The LIPE gene (lipase E, hormone-sensitive type), also known as hormone-sensitive lipase, acts as a primary regulator of lipid metabolism during lactation in cows. We studied a total of two hundred Holstein–Friesian cows and performed sequencing analysis that revealed two synonymous nucleotide changes within the LIPE gene: a transition change, c.276 T > C in exon 2 (g.50631651 T > C; position 351 of GenBank: ON638900) and a transversion change, c.219C > A in exon 6 (g.50635369C > A; position 1070 of GenBank: ON638901). The observed genotypes were TC and CC for the c.276 T > C SNP and CC and CA for the c.219C > A SNP. Notably, the heterozygous TC genotype of the T351C SNP exhibited a significant association with high milk yield. Furthermore, the T351C SNP displayed significant associations with various milk parameters, including temperature, freezing point, density and the percentages of fat, protein, lactose, solids and solids-not-fat, with the homozygous CC genotype showing higher values. The c.219C > A SNP also demonstrated a significant association with milk composition, with heterozygous genotypes (CA) exhibiting higher percentages of fat, protein, and lactose compared to homozygous genotypes (CC). This effect was consistent among both high and low milk producers for fat and lactose percentages, while high milk producers exhibited a higher protein percentage than low milk producers. These findings highlight the importance of considering the detected SNPs in marker-assisted selection and breeding programs for the identification of high milk-producing Holstein–Friesian cows and potentially other breeds. Moreover, this study strongly supports the fundamental role of the LIPE gene in milk production and composition in lactating animals.

Peanut shell plays key roles in protecting the seed from diseases and pest infestation but also in the processing of peanut and is an important byproduct of peanut production. Most studies on peanut shell have focused on the utilization of its chemical applications, but the genetic basis of shell-related traits is largely unknown. A panel of 320 peanut (Arachis hypogaea) accessions including var. hypogaea, var. vulgaris, var. fastigiata and var. hirsuta was used to study the genetic basis of two physical and five microstructure-related traits in peanut shell. Significant phenotypic differences were revealed among the accessions of var. hypogaea, var. hirsuta, var. vulgaris and var. fastigiata for mechanical strength, thickness, three sclerenchymatous layer projections and main cell shape of the sclerenchymatous layer. We identified 10 significant single nucleotide polymorphisms (SNPs) through genome-wide association study (P < 5.0 × 10−6) combining the shell-related traits and high-quality SNPs. In total, 192 genes were located in physical proximity to the significantly associated SNPs, and 11 candidate genes were predicted related to their potential contribution to the development and structure of the peanut shell. All SNPs were detected on the B genome demonstrating the biased contribution of the B genome for the phenotypical make-up of peanut. Exploring the newly identified candidate genes will provide insight into the molecular pathways that regulate peanut shell-related traits and provide valuable information for molecular marker-assisted breeding of an improved peanut shell.

Genotyping of lentil plant genetic resources holds the promise to increase the identification and utilization of useful genetic diversity for crop improvement. The International Center for Agriculture Research in the Dry Areas (ICARDA) lentil reference set plus collection of 176 accessions was genotyped using genotyping-by-sequencing (GBS) and 22,555 SNPs were identified. The population structure was investigated using Bayesian analysis (STRUCTURE, k = 3) and principal component analysis. The two methods are in concordance. Genome-wide association analysis (GWAS) using the filtered SNP set and ICARDA historical phenotypic data discovered putative markers for several agronomic traits including days to first flower, seeds per pod, seed weight and days to maturity. The genetic and genomic resources developed and utilized in this study are available to the research community interested in exploring the ICARDA reference set plus collection using GWAS.

Previous genetic studies on hair morphology focused on the overall morphology of the hair using data collected by self-report or researcher observation. Here, we present the first genome-wide association study (GWAS) of a micro-level quantitative measure of hair curvature. We compare these results to GWAS results obtained using a macro-level classification of observable hair curvature performed in the same sample of twins and siblings of European descent. Observational data were collected by trained observers, while quantitative data were acquired using an Optical Fibre Diameter Analyser (OFDA). The GWAS for both the observational and quantitative measures of hair curvature resulted in genome-wide significant signals at chromosome 1q21.3 close to the trichohyalin (TCHH) gene, previously shown to harbor variants associated with straight hair morphology in Europeans. All genetic variants reaching genome-wide significance for both GWAS (quantitative measure lead single-nucleotide polymorphism [SNP] rs12130862, p = 9.5 × 10–09; observational measure lead SNP rs11803731, p = 2.1 × 10–17) were in moderate to very high linkage disequilibrium (LD) with each other (minimum r2 = .45), indicating they represent the same genetic locus. Conditional analyses confirmed the presence of only one signal associated with each measure at this locus. Results from the quantitative measures reconfirmed the accuracy of observational measures.

