Levels of genetic diversity at different stages of the domestication cycle of interior spruce in British Columbia

Concerns over the reductionist nature of the domestication of forest-tree species focus on the possibility of potential genetic erosion during this process. To address these concerns, genetic diversity assessments in a breeding zone the Province of British Columbia “interior” spruce (Picea glauca×engelmanni) program was conducted using allozyme markers. Genetic-variation comparisons were made between natural and production (seed orchard) populations as well as seed and seedling crops produced from the same breeding zone’s seed orchard. The natural population sample consisted of a total of 360 trees representing three stands within each of three watersheds present in the Shuswap-Adams low-elevation zone of interior British Columbia. Small amounts of genetic differentiation were observed among the nine natural populations (4%) and this was attributable to extensive gene flow Consequently, the sum of these nine populations was considered as a baseline for the genetic variation present in the breeding zone. The comparisons between the seed orchard and the breeding zone produced a similar percentage of polymorphic loci while the expected hetrozygosity (0.207 vs 0.210) and the average number of alleles per locus (2.7 vs 2.4) were slightly lower in the seed orchard. A total of seven natural populations’ rare alleles were not present in the orchard population, while one allele was unique to the orchard. The %P increased to 70.6% in the seedlot, but dropped to the natural populations level (64.7%) in the plantation. The observed increase in %P was a result of pollen contamination in the orchard. It is suspected that the reduction in the plantation was caused by an unintentional selection in the nursery. Simulated roguing in the orchard did not drastically reduce even if up to 50% of the orchard’s clones were rogued. However, roguing was associated with a reduction in the average number of alleles per locus (i.e., sampling effect). Received: 2 January 1996 / Accepted: 24 May 1996     

Prd29A及DREB1A的克隆和干旱诱导型植物表达载体的构建与鉴定

从拟南芥中克隆了RD29A基因的启动子(Prd29A)及DREB1M基因的DNA片段,构建Prd29A:DREB1A融合基因,采用合成的接头将该融合基因插入到植物表达载体pBI121中,经鉴定,确认正确.     

Unravelling mitochondrial retrograde regulation in the abiotic stress induction of rice ALTERNATIVE OXIDASE 1 genes

Mitochondrial retrograde regulation (MRR) is the transduction of mitochondrial signals to mediate nuclear gene expression. It is not clear whether MRR is a common regulation mechanism in plant abiotic stress response. In this study, we analysed the early abiotic stress response of the rice OsAOX1 genes, and the induction of OsAOX1a and OsAOX1b (OsAOX1a/b) was selected as a working model for the stress‐induced MRR studies. We found that the induction mediated by the superoxide ion (O_2·^‐)‐generating chemical methyl viologen was stronger than that of hydrogen peroxide (H₂O₂). The addition of reactive oxygen species (ROS) scavengers demonstrated that the stress induction was reduced by eliminating O_2·^‐. Furthermore, the stress induction did not rely on chloroplast‐ or cytosol‐derived O_2·^‐. Next, we generated transgenic plants overexpressing the superoxide dismutase (SOD) gene at different subcellular locations. The results suggest that only the mitochondrial SOD, OsMSD, attenuated the stress induction of OsAOX1a/b specifically. Therefore, our findings demonstrate that abiotic stress initiates the MRR on OsAOX1a/b and that mitochondrial O_2·^– is involved in the process.     

新生儿肺炎的临床表现及x线特征的探讨

目的：探讨新生儿肺炎（neonatal pneumonia,NP）的临床表现及x线特征,以提高对NP的临床认识。方法：选择2011年6月至2012年10月在我院确诊为NP的新生儿73例,均经x线检查,回顾性分析患儿的临床资料,总结并分析患儿的临床表现及x线特征。结果：NP患儿的临床症状主要表现为呼吸急促、发绀、咳嗽、吐沫、呛奶和三凹征,部分患儿体温正常;NP的x线影像表现具有多样性,以不同程度的支气管肺炎多见,主要表现为肺纹理增多增密,局部肺野透光度降低或透光度增强。结论：NP患儿的临床症状以呼吸急促、发绀、咳嗽、吐沫、呛奶和三凹征为主,x线检查可为NP的早期诊断提供重要的临床信息,临床医师应根据NP患儿的x线影像的多样性,密切结合患儿的临床症状,做出综合分析。     

