Significant population genetic structuring in Rhyzopertha dominica across Turkey: Biogeographic and practical implications

Rhyzopertha dominica is a key pest of stored grain. Understanding the movement of this beetle on broad geographic scales is crucial, particularly when developing strategies to prevent the spread of phosphine resistance. We assessed population genetic structuring in this pest across Turkey, using a combination of mitochondrial (cytochrome oxidase I) and microsatellite markers. In addition, we screened samples for Wolbachia, as this endosymbiont has previously been suggested to be associated with low mitochondrial genetic diversity in this beetle. Mitochondrial genetic diversity was low, with only six haplotypes identified. The genetic diversity was, however, substantially higher than that previously found in Australia or India, suggesting that R. dominica may have originated in the Middle East. Wolbachia were detected only at a single site, indicating they are not impacting the mitochondrial genetic diversity of R. dominica across Turkey. Microsatellite markers indicated there is significant geographic genetic structuring across Turkey, even among sites less than 100 km apart, suggesting there is little movement of beetles across regions within the country. This contrasts with the significantly higher levels of gene-flow found in Australia and the United States. We suggest that the limited movement of beetles across Turkey may be due to a combination of the historically localised agricultural practices (which limits anthropogenic movement among regions), and the mountainous landscape (which limits active flight among regions). Our results demonstrate that the movement of stored product pests may differ significantly across studies conducted in different countries. As a consequence, phosphine resistance management strategies must incorporate region specific information on the extent of beetle movement.     

Microsatellite markers for Rhyzopertha dominica (Coleoptera: Bostrichidae)

Rhyzopertha dominica (F.) is a destructive insect pest of stored products. Due to this pest's broad host range, short life cycle, and high reproductive capacity, it has rapidly spread throughout the world. Understanding the population structuring of this important pest is vital for developing and implementing an effective integrated pest management strategy. In this study, we isolated 19 novel polymorphic microsatellite loci from an enriched genomic library based on a biotin/streptavidin capture protocol. The genetic parameters were estimated based on 80 individual R. dominica from two natural populations. The numbers of alleles ranged from 3 to 10, and sixteen loci exhibited polymorphic information contents (PICs) greater than 0.5. The observed (H_O) and expected (H_E) heterozygosities ranged from 0.033 to 0.900 and 0.310 to 0.882, respectively. Six locus/population combinations significantly deviated from Hardy–Weinberg equilibrium (HWE). These microsatellite markers will provide a valuable resource for studying the population genetic structure of this species.     

Breed assignment test in four Italian beef cattle breeds

The assessment of a method able to assign individuals to the breed of origin is needed to certify origin and quality of livestock products. A set of 21 microsatellites was tested for breed identification in four native Italian beef breeds: Chianina, Marchigiana, Romagnola, and Piemontese. Two statistical approaches, based on maximum likelihood and on a Bayesian method, were evaluated. Different marker sets, chosen in order of the highest gene diversity and F_ST estimates were also tested. The Bayesian method performed better, achieving a correct assignment rate of about 90% even with six microsatellites. The marker sets with the highest gene diversity were shown to perform best. Considering a threshold probability of 90%, only 52.5% of the genotypes were correctly allocated. Such results are mainly due to the low genetic differentiation estimates among breeds (F_ST = 0.049). These findings suggest that markers with high gene diversity and the presence of private alleles should be investigated and the Bayesian method used.     

Characterisation of Bobal and Crujidera grape cultivars,in comparison with Tempranillo and Cabernet Sauvignon: Evolution of leaf macronutrients and berry composition during grape ripening

We present characterisation data for two Spanish autochthonous grapevines, Bobal and Crujidera, in comparison with the well-known cultivars Tempranillo and Cabernet Sauvignon. Microsatellite markers were used for the molecular characterisation of Crujidera grapevines. Leaf macronutrient contents of the four cultivars were evaluated, as well as their changes at different vine developmental stages, and veraison was seen as the most suitable time to evaluate the nutritional status. Quantitative changes in some physiological parameters and the phenolic composition of the four grape varieties were measured during the last month of ripening. Polyphenols, tannins and anthocyanins increased with grape maturation, although the accumulation of these phenolic compounds and their patterns of evolution varied considerably with the cultivar. The biosynthetic potential of these grapes to produce resveratrol largely depended on the grape variety, with a remarkably high content found in Bobal berry skins.     

Traceability of 9 Portuguese cattle breeds with PDO products in the market using microsatellites

Assignment tests based on multilocus genotypes are becoming increasingly important to certify the origin of livestock products and assure food safety and authenticity. The potential of microsatellites for determining the origin of beef products among cattle breeds present in the Portuguese market with the Protected Denomination of Origin (PDO) was studied. Methodologies were used to establish the number of populations under study and to allocate individuals to their original population. The STRUCTURE program was used to perform the strictly Bayesian method and the GENECLASS 2 program was used to accomplish two types of assignment tests. The STRUCTURE program converged to 9 populations, precisely the number of populations under study. Regarding the individual allocation, the strictly Bayesian method implemented by the STRUCTURE program allowed 96% of correct allocations when running the program without the knowledge of the source populations and 98% when the STRUCTURE program was run knowing the source populations of the animals. In the assignment test performed by the GENECLASS 2, 95% and 97% of individuals were correctly allocated by the frequency and the Bayesian methods, respectively. These results show the potential feasibility for traceability scheme based on microsatellites.     

