Genetic variation and mRNA expression of the ELOVL6 and CRTC2 genes in Kalmyk cattle

Both Hemibarbus labeo and H. medius (Cypriniformes: Cyprinidae: Gobioninae) are primary freshwater fishes and are widely distributed. As such, they provide an ideal model for phylogeographical studies. However, the similarity in morphological characters between these two species made the description of their distributions and the validation of species quite challenging. Here we employed variations in the DNA sequences of mitochondrial COI and ND5 genes (2151 bp) to solve this challenge and to study the population genetics structure of these two species. Among the 130 specimens belonging to 8 populations of H. labeo and 9 populations of H. medius from 17 drainage systems in southern China,196 variable sites (9.1% in the full sequences) falling into 50 haplotypes were identified. The haplotype diversity (h) and the nucleotide diversity (π) were 0.964 and 0.019, respectively, indicating a high level of genetic diversity and an evolutionary potential in both species. The result of neighbor-joining tree based on composite nucleotide sequences of the mtDNA COI and ND5 genes showed that the H. labeo and H. medius fell into two major clades (clade1and clade2): clade1was composed of some specimens of Oujiang River, all the specimens of Hanjiang River and Jiulongjiang River, whereas all remaining populations fell in clade2. The genetic distance between clade I and clade II was 0.036, while that between H. labeo and H. medius was 0.027. The haplotype network analyses indicated that the populations of Hanjiang River and Jiulongjiang River had relatively high genetic variation with the rest rivers. The po-pulations of Hainan Island migrated northward to Moyangjaing River. Haplotypes of the rivers of Hainan Island and Moyangjang River had relatively higher genetic variation with the Yangtze River than Pearl River. The populations of Xiangjiang River had no genetic variation with the populations of Guijiang River and Liujiang River. Analysis of molecular variance (AMOVA) indicated that the genetic variance mainly presented in individuals between geographical regions. The genetic variation of populations among regions was 71.2%, the genetic variation among populations within regions was 16.6%, and that within populations within the regions was 12.2%, indicating that most of the genetic variations resided in the populations among regions. The results of mismatch distribution and tests of neutrality suggested that in all populations, H. labeo, H. medius, clade1and clade2 were relatively stable.

Meat production and quality traits in beef cattle are largely affected by genetic factors. Acetyl-Coenzyme A carboxylase-α (ACACA) plays a key role in the regulation and metabolism of fatty acid biosynthesis in mammalian animals. The gene encoding ACACA enzyme was chosen as a candidate gene for carcass and meat traits. In this study, we investigated effects of single nucleotide polymorphisms (SNPs) in the ACACA gene on beef carcass and meat traits in Hanwoo (Korean cattle) populations. We have sequenced a fragment of intron I region of the Hanwoo ACACA gene and identified two SNPs. Genotyping of the two SNP markers (g.2344T>C and g.2447C>A) was carried out using PCR-SSCP analysis in 309 Hanwoo steers to evaluate their association with carcass and meat production traits. The g.2344C SNP marker showed a significant increasing effect on LW (p = 0.009) and CW (p = 0.017). Animals with the CC genotype had higher CW and LW compared with TT and TC genotypes (p C and g.2447C>A in the LD analysis, four major haplotype classes were formed with two SNP information within the ACACA gene. We constructed haplotypes using the HaploView software package program and analyzed association between haplotypes and carcass traits. The haplotype of ACACA gene significantly affected the LW (p = 0.027), CW (p = 0.041) and MC (p = 0.036). The effect of h1 haplotype on LW and CW was larger than that of h3 haplotype. Animals with the h1 haplotype also had greater MC than did animals with h2 haplotype. Consequently, the ACACA gene could be useful as a DNA marker for meat production traits such as carcass yield and meat contents in Hanwoo. (Key

