Positive selection pressure on rice blast resistance allele Piz-t makes it divergent in Indian land races

Abstract

Allelic variants of the broad-spectrum blast resistance gene, Piz-t, have been analyzed in 48 rice lines selected after phenotyping across three blast hot-spot regions of India. Single Nucleotide Polymorhisms in the form of transitions were more frequent than the transversions in the alleles. On the basis of nucleotide polymorphism, 46 haplotypes have been identified, with major haplotypes forming three main haplogroups. The Piz-t alleles formed mostly region-specific clusters. Resistant and susceptible Piz-t alleles were grouped into separate sub-clusters. The value of Tajima's D was negative indicating positive selection on Piz-t locus. Sequence variations were more abundant in the leucine rich repeats (LRR) region than in the NB-ARC (nucleotide-binding adaptor shared by APAF-1,R proteins, and CED-4) region, indicating that the LRR region has played a more important role in the evolution of this allele. The detailed molecular analysis of the Piz-t locus provide insights to high degree of inter-and intra-specific relationship among the Indian land races of rice which will help in the selection of better alleles for future rice breeding programs.     

Effects of experimental warming on stomatal traits in leaves of maize (Zea may L.)

We examined the warming effects on the stomatal frequency, stomatal aperture size and shape, and their spatial distribution pattern of maize (Zea may L.) leaves using a light microscope, an electron scanning microscope, and geostatistic techniques. A field manipulative experiment was conducted to elevate canopy temperature by 2.08°C, on average. We found that experimental warming had little effect on stomatal density, but significantly increased stomatal index due to the reduction in the number of epidermal cells under the warming treatment. Warming also significantly decreased stomatal aperture length and increased stomatal aperture width. As a result, warming significantly increased the average stomatal aperture area and stomatal aperture circumference. In addition, warming dramatically changed the stomatal spatial distribution pattern with a substantial increase in the average nearest neighbor distance between stomata on both adaxial and abaxial surfaces. The spatial distribution pattern of stomata was scale dependent with regular patterns at small scales and random patterns at larger scales on both leaf surfaces. Warming caused the stomatal distribution to become more regular on both leaf surfaces with smaller L(t) values (Ripley's K‐function, L(t) is an expectation of zero for any value of t) in the warming plots than the control plots.     

Pool‐hmm: a Python program for estimating the allele frequency spectrum and detecting selective sweeps from next generation sequencing of pooled samples

Due to its cost effectiveness, next generation sequencing of pools of individuals (Pool‐Seq) is becoming a popular strategy for genome‐wide estimation of allele frequencies in population samples. As the allele frequency spectrum provides information about past episodes of selection, Pool‐seq is also a promising design for genomic scans for selection. However, no software tool has yet been developed for selection scans based on Pool‐Seq data. We introduce Pool‐hmm, a Python program for the estimation of allele frequencies and the detection of selective sweeps in a Pool‐Seq sample. Pool‐hmm includes several options that allow a flexible analysis of Pool‐Seq data, and can be run in parallel on several processors. Source code and documentation for Pool‐hmm is freely available at https://qgsp.jouy.inra.fr/ .     

Distribution,Disease Level and Virulence Variation of Bremia lactucae on Lactuca sativa in the Czech Republic in the Period 1999–2011

We report the distribution and disease level of downy mildew on lettuce (Lactuca sativa) and virulence variation in populations of its causal agent (Bremia lactucae) in the Czech Republic during the period 1999–2011. Disease incidence was not high; among a total of 92 different localities surveyed, 43.4% of them were infected by lettuce downy mildew at least once during the whole period. However, among individual years, differences were found in disease incidence that ranged from 4.8% (2009) to 66.7% (2004). A total of 128 isolates of B. lactucae collected from infected leaf samples in 35 different localities during the surveying period were included in the virulence analysis. Virulence was examined on a set of 19 differential genotypes of Lactuca sativa and Lactuca serriola (EU‐A test set). Isolates exhibited quite a broad variation in virulence to individual Lactuca differential genotypes. Eighteen of 19 virulence factors (v‐factors) tested were present in the samples. The most frequently detected factors were v1–4, v5/8, v6, v7, v10–14, v16, v36 and v38; factor v17 was not found. The most pronounced temporal shift was recorded for factors v36 and v38 whose frequency increased during the studied period. V‐factors 15, 17, 18 and 37 were present in low frequencies in a pathogen population, and their corresponding gene (Dm15) or resistance factors (R17, R18 and R37) may have the best potential for resistance breeding in the Czech Republic. Broad diversity of v‐phenotypes (63 different ones) was identified during the study period. The numbers of v‐factors per v‐phenotype (resp. isolate) varied within a range of 5–15. Within the 128 analysed isolates, only 9 v‐phenotypes were recorded repeatedly (three or more times). Possible reasons of recorded virulence variation are discussed.     

Vibrotactile thresholds at the sole of the foot: Effect of vibration frequency and contact location

Studies of vibration perception in the glabrous skin of the human hand have identified four mechanoreceptor channels, with each channel showing characteristic variations in thresholds with variations in the frequency of vibration and the area of vibration excitation. To advance understanding of the channels mediating vibration perception on the sole of the foot, this study determined how thresholds depend on the frequency of vibration, the location on the foot (the big toe, the ball of the foot, and the heel), and the gap between a vibrating probe and a fixed surround. Thresholds at the three locations were obtained at the 12 preferred one-third octave centre frequencies from 20 to 250?Hz using a 6-mm diameter probe with both a 10-mm and a 20-mm diameter surround. With the 10-mm surround, the displacement thresholds at all three locations showed flat responses from 20 to 40?Hz. With both the 10-mm and the 20-mm surround, the displacement thresholds at the three locations showed “U-shaped” responses from 40 to 250?Hz. Relative to thresholds obtained with the 20-mm surround, thresholds obtained with the 10-mm surround were lower at the toe and the heel with 20- and 25-Hz vibration, but higher at the ball of the foot with 31.5- to 250-Hz vibration. It is concluded that absolute thresholds for the perception of vibration at the sole of the foot show important variations with location and with contact conditions and tend to be mediated by the NP I channel in the range from about 20 to 40?Hz and the P channel from about 40 to 250?Hz.     

