Hardiness Test Research Articles

Associations between single nucleotide polymorphisms of GDF9 and BMP15 genes and litter size in two dairy sheep breeds of Greece

The aim of the present study was to assess the presence of single nucleotide polymorphisms (SNPs) in the Growth Differentiating Factor 9 (GDF9) and Bone Morphogenetic Protein 15 (BMP15) genes, in two Greek sheep breeds i.e. Chios and Karagouniki, with high and moderate litter size (LS) i.e. number of lambs born, respectively. An examination of association(s) between the polymorphisms and LS, within breeds, was also conducted. Blood samples from 92 Chios and 96 Karagouniki ewes were collected, while repeated records on LS, were also available (n=239 and 259, respectively). Detection of SNPs was performed on the DNA products by PCR-RLFP analysis. Data analysis included examination of allelic and genotypic differentiation between the breeds, testing for Hardy–Weinberg Equilibrium (HWE) and association analysis between polymorphisms and LS. Genetic analysis showed that the G1 and G8 mutations of the GDF9 gene were significantly over-presented only in the highly prolific breed (Chios). The B4 mutation of the BMP15 gene was significantly over-presented only in the low prolific breed (Karagouniki). Both breeds were in Hardy–Weinberg disequilibrium (HWD), possibly due to selection pressure, population sub-structure and genetic drift. Certain polymorphisms of the G1, G4 and G8 sites of the GDF9 gene in the Chios breed were found to show heterozygote advantage with no evidence of infertility for the homozygous females. A similar trend was observed in the BMP15 gene although at no statistically significant level. In the Karagouniki breed, no significant associations between the studied polymorphisms and LS were detected.

Optimal measurement bases for Bell tests based on the Clauser-Horne inequality

The Hardy test of nonlocality can be seen as a particular case of the Bell tests based on the Clauser-Horne (CH) inequality. Here we stress this connection when we analyze the relation between the CH-inequality violation, its threshold detection efficiency, and the measurement settings adopted in the test. It is well known that the threshold efficiencies decrease when one considers partially entangled states and that the use of these states, unfortunately, generates a reduction in the CH violation. Nevertheless, these quantities are both dependent on the measurement settings considered, and in this paper we show that there are measurement bases which allow for an optimal situation in this trade-off relation. These bases are given as a generalization of the Hardy measurement bases, and they will be relevant for future Bell tests relying on pairs of entangled qubits.

Exact Tests for Hardy–Weinberg Proportions

Exact conditional tests are often required to evaluate statistically whether a sample of diploids comes from a population with Hardy-Weinberg proportions or to confirm the accuracy of genotype assignments. This requirement is especially common when the sample includes multiple alleles and sparse data, thus rendering asymptotic methods, such as the common chi(2)-test, unreliable. Such an exact test can be performed using the likelihood ratio as its test statistic rather than the more commonly used probability test. Conceptual advantages in using the likelihood ratio are discussed. A substantially improved algorithm is described to permit the performance of a full-enumeration exact test on sample sizes that are too large for previous methods. An improved Monte Carlo algorithm is also proposed for samples that preclude full enumeration. These algorithms are about two orders of magnitude faster than those currently in use. Finally, methods are derived to compute the number of possible samples with a given set of allele counts, a useful quantity for evaluating the feasibility of the full enumeration procedure. Software implementing these methods, ExactoHW, is provided.

Use of X-linked short tandem repeats loci to confirm mutations in parentage caseworks