Improving the production traits and resistance against mastitis in dairy cattle is a challenge for animal scientists across the globe. The present study was designed to investigate the genetic effects of single nucleotide polymorphisms (SNPs) in Janus kinase 2 (JAK2) and diacylglycerol acyltransferase (DGAT1) genes with production and mastitis-related traits. Four SNPs in JAK2 and one in DGAT1 were analyzed through Chinese Cow's SNPs Chip-I (CCSC-I) and genotyped in a population of 312 Chinese Holsteins. Our findings demonstrated that milk fat percentage, somatic cell count (SCC), somatic cell score (SCS), serum cytokines interleukin 6 (IL-6) and interferon gamma (IFN-γ) showed significant associations (P < 0.05) with at least one or more identified SNPs. Consequently, the analysis based on haplotypes amongst the SNPs in JAK2 revealed noteworthy (P < 0.05) association with SCC and IL-6. Collectively, our results verified the pleiotropic ability of detected SNPs in bovine JAK2 and DGAT1 for milk fat percentage as well as mastitis-related traits. The significant SNPs in both the genes could serve as powerful genetic markers to minimize mastitis risk. In addition, besides SCC and SCS, the IFN-γ and IL-6 could also be used as indicators of improved genetic resistance against mastitis.

Silene ciliata (Caryophyllaceae) is a key species to test evolutionary hypotheses in a global warming context. The recent advances in Next Generation Sequencing technologies can help in providing clues about climate-mediated local adaptation. In the present study, we analysed the full transcriptome of six individuals of S. ciliata from Central Spain, by aligning it with the transcriptome of S. latifolia. We aimed (a) to identify Single Nucleotide Polymorphisms (SNPs) in the transcriptome of the species, (b) to describe the biological function of the polymorphic genes expressed and (c) to identify loci that may be involved in local adaptation processes at optimal and marginal populations of the species. We identified a total of 147,118 SNPs distributed throughout 12,688 sequences. The number of polymorphic sequences annotated was 8023. One hundred thirty sequences containing polymorphisms strongly associated with optimal and marginal conditions were selected. Gene ontology searches were successful for 118, and many of these were related to responses to stress (n = 19) and abiotic stimulus (n = 16). Genomic data generated provide a starting point for further research on the identification of candidate genes related to local adaptation and other processes in the species.

β-Carotene intake and tissue/blood concentrations have been associated with reduced incidence of several chronic diseases. Further bioactive carotenoid-metabolites can modulate the expression of specific genes mainly via the nuclear hormone receptors: retinoic acid receptor- and retinoid X receptor-mediated signalling. To better understand the metabolic conversion of β-carotene, inter-individual differences regarding β-carotene bioavailability and bioactivity are key steps that determine its further metabolism and bioactivation and mediated signalling. Major carotenoid metabolites, the retinoids, can be stored as esters or further oxidised and excreted via phase 2 metabolism pathways. In this review, we aim to highlight the major critical control points that determine the fate of β-carotene in the human body, with a special emphasis on β-carotene oxygenase 1. The hypothesis that higher dietary β-carotene intake and serum level results in higher β-carotene-mediated signalling is partly questioned. Alternative autoregulatory mechanisms in β-carotene / retinoid-mediated signalling are highlighted to better predict and optimise nutritional strategies involving β-carotene-related health beneficial mediated effects.

An adverse early life environment can increase the risk of metabolic and other disorders later in life. Genetic variation can modify an individual’s susceptibility to these environmental challenges. These gene by environment interactions are important, but difficult, to dissect. The nucleus is the primary organelle where environmental responses impact directly on the genetic variants within the genome, resulting in changes to the biology of the genome and ultimately the phenotype. Understanding genome biology requires the integration of the linear DNA sequence, epigenetic modifications and nuclear proteins that are present within the nucleus. The interactions between these layers of information may be captured in the emergent spatial genome organization. As such genome organization represents a key research area for decoding the role of genetic variation in the Developmental Origins of Health and Disease.

