中国林木遗传资源利用与可持续经营状况

中国经过遗传改良的重要造林树种有100多种,全国年均提供各类林木种子2300万kg,年均生产各类良种壮苗约130亿株。林木良种在生产上的应用产生了明显的综合增益,其中用材林平均生长增益达10%~30%,经济林平均产量增益达15%~68%。中国每年进口林木种子15万kg以上,涉及50多个树种;每年出口林木种子30万kg和苗木400多种。近10年来,中国林木遗传资源的可持续经营和利用已取得了明显的进步,但与一些发达国家相比还存在一定差距。今后,应优先考虑对已保存的林木遗传资源的维护和资金补贴,加强种苗市场监管和信息服务,进一步提高林木良种的基地供种率和良种使用率。     

Enumeration of Major Peripheral Blood Leukocyte Populations for Multicenter Clinical Trials Using a Whole Blood Phenotyping Assay

Cryopreservation of peripheral blood leukocytes is widely used to preserve cells for immune response evaluations in clinical trials and offers many advantages for ease and standardization of immunological assessments, but detrimental effects of this process have been observed on some cell subsets, such as granulocytes, B cells, and dendritic cells ^1-3. Assaying fresh leukocytes gives a more accurate picture of the in vivo state of the cells, but is often difficult to perform in the context of large clinical trials. Fresh cell assays are dependent upon volunteer commitments and timeframes and, if time-consuming, their application can be impractical due to the working hours required of laboratory personnel. In addition, when trials are conducted at multiple centers, laboratories with the resources and training necessary to perform the assays may not be located in sufficient proximity to clinical sites. To address these issues, we have developed an 11-color antibody staining panel that can be used with Trucount tubes (Becton Dickinson; San Jose, CA) to phenotype and enumerate the major leukocyte populations within the peripheral blood, yielding more robust cell-type specific information than assays such as a complete blood count (CBC) or assays with commercially-available panels designed for Trucount tubes that stain for only a few cell types. The staining procedure is simple, requires only 100 μl of fresh whole blood, and takes approximately 45 minutes, making it feasible for standard blood-processing labs to perform. It is adapted from the BD Trucount tube technical data sheet (version 8/2010). The staining antibody cocktail can be prepared in advance in bulk at a central assay laboratory and shipped to the site processing labs. Stained tubes can be fixed and frozen for shipment to the central assay laboratory for multicolor flow cytometry analysis. The data generated from this staining panel can be used to track changes in leukocyte concentrations over time in relation to intervention and could easily be further developed to assess activation states of specific cell types of interest. In this report, we demonstrate the procedure used by blood-processing lab technicians to perform staining on fresh whole blood and the steps to analyze these stained samples at a central assay laboratory supporting a multicenter clinical trial. The video details the procedure as it is performed in the context of a clinical trial blood draw in the HIV Vaccine Trials Network (HVTN).     

Phenotyping tree resistance to a bark‐chewing insect,the pine weevil Hylobius abietis

Breeding for resistance to forest pests and pathogens is emerging as a promising tool for minimising the impact of the increasing biotic threats that our forests are experiencing as a consequence of global change. Efficient phenotyping protocols of resistance are urgently needed. Here we present the results of two experiments aimed to determine whether the variation in resistance to the pine weevil Hylobius abietis, a harmful pest of European conifers, can be inferred by nondestructive bioassays using excised plant material collected in forest genetic trials. Weevil damage and amount of nonvolatile resin induced by weevil feeding were assessed in young trees and in branches of adult trees using several phenotyping procedures (bioassays using either living trees, excised plant material and cut stem twigs) on four pine species (Pinus pinaster, P. radiata, P. sylvestris and P. pinea). Half of the plants were previously induced with methyl jasmonate (MJ), a treatment that is known to affect resistance to the pine weevil. In Experiment 1, living and excised plants showed parallel results: MJ treatment significantly reduced weevil damage, and saplings responded to weevil damage locally increasing the nonvolatile resin (NVR) in the stems proportionally to the damage suffered. This response was, however, slightly lower in excised than in living saplings. On the contrary, patterns of weevil feeding on stem twigs completely departed from those observed in living and excised seedlings. Moreover, cut stem twigs were unable to respond to weevil feeding increasing NVR according to the weevil damage. In Experiment 2, assessment of weevil damage on excised branches explained around 50% of variation in damage on living branches. This relationship became much more pronounced (R² = 0.81) when explored at the mean treatment level; branch manipulation did not alter the patterns of variation in resistance across pine species or MJ treatments. Irrespective of the assessment procedure, MJ consistently decreased weevil damage in all pine species, with larger reduction in weevil damage in stone and maritime pine than in radiata and Scots pine. Radiata pine was the most resistant while Scots pine was the most susceptible to the pine weevil. Overall, results suggest that using excised plant material is an operative alternative for phenotyping weevil resistance whenever care is taken to maintain the functionality of the excised plant material. This will allow taking advantage of multiple available conifer genetic trials to deepen the ecological genetics of resistance to the pine weevil and to screen for resistance without compromising the long‐term utility of those genetic trials.     

