Functional validation of mouse tyrosinase non-coding regulatory DNA elements by CRISPR–Cas9-mediated mutagenesis

Newly developed genome-editing tools, such as the clustered regularly interspaced short palindromic repeat (CRISPR)–Cas9 system, allow simple and rapid genetic modification in most model organisms and human cell lines. Here, we report the production and analysis of mice carrying the inactivation via deletion of a genomic insulator, a key non-coding regulatory DNA element found 5′ upstream of the mouse tyrosinase (Tyr) gene. Targeting sequences flanking this boundary in mouse fertilized eggs resulted in the efficient deletion or inversion of large intervening DNA fragments delineated by the RNA guides. The resulting genome-edited mice showed a dramatic decrease in Tyr gene expression as inferred from the evident decrease of coat pigmentation, thus supporting the functionality of this boundary sequence in vivo, at the endogenous locus. Several potential off-targets bearing sequence similarity with each of the two RNA guides used were analyzed and found to be largely intact. This study reports how non-coding DNA elements, even if located in repeat-rich genomic sequences, can be efficiently and functionally evaluated in vivo and, furthermore, it illustrates how the regulatory elements described by the ENCODE and EPIGENOME projects, in the mouse and human genomes, can be systematically validated.     

Impact of single-site axonal GABAergic synaptic events on cerebellar interneuron activity

Axonal ionotropic receptors are present in a variety of neuronal types, and their function has largely been associated with the modulation of axonal activity and synaptic release. It is usually assumed that activation of axonal GABA_ARs comes from spillover, but in cerebellar molecular layer interneurons (MLIs) the GABA source is different: in these cells, GABA release activates presynaptic GABA_A autoreceptors (autoRs) together with postsynaptic targets, producing an autoR-mediated synaptic event. The frequency of presynaptic, autoR-mediated miniature currents is twice that of their somatodendritic counterparts, suggesting that autoR-mediated responses have an important effect on interneuron activity. Here, we used local Ca²⁺ photolysis in MLI axons of juvenile rats to evoke GABA release from individual varicosities to study the activation of axonal autoRs in single release sites. Our data show that single-site autoR conductances are similar to postsynaptic dendritic conductances. In conditions of high [Cl⁻]_i, autoR-mediated conductances range from 1 to 5 nS; this corresponds to ∼30–150 GABA_A channels per presynaptic varicosity, a value close to the number of channels in postsynaptic densities. Voltage responses produced by the activation of autoRs in single varicosities are amplified by a Na_v-dependent mechanism and propagate along the axon with a length constant of 91 µm. Immunolabeling determination of synapse location shows that on average, one third of the synapses produce autoR-mediated signals that are large enough to reach the axon initial segment. Finally, we show that single-site activation of presynaptic GABA_A autoRs leads to an increase in MLI excitability and thus conveys a strong feedback signal that contributes to spiking activity.     

Detecting inbreeding depression for reproductive traits in Iberian pigs using genome-wide data

Background

The current availability of genotypes for very large numbers of single nucleotide polymorphisms (SNPs) is leading to more accurate estimates of inbreeding coefficients and more detailed approaches for detecting inbreeding depression. In the present study, genome-wide information was used to detect inbreeding depression for two reproductive traits (total number of piglets born and number of piglets born alive) in an ancient strain of Iberian pigs (the Guadyerbas strain) that is currently under serious danger of extinction.

Methods

A total of 109 sows with phenotypic records were genotyped with the PorcineSNP60 BeadChip v1. Inbreeding depression was estimated using a bivariate animal model in which the inbreeding coefficient was included as a covariate. We used two different measures of genomic inbreeding to perform the analyses: inbreeding estimated on a SNP-by-SNP basis and inbreeding estimated from runs of homozygosity. We also performed the analyses using pedigree-based inbreeding.

Results

Significant inbreeding depression was detected for both traits using all three measures of inbreeding. Genome-wide information allowed us to identify one region on chromosome 13 associated with inbreeding depression. This region spans from 27 to 54 Mb and overlaps with a previously detected quantitative trait locus and includes the inter-alpha-trypsin inhibitor gene cluster that is involved with embryo implantation.

