An arrayed human genomic library constructed in the PAC shuttle vector pJCPAC-Mam2 for genome-wide association studies and gene therapy

The various iterations of the HapMap Project and many genome-wide association studies (GWAS) have identified hundreds of potential genes involved in monogenic and multifactorial traits. We constructed an arrayed 115,000-member human genomic library in the PAC shuttle vector pJCPAC-Mam2 that can be propagated in both bacterial and human cells. The library appears to represent a two-fold coverage of the human genome. Transient transfection of a p53-containing PAC clone into p53-null Saos-2 human osteosarcoma cells demonstrated that both p53 mRNA and protein were produced. Additionally, expression of the p53 protein triggered apoptosis in a subset of the Saos-2 cells. This library should serve as a valuable resource to validate potential disease genes identified by GWAS in human cell lines and in animal models. Also, individual library members could potentially be used for gene therapy trials for a variety of recessive disorders.     

Genetic architecture and adaptive significance of the selfing syndrome in Capsella

The transition from outcrossing to predominant self-fertilization is one of the most common evolutionary transitions in flowering plants. This shift is often accompanied by a suite of changes in floral and reproductive characters termed the selfing syndrome. Here, we characterize the genetic architecture and evolutionary forces underlying evolution of the selfing syndrome in Capsella rubella following its recent divergence from the outcrossing ancestor C. grandiflora. We conduct genotyping by multiplexed shotgun sequencing and map floral and reproductive traits in a large (N= 550) F2 population. Our results suggest that in contrast to previous studies of the selfing syndrome, changes at a few loci, some with major effects, have shaped the evolution of the selfing syndrome in Capsella. The directionality of QTL effects, as well as population genetic patterns of polymorphism and divergence at 318 loci, is consistent with a history of directional selection on the selfing syndrome. Our study is an important step toward characterizing the genetic basis and evolutionary forces underlying the evolution of the selfing syndrome in a genetically accessible model system.     

棉花“三桃”性状的QTL定位

棉花的"三桃"(伏前桃、伏桃和秋桃)一直以来被认为是棉花早熟高产的重要指标。文章以早熟高产棉百棉2号为核心亲本,分别与中晚熟材料TM-1和中棉所12杂交,获得两个组合的F2和F2:3家系群体。对两个组合进行了遗传连锁图谱构建,标记位点分别为269个和127个,图谱总长分别为1 837.8 cM和1 244.3 cM。两组合共检测到29个"三桃"性状QTL,包括16个可能性QTL和13个显著性QTL,其中,5个显著性QTL的LOD值既大于3又大于permutation阈值;16个QTL的贡献率大于10%,解释表型变异的10.9%～44.5%。在两组合的相同染色体共同标记附近检测到4个共同QTL,分别为伏前桃qPSB-17、伏桃qSB-17(qSB-17a/17b)和秋桃qAB-17、qAB-12/26,可用于棉花"三桃"性状的标记辅助选择;其中,伏桃qSB-17(qSB-17a/17b)在两个组合中的贡献率均大于10%,秋桃qAB-17、qAB-12/26在一个组合中的贡献率均大于10%,这些既共同又贡献率较大的QTL在标记辅助选择中应优先考虑。     

Ultrastructural features of agouti (Dasyprocta aguti) preantral follicles cryopreserved using dimethyl sulfoxide, ethylene glycol and propanediol

The objective was to develop an efficient protocol for cryopreservation of agouti (Dasyprocta aguti) ovarian tissue. Agouti ovarian fragments were placed, for 10 min, in a solution containing MEM and fetal bovine serum plus 1.5 M dimethyl sulfoxide (DMSO), ethylene glycol (EG) or propanediol (PROH); some of those fragments were subsequently cryopreserved in a programmable freezer. After exposure and/or thawing, all samples were fixed in Carnoy prior to histological analysis. To evaluate ultrastructure, follicles from the control and all cryopreserved treatments were fixed in Karnovsky and processed for transmission electron microscopy. After exposure and freezing, there was a significant decrease in the percentage of morphologically normal preantral follicles in all treatments when compared to the control (92.67 ± 2.79, mean ± SD). However, there were no significant difference when the exposure and freezing procedures were compared using the same cryoprotectant. Moreover, there was no significant difference among cryoprotectants at the time of exposure (DMSO: 64.7 ± 3.8; EG: 70.7 ± 11.2, PROH: 63.3 ± 8.5) or after freezing (DMSO: 60.6 ± 3.6, EG: 64.0 ± 11.9; PROH: 62.0 ± 6.9). However, only follicles frozen with PROH had normal ultrastructure. In conclusion, preantral follicles enclosed in agouti ovarian tissue were successfully cryopreserved using 1.5 M PROH, with satisfactory maintenance of follicle morphology and ultrastructure.     

