Strain Crosses Research Articles

Three-locus analysis in conjunction with strain crosses confirms the existence of reproductively isolated populations in Paramecium jenningsi

Paramecium jenningsi (Diller & Earl, 1958) was formerly considered to be a species with only one syngen (genetic species) based on an inter-strain cross of two strains, cytological analysis, and an investigation of esterases and acid phosphatases. However, the existence of syngens within the species was later suggested by genetic studies, i.e. classical strain crosses of new strains and molecular PCR-based analyses (RAPD, RFLP), as well as by sequencing the H4 gene fragment. This issue still needs to be clarified by the application of molecular markers, genetic tests and cytological preparations. In the present study, we tested 12 strains of P. jenningsi originating from Asia, North America and Africa. Trees reconstructed on the basis of three genome fragments (ITS1-5.8S-ITS2-5’LSU, COI and CytB) show that P. jenningsi is divided into two distinct clusters (PJ1, PJ3) and one branch (PJ2) which correspond to reproductively isolated groups revealed by strain crosses. A study based both on strain crosses and a three-locus comparison gives the opportunity for a more complete identification of the reproductively isolated populations of P. jenningsi and other ciliate species.

Strain-insensitive and high temperature fiber sensor based on a Mach–Zehnder modal interferometer

In this paper, a strain insensitive high temperature fiber sensor based on the modal interferometer is proposed. It is composed of a piece of small-core photosensitive fiber (SCPSF) which is spliced between two pieces of single mode fiber (SMF). Compared to other high temperature fiber sensor based on the modal interferometer, the sensor owns the highest temperature sensitivity of 106.64pm/°C from 200°C to 1000°C. The temperature to strain cross sensitivity of the sensor is low and only 0.00675°C/με. The reasons for realizing the high temperature sensitivity is also discussed.

Out of the bottleneck: the Diversity Outcross and Collaborative Cross mouse populations in behavioral genetics research

The historical origins of classical laboratory mouse strains have led to a relatively limited range of genetic and phenotypic variation, particularly for the study of behavior. Many recent efforts have resulted in improved diversity and precision of mouse genetic resources for behavioral research, including the Collaborative Cross and Diversity Outcross population. These two populations, derived from an eight way cross of common and wild-derived strains, have high precision and allelic diversity. Behavioral variation in the population is expanded, both qualitatively and quantitatively. Variation that had once been canalized among the various inbred lines has been made amenable to genetic dissection. The genetic attributes of these complementary populations, along with advances in genetic and genomic technologies, makes a systems genetic analyses of behavior more readily tractable, enabling discovery of a greater range of neurobiological phenomena underlying behavioral variation.

Investigating the Ustilago maydis/Zea mays pathosystem: Transcriptional responses and novel functional aspects of a fungal calcineurin regulatory B subunit

The sustainable control of basidiomycete biotrophic plant pathogenesis requires an understanding of host responses to infection, as well as the identification and functional analysis of fungal genes involved in disease development. The creation and analysis of a suppressive subtractive hybridization (SSH) cDNA library from Ustilago maydis-infected Zea mays seedlings enabled the identification of fungal and plant genes expressed during disease development, and uncovered new insights into the interactions of this model system. Candidate U. maydis pathogenesis genes were identified by using the current SSH cDNA library analysis, and by knowledge generated from previous cDNA microarray and comparative genomic analyses. These identifications were supported by the independent determination of transcript level changes in different cell-types and during pathogenic development. The basidiomycete specific um01632, the highly in planta expressed um03046 (zig1), and the calcineurin regulatory B subunit (um10226, cnb1), were chosen for deletion experiments. um01632 and zig1 mutants showed no difference in morphology and did not have a statistically significant impact on pathogenesis. cnb1 mutants had a distinct cell division phenotype and reduced virulence in seedling assays. Infections with reciprocal wild-type×Δcnb1 haploid strain crosses revealed that the wild-type allele was unable to fully compensate for the lack of a second cnb1 allele. This haploinsufficiency was undetected in other fungal cnb1 mutational analyses. The reported data improves U. maydis genome annotation and expands on the current understanding of pathogenesis genes in this model basidiomycete.