Conclusions

Our results highlight the value of high-density SNP genotyping for providing new insights on where genes causing inbreeding depression are located in the genome. Genomic measures of inbreeding obtained on a SNP-by-SNP basis or those based on the presence/absence of runs of homozygosity represent a suitable alternative to pedigree-based measures to detect inbreeding depression, and a useful tool for mapping studies. To our knowledge, this is the first study in domesticated animals using the SNP-by-SNP inbreeding coefficient to map specific regions within chromosomes associated with inbreeding depression.

Electronic supplementary material

The online version of this article (doi:10.1186/s12711-014-0081-5) contains supplementary material, which is available to authorized users.     

Direct versus indirect facilitation (herbivore mediated) among woody plants in a semiarid Chaco forest: A spatial association approach

In arid environments, direct facilitation (microhabitat amelioration) and indirect facilitation (‘associational resistance’ via protection from herbivory) among plants of different species may act simultaneously. Little is known about their relative effects. One way to disentangle the effects is by evaluating spatial associations. We examined the relative importance of these two mechanisms of facilitation in the semiarid Chaco vegetation of north‐central Argentina, through an eight‐way observational study in which we quantified the degree of spatial association between saplings of each of two key tree species, Schinopsis lorentzii (Anacardiaceae) and Aspidosperma quebracho‐blanco (Apocynaceae), with shrub neighbours either possessing spines or without spines and in both an ungrazed site and a site with a long history of cattle grazing. We analysed data across 400 subparcels at each site with spatial analysis by distance indices. Saplings of both tree species showed positive spatial associations with spiny shrubs in the grazed site but not in the ungrazed site, and never with non‐spiny shrubs. This result suggests that spiny shrubs may indeed provide associational resistance for saplings of key tree species in grazed habitats in these dry subtropical forests, that is, that indirect facilitation may predominate over direct facilitation. If confirmed by experimental studies, this result can have implications for the silvopastoral management of rapidly expanding ranches in the semiarid Chaco, where current practice includes the near elimination of native shrubs.     

Analysis of ven3 and ven6 reticulate mutants reveals the importance of arginine biosynthesis in Arabidopsis leaf development

Arabidopsis thaliana reticulate mutants exhibit differential pigmentation of the veinal and interveinal leaf regions, a visible phenotype that often indicates impaired mesophyll development. We performed a metabolomic analysis of one ven6 (venosa6) and three ven3 reticulate mutants that revealed altered levels of arginine precursors, namely increased ornithine and reduced citrulline levels. In addition, the mutants were more sensitive than the wild-type to exogenous ornithine, and leaf reticulation and mesophyll defects of these mutants were completely rescued by exogenous citrulline. Taken together, these results indicate that ven3 and ven6 mutants experience a blockage of the conversion of ornithine into citrulline in the arginine pathway. Consistent with the participation of VEN3 and VEN6 in the same pathway, the morphological phenotype of ven3 ven6 double mutants was synergistic. Map-based cloning showed that the VEN3 and VEN6 genes encode subunits of Arabidopsis carbamoyl phosphate synthetase (CPS), which is assumed to be required for the conversion of ornithine into citrulline in arginine biosynthesis. Heterologous expression of the Arabidopsis VEN3 and VEN6 genes in a CPS-deficient Escherichia coli strain fully restored bacterial growth in minimal medium, demonstrating the enzymatic activity of the VEN3 and VEN6 proteins, and indicating a conserved role for CPS in these distinct and distant species. Detailed study of the reticulate leaf phenotype in the ven3 and ven6 mutants revealed that mesophyll development is highly sensitive to impaired arginine biosynthesis.     

阿根廷种植转基因作物15年的经济影响

自1996年引入第一例抗除草剂大豆以后,阿根廷成为全球率先采用转基因作物的几个主要国家之一。2010年,全国转基因作物种植面积达到2290万公顷。新技术的采用过程稳定、迅速且品种多样化。目前,阿根廷所有的大豆、86%的玉米和99%的棉花都采用了转基因品种。本研究发现,1996~2010年间,农业生物技术使阿根廷获得的总收益达到726.45亿美元,创造了182万个工作机会。优先采用新技术为阿根廷带来的优势效益非常显著。收益是通过SIGMA数学模型进行评估的,该评估工具由阿根廷国家农业技术机构和全球乡村发展捐赠平台的支持。"此报告呼吁立即行动。"该委员会委员、威斯康星大学麦迪逊学院教授Molly, Jahn说,"全世界都要求增加粮食、饲料和生物能源作物。食品价格已涨至历史高位,极端天气事件在全球范围内频发,将导致粮食安全状况恶化。庆幸我们正在采取具体而明确的、科学的措施应对这一切。"委员会向政策制定者提出几点意见:一、将粮食安全和可持续农业纳入全球和国家政策;二、在减少温室气体排放和其他对农业的负面环境影响的同时,持续性地增加农业产出;三、锁定最易受气候变化和粮食危机影响的人群和部门;四、重新建立更适宜的食品获取和消费模式,确保满足人们的最基本营养需求,培养健康而可持续的进食习惯;五、减少粮食体系内的损失和浪费,尤其是基础设施、耕种技术、加工过程、运输以及贮藏习惯等;六、建立广泛、共享、综合的信息系统。     

