Inbreeding,which refers to situations where relatives are mating,is unavoidable in aquaculture populations because of their restricted population size.The rate of inbreeding in a population is roughly equal to one ove...Inbreeding,which refers to situations where relatives are mating,is unavoidable in aquaculture populations because of their restricted population size.The rate of inbreeding in a population is roughly equal to one over twice the ’effective population size’,1/(2N_e),but a more accurate ’inbreeding coefficient’(F) is usually used to quantify inbreeding in populations undergoing artificial and/or natural selection.Inbreeding usually leads to reductions of performance in aquaculture species.Such ’inbreeding depression’ is mainly the result of recessive deleterious genes being unmasked and expressed in homozygous individuals.All aquaculture populations will accumulate recessive deleterious genes because of mutations in the DNA.It is assumed that most aquaculture species have a ’genetic load’ of about 100 recessive deleterious genes,which would be more than enough to cause the extinction of that species if these genes were made homozygous through mating between relatives.A literature review confirmed that traits related to the overall fitness of aquaculture species are strongly affected by inbreeding(ranging between 3%-50% inbreeding depression per 10% increase of the inbreeding coefficient,F).Fast inbreeding through full-sib mating has resulted,on average,in three times higher inbreeding depression in growth compared to slow inbreeding in large-scale selective breeding programs.Studies with other species suggest that slow inbreeding usually lead to more effective purging of recessive deleterious genes than rapid full-sib inbreeding since fewer genes are fixed because of random drift.Inbreeding will also reduce the additive genetic variation within hatchery populations,but increases the additive genetic variation between isolated hatchery populations.Inbred populations usually show different responses in different environments due to the reduced additive genetic variance and their loss of ability to adapt to environmental changes.Therefore,efforts should be made to restrict inbreeding and its negative c展开更多
Low-coverage whole-genome sequencing is an effective strategy for genome-wide association studies in hu- mans, due to the availability of large reference panels for genotype imputation. However, it is unclear whether ...Low-coverage whole-genome sequencing is an effective strategy for genome-wide association studies in hu- mans, due to the availability of large reference panels for genotype imputation. However, it is unclear whether this strategy can be utilized in other species without reference panels. Using simulations, we show that this approach is even more relevant in inbred species such as rice （Oryza sativa L.）, which are effectively haploid, allowing easy haplotype construction and imputation-based genotype calling, even without the availability of large reference panels. We sequenced 203 rice varieties with well-characterized phenotypes from the United States Department of Agriculture Rice Mini-Core Collection at an average depth of 1.5~ and used the data for mapping three traits. For the first two traits, amylose content and seed length, our approach leads to direct identification of the previously identified causal SN Ps in the major-effect loci. For the third trait, pericarp color, an important trait underwent selection during domestication, we identified a new major-effect locus. Although known loci can explain color variation in the varieties of two main subspecies of Asian domesticated rice,japonica and indica, the new locus identified is unique to another domesticated rice subgroup, aus, and together with existing loci, can fully explain the major variation in pericarp color in aus. Our discovery of a unique genetic basis of white pericarp in aus provides an example of convergent evolution during rice domestication and suggests that aus may have a domestication history independent of japonica and indica.展开更多
Eight microsatellite markers were used to analyze genetic diversity, level of inbreeding, and effective population size of spawner and recaptured populations of Chinese shrimp（Fenneropenaeus chinensis） during stock ...Eight microsatellite markers were used to analyze genetic diversity, level of inbreeding, and effective population size of spawner and recaptured populations of Chinese shrimp（Fenneropenaeus chinensis） during stock enhancement in the Bohai Bay in 2013. A total of 254 and 238 alleles were identified in the spawner and recaptured populations, respectively, and the numbers of alleles（N_a） were 8–63 and 6–60, respectively. The numbers of effective alleles（N_e） were 2.52–21.60 and 2.67–20.72, respectively. The polymorphism information content ranged from 0.529 to 0.952. The observed heterozygosity（H_o） values（0.638–0.910 and 0.712–0.927） were lower than the expected heterozygosity（H_e） values（0.603–0.954 and 0.625–0.952）, which indicated that the two populations possessed a rich genetic diversity. In 16 tests（2 populations×8 loci）, 13 tests deviated from the HardyWeinberg equilibrium. F_（is） values were positive at seven loci and the inbreeding coefficients（F） of the two populations estimated by trio ML were 13.234% and 11.603%, suggesting that there was a relatively high degree of inbreeding. A certain level of inbreeding depression had occurred in the Chinese shrimp population. F_（st） values ranged from 0 to 0.059, with a mean of 0.028, displaying a low level of genetic differentiation in the two populations. Effective population sizes（3 060.2 and 3 842.8） were higher than the minimum number suggested for retaining the evolutionary potential to adapt to new environmental conditions. For enhancement activity in 2014,the ideal number of captured shrimp spawners should have ranged from 7 686 to 19 214 to maintain genetic diversity and effective population size. Further strategies to adjust the balance of economic cost, fishing effort and ideal number of shrimp spawners to maintain a satisfactory effective population size for ensuring the sustainability of Chinese shrimp are proposed.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