An apparent increase in meiotic silencing strength in crosses involving inbred Neurospora crassa strains

Meiotic silencing by unpaired DNA is a presumed RNAi-mediated elimination of the transcripts of any gene that is not properly paired with a homolog in meiosis. Wild-isolated strains of Neurospora crassa can be classified into three types based on the apparent strength of meiotic silencing of the bml (β-tubulin) and mei-3 genes in crosses of the wild strains with the tester strains ::Bmlr and ::mei-3. Crosses with “OR” and “Sad” type wild-isolates, respectively, did or did not silence both the genes, whereas crosses with the “Esm” type silenced bml, but not mei-3+. Presumably, bml is more sensitive to silencing than mei-3, and silencing is strongest in crosses with the OR type, weakest (or non-evident) in crosses with the Sad type, and of intermediate strength in crosses with Esm type. Now, while constructing recombinant inbred lines from the Sad type wild strains Bichpuri-1 a and Spurger-3 A, we found that although crosses of Bichpuri-1 a and Spurger-3 A, and of most of their f1 progeny, with the ::Bmlr and ::mei-3 testers were consistently and reproducibly Sad type, those of later generation strains of each line could show Sad, Esm, or a variably expressive Sad/Esm type. Since any genotype found in a later generation is, in principle, obtainable in the f1, the observed transition from an apparently stable Sad phenotype to an apparently unstable Sad/Esm phenotype appears not to be due to genotype differences between the generations. Therefore, the Sad versus Esm difference may have a genotype-independent basis.

An assessment of haplotype variation in ribosomal and mitochondrial DNA fragments suggests incomplete lineage sorting in some species of the Paramecium aurelia complex (Ciliophora, Protozoa)

The Paramecium aurelia complex (Ciliophora, Protozoa) Sonneborn (1975) is composed of 15 sibling species, which are morphologically indistinguishable but sexually isolated. Therefore, the P. aurelia complex seems to be an ideal model for testing hypotheses about recent speciation events. Here we present two-locus (ITS1-5.8S-ITS2-5′LSU rDNA and COI mtDNA) analyses using over 120 strains collected from around the world and representing all currently known species of the complex. According to our findings, the studied species show different levels of haplotype variability. Some of them appear on the obtained trees as polyphyletic (e.g., P. dodecaurelia), while others as monophyletic (e.g., P. quadecaurelia), clusters. The revealed discrepancies, which are manifested by different mating behavior and haplotypes not characteristic of particular species, may be explained by incomplete lineage sorting. Furthermore, the phenomena of hybridization and introgression are considered as another explanation for our results. Despite the above discrepancies, “polyphyletic taxa” should be considered true biological species based on the results of genetic crosses. Using a combination of both strain crosses (the biological species concept) and molecular methods (the phylogenetic species concept) seems to be the appropriate way of delimiting species in closely related eukaryotic microorganisms such as the P. aurelia complex.

Mild strain cross protection of tristeza: a review of research to protect against decline on sour orange in Florida.

Tristeza, caused by Citrus tristeza virus (CTV), has long been present in Florida but outbreaks of decline on sour orange rootstock were occasional events until the late 1970s. Sour orange rootstock was valued for the high quality of fruit produced and was widely used because of its tolerance of citrus blight, a disease of unknown etiology. Research was directed towards the selection and screening of mild strains of CTV which could protect against sour orange decline strains. Following the introduction of Toxoptera citricida (also known as the brown citrus aphid) in 1995 there was a greater concern for maintaining production of existing blocks of citrus on sour orange rootstock. Availability of the CTV genome sequence around the same time as well as molecular characterization of in planta CTV populations led to the selection of mild CTV isolates which when inoculated into existing field trees, extended the productive life of the groves and enabled a more graduate replanting of trees on CTV-tolerant rootstocks. The history of CTV in Florida and the methods developed to select mild isolates for use for mild strain cross protection will be reviewed.

