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901.
Niel Hens Christel Faes Marc Aerts Ziv Shkedy Koen Mintiens Hans Laevens Frank Boelaert 《Journal of Agricultural, Biological & Environmental Statistics》2007,12(4):498-513
Modeling infectious diseases data is a relatively young research area in which clustering and stratification are key features.
It is not unlikely for these data to have missing values. If values are missing completely at random, the analysis on the
complete cases is valid. However, in practice this assumption is usually not fulfilled. This article shows the effect of ignoring
missing data in modeling the force of infection of the bovine herpesvirus-1 in Belgian cattle and proposes the use of weighted
generalized estimating equations with constrained fractional polynomials as a flexible modeling tool. 相似文献
902.
Fujun Wang Melanie M. Wall 《Journal of Agricultural, Biological & Environmental Statistics》2003,8(3):296-309
In spatial predictions, researchers usually treat the estimated theoretical variogram parameters as known without error and ignore the variability of the parameter estimators. Although the prediction is still unbiased, the prediction error is usually underestimated. Therefore, the coverage probability of the prediction interval usually is lower than the nominal probability. A simulation study is performed to show how the coverage probability for prediction relates to the true range and sill of an exponential variogram. This article proposes two parametric bootstrap methods to incorporate the variability of the corresponding parameter estimators. A simulation study is performed to evaluate the coverage probability of these proposed methods. Finally, we apply the parametric bootstrap methods to a real dataset and compare the results with those from naive (i.e., treating estimated parameters as known) and Bayesian methods. 相似文献
903.
Nitrogen fixation in biological soil crusts from southeast Utah,USA 总被引:20,自引:0,他引:20
Jayne Belnap 《Biology and Fertility of Soils》2002,35(2):128-135
Biological soil crusts can be the dominant source of N for arid land ecosystems. We measured potential N fixation rates biweekly for 2 years, using three types of soil crusts: (1) crusts whose directly counted cells were >98% Microcoleus vaginatus (light crusts); (2) crusts dominated by M. vaginatus, but with 20% or more of the directly counted cells represented by Nostoc commune and Scytonema myochrous (dark crusts); and (3) the soil lichen Collema sp. At all observation times, Collema had higher nitrogenase activity (NA) than dark crusts, which had higher NA than light crusts, indicating that species composition is critical when estimating N inputs. In addition, all three types of crusts generally responded in a similar fashion to climate conditions. Without precipitation within a week of collection, no NA was recorded, regardless of other conditions being favorable. Low (<1°C) and high (>26°C) temperatures precluded NA, even if soils were moist. If rain or snow melt had occurred 3 or less days before collection, NA levels were highly correlated with daily average temperatures of the previous 3 days (r2=0.93 for Collema crusts; r2=0.86 for dark crusts and r2=0.83 for light crusts) for temperatures between 1°C and 26°C. If a precipitation event followed a long dry period, NA levels were lower than if collection followed a time when soils were wet for extended periods (e.g., winter). Using a combination of data from a recording weather datalogger, time-domain reflectometry, manual dry-down curves, and N fixation rates at different temperatures, annual N input from the different crust types was estimated. Annual N input from dark crusts found at relatively undisturbed sites was estimated at 9 kg ha-1 year-1. With 20% cover of the N-fixing soil lichen Collema, inputs are estimated at 13 kg ha-1 year-1. N input from light crusts, generally indicating soil surface disturbance, was estimated at 1.4 kg ha-1 year-1. The rates in light crusts are expected to be highly variable, as disturbance history will determine cyanobacterial biomass and therefore N fixation rates. 相似文献
904.
Genetic diversity of winter wheat in Shaanxi province, China, and other common wheat germplasm pools
Samuel P. Hazen Lieceng Zhu Hong-Sik Kim Guoshiun Tang Richard W. Ward 《Genetic Resources and Crop Evolution》2002,49(4):439-448
Cultivated Chinese wheat germplasm has been a valuable genetic resourcein international plant breeding. Landraces endemic to China are a geneticresource that is distinct from other wheat germplasm. Patterns of geneticdiversity among cultivated Chinese accessions and relationship to othergermplasm pools are unknown, despite the proven value and potential novelty. Theobjective of this work was to determine the level of genetic diversity withinimproved Chinese germplasm in the context of several other wheat germplasmpools. We analyzed a set of improved accessions cultivated from the 1940s to the1990s in Shaanxi province, China, using six simple sequence repeat (SSR) primerpairs and 30 restriction fragment length polymorphism - probe enzymecombinations (RFLP-PEC) previously used to characterize 21 geographically basedgermplasm pools. Shaanxi germplasm consists of three groups based on foreignintroductions from Italy, Australia, Denmark, and Russia. There was a decreasein genetic diversity among Shaanxi accessions cultivated in the 1970s and 1980sto the 1990s, and accession classifications based on primary decade ofcultivation were found to be significantly undifferentiated. The analysis of themean genetic distance among 22 geographically based pools of germplasm suggestsseveral regions are significantly undifferentiated. A vast majority of the totalamount of variation was found within pools; therefore, pools appear to belargely differentiated based on small differences in band relative frequency andfew if any unique bands. Previous studies have identified some Chinese landracepools as morphologically and genetically unique. The Shaanxi pool does not havethe same unique morphological or genetic features, nor is it more similar to thelandrace pools than other improved germplasm pools. 相似文献
905.
