In the current research,we investigated the impact of gradually increasing inbreeding on the life span and reproductive rate of yellow steppe lemmings,Eolagurus luteus,that reproduced in the Moscow Zoo.The focal capti...In the current research,we investigated the impact of gradually increasing inbreeding on the life span and reproductive rate of yellow steppe lemmings,Eolagurus luteus,that reproduced in the Moscow Zoo.The focal captive colony existed from 2017 to 2021.The studied animals belonged to the second to tenth generations.The founders of the colony were 5 females and 5 males originating from 3 females and 4 males livetrapped in the Zaisan basin(Kazakhstan).The degree of their descendant relatedness progressively increased.The animals intended to be used for reproduction were distributed to pairs with unfamiliar partners.We constructed the pedigree of 177 individuals and calculated their inbreeding coefficients.This parameter varied from O to 0.29,and the maximum values were registered in the lemmings of the seventh to tenth generations.We measured the life span of 61 individuals and used information about the reproduction or its absence in 45 pairs.A substantial decline in individual life span and reproductive parameters in the breeding pairs,along with a progressive increase in the inbreeding coefficients,was registered.The number of delivered litters,born pups,and young lived up to the age of puberty significantly depended on the level of mother inbreeding.The noticeable traits of inbreeding depression in the colony appeared in 2019-2020 when the offspring inbreeding coefficients reached approximately 0.2.Therefore,we assume that if the E.luteus population originates from a relatively small number of noninbred and unfamiliar individuals,then successful reproduction without significant inbreeding depression will continue for several generations of offspring.展开更多
Inbreeding increases genome homozygosity within populations,which can exacerbate inbreeding depression by exposing homozygous deleterious alleles that are responsible for declines in fitness traits.In small population...Inbreeding increases genome homozygosity within populations,which can exacerbate inbreeding depression by exposing homozygous deleterious alleles that are responsible for declines in fitness traits.In small populations,genetic purging that occurs under the pressure of natural selection acts as an opposing force,contributing to a reduction of deleterious alleles.Both inbreeding and genetic purging are paramount in the field of conservation genomics.The Amur tiger(Panthera tigris altaica)lives in small populations in the forests of Northeast Asia and is among the most endangered animals on the planet.Using genome-wide assessment and comparison,we reveal substantially higher and more extensive inbreeding in wild Amur tigers(F_(ROH)=0.50)than in captive individuals(F_(ROH)=0.24).However,a relatively reduced number of lossof-function mutations in wild Amur tigers is observed compared to captive individuals,indicating genetic purging of inbreeding load with relatively large-effect alleles.The higher ratio of homozygous mutation load and number of fixed damaging alleles in the wild population indicates a less-efficient genetic purging,with purifying selection also contributing to this process.These findings provide valuable insights for the future conservation of Amur tigers.展开更多
Inbreeding usually reduces the mean phenotypic value of various traits.In Crassostrea gigas,inbreeding depression at the early life stage might be particularly remarkable because of a high mutational load that is diff...Inbreeding usually reduces the mean phenotypic value of various traits.In Crassostrea gigas,inbreeding depression at the early life stage might be particularly remarkable because of a high mutational load that is difficult to purge.In this study,the ef-fects of inbreeding on the survival rate and gene expression at the early life stage were investigated.Two inbred groups containing five F1 families and five F2 families with a theoretically higher degree of inbreeding were constructed based on an inbred strain.Meanwhile,5 families were established as the control group(CF)based on the wild population.The results showed that the survival rate of the CF group was significantly higher than those of the two inbred groups.Differential gene analysis showed 1616 common differentially expressed genes(DEGs)in the two inbred groups,which were significantly enriched in pathways associated with im-mune response,nutrient restriction,and virus infection.By weighted gene co-expression network analysis(WGCNA),19 common DEGs were enriched in M21,the functional module most closely related to inbreeding,and 6 of them were related to immunity.No-tably,the survival rate of F2 was higher than that of F1.A total of 643 DEGs between F1 and CF were screened out,which did not show differential expression between F2 and CF,and these genes were significantly enriched in pathways associated with protein syn-thesis.These results contribute to a more comprehensive understanding of the genetic mechanism behind the effect of inbreeding on the early survival rate of oyster larvae.展开更多
Indian mustard is recognized as a resilient and economically important oilseed crop.However,its potential remains untapped due to the limited availability of short-duration,high-yielding varieties capable of out-compe...Indian mustard is recognized as a resilient and economically important oilseed crop.However,its potential remains untapped due to the limited availability of short-duration,high-yielding varieties capable of out-competing other rabi crops.Considering this notion,we have evaluated twenty-one F_(2) and six BC1F1 populations derived from seven diversified parents of Brassica juncea following a Randomized Complete Block Design at Sher-e-Bangla Agricultural University.Based on key agronomic traits,the genetic components,heterosis,inbreeding depression,and gene action were studied to select early maturing and high-yielding populations.The percentage of heterosis was manifested in various cross-combinations,including P4×P6(91.45%for yield per plant)and P5×P6(28.52%for thousand seed weight),emerging as promising candidates for increasing productivity while managing negative inbreeding effects.Conversely,significant inbreeding depression was noted in traits like days to siliquae maturity and yield,particularly in crosses,P1×P2(6.29%)and P3×P5(21.74%),underscoring the need for careful selection in breeding programs to mitigate these effects.Variance analysis indicated that both additive and non-additive genetic interactions play a pivotal role in the inheritance patterns of the traits of interest.Among the six backcrosses,one promising line was(P5×P6)×P5,demonstrating early maturity(107.00 DAS)with improved seed yield(12.47 g).This combination exhibited the potential for enhancing the adaptability and productivity by maintaining the maturity index and accelerating yield.Furthermore,significant phenotypic variation across yield-contributing traits was notable,whereas thousand seed weight and yield per plant showed high broad-sense and narrow-sense of heritability.Besides,positive correlations between seed yield and its attributing traits were noted,suggesting potential avenues for selection breeding.Collectively,the ob-tained findings enhance the understanding of genetic mechanisms underlying heterosis and inbreeding depres-sion in B.juncea,providing insights and effective strategies for developing superior cultivars with optimized agronomic traits.展开更多
Genetic load and inbreeding are recognized as important factors to be considered in conservation programs.Elevated levels of both can increase the risk of population extinction by negatively impacting fitness-related ...Genetic load and inbreeding are recognized as important factors to be considered in conservation programs.Elevated levels of both can increase the risk of population extinction by negatively impacting fitness-related characters in many species of plants and animals,including humans(inbreeding depression).Genomic tech-niques are increasingly used in measuring and understanding genetic load and inbreeding and their importance in evolution and conservation.We used whole genome resequencing data from two sibling grouse species in subarctic Eurasia to quantify both.We found a large range of inbreeding measured as FROH(fraction of runs of homozygosity)in individuals from different populations of Chinese Grouse(Tetrastes sewerzowi)and Hazel Grouse(T.bonasia).FROH estimated from genome-wide runs of homozygosity(ROH)ranged from 0.02 to 0.24 among Chinese Grouse populations and from 0.01 to 0.44 in Hazel Grouse.Individuals from a population of Chinese Grouse residing in the Qilian mountains and from the European populations of Hazel Grouse(including samples from Sweden,Germany and Northeast Poland)were the most inbred(FROH ranged from 0.10 to 0.23 and 0.11 to 0.44,respectively).These levels are comparable to other highly inbred populations of birds.Hazel Grouse from northern China and Chinese Grouse residing in the Qinghai-Tibetan Plateau showed relatively lower inbreeding levels.Comparisons of the ratio between deleterious missense mutations and synonymous mutations revealed higher levels in Chinese Grouse as compared to Hazel Grouse.These results are possibly explained by higher fixation rates,mutational melt down,in the range-restricted Chinese Grouse compared to the wide-ranging Hazel Grouse.However,when we compared the relatively more severe class of loss-of-function muta-tions,Hazel Grouse had slightly higher levels than Chinese Grouse,a result which may indicate that purifying selection(purging)has been more efficient in Chinese Grouse on this class of mutations.展开更多
