Over the years, numerous observational studies have substantiated that various dietary choices have opposing effects on CVD. However, the causal effect has not yet been established. Thus, we conducted a Mendelian randomisation (MR) analysis to reveal the causal impact of dietary habits on CVD. Genetic variants strongly associated with 20 dietary habits were selected from publicly available genome-wide association studies conducted on the UK Biobank cohort (n 449 210). Summary-level data on CVD were obtained from different consortia (n 159 836–977 323). The inverse-variance weighted method (IVW) was the primary outcome, while MR-Egger, weighted median and MR Pleiotropy RESidual Sum and Outlier were used to assess heterogeneity and pleiotropy. We found compelling evidence of a protective causal effect of genetic predisposition towards cheese consumption on myocardial infarction (IVW OR = 0·67; 95 % CI = 0·544, 0·826; P = 1·784 × 10−4) and heart failure (IVW OR = 0·646; 95 % CI = 0·513, 0·814; P = 2·135 × 10−4). Poultry intake was found to be a detrimental factor for hypertension (IVW OR = 4·306; 95 % CI = 2·158, 8·589; P = 3·416 × 10−5), while dried fruit intake was protective against hypertension (IVW OR = 0·473; 95 % CI = 0·348, 0·642; P = 1·683 × 10−6). Importantly, no evidence of pleiotropy was detected. MR estimates provide robust evidence for a causal relationship between genetic predisposition to 20 dietary habits and CVD risk, suggesting that well-planned diets may help prevent and reduce the risk of CVD.

Tuberculosis (TB) is the leading cause of death caused by single pathogenic microorganism, Mycobacterium tuberculosis (MTB). The study aims to explore the associations of microRNA (miRNA) single-nucleotide polymorphisms (SNPs) with pulmonary TB (PTB) risk. A population-based case−control study was conducted, and 168 newly diagnosed smear-positive PTB cases and 251 non-TB controls were recruited. SNPs located within miR-27a (rs895819), miR-423 (rs6505162), miR-196a-2 (rs11614913), miR-146a (rs2910164), miR-618 (rs2682818) were selected and MassARRAY® MALDI-TOF System was employed for genotyping. SPSS19.0 was adopted for statistical analysis, non-conditional logistic regression was performed. Odds ratios (ORs) and 95% confidence intervals (95% CIs) were computed to estimate the associations. Associations of haplotypes with PTB risk were performed with online tool. Rs895819 CT/CC genotype was associated with reduced PTB risk among female population (OR = 0.45, 95% CI: 0.23–0.98), P = 0.045. Haplotypes (combined with rs895819, rs2682818, rs2910164, rs6505162 and rs11614913) TCCCT, TAGCC, CCCCC, CCGCT and TCGAT were associated with reduced PTB risk and the ORs were 0.67 (95% CI: 0.45–0.99), 0.49 (0.25–0.94), 0.34 (95% CI: 0.14–0.81), 0.22 (95% CI: 0.06–0.84) and 0.24 (95% CI: 0.07–0.79), respectively; while the haplotypes of TAGCT, CCCCT, CACCT and TCCAT were associated with increased PTB risk, and the ORs were 3.63 (95% CI: 1.54–8.55), 2.20 (95% CI: 1.00–4.86), 3.90 (95% CI: 1.47–10.36) and 2.95 (95% CI: 1.09–7.99), respectively. Rs895819 CT/CC genotype was associated with reduced female PTB risk and haplotype TCCCT, TAGCC, CCCCC, CCGCT and TCGAT were associated with reduced PTB risk, while TAGCT, CCCCT, CACCT and TCCAT were associated with increased risk.

Based on the sequences of Brassica rapa ssp. pekinensis, we carried out a single-nucleotide polymorphism (SNP) study for genes controlling disease resistance (clubroot, turnip mosaic virus and soft rot) and leaf traits in B. rapa leafy genotypes ‘VC40’ and ‘SR5’. In total, 7645 SNP markers were obtained based on the annotation of a B. rapa database for disease resistance. Among these 7645 SNP markers, 141 were related to 125 genes linked to leaf traits. From these 141 SNP markers, 63 were screened and High Resolution Melt (HRM) primers were designed for genomic studies. A total of 20 polymorphic SNP primers were finally obtained. Eventually, these markers will be further used for the detection of quantitative trait loci and mapping studies.

