Single nucleotide polymorphisms (SNPs) discovery and linkage disequilibrium (LD) in forest trees

With completion of the Populus genome sequencing project and the availability of many expressed sequence tags （ESTs） databases in forest trees, attention is now rapidly shifting towards the study of individual genetic variation in natural populations. The most abundant form of genetic variation in many eukaryotic species is represented by single nucleotide polymorphisms （SNPs）, which can account for heritable inter-individual differences in complex phenotypes. Unlike humans, the linkage disequilibrium （LD） rapidly decays within candidate genes in forest trees. Thus, SNPs-based candidate gene association studies are considered to be a most effective approach to dissect the complex quantitative traits in forest trees. The present study demonstrates that LD mapping can be used to identify alleles associated with quantitative traits and suggests that this new approach could be particularly useful for performing breeding programs in forest trees. In this review, we will describe the fundamentals, patterns of SNPs distribution and frequency, summarize recent advances in SNPs discovery and LD and comment on the application of LD in the dissection of complex quantitative traits in forest tress. We also put forward the outlook for future SNPs-based association analysis of quantitative traits in forest trees.     

Mega-trap-plots: a novel method of Sirex woodwasp management on Pinus radiata plantations in Chile

Sirex noctilio is one of the most important invasive pests that affect Pinus radiata plantations in Chile. Its management is based on a biological control complex, the most important component of which is the nematode, Deladenus siricidicola. However, in some areas, S. noctilio populations attain epidemic levels and no effective control methods exist to reduce large populations in a short period. In this study, we evaluated a novel method called mega-trap-plots (MTPs), which consist of an area of 1 ha with trap trees, which were debilitated in four different months (from November to February) with the purpose of reducing the Sirex wasp population through harvesting of trees attacked. The main objective was to reduce the potential population of S. noctilio, by evaluating four periods or months of MTP installation to maximise the colonisation of trap trees by wood wasps. The results showed that the MTPs that were installed from November to January had the highest wood wasp infestation, which was coincident with the flight period of the insect. The trap trees were clearly attractive to S. noctilio females up to 90 d following their establishment. The MTPs that were established in November concentrated a potential population of 57 901 females of S. noctilio, which represents a population 5.4 times greater than that in the control, with 10 701 females. The population of S. noctilio attracted between November and January shows that the use of MTPs is an effective system for the management of wood wasps on plantations with a high level of infestation and thereby can reduce their spread and the attack of new trees within the same forest compartments.     

一种利用黑松枝条筛选杀松材线虫剂的生测方法

该文介绍了一种利用黑松枝条进行化合物对松材线虫作用的生测方法。通过研究枝条的接种线虫数量、含水量以及灭菌处理后对松材线虫繁殖的影响,确定了合适的生测条件,并对几种生测方法的优缺点进行了讨论。     

日本落叶松杂种及亲本 4CL基因的克隆和SNP多态性分析

以日本落叶松(Larix kaempferi)不同杂交组合为材料,依据转录组测序信息,成功获得了11种日本落叶松材料的4 CL基因的编码区序列,该序列长1 537 bp,包含完整ORF片段1 368 bp,编码455个氨基酸。qRT-PCR结果分析表明,除日本落叶松Larix16×Larix61组合外,Larix82×Larix13、Larix40×Larix10和Larix82×Larix61子代的表达均高于双亲,推测4 CL基因差异表达与落叶松杂种的木质素生物合成有关。进一步采用SNP标记方法和DNAMAN软件对不同日本落叶松杂种和亲本组合的单核苷酸多态性进行分析。共检测到66个SNP多态性位点,表明日本落叶松4CL 具有丰富的遗传多样性。66个SNP变异中,属于三突变1个;转换类型45个,占总变异的68.18%;20个属于颠换类型,占总变异的30.30%,转换:颠换=9:4。在转换类型中,A/G和C/T转换分别占28.79%和39.39%;颠换类型中A/C、A/T、G/C、G/T分别占4.55%、9.09%、9.09%和7.58%。采用NJ 聚类法对克隆片段的氨基酸序列进行了遗传多样性分析。