Isolation and phylogenetic analysis of orf virus from the sheep herd outbreak in northeast China

BackgroundOrf is a zoonotic and epitheliotrophic contagious disease that mainly affects sheep, goats, wild ruminants, and humans with a worldwide distribution. To date, there is little information on the characterization of ORFV strains that are endemic in Mainland China. In addition, the relationship between the severity of disease and the molecular profile of ORFV strains has not been fully elucidated.ResultsFrom the recent outbreak of a sheep herd in Nongan, northeast of China, the novel orf virus (ORFV) strain NA1/11 was successfully isolated. Western blot analysis indicated that the NA1/11 strain cross reacts with monoclonal antibody A3 and infected sheep ORFV antiserum. The purified virions revealed the typical ovoid shape when observed by atomic force microscopy. To determine the genetic characteristics of the NA1/11 strain, the sequences of ORFV011 (B2L), ORFV059 (F1L), ORFV109, ORFV110 and ORFv132 (VEGF) genes were amplified and compared with reference parapoxvirus strains. Non-metric multidimensional scaling (nMDS) was performed to analyze the nucleotide similarities between different ORFV strains.ConclusionsPhylogenetic analysis based on ORFV 011 nucleotide sequences showed that the NA1/11strain was closely related to Xinjiang and Gansu strains. ORFV110 and ORFV132 genes are highly variable. The results revealed that precise phylogenetic analysis might provide evidence for genetic variation and movement of circulating ORFV strains in Northeast China. In addition, nMDS analysis showed that geographic isolation and animal host are likely major factors resulting in genetic differences between ORFV strains.

Induction and regulation of pathogenic Th17 cell responses in schistosomiasis

Schistosomiasis is a major tropical disease caused by trematode helminths in which the host mounts a pathogenic immune response against tissue-trapped parasite eggs. The immunopathology consists of egg antigen-specific CD4 T cell-mediated granulomatous inflammation that varies greatly in magnitude in humans and among mouse strains in an experimental model. New evidence, covered in this review, intimately ties the development of severe pathology to IL-17-producing CD4 T helper (Th17) cells, a finding that adds a new dimension to the traditional CD4 Th1 vs. Th2 cell paradigm. Most examined mouse strains, in fact, develop severe immunopathology with substantial Th17 as well as Th1 and Th2 cell responses; a solely Th2-polarized response is an exception that is only observed in low-pathology strains such as the C57BL/6. The ability to mount pathogenic Th17 cell responses is genetically determined and depends on the production of IL-23 and IL-1β by antigen presenting cells following recognition of egg antigens; analyses of several F2 progenies of (high × low)-pathology strain crosses demonstrated that quantitative trait loci governing IL-17 levels and disease severity vary substantially from cross to cross. Low pathology is dominant, which may explain the low incidence of severe disease in humans; however, coinfection with intestinal nematodes can also dampen pathogenic Th17 cell responses by promoting regulatory mechanisms such as those afforded by alternatively activated macrophages and T regulatory cells. A better understanding of the pathways conducive to severe forms of schistosomiasis and their regulation should lead to interventions similar to those presently used to manage other immune-mediated diseases.

Strain and sex effects on growth performance and carcass traits of contemporary commercial broiler crosses

In total, 3,840 sexed birds from 6 commercial cross broiler strains (4 male and 3 female) were raised and processed to analyze the effect of strain and sex on growth performance and carcass traits. Chicks from M1 × F1, M2 × F1, M3 × F1, M4 × F1, M3 × F2, and M4 × F3 crosses were sexed. Fifty female and 40 male chicks were randomly allocated to 24 floor pens (119 × 300 cm) covered with pine shavings in each of 4 rooms. The FCR was adjusted for the weight of dead birds (AFCR). Four birds/pen were processed at 7 wk of age. Carcasses were deboned after 2 h of chilling (n = 32 birds per treatment). There were significant strain by sex interactions for BW gain from 0 to 21 and 0 to 48 d. Strain differences in growth rate and mortality increased with age. The cross with the fastest growth rate also had the highest mortality. Because of differences in mortality and carcass yields, birds with the fastest growth (0-48 d) did not produce the most salable meat. Both the heaviest live BW per bird at 48 d (3.45 kg) and highest mortality (13.40%) were observed with the M4 × F3 cross. However, the heaviest live BW per 1,000 chicks placed was from the M3 × F2 cross (3,107 kg). The highest chilled carcass yield was from the M3 × F2 cross (76.05% of live BW) as was the highest meat yield (2,364 kg per 1,000 chicks placed) and highest pectoralis meat yield (805 kg per 1,000 chicks placed). The M3 × F2 cross produced the most total white meat (1,058 kg per 1,000 chicks placed), but interestingly the slowest-growing strain (M1 × F1) produced more white meat (breast + tenders + wings) than did the fastest-growing M4 × F3 strain (980 kg vs. 1,002 kg per 1,000 chicks placed). These results demonstrate the complexity of choosing between commercial strain crosses. The most profitable choice will be dependent on whether whole birds or parts are marketed and the relative values of the parts.

