizes.  相似文献   

20.
旨在通过分析娄门鸭保种群体的遗传多样性和群体结构来评估保种效果。本研究在娄门鸭保种群中随机选择同一世代163只90日龄的健康个体(39公，124母)，翅静脉采血后提取基因组DNA，利用简化基因组测序技术检测全基因组范围内的单核苷酸多态性(SNPs); 利用R软件计算个体水平的多态信息含量(PIC)、固定指数(Fix-index)、香农信息指数(SHI)、基因多样性指数(Nei)、有效等位基因数(Ne)以及本研究自创的相对多态信息含量(rPIC)等6个遗传多样性指标，并比较分析了不同染色体水平的遗传多样性指标; 同时利用admixture软件分析群体遗传结构，gcta软件分析群体主成分和个体间的亲缘关系，并分析连续性纯合片段(runs of homozygosity，ROH)以及基因组近交系数FROH，评估保种效果。结果显示，163只娄门鸭个体共检测到622 205个SNPs位点，质控过滤后得到374 455个高质量SNPs位点，其中50.70%的位点分布在NC_040046、NC_040047、NC_040048和NC_040049四个染色体中。娄门鸭群体PIC、Nei、Ne、SHI和rPIC指标值分别为0.154 1、0.192 9、1.336、0.296 9和0.410 9，对于SNPs而言，该群体38.80%的SNPs位点属于高度多态性位点，遗传多样性较为丰富; Fix-index值为0.320 8，说明娄门鸭群体出现了分化，这与遗传结构、PCA和亲缘关系分析将娄门鸭群体划分为3个群体的结果一致。PIC、Nei、Ne和SHI四个指标分别在不同染色体上的分布规律均一致，且4个指标两两相关性均达到0.97以上，而Fix-index与其他4个指标的相关性较低，在0.23以下，说明可以选择Fix-index以及PIC等少数指标来评估娄门鸭群体的遗传多样性。163只娄门鸭个体共检测到2 966条ROH，ROH片段长度主要集中在0~2 Mb区间; 基于ROH得到的基因组近交系数FROH在公、母鸭中分别为0.027 5和0.043 3，说明娄门鸭保种群近交程度较低; 具体到染色体水平，NC_040068、NC_040074染色体的FROH值分别达到0.352 4和0.319 3。结果提示，娄门鸭保种群的遗传多样性较丰富，群体基因组近交系数较低，但个别染色体的近交系数较高，且群体出现了部分分化。后续保种中可以将遗传结构分析得到的3个分化的亚群个体之间进行适当的非随机交配，消除目前的群体分化现象，并重点监测染色体近交系数较高的基因组区域，避免个别染色体近交系数上升过快。  相似文献   

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