遗传标记及其在林木研究中的应用

遗传标记经历了形态标记、细胞学标记、生化标记和分子标记等4个阶段,其中分子标记的发展最为迅猛和有效。本文比较了几种主要分子标记方法的特点,为更好地利用分子标记提供了理论依据,并对分子标记在林木遗传多样性研究、遗传育种、DNA指纹图谱的构建、亲缘关系鉴定及分类研究等方面的应用做了介绍。     

Forestry Matters: Decline of Oaks Will Impact Wildlife in Hardwood Forests

Abstract: Acom production by oaks (Quercus spp.) is an important food resource for wildlife in many deciduous forests. Its role as a hard mast crop that can be either stored or used to build fat reserves for winter survival cannot be replaced by most other potential foods. Changes in forest management, introduced pests and pathogens, and increased deer populations have resulted in significant changes in the demography of oaks in eastern North America, as evident in Forest Inventory and Analysis data. Specifically, maples (Acer spp.) are replacing oaks in many forests through dominance of the younger age classes. These changes are not yet obvious in mast production but will take decades to reverse. Effective forest management for mast production is arguably one of the more important tasks facing wildlife professionals, yet receives scant attention by both public and private land managers. Public forests need to explicitly include mast production in their forest planning and reduce adversarial relationships over forest management. Market forces are driving commercial forests toward forest certification. Private forests compose 80% of our oak forests and are the hardest group to influence. States have not been able to effectively market forest plans and we recommend joining with advocacy groups more adept at motivating the public. Increased communication between wildlife and forestry professionals is needed through agency restructuring and joint meetings of professional agencies at the state level. Professional wildlife and forest managers are encouraged to make increased use of monitoring data and form a multiagency cooperative using a joint venture model, which has been successful for other organizations.     

基于BP人工神经网络的兴安落叶松天然林全林分生长模型的研究

以大兴安岭地区兴安落叶松天然林为研究对象,基于688块固定标准地数据,采用MATLAB中log-sigmoid型函数(logsig)和线性函数(purelin)为神经元的作用函数,依据全林分生长模型的概念,以年龄（A）、地位级指数（SCI）和林分密度指数（SDI）作为输入变量,以林分每公顷蓄积量（M）作为输出变量,构建和训练了全林分生长的BP人工神经网络模型,并与常规建模方法进行了对比研究。结果表明,BP人工神经网络模型的拟合精度高达99.6%,检验精度为98.9%,说明与其它建模方法相比人工神经网络建模具有较高的拟合精度和适应性,对林分生长具有更好的预测能力。     

The Performance of Whole Genome Amplification Methods and Next-Generation Sequencing for Pre-Implantation Genetic Diagnosis of Chromosomal Abnormalities

Reliable and accurate pre-implantation genetic diagnosis(PGD) of patient’s embryos by next-generation sequencing(NGS) is dependent on efficient whole genome amplification(WGA) of a representative biopsy sample. However, the performance of the current state of the art WGA methods has not been evaluated for sequencing. Using low template DNA(15 pg) and single cells, we showed that the two PCR-based WGA systems Sure Plex and MALBAC are superior to the REPLI-g WGA multiple displacement amplification(MDA) system in terms of consistent and reproducible genome coverage and sequence bias across the 24 chromosomes, allowing better normalization of test to reference sequencing data. When copy number variation sequencing(CNV-Seq) was applied to single cell WGA products derived by either Sure Plex or MALBAC amplification, we showed that known disease CNVs in the range of 3e15 Mb could be reliably and accurately detected at the correct genomic positions. These findings indicate that our CNV-Seq pipeline incorporating either Sure Plex or MALBAC as the key initial WGA step is a powerful methodology for clinical PGD to identify euploid embryos in a patient’s cohort for uterine transplantation.     