With F1 of self pollinated Eucalyptus urophylla, F1 of inter tree pollinated E.urophylla, F1of open pollinated E.urophylla and F1 of E.urophylla×grandis as materials,inbreeding depression and hy...With F1 of self pollinated Eucalyptus urophylla, F1 of inter tree pollinated E.urophylla, F1of open pollinated E.urophylla and F1 of E.urophylla×grandis as materials,inbreeding depression and hybrid superiority in growth and wood traits are analyzed and discussed.The results are as follows.①There was a regularity for E.urophylla that F1 of self pollinated was subjected to more intense depression than F1 of open pollinated,and growth traits showed more signifcant depression than wood traits.②As to F1 of self pollinated E.urophylla, height,DBH and volume showed significant or extremely significant depression,while water content of green wood,wood density and bark thickness showed no significant depression.③As to F1 of open pollinated E.urophylla, height,DBH and volume showed depression to a certain degree,but not significant;Here again,water content of green wood,wood density and bark thickness showed no significant depression.④F1 of E.urophylla×grandis showed significant hybrid superiority in height,DBH and volume,but the hybrid superiority percentage of different cross pairs varied greatly;It showed no hybrid superiority in water content of green wood,wood density and fiber length;Its bark thickness and content of 1% NaOH extractives decreased evidently.展开更多
Background:Estimating inbreeding,which is omnipresent and inevitable in livestock populations,is a primary goal for management and animal breeding especially for those interested in mitigating the negative consequence...Background:Estimating inbreeding,which is omnipresent and inevitable in livestock populations,is a primary goal for management and animal breeding especially for those interested in mitigating the negative consequences of inbreeding.Inbreeding coefficients have been historically estimated by using pedigree information;however,over the last decade,genome-base inbreeding coefficients have come to the forefront in this field.The Pura Raza Espanola(PRE)horse is an autochthonous Spanish horse breed which has been recognised since 1912.The total PRE population(344,718 horses)was used to estimate Classical(F),Ballou’s ancestral,Kalinowski’s ancestral,Kalinowski’s new and the ancestral history coefficient values.In addition,genotypic data from a selected population of 805 PRE individuals was used to determine the individual inbreeding coefficient using SNP-by-SNP-based techniques(methods of moments-FHOM-,the diagonal elements of the genomic-FG-,and hybrid matrixes-FH-)and ROH measures(FRZ).The analyse of both pedigree and genomic based inbreeding coefficients in a large and robust population such as the PRE horse,with proven parenteral information for the last 40 years and a high degree of completeness(over 90%for the last 70 years)will allow us to understand PRE genetic variability better and the correlations between the estimations will give the data greater reliability.Results:The mean values of the pedigree-based inbreeding coefficients ranged from 0.01(F for the last 3 generations-F3-)to 0.44(ancestral history coefficient)and the mean values of genomic-based inbreeding coefficients varied from 0.05(FRZ for three generations,FH and FHOM)to 0.11(FRZ for nine generations).Significant correlations were also found between pedigree and genomic inbreeding values,which ranged between 0.58(F3 with FHOM)and 0.79(F with FRZ).In addition,the correlations between FRZ estimated for the last 20 generations and the pedigree-based inbreeding highlight the fact that fewer generations of genomic data are required when comparing total inbreeding values,and the opposite when ancient values are calculated.Conclusions:Ultimately,our results show that it is still useful to work with a deep and reliable pedigree in pedigreebased genetic studies with very large effective population sizes.Obtaining a satisfactory parameter will always be desirable,but the approximation obtained with a robust pedigree will allow us to work more efficiently and economically than with massive genotyping.展开更多
Authors conducted pollination experiments and genetic analyses using microsatellite loci for a natural population of a shrub species,Magnolia salicifolia,in a secondary Japanese beech forest in Hakkoda mountains,north...Authors conducted pollination experiments and genetic analyses using microsatellite loci for a natural population of a shrub species,Magnolia salicifolia,in a secondary Japanese beech forest in Hakkoda mountains,northern Japan,to analyze inbreeding and inbreeding depression that involve sexual reproduction and population genetic structure of the species.The pollination experiments revealed that self-fertilization through geitonogamy is possible and that the magnitude of inbreeding depression(δ)at the embryonic stage is substantial(δ=0.42),suggesting that the inbreeding depression due to self-fertilization decreases seed production of the natural population.The genetic analyses showed discrepancy in the level of inbreeding between life history stages:the inbreeding coefficient for the juvenile and adult stage was 0.17 and 0.01,respectively,implying that most of inbred progenies cannot grow to the adult stage in the population,since the cumulative inbreeding depression is severe.These results are consistent with the hypothesis that explains mechanisms causing stable maintenance of severe inbreeding depression in partially inbred populations by focusing on the selective interference among deleterious mutations.It is suggested that some reproductive traits facilitating outcrossing in the species would be attributed to the severe cumulative inbreeding depression.展开更多
Background: Runs of homozygosity(ROHs) are homozygous segments of the genome where the two haplotypes inherited from the parents are identical. The current availability of genotypes for a very large number of single n...Background: Runs of homozygosity(ROHs) are homozygous segments of the genome where the two haplotypes inherited from the parents are identical. The current availability of genotypes for a very large number of single nucleotide polymorphisms(SNPs) is leading to more accurate characterization of ROHs in the whole genome. Here,we investigated the occurrence and distribution of ROHs in 3,692 Large White pigs and compared estimates of inbreeding coefficients calculated based on ROHs(FROH), homozygosity(FHOM), genomic relationship matrix(FGRM)and pedigree(FPED). Furthermore, we identified genomic regions with high ROH frequencies and annotated their candidate genes.Results: In total, 176,182 ROHs were identified from 3,569 animals, and all individuals displayed at least one ROH longer than 1 Mb. The ROHs identified were unevenly distributed on the autosomes. The highest and lowest coverages of Sus scrofa chromosomes(SSC) by ROH were on SSC14 and SSC13, respectively. The highest pairwise correlation among the different inbreeding coefficient estimates was 0.95 between FROH_totaland FHOM, while the lowest was-0.083 between FGRMand FPED. The correlations between FPEDand FROHusing four classes of ROH lengths ranged from 0.18 to 0.37 and increased with increasing ROH length, except for ROH > 10 Mb. Twelve ROH islands were located on four chromosomes(SSC1, 4, 6 and 14). These ROH islands harboured genes associated with reproduction, muscular development, fat deposition and adaptation, such as SIRT1, MYPN, SETDB1 and PSMD4.Conclusion: FROHcan be used to accurately assess individual inbreeding levels compared to other inbreeding coefficient estimators. In the absence of pedigree records, FROHcan provide an alternative to inbreeding estimates.Our findings can be used not only to effectively increase the response to selection by appropriately managing the rate of inbreeding and minimizing the negative effects of inbreeding depression but also to help detect genomic regions with an effect on traits under selection.展开更多