Complex genetics controls natural variation among seed quality phenotypes in a recombinant inbred population of an interspecific cross between Solanum lycopersicum × Solanum pimpinellifolium

Seed quality in tomato is associated with many complex physiological and genetic traits. While plant processes are frequently controlled by the action of small‐ to large‐effect genes that follow classic Mendelian inheritance, our study suggests that seed quality is primarily quantitative and genetically complex. Using a recombinant inbred line population of Solanum lycopersicum × Solanum pimpinellifolium, we identified quantitative trait loci (QTLs) influencing seed quality phenotypes under non‐stress, as well as salt, osmotic, cold, high‐temperature and oxidative stress conditions. In total, 42 seed quality traits were analysed and 120 QTLs were identified for germination traits under different conditions. Significant phenotypic correlations were observed between germination traits under optimal conditions, as well as under different stress conditions. In conclusion, one or more QTLs were identified for each trait with some of these QTLs co‐locating. Co‐location of QTLs for different traits can be an indication that a locus has pleiotropic effects on multiple traits due to a common mechanistic basis. However, several QTLs also dissected seed quality in its separate components, suggesting different physiological mechanisms and signalling pathways for different seed quality attributes.     

Novel natural alleles at FLC and LVR loci account for enhanced vernalization responses in Arabidopsis thaliana

Vernalization, the induction of flowering by low winter temperatures, is likely to be involved in plant climatic adaptation. However, the genetic, molecular and ecological bases underlying the quantitative variation that tunes vernalization sensitivity to natural environments are largely unknown. To address these questions, we have studied the enhanced vernalization response shown by the Ll-0 accession of Arabidopsis thaliana. Quantitative trait locus (QTL) mapping for several flowering initiation traits in relation to vernalization, in a new Ler × Ll-0 recombinant inbred line (RIL) population, identified large effect alleles at FRI, FLC and HUA2, together with two small effect loci named as Llagostera vernalization response (LVR) 1 and 2. Phenotypic analyses of near isogenic lines validated LVR1 effect on flowering vernalization responses. To further characterize the FLC allele from Ll-0, we carried out genetic association analyses using a regional collection of wild genotypes. FLC-Ll-0 appeared as a low-frequency allele that is distinguished by polymorphism Del(-57), a 50-bp-deletion in the 5'-UTR. Del(-57) was significantly associated with enhanced vernalization responses and FLC RNA expression, as well as with altitude and minimum temperatures. These results are consistent with Del(-57) acting as a novel cis-regulatory FLC polymorphism that may confer climatic adaptation by increasing vernalization sensitivity.     

Effects of vicariant barriers, habitat stability, population isolation and environmental features on species divergence in the south-western Australian coastal reptile community

Identifying explicit hypotheses regarding the factors determining genetic structuring within species can be difficult, especially in species distributed in historically dynamic regions. To contend with these challenges, we use a framework that combines species distribution models, environmental data and multi-locus genetic data to generate and explore phylogeographic hypotheses for reptile species occupying the coastal sand-dune and sand-plain habitats of the south-western Australian biodiversity hotspot, a community which has both a high diversity of endemics and has varied dramatically in spatial extent over time. We use hierarchical amova, summary statistic and distance-based analyses to explicitly test specific phylogeographic hypotheses. Namely, we test if biogeographic vicariance across barriers, habitat stability, population isolation along a linear habitat or fragmentation across different environments can explain genetic divergence within five co-distributed squamate reptile species. Our results show that patterns of genetic variation reflect complex and species-specific interactions related to the spatial distribution of habitats present currently and during repeated glacial minima, as opposed to being associated with historical factors such as habitat stability between glacial and inter-glacial periods or vicariant barriers. We suggest that the large impact of habitat characteristics over time (i.e. relative levels of habitat connectivity, climatic gradients and spatial heterogeneity of soil types) reflects the ecological restrictions of the sand-dune and sand-plain reptile communities and may explain the lack of concordance across taxa. The study demonstrates the general utility of the approach for assemblage-level, as well as single species, phylogeographic study, including its usefulness for exploring biologically informed hypotheses about what factors have influenced patterns of genetic variation.