Hydroacoustic assessment of mono‐ and polymorphic Coregonus density and biomass in subarctic lakes

Density and biomass estimates of pelagic fish are essential to understand food web interactions and ecosystem functioning. We conducted surveys of six subarctic lakes for assessing both mono‐ and polymorphic whitefish Coregonus lavaretus (L.) populations. Monomorphic whitefish lakes were inhabited by a habitat and diet generalist, large sparsely rakered (LSR) morph, whereas polymorphic whitefish lakes had a littoral benthivorous LSR morph, a pelagic planktivorous densely rakered (DR) morph and in two cases a benthivorous small sparsely rakered (SSR) morph inhabiting the profundal zone. In addition, an introduced specialist zooplanktivore, vendace Coregonus albula (L.), inhabited one of the monomorphic lakes. Hydroacoustics was found to be an appropriate method for estimating coregonid densities and biomasses in large and deep polymorphic lakes occupied by the planktivorous DR morph or vendace, but only during dark nights in autumn. The suitability of hydroacoustic assessment for benthivorous LSR and SSR morphs was low, especially in polymorphic whitefish lakes due to their preference for near‐bottom habitat or shallow areas not sampled with hydroacoustics. The pelagic density of DR morph varied from 330 to 1780 fish·ha^?1 and biomass from 1.4 to 13.3 kg·ha^?1 in polymorphic whitefish lakes, whereas corresponding estimates for LSR morph were 10–320 fish·ha^?1 and 0.5–8.4 kg·ha^?1 in monomorphic whitefish lakes. In general, polymorphism tended to increase the density and biomass of whitefish in the pelagic area compared with monomorphic systems.     

香蕉GAPDH基因家族的生物信息学及转录表达分析

从香蕉基因组数据库和NCBI数据库中检索香蕉GAPDH基因家族的所有成员,并采用生物信息学方法对其进行亚细胞定位、进化树分析和保守结构域预测。克隆测序发现,巴西蕉内的GAPDH基因家族成员序列与小果野蕉基因组数据库中提供的序列基本一致,同源性超过98%。转录表达分析表明,GAPDH基因家族成员在巴西蕉不同器官的表达模式多样:MaGAPCP1,MaGAPC6/8/10/11成组成型表达,其余的基因则在各组织器官间成差异型表达,且差异型表达的基因在不同组织器官中表达模式也不相同,组成型表达的基因在不同组织器官中表达模式虽相同,但表达量有差异。GAPDH基因家族成员在表达模式上的多样化,可能暗示其功能的多样化,这种多样化可能是在进化过程中为适应环境而出现的功能分化或冗余。结果为进一步研究GAPDH基因家族成员在香蕉生长、发育,非生物胁迫,果实后熟等重要生物学过程中的功能奠定基础。     

莫氏兰的品种选育和栽培技术研究

对从新加坡引进的莫氏兰进行适应性栽培。筛选出Mokara Adisa、M. Red、M. Dinah Shore、M. Chittl Orange Spot、M. Chao Praya Gold、M. Chao Praya Boy、M. Chark Kuan Pink、M. Kitiya共8个适宜在海南省三亚市栽培的莫氏兰优良切花品种，并对莫氏兰优良品种的主要栽培技术进行介绍。     