异丙酚和氯胺酮对大鼠离体缺血再灌注损伤心肌脂质过氧化的影响

目的：比较异丙酚和氯胺酮对大鼠离体缺血再灌注损伤心肌脂质过氧化的影响。方法：成年Wistar大鼠18只,雌雄不拘。体重240-300g,随机分为3组（T1=6）：心肌缺血再灌注损伤组（I／R组）,异丙酚组（P组）,氯胺酮组（K组）。采用Langendorff灌装置建立离体心脏缺血再灌注模型,将心脏连接至Langendorff逆灌装置,3组均以K-H液平衡灌注10min后,再分别以K．H液、含30μmol/L。异丙酚的K-H液、含10μmol-L-1氯胺酮的K-H液灌注10min,然后全心停灌25min,再分别以停灌前相同的灌注液恢复灌注30min。留取冠脉流出液测定总LDH活性;灌注末取左室心肌组织置于2．5％的戊二醛固定,观察心肌的超微结构;心尖部心肌组织留待检测8-异前列腺素和SOD活性。结果：与I／R组比较,P组8-异前列腺素含量降低,SOD活性升高,LDH活性降低（P〈0．05）;K组8-异前列腺素含量,SOD及LDH活性均无统计学意义（P〉0．05）;与P组比较,K组8-异前列腺素含量升高,SOD及LDH活性降低（P〈0．05）;P组心肌超微结构损伤较m组和K组也明显改善。结论：异丙酚可显著减轻心肌缺血再灌注损伤大鼠的脂质过氧化和心肌缺血再灌注损伤,而氯胺酮没有抗心肌缺血再灌注损伤心肌脂质过氧化的作用。     

Prediction accuracies for growth and wood attributes of interior spruce in space using genotyping-by-sequencing

Background

Genomic selection (GS) in forestry can substantially reduce the length of breeding cycle and increase gain per unit time through early selection and greater selection intensity, particularly for traits of low heritability and late expression. Affordable next-generation sequencing technologies made it possible to genotype large numbers of trees at a reasonable cost.

Results

Genotyping-by-sequencing was used to genotype 1,126 Interior spruce trees representing 25 open-pollinated families planted over three sites in British Columbia, Canada. Four imputation algorithms were compared (mean value (MI), singular value decomposition (SVD), expectation maximization (EM), and a newly derived, family-based k-nearest neighbor (kNN-Fam)). Trees were phenotyped for several yield and wood attributes. Single- and multi-site GS prediction models were developed using the Ridge Regression Best Linear Unbiased Predictor (RR-BLUP) and the Generalized Ridge Regression (GRR) to test different assumption about trait architecture. Finally, using PCA, multi-trait GS prediction models were developed. The EM and kNN-Fam imputation methods were superior for 30 and 60% missing data, respectively. The RR-BLUP GS prediction model produced better accuracies than the GRR indicating that the genetic architecture for these traits is complex. GS prediction accuracies for multi-site were high and better than those of single-sites while multi-site predictability produced the lowest accuracies reflecting type-b genetic correlations and deemed unreliable. The incorporation of genomic information in quantitative genetics analyses produced more realistic heritability estimates as half-sib pedigree tended to inflate the additive genetic variance and subsequently both heritability and gain estimates. Principle component scores as representatives of multi-trait GS prediction models produced surprising results where negatively correlated traits could be concurrently selected for using PCA2 and PCA3.

Conclusions

The application of GS to open-pollinated family testing, the simplest form of tree improvement evaluation methods, was proven to be effective. Prediction accuracies obtained for all traits greatly support the integration of GS in tree breeding. While the within-site GS prediction accuracies were high, the results clearly indicate that single-site GS models ability to predict other sites are unreliable supporting the utilization of multi-site approach. Principle component scores provided an opportunity for the concurrent selection of traits with different phenotypic optima.

Electronic supplementary material

The online version of this article (doi:10.1186/s12864-015-1597-y) contains supplementary material, which is available to authorized users.     

