Effect of genotyping strategies on the sustained benefit of single-step genomic BLUP over multiple generations.

BACKGROUND: Single-step genomic best linear unbiased prediction (ssGBLUP) allows the inclusion of information from genotyped and ungenotyped individuals in a single analysis. This avoids the need to genotype all candidates with the potential benefit of reducing overall costs. The aim of this study was to assess the effect of genotyping strategies, the proportion of genotyped candidates and the genotyping criterion to rank candidates to be genotyped, when using ssGBLUP evaluation. A simulation study was carried out assuming selection over several discrete generations where a proportion of the candidates were genotyped and evaluation was done using ssGBLUP. The scenarios compared were: (i) three genotyping strategies defined by their protocol for choosing candidates to be genotyped (RANDOM: candidates were chosen at random; TOP: candidates with the best genotyping criterion were genotyped; and EXTREME: candidates with the best and worse criterion were genotyped); (ii) eight proportions of genotyped candidates (p); and (iii) two genotyping criteria to rank candidates to be genotyped (candidates' own phenotype or estimated breeding values). The criteria of the comparison were the cumulated gain and reliability of the genomic estimated breeding values (GEBV). RESULTS: The genotyping strategy with the greatest cumulated gain was TOP followed by RANDOM, with EXTREME behaving as RANDOM at low p and as TOP with high p. However, the reliability of GEBV was higher with RANDOM than with TOP. This disparity between the trend of the gain and the reliability is due to the TOP scheme genotyping the candidates with the greater chances of being selected. The extra gain obtained with TOP increases when the accuracy of the selection criterion to rank candidates to be genotyped increases. CONCLUSIONS: The best strategy to maximise genetic gain when only a proportion of the candidates are to be genotyped is TOP, since it prioritises the genotyping of candidates which are more likely to be selected. However, the strategy with the greatest GEBV reliability does not achieve the largest gain, thus reliability cannot be considered as an absolute and sufficient criterion for determining the scheme which maximises genetic gain.

Metabolic Profiling of Vasorelaxant Extract from Malvaviscus arboreus by LC/QTOF-MS.

We aimed to develop a standardized methodology to determine the metabolic profile of organic extracts from Malvaviscus arboreus Cav. (Malvaceae), a Mexican plant used in traditional medicine for the treatment of hypertension and other illnesses. Also, we determined the vasorelaxant activity of these extracts by ex vivo rat thoracic aorta assay. Organic extracts of stems and leaves were prepared by a comprehensive maceration process. The vasorelaxant activity was determined by measuring the relaxant capability of the extract to decrease a contraction induced by noradrenaline (0.1 µM). The hexane extract induced a significant vasorelaxant effect in a concentration- and endothelium-dependent manner. Secondary metabolites, such as polyunsaturated fatty acids, terpenes and one flavonoid, were annotated by liquid chromatography/quadrupole time-of-flight mass spectrometry (LC/QTOF-MS) in positive ion mode. This exploratory study allowed us to identify bioactive secondary metabolites from Malvaviscus arboreus, as well as identify potentially-new vasorelaxant molecules and scaffolds for drug discovery.

Metagenomic analysis and antimicrobial activity of two fermented milk kefir samples.

In recent years, the fermented milk product kefir has been intensively studied because of its health benefits. Here, we evaluated the microbial consortia of two kefir samples, from Escarcega, Campeche, and Campeche (México). We considered a functional comparison between both samples, including fungal and bacterial inhibition; second, we applied shotgun metagenomics to assess the structure and functional diversity of the communities of microorganisms. These two samples exhibited antagonisms against bacterial and fungal pathogens. Bioactive polyketides and nonribosomal peptides were identified by LC-HRMS analysis. We also observed a high bacterial diversity and an abundance of Actinobacteria in both kefir samples, and a greater abundance of Saccharomyces species in kefir of Escarcega than in the Campeche kefir. When the prophage compositions were evaluated, the Campeche sample showed a higher diversity of prophage sequences. In Escarcega, we observed a prevalence of prophage families that infect Enterobacteria and Lactobacillus. The sequences associated with secondary metabolites, such as plipastatin, fengycin, and bacillaene, and also bacteriocins like helveticin and zoocin, were also found in different proportions, with greater diversity in the Escarcega sample. The analyses described in this work open the opportunity to understand the microbial diversity in kefir samples from two distant localities.

Quantitative trait loci for resistance to trichostrongylid infection in Spanish Churra sheep.

BACKGROUND: For ruminants reared on grazing systems, gastrointestinal nematode (GIN) parasite infections represent the class of diseases with the greatest impact on animal health and productivity. Among the many possible strategies for controlling GIN infection, the enhancement of host resistance through the selection of resistant animals has been suggested by many authors. Because of the difficulty of routinely collecting phenotypic indicators of parasite resistance, information derived from molecular markers may be used to improve the efficiency of classical genetic breeding. METHODS: A total of 181 microsatellite markers evenly distributed along the 26 sheep autosomes were used in a genome scan analysis performed in a commercial population of Spanish Churra sheep to detect chromosomal regions associated with parasite resistance. Following a daughter design, we analysed 322 ewes distributed in eight half-sib families. The phenotypes studied included two faecal egg counts (LFEC0 and LFEC1), anti-Teladorsagia circumcincta LIV IgA levels (IgA) and serum pepsinogen levels (Peps). RESULTS: The regression analysis revealed one QTL at the 5% genome-wise significance level on chromosome 6 for LFEC1 within the marker interval BM4621-CSN3. This QTL was found to be segregating in three out of the eight families analysed. Four other QTL were identified at the 5% chromosome-wise level on chromosomes 1, 10 and 14. Three of these QTL influenced faecal egg count, and the other one had an effect on IgA levels. CONCLUSION: This study has successfully identified segregating QTL for parasite resistance traits in a commercial population. For some of the QTL detected, we have identified interesting coincidences with QTL previously reported in sheep, although most of those studies have been focused on young animals. Some of these coincidences might indicate that some common underlying loci affect parasite resistance traits in different sheep breeds. The identification of new QTL may suggest the existence of complex host-parasite relationships that have unique features depending on the host-parasite combination, perhaps due to the different mechanisms underlying resistance in adult sheep (hypersensitivity reactions) and lambs (immunity). The most significant QTL identified on chromosome 6 for LFEC(1) may be the target for future fine-mapping research efforts.

Genetic parameters for lactation traits of milking ewes: protein content and composition, fat, somatic cells and individual laboratory cheese yield.

The effects of some environmental variation factors and the genetic parameters for total milk traits (fat content, protein content, casein content, serum protein content, lactation mean of individual laboratory cheese yield (LILCY), lactation mean of somatic cell count (LSCC), and milk yield) were estimated from the records of 1,111 Churra ewes. Genetic parameters were estimated by multivariate REML. Heritability for fat content was low (0.10) as is usually found in the Churra breed. Heritabilities for protein content, casein content, serum protein content, LILCY, milk yield and somatic cell count were 0.31, 0.30, 0.22, 0.09, 0.26 and 0.11, respectively. The highest heritability estimates were for protein and casein contents. Casein content is not advisable as an alternative to protein content as a selection criterion for cheese yield improvement; it does not have any compelling advantages and its measurement is costly. Our results for LSCC indicated that efforts should focus on improving the level of management rather than selecting for somatic cells, in the actual conditions of the Churra breed.