Pan-genome and transcriptome analyses provide insights into genomic variation and differential gene expression profiles related to disease resistance and fatty acid biosynthesis in eastern black walnut (Juglans nigra)

Walnut(Juglans)species are used as nut crops worldwide.Eastern black walnut(EBW,Juglans nigra),a diploid,horticultural important woody species is native to much of eastern North America.Although it is highly valued for its wood and nut,there are few resources for understanding EBW genetics.Here,we present a high-quality genome assembly of J.nigra based on Illumina,Pacbio,and HiC technologies.The genome size was 540.8 Mb,with a scaffold N50 size of 35.1 Mb,and 99.0%of the assembly was anchored to 16 chromosomes.Using this genome as a reference,the resequencing of 74 accessions revealed the effective population size of J.nigra declined during the glacial maximum.A single whole-genome duplication event was identified in the J.nigra genome.Large syntenic blocks among J.nigra,Juglans regia,and Juglans microcarpa predominated,but inversions of more than 600 kb were identified.By comparing the EBW genome with those of J.regia and J.microcarpa,we detected InDel sizes of 34.9 Mb in J.regia and 18.3 Mb in J.microcarpa,respectively.Transcriptomic analysis of differentially expressed genes identified five presumed NBS-LRR(NUCLEOTIDE BINDING SITELEUCINE-RICH REPEAT)genes were upregulated during the development of walnut husks and shells compared to developing embryos.We also identified candidate genes with essential roles in seed oil synthesis,including FAD(FATTY ACID DESATURASE)and OLE(OLEOSIN).Our work advances the understanding of fatty acid bioaccumulation and disease resistance in nut crops,and also provides an essential resource for conducting genomics-enabled breeding in walnut.

Population genetic insights into the conservation of common walnut(Juglans regia)in Central Asia

The common walnut(Juglans regia)is one of the most economically important nut trees cultivated worldwide.Despite its importance,no comprehensive evaluation of walnut tree population genetics has been undertaken across the range where it originated,Central Asia.In this study,we investigated the genetic diversity and population structure of 1082 individuals from 46 populations across Central Asia.We found moderate genetic diversity of J.regia across Central Asia,with 46 populations clustered into three groups with a weak relationship between genetic and geographic distance.Our findings reveal that the western Himalaya might be the core region of common walnut genetic diversity in Central Asia and that,except for two populations in Gongliu Wild Walnut Valley,humans might have introduced walnut populations to Xinjiang,China.The observed distribution of the genetic landscape has probably been affected by historical climate fluctuation,breeding system,and prolonged anthropogenic activity.We propose the conservation of the core genetic diversity resources in the western Himalaya and pay special attention to populations from Gongliu in Xinjiang.These findings enhance our understanding of the genetic variation throughout the distribution range of J.regia in Central Asia,which will provide a key prerequisite for evidence-based conservation and management.

Application of GIS in Ecological Land Type(ELT)mapping--A case in Changbai Mountain area

This paper depicted the physiographic landscape features and natural vegetation situation of study area (the eastern Jilin Province), and expatiates the definition, basic characters and its development of Ecological Land Classification (ELC). Based on the combination of relief map, satellite photography for study area and vegetation inventory data of 480 sample sites, a 5-class and a 15-class ecological land type map was concluded according to 4 important factors including slope, aspect, vegetation and elevation. Ecological Classification System (ECS) is a method to identify, characterize, and map ecosystems. The Ecological Land Type (ELT) was examined and applied initially in eastern Jilin Province.

Urban Three-dimensional Expansion and Its Driving Forces——A Case Study of Shanghai,China

Urban expansion is a phenomenon of urban space increase,and an important measuring index of the process of urbanization.Taking Shanghai as an example,the changes of urban average height and built-up area were studied to represent city's vertical and horizontal increases respectively,and statistical methods were used to analyze the driving forces of urban expansion.The research drew following conclusions:1) The urban expansion process of Shanghai from 1985 to 2006 had a clear periodic feature,and could be divided into three stages:vertical expansion in dominance,coordinated vertical and horizontal expansion,and horizontal expansion in dominance.2) The average height and quantity of buildings in core city were significantly bigger than those in suburbs,but the changing speed of the latter was faster.And 3) urbanization process was the major driving force for the city's horizontal expansion,while industrial structure improvement was the key driving factor for the vertical expansion.Those two driving forces were simultaneously affected by city's political factors.

