Molecular identification of blast resistance genes in rice landraces from northeastern India

Rice blast disease caused by the fungus Magnaporthe oryzae is one of the most devastating diseases causing huge losses worldwide. In the present study, major blast resistance genes were investigated in landraces originating from northeastern India. Based on phenotypic evaluation, 288 landraces were classified into three distinct groups: resistant (75), moderately resistant (127) and susceptible (86). The genetic frequencies of the 18 major blast resistance genes were between 6.2% and 27.4%, with only two genotypes possessing a maximum of nine blast resistance genes. The cluster and population structure analysis grouped the landraces into two groups. Through principal coordinate analysis, the scatter plots partitioned the resistant and moderately resistant landraces into different groups. Analysis of molecular variance showed maximum (96%) diversity within populations and least (4%) diversity between populations. Association analysis identified six markers, CRG4_2, RM72, tk59-2, pi21_79-3, RM1233 and RM6648, that are significantly associated with blast disease and explained a phenotypic variance of 1.1–6.5%. The associated genes could be used in marker-assisted rice breeding programmes for gene pyramiding to develop rice varietal resistance against blast disease. The present study represents a valuable blast resistance genetic resource that could be used for identification of new R genes, donors for blast resistance, and genomic studies.     

Control of lettuce big-vein disease by application of fungicides and crop covers

One of the economically important diseases of lettuce is lettuce big-vein disease (LBVD), which leads to severe yield losses. LBVD is associated with a complex of two viruses, Lettuce big-vein associated virus (LBVaV) and Mirafiori lettuce big-vein virus (MLBVV). These viruses are transmitted by motile zoospores of Olpidium spp. fungi, which persist in the soil for decades through resting spores. In greenhouse and field experiments, this study tested whether changing plant and soil temperatures together with fungicide application would have a significant effect on controlling LBVD in lettuce. Soil fumigation with metam sodium was not effective at controlling the disease, as opposed to treatment with chloropicrin and methyl bromide. Moreover, the fungicides carbendazim and fluazinam were effective in reducing the incidence of Olpidium virulentus. Nevertheless, control of the fungal vector did not seem to be sufficient to control the disease due to the transition ability of the virus under low vector abundance. Crop covers, which affect the favourable environmental conditions for the viruses by lowering soil temperature and raising air temperature, reduced the disease symptoms. Combining fungicides with crop cover had a synergistic effect on reducing disease symptoms, thus providing a sustainable solution for LBVD.     

Cryptic species and population genetic structure of Plasmopara viticola in São Paulo State,Brazil

Downy mildew (Plasmopara viticola) is one of the most important diseases in grape-growing areas worldwide, including Brazil. To examine pathogen population biology and structure, P. viticola was sampled during the 2015/16 growing season from 516 lesions on nine grape cultivars in 11 locations in subtropical areas of São Paulo State, Brazil. For identification of cryptic species, a subsample of 130 isolates was subjected to cleaved amplified polymorphic sequence (CAPS) analysis, and for 91 of these isolates the ITS1 region was sequenced. These analyses suggest that the population of P. viticola in São Paulo State consists of a single cryptic species, P. viticola clade aestivalis. Seven microsatellite markers were used to determine the genetic structure of all 516 P. viticola isolates, identifying 23 alleles and 55 multilocus genotypes (MLGs). Among these MLGs, 34.5% were clonal and represented 93% of the isolates sampled. Four dominant genotypes were present in at least five different locations, corresponding to 65.7% of the isolates sampled. Genotypic diversity (Ĝ = 0.21–0.89) and clonal fraction (0.58–0.96) varied among locations (populations). Most populations showed significant deviation from Hardy–Weinberg expectations; in addition, excess of heterozygosity was verified for many loci. However, principal coordinate analysis revealed no clusters among locations and no significant isolation by distance was found, suggesting high levels of migration. The results indicate that downy mildew epidemics result from multiple clonal infections caused by a few genotypes of P. viticola, and reproduction of P. viticola in São Paulo State is predominantly asexual.     

