Assessment of rice genotypes for salt tolerance using microsatellite markers associated with the saltol QTL

A major quantitative trait locus (QTL) for salt tolerance named Saltol was mapped on chromosome 1 using F8 recombinant inbred lines (RILs) of Pokkali/IR29 cross, which is responsible for low Na+, highK+ uptake and maintaining Na+/K+ homeostasis in the rice shoots. To test the usefulness of microsatellite (SSR) markers associated with Saltol QTL, a collection of 36 diverse rice genotypes wereused. Phenotypic response of the genotypes to salt stress with EC=12 was assessed under controlled environmental conditions at seedling stage using a visual score of 1 to 9 scale. Thirty three polymorphic SSR markers located on chromosome 1 were also used to determine the impact of these markers associated with salt tolerance in rice. The results of phenotypic response of rice genotypes to salinity stress at the seedling stage indicated the varied genotypic responses. The genotypes were classified into five groups from highly tolerant (score 1) to highly sensitive (score 9). Number of alleles of the SSR markers ranged from 3 for RM10702 to 14 for RM8094. Polymorphic information content (PIC) value varied from 0.28 for RM8095 to 0.88 for RM8094 with an average of 0.73. The SSR marker, RM8094, was found to be superior for analysis of genetic diversity in this study. Cluster analysis of the rice genotypes based on SSR data divided the genotypes into three groups each of which having 12, 8 and 16 genotypes including highly salt-tolerant IRRI elite lines (cluster 1), salt tolerant and moderate tolerant genotypes as well as Pokkali and FL478 (cluster 2), sensitive and highly sensitive genotypes (cluster 3), respectively. The impact of chromosome 1 for tolerance to salinity at the seedling stage in rice was emphasized by the results. Thirty six rice genotypes divided into 18 different haplotypes based on Saltol QTL located on chromosome 1 using Pokkali cultivar as the reference. The haplotypespossessing RM8094 and RM10745 markers could discriminate the tolerant genotypes and hence could be useful for marker-assisted selection of Saltol QTL

Multiple QTL-effects of wheat Gpc-B1 locus on grain protein and micronutrient concentrations

Micronutrient malnutrition afflicts over three billion peopleworldwide and the numbers are continuously increasing. Developing genetically micronutrientenriched cereals, which are the predominant source of human dietary, is essential to alleviate malnutrition worldwide. Wheat chromosome 6B derived from wild emmerwheat [Triticum turgidum ssp. dicoccoides (Körn.) Thell] was previously reported to be a source for high Zn concentration in the grain. In the present study, recombinant chromosome substitution lines (RSLs), previously constructed for genetic and physical maps of Gpc-B1 (a 250-kb locus affecting grain protein concentration), were used to identify the effects of the Gpc-B1 locus on grain micronutrient concentrations. RSLs carrying the Gpc-B1 allele of T. dicoccoides accumulated on average 12% higher concentration of Zn, 18% higher concentration of Fe, 29% higher concentration of Mn and 38% higher concentration of protein in the grain as compared with RSLs carrying the allele from cultivated wheat (Triticum durum). Furthermore, the high grain Zn, Fe and Mn concentrations were consistently expressed in five different environments with an absence of genotype by environment interaction. The results obtained in the present study also confirmed the previously reported effect of the wild-type allele of Gpc-B1 on earlier senescence of flag leaves. We suggest that the Gpc-B1 locus is involved in more efficient remobilization of protein, zinc, iron and manganese from leaves to the grains, in addition to its effect on earlier senescence of the green tissues

EGRINs (Environmental Gene Regulatory Influence Networks) in Rice That Function in the Response to Water Deficit, High Temperature, and Agricultural Environments

Environmental gene regulatory influence networks (EGRINs) coordinate the timing and rate of gene expression in response to environmental signals. EGRINs encompass many layers of regulation, which culminate in changes in accumulated transcript levels. Here, we inferred EGRINs for the response of five tropical Asian rice (Oryza sativa) cultivars to high temperatures, water deficit, and agricultural field conditions by systematically integrating time-series transcriptome data, patterns of nucleosome-free chromatin, and the occurrence of known cis-regulatory elements. First, we identified 5447 putative target genes for 445 transcription factors (TFs) by connecting TFs with genes harboring known cis-regulatory motifs in nucleosome-free regions proximal to their transcriptional start sites. We then used network component analysis to estimate the regulatory activity for each TF based on the expression of its putative target genes. Finally, we inferred an EGRIN using the estimated transcription factor activity (TFA) as the regulator. The EGRINs include regulatory interactions between 4052 target genes regulated by 113 TFs. We resolved distinct regulatory roles for members of the heat shock factor family, including a putative regulatory connection between abiotic stress and the circadian clock. TFA estimation using network component analysis is an effective way of incorporating multiple genome-scale measurements into network inference

