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Claudia A Sevillano Marcos S Lopes Barbara Harlizius Egiel HAT Hanenberg Egbert F Knol John WM Bastiaansen 《遗传、选种与进化》2015,47(1)
Background
Cryptorchidism and scrotal/inguinal hernia are the most frequent congenital defects in pigs. Identification of genomic regions that control these congenital defects is of great interest to breeding programs, both from an animal welfare point of view as well as for economic reasons. The aim of this genome-wide association study (GWAS) was to identify single nucleotide polymorphisms (SNPs) that are strongly associated with these congenital defects. Genotypes were available for 2570 Large White (LW) and 2272 Landrace (LR) pigs. Breeding values were estimated based on 1 359 765 purebred and crossbred male offspring, using a binary trait animal model. Estimated breeding values were deregressed (DEBV) and taken as the response variable in the GWAS.Results
Heritability estimates were equal to 0.26 ± 0.02 for cryptorchidism and to 0.31 ± 0.01 for scrotal/inguinal hernia. Seven and 31 distinct QTL regions were associated with cryptorchidism in the LW and LR datasets, respectively. The top SNP per region explained between 0.96% and 1.10% and between 0.48% and 2.77% of the total variance of cryptorchidism incidence in the LW and LR populations, respectively. Five distinct QTL regions associated with scrotal/inguinal hernia were detected in both LW and LR datasets. The top SNP per region explained between 1.22% and 1.60% and between 1.15% and 1.46% of the total variance of scrotal/inguinal hernia incidence in the LW and LR populations, respectively. For each trait, we identified one overlapping region between the LW and LR datasets, i.e. a region on SSC8 (Sus scrofa chromosome) between 65 and 73 Mb for cryptorchidism and a region on SSC13 between 34 and 37 Mb for scrotal/inguinal hernia.Conclusions
The use of DEBV in combination with a binary trait model was a powerful approach to detect regions associated with difficult traits such as cryptorchidism and scrotal/inguinal hernia that have a low incidence and for which affected animals are generally not available for genotyping. Several novel QTL regions were detected for cryptorchidism and scrotal/inguinal hernia, and for several previously known QTL regions, the confidence interval was narrowed down.Electronic supplementary material
The online version of this article (doi:10.1186/s12711-015-0096-6) contains supplementary material, which is available to authorized users. 相似文献98.
John WM Bastiaansen Albart Coster Mario PL Calus Johan AM van Arendonk Henk Bovenhuis 《遗传、选种与进化》2012,44(1):3
Background
Genomic selection has become an important tool in the genetic improvement of animals and plants. The objective of this study was to investigate the impacts of breeding value estimation method, reference population structure, and trait genetic architecture, on long-term response to genomic selection without updating marker effects.Methods
Three methods were used to estimate genomic breeding values: a BLUP method with relationships estimated from genome-wide markers (GBLUP), a Bayesian method, and a partial least squares regression method (PLSR). A shallow (individuals from one generation) or deep reference population (individuals from five generations) was used with each method. The effects of the different selection approaches were compared under four different genetic architectures for the trait under selection. Selection was based on one of the three genomic breeding values, on pedigree BLUP breeding values, or performed at random. Selection continued for ten generations.Results
Differences in long-term selection response were small. For a genetic architecture with a very small number of three to four quantitative trait loci (QTL), the Bayesian method achieved a response that was 0.05 to 0.1 genetic standard deviation higher than other methods in generation 10. For genetic architectures with approximately 30 to 300 QTL, PLSR (shallow reference) or GBLUP (deep reference) had an average advantage of 0.2 genetic standard deviation over the Bayesian method in generation 10. GBLUP resulted in 0.6% and 0.9% less inbreeding than PLSR and BM and on average a one third smaller reduction of genetic variance. Responses in early generations were greater with the shallow reference population while long-term response was not affected by reference population structure.Conclusions
The ranking of estimation methods was different with than without selection. Under selection, applying GBLUP led to lower inbreeding and a smaller reduction of genetic variance while a similar response to selection was achieved. The reference population structure had a limited effect on long-term accuracy and response. Use of a shallow reference population, most closely related to the selection candidates, gave early benefits while in later generations, when marker effects were not updated, the estimation of marker effects based on a deeper reference population did not pay off. 相似文献99.
Jouvin-Marche E; Cuddihy A; Butler S; Hansen JN; Fitch WM; Rudikoff S 《Molecular biology and evolution》1988,5(5):500-511
The immunoglobulin kappa light-chain constant region gene (C kappa) has
been cloned and sequenced from five wild mouse species. Analysis of these
data has permitted an assessment of single-copy gene evolution during a
limited time period as defined by the genus Mus. Sequence conservation was
found to be as high (or higher) in the 5' and enhancer regions as in the
coding region. The pattern of substitutions throughout these genes suggests
that parallel evolution has occurred frequently and that substitutions at
replacement sites have not decreased significantly, owing to saturation
during this period of approximately 10 Myr. Phylogenetic relationships have
been determined among these wild species as well as among members of the
genus Rattus.
相似文献
100.
Evidence from nuclear sequences that invariable sites should be considered when sequence divergence is calculated 总被引:3,自引:1,他引:2
It has long been known, from the distribution of multiple amino acid
replacements, that not all amino acids of a sequence are replaceable. More
recently, the phenomenon was observed at the nucleotide level in
mitochondrial DNA even after allowing for different rates of transition and
transversion substitutions. We have extended the search to globin gene
sequences from various organisms, with the following results: (1) Nearly
every data set showed evidence of invariable nucleotide positions. (2) In
all data sets, substitution rates of transversions and transitions were
never in the ratio of 2/1, and rarely was the ratio even constant. (3) Only
rarely (e.g., the third codon position of beta hemoglobins) was it possible
to fit the data set solely by making allowance for the number of invariable
positions and for the relative rates of transversion and transition
substitutions. (4) For one data set (the second codon position of beta
hemoglobins) we were able to simulate the observed data by making the
allowance in (3) and having the set of covariotides (concomitantly variable
nucleotides) be small in number and be turned over in a stochastic manner
with a probability that was appreciable. (5) The fit in the latter case
suggests, if the assumptions are correct and at all common, that current
procedures for estimating the total number of nucleotide substitutions in
two genes since their divergence from their common ancestor could be low by
as much as an order of magnitude. (6) The fact that only a small fraction
of the nucleotide positions differ is no guarantee that one is not
seriously underestimating the total amount of divergence (substitutions).
(7) Most data sets are so heterogeneous in their number of transition and
transversion differences that none of the current models of nucleotide
substitution seem to fit them even after (a) segregation of coding from
noncoding sequences and (b) splitting of the codon into three subsets by
codon position. (8) These frequently occurring problems cannot be seen
unless several reasonably divergent orthologous genes are examined
together.
相似文献