溪岸蠼螋对棉铃虫的捕食能力

为明确棉田溪岸蠼螋 Labidura riparia 对棉铃虫的控害潜能, 在实验室条件下观察和测定了溪岸蠼螋不同龄期的若虫、雌雄成虫对棉铃虫幼虫、蛹和成虫的捕食能力以及其5龄若虫和雌雄成虫的捕食选择性。结果表明:不同发育阶段的溪岸蠼螋都不捕食棉铃虫完整的蛹体, 但对棉铃虫幼虫和成虫都具有较强的捕食能力。其中, 雌性溪岸蠼螋成虫的捕食能力最强, 对棉铃虫1龄幼虫日捕食量最大, 为(31.3±1.1)头。1龄溪岸蠼螋若虫也具有一定的捕食能力, 对棉铃虫1龄幼虫日捕食量为(1.7±0.7)头。不同龄期的溪岸蠼螋对相同龄期棉铃虫幼虫的捕食能力随龄期增加而增大。对1~3龄棉铃虫幼虫,溪岸蠼螋雌成虫捕食能力最强,其次是溪岸蠼螋雄成虫,再次是溪岸蠼螋5龄若虫。但是,对棉铃虫4~6龄幼虫和雌雄成虫,溪岸蠼螋雌雄成虫和5龄若虫的捕食量差异不显著。捕食选择试验表明:溪岸蠼螋5龄若虫和雌雄成虫对棉铃虫1～4龄幼虫均表现正喜好性, 对5～6龄棉铃虫幼虫和雌雄成虫表现负喜好性。     

三七NAC基因家族全基因组鉴定与表达分析

为明确三七Panax notoginseng NAC转录因子基因家族的分布、功能和结构,通过生物信息学分析法进行鉴定,对其理化特性、染色体位置和进化特征进行分析,并根据RNA-seq数据分析其家族成员的时空表达模式和受黑斑病菌Alternaria panax诱导后的表达情况。结果显示,三七中共有98个NAC基因家族成员,其编码蛋白质长度介于104～882个氨基酸之间,分子量在11.78～100.20 kD之间,等电点在4.12～9.75之间。这98个NAC基因家族不均匀地分布在三七的12条染色体上,其中1号染色体分布最多（16个）,而11号染色体上分布最少（1个）。三七NAC基因启动子区域存在与光响应、生长素响应、赤霉素响应及茉莉酸甲酯响应等相关的多种顺式作用元件。NAC基因在三七不同组织及根部不同发育时期均有表达,在受到黑斑病菌侵染的叶片中NAC部分基因家族成员显著上调表达。表明NAC基因家族在三七的生长发育和响应黑斑病菌侵染过程中具有重要作用。     

Effective population size and inbreeding depression on litter size in rabbits. A case study

The purpose of this study is to use demographic and litter size data on four Spanish maternal lines of rabbits (A, V, H and LP), as a case study, in order to: (i) estimate the effective population size of the lines, as a measure of the rate of increase of inbreeding, and (ii) study whether the inbreeding effect on litter size traits depends on the pattern of its accumulation over time. The lines are being selected for litter size at weaning and are kept closed at the same selection nucleus under the same selection and management programme. The study considered 47 794 l and a pedigree of 14 622 animals. Some practices in mating and selection management allow an increase of the inbreeding coefficient lower than 0.01 per generation in these lines of around 25 males and 125 females. Their effective population size (Ne) was around 57.3, showing that the effect of selection, increasing the inbreeding, was counterbalanced by the management practices, intended to reduce the rate of inbreeding increase. The inbreeding of each individual was broken down into three components: old, intermediate and new inbreeding. The coefficients of regression of the old, intermediate and new inbreeding on total born (TB), number born alive (NBA) and number weaned (NW) per litter showed a decreasing trend from positive to negative values. Regression coefficients significantly different from zero were those for the old inbreeding on TB (6.79 ± 2.37) and NBA (5.92 ± 2.37). The contrast between the coefficients of regression between the old and new inbreeding were significant for the three litter size traits: 7.57 ± 1.72 for TB; 6.66 ± 1.73 for NBA and 5.13 ± 1.67 for NW. These results have been interpreted as the combined action of purging unfavourable genes and artificial selection favoured by the inbreeding throughout the generations of selection.     

Is the use of formulae a reliable way to predict the accuracy of genomic selection?

