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131.
Background
To obtain predictions that are not biased by selection, the conditional mean of the breeding values must be computed given the data that were used for selection. When single nucleotide polymorphism (SNP) effects have a normal distribution, it can be argued that single-step best linear unbiased prediction (SS-BLUP) yields a conditional mean of the breeding values. Obtaining SS-BLUP, however, requires computing the inverse of the dense matrix G of genomic relationships, which will become infeasible as the number of genotyped animals increases. Also, computing G requires the frequencies of SNP alleles in the founders, which are not available in most situations. Furthermore, SS-BLUP is expected to perform poorly relative to variable selection models such as BayesB and BayesC as marker densities increase.Methods
A strategy is presented for Bayesian regression models (SSBR) that combines all available data from genotyped and non-genotyped animals, as in SS-BLUP, but accommodates a wider class of models. Our strategy uses imputed marker covariates for animals that are not genotyped, together with an appropriate residual genetic effect to accommodate deviations between true and imputed genotypes. Under normality, one formulation of SSBR yields results identical to SS-BLUP, but does not require computing G or its inverse and provides richer inferences. At present, Bayesian regression analyses are used with a few thousand genotyped individuals. However, when SSBR is applied to all animals in a breeding program, there will be a 100 to 200-fold increase in the number of animals and an associated 100 to 200-fold increase in computing time. Parallel computing strategies can be used to reduce computing time. In one such strategy, a 58-fold speedup was achieved using 120 cores.Discussion
In SSBR and SS-BLUP, phenotype, genotype and pedigree information are combined in a single-step. Unlike SS-BLUP, SSBR is not limited to normally distributed marker effects; it can be used when marker effects have a t distribution, as in BayesA, or mixture distributions, as in BayesB or BayesC π. Furthermore, it has the advantage that matrix inversion is not required. We have investigated parallel computing to speedup SSBR analyses so they can be used for routine applications.Electronic supplementary material
The online version of this article (doi:10.1186/1297-9686-46-50) contains supplementary material, which is available to authorized users. 相似文献132.
A Geert Heidema Jolanda MA Boer Nico Nagelkerke Edwin CM Mariman Daphne L van der A Edith JM Feskens 《BMC genetics》2006,7(1):1-15
Background
Molecular genetic approaches have much to offer population biology. Despite recent advances, convenient techniques to develop and screen highly-resolving markers can be limiting for some applications and taxa. We describe an improved PCR-based, cloning-free, nuclear marker development procedure, in which single-stranded conformation polymorphism (SSCP) plays a central role. Sequence-variable alleles at putative nuclear loci are simultaneously identified and isolated from diploid tissues. Based on a multiple allele alignment, locus-specific primers are designed in conserved regions, minimizing 'null' alleles. Using two undescribed endemic Australian Collembola as exemplars, we outline a comprehensive approach to generating and validating suites of codominant, sequence-yielding nuclear loci for previously unstudied invertebrates.Results
Six markers per species were developed without any baseline genetic information. After evaluating the characteristics of each new locus via SSCP pre-screening, population samples were genotyped on the basis of either DNA sequence, restriction site, or insertion/deletion variation, depending on which assay was deemed most appropriate. Polymorphism was generally high (mean of nine alleles per locus), and the markers were capable of resolving population structuring over very fine spatial scales (<100 km). SSCP coupled with targeted DNA sequencing was used to obtain genotypic, genic and genealogical information from six loci (three per species). Phylogeographic analysis identified introns as being most informative.Conclusion
The comprehensive approach presented here feasibly overcomes technical hurdles of (i) developing suitably polymorphic nuclear loci for non-model organisms, (ii) physically isolating nuclear allele haplotypes from diploid tissues without cloning, and (iii) genotyping population samples on the basis of nuclear DNA sequence variation. 相似文献133.
Survey of Malassezia sp and dermatophytes in the cutaneous microbiome of free‐ranging golden‐headed lion tamarins (Leontopithecus chrysomelas ‐ Kuhl, 1820) 下载免费PDF全文
134.