基于戴云山固定样地黄山松群落物种组成与结构研究

黄山松是亚热带中部山区主要建群种,研究其物种组成及群落结构对探讨中亚热带植被演替规律具有重要意义。戴云山自然保护区分布有大面积黄山松群落,该研究采用网格布点法,建立86块(25.82 m×25.82 m)共5.7 hm~2固定样地,对样地内黄山松群落的物种组成特征、分布区类型、胸径和树高结构、空间分布格局4个方面特征进行了探讨。结果表明:(1)样地内共出现木本植物32 603株219种,隶属于59科108属。乔灌木优势种有黄山松、马尾松、木荷、肿节少穗竹、岩柃、窄基红褐柃等,其中稀有种和偶见种分别占总物种数的33.79%、25.75%和45.21%、24.66%。(2)在区系分布类型上,热带分布类型的科属多于温带分布类型的科属,热带分布类型中又以泛热带分布类型,温带分布类型以北温带占据最大比例。(3)样地内优势种的胸径分布呈倒"J"型,表明更新状态良好。垂直结构上,各优势种树高为倒"J"型或近似倒"J"型。黄山松和其他优势乔木大部分树高为4~10 m,灌木除短尾越桔0~1 m个体数最多外,其他优势灌木1~2 m个体数最多。(4)经计算,样地内乔灌木各优势种均呈聚集分布,聚集程度有所差异,乔木层黄山松最低,灌木层短尾越桔最低。该研究结果表明戴云山保护区黄山松群落物种组成丰富、更新良好,反映了亚热带高山针叶林的典型特征,其空间分布格局可能与取样方式等因素有关。     

Practical application of genomic selection in a doubled-haploid winter wheat breeding program

Crop improvement is a long-term, expensive institutional endeavor. Genomic selection (GS), which uses single nucleotide polymorphism (SNP) information to estimate genomic breeding values, has proven efficient to increasing genetic gain by accelerating the breeding process in animal breeding programs. As for crop improvement, with few exceptions, GS applicability remains in the evaluation of algorithm performance. In this study, we examined factors related to GS applicability in line development stage for grain yield using a hard red winter wheat (Triticum aestivum L.) doubled-haploid population. The performance of GS was evaluated in two consecutive years to predict grain yield. In general, the semi-parametric reproducing kernel Hilbert space prediction algorithm outperformed parametric genomic best linear unbiased prediction. For both parametric and semi-parametric algorithms, an upward bias in predictability was apparent in within-year cross-validation, suggesting the prerequisite of cross-year validation for a more reliable prediction. Adjusting the training population’s phenotype for genotype by environment effect had a positive impact on GS model’s predictive ability. Possibly due to marker redundancy, a selected subset of SNPs at an absolute pairwise correlation coefficient threshold value of 0.4 produced comparable results and reduced the computational burden of considering the full SNP set. Finally, in the context of an ongoing breeding and selection effort, the present study has provided a measure of confidence based on the deviation of line selection from GS results, supporting the implementation of GS in wheat variety development.     

Optimization of combined genetic gain and diversity for collection and deployment of seed orchard crops

Genetic gain and diversity of seed orchards’ crops are determined by the number of parents, their breeding values and relatedness, within-orchard pollination efficiency, and level of pollen contamination. These parameters can be manipulated at establishment by varying clonal representation (e.g., linear deployment), during orchard development by genetic thinning, or by selective harvesting. Since clonal fecundities are known to vary both within and among years, then each seed crop has a unique genetic composition and, therefore, crops should be treated on a yearly basis. Here we present an optimization protocol that maximizes crop’s genetic gain at any desired genetic diversity through the selection of a subset of the crop that meets both parameters. The genetic gain is maximized within the biological limit set by each clone’s seed-cone production and effective population size is used as a proxy to genetic diversity whereby any relationship among clones is considered. The optimization was illustrated using 3 years’ reproductive output data from a first-generation western larch seed orchard and was tested under various scenarios including actual male and female reproductive output and male reproductive output assumed to be either equal to that of female or a function of clonal representation. Furthermore, various levels of co-ancestry were assigned to the orchard’s clones in supplementary simulations. Following the optimization, all solutions were effective in creating custom seedlots with different gain and diversity levels and provided the means to estimate the genetic properties of composite seedlots encompassing the remaining “unused” seed from a number of years.