Background Analysis of short tandem repeats (STRs) has become wide-spread in routine for parentage test. However, the accuracy of STR is sometimes interfered by the presence of microsatellite mutations. Analysis of other DNA markers such as the HV1 and HV2 hypervariable regions of mitochondrial DNA or the Y-STR becomes essential to settle the noncongruence. Owing to the time-consuming nature of these tests, we explored here the use of X-chromosome STR (X-STR) to resolve the paternity and maternity disputes. Methods At first, the autosomal STR mutation frequencies among 4758 Taiwanese were analyzed. Population data were obtained from randomly selected 99 females and 101 males to setup the X-STR database. Two families with a mismatch of one allele in autosomal STR analysis were subjected to the X-STR test to explore its clinical application. Results The STR mutations occurred in all 15 autosomal STR loci with the exception of TH01 and TPOX. The mutation rates could reach as high as 0.106% for the loci of D8S1179 and D18S51. As to the X-STR frequencies, the probability values of exact tests for Hardy–Weinberg equilibrium were 0.1471, 0.0019, 0.0025, 0.1427, and 0.1167 for the loci of DXS7132, DXS981, DXS6789, DXS101, and HPRTB, respectively. In addition, 33 and 34 different haplotypes were revealed for DXS101-DXS6789 and DXS7132-DXS981, respectively. Furthermore, two cases with one allele mismatch in routine parentage test were resolved by performing X-STR analysis. Conclusion Typing of X-STR markers is recommended for parentage test when 1 or 2 alleles mismatch is present or when the samples are difficult to be analyzed.

Hardy’s test versus the Clauser-Horne-Shimony-Holt test of quantum nonlocality: Fundamental and practical aspects

We compare two different tests of quantum nonlocality, both in theoretical terms and with respect to a possible implementation in a mesoscopic circuit: Hardy's test [L. Hardy, Phys. Rev. Lett. 68, 2981 (1992)] and the Clauser-Horne-Shimony-Holt (CHSH) test, the latter including a recently discovered inequality relevant for experiments with three possible outcomes [D. Collins and N. Gisin, J. Phys. A 37, 1775 (2004)]. We clarify the geometry of the correlations defined by Hardy's equations with respect to the polytope of causal correlations, and show that these equations generalize to the CHSH inequality if the slightest imperfections in the setup need to be taken into account. We propose a mesoscopic circuit consisting of two interacting Mach-Zehnder interferometers in a Hall bar system for which both Hardy's test and the CHSH test can be realized with a simple change of gate voltages, and evaluate the robustness of the two tests in the case of fluctuating experimental parameters. The proposed setup is remarkably robust and should work for fluctuations of beam splitter angles or phases up to the order of 1 radian, or single particle loss rates up to about 15%.

A Conversation with Seymour Geisser

A Conversation with Seymour Geisser

Microsatellite variability and heterozygote excess in Elymus trachycaulus populations from British Columbia in Canada

Microsatellite markers were used to assess the genetic diversity and population structure in four populations of Elymus trachycaulus from British Columbia and one population of Elymus alaskanus from Northwest Territories. Fourteen microsatellite loci were used in this study. Our results indicated that E. trachycaulus is highly polymorphic, with an average percentage of polymorphic loci of 96.5% over the four populations. Average expected heterozygosity values ( H E or gene diversity) varied from 0.418 to 0.585 with a mean of 0.497. Most of the genetic variation was found within populations (85%) and the differentiation among populations was found to be 15% ( F st = 0.15). Interpopulation genetic distances corresponded well with the geographic distance between the population sites of origin, as well as morphological characteristics. Tests for Hardy–Weinberg equilibrium (HWE) for all loci and all populations revealed that all loci significantly differ from HWE. Subsequent analysis indicated that departure from HWE at some loci was due to an excess of heterozygotes. Possible explanations for heterozygote excess are discussed. The most likely reason for observed heterozygote excess could be due to the polyploidy nature of the species.

Overwintering and population dynamics of Bemisia tabaci biotype B in greenhouse during the spring in northern China

Since the sweetpotato whitefly, Bemisia tabaci (Gennadius) biotype B invaded southern China in the mid-1990s, it had spread to most other regions of the country, and become an important pest in agricultural and horticultural production. Investigations on overwintering of B. tabaci biotype B and its spring reproduction in northern China were conducted to determine the main factors that might contribute to an understanding of the population dynamics of this pest for developing improved pest control strategies. A cold hardiness test showed that when exposed for 10 h at −10 °C, mortalities of eggs, nymphs, and adults reached to 86.6%, 88.4%, and 100%, respectively, suggesting that it is probably impossible for feral populations of B. tabaci to survive in the winter under natural environmental conditions in northern China. A survey on vegetables, ornamental plants and weeds in greenhouses at Hebei Province and Beijing in northern China revealed at least 14 species of plants on which B. tabaci fed during the winter and spring. Lycopersicon esculentum Mill, Brassica alboglabra Bailey, Ficus carica L., Euphorbia pulcerrima Wild, and Hemelia patens Haence were the main host plants. Further research on the population dynamics of B. tabaci on three major greenhouse hosts; tomato, cucumber, and melon, indicated that densities remained at a low level during the winter, but increased steadily from February to March until migration into field crops in April. It is concluded that the control of the insect in greenhouse in winter and spring can play an important role for seasonal management of this pest in northern China.