Quantitative Phenotyping as an Efficient Means to Estimate C-Cell Number in a Knock-in Mouse Model of MEN2B

Over the last two decades we have witnessed the generation of hundreds, if not thousands, of lines of genetically altered mice, large numbers of which are being produced in order to model human disease. Given that their creation is still rather technically demanding and labour intensive, the time taken analysing the resultant phenotypes should be such that the maximal amount of information can be gleaned efficiently in an unbiased manner so as to be as close to the 'true' value as possible. In an attempt to characterise a cell-specific phenotype in a genetically defined knock-in mouse model of multiple endocrine neoplasia type 2B (MEN2B) we used a modern, unbiased, stereological approach called the optical fractionator to estimate total cell number in 3-D space. By applying a sampling technique to tissue blocks in a systematic random uniform manner, we demonstrate that the total number of calcitonin-immunoreactive C-cells in the thyroid glands of littermate mice harbouring activating mutations in one or both alleles of ret does not vary significantly (p = 0.46) from an unbiased estimate of 23,000 in wild-type controls; likewise, neither does mean thyroid volume (p = 0.78) when estimated using Cavalieri's principle. We demonstrate that the variation associated with the quantitative phenotyping method is negligible. Using this efficient, unbiased stereological method our results provide new insights into cell number and positioning with consequences for both normal and disease states. In summary, this unbiased stereological technique is conceptually simple, can be applied efficiently, and is pertinent to quantitating a wide variety of cell phenotypes thereby bridging specialisation boundaries. We propose the adoption of this technique to mouse experimental geneticists and recommend its horizontal transmission across all fields within experimental biology.     

基于全基因组测序的法医单核苷酸多态性系谱推断研究

目的 通过全基因组测序（whole genome sequencing，WGS）获得高密度单核苷酸多态性（single nucleotide polymorphism，SNP）分型数据，评估分型准确性，研究建立WGS数据用于法医SNP系谱推断的方法。方法 通过华大MGISEQ-200RS测序平台对样本进行深度为30×的WGS，从测序数据中提取Wegene GSA芯片中的645 199个常染色体SNP位点，质控过滤后运用IBS/IBD算法计算预测亲缘关系，并对样本的族群来源进行分析。结果 从测序数据中提取的SNP分型与Wegene GSA芯片分型的一致率大于99.62%。测序获得的SNP数据使用IBS算法可预测1~4级亲缘关系，4级亲缘预测置信区间准确性达100%，使用IBD算法可预测1~7级亲缘关系，7级亲缘预测为有亲缘关系的准确性达100%，通过高深度WGS数据获取的SNP系谱推断能力与芯片预测结果无显著差异。同时，WGS数据用于族群推断与调查结果一致。结论 WGS技术可应用于法医SNP系谱推断，为案件侦破提供线索。     

林木分子遗传图谱的构建

介绍了林木分遗传图谱构建中所使用的分离群体和分子标记,着重综述了国内外林木遗传图谱研究的现状,对已建立图谱的树种的作图情况作了较尽的总结。     

Simulating the Long-term Response of Tropical Wet Forests to Fragmentation

In the coming decades, a large fraction of the world's tropical forests will be fragmented into remnants surrounded by secondary vegetation, land-use areas, or roads. It is important to develop integrative tools to monitor the evolution of these fragmented ecosystems. We used the individual-oriented and process-based forest growth simulator FORMIND2.0 to investigate the spatial and temporal effects on standing biomass and functional diversity of various intensities and patterns of fragmentation within a forest landscape. The simulator was calibrated for an old-growth wet forest in French Guiana, South America. We found that the standing biomass of forest remnants was reduced significantly compared to a similar area of nonfragmented forest. When fewer but larger remnants were created rather than many small ones, the total loss in biomass and the increase in the abundance of early-successional species were significantly reduced, confirming that edge effects dominate the functioning of forest remnants. We also performed simulations of secondary succession after the landscape had been abandoned. The simulated recovery time in those secondary forests depends on both the size of cleared area and the spatial pattern of the remnant forests. Received 30 January 2002; accepted 16 July 2002.     

Bird Response to Prescribed Silvicultural Treatments in Bottomland Hardwood Forests

ABSTRACT Silvicultural treatments prescribed to enhance wildlife habitat by promoting structural heterogeneity via retention of large live trees, snags, and coarse woody debris has been termed wildlife-forestry. Wildlife-forestry has been advocated for management of bottomland hardwood forests on public conservation lands within the Mississippi Alluvial Valley, USA. On Tensas River National Wildlife Refuge in northeast Louisiana, we used distance sampling during 6 visits to 138 point locations to estimate avian densities within stands subjected to variable-retention harvests, within a 13-year chronosequence, and untreated control stands. Densities of 9 species, including 6 species of conservation concern, were greater in treated stands than on untreated stands. Five species responded negatively to treatments and had greater densities in untreated control stands. Based on conservation concern scores established by Partners in Flight and annual detections of each of 30 species, treated stands afforded greater community-wide bird conservation than did untreated stands. For most species, maximum treatment response was between 5 years and 8 years posttreatment with duration of treatment effect <13 years. Therefore, habitat conditions on treated stands should be reevaluated at circa 15-year intervals and, if warranted, additional silvicultural treatment prescribed to rejuvenate habitat conditions.     