Next-generation sequencing technique has been known as a useful tool for de novo transcriptome assembly, functional annotation of genes and identification of molecular markers. This study was carried out to mine molecular markers from de novo assembled transcriptomes of four chilli pepper varieties, the highly pungent ‘Saengryeg 211’ and non-pungent ‘Saengryeg 213’ and variably pigmented ‘Mandarin’ and ‘Blackcluster’. Pyrosequencing of the complementary DNA library resulted in 361,671, 274,269, 279,221, and 316,357 raw reads, which were assembled in 23,607, 19,894, 18,340 and 20,357 contigs, for the four varieties, respectively. Detailed sequence variant analysis identified numerous potential single-nucleotide polymorphisms (SNPs) and simple sequence repeats (SSRs) for all the varieties for which the primers were designed. The transcriptome information and SNP/SSR markers generated in this study provide valuable resources for high-density molecular genetic mapping in chilli pepper and Quantitative trait loci analysis related to fruit qualities. These markers for pepper will be highly valuable for marker-assisted breeding and other genetic studies.

The characterization of genetic diversity and structure for improved cultivated varieties/elite lines is tremendously important to assist breeders in parental selection for inbred and hybrid breeding and heterotic group construction. In this study, a total of 737 improved indica varieties/lines developed recently and/or widely used by present indica breeding programmes worldwide were genotyped with a 384-single-nucleotide polymorphism assay. Model-based population structure analysis revealed the presence of two major groups with six subgroups (SGs), wherein no clear correlation was found between the groups/SGs and breeding programmes or geographical origin of the accessions. Over half of the accessions (51.8%) appeared to have less than 0.6 memberships assigned to any one of the six model-based groups, highlighting the wide range of gene flow within improved indica varieties/lines and the genetic integration of valuable alleles shared by ancestries among improved high-yielding varieties/lines through germplasm exchanges. Distance-based clustering revealed that Latin-American cultivated indica lines have tended to form their own ecological cline, which could serve as a potential heterotic ecotype for hybrid rice breeding, although they are still closely related to Asian indica lines. African cultivated indica lines, on the other hand, have not yet formed their own ecological cline. It was also observed that the most well-known hybrid rice parents, Zhenshan97B and Minghui63, were unexpectedly clustered in the same SG with a relatively narrow genetic distance, which suggests that a significant genetic distance between parents is not a prerequisite for all elite hybrid rice lines with high heterosis.

WRKY transcription factors are one of the largest families of transcriptional regulators and form an integral part of signalling webs which modulate many plant processes, such as abiotic stress tolerance. In the present paper, an innovative method has been applied to identify novel WRKY-1 alleles involved in the responses to salt and drought stresses in Triticum durum. This technique involves scanning for sequencing variations in cDNA-derived PCR amplicons, using high-resolution melting (HRM) followed by direct Sanger sequencing of only those amplicons which were predicted to carry nucleotide changes. HRM represents a novel advance in detection of single-nucleotide polymorphisms (SNPs) by measuring temperature-induced strand separation of short PCR amplicons. The use of this approach is still limited in the field of plant biology. Here, HRM analysis has been applied to the discovery and genotyping of durum wheat SNPs. Specific primers have been designed, starting at multi-alignment of WRKY-1-conserved portions. The PCR amplicons, containing single SNPs, produce distinctive HRM profiles, and by sequencing the PCR products identified, SNPs have been characterized and validated. The results showed that all the revealed SNPs are located on salt-tolerant varieties, confirming their value in breeding activities.

The inflammatory response to injury and infection, although an essential part of immune function, carries the risk of severe tissue depletion and immunosuppression. These outcomes increase morbidity and delay recovery. Evidence is accumulating that single-nucleotide polymorphisms in the genes controlling pro-inflammatory cytokine production adversely influence the response. Immunonutrition provides a means of modulating the inflammatory response to injury and infection, and thereby improves clinical outcome. n-3 Polyunsaturated fatty acids (n-3 PUFA), glutamine, arginine, S amino acids and nucleotides are important components of immunonutrient mixes. While animal model studies suggest that all these components may exert a beneficial effect in patients, the number of large randomized placebo-controlled trials utilizing immunonutrition is fairly limited and the observed effects are relatively small. Meta-analyses suggest that while immunonutrition may not reduce mortality rates, a reduction in hospital length of stay, decreased requirements for ventilation and lower infection rates are achieved by this mode of nutrition. The present paper discusses some underlying reasons for the difficulty in demonstrating the clinical efficacy of immunonutrition. Paramount among these reasons is the antioxidant status and genetic background of the patient. A number of studies suggest that there is an inverse relationship between inflammation and T-cell function. Immuno-enhancive effects have been shown in a number of studies in which n-3 PUFA, glutamine and N-acetyl cysteine have been employed. All these nutrients may exert their effects by suppressing inflammation; n-3 PUFA by direct suppression of the process and glutamine and N-acetyl cysteine by acting indirectly on antioxidant status. Glutamine and nucleotides exert a direct effect on lymphocyte proliferation. Preliminary data suggests that not all genotypes are equally sensitive to the effects of immunonutrition. When further studies have been conducted to discern the precise interaction between each individual's genotype of relevance to the response to injury and infection, and immunonutrients, the level of precision in the application of immunonutrition will undoubtedly improve.