Background Genomic selection involves choosing as parents those elite individuals with the higher genomic estimated breeding values(GEBV)to accelerate the speed of genetic improvement in domestic animals.But after mul...Background Genomic selection involves choosing as parents those elite individuals with the higher genomic estimated breeding values(GEBV)to accelerate the speed of genetic improvement in domestic animals.But after multi-generation selection,the rate of inbreeding and the occurrence of homozygous harmful alleles might increase,which would reduce performance and genetic diversity.To mitigate the above problems,we can utilize genomic mating(GM)based upon optimal mate allocation to construct the best genotypic combinations in the next generation.In this study,we used stochastic simulation to investigate the impact of various factors on the efficiencies of GM to optimize pairing combinations after genomic selection of candidates in a pig population.These factors included:the algorithm used to derive inbreeding coefficients;the trait heritability(0.1,0.3 or 0.5);the kind of GM scheme(focused average GEBV or inbreeding);the approach for computing the genomic relationship matrix(by SNP or runs of homozygosity(ROH)).The outcomes were compared to three traditional mating schemes(random,positive assortative or negative assortative matings).In addition,the performance of the GM approach was tested on real datasets obtained from a Large White pig breeding population.Results Genomic mating outperforms other approaches in limiting the inbreeding accumulation for the same expected genetic gain.The use of ROH-based genealogical relatedness in GM achieved faster genetic gains than using relatedness based on individual SNPs.The GROH-based GM schemes with the maximum genetic gain resulted in 0.9%-2.6%higher rates of genetic gainΔG,and 13%-83.3%lowerΔF than positive assortative mating regardless of heritability.The rates of inbreeding were always the fastest with positive assortative mating.Results from a purebred Large White pig population,confirmed that GM with ROH-based GRM was more efficient than traditional mating schemes.Conclusion Compared with traditional mating schemes,genomic mating can not only achieve sustainable genetic progress but also effectively control the rates of inbreeding accumulation in the population.Our findings demonstrated that breeders should consider using genomic mating for genetic improvement of pigs.展开更多
In present study, the inbreeding depression(ID) of growth and survival of Manila clam(Ruditapes philippinarum) was investigated at larval and juvenile stages. Nine inbred families(A_2, B_2, C_2, D_2, E_2, F_2, G_2, H_...In present study, the inbreeding depression(ID) of growth and survival of Manila clam(Ruditapes philippinarum) was investigated at larval and juvenile stages. Nine inbred families(A_2, B_2, C_2, D_2, E_2, F_2, G_2, H_2 and I_2) were established by mating within nine full-sib families with expected inbreeding coefficient of 0.25. Inbred families showed significant differences in shell length and hatching rate of D-larvae(straight-hinged larvae). The larvae of the nine inbred families grew slower than those of control group(CG), and their ID value ranged from 0.81% ± 6.09% to 16.10% ± 1.49%. The ID value of larval survival rate varied between 27.47% ± 9.36% and 70.50% ± 13.66%. The ID was also detected for juvenile growth in A_2, B_2, C_2, and D_2, which ranged from 4.60 ± 2.21 to 17.71 ± 7.73. The A_2 family maintained the highest juvenile survival rate, whereas the other inbred families exhibited ID values varying between 62.79% ± 4.54% and 96.14% ± 0.87%. The linear relationship of estimated ID between growth and survival was negatively correlated(R =-0.434, P < 0.05). The results of this study suggested that the ID of growth was common at the larval stage but was less prevalent at juvenile stage. In contrast, the ID of survival increased from larval to juvenile stage. A better understanding of the effect of inbreeding may aid to selective breeding of Manila clam.展开更多
The genetic basis of heterosis was studied through mid-parent, standard variety and better parent for 11 quantitative traits in 17 parental lines and their 10 selected hybrids in rice (Oryza sativa L.).The characters ...The genetic basis of heterosis was studied through mid-parent, standard variety and better parent for 11 quantitative traits in 17 parental lines and their 10 selected hybrids in rice (Oryza sativa L.).The characters were plant height,days to flag leaf initiation, days to first panicle initiation, days to 100% flowering, panicle length,flag leaf length, days to maturity, number of fertile spikelet/panicle, number of effective tillers/hill, grain yield/10-hill, and 1000-grain weight.In general the hybrids performed significantly better than the respective parents.Significant heterosis was observed for most of the studied characters. Among the 10 hybrids, four hybrids viz., 17A×45R,25A×37R,27A×39R,31A×47R,and 35A×47R showed highest heterosis in 10-hill grain yield/10-hill. Inbreeding depression of F2 progeny was also studied for 11 characters of 10 hybrids.Both positive and negative inbreeding depression were found in many crosses for the studied characters,but none was found significant. Selection of good parents was found to be the most important for developing high yielding hybrid rice varieties.展开更多
The population characteristics of distylous species are highly sensitive to stochastic natural selection pressure.Therefore,populations growing under different environmental conditions may vary in floral morph ratios,...The population characteristics of distylous species are highly sensitive to stochastic natural selection pressure.Therefore,populations growing under different environmental conditions may vary in floral morph ratios,potentially affecting female fitness and leading to inbreeding depression.However,the variation in offspring quality among populations as a result of inbreeding depression is poorly understood in distylous species.This study investigates variations in plant density,seed mass,seed viabilityfemale fitness,and post-dispersal inbreeding depression in both sexual morphs(long-styled and shortstyled plants)of the distylous Primula nivalis that were subjected to different pollination treatments along an elevational gradient from 1657 to 2704 m a.s.l.Population characteristics(morph plant density and ratio)and fruit set were significantly affected by sexual morph and elevation.Plant density and fruitset frequencies were lower for short-styled than for long-styled plants at 2704 m a.s.l.The seeds from the cross-pollinated flowers of both morphs were higher in quality than those of self-pollinated flowers.The female fitness of seeds from cross-pollinated flowers of both morphs was higher than that of seeds from open-pollinated and self-pollinated flowers.The female fitness of seeds from long-styled flowers was higher than that of seeds from short-styled flowers at all elevations.Inbreeding depression increased with elevation among plants with short-styled flowers but not among those with long-styled flowers.Variation in the elevation-dependent mating system might influence female fitness and affect inbreeding depression in both floral morphs.In conclusion,the low quality of seeds from short-styled flowers at high elevations might decrease short-styled flower frequency,affecting population characteristics.展开更多
Background:A run of homozygosity(ROH)is a consecutive tract of homozygous genotypes in an individual that indicates it has inherited the same ancestral haplotype from both parents.Genomic inbreeding can be quantified ...Background:A run of homozygosity(ROH)is a consecutive tract of homozygous genotypes in an individual that indicates it has inherited the same ancestral haplotype from both parents.Genomic inbreeding can be quantified based on ROH.Genomic regions enriched with ROH may be indicative of selection sweeps and are known as ROH islands.We carried out ROH analyses in five Chinese indigenous sheep breeds;Altay sheep(n=50 individuals),Large-tailed Han sheep(n=50),Hulun Buir sheep(n=150),Short-tailed grassland sheep(n=150),and Tibetan sheep(n=50),using genotypes from an Ovine Infinium HD SNP BeadChip.Results:A total of 18,288 ROH were identified.The average number of ROH per individual across the five sheep breeds ranged from 39(Hulun Buir sheep)to 78(Large-tailed Han sheep)and the average length of ROH ranged from 0.929 Mb(Hulun Buir sheep)to 2.544 Mb(Large-tailed Han sheep).The effective population size(Ne)of Altay sheep,Large-tailed Han sheep,Hulun Buir sheep,Short-tailed grassland sheep and Tibetan sheep were estimated to be 81,78,253,238 and 70 five generations ago.The highest ROH-based inbreeding estimate(FROH)was 0.0808 in Large-tailed Han sheep,whereas the lowest F_(ROH)was 0.0148 in Hulun Buir sheep.Furthermore,the highest proportion of long ROH fragments(>5 Mb)was observed in the Large-tailed Han sheep breed which indicated recent inbreeding.In total,49 ROH islands(the top 0.1% of the SNPs most commonly observed in ROH)were identified in the five sheep breeds.Three ROH islands were common to all the five sheep breeds,and were located on OAR2:12.2-12.3 Mb,OAR12:78.4-79.1 Mb and OAR13:53.0-53.6 Mb.Three breed-specific ROH islands were observed in Altay sheep(OAR15:3.4-3.8 Mb),Large-tailed Han sheep(ORA17:53.5-53.8 Mb)and Tibetan sheep(ORA5:19.8-20.2 Mb).Collectively,the ROH islands harbored 78 unique genes,including 19 genes that have been documented as having associations with tail types,adaptation,growth,body size,reproduction or immune response.Conclusion:Different ROH patterns were observed in five Chinese indigenous sheep breeds,which reflected their different population histories.Large-tailed Han sheep had the highest genomic inbreeding coefficients and the highest proportion of long ROH fragments indicating recent inbreeding.Candidate genes in ROH islands could be used to illustrate the genetic characteristics of these five sheep breeds.Our findings contribute to the understanding of genetic diversity and population demography,and help design and implement breeding and conservation strategies for Chinese sheep.展开更多