Data from the first four cycles of the Germplasm Evaluation Program at the U.S. Meat Animal Research Center (USMARC) were used to investigate genetic relationships between mature weight (MW, n = 37,710), mature weight adjusted for body condition score (AMW, n = 37,676), mature height (HT, n = 37,123), and BCS (n = 37,676) from 4- to 8-yr old cows (n = 1,800) and carcass traits (n = 4,027) measured on their crossbred paternal half-sib steers. Covariance components among traits were estimated using REML. Carcass traits were adjusted for age at slaughter. Estimates of heritability for hot carcass weight (HCWT); percentage of retail product; percentage of fat; percentage of bone; longissimus muscle area; fat thickness adjusted visually; estimated kidney, pelvic, and heart fat percentage; marbling score; Warner-Bratzler shear force; and taste panel tenderness measured on steers were moderate to high (0.26 to 0.65), suggesting that selection for carcass and meat traits could be effective. Estimates of heritability for taste panel flavor and taste panel juiciness were low and negligible (0.05 and 0.01, respectively). Estimates of heritability from cow data over all ages and seasons were high for MW, AMW, and HT (0.52, 0.57, 0.71; respectively) and relatively low for BCS (0.16). Pairwise analyses for each female mature trait with each carcass trait were done with bivariate animal models. Estimates of genetic correlations between cow mature size and carcass composition or meat quality traits, with the exception of HCWT, were relatively low. Selection for cow mature size (weight and/or height) could be effective and would not be expected to result in much, if any, correlated changes in carcass and meat composition traits. However, genetic correlations of cow traits, with the possible exception of BCS, with HCWT may be too large to ignore. Selection for steers with greater HCWT would lead to larger cows.

Data from the first four cycles of the Germplasm Evaluation Program at the U.S. Meat Animal Research Center (USMARC) were used to investigate genetic relationships between mature weight (MW, n = 37,710), mature weight adjusted for body condition score (AMW, n = 37,676), mature height (HT, n = 37,123), and BCS (n = 37,676) from 4- to 8-yr old cows (n = 1,800) and carcass traits (n = 4,027) measured on their crossbred paternal half-sib steers. Covariance components among traits were estimated using REML. Carcass traits were adjusted for age at slaughter. Estimates of heritability for hot carcass weight (HCWT); percentage of retail product; percentage of fat; percentage of bone; longissimus muscle area; fat thickness adjusted visually; estimated kidney, pelvic, and heart fat percentage; marbling score; Warner-Bratzler shear force; and taste panel tenderness measured on steers were moderate to high (0.26 to 0.65), suggesting that selection for carcass and meat traits could be effective. Estimates of heritability for taste panel flavor and taste panel juiciness were low and negligible (0.05 and 0.01, respectively). Estimates of heritability from cow data over all ages and seasons were high for MW, AMW, and HT (0.52, 0.57, 0.71; respectively) and relatively low for BCS (0.16). Pairwise analyses for each female mature trait with each carcass trait were done with bivariate animal models. Estimates of genetic correlations between cow mature size and carcass composition or meat quality traits, with the exception of HCWT, were relatively low. Selection for cow mature size (weight and/or height) could be effective and would not be expected to result in much, if any, correlated changes in carcass and meat composition traits. However, genetic correlations of cow traits, with the possible exception of BCS, with HCWT may be too large to ignore. Selection for steers with greater HCWT would lead to larger cows.

In the 21st century, one of the major scientific challenges is to clarify and understand the significance of genetic variations in human health and diseases. Human genetic variations are usually correlated with the regular physiological function, so it has a tremendous boost for scientific researches and clinical testing in order to understand the effect of human genetic variations on human health. Related researches published after the Human Genome Project have enriched our knowledge of different human genetic variations and their evolutionary history and relationships. Many diseases are associated with clinical genetic variations which are prevalent in the genome. The phenotypic diversity, inherited diseases and susceptibility to complex diseases among individuals are considered to be caused by these genetic variations and non-genetic factors (e.g. environmental factors). Each genetic variation tends to have specific effects on human health. Most common genetic variations like SNPs, structural variations, chromosomal aberrations and genetic susceptibility are correlated with human health. The studies in this field will be greatly facilitated by deep understanding of the mechanisms by which mutations exert their dominant effects on human health. Moreover, understanding the effects of environmental factors and genetic variations including their interaction on human health are of the great challenging. Recent advances in technologies, especially the high-throughput sequencing technology and progressive development of related technologies, like next generation sequencing including whole genome sequencing, whole exome sequencing and targeted exome capture based sequencing have promoted scientific researches and clinical applications, which subsequently creates great improvement in the genetic diagnosis and treatment programs. Currently, the use of high-throughput technology on genetic testing has greatly expanded its scope from a single genetic disease screening to the detection of complex diseases and hereditary cancers. In present days, it is widely used in non-invasive prenatal testing, neonatal genetic testing, pedigree analysis and carrier screening. Simultaneously, technological improvement is also helping development in the field of pharmacogenomics and nutrigenomics. Genetic testing benefits research and clinical development greatly. Development and application of DNA sequencing technology has significantly promoted the study of human genetic variation and phenotypic differences relationship, and in particular to identify susceptible genes for complex diseases. Additionally, it has also contributed to studying the relationship between genetic variation and various drug ressistance or sensitivity, and the specific reactions of individuals to environmental factors. This article focuses on the impact and mechanism of different genetic variations of human health, and progress on scientific research and clinical applications led by technological advances, including the prevention and treatment of genetic diseases. At the same time, we also engage with future research trend of genetic variations, hoping to provide a reference for related research on human health.