Drone remote sensing for forestry research and practices

Drones of various shapes, sizes, and functionalities have emerged over the past few decades, and their civilian applications are becoming increasingly appealing. Flexible, low-cost, and high-resolution remote sensing systems that use drones as platforms are important for filling data gaps and supplementing the capabilities of crewed/manned aircraft and satellite remote sensing systems. Here, we refer to this growing remote sensing ini- tiative as drone remote sensing and explain its unique advantages in forestry research and practices. Furthermore, we summarize the various approaches of drone remote sensing to surveying forests, mapping canopy gaps, mea- suring forest canopy height, tracking forest wildfires, and supporting intensive forest management. The benefits of drone remote sensing include low material and operational costs, flexible control of spatial and temporal resolution, high-intensity data collection, and the absence of risk to crews. The current forestry applications of drone remote sensing are still at an experimental stage, but they are expected to expand rapidly. To better guide the development of drone remote sensing for sustainable forestry, it isimportant to systematically and continuously conduct comparative studies to determine the appropriate drone remote sensing technologies for various forest conditions and/or forestry applications.

Development of cork oak (Quercus suber L.) seedlings in response to tree shelters and mulching in northwestern Tunisia

The need for reforestation in cork oak （Quercus suber L.） areas is challenged by difficulties. Principal among these is herbivory of young plants, vegetative competition, and slow growth rates of cork oak seedlings. We evaluated the early development of cork oak seedlings treated using tree shelters and mulching in northwestern Tunisia. We tested three tree shelter treatments （non-vented, vented, and control） to shield seedlings from animal damage and five mulch types to control competing vegetation （Italian Stone Pine, Lentisk, combination of Italian Stone Pine and Lentisk （organic mulches）, gravel （inorganic mulch） and no mulch）. At the end of the two-year experiment, sheltered seedlings were 89-99% taller than unshelteredseedlings and had higher numbers and lengths of shoot growth flushes. In contrast, both stem diameter growth and dry weight biomass （from samples extracted after two years） were significantly reduced inside tree shelters. Root-to-shoot ratio was not significantly different in sheltered vs. unsheltered seedlings, suggesting that tree shelters do not adversely affect this parameter. Mulching alone did not favour growth, but could be beneficial when combined with tree shelters. The combination of vented tree shelters and gravel mulch was the most effective treatment for promoting diameter, height and stem volume growth.

Diversity and regeneration status of Sarkot Van Panchyat in Garhwal Himalaya, India

We investigated the floristic composition, phytosociological and regeneration status of Sarkot Van Panchyat （community forest） in Chamoli district of Garhwal Himalaya. A total of 52 plant species of 46 genera and 26 families were recorded, which included 12 trees, 18 shrubs and 22 herb species. Quercus leucotrichophora was dominant tree species in sapling and seedling layers, followed by Lyonia ovalifolia and Rhododendron arboreum. Out of 12 tree species, 7 species in seedling stage and 8 species in sapling stage were recorded in the study area. The 44.41% species in the study area showed good regeneration status, 16.66% species were fairly regenerating, and 8.33% species showed poor regeneration status, while 33% species were not regenerating. Number of individuals from lower girth classes （0--10 cm and 10-30 cm） showed decreasing trend with the increase in size of girth class. Shannon index （H） for trees, shrubs and herbs was recorded as 1.82, 2.24 and 2.41 respectively. Simpsons index （Co） was recorded as 0.21, 0.12 and 0.12 for trees, shrubs and herbs respectively. The forest should be di- vided into compartments for better management purpose and each compartment should be closed for five years to assist regeneration and enrichment planting may also be carried out for sustainable management.