Reproductive mode and life cycle of the ash dieback pathogen Hymenoscyphus pseudoalbidus

Ash dieback caused by the fungal pathogen Hymenoscyphus pseudoalbidus is currently ravaging in Europe, killing Fraxinus excelsior and Fraxinus angustifolia trees of all age classes. The aim of this work was to elucidate aspects of the reproduction biology of this fungal pathogen and its cryptic, non-pathogenic sister species Hymenoscyphus albidus. The mating type (MAT) locus of both species was identified, partly sequenced and characterized. Whereas a heterothallic MAT organization was detected in H. pseudoalbidus, H. albidus was shown to be structurally homothallic. The molecular MAT determination of H. pseudoalbidus was confirmed by crossing experiments on sterile ash petioles. Crossings of strains exhibiting alternate MAT idiomorphs produced fertile apothecia whereas crosses of strains with identical MAT idiomorphs were never successful. Offspring genotyping with microsatellites (MSs) and the MAT marker confirmed that both parental strains were involved in apothecia formation. In addition, polymorphic MS were shown to follow Mendelian inheritance. However, for yet unknown reasons the MAT ratio of progenies of one successful cross revealed a significant segregation distortion. Based on the MAT sequences of H. pseudoalbidus a multiplex PCR was developed, allowing for a quick and reliable MAT determination. The PCR was applied to screen the MAT ratio of two H. pseudoalbidus populations derived from the country of the disease outbreak in Poland and two populations from the disease periphery in Switzerland. None of the screened populations showed a significant deviation from the 1:1 ratio, expected under random mating. Therefore, an initial clonal distribution through asexually produced conidiospores as observed for other fungal pathogens holds not true for H. pseudoalbidus. Instead, our data is highly supportive for a distribution through ascospores. Leaf petioles collected in the field were thoroughly analyzed for the number of different colonizing strains and their mating behavior. Up to eight different H. pseudoalbidus genotypes were found on a single petiole. Cross-fertilizations of strains on the same petiole and fertilizations of unknown strains from outside were found, indicating that fertilization is mediated by spermatia. The presented study complements our understanding of the life cycle of this highly destructive pathogen. The possibility to perform sexual crosses in the lab provides ample opportunities for further genetic studies of H. pseudoalbidus and related species in the future.

A general Bayesian approach to analyzing diallel crosses of inbred strains.

The classic diallel takes a set of parents and produces offspring from all possible mating pairs. Phenotype values among the offspring can then be related back to their respective parentage. When the parents are diploid, sexed, and inbred, the diallel can characterize aggregate effects of genetic background on a phenotype, revealing effects of strain dosage, heterosis, parent of origin, epistasis, and sex-specific versions thereof. However, its analysis is traditionally intricate, unforgiving of unplanned missing information, and highly sensitive to imbalance, making the diallel unapproachable to many geneticists. Nonetheless, imbalanced and incomplete diallels arise frequently, albeit unintentionally, as by-products of larger-scale experiments that collect F1 data, for example, pilot studies or multiparent breeding efforts such as the Collaborative Cross or the Arabidopsis MAGIC lines. We present a general Bayesian model for analyzing diallel data on dioecious diploid inbred strains that cleanly decomposes the observed patterns of variation into biologically intuitive components, simultaneously models and accommodates outliers, and provides shrinkage estimates of effects that automatically incorporate uncertainty due to imbalance, missing data, and small sample size. We further present a model selection procedure for weighing evidence for or against the inclusion of those components in a predictive model. We evaluate our method through simulation and apply it to incomplete diallel data on the founders and F1's of the Collaborative Cross, robustly characterizing the genetic architecture of 48 phenotypes.