Background:Inbreeding in seed orchards is expected to increase with the advancement of breeding cycles,which results in the delivery of crops with suboptimal genetic gain,reduced genetic diversity,and lower seed set.H...Background:Inbreeding in seed orchards is expected to increase with the advancement of breeding cycles,which results in the delivery of crops with suboptimal genetic gain,reduced genetic diversity,and lower seed set.Here,a genetic distance-dependent method for clonal spatial deployment in seed orchards was developed and demonstrated,which reduced the inbreeding levels.The method’s main evaluation parameter of inbreeding is the genetic distance among individuals and the deployment method used an improved adaptive parallel genetic algorithm(IAPGA)based on Python language.Using inbreeding-prone Chinese Mongolian pine breeding population material originating from a single natural population,the proposed method was compared to a traditional orchard design and a distance-based design;namely,complete randomized block(RCB)and optimum neighborhood(ONA)designs,respectively.Results:With the advancement of selective breeding cycles,group separation among orchard related individuals is expected to increase.Based on the genetic distance among individuals,the IAPGA design was superior in significantly reducing the inbreeding level as compared to the two existing designs,confirming its suitability to advanced-generation orchards where relatedness among parents is common.In the 1st,2nd,and mixed generations clonal deployment schemes,the IAPGA design produced lower inbreeding with 87.22%,81.49%,and 87.23%of RCB,and 92.78%,91.30%,and 91.67%of ONA designs,respectively.Conclusions:The IAPGA clonal deployment proposed in this study has the obvious advantage of controlling inbreeding,and it is expected to be used in clonal deployment in seed orchards on a large-scale.Further studies are needed to focus on the actual states of pollen dispersal and mating in seed orchards,and more assumptions should be taken into account for the optimized deployment method.展开更多
Ten microsatellite markers were used to analyze the levels of genetic diversity and inbreeding in a hatchery release population of Rhopilema esculentum Kishinouye （Scypbozoa： Rhizostomatidae）. A total of 85 alleles...Ten microsatellite markers were used to analyze the levels of genetic diversity and inbreeding in a hatchery release population of Rhopilema esculentum Kishinouye （Scypbozoa： Rhizostomatidae）. A total of 85 alleles were detected in 600 individuals. Within-population levels of observed （Ho） and expected （He） heterozygosity ranged from 0.152 to 0.839 （mean=0.464） and from 0.235 to 0.821 （mean=0.618）, respectively. The polymorphism information content （PIC） of each marker ranged from 0.207 to 0.795 with an average of 0.580, indicating that the hatchery population maintained a high level of genetic diversity. Inbreeding levels were estimated in the hatchery population and the inbreeding coefficient was 0.203. This result revealed that a certain level of inbreeding occurred within the population. Meanwhile, we also determined genetic diversity at the clone level. Several polyps from the same scyphistomae were genotyped at the ten microsatellite loci and there was virtually no difference in their genotypes. Furthermore, we calculated the probabilities of exclusion. When both parents were known, the average exclusion probability often loci was 99.99%. Our data suggest that the ten microsatellite markers can not only be used to analyze the identity of individuals but they can also be applied to parentage identification. Our research provides a theoretical basis and technical support for genetic diversity detection and reasonable selection of R. esculentum hatchery populations. These findings support the use of releasing studies and conservation of R. esculentum germplasm resources.展开更多
Background:Inbreeding depression can adversely affect traits related to fitness,reproduction and productive performance.Although current research suggests that inbreeding levels are generally low in most goat breeds,t...Background:Inbreeding depression can adversely affect traits related to fitness,reproduction and productive performance.Although current research suggests that inbreeding levels are generally low in most goat breeds,the impact of inbreeding depression on phenotypes of economic interest has only been investigated in a few studies based on genealogical data.Results:We genotyped 1040 goats with the Goat SNP50 BeadChip.This information was used to estimate different molecular inbreeding coefficients and characterise runs of homozygosity and homozygosity patterns.We detected38 genomic regions with increased homozygosity as well as 8 ROH hotspots mapping to chromosomes 1,2,4,6,14,16 and 17.Eight hundred seventeen goats with available records for dairy traits were analysed to evaluate the potential consequences of inbreeding depression on milk phenotypes.Four regions on chromosomes 8 and 25were significantly associated with inbreeding depression for the natural logarithm of the somatic cell count.Notably,these regions contain several genes related with immunity,such as SYK,IL27,CCL19 and CCL21.Moreover,one region on chromosome 2 was significantly associated with inbreeding depression for milk yield.Conclusions:Although genomic inbreeding levels are low in Murciano-Granadina goats,significant evidence of inbreeding depression for the logarithm of the somatic cell count,a phenotype closely associated with udder health and milk yield,have been detected in this population.Minimising inbreeding would be expected to augment economic gain by increasing milk yield and reducing the incidence of mastitis,which is one of the main causes of dairy goat culling.展开更多
Island species and their ecosystems play an important role in global biodiversity preservation,and many vulnerable island species are conservation priorities.Although insular habitat likely facilitates the species div...Island species and their ecosystems play an important role in global biodiversity preservation,and many vulnerable island species are conservation priorities.Although insular habitat likely facilitates the species diversification process,it may also aggravate the fragility of these species with high risk of inbreeding.The Shedao pit-viper Gloydius shedaoensis is an island endemic species with an extremely high population density,which has been categorized as vulnerable in the IUCN(International Union for the Conservation of Nature and Natural Resources)Red List.We collected 13,148 SNP(Single Nucleotide Polymorphism)from across its genome and examined its genetic diversity and demographic history.The Shedao pit-viper has a low genetic diversity but shows no sign of inbreeding.Furthermore,population genetic structure analysis,including the neighbor-joining tree,principal coordinate analysis,clustering,and spatial autocorrelation,revealed a general lack of spatial structure.Only the isolation by distance residues suggested a weak patchiness.Overall,the population is nearly panmictic and gene flow is evenly distributed across the island.A large number of individuals,small size of the island,and the lack of population structure likely all contribute to the lack of inbreeding in this species.We also detected signs of male-biased dispersal,which likely is another inbreeding avoidance strategy.Historical demographic analysis suggested that the historical population size and distribution of the species are much larger than their current ones.The multiple transgressive–regressive events since the Late Pleistocene are likely the main cause of the population size changes.Taken together,our results provide a basic scientific foundation for the conservation of this interesting and important species.展开更多
To elucidate the structure of SLA-3 alleles on inbred line of Wuzhishan pig （WZSP） population, we examined the partial exon 1, completed exon 2, and partial exon 3 of SLA-3 loci using the reverse transcription-polym...To elucidate the structure of SLA-3 alleles on inbred line of Wuzhishan pig （WZSP） population, we examined the partial exon 1, completed exon 2, and partial exon 3 of SLA-3 loci using the reverse transcription-polymerase chain reaction （RT- PCR） and the sequencing-based method in 32 WZSPs. According to pedigree and amplification results, PCR products of 8 WZSPs were selected to clone and sequence. Nine different nucleotide sequences were obtained. After comparing the DNA and protein sequences of the WZSPs SLA-3 alleles with the published GenBank SLA sequences, it was found that the SLA-3 alleles in WZSPs were all novel, but there were very few variations among them. Comparision of SLA-3 and HLA-A protein sequences indicated that there was more sequence homology. Meanwhile, the construction of a phylogenetic tree using the nucleotide sequences of 23 SLA-3 alleles and 1 HLA-A allele represented that the WZSP population owns its unique genetics resource. In this study, the alleles of SLA-3 on WZSP group were successfully detected and analyzed, which provided the firm basis on the genotype of SLA-3 for breeding specific haplotypes WZSPs.展开更多
基金carried out within the framework of the theme of a State Assignment of the Severtsov Institute of Ecology and Evolution,Russian Academy of Sciences,"Ecological and Evolutionary Aspects of Animal Behavior and Communication,"project no.AAAA-A18-118042690110-1.