Interspecific phenotypic variation in plant secondary metabolites (PSM) is often explained by biotic and abiotic factors. However, patterns of variation within species do not clearly fit the theoretical predictions. Exploring how genetics, environment and demographic processes shape such variation among and within populations is crucial for understanding evolution of PSM, particularly in long‐lived plants such as forest trees. Here, we quantified genetic variation in PSM among and within populations, and explored drivers of local adaptation by studying the role of climate as a source of population differentiation in PSM of maritime pine. Constitutive profile and concentrations of 63 PSM and their herbivory‐associated inducibility were determined in the bark of 130 clonally replicated genotypes with known familial structure from 10 populations covering the distribution range of the species. We compared neutral and quantitative population genetic differentiation of PSM (FST and QST). Also, we accounted for population genetic structure and kinship among individuals when exploring climate–trait relationships. We found large population differentiation and additive genetic variation in constitutive PSM. Many PSM were inducible, although very low genetic variation was observed with respect to their inducibility. QST–FST comparisons suggest that differentiation of most diterpenes, monoterpenes, and phenolics can be explained by neutral demographic processes. Spatially heterogeneous selection across populations leading to local adaptation was only found for total constitutive sesquiterpenes and a few individual PSM. After accounting for population genetic structure, only the constitutive concentration of two sesquiterpenes showing signs of diversifying selection was predicted by climate, with decreasing concentrations along a growth‐prone climatic gradient. Synthesis. Evolutionary patterns of plant secondary metabolites depended on their chemical nature, with neutral differentiation governing most plant secondary metabolites. Evidence of local adaptation was only found for total constitutive sesquiterpenes and a few individual plant secondary metabolites. The low genetic variation in the inducibility of plant secondary metabolites suggests a conserved model of defensive induction in this species. Since population differentiation linked to past demographic history could lead to false positives of adaptive differentiation signals, accounting for the genetic relatedness among populations is required to infer the environmental determinants of intraspecific genetic variation in putatively adaptive traits such as plant defences.

La variabilidad genética es de gran importancia cuando se analiza la conservación de los recursos genéticos, además se constituye en la base para los procesos de selección y mejoramiento genético. El objetivo principal de este estudio fue determinar la variabilidad genética de la raza Romosinuano existente en Colombia por medio de técnicas moleculares. En este estudio se utilizaron 12 marcadores tipo microsatélites para determinar la diversidad genética y estructura poblacional en un total de 119 individuos de la raza Romosinuano y 42 de la raza Cebú, distribuidos en diferentes zonas geográficas del país. El valor más alto del número promedio de alelos (NPA) fue para la subpoblación de Universidad del Tolima (UT: 7,92) y el menor valor en la subpoblación Bonanza (BO: 4,08). El contenido de información polimórfica (PIC), para todos los marcadores estudiados fueron informativos, encontrándose rangos entre 0,47 (BM 1818) y 0,71 (BM 2113), con un promedio en la población de 0,64. Los índices de fijación FIS (-0,20), FIT (0,37) y FST (0,14), indicaron un déficit de heterocigotos. Se construyó el árbol filogenético, empleando la metodología de Nei, la menor distancia genética se presentó entre las subpoblaciones de Guillermo Soto (GS) y el Edem (ED), mientras que la mayor medida se presentó entre las subpoblaciones. El Brillante (BR), universidad del Tolima (UT) y Fabio Torres (FT). Existe una alta variabilidad genética entre las poblaciones, pero valores moderados de homocigosidad dentro de ellas, por lo que es necesario dar más relevancia al manejo de este flujo genético para reducir la consanguinidad. Estos resultados son una base importante para definir nuevos planes de apareamiento y selección asistida.