Genetic variation in TRPS1 may regulate hip geometry as well as bone mineral density

Trps1 has been proposed as a candidate gene for a mouse bone mineral density (BMD) QTL on Chromosome (Chr) 15, but it remained unclear if this gene was associated with BMD in humans. We used newly available data and advanced bioinformatics techniques to confirm that Trps1 is the most likely candidate gene for the mouse QTL. In short, by combining the raw genetic mapping data from two F2 generation crosses of inbred strains of mice, we narrowed the 95% confidence interval of this QTL down to the Chr 15 region spanning from 6 to 24cM. This region contains 131 annotated genes. Using block haplotyping, all other genes except Trps1 were eliminated as candidates for this QTL. We then examined associations of 208 SNPs within 10kb of TRPS1 with BMD and hip geometry, using human genome-wide association study (GWAS) data from the GEFOS consortium. After correction for multiple testing, six TRPS1 SNPs were significantly associated with femoral neck BMD (P=0.0015–0.0019; adjusted P=0.038–0.048). We also found that three SNPs were highly associated with femoral neck width in women (rs10505257, P=8.6×10−5, adjusted P=2.15×10−3; rs7002384, P=5.5×10−4, adjusted P=01.38×10−2). In conclusion, we demonstrated that combining association studies in humans with murine models provides an efficient strategy to identify new candidate genes for bone phenotypes.

A General Bayesian Approach to Analyzing Diallel Crosses of Inbred Strains

A General Bayesian Approach to Analyzing Diallel Crosses of Inbred Strains

Effect of Selection Response on F3 and F4 Generation for Yield and Yield Component Characters in Mutant Rice Strain (Oryza sativa L.)

Using the variability present in the F2 population originating from six crosses of rice mutant strains, selection was practiced for high grain yield. Expected response to selection was estimated in F3 generation and compared with F2 generation. Similar selection practices were made in F3 generation and selection response was estimated in F4 generation. F3 generation showed significant positive selection response for plant height, number of panicles per plant, grain density and days to 50% flowering, thus indicating the effectiveness of selection for these characters. Grain yield showed non significant response in F2 generation which indicates straight selection for this character during early generation may not be effective. F4 generation showed positive selection response for all the characters i.e. plant height, number of panicles per plant, grain density, days to 50% flowering and grain yield. This indicates the effectiveness of selection for these characters in F3 or latter generation. The regression coefficient between F2 and F3 generation and F3 and F4 generation was significant for all the characters. Selection for plant height, number of panicles per plant and days to 50 percent flowering can be made in the early segregating generation. Grain yield per plant and grain density is effective for selection in later generation.

Healing quantitative trait loci in a combined cross analysis using related mouse strain crosses

Inbred mouse strains MRL and LG share the ability to fully heal ear hole punches with the full range of appropriate tissues without scarring. They also share a common ancestry, MRL being formed from a multi-strain cross with two final backcrosses to LG before being inbred by brother-sister mating. Many gene-mapping studies for healing ability have been performed using these two strains, resulting in the location of about 20 quantitative trait loci (QTLs). Here, we combine two of these crosses (N = 638), MRL/lpr × C57BL/6NTac and LG/J × SM/J, in a single combined cross analysis to increase the mapping power, decrease QTL support intervals, separate multiple QTLs and establish allelic states at individual QTL. The combined cross analysis located 11 QTLs, 6 affecting only one cross (5 LG × SM and 1 MRL × B6) and 5 affecting both crosses, approximately the number of common QTLs expected given strain SNP similarity. Amongst the five QTLs mapped in both crosses, three had significantly different genetic effects, additive in one cross and over or underdominant in the other. It is possible that allelic states at these three loci are different in SM and B6 because they lead to differences in dominance interactions with the LG and MRL alleles. QTL support intervals are 40% smaller in the combined cross analysis than in either of the single crosses. Combined cross analysis was successful in enhancing the interpretation of earlier QTL results for these strains.