文摘In the current research,we investigated the impact of gradually increasing inbreeding on the life span and reproductive rate of yellow steppe lemmings,Eolagurus luteus,that reproduced in the Moscow Zoo.The focal captive colony existed from 2017 to 2021.The studied animals belonged to the second to tenth generations.The founders of the colony were 5 females and 5 males originating from 3 females and 4 males livetrapped in the Zaisan basin(Kazakhstan).The degree of their descendant relatedness progressively increased.The animals intended to be used for reproduction were distributed to pairs with unfamiliar partners.We constructed the pedigree of 177 individuals and calculated their inbreeding coefficients.This parameter varied from O to 0.29,and the maximum values were registered in the lemmings of the seventh to tenth generations.We measured the life span of 61 individuals and used information about the reproduction or its absence in 45 pairs.A substantial decline in individual life span and reproductive parameters in the breeding pairs,along with a progressive increase in the inbreeding coefficients,was registered.The number of delivered litters,born pups,and young lived up to the age of puberty significantly depended on the level of mother inbreeding.The noticeable traits of inbreeding depression in the colony appeared in 2019-2020 when the offspring inbreeding coefficients reached approximately 0.2.Therefore,we assume that if the E.luteus population originates from a relatively small number of noninbred and unfamiliar individuals,then successful reproduction without significant inbreeding depression will continue for several generations of offspring.
基金supported by the Fundamental Research Funds for the Central Universities of China(2572022DQ03)the National Natural Science Foundation of China(32170517)+2 种基金the Guangdong Provincial Key Laboratory of Genome Read and Write(2017B030301011)the Start-up Scientific Foundation of Northeast Forestry University(60201524043)supported by China National GeneBank(CNGB).
文摘Inbreeding increases genome homozygosity within populations,which can exacerbate inbreeding depression by exposing homozygous deleterious alleles that are responsible for declines in fitness traits.In small populations,genetic purging that occurs under the pressure of natural selection acts as an opposing force,contributing to a reduction of deleterious alleles.Both inbreeding and genetic purging are paramount in the field of conservation genomics.The Amur tiger(Panthera tigris altaica)lives in small populations in the forests of Northeast Asia and is among the most endangered animals on the planet.Using genome-wide assessment and comparison,we reveal substantially higher and more extensive inbreeding in wild Amur tigers(F_(ROH)=0.50)than in captive individuals(F_(ROH)=0.24).However,a relatively reduced number of lossof-function mutations in wild Amur tigers is observed compared to captive individuals,indicating genetic purging of inbreeding load with relatively large-effect alleles.The higher ratio of homozygous mutation load and number of fixed damaging alleles in the wild population indicates a less-efficient genetic purging,with purifying selection also contributing to this process.These findings provide valuable insights for the future conservation of Amur tigers.
基金supported by grants from the National Natural Science Foundation of China(Nos.W2411019 and 32373115)the China Agriculture Research System Project(No.CARS-49)the Laoshan Laboratory.
文摘Inbreeding usually reduces the mean phenotypic value of various traits.In Crassostrea gigas,inbreeding depression at the early life stage might be particularly remarkable because of a high mutational load that is difficult to purge.In this study,the ef-fects of inbreeding on the survival rate and gene expression at the early life stage were investigated.Two inbred groups containing five F1 families and five F2 families with a theoretically higher degree of inbreeding were constructed based on an inbred strain.Meanwhile,5 families were established as the control group(CF)based on the wild population.The results showed that the survival rate of the CF group was significantly higher than those of the two inbred groups.Differential gene analysis showed 1616 common differentially expressed genes(DEGs)in the two inbred groups,which were significantly enriched in pathways associated with im-mune response,nutrient restriction,and virus infection.By weighted gene co-expression network analysis(WGCNA),19 common DEGs were enriched in M21,the functional module most closely related to inbreeding,and 6 of them were related to immunity.No-tably,the survival rate of F2 was higher than that of F1.A total of 643 DEGs between F1 and CF were screened out,which did not show differential expression between F2 and CF,and these genes were significantly enriched in pathways associated with protein syn-thesis.These results contribute to a more comprehensive understanding of the genetic mechanism behind the effect of inbreeding on the early survival rate of oyster larvae.
基金funded by Bangladesh Academy of Sciences(BAS),and Fund ID:BAS-USDA SAU CR02.
文摘Indian mustard is recognized as a resilient and economically important oilseed crop.However,its potential remains untapped due to the limited availability of short-duration,high-yielding varieties capable of out-competing other rabi crops.Considering this notion,we have evaluated twenty-one F_(2) and six BC1F1 populations derived from seven diversified parents of Brassica juncea following a Randomized Complete Block Design at Sher-e-Bangla Agricultural University.Based on key agronomic traits,the genetic components,heterosis,inbreeding depression,and gene action were studied to select early maturing and high-yielding populations.The percentage of heterosis was manifested in various cross-combinations,including P4×P6(91.45%for yield per plant)and P5×P6(28.52%for thousand seed weight),emerging as promising candidates for increasing productivity while managing negative inbreeding effects.Conversely,significant inbreeding depression was noted in traits like days to siliquae maturity and yield,particularly in crosses,P1×P2(6.29%)and P3×P5(21.74%),underscoring the need for careful selection in breeding programs to mitigate these effects.Variance analysis indicated that both additive and non-additive genetic interactions play a pivotal role in the inheritance patterns of the traits of interest.Among the six backcrosses,one promising line was(P5×P6)×P5,demonstrating early maturity(107.00 DAS)with improved seed yield(12.47 g).This combination exhibited the potential for enhancing the adaptability and productivity by maintaining the maturity index and accelerating yield.Furthermore,significant phenotypic variation across yield-contributing traits was notable,whereas thousand seed weight and yield per plant showed high broad-sense and narrow-sense of heritability.Besides,positive correlations between seed yield and its attributing traits were noted,suggesting potential avenues for selection breeding.Collectively,the ob-tained findings enhance the understanding of genetic mechanisms underlying heterosis and inbreeding depres-sion in B.juncea,providing insights and effective strategies for developing superior cultivars with optimized agronomic traits.
基金funded by the National Natural Science Foundation of China(NSFC,Grant No.31520103903 to Y.-H.Sun and J.Hoglund)the Biodiversity Conservation Project of the Second Forest and Grass Ecosystem Recovery(Grant No.QHTX-2021-016).
文摘Genetic load and inbreeding are recognized as important factors to be considered in conservation programs.Elevated levels of both can increase the risk of population extinction by negatively impacting fitness-related characters in many species of plants and animals,including humans(inbreeding depression).Genomic tech-niques are increasingly used in measuring and understanding genetic load and inbreeding and their importance in evolution and conservation.We used whole genome resequencing data from two sibling grouse species in subarctic Eurasia to quantify both.We found a large range of inbreeding measured as FROH(fraction of runs of homozygosity)in individuals from different populations of Chinese Grouse(Tetrastes sewerzowi)and Hazel Grouse(T.bonasia).FROH estimated from genome-wide runs of homozygosity(ROH)ranged from 0.02 to 0.24 among Chinese Grouse populations and from 0.01 to 0.44 in Hazel Grouse.Individuals from a population of Chinese Grouse residing in the Qilian mountains and from the European populations of Hazel Grouse(including samples from Sweden,Germany and Northeast Poland)were the most inbred(FROH ranged from 0.10 to 0.23 and 0.11 to 0.44,respectively).These levels are comparable to other highly inbred populations of birds.Hazel Grouse from northern China and Chinese Grouse residing in the Qinghai-Tibetan Plateau showed relatively lower inbreeding levels.Comparisons of the ratio between deleterious missense mutations and synonymous mutations revealed higher levels in Chinese Grouse as compared to Hazel Grouse.These results are possibly explained by higher fixation rates,mutational melt down,in the range-restricted Chinese Grouse compared to the wide-ranging Hazel Grouse.However,when we compared the relatively more severe class of loss-of-function muta-tions,Hazel Grouse had slightly higher levels than Chinese Grouse,a result which may indicate that purifying selection(purging)has been more efficient in Chinese Grouse on this class of mutations.