Effects of gibberellin A_(4/7), 6-benzylaminopurine and chlormequat chloride on the number of male and female strobili and immature cones in Chinese Pine (Pinus tabuliformis) with foliar sprays

Three kinds of plant growth regulators, gibberellinA 4/7 （GA 4/7 ）, 6-benzylaminopurine （BA）, and chlormequat chloride （CCC）, were evaluated for their ability to promote strobilus and cone production in a Chinese pine （Pinus tabuliformis Carr.） clonal seed orchard. Treatments （0, 250, 500, or 1000 mg L -1 ） were applied during three periods （June- July, July-August and August-September） in 2005. Of the three plant growth regulators, GA 4/7 was the best for promoting flower and cone production. Trees sprayed with GA 4/7 （500 mg L -1 ） from June to September had significantly more female strobili and immature cones than controls and other treatments （p≤0.0001）. The best time to apply GA 4/7 was in June. BA at 500 mg L -1 significantly increased female flower and immature cone production, compared to other treatments and controls （p≤0.0001）, while promotion of male strobili was unchanged. Chlormequat chloride at 1000 mg L -1 significantly increased the number of male strobili, compared to the other treatments （p≤0.0001）. Spraying CCC at500 mg L -1 significantly increased the number of female strobili, compared to controls （p0.05）, but it had no effect on immature cone production （p0.05）. These results are important for improving seed production and seed orchard management of Chinese pine.

Influence of mulching and tree shelters on 4-year survival and growth of zeen oak (Quercus canariensis) seedlings

We assessed the effect of mulching and tree shelters on the establishment and early growth of zeen oak(Quercus canariensis Willd.) during the first 4 years after planting in Northwestern Tunisia. Five mulch types(Italian Stone Pine(Pinus pinea L.), Lentisk(Pistacia lentiscus L.),and a combination of Italian Stone Pine and Lentisk(organic mulches), gravel(inorganic mulch) and control), and three tree shelter types(non-vented and vented tree shelters, and control) were tested. An increase in the number of internodes occurred under the gravel mulch, while a reduction in survival was found for the lentisk mulch. Tree shelters had no effect on survival, but increased mean height growth and reduced mean diameter growth during the 4 years(excepting a non-significant effect for vented tree shelter at year four). Comparison of the annual shoots and growth units(GU) between sheltered and unsheltered plants according to year of formation revealed two growth phases. In first phase, shoots were totally or partially inside the shelters; mean length of annual shoots and GU were greater for sheltered plants. The second phase was characterized by shoots emerging from shelters; mean length of annual shoots and GU were similar for all plants, with or without tree shelters. Results suggest that the use of tree shelters, particularly vented shelters, could contribute to the improvement of the artificial regeneration of zeen oak.The use of mulching alone or in combination with tree shelters did not improve zeen oak performance in the field.

Changes in soil properties under Eucalyptus relative to Pinus massoniana and natural broadleaved forests in South China

The ecological effects of eucalypt plantations（EPs） have garnered increasing attention.To understand their effect on soil quality at a landscape scale,and to determine whether soil quality parameters differ due to different stand types,we evaluated soil characteristics in twenty-one groups of EPs,Pinus massoniana Lamb.plantations（PMPs） and natural broadleaved forests（NBFs）across Guangdong Province,China.Both the physical characteristics of soil hydrology and the properties of soil nutrients in A and B horizons were determined.Results showed that,compared to NBFs,EPs and PMPs produced a shallower litter layer,reduced canopy density,higher soil bulk density,significantly lower total porosity,non-capillary porosity,total water volume,and hygroscopic water in the A horizon（P〈0.05）.Moreover,total N,available K,and soil organic carbon（SOC） in EPs and PMPs were significantly lower than in NBFs.EPs and PMPs did not differ significantly in N,P or K content,but PMPs had significantly lower SOC and boron in the A horizon than EPs.Low p H and poor capacity to buffer acidification generally occurred in all cover types.Both EPs and PMPs showed a decline in soil properties relative to NBFs,but EPs and PMPs exhibited no significant difference.These results indicate that actions are needed to ameliorate the potential negative effects on soil quality in forestry plantations.

