Biology subjects

Simic, D.

Publications and source records attributed to Simic, D..

3 recordsLinked to original sources

bioRxiv2020

First results on diversity patterns and selective sweeps in a Southeast European panel of maize inbred lines as combined with two West European panels

More than one third of European grain maize is produced in South Eastearn Europe (SEE) and utilization of historical maize material developed in SEE for its favorable alleles and diversity has long been speculated. However, molecular diversity of the SEE maize genetic material is scarce. The objectives of this study were i) to analyze diversity patterns in a large panel of densely genotyped historical accessions from SEE, ii) to compare the data with those obtained from other two European panels, and iii) to identify genomic regions that have undergone selection (selective sweeps) in response to adaptation to SEE conditions. 572 accessions of the historical inbred lines from Maize Research Institute Zemun Polje representing the SEE material were genotyped using the 600k maize genotyping Axiom array. The genotyping results were merged with two European panels DROPS and TUM. Genetic structure and diversity were analyzed using neighbor-joining cladogram, PcoA, Admixture, Structure and sNMF. To detect the selective sweep signals, Tajimas D statistic and RAiSD were employed. The best number of ancestral populations was K=7, whereby one of them is a subpopulation containing inbreds belong exclusively to the SEE panel. The prevalence of inbreds linked to historical US inbred lines Wf9, Oh43, Pa91 and A374 was detected in SEE. Possible soft selective sweep was detected in chromosome 2 in region harboring a gene linked to promotion of flowering FPF1. Additional scan for selective sweeps using the RAiSD methodology yielded four signals in chromosomes 5 and 6, all in gene-rich regions. Several candidates of selection were identified, influencing the plant morphology and adaptation. Our study provides the first step towards the utilization of the SEE genetic materials for use in maize breeding. Phenotypic analysis is needed for assessment of SEE accessions for favorable alleles, and identification of breeding targets.

genetics↗

bioRxiv2019

Genomewide analysis of biomass responses to water withholding in young plants of maize inbred lines with expired plant variety protection certificate

Patterns of seasonal variations in rainfall are changing which affects rain-fed agricultural areas. Water deficit during the early vegetative growth poses threat as it causes variability in plant development, makes plant susceptible to other stresses and deteriorates the stands. Plants responses to water deficit are reflected in biomass traits which represent the morpho-physiological adjustments of plant to new conditions. The aims of this study were to assess the biomass responses of maize inbred lines with expired plant variety protection certificate that are freely distributed worldwide using genomewide analysis approach. The collection of 109 maize inbred lines, genotyped using genotyping-by-sequencing, was planted in controlled conditions (16/8 day/night, 25{degrees}C, 50% RH, 200 Mol/m2/s) in trays filled with soil in three replicates. Plants in control (C) were watered every two days with 8 mlH2O, while watering was stopped for 10 days in water withholding (WW) treatment. Fourteen days old plants were harvested and fresh weight (FW), dry weight (DW) and dry matter content (DMC, % of FW) were measured. Different responses to WW were detected in two genetic subgroups: Stiff Stalk and Non-Stiff Stalk. Totally 29 QTLs were detected, and it was shown that genetic regulation of DMC is different than regulation of FW and DW. This was further supported with correlations of rrBLUP marker effects among the traits. It was concluded that measurements of biomass traits in this manner are fast and reliable indicator of plants response to water deficit and can be used for effective screening of breeding progenies.

genetics↗

bioRxiv2019

Liver-Chip: Reproducing Human and Cross-Species Toxicities

Nonclinical rodent and non-rodent toxicity models used to support clinical trials of candidate drugs may produce discordant results or fail to predict complications in humans contributing to drug failures in the clinic. Here we applied microengineered Organ-on-Chip (Organ-Chip) technology to design rat, dog, and human Liver-Chips containing species-specific primary hepatocytes interfaced with liver sinusoidal endothelial cells, with or without Kupffer cells and hepatic stellate cells, cultured under physiological fluid flow. The Liver-Chips detected diverse phenotypes of liver toxicity including hepatocellular injury, steatosis, cholestasis, and fibrosis as well as species-specific toxicities when treated with tool compounds. Multi-species Liver-Chips may provide a useful platform for prediction of liver toxicity and inform human relevance of liver toxicities detected in animal studies to better determine safety and human risk.\n\nOne Sentence SummaryMicroengineered Organ-Chip technology has been used to design rat, dog and human Liver-Chips that recapitulate species-specific liver toxicities.

pharmacology and toxicology↗