Meat quality of tenderloin from Iberian pigs as affected by breed strain and crossbreeding

In 2007, a new National Quality Standard was published in Spain to regulate the products derived from the Iberian pig carcass, including for the first time fresh meat. In the same way, four different Iberian strains were recognized as official (Lampiño, Entrepelado, Retinto and Torbiscal). A batch (n = 10) of each pig strain was selected using neutral DNA markers, and another batch of the most common crossbreeding pigs (Iberian × Duroc) was included into the study as a control. The main meat quality parameters of tenderloin, the most expensive meat cut for fresh consumption, from those five pig groups were analysed. Retinto and Lampiño strains showed the closest phenotypic distances, followed by Entrepelado strain. Meat from crossed and Torbiscal pigs had lower water holding capacity, L∗ and a∗, and higher SFA than meat from the other three strains. Crossbred pigs had the lowest protein, intramuscular fat and PUFA contents.     

Detection of DNA in virgin olive oils extracted from destoned fruits

Characterization of genetic identity using DNA extracted from olive oil has the potential to facilitate assessment of origin and varietal conformity. Such a prospect is particularly interesting in light of the increased regional spread of olive cultivars and their various contributions to olive oil mixtures for certification of denomination of origin. Towards this goal, we have devised a reliable method for extracting DNA from virgin olive oil that was utilized on monovariety oils from the single, self-sterile cultivar ‘Ogliarola salentina’. We show that DNA purified from oil can be used for microsatellite analysis and that the profile of DNA purified from a monovariety oil corresponds to the profile of DNA purified from the leaves of the same cultivar. While DNA from the pollinators present in the genome of the seed embryo, could potentially contain alleles not present in the genome fruit pulp, invalidating the molecular traceability of olive oil, we show for the first time that there is no contamination of seed embryo DNA in a monovariety oil. Thus, this molecular assay is applicable for monovariety olive oils.     

Investigating population genetics of invasive rainbow smelt in the Great Lakes Region

Increasing our understanding of invasive species is important because of the negative impacts they can have on the economies and ecosystems of invaded regions. There is growing interest in how environmental variability (e.g. temperature) and stochastic invasion events (e.g. founder effects) affect the genetic composition of populations of invasive species. Rainbow smelt (Osmerus mordax) are a cold-water, planktivorous fish that spread into the Great Lakes basin in the early 1900s. We performed genetic analyses using microsatellites (N = 10) to investigate the influence stochastic invasion events have had on the genetic composition of invasive rainbow smelt populations across a broad geographic range. Genetic analyses were conducted on rainbow smelt populations (N = 30/population) from Lake Ontario, Lake Michigan, Lake Superior, and four inland lakes in Northern Wisconsin. Populations from the Great Lakes were generally less differentiated than inland populations. Additionally, we found evidence of a significant bottleneck in two inland populations and evidence for two distinct genetic strains of rainbow smelt in Lake Ontario. We also performed genetic analyses using microsatellites to determine if a thermally-induced extreme mortality event had an effect on a population of rainbow smelt and found that there was no measurable genetic effect on the population. Overall, this study provides evidence that the genetic structure and diversity of introduced populations can vary significantly, and are likely influenced by factors such as the frequency and magnitude of introductions. Also the resiliency of an invasive species can be high despite a history of bottlenecks and low genetic diversity.     

TA-repeat microsatellites are closely associated with ARS consensus sequences in yeast chromosome III

Microsatellites are repeats of very short sequences of DNA, interspersed in the genome. In this paper, the occurrence of the two-base repeat microsatellites has been investigated in the DNA sequence of yeast chromosome III. Only AT-repeats were found at a significantly high frequency. Some of the regions with the highest concentration of AT-repeats were located and further analysed, showing a close association with the core consensus of autonomously replicating sequences.     

中国对虾部分基因组文库构建和微卫星DNA序列的筛选

以中国对虾为实验材料,提取肌肉的基因组DNA。经Bsp143Ⅰ酶切后,回收500～1000bp的DNA片段,与经BamHⅠ酶切并去磷酸化的PUC19重组,将重组载体转入大肠杆菌DH5α中。然后将其涂布于含氨苄青霉素的LB平板上,过夜培养后,经蓝白斑筛选,构建对虾部分基因组文库。采用载体质粒的通用引物进行PCR检测插入片段的大小,对基因组文库进一步进行筛选。从建立的文库中选取100个片段大小合适的克隆进行测序,其中54个克隆的DNA插入片段含有微卫星序列,共获得了111个微卫星序列,在GenBank中注册了12个微卫星序列。本实验中还发现1个含有23bp的小卫星序列。