Population genetic data on D1S80, D17S5, ApoB, COL2A1 and Ig-JH in Northeastern Thais

Allele frequency distributions at five VNTR loci namely; D1S80, D17S5, ApoB, COL2A1 and Ig-JH were examined in Northeastern Thais. The number of alleles at each locus were 19, 13, 14, 6 and 8 with the heterozygous frequencies of 0.814, 0.818, 0.676, 0.579 and 0.288, respectively. No significant deviations were found by statistical tests for Hardy–Weinberg equilibrium. The combined power of discrimination for all five loci was 0.99998.

Characterization of nine microsatellite loci in impala (Aepyceros melampus)

AbstractNine microsatellite loci were isolated from a genomic DNA library created from impala (Aepyceros melampus). Observed and expected levels of heterozygosity were computed utilizing 25 individuals from a population in central Kenya. Tests for Hardy–Weinberg equilibria were conducted and found that three of the nine loci deviated from equilibrium in this population. These markers were developed to analyse the genetic effects of culling and isolation on a game preserve in Kenya.

Characterization of eight microsatellite loci in Grant's gazelle (Gazella granti)

AbstractEight microsatellite loci were isolated from a genomic DNA library created from Grant's gazelle (Gazella granti). Observed and expected levels of heterozygosity were computed utilizing 20 individuals from a population in Central Kenya. Tests for Hardy–Weinberg equilibria were conducted and found that two of the eight loci deviated from equilibrium in this population. These markers were developed to analyse the genetic effects of culling and isolation on a game preserve in Kenya.

Ultraviolet Radiation and Plant Frost Hardiness in the Subarctic

The effects of ultraviolet radiation on plant frost hardiness were studied at two subarctic experimental sites, namely Abisko (northern Sweden, 68°N) and Sodankylä (northern Finland, 67°N). The Abisko treatment mimicked 15% ozone depletion and had been running for 7 yr. The investigated plant species was bilberry (Vaccinium myrtillus L.). The Sodankylä treatment consisted of lingonberry (V. vitis-idaea) and seedlings of mountain birch (Betula pubescens ssp. czerepanovii), which were exposed to both elevated UV-B and UV-A radiation in a modulated system corresponding to about 20% loss of the ozone layer. The frost hardiness tests in the Sodankylä experiment were carried out after UV exposure for one growing season. The frost hardiness of bilberry in Abisko was marginally decreased as a consequence of elevated UV-B exposure similarly to the frost hardiness of lingonberry and mountain birch in the Sodankylä experiment in August. The work provides evidence for rather than against a reducing effect of ultraviolet radiation on plant frost hardiness. The results suggest that elevated UV-A radiation probably reduces plant frost hardiness more efficiently than UV-B radiation.

Optimal testing strategies for large, sparse multinomial models

Much has been written in the literature on testing for independence in contingency tables. A number of related topics have been studied, including the choice of test statistic, the appropriateness of asymptotic results versus exact tests, and the use of conditional or unconditional analyses. Much of the work to date has focused on relatively small contingency tables. The literature on testing for Hardy–Weinberg equilibrium (HWE) is substantive as well. Most of the focus to date has been on loci with relatively small numbers of alleles. The increased use of genetic markers with large numbers of alleles (e.g., forensic DNA profiling) is quickly dating this previous work. The size of the multinomial vectors under consideration grows quickly. Even relatively large samples will produce somewhat sparse multinomial data sets with small expected frequencies, calling asymptotic results into question. In the face of large, sparse multinomials, we provide a comprehensive comparison of test statistics and testing strategies (asymptotic versus exact, conditional versus unconditional) to test for independence (i.e., the presence of HWE) at one locus with many alleles. Attained significance level and power are evaluated. We find that Fisher's exact test is most appropriate for small samples, and the asymptotic chi-square goodness-of-fit statistic works well with large samples, relative to the number of multinomial categories. The log-likelihood ratio statistic performs poorly.