Olive (Olea europaea L.) is one of the most economically important crop from east to the west around the world. The aim of this research was to investigate the genetic relationship among 41 olive genotypes, including 11 well-known Turkish cultivars and 30 Azerbaijani olive genotypes using simple sequence repeat (SSR) markers. In this study, 19 SSR markers were amplified 115 polymorphic SSR alleles. The number of polymorphic alleles ranged from 3 to 10 with an average of 6.05. The observed heterozygosity (Ho) varied from 0.05 to 0.93 with an average of 0.63 and expected heterozygosity (He) differed from 0.26 to 0.86 with an average of 0.72. The polymorphism information content (PIC) ranged from 0.23 to 0.85 with a mean of 0.68. A UPGMA cluster analysis grouped olive genotypes into two distinct clusters and both clusters were divided into two subgroups. Similarly, STRUCTURE analysis assigned olive genotypes into two different gene pools (K = 2) and four gene pools were identified representing the two subgroups by STRUCTURE analysis for K = 4. The genetic similarity of olive genotypes ranged from 0.36 to 0.95. These results revealed that there was a high genetic variation among 30 Azerbaijani olive genotypes. 'Ayvalık 1'and 'Ayvalık 2' from Azerbaijani olive genotypes were different from Turkish local olive cultivar, "Ayvalık" indicating homonymy. This research also highlighted that Azerbaijani olive genotypes were totally distinct from Turkish olive cultivars demonstrating that these olive genotypes might have been imported to Azerbaijan from different countries other than Turkey. The outcomes of this study indicated that these diverse olive genotypes could be useful for development of new olive varieties in Azerbaijan and future breeding programs between two countries could be enhanced by means of these results.

Simple SummaryAnimal production in mountain regions is changing and improvements to maintain autochthonous breeds and traditions should be defined. One of the strategies to add value and improve productivity is to produce meat with a PDO (protected denomination of origin) label. One example in Portugal is the Arouquesa PDO beef. This work aimed to compare different production systems and understand if they affect growth performance, carcass, and meat parameters for the Arouquesa PDO beef. Systems using supplementation had better results regarding live weight and average daily gain. The finishing period increased subcutaneous fat. The meat quality parameters differ in the improved production system with early weaning leading to lesser exudative and cooking losses. In conclusion, the traditional systems improved with practices, such as supplementation, can in turn improve meat production without affecting beef quality or PDO certification. This study demonstrates that improved production systems can advance the Arouquesa autochthonous breed production, while in turn maintaining the valued characteristics of a PDO product.Arouquesa is an autochthonous bovine breed known for its Arouquesa PDO beef labeling. There are several production systems under the definition of PDO labeling. This study aimed to compare the effect of different production systems on carcass and meat traits for the Arouquesa breed. Two trials differing in diet and weaning age were conducted. The first trial included a TF group fed the traditional way and weaned at 9 months; a TF + S1 group, equal to TF, but with a starter supplement; and finally, a S1 + S2 group that was fed with a starter and a growth supplement and weaned at 5 months. The second trial was composed of a TF + S3 group fed like the TF + S1 group but reared until 12 months with a finishing supplement, and finally, the S3 group fed like the S1 + S2 group but reared until 12 months. In the first trial, the TF + S1 and S1 + S2 groups showed higher final live weight and average daily gain. In the second trial, we observed differences in the subcutaneous fat that was higher in the S3 group. Regarding meat traits, we observed differences in exudative and cooking losses in the first trial. In general, supplementation improved meat production without affecting meat quality parameters.

IL28B single nucleotide polymorphisms in the treatment of hepatitis C

Genetic variation in targets of antihyperglycemic drugs and inflammatory bowel disease' risk: A mendelian randomization study.

