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1.
Background
Chow and Liu showed that the maximum likelihood tree for multivariate discrete distributions may be found using a maximum weight spanning tree algorithm, for example Kruskal's algorithm. The efficiency of the algorithm makes it tractable for high-dimensional problems. 相似文献2.
Background
The most common application of imputation is to infer genotypes of a high-density panel of markers on animals that are genotyped for a low-density panel. However, the increase in accuracy of genomic predictions resulting from an increase in the number of markers tends to reach a plateau beyond a certain density. Another application of imputation is to increase the size of the training set with un-genotyped animals. This strategy can be particularly successful when a set of closely related individuals are genotyped.Methods
Imputation on completely un-genotyped dams was performed using known genotypes from the sire of each dam, one offspring and the offspring’s sire. Two methods were applied based on either allele or haplotype frequencies to infer genotypes at ambiguous loci. Results of these methods and of two available software packages were compared. Quality of imputation under different population structures was assessed. The impact of using imputed dams to enlarge training sets on the accuracy of genomic predictions was evaluated for different populations, heritabilities and sizes of training sets.Results
Imputation accuracy ranged from 0.52 to 0.93 depending on the population structure and the method used. The method that used allele frequencies performed better than the method based on haplotype frequencies. Accuracy of imputation was higher for populations with higher levels of linkage disequilibrium and with larger proportions of markers with more extreme allele frequencies. Inclusion of imputed dams in the training set increased the accuracy of genomic predictions. Gains in accuracy ranged from close to zero to 37.14%, depending on the simulated scenario. Generally, the larger the accuracy already obtained with the genotyped training set, the lower the increase in accuracy achieved by adding imputed dams.Conclusions
Whenever a reference population resembling the family configuration considered here is available, imputation can be used to achieve an extra increase in accuracy of genomic predictions by enlarging the training set with completely un-genotyped dams. This strategy was shown to be particularly useful for populations with lower levels of linkage disequilibrium, for genomic selection on traits with low heritability, and for species or breeds for which the size of the reference population is limited. 相似文献3.
S?ren Franzenburg Sebastian Fraune Philipp M Altrock Sven Künzel John F Baines Arne Traulsen Thomas CG Bosch 《The ISME journal》2013,7(4):781-790
Animals are colonized by complex bacterial communities. The processes controlling community membership and influencing the establishment of the microbial ecosystem during development are poorly understood. Here we aimed to explore the assembly of bacterial communities in Hydra with the broader goal of elucidating the general rules that determine the temporal progression of bacterial colonization of animal epithelia. We profiled the microbial communities in polyps at various time points after hatching in four replicates. The composition and temporal patterns of the bacterial communities were strikingly similar in all replicates. Distinct features included high diversity of community profiles in the first week, a remarkable but transient adult-like profile 2 weeks after hatching, followed by progressive emergence of a stable adult-like pattern characterized by low species diversity and the preponderance of the Betaproteobacterium Curvibacter. Intriguingly, this process displayed important parallels to the assembly of human fecal communities after birth. In addition, a mathematical modeling approach was used to uncover the organizational principles of this colonization process, suggesting that both, local environmental or host-derived factor(s) modulating the colonization rate, as well as frequency-dependent interactions of individual bacterial community members are important aspects in the emergence of a stable bacterial community at the end of development. 相似文献
4.
PR Marcelino MS Aoki AFS Arruda CG Freitas A Mendez-Villanueva A Moreira 《Biology of sport / Institute of Sport》2016,33(1):37-42
The purpose of this study was to investigate the effect of court size on physiological responses and physical performance of young elite basketball players. Twelve male basketball players (18.6 ± 0.5 years; 88.8 ± 14.5 kg; 192.6 ± 6.5 cm) from an under-19 team performed two small-sided games (matches) with different court areas (28x15 m and 28x9 m; 28x15 and 28x9 protocols). The number of players (3x3) was kept the same in each protocol. The players performed a repeated-sprint ability (RSA) test before and after each match. Blood lactate concentration was collected before (pre) and after (post) the matches, and the session rating of perceived exertion (session-RPE) was determined 30 minutes after the match. Best and mean time in the RSA test were not different between the 28x15 and the 28x9 match protocols (p > 0.05). A significant difference was observed for lactate concentration from pre- to post-match (p < 0.05) in both protocols (28x15 and 28x9); however, there was no significant interaction between protocols. A similar session-RPE mean score (28x15: 7.2 ± 1.4 and 28x9: 6.6 ± 1.4) was detected for both protocols (p > 0.05, ES=0.41). In summary, the results of the current study suggest that the different court areas induced similar responses. Although there was no significant difference in effort perception, players tended to perceive a greater effort in the larger court size. 相似文献
5.