Design and Application of Long Distance Oil & Gas Pipeline Stress & Strain Monitoring Sensor

As Oil & Gas Pipeline of Long Distance has potential mechanical risks caused by geologic hazards, based on sensing technique, Fiber Bragg Grating (FBG) strain sensor, for which unstressed grating temperature compensation method is adopted, is designed to solve problems of FBG temperature and strain cross sensitivity. According to experimental tests, strain sensitive coefficients of the sensor before and after sticking on pipeline sample are 1.20 pm/με and 1.09 pm/με in separate. Finally, applied to a landslide area for monitoring pipeline stress, the sensor got the impact of Wenchuan Earthquake on May 12, 2008 on the pipeline.

Photonic Crystal Fiber Strain-Independent Temperature Sensing Based on Modal Interferometer

In this letter, the nonlinear photonic crystal fiber (NLPCF) has been exploited for the first time, as a high-temperature sensor based on the modal interferometric technique with a sensitivity that is remarkably higher along with low strain sensitivity. We have obtained a very high temperature sensitivity of 73 pm/°C and a very low strain sensitivity of 0.93 pm/με. The temperature to strain cross sensitivity is found to be significantly low in the very high range of temperature and strain. The proposed sensor may find application in strain-effective areas requiring accurate temperature measurement even at a high temperature range.

발색반응 분석법을 이용한 표고 교배균주의 세포외효소 분비 능력 평가

Shiitake breeding requires the procedures of mating of two different parental strains and selection of hybrid strains that have good traits for the mushroom production. In this study, we tested the possibility of the use of chromogenic plate-based assay for extracellular enzyme production in order to assess and find good biochemical properties-possessed hybrid strains that were generated from genetic cross of the monokaryotic strains derived from two different parental strains of Lentinula edodes Sanjo-101ho and Sanjo-108ho. We observed that there was difference in the ability of producing -glucosidase, avicelase, CM-cellulase, amylase, pectinase, xylanase, and protease among the monokaryotic strains. We could also comparatively assess that the ability of the seven extracellular enzymes production in the hybrid strains depended on the mating combination of the monokaryotic strains. Our results demonstrate that the assessment method for extracellular enzyme production using chromogenic plate assay could be usefully applied to the assessment of the hybrid strains derived from the breeding procedure of L. edodes.

Broiler genetic strain and sex effects on meat characteristics

A randomized complete block design within a factorial arrangement of treatments was used to evaluate the effect of strain and sex on carcass characteristics, meat quality, and sensory acceptability. Two broiler strains were reared: a commercially available strain (strain A) and a strain currently in the test phase (strain B) that has been genetically selected to maximize breast yield. Broilers were harvested in a pilot scale processing plant using commercial prototype equipment at 42 d of age. Carcasses were deboned at 4 h postmortem. The left half of each breast was evaluated for pH, color, cooking loss, shear force, and proximate analysis. The right side of each breast was used for consumer acceptability testing. Thigh meat was evaluated for proximate composition. No interactions were observed throughout the study. Male broilers had a higher (P < 0.05) live BW, carcass weight, and breast weight and lower (P < 0.05) dressing percentage and breast meat yield when compared with females. Broilers from strain B presented a higher (P < 0.05) breast yield and dressing percentage than those broilers corresponding to the commercially available broiler strain. At 24 h postmortem, female broilers presented a lower ultimate pH and higher Commission internationale de l'éclairage yellowness values (ventral side of the pectoralis major) when compared with male broilers. On average, no differences existed (P > 0.05) among treatments with respect to pH decline, cooking loss, shear values, and proximate composition. In addition, no differences (P > 0.05) existed among breast meat from the different strains with respect to consumer acceptability of appearance, texture, flavor, and overall acceptability, but breast meat from strain B was slightly preferred (P < 0.05) over that of strain A with respect to aroma. However, breast meat from both strains received scores in the range of “like slightly to like moderately.” Overall data suggest that all treatments yielded high quality breast and thigh meat and strain cross did not present variability in terms of consumer acceptability.