Follicular wave status at the beginning of the FSH treatment modifies reproductive features in superovulated sheep

In the current study we investigated whether the developmental status of the two largest follicles (LF1 and LF2) at the time of administration of the first two doses (0 and 12 h) of FSH of a superovulatory treatment influences periovulatory events and embryo yields in sheep. A larger size of LF1 was negatively correlated with embryo recovery (r=-0.608 for 0 h and r=-523 for 12 h, p<0.05), fertilization (r=-0.464 for 12 h, p<0.05) and viability (r=-0.775 for 12 h, p<0.005). Embryo viability rates were also lower when a higher difference between LF1 and LF2 (r=-0.839 for 0 h and r=-0.761 for 12 h, p<0.01) and a smaller size of LF2 (r=0.877 for 0 h and r=0.622 for 12 h, p<0.01) were observed. This indicates the existence of a limit in the follicular size that will be able to give rise a viable embryo. Conversely, a larger size of LF2 at the time of administration of the first two FSH doses was correlated with reduced recovery rates (r=-0.884 for 0 h and r=-0.706 for 12 h, p<0.01), whilst a decreasing size of LF1 and LF2 was correlated with an increased ovulation rate and recovered embryos. The dominance effect appeared to affect the timing of the preovulatory LH surge. Ewes with a higher difference between LF1 and LF2 displayed earlier LH surges (r=-0.420 for 0 h and r=-0.401 for 12 h, p<0.05) which were related to a higher number of non viable embryos (r=-0.777, p<0.05). The fact that superovulatory yields were affected by, both LF1 and LF2 supports the hypothesis of co-dominance effects in sheep.     

Non-additive effects of RBP4, ESR1 and IGF2 polymorphisms on litter size at different parities in a Chinese-European porcine line

Background

The aim of this work was to study the effects on litter size of variants of the porcine genes RBP4, ESR1 and IGF2, currently used in genetic tests for different purposes. Moreover, we investigated a possible effect of the interaction between RBP4-MspI and ESR1-PvuII polymorphisms. The IGF2-intron3-G3072A polymorphism is actually used to select lean growth, but other possible effects of this polymorphism on reproductive traits need to be evaluated.

Methods

Detection of polymorphisms in the genomic and cDNA sequences of RBP4 gene was carried out. RBP4-MspI and IGF2-intron3-G3072A were genotyped in a hyperprolific Chinese-European line (Tai-Zumu) and three new RBP4 polymorphisms were genotyped in different pig breeds. A bivariate animal model was implemented in association analyses considering the number of piglets born alive at early (NBA₁₂) and later parities (NBA₃₊ ) as different traits. A joint analysis of RBP4-MspI and ESR1-PvuII was performed to test their possible interaction. In the IGF2 analysis, paternal or maternal imprinting effects were also considered.

Results

Four different RBP4 haplotypes were detected (TGAC, GGAG, GAAG and GATG) in different pig breeds and wild boars. A significant interaction effect between RBP4-MspI and ESR1-PvuII polymorphisms of 0.61 ± 0.29 piglets was detected on NBA₃₊. The IGF2 analysis revealed a significant increase on NBA₃₊ of 0.74 ± 0.37 piglets for the paternally inherited allele A.

Conclusions

All the analyzed pig and wild boar populations shared one of the four detected RBP4 haplotypes. This suggests an ancestral origin of the quoted haplotype. The joint use of RBP4-MspI and ESR1-PvuII polymorphisms could be implemented to select for higher prolificacy in the Tai-Zumu line. In this population, the paternal allele IGF2-intron3-3072A increased litter size from the third parity. The non-additive effects on litter size reported here should be tested before implementation in other pig breeding schemes.