文摘With F1 of self pollinated Eucalyptus urophylla, F1 of inter tree pollinated E.urophylla, F1of open pollinated E.urophylla and F1 of E.urophylla×grandis as materials,inbreeding depression and hybrid superiority in growth and wood traits are analyzed and discussed.The results are as follows.①There was a regularity for E.urophylla that F1 of self pollinated was subjected to more intense depression than F1 of open pollinated,and growth traits showed more signifcant depression than wood traits.②As to F1 of self pollinated E.urophylla, height,DBH and volume showed significant or extremely significant depression,while water content of green wood,wood density and bark thickness showed no significant depression.③As to F1 of open pollinated E.urophylla, height,DBH and volume showed depression to a certain degree,but not significant;Here again,water content of green wood,wood density and bark thickness showed no significant depression.④F1 of E.urophylla×grandis showed significant hybrid superiority in height,DBH and volume,but the hybrid superiority percentage of different cross pairs varied greatly;It showed no hybrid superiority in water content of green wood,wood density and fiber length;Its bark thickness and content of 1% NaOH extractives decreased evidently.
基金funded by the AGL-2017-84217-P Research project from Ministerio de Economia,Industria y Competitividad,Gobierno de Espana.
文摘Background:Estimating inbreeding,which is omnipresent and inevitable in livestock populations,is a primary goal for management and animal breeding especially for those interested in mitigating the negative consequences of inbreeding.Inbreeding coefficients have been historically estimated by using pedigree information;however,over the last decade,genome-base inbreeding coefficients have come to the forefront in this field.The Pura Raza Espanola(PRE)horse is an autochthonous Spanish horse breed which has been recognised since 1912.The total PRE population(344,718 horses)was used to estimate Classical(F),Ballou’s ancestral,Kalinowski’s ancestral,Kalinowski’s new and the ancestral history coefficient values.In addition,genotypic data from a selected population of 805 PRE individuals was used to determine the individual inbreeding coefficient using SNP-by-SNP-based techniques(methods of moments-FHOM-,the diagonal elements of the genomic-FG-,and hybrid matrixes-FH-)and ROH measures(FRZ).The analyse of both pedigree and genomic based inbreeding coefficients in a large and robust population such as the PRE horse,with proven parenteral information for the last 40 years and a high degree of completeness(over 90%for the last 70 years)will allow us to understand PRE genetic variability better and the correlations between the estimations will give the data greater reliability.Results:The mean values of the pedigree-based inbreeding coefficients ranged from 0.01(F for the last 3 generations-F3-)to 0.44(ancestral history coefficient)and the mean values of genomic-based inbreeding coefficients varied from 0.05(FRZ for three generations,FH and FHOM)to 0.11(FRZ for nine generations).Significant correlations were also found between pedigree and genomic inbreeding values,which ranged between 0.58(F3 with FHOM)and 0.79(F with FRZ).In addition,the correlations between FRZ estimated for the last 20 generations and the pedigree-based inbreeding highlight the fact that fewer generations of genomic data are required when comparing total inbreeding values,and the opposite when ancient values are calculated.Conclusions:Ultimately,our results show that it is still useful to work with a deep and reliable pedigree in pedigreebased genetic studies with very large effective population sizes.Obtaining a satisfactory parameter will always be desirable,but the approximation obtained with a robust pedigree will allow us to work more efficiently and economically than with massive genotyping.
基金supported by JSPS KAKENHI(Grant number 18380099).
文摘Authors conducted pollination experiments and genetic analyses using microsatellite loci for a natural population of a shrub species,Magnolia salicifolia,in a secondary Japanese beech forest in Hakkoda mountains,northern Japan,to analyze inbreeding and inbreeding depression that involve sexual reproduction and population genetic structure of the species.The pollination experiments revealed that self-fertilization through geitonogamy is possible and that the magnitude of inbreeding depression(δ)at the embryonic stage is substantial(δ=0.42),suggesting that the inbreeding depression due to self-fertilization decreases seed production of the natural population.The genetic analyses showed discrepancy in the level of inbreeding between life history stages:the inbreeding coefficient for the juvenile and adult stage was 0.17 and 0.01,respectively,implying that most of inbred progenies cannot grow to the adult stage in the population,since the cumulative inbreeding depression is severe.These results are consistent with the hypothesis that explains mechanisms causing stable maintenance of severe inbreeding depression in partially inbred populations by focusing on the selective interference among deleterious mutations.It is suggested that some reproductive traits facilitating outcrossing in the species would be attributed to the severe cumulative inbreeding depression.
基金supported by the Natural Science Foundation of China (No.31572357) to FPZthe National Swine Industry Technology System(CARS-35) to LXW。
文摘Background: Runs of homozygosity(ROHs) are homozygous segments of the genome where the two haplotypes inherited from the parents are identical. The current availability of genotypes for a very large number of single nucleotide polymorphisms(SNPs) is leading to more accurate characterization of ROHs in the whole genome. Here,we investigated the occurrence and distribution of ROHs in 3,692 Large White pigs and compared estimates of inbreeding coefficients calculated based on ROHs(FROH), homozygosity(FHOM), genomic relationship matrix(FGRM)and pedigree(FPED). Furthermore, we identified genomic regions with high ROH frequencies and annotated their candidate genes.Results: In total, 176,182 ROHs were identified from 3,569 animals, and all individuals displayed at least one ROH longer than 1 Mb. The ROHs identified were unevenly distributed on the autosomes. The highest and lowest coverages of Sus scrofa chromosomes(SSC) by ROH were on SSC14 and SSC13, respectively. The highest pairwise correlation among the different inbreeding coefficient estimates was 0.95 between FROH_totaland FHOM, while the lowest was-0.083 between FGRMand FPED. The correlations between FPEDand FROHusing four classes of ROH lengths ranged from 0.18 to 0.37 and increased with increasing ROH length, except for ROH > 10 Mb. Twelve ROH islands were located on four chromosomes(SSC1, 4, 6 and 14). These ROH islands harboured genes associated with reproduction, muscular development, fat deposition and adaptation, such as SIRT1, MYPN, SETDB1 and PSMD4.Conclusion: FROHcan be used to accurately assess individual inbreeding levels compared to other inbreeding coefficient estimators. In the absence of pedigree records, FROHcan provide an alternative to inbreeding estimates.Our findings can be used not only to effectively increase the response to selection by appropriately managing the rate of inbreeding and minimizing the negative effects of inbreeding depression but also to help detect genomic regions with an effect on traits under selection.
基金funded by the Natural Science Foundations of China(No.32172702)National Key Research and Development Program of China(2021YFD1301101)Agricultural Science and Technology Innovation Program(ASTIP-IAS02)。
文摘Background Genomic selection involves choosing as parents those elite individuals with the higher genomic estimated breeding values(GEBV)to accelerate the speed of genetic improvement in domestic animals.But after multi-generation selection,the rate of inbreeding and the occurrence of homozygous harmful alleles might increase,which would reduce performance and genetic diversity.To mitigate the above problems,we can utilize genomic mating(GM)based upon optimal mate allocation to construct the best genotypic combinations in the next generation.In this study,we used stochastic simulation to investigate the impact of various factors on the efficiencies of GM to optimize pairing combinations after genomic selection of candidates in a pig population.These factors included:the algorithm used to derive inbreeding coefficients;the trait heritability(0.1,0.3 or 0.5);the kind of GM scheme(focused average GEBV or inbreeding);the approach for computing the genomic relationship matrix(by SNP or runs of homozygosity(ROH)).The outcomes were compared to three traditional mating schemes(random,positive assortative or negative assortative matings).In addition,the performance of the GM approach was tested on real datasets obtained from a Large White pig breeding population.Results Genomic mating outperforms other approaches in limiting the inbreeding accumulation for the same expected genetic gain.The use of ROH-based genealogical relatedness in GM achieved faster genetic gains than using relatedness based on individual SNPs.The GROH-based GM schemes with the maximum genetic gain resulted in 0.9%-2.6%higher rates of genetic gainΔG,and 13%-83.3%lowerΔF than positive assortative mating regardless of heritability.The rates of inbreeding were always the fastest with positive assortative mating.Results from a purebred Large White pig population,confirmed that GM with ROH-based GRM was more efficient than traditional mating schemes.Conclusion Compared with traditional mating schemes,genomic mating can not only achieve sustainable genetic progress but also effectively control the rates of inbreeding accumulation in the population.Our findings demonstrated that breeders should consider using genomic mating for genetic improvement of pigs.