Development of the X-linked tetrameric microsatellite markers HumDXS6803 and HumDXS9895 for forensic purpose

This paper presents sequence and population genetic data of the X-linked DXS6803 and DXS9895 short tandem repeat (STR). The tetranucleotide repeat polymorphism DXS6803 (also known as CHLC.GATA45H11) and DXS9895 (also known as CHLC.GATA124B04) are located at the Xq12-Xq21.33 and Xpter-Xp22.2 region, respectively. In kinship testing, DXS6803 and DXS9895 are suitable for concomitant use. Population genetic data were obtained by analyzing 182 unrelated females and 110 males from Chinese Han population. In this population, both DXS6803 and DXS9895 exhibited seven clearly distinguishable alleles ranging from 109 bp to 128 bp and 139 bp to 163 bp in length, respectively. Testing for Hardy–Weinberg equilibrium (HWE) showed no significant deviation for these two loci. The polymorphism information content (PIC), observed heterozygosity ( H obs) and power of exclusion for parentage testing of a girl for trios (PE trio) and duos (PE duo) were 0.67, 0.687, 0.673 and 0.530 for DXS6803, and 0.69, 0.736, 0.688 and 0.547 for DXS9895, respectively. Seventy-eight families studies of these two loci confirmed X-linked codominant inheritance and mutations were not found.

Allele sharing in first-degree and unrelated pairs of individuals in the Ge.F.I. AmpFlSTR® Profiler Plus™ database

Eleven Italian forensic laboratories participated in a population study based on the AB Profiler Plus™ loci with proficiency testing. The validated database, including 1340 individuals, is available on-line. Tests for Hardy–Weinberg equilibrium, gametic unbalance, and heterogeneity of gene frequency were generally not significant. Gene frequencies at each locus were consistent with those of two previously published Italian studies, but different from a third. Individuals of each subsample were paired, and the total number of alleles shared across the nine loci was determined in each pair. The analysis was replicated over the total sample. In addition, two samples of mother–child pairs (N=315) and full-sib pairs (N=91) were subjected to allele sharing analysis. The resulting distributions were sufficiently distinct from the sample of unrelated pairs as to be of practical usefulness.

Growth, morphology, and cold hardiness of Chamaecyparis nootkatensis seedlings originating from an abbreviated reproductive cycle

A common garden study investigated growth, morphology, and cold hardiness of yellow-cedar (Chamaecyparis nootkatensis (D. Don) Spach) seedlings originating from seed that had matured at an accelerated rate. This early maturing seed, produced at a low-elevation southern Vancouver Island seed orchard, was known to have similar germinability and seedling morphology as high-elevation normally maturing seeds. Population differences in 3-year-old seedlings were evident only in shoot harvest index (ratio of stem/shoot dry weight). The amount of stem elongation that occurred prior to the formation of secondary foliage (juvenile height) and harvest index were weakly correlated with source elevation at which maternal parents were developed. Traits that exhibited no discernable differences between progeny from early maturing seed and the control normally maturing seed included midwinter cold hardiness testing and selected measures of shoot morphology and growth. The control seedlings had significantly less height growth prior to the transition of primary foliage to secondary foliage formation than did the seedlings originating from early maturing seed.

Patterns of genetic variation in mountain hemlock ( Tsuga mertensiana (Bong.) Carr.) with respect to height growth and frost hardiness