Dong Fu Liang Chen Guohui Yu Yi Liu Qiaojun Lou Hanwei Mei Liang Xiong Mingshou Li Xiaoyan Xu Lijun Luo 《Euphytica》2011,180(2):209-218
Sheath blight, caused by the pathogen Rhizoctonia solani Kühn, is one of the most serious diseases of rice and leads to severe yield loss worldwide. A recombinant inbred line (RIL)
population consisting of 121 lines was constructed from a cross between HH1B and RSB03, the latter of which is a deep-water
rice variety. Five traits were used to evaluate sheath blight resistance, namely disease rating (DR), lesion length (LL),
lesion height (LH), relative lesion length [RLL, the ratio of LL to plant height (PH)], and relative LH (RLH, the ratio of
LH to PH). Using the RIL population and 123 molecular markers, we identified 28 quantitative trait loci (QTLs) for the five
traits in two environments. These QTLs are located on nine chromosomes and most of them are environment specific. A major
QTL for DR (qSBR1) on chromosome 1 was identified with contributions of 12.7% at Shanghai and 42.6% at Hainan, and it collocated with a QTL
for PH. The allele at this locus from RSB03 enhances sheath blight resistance and increases PH. Another QTL for DR on chromosome 7
was adjacent to QTLs for heading date (HD) and four other disease traits. RSB03 also carries the resistant allele at this
locus and shortens HD. The susceptible parent, HH1B, provides the resistance allele at the locus qSBR8, where QTLs for four other disease traits were identified. QTL mapping results showed that most QTLs for LL, LH, RLL, and
RLH are collocated with QTLs for DR. Three QTLs for DR are independent from HD, PH, and four other disease traits, while four
QTLs are closely related to HD and PH. Four QTLs for LL, LH, RLL, and RLH are independent from DR, HD, and PH, while there
is only one region harboring QTLs for these four traits and HD. Correlation analysis and QTL mapping results indicated that
LL, LH, RLL, and RLH might be important indices, like DR, for evaluating the level of resistance to rice sheath blight. 相似文献
906.
András Cseri Mátyás Cserháti Maria von Korff Bettina Nagy Gábor V. Horváth András Palágyi János Pauk Dénes Dudits Ottó Törjék 《Euphytica》2011,181(3):341-356
In the present study, allele mining was conducted on a panel of drought related candidate genes in a set of 96 barley genotypes
using EcoTILLING, which is a variant of the targeting induced local lesions in genomes (TILLING) technology. Analyzing approximately
1.5 million basepairs in barley a total number of 94 verified unique haplotypes were identified in 18 amplicons designed for
9 genes. Overall, 185 single nucleotide polymorphisms (SNPs) and 46 insertions/deletions (INDELs) were detected with a mean
of 1SNP/92 bp and 1INDEL/372 bp genomic sequence. Based on overlapping haplotype sequences, markers were developed for four
candidate genes (HvARH1, HvSRG6, HvDRF1, HVA1), which allows distinguishing between the main haplotypes showing either differences in amino acid sequence or which have
larger INDELs in the promoter region. As “proof of concept”, the HvARH1 and HvSRG6 haplotypes were tested for the level of abscisic acid-induced gene expression in subsets of genotypes belonging to different
haplotype categories. An integrated database was developed to contain information about the genes, genotypes, and haplotypes
analyzed in this study. The database supplies profound information about the natural variation in the tested drought related
candidate genes providing a significant asset for further mapping studies dealing with this highly polygenic trait. 相似文献
907.
Zhenfeng Jiang Binbin Zhang Weili Teng Yingpeng Han Xue Zhao Desheng Sun Zhongchen Zhang Wenbin Li 《Euphytica》2011,177(3):431-442
The oil accumulation in the developing soybean seed has been shown to be a dynamic process with different rates and activities
at different phases affected by both genotype and environment. The objective of the present study was to investigate additive,
epistatic and quantitative trait loci (QTL) × environment interaction (QE) effects of the QTL controlling oil filling rate
in soybean seed. A total of 143 recombinant inbred lines (RILs) derived from the cross of Charleston and Dongnong 594 were
used in this study to obtain 2 years of field data (2004 and 2005). A total of 26 QTL with significantly unconditional and
conditional additive (a) effect and/or additive × environment interaction (ae) effect at different filling stages were identified on 14 linkage groups. Among the QTL with significant a effects, 18 QTL showed positive effects and 6 QTL had negative effects on seed filling rate of oil content during seed development.