G. C. Yencho S. P. Kowalski R. S. Kobayashi S. L. Sinden M. W. Bonierbale K. L. Deahl 《TAG. Theoretical and applied genetics. Theoretische und angewandte Genetik》1998,97(4):563-574
Glycoalkaloids are quantitatively inherited in Solanum, and in high concentrations they can be toxic to humans. The increased use of wild potato germplasm to improve the pest resistance,
yield, and quality characteristics of cultivated potato may elevate or introduce new, more toxic glycoalkaloids into the cultivated
gene pool. Therefore, it is important to increase our understanding of their inheritance, accumulation, and biosynthesis.
Glycoalkaloids have two basic constituents – a glycosidic grouping and a steroid alkaloid skeleton. Steroid alkaloids are
classified as solanidanes and spirosolanes, of which solanidine and solasodine are, respectively, representatives. RFLP-mapped,
diploid, reciprocal backcross potato progenies involving the parents S. tuberosum and S. berthaultii, which produce solanidine and solasodine, respectively, were analyzed for segregation of the glycoalkaloids solanine, chaconine,
solasodine and solamargine to identify quantitative trait loci (QTLs) for the production of the aglycones solanidine and solasodine.
The F1 clone M200-30 exhibited low to nondetectable levels of solasodine and solanidine, suggesting that expression was controlled
by recessive genes. In a backcross to berthaultii (BCB) and backcross to tuberosum (BCT), several QTLs for the accumulation of solasodine and solanidine were identified. Three QTLs explaining approximately
20% of the variation in solasodine were identified in BCB on chromosomes 4, 6, and 12. Similarly, three QTLs were identified
in BCT on chromosomes 4, 8 and 11, but these accounted for only 10% of the variation observed in solasodine accumulation.
Two QTLs for solanidine were identified in BCT on chromosomes 1 and 4. The QTL located on chromosome 1 was highly significant,
accounting for 17% and 22% of the variation in solanidine accumulation in 1994 and 1995, respectively. This same QTL was also
detected in BCB. The QTLs detected in this study probably represent structural and/or regulatory genes controlling the accumulation
of solasodine and solanidine. Results are discussed in the context of steroid alkaloid accumulation and biosynthesis.
Received: 27 August 1997 / Accepted: 16 March 1998 相似文献
6.
Background
The ability to regulate transgene expression has many applications, mostly concerning the analysis of gene function. Desirable induction characteristics, such as low un-induced expression, high induced expression and limited cellular heterogeneity, can be seriously impaired by chromosomal position effects at the site of transgene integration. Many clones may therefore need to be screened before one with optimal induction characteristics is identified. Furthermore, such screens must be repeated for each new transgene investigated, and comparisons between clones with different transgenes is complicated by their different integration sites. 相似文献7.
BACKGROUND: Biochemical testing for pheochromocytoma by measurement of fractionated plasma metanephrines is limited by false positive rates of up to 18% in people without known genetic predisposition to the disease. The plasma normetanephrine fraction is responsible for most false positives and plasma normetanephrine increases with age. The objective of this study was to determine if we could improve the specificity of fractionated plasma measurements, by statistically adjusting for age. METHODS: An age-adjusted metanephrine score was derived using logistic regression from 343 subjects (including 33 people with pheochromocytoma) who underwent fractionated plasma metanephrine measurements as part of investigations for suspected pheochromocytoma at Mayo Clinic Rochester (derivation set). The performance of the age-adjusted score was validated in a dataset of 158 subjects (including patients 23 with pheochromocytoma) that underwent measurements of fractionated plasma metanephrines at Mayo Clinic the following year (validation dataset). None of the participants in the validation dataset had known genetic predisposition to pheochromocytoma. RESULTS: The sensitivity of the age-adjusted metanephrine score was the same as that of traditional interpretation of fractionated plasma metanephrine measurements, yielding a sensitivity of 100% (23/23, 95% confidence interval [CI] 85.7%, 100%). However, the false positive rate with traditional interpretation of fractionated plasma metanephrine measurements was 16.3% (22/135, 95% CI, 11.0%, 23.4%) and that of the age-adjusted score was significantly lower at 3.0% (4/135, 95% CI, 1.2%, 7.4%) (p < 0.001 using McNemar's test). CONCLUSION: An adjustment for age in the interpretation of results of fractionated plasma metanephrines may significantly decrease false positives when using this test to exclude sporadic pheochromocytoma. Such improvements in false positive rate may result in savings of expenditures related to confirmatory imaging. 相似文献
8.