Genetic structure (variance among and within populations) and geographic pattern of variations in growth and frost hardiness of mountain hemlock ( Tsuga mertensiana (Bong.) Carr.) populations from coastal British Columbia (BC) were examined. Populations fell into two main groups — south coast (16 sources) and north coast (two sources). Height growth of greenhouse grown seedlings was measured during the first growing season on a weekly basis whereas frost hardiness and branch water content were evaluated during the fall at monthly intervals. Significant differences among the populations were found in maximum instantaneous growth rate, height at the end of the growing season and in October and November frost hardiness. There were no differences in date of maximum growth rate, branch water content and September frost hardiness. Most of the genetic variance was found within populations: 77% for height, maximum growth rate and November frost hardiness and 87% for October frost hardiness. Geographic trends were identified using multiple linear regression and canonical correlation analyses based on population means and latitude, longitude and elevation of the population origin. The uneven distribution of sources limited the extrapolation, but some general trends appeared. Maximum instantaneous growth rates increased with latitude, elevation and decreased with longitude ( R 2=0.64) and consequently were negatively correlated with the length of the growing season in the seed collection sites. Both populations from the north coast developed frost hardiness earlier than any population from the south coast. The relationship between climate coldness and growth rates has potential implications for seed transfer guidelines. Due to their higher growth rates, plants from higher altitudes may accomplish the same amount of growth within a shorter period compared to plants from lower altitudes when both are transferred north. Results of the frost hardiness tests indicate that seed transfer along the British Columbia coast of more than 3° northward will considerably increase chances of frost damage in plantations.

Cold Hardiness Testing for Douglas-Fir Tree Improvement Programs: Guidelines for a Simple, Robust, and Inexpensive Screening Method

Abstract Operational methods are needed for screening genotypes in breeding programs for adaptive traits. In this article, we present a detailed description of one procedure for screening improved coastal Douglas-fir seedlings and saplings for cold hardiness, based on research results of the Pacific Northwest Tree Improvement Research Cooperative. Artificial freeze testing of detached shoots from genetic tests, followed by visual scoring of injury, has proved to be an efficient, reliable, and cost-effective method of screening large numbers of genotypes. Relevant research results are summarized, and practical details of this methodology are presented for straightforward implementation by Douglas-fir breeders and researchers. West. J. Appl. For. 15(3):129-136.

424 A Comparison of Techniques Used for Determining Freezing Injury on Two Apple (Malus × domestica Borkh.) Cultivars: Liberty and RedMax

Hardiness testing of the wood of deciduous fruit trees has been conducted using a variety of techniques. In our studies, the objective was to determine an efficient method of determining freezing injury for apple (Malus × domestica Borkh.) wood. We tested 1-year old wood of two cultivars: Liberty and RedMax. The wood was tested over the course of 2 years (1998 and 1999). Collection began in the late fall and continued throughout the winter (until it was determined full hardiness had been achieved) and then again in the early spring. The wood was cut into 1-cm sections and frozen. The artificial freezing was conducted in an ethanol bath, with the temperature lowered at 5 °C/h. Samples were removed in 3-min intervals. After freezing, the wood was acclimated to 4 °C for 12 h. Three tests were conducted to determine the hardiness/injury to the tissues. The tests used were: discoloration, callus growth and vital staining (with 2,3,5-triphenyltetrazolium chloride). This was a split block design with samples collected randomly from each tree. Four replicates (12 trees) of each cultivar were tested. Results showed that the callus test predicted the same LT50 as the other two tests, discoloration and vital staining. Discoloration was not easy to differentiate and was the most time-consuming. The callus grown by the apple wood was easily formed and distinguished. The callus test does not require the tetrazolium stain; therefore, one less step was needed in comparison to the vital staining test. This reduced testing time by over 6 h.

High Levels of Gene Flow and Heterozygote Excess Characterize Rhizoctonia solani AG-1 IA (Thanatephorus cucumeris) from Texas

To date, much of the genetics of the basidiomycete Thanatephorus cucumeris (anamorph=Rhizoctonia solani) remains unknown. Here, we present a population genetics study using codominant markers to augment laboratory analyses. Seven single-copy nuclear RFLP markers were used to examine 182 isolates of Rhizoctonia solani AG-1 IA collected from six commercial rice fields in Texas. Thirty-six multilocus RFLP genotypes were identified. Population subdivision analyses indicated a high degree of gene flow/migration between the six geographic populations. Tests for Hardy–Weinberg equilibrium (HWE) among the 36 multilocus RFLP genotypes revealed that four of the seven loci did not significantly differ from HWE. Subsequent analysis demonstrated that departures from HWE at the three remaining loci were due to an excess of heterozygotes. Data presented here suggest that R. solani AG-1 IA is actively outbreeding (heterothallic). Possible explanations for heterozygote excess, which was observed at all seven RFLP loci, are discussed.