Biomass and Carbon Sequestration Potential of Poplar-Wheat Inter-cropping System in Irrigated Agro-ecosystem in India

An attempt has been made to assess the productivity as well as the carbon sequestration potential of this mixture. The grain as well as straw yields were significantly lower in poplar block plantations than in the open （14 to 64% and 13 to 66% grain and straw yield, respectively under one to six year plantation）. The annual productivity of poplars was recorded maximum after fourth year and later the annual wood increment decreased （42.4, 39.8 and 35.6 m^3/ha/yr after 4^th, 5^th and 6^th year, respectively）. The enrichment of soil through litter and roots enhanced the organic carbon in the surface layer of soil （0-15 cm） under poplar blocks as compared to open fields with wheat crop only. The carbon storage potential in agroforestry system was recorded very high in comparison to sole crop. The carbon storage in agroforestry system increased with the age of the plantation and the major contribution came from the timber, roots and litter （37.30 mg/ha after six years）. However, wheat crop yield decreased under poplar but this may be compensated by the poplar trees in terms of biomass, economic returns and the carbon sequestration potential.

Ovipositional preference and larval performance of poplar defoliator,Clostera restitura on different poplar clones in north-western India

We evaluated ten poplar clones （G-3, G-48, L-50/88, L- 154/84, L-156/89, S7C8, S7C15 WSL-22, WSL-29 and Uday） for ovi- positional preference and larval performance of Clostera restitura. Fe- male moths did not show any preference with respect to clones for ovi- position. Significant differences were observed for number of eggs laid on different plant parts. C. restitura laid eggs in clusters, preferably on upper surface of leaf and size of the egg cluster varied from 15 to 167 eggs. Clones varied for their relative resistance and susceptibility to C. restitura. L-50/88; L-156/89 were identified as most resistant clone based on minimum leaf consumption, whereas S7C15 was found to be most susceptible clone to C. restitura. In multiple choice experiments, no feeding preference by C. restitura larvae was detected amongst different poplar clones. After initial settlement of larvae on a particular clone, the larvae remained confined to that clone and negligible inter-clonal move- ment was noticed subsequently. The fresh pupal weight was correlated negatively （r = -0.37） with percentage surface leaf area eaten and positively （r = 0.47） with length of larval period, measured on different clones. Relationship between percentage leaf area eaten and length of larval period was negative （r = -0.23）. Owing to relative resistance of L- 50/88 and L-156/89 against C. restitura, these clones can be recom- mended for plantation in defoliator prone areas in north-western India.

Performance of statistical and machine learning-based methods for predicting biogeographical patterns of fungal productivity in forest ecosystems

Background:The prediction of biogeographical patterns from a large number of driving factors with complex interactions,correlations and non-linear dependences require advanced analytical methods and modeling tools.This study compares different statistical and machine learning-based models for predicting fungal productivity biogeographical patterns as a case study for the thorough assessment of the performance of alternative modeling approaches to provide accurate and ecologically-consistent predictions.Methods:We evaluated and compared the performance of two statistical modeling techniques,namely,generalized linear mixed models and geographically weighted regression,and four techniques based on different machine learning algorithms,namely,random forest,extreme gradient boosting,support vector machine and artificial neural network to predict fungal productivity.Model evaluation was conducted using a systematic methodology combining random,spatial and environmental blocking together with the assessment of the ecological consistency of spatially-explicit model predictions according to scientific knowledge.Results:Fungal productivity predictions were sensitive to the modeling approach and the number of predictors used.Moreover,the importance assigned to different predictors varied between machine learning modeling approaches.Decision tree-based models increased prediction accuracy by more than 10%compared to other machine learning approaches,and by more than 20%compared to statistical models,and resulted in higher ecological consistence of the predicted biogeographical patterns of fungal productivity.Conclusions:Decision tree-based models were the best approach for prediction both in sampling-like environments as well as in extrapolation beyond the spatial and climatic range of the modeling data.In this study,we show that proper variable selection is crucial to create robust models for extrapolation in biophysically differentiated areas.This allows for reducing the dimensions of the ecosystem space described by the predictors of the models,resulting in higher similarity between the modeling data and the environmental conditions over the whole study area.When dealing with spatial-temporal data in the analysis of biogeographical patterns,environmental blocking is postulated as a highly informative technique to be used in cross-validation to assess the prediction error over larger scales.