Quantitative trait loci conferring grain mineral nutrient concentrations in durum wheat 3 wild emmer wheat RIL population

Mineral nutrient malnutrition, and particularly deficiency in zinc and iron, afflicts over 3 billion people worldwide. Wild emmer wheat, Triticum turgidum ssp. dicoccoides, genepool harbors a rich allelic repertoire for mineral nutrients in the grain. The genetic and physiological basis of grain protein, micronutrients (zinc, iron, copper and manganese) and macronutrients (calcium, magnesium, potassium, phosphorus and sulfur) concentration was studied in tetraploid wheat population of 152 recombinant inbred lines (RILs), derived from a cross between durum wheat (cv. Langdon) and wild emmer (accession G18-16). Wide genetic variation was found among the RILs for all grain minerals, with considerable transgressive effect. A total of 82 QTLs were mapped for 10 minerals with LOD score range of 3.2–16.7. Most QTLs were in favor of the wild allele (50 QTLs). Fourteen pairs of QTLs for the same trait were mapped to seemingly homoeologous positions, reflecting synteny between the A and B genomes. Significant positive correlation was found between grain protein concentration (GPC), Zn, Fe and Cu, which was supported by significant overlap between the respective QTLs, suggesting common physiological and/or genetic factors controlling the concentrations of these mineral nutrients. Few genomic regions (chromosomes 2A, 5A, 6B and 7A) were found to harbor clusters of QTLs for GPC and other nutrients. These identified QTLs may facilitate the use of wild alleles for improving grain nutritional quality of elite wheat cultivars, especially in terms of protein, Zn and Fe

Development of a Surface Plasmon Resonance Biosensor for Real-Time Detection of Osteogenic Differentiation in Live Mesenchymal Stem Cells

Surface plasmon resonance (SPR) biosensors have been recognized as a useful tool and widely used for real-time dynamic analysis of molecular binding affinity because of its high sensitivity to the change of the refractive index of tested objects. The conventional methods in molecular biology to evaluate cell differentiation require cell lysis or fixation, which make investigation in live cells difficult. In addition, a certain amount of cells are needed in order to obtain adequate protein or messenger ribonucleic acid for various assays. To overcome this limitation, we developed a unique SPR-based biosensing apparatus for real-time detection of cell differentiation in live cells according to the differences of optical properties of the cell surface caused by specific antigen-antibody binding. In this study, we reported the application of this SPR-based system to evaluate the osteogenic differentiation of mesenchymal stem cells (MSCs). OB-cadherin expression, which is up-regulated during osteogenic differentiation, was targeted under our SPR system by conjugating antibodies against OB-cadherin on the surface of the object. A linear relationship between the duration of osteogenic induction and the difference in refractive angle shift with very high correlation coefficient was observed. To sum up, the SPR system and the protocol reported in this study can rapidly and accurately define osteogenic maturation of MSCs in a live cell and label-free manner with no need of cell breakage. This SPR biosensor will facilitate future advances in a vast array of fields in biomedical research and medical diagnosis

Effects of Inhibition of Interleukin-6 Signalling on Insulin Sensitivity and Lipoprotein (A) Levels in Human Subjects with Rheumatoid Diseases

Interleukin-6 (IL-6) is a pro-inflammatory cytokine that has been found to be increased in type 2 diabetic subjects. However, it still remains unclear if these elevated IL-6 levels are co-incidental or if this cytokine is causally related to the development of insulin resistance and type 2 diabetes in humans. Therefore, in the present study we examined insulin sensitivity, serum adipokine levels and lipid parameters in human subjects before and after treatment with the IL-6 receptor antibody Tocilizumab.11 non-diabetic patients with rheumatoid disease were included in the study. HOMA-IR was calculated and serum levels for leptin, adiponectin, triglycerides, LDL-cholesterol, HDL-cholesterol and lipoprotein (a) (Lp (a)) were measured before as well as one and three months after Tocilizumab treatment. The HOMA index for insulin resistance decreased significantly. While leptin concentrations were not altered by inhibition of IL-6 signalling, adiponectin concentrations significantly increased. Thus the leptin to adiponectin ratio, a novel marker for insulin resistance, exhibited a significant decrease. Serum triglycerides, LDL-cholesterol and HDL-cholesterol tended to be increased whereas Lp (a) levels significantly decreased.Inhibition of IL-6 signalling improves insulin sensitivity in humans with immunological disease suggesting that elevated IL-6 levels in type 2 diabetic subjects might be causally involved in the pathogenesis of insulin resistance. Furthermore, our data indicate that inhibition of IL-6 signalling decreases Lp (a) serum levels, which might reduce the cardiovascular risk of human subjects