Genetic markers have been used in horticulture and conservation biology to identify breeding lines, assess genetic diversity, and examine gene flow. In weed science, analysis of genetic markers is not as common, as the focus often lies in the development of control methods. This is unfortunate, because advances in genetic marker techniques may lead to innovative methods in controlling weedy plants. Microsatellites, random amplified polymorphic DNA (RAPDs), intersimple sequence repeats (ISSRs), amplified fragment length polymorphisms (AFLPs), DNA sequences, single nucleotide polymorphisms (SNPs), and derived cleaved amplified polymorphic sequences (dCAPS) have been used in studying genetics of weedy plants. Beyond assessing genetic diversity of weeds, markers have been used to examine gene flow, patterns of dispersal, ploidy levels, and relationships of weedy and nonweedy species, as well as identifying founder populations. Identification of closely related species may indicate the potential for hybridization, cross reactivity of chemical applications, or nontarget biological control effects. Furthermore, markers have been used in identification of mutations conferring herbicide resistance and identification of regions correlating fitness of weedy and hybrid plants in new habitats. Knowledge from genetic markers provides fundamental information that can be used in advancing chemical and biological control in weed management. This article serves as a review of these marker types and their application to weed science.

Watermelon [Citrullus lanatus (Thunb.) Matsum. & Nakai var. lanatus] is an economically important vegetable belonging to the Cucurbitaceae family. Genotypes that exhibit agronomically important traits are selected for the development of elite cultivars. Understanding the genetic diversity and the genotype population structure based on molecular markers at the genome level can speed up the utilization of diverse genetic resources for varietal improvement. In the present study, we carried out an analysis of genetic diversity based on 3882 SNP markers across 37 core watermelon genotypes, including the most widely used watermelon varieties and wild watermelon. Based on the SNP genotyping data of the 37 watermelon genotypes screened, gene diversity and polymorphism information content values across chromosomes varied between 0.03–0.5 and 0.02–0.38, with averages of 0.14 and 0.13, respectively. The two wild watermelon genotypes were distinct from cultivated varieties and the remaining 35 cultivated genotypes were differentiated into three major clusters: 20 genotypes were grouped in cluster I; 11 genotypes were grouped in cluster II; three advanced breeding lines of yellow fruit flesh and genotype SW043 were grouped in cluster III. The results from neighbour-joining dendrogram, principal coordinate analysis and STRUCTURE analysis approaches were consistent, and the grouping of genotypes was generally in agreement with their origins. Here we reveal the genetic relationships among the core watermelon genotypes maintained at the Jiangsu Academy of Agricultural Sciences, China. The molecular and phenotypic characterization of the existing core watermelon genotypes, together with specific agronomic characteristics, can be utilized by researchers and breeders for future watermelon improvement.

Cassava germplasm collection is important for the preservation of genetic variability, allowing the development of improved cultivars with desirable traits such as drought and disease tolerance, better starch quality and yield. Therefore, the assessment of diversity in cassava germplasm maintained by farmers is important for maintaining biodiversity and crop improvement. Herein, we report genetic diversity relationships of 52 farmer-preferred cassava landraces from the eastern zone of Tanzania based on morphological descriptors and single nucleotide polymorphisms (SNPs). Cluster analysis was performed for both morphological traits (genetic distance 1.18–0.15) and SNPs (genetic distance 0.078–0.002). The analysis revealed that there were a total of 17,393 variant positions, and that several of the SNPs were distributed across all the chromosomes. The abundance of SNP varied remarkably among the 18 cassava chromosomes, with chromosome 2 having the highest number of SNPs (1335) and chromosome 18 having the lowest number of SNPs (734). The power of SNPs in distinguishing morphologically similar landraces was shown. Both analyses did not group landraces according to geographical locations, suggesting that farmers were moving cassava germplasm to different areas. Their diversity was mainly due to adaptation and preferential selection by farmers. This further implied that within a geographical location, the cultivars were more diverse and there was no misnaming of cassava cultivars by farmers. The collection revealed a wide range of genetic diversity, and represented a valuable resource for trait improvement, allowing the capture of farmer-preferred traits in future cassava breeding programmes.