A total of 29 epistatic pairwise QTL underlying seed filling rate were identified at different filling stages. About 28 pairs
of the QTL showed additive × additive epistatic (aa) effects and 14 pairs of the QTL showed aa × environment interaction (aae) effects at different filling stages. QTL with aa and aae (additive × additive × environment) effects appeared to vary at different filling stages. Our results demonstrated that oil
filling rate in soybean seed were under genetic, developmental and environmental control. 相似文献
908.
Molecular genetics of race non-specific rust resistance in wheat 总被引:1,自引:0,他引:1
Evans S. Lagudah 《Euphytica》2011,179(1):81-91
Over 150 resistance genes that confer resistance to either leaf rust, stripe rust or stem rust have been catalogued in wheat
or introgressed into wheat from related species. A few of these genes from the ‘slow-rusting’ adult plant resistance (APR)
class confer partial resistance in a race non-specific manner to one or multiple rust diseases. The recent cloning of two
of these genes, Lr34/Yr18, a dual APR for leaf rust and stripe rust, and Yr36, a stripe rust APR gene, showed that they differ from other classes of plant resistance genes. Currently, seven Lr34/Yr18 haplotypes have been identified from sequencing the encoding ATP Binding Cassette transporter gene from diverse wheat germplasm
of which one haplotype is commonly associated with the resistance phenotype. The paucity of well characterised APR genes,
particularly for stem rust, calls for a focused effort in developing critical genetic stocks to delineate quantitative trait
loci, construct specific BAC libraries for targeted APR genes to facilitate robust marker development for breeding applications,
and the eventual cloning of the encoding genes. 相似文献
909.
Haejeen Bang Dong Youn Cho Kil-Sun Yoo Moo-Kyoung Yoon Bhimanagouda S. Patil Sunggil Kim 《Euphytica》2011,179(3):439-449
In order to implement reliable marker-assisted selection systems for the restorer-of-fertility locus (Ms) in onions (Allium cepa L.), simple PCR-based codominant markers linked to the Ms locus were developed. Based on the EST probe sequences of previously reported RFLP markers, full-length genomic sequences
of the gene encoding putative oligopeptide transporter (OPT) was obtained by RACE. The first intron contained two 108 and
439-bp indel polymorphisms between the two Ms allele-linked OPT alleles. A simple PCR marker for OPT was developed by designing a primer pair on the flanking regions of
the 108-bp indel which is created by two tandem repeats. The second simple PCR marker was developed from the EST probe encoding
photosystem I subunit O (PsaO). Two 14 and 39-bp tandem repeats were identified from the 5′ upstream sequences of the PsaO-coding
gene, which were isolated by genome walking. Three different compositions of these tandem repeats were identified from diverse
onion germplasm. A primer set binding to the flanking sequence of these polymorphic repeats was used to amplify three different
marker haplotypes. The OPT marker was tightly linked to the Ms locus at a distance of 1.5 cM, but the analysis of the linkage relationship showed little linkage disequilibrium between
the marker and the Ms locus. Even so, these simple PCR markers are valuable tools for the marker-assisted selection of segregating individuals
in onion F1 hybrid breeding programs. 相似文献
910.
Abbas Rezaeizad Benjamin Wittkop Rod Snowdon Maen Hasan Valiollah Mohammadi Abbas Zali Wolfgang Friedt 《Euphytica》2011,177(3):335-342
Association mapping identifies quantitative trait loci (QTLs) by examining the marker-trait associations that can be attributed
to the strength of linkage disequilibrium between markers and functional polymorphisms across a set of diverse germplasm.
In this study, association mapping was performed to detect QTL-linked and genome wide SSR markers linked to phenolic compounds
of extraction meal in a population of 49 genetically diverse oilseed rape cultivars of dark-seeded, winter-type oilseed rape
accessions. Correction for population structure was performed using 559 genome wide SSR markers. Results showed that seed
colour is an important contributor to seed meal quality. Totally, 52 SSR markers linked to phenolic compounds were detected,
five of them being QTL linked markers. Some of these markers were already mapped on Brassica napus chromosomes that contain known QTL controlling oilseed rape meal quality traits. Our results demonstrate that association
mapping is a useful approach to complement and enhance previous QTL information for marker-assisted selection. 相似文献