Population structure and regeneration patterns of tree species in climate-sensitive subalpine forests of Indian western Himalaya

The population structure of tree species has been explored in order to elucidate regeneration potential of the subalpine forests of Indian western Himalaya. For this study, the subalpine forest area was divided into three strata, i.e., lower altitude （〈3000 m）; mid-altitude （3000-3200 m）; and high altitude （〉3200m）. Considering the major compositional attributes, an increase in altitude came with a significant decline in tree density and the total basal area for all the sites. However, no such clear trends were observed for recruits （i.e., seedlings and saplings）. Seedling density did not exhibit uniform patterns for sites and altitude strata. In general, overall seedling density was greater at the Pindari site compared to the Lata and Tungnath sites. By comparison, significant variation in seedling density along the altitude strata was recorded for the Tungnath and Pindari sites only. Likewise, sapling density patterns varied across the sites and altitude strata, and significant variation in sapling density along the altitude strata was recorded only for the Lata site. At the Pin- daft site, the continuous increase in sapling density along with increasing altitude was revealing. The Pindari forests of exhibited expanding population structure. In contrast, greater accumulation of individuals in the sapling class and sharp decline toward both higher tree classes and lower seedling classes was generally apparent for the Lata and Tungnath sites. This indicates that the replacement in tree size classes from sapling stage is not proportional and the population may decline in the long-term. Considerable variation in patterns of forest and dominant species popula- tion structure were evident across altitude strata. But in all cases irrespective of sites, we found growth at the high-altitude stratum, in the form of entire forests or dominant species. This trend deserves further investigation to explore its relevance under changing climate scenarios.

Net Primary Productivity and Species Diversity of Herbaceous Vegetation in Banj-oak (Quercus leucotri-chophora A.Camus) Forest in Kumaun Himalaya,India

Net primary productivity and species diversity of herbaceous vegetation of banj-oak （Quercus leucotrichophora A. Camus） forest in Kumaun Himalaya, India were analyzed. Across different growth forms （tall forbs, short forbs, cushion and spreading forbs, grasses）, short forbs were most dominant component during rainy season （1VI=152） and winter season （IVI=167） and grasses during the winter season （IVI=148）. Maximum above-ground production occurred during rainy season （132.5 g m-2） and minimum during winter season （2.8 g m-~）. Below-ground production was maximum （85.9 g m-x） during winter season and minimum （14.9 g m-x） during summer season. Annual net shoot production was 15o g m-~ and below-ground production was 138 g m-~. Of the total input 61% was channeled to above- ground parts and 39% to below-ground parts.

Effects of cutting types and hormonal concentration on vegetative propagation of Zanthoxylum armatum in Garhwal Himalaya,India

Experiments were carried out to define the effects of hormonal concentrations on semi-hard wood（SHW） and hard-wood（HW） branch cuttings of the Z.armatum. SHW and HW cuttings were collected in the month of March. The SHW and HW cuttings were treated with different concentration of indole-3-acetic acid and indole-3-butyric acid（IAA and IBA） and placed in vermiculite rooting medium for 90 days under 1-min misting after 10 min. Sprouting, rooting percentage, sprout number, sprout length, root number, and length were measured.The highest rooting and sprouting rate, 64.0 %, was obtained at the 0.3 % IBA treatment in the SHW cuttings.Similarly sprout length and number of roots per cutting were also higher at the 0.3 % IBA treatment in the SHW cuttings. The number of shoots per cutting was higher at the 0.3 % IAA treatment in the SHW cuttings. Root length per cutting was higher in 0.4 % IBA treatment in the SHW cuttings. The results indicated that 0.3 and 0.4 % IBA treatment produce higher rooting percentages as well as the number of roots and their length in SHW cuttings. The HW cuttings produced maximum rate of 18.0 % rooting in0.5 % IBA treatment. The control set and lower concentrations of IBA and IAA completely failed to root in the mist chamber.