Smallholder farmers in Africa and other developing countries raise village chickens under low input production systems characterised by minimal management and veterinary interventions. However, village chickens have a major contribution to village communities as a source of protein, income and cultural needs. The village chickens are described as nondescript birds that have not been developed as a breed and with uncharacterised genetic attributes. Local chickens are found in the most marginalised farming systems, to which they have adapted and survived the harsh production and environmental conditions. Such survival and adaptive attributes need to be characterised, conserved, and utilised. Several studies on Southern African local chickens have revealed high genetic variation within and among the village chicken populations and indicated that village chickens contribute diversity that is unique and different from that of commercial and specialised chicken populations. The availability of whole genome single nucleotide polymorphism (SNP) data facilitates the use of powerful statistical methods for in depth investigations into the evolutionary history and population demographics of village chickens. Linkage disequilibrium (LD), as a function of effective population size, has been used to estimate rate and level of inbreeding as well as selection pressures in the absence of pedigree information. The extent and distribution of LD in the genome has been exploited to shed light on the origin and domestication of animals and facilitate an understanding of breeds’ relatedness. The Illumina iSelect chicken 60K SNP chip has over 54 000 SNPs that have found application in population and quantitative genetics studies and has revealed demographic history, effective population size and level of genetic erosion in commercial and traditional/village chicken populations. The recent launching of the 600 K Affymetrix® Axiom® HD genotyping array for chickens and the ever decreasing cost of sequencing will see improved estimation of LD and the associated population parameters.

MC4R (melanocortin 4 receptor) is expressed in the appetite-regulating areas of the brain and takes part in leptin signaling pathways. Sequencing of the coding region of the MC4R gene for 354 yaks identified the following five single nucleotide polymorphisms (SNPs): SNP1 (273C>T), SNP2 (321 G>T), SNP3 (864 C>A), SNP4 (1069G>C) and SNP5 (1206 G>C). SNP1, SNP2 and SNP3 were synonymous mutations, whereas SNP4 and SNP5 were missense mutations resulting in amino acid substitutions (V286L and R331S). Pairwise linkage disequilibrium (LD) analysis indicated that two pairs of SNPs, SNP2 and SNP5 (r2=0.81027) and SNP4 and SNP5 (r2=0.53816), exhibited higher degrees of LD. CC genotype of SNP4, CGACG and CTCCC haplotypes for all SNPs were associated with increased BW of animals that were 18 months old and with the average daily gain. The secondary structure and transmembrane region prediction of the yak MC4R protein suggested that SNP4 was correlated with influential changes in the seventh transmembrane domain of the MC4R protein and with the functional deterioration or even incapacitation of MC4R, which may contribute to the increased feed intake, BW and average daily gain of the yaks with CC genotypes. The data from this study suggested that 1069G>C SNP of the MC4R gene could be used in marker-assisted selection of growth traits in the Maiwa yak breed.

Despite years of investigation into triclabendazole (TCBZ) resistance in Fasciola hepatica, the genetic mechanisms responsible remain unknown. Extensive analysis of multiple triclabendazole-susceptible and -resistant isolates using a combination of experimental in vivo and in vitro approaches has been carried out, yet few, if any, genes have been demonstrated experimentally to be associated with resistance phenotypes in the field. In this review we summarize the current understanding of TCBZ resistance from the approaches employed to date. We report the current genomic and genetic resources for F. hepatica that are available to facilitate novel functional genomics and genetic experiments for this parasite in the future. Finally, we describe our own non-biased approach to mapping the major genetic loci involved in conferring TCBZ resistance in F. hepatica.

Blood lipid response to a given dietary intervention could be determined by the effect of diet, gene variants or gene–diet interactions. The objective of the present study was to investigate whether variants in presumed nutrient-sensitive genes involved in lipid metabolism modified lipid profile after weight loss and in response to a given diet, among overweight European adults participating in the Diet Obesity and Genes study. By multiple linear regressions, 240 SNPs in twenty-four candidate genes were investigated for SNP main and SNP–diet interaction effects on total cholesterol, LDL-cholesterol, HDL-cholesterol and TAG after an 8-week low-energy diet (only main effect), and a 6-month ad libitum weight maintenance diet, with different contents of dietary protein or glycaemic index. After adjusting for multiple testing, a SNP–dietary protein interaction effect on TAG was identified for lipin 1 (LPIN1) rs4315495, with a decrease in TAG of − 0·26 mmol/l per A-allele/protein unit (95 % CI − 0·38, − 0·14, P= 0·000043). In conclusion, we investigated SNP–diet interactions for blood lipid profiles for 240 SNPs in twenty-four candidate genes, selected for their involvement in lipid metabolism pathways, and identified one significant interaction between LPIN1 rs4315495 and dietary protein for TAG concentration.