Phytophagous insect fauna of Onopordum spp. thistles in the south of Syria

Thistles from the genus Onopordum (Asteraceae) are of Mediterranean and Eurasian origin. They are very common in the south of Syria, in particular in Damascus and Al Suwayda, and are found in fallow fields, pastures, roadsides and neglected areas. In 2015–2017, several sites with large populations of Onopordum spp. were identified. Weekly surveys of some of the sites, mainly in the regions of Damascus and Al Suwayda, revealed a significant diversity of phytophagous insect species, some of which had a very high population density. A total of 29 insect species were detected, belonging to four orders and 21 families. The most abundant species were from the order Coleoptera. These were observed to be feeding on different plant parts of Onopordum spp. Purely endophagous species comprised 38% of the species observed on Onopordum spp., ectophagous species comprised 45% with 17% of species mixed ectophagous and endophagous. Species that only fed on Onopordum spp. represented 34% of all the species observed.     

Genetic diversity of the pine pathogen Lecanosticta acicola in Slovenia and Croatia

Brown spot needle blight (BSNB), a disease of pine trees caused by the fungus Lecanosticta acicola, has been known in Slovenia since 2008 and in Croatia since 1975. Recent outbreaks in Slovenia prompted this study to compare L. acicola populations in these two neighbouring European countries. Sixty-nine isolates collected from three pine species (Pinus mugo, P. halepensis and P. nigra) were used to determine the phylogenetic relationships, genetic structure, and reproductive strategy of the pathogen. EF1-α sequences showed that Slovenian and Croatian isolates share a common ancestry with individuals from central and northern Europe. Population structure analysis revealed four distinct population clusters of L. acicola in these two countries, generally corresponding to their respective geographic location and host. An unequal ratio of mating types and a low overall genetic diversity in the population indicated a strong influence of asexual reproduction. Although some of the oldest recorded European occurrences of BSNB are from Croatia, this study provided no evidence that the population studied in Croatia was the source of the sampled outbreaks in Slovenia. Recent outbreaks of L. acicola in Slovenia are most likely due to introductions from other, yet to be identified, sources.     

The value of linking paleoecological and neoecological perspectives to understand spatially-explicit ecosystem resilience

Context

Predicting ecosystem resilience is a challenge, especially as climate change alters disturbance regimes and conditions for recovery. Recent research has highlighted the importance of spatially-explicit disturbance and resilience processes to long-term ecosystem dynamics. “Neoecological” approaches characterize resilience mechanisms at relatively fine spatio-temporal resolutions, but results are difficult to extrapolate across broad temporal scales or climatic ranges. Paleoecological methodologies can consider the effects of climates that differ from today. However, they are often limited to coarse-grained spatio-temporal resolutions.

Methods

In this synthesis, we describe implicit and explicit examples of studies that incorporate both neo- and paleoecological approaches. We propose ways to build on the strengths of both approaches in an explicit and proactive fashion.

Results

Linking the two approaches is a powerful way to surpass their respective limitations. Aligning spatial scales is critical: Paleoecological sampling design should incorporate knowledge of the spatial characteristics of the disturbance process, and neoecological studies benefit from a longer-term context to their conclusions. In some cases, modeling can incorporate non-spatial data from paleoecological records or emerging spatial paleo-data networks with mechanistic disturbance/recovery processes that operate at fine spatiotemporal scales.

Conclusions

Linking these two complementary approaches is a powerful way to build a complete understanding of ecosystem disturbance and resilience.

     

Landscape-level naturalness of conservation easements in a mixed-use matrix

Context

With underrepresentation of habitats in publicly protected areas, attention has focused on the function of alternative land conservation mechanisms. Private conservation easements (CEs) have proliferated in the United States, yet assessing landscape-level function is confounded by varying extent, resolution, and temporal scale.

Objectives

We developed and tested an assessment tool to evaluate interacting spatial, social, and environmental attributes of easements relative to the degree of human modification (HM). We hypothesized that on both private and public conservation properties HM would be lower than on non-conserved parcels, and that for fine-scale features (most CEs), the level of HM would be driven by the variables used to create the coarser scale HM measure.