Seasonal variations in species diversity, dry matter and net primary productivity of herb layer of Quercus leucotrichophora-Pinus roxburghii mixed forest in Kumaun Himalaya, India

Plant biomass, species diversity and net primary productivity are presented for herb layer of banj oak （Quercus leucotrichophora A. Camus）-chir pine （Pinus roxburghii Sarg.） mixed forest in Kumaun, central Himalaya, India. The species diversity declined from a maximum （3.56） in September to a minimum （2.11） in December. The monthly live shoots biomass exhibited a single peak growth pattern with highest live shoot biomass of 185 g·m^-2 in August. The seasonal pattem showed that the maximum above-ground production （131 g·m^-2） occurred during the rainy season and the minimum （1 g·m^-2） during winter season. The be- low-ground production was maximum during winter season （84 g·m^2） and minimum during summer season （34 g＇m＇2）. The annual net shoot production was 171 g·^2m^-1 and total below-ground production was 165 g·m^2. Of the total input 61% was channeled to above-ground parts and 39% to below-ground parts. Transfer of live shoots to dead shoots compartments and that of dead shoots to litter compartments was 61% and 66%, respectively. The total dry matter disappearance was 61% of the total input within annual cycle. The herb layer showed a net accumulation of organic matter, indicating the seral nature of the community.

Above and below ground organic carbon stocks in a sub-tropical Pinus roxburghii Sargent forest of the Garhwal Himalayas

Accurate estimates of tree carbon, forest floor carbon and organic carbon in forest soils （SOC） are important in order to determine their contribution to global carbon （C） stocks. However, information about these carbon stocks is lacking. Some studies have investigated regional and continental scale patterns of carbon stocks in forest ecosystems; however, the changes in C storage in dif- ferent components （vegetation, forest floor and soil） as a function of elevation in forest ecosystems remain poorly understood. In this study, we estimate C stocks of vegetation, forest floor and soils of a Pinus roxburghii Sargent forest in the Garhwal Himalayas along a gradient to quantify changes in carbon stock due to differences in elevation at three sites. The biomass of the vegetation changes drastically with increasing elevation among the three sites. The above-ground biomass （AGB） and below-ground biomass （BGB） were highest at site I （184.46 and 46.386 t·ha^-1 respectively） at an elevation of 1300 m followed by site II （173.99 and 44.057 t·ha^-1 AGB and BGB respectively） at 1400 m and the lowest AGB and BGB were estimated at site III （161.72 and 41.301t·ha^-1） at 1500 m. The trend for SOC stock was similar to that of biomass. Our results suggest that carbon storage （in both soil and biomass） is nega- tively correlated with elevation.

Polymorphism and heredity of cpDNA and mtDNA in the Section Leuce of Populus

The chloroplast DNA （cpDNA） and mitochondrial DNA （mtDNA） of 16 Populus species （Section Leuce） and their F1 generation were detected using PCR-RFLP technique. The results show that cpDNA in the F1 generation of 22 hybrid combinations was inherited maternally, which supported the conclusions of the study of plasmid cytology. The mtDNA fragments amplified by PCR were consistent with the restriction maps in all hybrid combinations and no polymorphism was detected, indicating that the Section Leuce is highly conserved in mitochondrial gene sequences. These results provided direct evidence of maternal chloroplast inheritance in Populus tomentosa, P. bolleana, P. davidiana, P. adenopoda, P. tomentosa × P. bolleana, P. alba × P. glandulosa and P. alba × P. tomentosa.

The de novo genome assembly of Tapiscia sinensis and the transcriptomic and developmental bases of androdioecy

Tapiscia sinensis(Tapisciaceae)possesses an unusual androdioecious breeding system that has attracted considerable interest from evolutionary biologists.Key aspects of T.sinensis biology,including its biogeography,genomics,and sexlinked genes,are unknown.Here,we report the first de novo assembly of the genome of T.sinensis.The genome size was 410 Mb,with 22,251 predicted genes.Based on whole-genome resequencing of 55 trees from 10 locations,an analysis of population genetic structure indicated that T.sinensis has fragmented into five lineages,with low intrapopulation genetic diversity and little gene flow among populations.By comparing whole-genome scans of male versus hermaphroditic pools,we identified 303 candidate sex-linked genes,79 of which(25.9%)were located on scaffold 25.A 24-kb region was absent in hermaphroditic individuals,and five genes in that region,TsF-box4,TsF-box10,TsF-box13,TsSUT1,and TsSUT4,showed expression differences between mature male and hermaphroditic flowers.The results of this study shed light on the breeding system evolution and conservation genetics of the Tapisciaceae.