In 2002, six cohorts ofbroodstock bay scallop Argopecten irradians irradians （Ne=1, 2, 10, 30, 50 and control） were randomly chosen from a population of bay scallop to produce offspring. After one year rearing, with...In 2002, six cohorts ofbroodstock bay scallop Argopecten irradians irradians （Ne=1, 2, 10, 30, 50 and control） were randomly chosen from a population of bay scallop to produce offspring. After one year rearing, with the progeny matured, the similar experiment was done to produce the F2 generation. To determine the magnitude of Ne effects, the growth and survival rates in larvae and adult of six F2 groups were compared. Results showed that inbreeding depression existed not only in the Ne=1 group but also in the Ne=2 group. The growth and survival rates of the two groups were significantly lower than those of the other groups （Ne=10, 30, 50, control）, and there were no significant differences among the latter （P〉0.05）. At the same time, the amount of depression in the Ne=1 group was significantly higher than that of the Ne=2 group （P〈0.05）. These results indicated that the low effective population size （Ne）, which increases the possibility of inbreeding, could lead to some harmful effects on the offspring. So it is essential to maintain a high level of Ne in commercial seed production. Fta＇thermore, as the high fecundity of bay scallop might lead to increased inbreeding, selecting broodstock from different growout sites is recommended.展开更多
文摘Inbreeding,which refers to situations where relatives are mating,is unavoidable in aquaculture populations because of their restricted population size.The rate of inbreeding in a population is roughly equal to one over twice the ’effective population size’,1/(2N_e),but a more accurate ’inbreeding coefficient’(F) is usually used to quantify inbreeding in populations undergoing artificial and/or natural selection.Inbreeding usually leads to reductions of performance in aquaculture species.Such ’inbreeding depression’ is mainly the result of recessive deleterious genes being unmasked and expressed in homozygous individuals.All aquaculture populations will accumulate recessive deleterious genes because of mutations in the DNA.It is assumed that most aquaculture species have a ’genetic load’ of about 100 recessive deleterious genes,which would be more than enough to cause the extinction of that species if these genes were made homozygous through mating between relatives.A literature review confirmed that traits related to the overall fitness of aquaculture species are strongly affected by inbreeding(ranging between 3%-50% inbreeding depression per 10% increase of the inbreeding coefficient,F).Fast inbreeding through full-sib mating has resulted,on average,in three times higher inbreeding depression in growth compared to slow inbreeding in large-scale selective breeding programs.Studies with other species suggest that slow inbreeding usually lead to more effective purging of recessive deleterious genes than rapid full-sib inbreeding since fewer genes are fixed because of random drift.Inbreeding will also reduce the additive genetic variation within hatchery populations,but increases the additive genetic variation between isolated hatchery populations.Inbred populations usually show different responses in different environments due to the reduced additive genetic variance and their loss of ability to adapt to environmental changes.Therefore,efforts should be made to restrict inbreeding and its negative c
文摘Low-coverage whole-genome sequencing is an effective strategy for genome-wide association studies in hu- mans, due to the availability of large reference panels for genotype imputation. However, it is unclear whether this strategy can be utilized in other species without reference panels. Using simulations, we show that this approach is even more relevant in inbred species such as rice （Oryza sativa L.）, which are effectively haploid, allowing easy haplotype construction and imputation-based genotype calling, even without the availability of large reference panels. We sequenced 203 rice varieties with well-characterized phenotypes from the United States Department of Agriculture Rice Mini-Core Collection at an average depth of 1.5~ and used the data for mapping three traits. For the first two traits, amylose content and seed length, our approach leads to direct identification of the previously identified causal SN Ps in the major-effect loci. For the third trait, pericarp color, an important trait underwent selection during domestication, we identified a new major-effect locus. Although known loci can explain color variation in the varieties of two main subspecies of Asian domesticated rice,japonica and indica, the new locus identified is unique to another domesticated rice subgroup, aus, and together with existing loci, can fully explain the major variation in pericarp color in aus. Our discovery of a unique genetic basis of white pericarp in aus provides an example of convergent evolution during rice domestication and suggests that aus may have a domestication history independent of japonica and indica.