Imputation of high-density genotypes from low- or medium-density platforms is a promising way to enhance the efficiency of whole-genome selection programs at low cost. In this study, we compared the efficiency of three widely used imputation algorithms (fastPHASE, BEAGLE and findhap) using Chinese Holstein cattle with Illumina BovineSNP50 genotypes. A total of 2108 cattle were randomly divided into a reference population and a test population to evaluate the influence of the reference population size. Three bovine chromosomes, BTA1, 16 and 28, were used to represent large, medium and small chromosome size, respectively. We simulated different scenarios by randomly masking 20%, 40%, 80% and 95% single-nucleotide polymorphisms (SNPs) on each chromosome in the test population to mimic different SNP density panels. Illumina Bovine3K and Illumina BovineLD (6909 SNPs) information was also used. We found that the three methods showed comparable accuracy when the proportion of masked SNPs was low. However, the difference became larger when more SNPs were masked. BEAGLE performed the best and was most robust with imputation accuracies >90% in almost all situations. fastPHASE was affected by the proportion of masked SNPs, especially when the masked SNP rate was high. findhap ran the fastest, whereas its accuracies were lower than those of BEAGLE but higher than those of fastPHASE. In addition, enlarging the reference population improved the imputation accuracy for BEAGLE and findhap, but did not affect fastPHASE. Considering imputation accuracy and computational requirements, BEAGLE has been found to be more reliable for imputing genotypes from low- to high-density genotyping platforms.

Multilocus sequence typing (MLST) and multilocus sequence analysis (MLSA) have revolutionized understanding the global epidemiology of many medically relevant bacteria utilizing a number, mostly seven, of housekeeping genes. A more recent introduction, single nucleotide polymorphisms (SNPs), constitutes an even more powerful tool for bacterial typing, population genetic studies and phylogeography. The introduction of massive parallel sequencing has made genome re-sequencing and SNP discovery more economical for investigations of microbial organisms. In this paper we review phylogeographic studies on Lyme borreliosis (LB)-group spirochetes and methicillin-resistant Staphylococcus aureus (MRSA). Members of the LB-group spirochetes are tick-transmitted zoonotic bacteria that have many hosts and differ in their degree of host specialism, constituting a highly complex system. MRSA is a directly transmitted pathogen that may be acquired by contact with infected people, animals or MRSA-contaminated objects. For the LB-group spirochetes, MLSA has proved a powerful tool for species assignment and phylogeographic investigations while for S. aureus, genome-wide SNP data have been used to study the very short-term evolution of two important MRSA lineages, ST239 and ST225. These data are detailed in this review.

In the mammary gland, Wnt signals are strongly implicated in initial development of the mammary rudiments and in the ductal branching and alveolar morphogenesis that occurs during pregnancy. Previously, we identified two Wnt signaling pathway-implicated genes, PPP3CA and MARK4, as having a role in more aggressive and potentially metastatic breast tumors. In this study, we examined two SNPs within PPP3CA and MARK4 in an Australian case-control study population for a potential role in human breast cancers. 182 cases and 180 controls were successfully genotyped for the PPP3CA SNP (rs2850328) and 182 cases and 177 controls were successfully genotyped for the MARK4 SNP (rs2395) using High Resolution Melt (HRM) analysis. Genotypes of randomly selected samples for both SNPs were validated by dye terminator sequencing. Chi-square tests were performed to determine any significant differences in the genotype and allele frequencies between the cases and controls. Chi-square analysis showed no statistically significant difference (ρ > .05) for genotype frequencies between cases and controls for rs2850328 (χ2 = 1.2, p = .5476) or rs2395 (χ2 = .3, p = .8608). Similarly, no statistical difference was observed for allele frequencies for rs2850328 (χ2 = .68, p = .4108) or rs2395 (χ2 = .02, p = .893). Even though an association of the polymorphisms rs2850328 and rs2395 and breast cancer was not detected in our case-control study population, other variants within the PPP3CA and MARK4 genes may still be associated with breast cancer, as both genes are implicated with processes involved in the disease as well as their mutual partaking in the Wnt signaling pathway.

Single-nucleotide polymorphisms (SNPs) of exon 8 of the GHR gene were detected in Chinese Holstein cows by polymerase chain reaction restriction fragment length polymorphism (PCR-RFLP). The results showed that exon 8 of the GHR gene digested by TasI could be divided into two kinds of alleles and three kinds of genotypes. The frequencies of allele A and T were 0.6339 and 0.3661, respectively. The frequencies of genotypes AA, AT and TT were 0.459, 0.350 and 0.191, respectively. Sequencing showed one single nucleotide mutation T→A at 4962 bp of the gene in genotype TT when compared with genotype AA, and this mutation resulted in an amino acid change of phenylalanine (TTT)→tyrosine (TAT). The result of χ2 testing indicated that the genotypic frequency of the GHR gene digested by TasI did not fit with Hardy–Weinberg equilibrium in this population (P<0.05). The least-square mean of the fat percentage of this population was higher for genotype TT than for genotype AA (P<0.05).