Using Genetic Tools to Track Desert Bighorn Sheep Colonizations

ABSTRACT Understanding colonization is vital for managing fragmented populations. We employed mitochondrial DNA haplotypes and 14 microsatellite (nuclear DNA) markers to infer the origins of newly established populations of desert bighorn sheep (Ovis canadensis nelsoni) and to assess loss of genetic diversity during natural colonizations. We used haplotype distribution, F-statistics, Bayesian population clustering, and assignment tests to infer source populations for 3 recent colonies and identified a previously undetected colonization from multiple source populations. Allelic richness declined in 3 of 4 colonies in comparison to the primary source populations, but not as much as has been reported for translocated populations. Heterozygosity declined in only one colony. We also demonstrated that both native and translocated desert bighorn sheep have naturally recolonized empty habitats and suggest that colonization may partially offset population extinction in the region as long as connectivity is maintained. Genetic techniques and mitochondrial DNA haplotypes we described will allow managers to determine the origins of future colonizations by bighorn sheep in California, USA, and prioritize protection of linkages between known sources and colonies.     

Genetic mapping of the early responses to salt stress in Arabidopsis thaliana

Salt stress decreases plant growth prior to significant ion accumulation in the shoot. However, the processes underlying this rapid reduction in growth are still unknown. To understand the changes in salt stress responses through time and at multiple physiological levels, examining different plant processes within a single set-up is required. Recent advances in phenotyping has allowed the image-based estimation of plant growth, morphology, colour and photosynthetic activity. In this study, we examined the salt stress-induced responses of 191 Arabidopsis accessions from 1 h to 7 days after treatment using high-throughput phenotyping. Multivariate analyses and machine learning algorithms identified that quantum yield measured in the light-adapted state (F_v′/F_m′) greatly affected growth maintenance in the early phase of salt stress, whereas the maximum quantum yield (QY_max) was crucial at a later stage. In addition, our genome-wide association study (GWAS) identified 770 loci that were specific to salt stress, in which two loci associated with QY_max and F_v′/F_m′ were selected for validation using T-DNA insertion lines. We characterized an unknown protein kinase found in the QY_max locus that reduced photosynthetic efficiency and growth maintenance under salt stress. Understanding the molecular context of the candidate genes identified will provide valuable insights into the early plant responses to salt stress. Furthermore, our work incorporates high-throughput phenotyping, multivariate analyses and GWAS, uncovering details of temporal stress responses and identifying associations across different traits and time points, which are likely to constitute the genetic components of salinity tolerance.     

Revisiting the historical distribution of Seasonally Dry Tropical Forests: new insights based on palaeodistribution modelling and palynological evidencegeb

Aim To investigate the potential distribution of Seasonally Dry Tropical Forests (SDTFs) during the Quaternary climatic fluctuations; to reassess the formerly proposed ‘Pleistocenic arc hypothesis’ (PAH); and to identify historically stable and unstable areas of SDTF distributions in the light of palaeodistribution modelling. Location SDTFs in lowland cis‐Andean eastern‐central South America. Methods We first developed georeferenced maps depicting the current distributional extent of SDTFs under two distinct definitions (narrow and broad). We then generated occurrence datasets, which were used with current and past bioclimatic variables to predict SDTF occurrence by implementing the maximum entropy machine‐learning algorithm. We obtained historical stability maps by overlapping the presence/absence projections of each of three climatic scenarios [current, 6 kyr bp during the Holocene, and 21 kyr bp during the Last Glacial Maximum (LGM)]. Finally, we checked the consistencies of the model prediction with qualitative comparisons of vegetation types inferred from available fossil pollen records. Results The present‐day SDTF distribution is disjunct, but we provide evidence that it was even more disjunct during the LGM. Reconstructions support a progressive southward and eastward expansion of SDTFs on a continental scale since the LGM. No significant expansion of SDTFs into the Amazon Basin was detected. Areas of presumed long‐term stability are identified and confirmed (the three nuclear regions, Caatinga, Misiones and Piedmont, plus the Chiquitano region), and these possibly acted as current and historical refugial areas. Main conclusions The LGM climate was probably too dry and cold to support large tracts of SDTF, which were restricted to climatically favourable areas relative to the present day (in contrast with the PAH, as it was originally conceived). Expansions of SDTFs are proposed to have occupied the southern portion of Caatinga nucleus more recently during the early–middle Holocene transition. We propose an alternative scenario amenable to further testing of an earlier SDTF expansion (either at the Lower Pleistocene or the Tertiary), followed by fragmentation in the LGM and secondary expansion in the Holocene. The stability maps were used to generate specific genetic predictions at both continental and regional scales (stable areas are expected to have higher genetic diversity and endemism levels than adjacent unstable areas) that can be used to direct field sampling to cover both stable (predicted refugia) and unstable (recently colonized) areas. Lastly, we discuss the possibility that SDTFs may experience future expansion under changing climate scenarios and that both stable and unstable areas should be prioritized by conservation initiatives.     