基金The National Basic Research Program of China(973 Program)Adaptive Response of Fishery Species to Environmental Changes and Their Effects on Population Dynamics under contract No.2015CB453303the International Science&Technology Cooperation Program of China under contract No.2013DFA31410
文摘Eight microsatellite markers were used to analyze genetic diversity, level of inbreeding, and effective population size of spawner and recaptured populations of Chinese shrimp（Fenneropenaeus chinensis） during stock enhancement in the Bohai Bay in 2013. A total of 254 and 238 alleles were identified in the spawner and recaptured populations, respectively, and the numbers of alleles（N_a） were 8–63 and 6–60, respectively. The numbers of effective alleles（N_e） were 2.52–21.60 and 2.67–20.72, respectively. The polymorphism information content ranged from 0.529 to 0.952. The observed heterozygosity（H_o） values（0.638–0.910 and 0.712–0.927） were lower than the expected heterozygosity（H_e） values（0.603–0.954 and 0.625–0.952）, which indicated that the two populations possessed a rich genetic diversity. In 16 tests（2 populations×8 loci）, 13 tests deviated from the HardyWeinberg equilibrium. F_（is） values were positive at seven loci and the inbreeding coefficients（F） of the two populations estimated by trio ML were 13.234% and 11.603%, suggesting that there was a relatively high degree of inbreeding. A certain level of inbreeding depression had occurred in the Chinese shrimp population. F_（st） values ranged from 0 to 0.059, with a mean of 0.028, displaying a low level of genetic differentiation in the two populations. Effective population sizes（3 060.2 and 3 842.8） were higher than the minimum number suggested for retaining the evolutionary potential to adapt to new environmental conditions. For enhancement activity in 2014,the ideal number of captured shrimp spawners should have ranged from 7 686 to 19 214 to maintain genetic diversity and effective population size. Further strategies to adjust the balance of economic cost, fishing effort and ideal number of shrimp spawners to maintain a satisfactory effective population size for ensuring the sustainability of Chinese shrimp are proposed.
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This study was supported by the Project of Scientific Innovation of the Chinese Academy of Sciences under contract No.ZKCX2-211the Science and Technology Plans of Shandong Province under contract No.022110107the Science and Technology Plans of Qingdao under contract No.03-1-HH-10.
文摘In 2002, six cohorts ofbroodstock bay scallop Argopecten irradians irradians （Ne=1, 2, 10, 30, 50 and control） were randomly chosen from a population of bay scallop to produce offspring. After one year rearing, with the progeny matured, the similar experiment was done to produce the F2 generation. To determine the magnitude of Ne effects, the growth and survival rates in larvae and adult of six F2 groups were compared. Results showed that inbreeding depression existed not only in the Ne=1 group but also in the Ne=2 group. The growth and survival rates of the two groups were significantly lower than those of the other groups （Ne=10, 30, 50, control）, and there were no significant differences among the latter （P〉0.05）. At the same time, the amount of depression in the Ne=1 group was significantly higher than that of the Ne=2 group （P〈0.05）. These results indicated that the low effective population size （Ne）, which increases the possibility of inbreeding, could lead to some harmful effects on the offspring. So it is essential to maintain a high level of Ne in commercial seed production. Fta＇thermore, as the high fecundity of bay scallop might lead to increased inbreeding, selecting broodstock from different growout sites is recommended.