Estimation of population allele frequencies from next‐generation sequencing data: pool‐versus individual‐based genotyping

Molecular markers produced by next‐generation sequencing (NGS) technologies are revolutionizing genetic research. However, the costs of analysing large numbers of individual genomes remain prohibitive for most population genetics studies. Here, we present results based on mathematical derivations showing that, under many realistic experimental designs, NGS of DNA pools from diploid individuals allows to estimate the allele frequencies at single nucleotide polymorphisms (SNPs) with at least the same accuracy as individual‐based analyses, for considerably lower library construction and sequencing efforts. These findings remain true when taking into account the possibility of substantially unequal contributions of each individual to the final pool of sequence reads. We propose the intuitive notion of effective pool size to account for unequal pooling and derive a Bayesian hierarchical model to estimate this parameter directly from the data. We provide a user‐friendly application assessing the accuracy of allele frequency estimation from both pool‐ and individual‐based NGS population data under various sampling, sequencing depth and experimental error designs. We illustrate our findings with theoretical examples and real data sets corresponding to SNP loci obtained using restriction site–associated DNA (RAD) sequencing in pool‐ and individual‐based experiments carried out on the same population of the pine processionary moth (Thaumetopoea pityocampa). NGS of DNA pools might not be optimal for all types of studies but provides a cost‐effective approach for estimating allele frequencies for very large numbers of SNPs. It thus allows comparison of genome‐wide patterns of genetic variation for large numbers of individuals in multiple populations.     

Development of genetic diversity,differentiation and structure over 500 years in four ponderosa pine populations

Population history plays an important role in shaping contemporary levels of genetic variation and geographic structure. This is especially true in small, isolated range‐margin populations, where effects of inbreeding, genetic drift and gene flow may be more pronounced than in large continuous populations. Effects of landscape fragmentation and isolation distance may have implications for persistence of range‐margin populations if they are demographic sinks. We studied four small, disjunct populations of ponderosa pine over a 500‐year period. We coupled demographic data obtained through dendroecological methods with microsatellite data to discern how and when contemporary levels of allelic diversity, among and within‐population levels of differentiation, and geographic structure, arose. Alleles accumulated rapidly following initial colonization, demonstrating proportionally high levels of gene flow into the populations. At population sizes of approximately 100 individuals, allele accumulation saturated. Levels of genetic differentiation among populations (F_ST and Jost's D_est) and diversity within populations (F_IS) remained stable through time. There was no evidence of geographic genetic structure at any time in the populations' history. Proportionally, high gene flow in the early stages of population growth resulted in rapid accumulation of alleles and quickly created relatively homogenous genetic patterns among populations. Our study demonstrates that contemporary levels of genetic diversity were formed quickly and early in population development. How contemporary genetic diversity accumulates over time is a key facet of understanding population growth and development. This is especially relevant given the extent and speed at which species ranges are predicted to shift in the coming century.     

Changes in homologous recombination frequency in Arabidopsis thaliana plants exposed to stress depend on time of exposure during development and on duration of stress exposure

In the past, we showed that exposure to abiotic and biotic stresses changes the homologous recombination frequency (HRF) in somatic tissue and in the progeny. In current work we planned to answer the following question: do stress intensity/duration and time during exposure influence changes in somatic HRF and transgenerational changes in HRF? Here, we tested the effects of exposure to UV-C, cold and heat on HRF at 7, 14, 21 and 28 days post germination (dpg). We found that exposure at 14 and 21 dpg resulted in a higher increase in HRF as compared to exposure at 7 dpg; longer exposure to UV-C resulted in a higher frequency of HR, whereas prolonged exposure to cold or heat, especially at later developmental stages, had almost no effect on somatic HRF. Exposure at 7 dpg had a positive effect on somatic growth of plants; plants exposed to stress at this age had larger leaves. The analysis of HRF in the progeny showed that the progeny of plants exposed to stress at 7 dpg had an increase in somatic HRF and showed larger sizes of recombination spots on leaves. The progeny of plants exposed to UV-C at 7 dpg and the progeny of plants exposed to cold or heat at 28 dpg had larger leaves as compared to control plants. To summarize, our experiments showed that changes in somatic and transgenerational HRF depend on the type of stress plants are exposed to, time of exposure during development and the duration of exposure.

Electronic supplementary material

The online version of this article (doi:10.1007/s12298-013-0197-z) contains supplementary material, which is available to authorized users.     

比亚芬对微等离子体治疗疤痕术后创面修复的临床观察

目的：对比观察比亚芬对微等离子体术后创面修复的临床疗效.方法：将46例需进行微等离子体治疗的萎缩性痤疮瘢痕患者随机分成2组,治疗组31例术后即刻外用比亚芬,对照组15例术后不使用任何药物.结果：治疗组的红斑消退时间、痂皮脱落时间、创面愈合时间明显快于对照组,P〈0.05,差异有统计学意义.结论：比亚芬对微等离子体术后的创面愈合有明显的促进作用.