基金supported by grants from National Science Foundation of China(31502163)the fund earmarked for Modern Agroindustry Technology Research System(CARS-48)
文摘In present study, the inbreeding depression(ID) of growth and survival of Manila clam(Ruditapes philippinarum) was investigated at larval and juvenile stages. Nine inbred families(A_2, B_2, C_2, D_2, E_2, F_2, G_2, H_2 and I_2) were established by mating within nine full-sib families with expected inbreeding coefficient of 0.25. Inbred families showed significant differences in shell length and hatching rate of D-larvae(straight-hinged larvae). The larvae of the nine inbred families grew slower than those of control group(CG), and their ID value ranged from 0.81% ± 6.09% to 16.10% ± 1.49%. The ID value of larval survival rate varied between 27.47% ± 9.36% and 70.50% ± 13.66%. The ID was also detected for juvenile growth in A_2, B_2, C_2, and D_2, which ranged from 4.60 ± 2.21 to 17.71 ± 7.73. The A_2 family maintained the highest juvenile survival rate, whereas the other inbred families exhibited ID values varying between 62.79% ± 4.54% and 96.14% ± 0.87%. The linear relationship of estimated ID between growth and survival was negatively correlated(R =-0.434, P < 0.05). The results of this study suggested that the ID of growth was common at the larval stage but was less prevalent at juvenile stage. In contrast, the ID of survival increased from larval to juvenile stage. A better understanding of the effect of inbreeding may aid to selective breeding of Manila clam.
文摘The genetic basis of heterosis was studied through mid-parent, standard variety and better parent for 11 quantitative traits in 17 parental lines and their 10 selected hybrids in rice (Oryza sativa L.).The characters were plant height,days to flag leaf initiation, days to first panicle initiation, days to 100% flowering, panicle length,flag leaf length, days to maturity, number of fertile spikelet/panicle, number of effective tillers/hill, grain yield/10-hill, and 1000-grain weight.In general the hybrids performed significantly better than the respective parents.Significant heterosis was observed for most of the studied characters. Among the 10 hybrids, four hybrids viz., 17A×45R,25A×37R,27A×39R,31A×47R,and 35A×47R showed highest heterosis in 10-hill grain yield/10-hill. Inbreeding depression of F2 progeny was also studied for 11 characters of 10 hybrids.Both positive and negative inbreeding depression were found in many crosses for the studied characters,but none was found significant. Selection of good parents was found to be the most important for developing high yielding hybrid rice varieties.
基金supported in part by the National Natural Science Foundation of China (NSFC 31400279, 31860121)Funded by the Scientific Research Program of the Higher Education Institution of Xinjiang (XJEDU2016I042)High-level Scientific Research Foundation of Kashi University (GCCZK-004), China
文摘The population characteristics of distylous species are highly sensitive to stochastic natural selection pressure.Therefore,populations growing under different environmental conditions may vary in floral morph ratios,potentially affecting female fitness and leading to inbreeding depression.However,the variation in offspring quality among populations as a result of inbreeding depression is poorly understood in distylous species.This study investigates variations in plant density,seed mass,seed viabilityfemale fitness,and post-dispersal inbreeding depression in both sexual morphs(long-styled and shortstyled plants)of the distylous Primula nivalis that were subjected to different pollination treatments along an elevational gradient from 1657 to 2704 m a.s.l.Population characteristics(morph plant density and ratio)and fruit set were significantly affected by sexual morph and elevation.Plant density and fruitset frequencies were lower for short-styled than for long-styled plants at 2704 m a.s.l.The seeds from the cross-pollinated flowers of both morphs were higher in quality than those of self-pollinated flowers.The female fitness of seeds from cross-pollinated flowers of both morphs was higher than that of seeds from open-pollinated and self-pollinated flowers.The female fitness of seeds from long-styled flowers was higher than that of seeds from short-styled flowers at all elevations.Inbreeding depression increased with elevation among plants with short-styled flowers but not among those with long-styled flowers.Variation in the elevation-dependent mating system might influence female fitness and affect inbreeding depression in both floral morphs.In conclusion,the low quality of seeds from short-styled flowers at high elevations might decrease short-styled flower frequency,affecting population characteristics.
基金funded by the Natural Science Foundations of China(No.31572357)to FPZAgricultural Science and Technology Innovation Program(ASTIP-IAS02)to LXW.
文摘Background:A run of homozygosity(ROH)is a consecutive tract of homozygous genotypes in an individual that indicates it has inherited the same ancestral haplotype from both parents.Genomic inbreeding can be quantified based on ROH.Genomic regions enriched with ROH may be indicative of selection sweeps and are known as ROH islands.We carried out ROH analyses in five Chinese indigenous sheep breeds;Altay sheep(n=50 individuals),Large-tailed Han sheep(n=50),Hulun Buir sheep(n=150),Short-tailed grassland sheep(n=150),and Tibetan sheep(n=50),using genotypes from an Ovine Infinium HD SNP BeadChip.Results:A total of 18,288 ROH were identified.The average number of ROH per individual across the five sheep breeds ranged from 39(Hulun Buir sheep)to 78(Large-tailed Han sheep)and the average length of ROH ranged from 0.929 Mb(Hulun Buir sheep)to 2.544 Mb(Large-tailed Han sheep).The effective population size(Ne)of Altay sheep,Large-tailed Han sheep,Hulun Buir sheep,Short-tailed grassland sheep and Tibetan sheep were estimated to be 81,78,253,238 and 70 five generations ago.The highest ROH-based inbreeding estimate(FROH)was 0.0808 in Large-tailed Han sheep,whereas the lowest F_(ROH)was 0.0148 in Hulun Buir sheep.Furthermore,the highest proportion of long ROH fragments(>5 Mb)was observed in the Large-tailed Han sheep breed which indicated recent inbreeding.In total,49 ROH islands(the top 0.1% of the SNPs most commonly observed in ROH)were identified in the five sheep breeds.Three ROH islands were common to all the five sheep breeds,and were located on OAR2:12.2-12.3 Mb,OAR12:78.4-79.1 Mb and OAR13:53.0-53.6 Mb.Three breed-specific ROH islands were observed in Altay sheep(OAR15:3.4-3.8 Mb),Large-tailed Han sheep(ORA17:53.5-53.8 Mb)and Tibetan sheep(ORA5:19.8-20.2 Mb).Collectively,the ROH islands harbored 78 unique genes,including 19 genes that have been documented as having associations with tail types,adaptation,growth,body size,reproduction or immune response.Conclusion:Different ROH patterns were observed in five Chinese indigenous sheep breeds,which reflected their different population histories.Large-tailed Han sheep had the highest genomic inbreeding coefficients and the highest proportion of long ROH fragments indicating recent inbreeding.Candidate genes in ROH islands could be used to illustrate the genetic characteristics of these five sheep breeds.Our findings contribute to the understanding of genetic diversity and population demography,and help design and implement breeding and conservation strategies for Chinese sheep.
基金grants from The Fundamental Research Funds for the Central Universities(2015-02)the National Natural Science Foundation of China(Nos.31770713,31860221).