Vulnerability of dynamic genetic conservation units of forest trees in Europe to climate change

A transnational network of genetic conservation units for forest trees was recently documented in Europe aiming at the conservation of evolutionary processes and the adaptive potential of natural or man‐made tree populations. In this study, we quantified the vulnerability of individual conservation units and the whole network to climate change using climate favourability models and the estimated velocity of climate change. Compared to the overall climate niche of the analysed target species populations at the warm and dry end of the species niche are underrepresented in the network. However, by 2100, target species in 33–65 % of conservation units, mostly located in southern Europe, will be at the limit or outside the species' current climatic niche as demonstrated by favourabilities below required model sensitivities of 95%. The highest average decrease in favourabilities throughout the network can be expected for coniferous trees although they are mainly occurring within units in mountainous landscapes for which we estimated lower velocities of change. Generally, the species‐specific estimates of favourabilities showed only low correlations to the velocity of climate change in individual units, indicating that both vulnerability measures should be considered for climate risk analysis. The variation in favourabilities among target species within the same conservation units is expected to increase with climate change and will likely require a prioritization among co‐occurring species. The present results suggest that there is a strong need to intensify monitoring efforts and to develop additional conservation measures for populations in the most vulnerable units. Also, our results call for continued transnational actions for genetic conservation of European forest trees, including the establishment of dynamic conservation populations outside the current species distribution ranges within European assisted migration schemes.     

Genetic variation within a fragmented population of swietenia humilis zucc

With large tracts of once continuous forest now modified by human use to leave reduced and highly fragmented stands of trees, the determination of the genetic consequences of forest fragmentation is a priority for ascertaining the conservation value of resultant stands, and in formulating sustainable management strategies. The levels and distribution of genetic diversity over 10 microsatellite loci were investigated within a fragmented population of the neotropical tree Swietenia humilis Zucc. High levels of genetic variation, typical of a highly outcrossing species, were found in all fragments at all loci (mean HE = 0.548). The majority of the variation was within rather than between fragments (RST = 0.032), giving high indirect estimates of gene flow (Nm = 8.9), probably reflecting the genetic structure of the trees present under more continuous forest. A high proportion of loci also showed significant departures from Hardy-Weinberg equilibrium with associated significant levels of FIS. The initial effects of fragmentation were, however, seen in the fragments through the loss of low-frequency alleles present in the continuous 'control' stand. The percentage of this allelic loss increased with a decrease in fragment size.     

Exploiting the Extraordinary Genetic Polymorphism of Ciona for Developmental Genetics with Whole Genome Sequencing

Studies in tunicates such as Ciona have revealed new insights into the evolutionary origins of chordate development. Ciona populations are characterized by high levels of natural genetic variation, between 1 and 5%. This variation has provided abundant material for forward genetic studies. In the current study, we make use of deep sequencing and homozygosity mapping to map spontaneous mutations in outbred populations. With this method we have mapped two spontaneous developmental mutants. In Ciona intestinalis we mapped a short-tail mutation with strong phenotypic similarity to a previously identified mutant in the related species Ciona savignyi. Our bioinformatic approach mapped the mutation to a narrow interval containing a single mutated gene, α-laminin3,4,5, which is the gene previously implicated in C. savignyi. In addition, we mapped a novel genetic mutation disrupting neural tube closure in C. savignyi to a T-type Ca²⁺ channel gene. The high efficiency and unprecedented mapping resolution of our study is a powerful advantage for developmental genetics in Ciona, and may find application in other outbred species.