Climate warming alters plant composition and population dynamics of arctic ecosystems. In particular, an increase in relative abundance and cover of deciduous shrub species (shrubification) has been recorded. We inferred genetic variation of common shrub species (Alnus alnobetula, Betula nana, Salix sp.) through time. Chloroplast genomes were assembled from modern plants (n = 15) from the Siberian forest‐tundra ecotone. Sedimentary ancient DNA (sedaDNA; n = 4) was retrieved from a lake on the southern Taymyr Peninsula and analyzed by metagenomics shotgun sequencing and a hybridization capture approach. For A. alnobetula, analyses of modern DNA showed low intraspecies genetic variability and a clear geographical structure in haplotype distribution. In contrast, B. nana showed high intraspecies genetic diversity and weak geographical structure. Analyses of sedaDNA revealed a decreasing relative abundance of Alnus since 5,400 cal yr BP, whereas Betula and Salix increased. A comparison between genetic variations identified in modern DNA and sedaDNA showed that Alnus variants were maintained over the last 6,700 years in the Taymyr region. In accordance with modern individuals, the variants retrieved from Betula and Salix sedaDNA showed higher genetic diversity. The success of the hybridization capture in retrieving diverged sequences demonstrates the high potential for future studies of plant biodiversity as well as specific genetic variation on ancient DNA from lake sediments. Overall, our results suggest that shrubification has species‐specific trajectories. The low genetic diversity in A. alnobetula suggests a local population recruitment and growth response of the already present communities, whereas the higher genetic variability and lack of geographical structure in B. nana may indicate a recruitment from different populations due to more efficient seed dispersal, increasing the genetic connectivity over long distances.

Lonicera caerulea var. edulis is a rare species found in some alpine region of Korea. Genetic variation in L. caerulea var. edulis has been investigated by examining 161 individuals from six natural populations: Mt. Seorak 1, Mt. Seorak 2, Mt. Jeombong, Mt. Bangtae, Mt. Gyebang, Mt. Halla. The mean genetic diversity for all the six populations was 0.25 (S.I.). The highest genetic diversity was found in Mt. Seorak (S.I.=0.3158) and the lowest was in Mt. Gyebang (S.I.=0.1047). Comparatively low level of genetic diversity was observed (Ae=1.25, P= 64.6%, S.I.=0.25), which is a typical pattern for rare tree species. AMOVA showed exceptionally large proportion of genetic variations both for among populations (34.69%) and within populations (65.31%). Excluding Mt. Gyebang, the genetic variation among and within population was 18.71% and 81.29% respectively. The UPGMA dendrogram based on genetic distance is not suitable for geographic relationship. Genetic distance of Mt. Gyebang was most distant from the other populations. Excluding Mt. Gyebang, the genetic identities among the five populations were 0.95 to 0.97, which is very high similarity level of genetic identity. This low level of genetic variations and the lack of site in nature indicates that Lonicera caerulea var. edulis demanded a serious conservation.

The theory of evolution via natural selection predicts that the genetic composition of wild populations changes over time in response to the environment. Different genotypes should exhibit different demographic patterns, but genetic variation in demography is often impossible to separate from environmental variation. Here, we asked if genetic variation is important in determining demographic patterns. We answer this question using a long-term field experiment combined with general linear modeling of deterministic population growth rates (lambda), deterministic life table response experiment (LTRE) analysis, and stochastic simulation of demography by paternal lineage in a short-lived perennial plant, Plantago lanceolata, in which we replicated genotypes across four cohorts using a standard breeding design. General linear modeling showed that growth rate varied significantly with year, spatial block, and sire. In LTRE analysis of all cohorts, the strongest influences on growth rate were from year x spatial block, and cohort x year x spatial block interactions. In analysis of genetics vs. temporal environmental variation, the strongest impacts on growth rate were from year and year x sire. Finally, stochastic simulation suggested different genetic composition among cohorts after 100 years, and different population growth rates when genetic differences were accounted for than when they were not. We argue that genetic variation, genotype x environment interactions, natural selection, and cohort effects should be better integrated into population ecological studies, as these processes should result in deviations from projected deterministic and stochastic population parameters.

BackgroundInflammatory bowel disease (IBD), including Crohn’s disease (CD) and ulcerative colitis (UC), poses a substantial disease burden worldwide. Recent studies have indicated that anti-diabetic drugs like metformin may attenuate intestinal...