Abstract Helicoverpa armigera oviposition preference for, and larval development on sorghum hybrids with differing resistance to sorghum midge, Stenodiplosis sorghicola , were investigated. When H. armigera larvae were fed seed of resistant and susceptible hybrids in the laboratory there were no differences in larval and pupal sizes or the rate of development. The same result was recorded when larvae fed on panicles on plants in a glasshouse. On some sampling occasions, significantly more eggs were laid on panicles of resistant hybrids in the field. This occurred when plants were in plots and also in a mixed planting. Midge-resistance status did not affect levels of egg parasitism. In a field study using recombinant inbred lines between a midge-resistant and a midge-susceptible line, no relationship was found between level of resistance and oviposition of H. armigera . We conclude that, although midge-resistant hybrids are sometimes preferred for oviposition by H. armigera, the resistance per se does not determine this preference. Egg survival, larval survival, development and resultant damage are not significantly affected by the midge-resistance status of the host. 相似文献
9.
Development of a genetic linkage map and identification of homologous linkage groups in sweetpotato using multiple-dose AFLP markers 总被引:1,自引:0,他引:1
Jim C. Cervantes-Flores G. Craig Yencho Albert Kriegner Kenneth V. Pecota Maria A. Faulk Robert O. M. Mwanga Bryon R. Sosinski 《Molecular breeding : new strategies in plant improvement》2008,21(4):511-532
Sweetpotato genomic research is minimal compared to most other major crops despite its worldwide importance as a food crop.
The development of a genetic linkage map in sweetpotato will provide valuable information about the genomic organization of
this important species that can be used by breeders to accelerate the introgression of desired traits into breeding lines.
We developed a mapping population consisting of 240 individuals of a cross between ‘Tanzania’, a cream-fleshed African landrace,
and ‘Beauregard’, an orange-fleshed US sweetpotato cultivar. The genetic linkage map of this population was constructed using
Amplified Fragment Length Polymorphism (AFLP) markers. A total of 1944 (‘Tanzania’) and 1751 (‘Beauregard’) AFLP markers,
of which 1511 and 1303 were single-dose markers respectively, were scored. Framework maps consisting of 86 and 90 linkage
groups for ‘Tanzania’ and ‘Beauregard’ respectively, were developed using a combination of JoinMap 3.0 and MAPMAKER/EXP 3.0.
A total of 947 single-dose markers were placed in the final framework linkage map for ‘Tanzania’. The linkage map size was
estimated as 5792 cM, with an average distance between markers of 4.5 cM. A total of 726 single-dose markers were placed in
the final framework map for ‘Beauregard’. The linkage map length was estimated as 5276 cM, with an average distance between
markers of 4.8 cM. Duplex and triple-dose markers were used to identify the corresponding homologous groups in the maps. Our
research supports the hypothesis that sweetpotato is an autopolyploid. Distorted segregation in some markers of different
dosages in this study suggests that some preferential pairing occurs in sweetpotato. However, strict allopolyploid inheritance
in sweetpotato can be ruled out due to the observed segregation ratios of the markers, and the proportion of simplex to multiple-dose
markers.
Electronic supplementary material The online version of this article (doi:) contains supplementary material, which is available to authorized users.
This paper is a portion of a dissertation submitted by Jim C. Cervantes-Flores. 相似文献
10.
D Taruscio C Morciano P Laricchiuta P Mincarone F Palazzo CG Leo S Sabina R Guarino J Auld T Sejersen D Gavhed K Ritchie M Hilton-Boon J Manson PG Kanavos D Tordrup V Tzouma Y Le Cam J Senecat G Filippini S Minozzi C Del Giovane H Schünemann JJ Meerpohl B Prediger L Schell R Stefanov G Iskrov T Miteva-Katrandzhieva P Serrano-Aguilar L Perestelo-Perez MM Trujillo-Martín J Pérez-Ramos A Rivero-Santana A Brand H van Kranen K Bushby A Atalaia J Ramet L Siderius M Posada I Abaitua-Borda V Alonso Ferreira M Hens-Pérez FJ Manzanares 《Orphanet journal of rare diseases》2014,9(Z1):O14