The mutation rates of di-, tri- and tetranucleotide repeats in Drosophila melanogaster 总被引:3,自引:1,他引:3
Schug MD; Hutter CM; Wetterstrand KA; Gaudette MS; Mackay TF; Aquadro CF 《Molecular biology and evolution》1998,15(12):1751-1760
In a recent study, we reported that the combined average mutation rate of
10 di-, 6 tri-, and 8 tetranucleotide repeats in Drosophila melanogaster
was 6.3 x 10(-6) mutations per locus per generation, a rate substantially
below that of microsatellite repeat units in mammals studied to date (range
= 10(-2)-10(-5) per locus per generation). To obtain a more precise
estimate of mutation rate for dinucleotide repeat motifs alone, we assayed
39 new dinucleotide repeat microsatellite loci in the mutation accumulation
lines from our earlier study. Our estimate of mutation rate for a total of
49 dinucleotide repeats is 9.3 x 10(-6) per locus per generation, only
slightly higher than the estimate from our earlier study. We also estimated
the relative difference in microsatellite mutation rate among di-, tri-,
and tetranucleotide repeats in the genome of D. melanogaster using a method
based on population variation, and we found that tri- and tetranucleotide
repeats mutate at rates 6.4 and 8.4 times slower than that of dinucleotide
repeats, respectively. The slower mutation rates of tri- and
tetranucleotide repeats appear to be associated with a relatively short
repeat unit length of these repeat motifs in the genome of D. melanogaster.
A positive correlation between repeat unit length and allelic variation
suggests that mutation rate increases as the repeat unit lengths of
microsatellites increase.
相似文献
135.
Several studies have indicated that olfactory responses are impeded by
amiloride. Therefore, it was of interest to see whether, and if so which,
olfactory epithelial cellular compartments have amiloride- sensitive
structures. Using ultrastructural methods that involved rapid freezing,
freeze-substitution and low temperature embedding of olfactory epithelia,
this study shows that, in the rat, this tissue is immunoreactive to
antibodies against amiloride sensitive Na(+)- channels. However, microvilli
of olfactory supporting cells, as opposed to receptor cilia, contained most
of the immunoreactive sites. Apices from which the microvilli sprout and
receptor cell dendritic knobs had much less if any of the
amiloride-antibody binding sites. Using a direct ligand-binding
cytochemical method, this study also confirms earlier ones that showed that
olfactory receptor cell cilia have Na+, K(+)-ATPase. It is proposed that
supporting cell microvilli and the receptor cilia themselves have
mechanisms, different but likely complementary, that participate in
regulating the salt concentration around the receptor cell cilia. In this
way, both structures help to provide the ambient mucous environment for
receptor cells to function properly. This regulation of the salt
concentration of an ambient fluid environment is a function that the
olfactory epithelium shares with cells of transporting epithelia, such as
those of kidney.
相似文献
136.
137.
Adelmo L Cechin Marialva Sinigaglia Ney Lemke Sérgio Echeverrigaray Odalys G Cabrera Gonçalo AG Pereira José CM Mombach 《BMC plant biology》2008,8(1):50
Background
NEP1-like proteins (NLPs) are a novel family of microbial elicitors of plant necrosis. Some NLPs induce a hypersensitive-like response in dicot plants though the basis for this response remains unclear. In addition, the spatial structure and the role of these highly conserved proteins are not known. 相似文献138.
139.
Jesús Aguirre-Hernández Bruce S Milne Chris Queen Patricia CM O'Brien Tess Hoather Sean Haugland Malcolm A Ferguson-Smith Jane M Dobson David R Sargan 《BMC veterinary research》2009,5(1):1-18
Background
In dogs in the western world neoplasia constitutes the most frequently diagnosed cause of death. Although there appear to be similarities between canine and human cancers, rather little is known about the cytogenetic and molecular alterations in canine tumours. Different dog breeds are susceptible to different types of cancer, but the genetic basis of the great majority of these predispositions has yet to be discovered. In some retriever breeds there is a high incidence of soft tissue sarcomas and we have previously reported alterations of chromosomes 11 and 30 in two poorly differentiated fibrosarcomas. Here we extend our observations and present a case report on detail rearrangements on chromosome 11 as well as genetic variations in a tumour suppressor gene in normal dogs. 相似文献140.
Smid Eddy J Erkus Oylum Spus Maciej Wolkers-Rooijackers Judith CM Alexeeva Svetlana Kleerebezem Michiel 《Microbial cell factories》2014,13(1):1-9
This review describes the recent advances made in the studies of the microbial community of complex and undefined cheese starter cultures. We report on work related to the composition of the cultures at the level of genetic lineages, on the presence and activity of bacteriophages and on the population dynamics during cheese making and during starter culture propagation. Furthermore, the link between starter composition and starter functionality will be discussed. Finally, recent advances in predictive metabolic modelling of the multi-strain cultures will be discussed in the context of microbe-microbe interactions.
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