We studied four formulae used to predict the accuracy of genomic selection prior to genotyping. The objectives of our study were to investigate the impact of the parameters of each formula on the values of accuracy calculated using these formulae, and to check whether the accuracies reported in the literature are in agreement with the formulae. First, we computed the marginal distribution of accuracy (by integration) for each parameter of all four formulae: heritability h², reference population size T, number of markers M and number of effective segments in the genome M_e. Then, we collected 145 accuracies and corresponding parameters reported in 13 publications on genomic selection (mainly in dairy cattle), and performed analysis of variance to test the differences between observed and predicted accuracy with effects of formulae and parameters. The variation of accuracy for different values of each parameter indicated that two parameters, T and M_e, had a significant impact and that considerable differences existed between the formulae (mean accuracies differed by up to 0.20 point). The results of our meta‐analysis showed a big formula effect on the accuracies predicted using each formula, and also a significant effect of the value obtained for M_e calculated from N_e (effective population size). Each formula can therefore be demonstrated to be optimal depending on the assumption used for M_e. In conclusion, no rules can be applied to predict the reliability of genomic selection using these formulae.     

Use of genomic recursions and algorithm for proven and young animals for single‐step genomic BLUP analyses – a simulation study

The purpose of this study was to examine accuracy of genomic selection via single‐step genomic BLUP (ssGBLUP) when the direct inverse of the genomic relationship matrix ( G ) is replaced by an approximation of G ^?1 based on recursions for young genotyped animals conditioned on a subset of proven animals, termed algorithm for proven and young animals (APY). With the efficient implementation, this algorithm has a cubic cost with proven animals and linear with young animals. Ten duplicate data sets mimicking a dairy cattle population were simulated. In a first scenario, genomic information for 20k genotyped bulls, divided in 7k proven and 13k young bulls, was generated for each replicate. In a second scenario, 5k genotyped cows with phenotypes were included in the analysis as young animals. Accuracies (average for the 10 replicates) in regular EBV were 0.72 and 0.34 for proven and young animals, respectively. When genomic information was included, they increased to 0.75 and 0.50. No differences between genomic EBV (GEBV) obtained with the regular G ^?1 and the approximated G ^?1 via the recursive method were observed. In the second scenario, accuracies in GEBV (0.76, 0.51 and 0.59 for proven bulls, young males and young females, respectively) were also higher than those in EBV (0.72, 0.35 and 0.49). Again, no differences between GEBV with regular G ^?1 and with recursions were observed. With the recursive algorithm, the number of iterations to achieve convergence was reduced from 227 to 206 in the first scenario and from 232 to 209 in the second scenario. Cows can be treated as young animals in APY without reducing the accuracy. The proposed algorithm can be implemented to reduce computing costs and to overcome current limitations on the number of genotyped animals in the ssGBLUP method.     

Genomic best linear unbiased prediction method reflecting the degree of linkage disequilibrium

The degree of linkage disequilibrium (LD) between markers differs depending on the location of the genome; this difference biases genetic evaluation by genomic best linear unbiased prediction (GBLUP). To correct this bias, we used three GBLUP methods reflecting the degree of LD (GBLUP‐LD). In the three GBLUP‐LD methods, genomic relationship matrices were conducted from single nucleotide polymorphism markers weighted according to local LD levels. The predictive abilities of GBLUP‐LD were investigated by estimating variance components and assessing the accuracies of estimated breeding values using simulation data. When quantitative trait loci (QTL) were located at weak LD regions, the predictive abilities of the three GBLUP‐LD methods were superior to those of GBLUP and Bayesian lasso except when the number of QTL was small. In particular, the superiority of GBLUP‐LD increased with decreasing trait heritability. The rates of QTL at weak LD regions would increase when selection by GBLUP continues; this consequently decreases the predictive ability of GBLUP. Thus, the GBLUP‐LD could be applicable for populations selected by GBLUP for a long time. However, if QTL were located at strong LD regions, the accuracies of three GBLUP‐LD methods were lower than GBLUP and Bayesian lasso.     

天然林林木空间格局的随机性检验和调整

通过对帽儿山林场101块固定标准地的林木空间分布格局的检验发现,对天然林而言空间格局以随机格局和均匀格局为主。集聚格局一般是由林窗引起的,而有林窗不一定都是集聚格局,但择伐过程中如果人为扩大林窗则会使随机格局变为集聚格局。在择伐设计中适当保留林窗周围的林木,一般能避免对原有空间格局的改变。