A simple method to separate base population and segregation effects in genomic relationship matrices

Background

Genomic selection and estimation of genomic breeding values (GBV) are widely used in cattle and plant breeding. Several studies have attempted to detect population subdivision by investigating the structure of the genomic relationship matrix G. However, the question of how these effects influence GBV estimation using genomic best linear unbiased prediction (GBLUP) has received little attention.

Methods

We propose a simple method to decompose G into two independent covariance matrices, one describing the covariance that results from systematic differences in allele frequencies between groups at the pedigree base (G_A^*) and the other describing genomic relationships (G_S) corrected for these differences. Using this decomposition and F_st statistics, we examined whether observed genetic distances between genotyped subgroups within populations resulted from the heterogeneous genetic structure present at the base of the pedigree and/or from breed divergence. Using this decomposition, we tested three models in a forward prediction validation scenario on six traits using Brown Swiss and dual-purpose Fleckvieh cattle data. Model 0 (M0) used both components and is equivalent to the model using the standard G-matrix. Model 1 (M1) used G_S only and model 2 (M2), an extension of M1, included a fixed genetic group effect. Moreover, we analyzed the matrix of contributions of each base group (Q) and estimated the effects and prediction errors of each base group using M0 and M1.

Results

The proposed decomposition of G helped to examine the relative importance of the effects of base groups and segregation in a given population. We found significant differences between the effects of base groups for each breed. In forward prediction, differences between models in terms of validation reliability of estimated direct genomic values were small but predictive power was consistently lowest for M1. The relative advantage of M0 or M2 in prediction depended on breed, trait and genetic composition of the validation group. Our approach presents a general analogy with the use of genetic groups in conventional animal models and provides proof that standard GBLUP using G yields solutions equivalent to M0, where base groups are considered as correlated random effects within the additive genetic variance assigned to the genetic base.     

Reference genes for quantitative reverse transcription-polymerase chain reaction expression studies in wild and cultivated peanut

Background

Molecular genetic studies on rare tumour entities, such as bone tumours, often require the use of decalcified, formalin-fixed, paraffin-embedded tissue (dFFPE) samples. Regardless of which decalcification procedure is used, this introduces a vast breakdown of DNA that precludes the possibility of further molecular genetic testing. We set out to establish a robust protocol that would overcome these intrinsic hurdles for bone tumour research.

Findings

The goal of our study was to establish a protocol, using a modified DNA isolation procedure and quality controls, to select decalcified samples suitable for array-CGH testing. Archival paraffin blocks were obtained from 9 different pathology departments throughout Europe, using different fixation, embedding and decalcification procedures, in order to preclude a bias for certain lab protocols. Isolated DNA samples were subjected to direct chemical labelling and enzymatic labelling systems and were hybridised on a high resolution oligonucleotide chip containing 44,000 reporter elements. Genomic alterations (gains and losses) were readily detected in most of the samples analysed. For example, both homozygous deletions of 0.6 Mb and high level of amplifications of 0.7 Mb were identified.

Conclusions

We established a robust protocol for molecular genetic testing of dFFPE derived DNA, irrespective of fixation, decalcification or sample type used. This approach may greatly facilitate further genetic testing on rare tumour entities where archival decalcified, formalin fixed samples are the only source.     

Seasonal variation and natural infection of Lutzomyia antunesi (Diptera: Psychodidae: Phlebotominae), an endemic species in the Orinoquia region of Colombia

Lutzomyia antunesi has been commonly reported in outbreaks of cutaneous leishmaniasis (CL) in the Orinoquia region of Colombia. The bionomics of this species were studied in the municipality of Villavicencio (Meta, Colombia). Sandflies were captured over the course of one week per month for one year in intradomiciliary, peridomiciliary and extradomiciliary housing areas. The captures were performed from 06:00 pm-06:00 am using CDC light traps and the females were processed for polymerase chain reaction (PCR) to detect Leishmania spp. A total of 22,097 specimens and 19 species were captured of which Lu. antunesi (89%) and Lutzomyia walkeri (5%) were the most abundant. Other species recognised as anthropophilic (Lutzomyia panamensis, Lutzomyia gomezi, Lutzomyia flaviscutellata and Lutzomyia fairtigi) were present in very low abundance (< 2%). Natural infection with Leishmania spp was detected using PCR in Lu. antunesi, Lu. panamensis and Lu. flavicutellata, showing infection rates of 1%, 4.8% and 7.5%, respectively. The present paper provides information on various ecological aspects of Lu. antunesi. An analysis of seasonality shows that this species increases in abundance in the hottest months (December, January and February), directly correlating with the maximum temperature and inversely correlating with precipitation. The natural infection rate is associated with the peaks of highest abundance.     

Wild Populations of Triatoma infestans Are Highly Connected to Intra-Peridomestic Conspecific Populations in the Bolivian Andes

Triatoma infestans, the major vector of Chagas disease south of the Amazon in South America, has a large distribution of wild populations, contrary to what has previously been stated. These populations have been suspected of being the source of reinfestation of human habitats and could impede the full success of vector control campaigns. This study examined gene flow between intra-peridomestic populations and wild populations collected in the surround areas in three Andean localities in Bolivia. The populations were defined according to temporal, ecological, and spatial criteria. After DNA extraction from the legs of each insect, the samples were analyzed using seven microsatellite markers. First, the analysis of molecular variance (AMOVA) detected an absence of differentiation between wild and intra-peridomestic populations, although strong structuring was observed between the populations within each environment. Then for some populations, the Bayesian method of assignment to inferred populations showed very similar assignment patterns of the members of wild or intra-peridomestic populations in each locality. Finally, the detection of the first-generation migrants within the different populations provided evidence of insect displacement from the wild to the intra-peridomestic environment. This result indicates that, after control campaigns in the Andes, controlling this new paradigm of vector transmission risk stemming from the invasion of human habitats by wild populations of T. infestans requires long-term maintenance of public monitoring to keep the risk at a minimal level. Since wild populations of T. infestans have also been detected elsewhere in Argentina, Paraguay, and Chile, there is an urgent need to take these populations into account in future monitoring of Chagas disease transmission.     

Structure of the pigeon lysozyme and its relationship with other type c lysozymes

1. The secondary structure of the pigeon egg-white lysozyme shows important differences when compared to other type c lysozymes. These differences are mainly located at the region comprising residues 77-84. This segment contains one alpha-helix in the lysozymes c studied by means of an X-ray analysis, while the residues at such positions in pigeon lysozyme would form two beta-bends. 2. Analysis of the tertiary structure of the pigeon lysozyme by means of hydropathy profiles reveals that the above segment seems to be more hydrophilic in the pigeon enzyme than in other type c lysozymes. 3. Though a certain similarity to the calcium-binding loop of alpha-lactalbumins is detected in pigeon lysozyme, the circular dichroism spectra of the protein at neutral pH do not change in the presence of Ca2+ ions. 4. The presented structural analysis is discussed in terms of function-structure and antigenicity relationships between the type c lysozymes.