文摘Background:Inbreeding in seed orchards is expected to increase with the advancement of breeding cycles,which results in the delivery of crops with suboptimal genetic gain,reduced genetic diversity,and lower seed set.Here,a genetic distance-dependent method for clonal spatial deployment in seed orchards was developed and demonstrated,which reduced the inbreeding levels.The method’s main evaluation parameter of inbreeding is the genetic distance among individuals and the deployment method used an improved adaptive parallel genetic algorithm(IAPGA)based on Python language.Using inbreeding-prone Chinese Mongolian pine breeding population material originating from a single natural population,the proposed method was compared to a traditional orchard design and a distance-based design;namely,complete randomized block(RCB)and optimum neighborhood(ONA)designs,respectively.Results:With the advancement of selective breeding cycles,group separation among orchard related individuals is expected to increase.Based on the genetic distance among individuals,the IAPGA design was superior in significantly reducing the inbreeding level as compared to the two existing designs,confirming its suitability to advanced-generation orchards where relatedness among parents is common.In the 1st,2nd,and mixed generations clonal deployment schemes,the IAPGA design produced lower inbreeding with 87.22%,81.49%,and 87.23%of RCB,and 92.78%,91.30%,and 91.67%of ONA designs,respectively.Conclusions:The IAPGA clonal deployment proposed in this study has the obvious advantage of controlling inbreeding,and it is expected to be used in clonal deployment in seed orchards on a large-scale.Further studies are needed to focus on the actual states of pollen dispersal and mating in seed orchards,and more assumptions should be taken into account for the optimized deployment method.
基金Supported by the International Science&Technology Cooperation Program of China(No.2013DFA31410)the Adaptive Response of Fishery Species to Environmental Changes and their Effects on Population Dynamics(No.2015CB453303)
文摘Ten microsatellite markers were used to analyze the levels of genetic diversity and inbreeding in a hatchery release population of Rhopilema esculentum Kishinouye （Scypbozoa： Rhizostomatidae）. A total of 85 alleles were detected in 600 individuals. Within-population levels of observed （Ho） and expected （He） heterozygosity ranged from 0.152 to 0.839 （mean=0.464） and from 0.235 to 0.821 （mean=0.618）, respectively. The polymorphism information content （PIC） of each marker ranged from 0.207 to 0.795 with an average of 0.580, indicating that the hatchery population maintained a high level of genetic diversity. Inbreeding levels were estimated in the hatchery population and the inbreeding coefficient was 0.203. This result revealed that a certain level of inbreeding occurred within the population. Meanwhile, we also determined genetic diversity at the clone level. Several polyps from the same scyphistomae were genotyped at the ten microsatellite loci and there was virtually no difference in their genotypes. Furthermore, we calculated the probabilities of exclusion. When both parents were known, the average exclusion probability often loci was 99.99%. Our data suggest that the ten microsatellite markers can not only be used to analyze the identity of individuals but they can also be applied to parentage identification. Our research provides a theoretical basis and technical support for genetic diversity detection and reasonable selection of R. esculentum hatchery populations. These findings support the use of releasing studies and conservation of R. esculentum germplasm resources.
基金funded by the European Regional Development Fund(FEDER)/Ministerio de Ciencia e Innovación-Agencia Estatal de Investigación/Project Reference grant:PID2019-105805RB-I00by the CERCA Programme/Generalitat de Catalunya+3 种基金the support of the Spanish Ministerio de Ciencia e Innovación for the Center of Excellence Severo Ochoa 2020–2023(CEX2019–000902-S)grant awarded to the Centre for Research in Agricultural Genomics(CRAG,Bellaterra,Spain)the support of the CERCA programme of the Generalitat de Catalunyafunded by a PhD fellowship from the China Scholarship Council(CSC)funded with a PhD fellowship Formación de Personal Investigador(BES-C-2017-079709)awarded by the Spanish Ministry of Economy and Competitivity。
文摘Background:Inbreeding depression can adversely affect traits related to fitness,reproduction and productive performance.Although current research suggests that inbreeding levels are generally low in most goat breeds,the impact of inbreeding depression on phenotypes of economic interest has only been investigated in a few studies based on genealogical data.Results:We genotyped 1040 goats with the Goat SNP50 BeadChip.This information was used to estimate different molecular inbreeding coefficients and characterise runs of homozygosity and homozygosity patterns.We detected38 genomic regions with increased homozygosity as well as 8 ROH hotspots mapping to chromosomes 1,2,4,6,14,16 and 17.Eight hundred seventeen goats with available records for dairy traits were analysed to evaluate the potential consequences of inbreeding depression on milk phenotypes.Four regions on chromosomes 8 and 25were significantly associated with inbreeding depression for the natural logarithm of the somatic cell count.Notably,these regions contain several genes related with immunity,such as SYK,IL27,CCL19 and CCL21.Moreover,one region on chromosome 2 was significantly associated with inbreeding depression for milk yield.Conclusions:Although genomic inbreeding levels are low in Murciano-Granadina goats,significant evidence of inbreeding depression for the logarithm of the somatic cell count,a phenotype closely associated with udder health and milk yield,have been detected in this population.Minimising inbreeding would be expected to augment economic gain by increasing milk yield and reducing the incidence of mastitis,which is one of the main causes of dairy goat culling.
基金Key Laboratory of Southwest China Wildlife Resources Conservation(Ministry of Education),China West Normal University(XNYB18-02)Nature Conservation of Snake Island and Laotieshan Mountain,Dalian,China(Y8Y3041).
文摘Island species and their ecosystems play an important role in global biodiversity preservation,and many vulnerable island species are conservation priorities.Although insular habitat likely facilitates the species diversification process,it may also aggravate the fragility of these species with high risk of inbreeding.The Shedao pit-viper Gloydius shedaoensis is an island endemic species with an extremely high population density,which has been categorized as vulnerable in the IUCN(International Union for the Conservation of Nature and Natural Resources)Red List.We collected 13,148 SNP(Single Nucleotide Polymorphism)from across its genome and examined its genetic diversity and demographic history.The Shedao pit-viper has a low genetic diversity but shows no sign of inbreeding.Furthermore,population genetic structure analysis,including the neighbor-joining tree,principal coordinate analysis,clustering,and spatial autocorrelation,revealed a general lack of spatial structure.Only the isolation by distance residues suggested a weak patchiness.Overall,the population is nearly panmictic and gene flow is evenly distributed across the island.A large number of individuals,small size of the island,and the lack of population structure likely all contribute to the lack of inbreeding in this species.We also detected signs of male-biased dispersal,which likely is another inbreeding avoidance strategy.Historical demographic analysis suggested that the historical population size and distribution of the species are much larger than their current ones.The multiple transgressive–regressive events since the Late Pleistocene are likely the main cause of the population size changes.Taken together,our results provide a basic scientific foundation for the conservation of this interesting and important species.
文摘To elucidate the structure of SLA-3 alleles on inbred line of Wuzhishan pig （WZSP） population, we examined the partial exon 1, completed exon 2, and partial exon 3 of SLA-3 loci using the reverse transcription-polymerase chain reaction （RT- PCR） and the sequencing-based method in 32 WZSPs. According to pedigree and amplification results, PCR products of 8 WZSPs were selected to clone and sequence. Nine different nucleotide sequences were obtained. After comparing the DNA and protein sequences of the WZSPs SLA-3 alleles with the published GenBank SLA sequences, it was found that the SLA-3 alleles in WZSPs were all novel, but there were very few variations among them. Comparision of SLA-3 and HLA-A protein sequences indicated that there was more sequence homology. Meanwhile, the construction of a phylogenetic tree using the nucleotide sequences of 23 SLA-3 alleles and 1 HLA-A allele represented that the WZSP population owns its unique genetics resource. In this study, the alleles of SLA-3 on WZSP group were successfully detected and analyzed, which provided the firm basis on the genotype of SLA-3 for breeding specific haplotypes WZSPs.