Methods

Variation in HM between private, public, and non-conserved was tested via pairwise parcel sampling. Composition was evaluated using multiple geographic bounds and edge characteristics. We assessed both environmental and social predictors using multinomial logistic regression.

Results

Privately conserved lands did not differ significantly from non-conserved lands. Publicly conserved lands had lower HM than both privately conserved and non-conserved lands. Edge contrast was similar between private and matched non-conserved patches. The level of HM was not driven by distance to roads, or by elevation in this mixed-use setting.

Conclusions

Variation in tests for differences, land characteristics, and HM variables confirmed the significantly lower HM of publicly protected lands, and opens the question as to naturalness of easements in some contexts. CEs in this location may be representative of the mixed rural-forested landscape instead of more natural land cover.

     

白茶萎凋过程萜烯类合成相关基因的鉴定和表达分析

萜烯类化合物是植物中重要的次生代谢产物之一,对茶树挥发性香气的组成起着重要作用。从茶树基因组数据库中鉴定获得了141个茶树萜烯类合成相关基因,并对其不同组织表达特异性进行分析,筛选出16个在茶树顶芽和嫩叶中高表达的萜烯类合成代表基因。生物信息学分析结果表明,系统进化关系将茶树与拟南芥和葡萄的萜烯类合成相关基因分成了4个亚家族;茶树萜烯类合成相关基因含有5~14个外显子,在上游启动子区域分析发现了大量与光响应、植物生长发育、激素和胁迫响应密切相关的顺式作用元件。荧光定量检测发现,CsMVK、CsDXS和CsGGPS在白茶萎凋过程中的表达显著上调;CsDXR、CsMCT、CsCMK、CsMCS、CsHDS、CsGPPS和CsGGPPS在萎凋4 h和24 h的表达达到峰值。本研究结果为进一步挖掘茶叶萎凋过程中萜烯类合成相关基因对茶叶香气组分积累提供了理论依据。     

茶叶微生物固态发酵中咖啡碱降解途径初探

为探究微生物作用下咖啡碱的降解产物与途径,将普洱茶发酵中筛选鉴定的Aspergillus sydowii NRRL250（聚多曲霉）、Aspergillus pallidofulvus NRRL4789、Aspergillus sesamicola CBS137324和Penicillium mangini CBS253.31等优势菌株分别接种至晒青毛茶进行单菌种固态发酵,并采用高效液相色谱（HPLC）测定咖啡碱、可可碱、茶碱的含量,探究微生物对咖啡碱代谢的影响;另外,基于UHPLC-QTOF-MS代谢组学技术,以灭菌处理组（ST组）和原料组（RM组）为对照,对聚多曲霉接种发酵样进行代谢组学分析。结果表明,A. pallidofulvus NRRL4789、A. sesamicola CBS137324和Penicillium mangini CBS253.31等优势菌株对咖啡碱等嘌呤类碱代谢均无显著影响,而在聚多曲霉接种发酵中,咖啡碱含量显著下降（P<0.05）,降幅达83.89%;茶碱含量显著增加（P<0.05）,发酵末期含量为(25.03±1.17) mg·g^-1;而可可碱保持基本稳定。由此可知,聚多曲霉对咖啡碱降解代谢有显著影响。采用UHPLC-QTOF-MS方法检出茶碱、3-甲基黄嘌呤、1,7-二甲基黄嘌呤等9种与咖啡碱降解相关的代谢物。在聚多曲霉作用下,茶碱、3-甲基黄嘌呤、1,7-二甲基黄嘌呤、7-甲基黄嘌呤含量显著提高（P<0.05）。茶碱、3-甲基黄嘌呤、1,7-二甲基黄嘌呤和1-甲基黄嘌呤与咖啡碱及其相关代谢物的N-脱甲基化途径相关。1,7-二甲基尿酸、1-甲基尿酸与咖啡碱相关代谢物的氧化途径相关。由此可知,聚多曲霉为降解普洱茶咖啡碱的优势菌株,且具有将咖啡碱转化为茶碱的潜在能力;在咖啡碱降解代谢过程中,存在聚多曲霉作用下的N-脱甲基化和氧化,并以N-脱甲基化为主。