Phylogenomic investigation of safflower (Carthamus tinctorius) and related species using genotyping-by-sequencing (GBS).

Safflower (Carthamus tinctorius, Asteraceae) is a source of high-quality edible oil growing in moisture-limited environments. Despite its economic importance, the relationships to close wild species in Carthamus and the presence and relationships of ecotypes within safflower are still not fully clarified. Here we use genotyping-by-sequencing to identify the wild progenitor of C. tinctorius, infer phylogenetic relationship within the series Carthamus and identify groups of closely related lineages within cultivated safflower. Phylogenetic and population genomic analyses found C. palaestinus to be the closest relative and single progenitor of C. tinctorius, which confirms the Levant as the area of domestication of the crop. Flow cytometry showed all analyzed samples of C. oxyacantha, C. palaestinus and C. tinctorius to be diploid (2n = 2x = 24) with 2C genome sizes of 2.4-2.7 pg. Analyses of a set of 114 worldwide distributed safflower accessions arrived at two to five genetic groups, which showed, however, no correlation with the geographic origins of these accessions. From this, we conclude that the trade of safflower seeds resulted in multiple introductions of genotypes from the Levant into other areas with suitable climate conditions for the plant, as well as exchange of genotypes among these areas.

Candidate genes for anthocyanin pigmentation in rice stem revealed by GWAS and whole-genome resequencing.

Anthocyanin pigment as a phenolic secondary metabolite is accumulated in areal organs of some rice cultivars. Despite several research attempts, the majority of genomic regions and candidate genes for purple-colored stem (Ps) resulting from anthocyanin pigmentation of rice leaf sheath have not been identified. A genome-wide association study (GWAS) and whole-genome resequencing (WGR) analysis was applied for genetic dissection of anthocyanin pigmentation of rice stem. Using GWAS, the genomic regions (on chromosomes 2, 4, and 6) tagged to eight single-nucleotide polymorphisms (SNPs) were identified to be significantly associated with purple stem, and in the vicinity of GWAS signals, 19 genes were highlighted as putative candidate genes. To narrow down the genomic regions more highly associated to the trait, a WGR study on recombinant inbred lines (RIL) with opposite phenotypes was conducted. After defining the DNA variation between reference genome, maternal parent and the two sister lines, a narrow genomic region on the short arm of chromosome 6 (4.7-6.2 Mbp interval) was identified to be highly associated with anthocyanin pigmentation of rice stem. In the interval, a few candidate genes with probable role in anthocyanin biosynthesis and accumulation were identified, which included five structural genes involved in the known pathways [one chalcone isomerase (CHI), two glycosyl transferases, and two UDP-flavonoid-3-O-glucosyl (UFGT) transferases] and two transcription factors [one basic helix-loop-helix (bHLH)- and one myeloblastosis (MYB)-coding genes]. The identified candidate genes can be used in breeding programs of rice or other Gramineae species for anthocyanin accumulation in areal organs.

Rapid extraction of high- and low-density microplastics from soil using high-gradient magnetic separation.

Microplastics (MPs) are present in all environments, and concerns over their possible detrimental effects on flora and fauna have arisen. Density separation (DS) is commonly used to separate MPs from soils to allow MP quantification; however, it frequently fails to extract high-density MPs sufficiently, resulting in under-estimation of MP abundances. In this proof-of-concept study, a novel three-stage extraction method was developed, involving high-gradient magnetic separation and removal of magnetic soil (Stage 1), magnetic tagging of MPs using surface modified iron nanoparticles (Stage 2), and high-gradient magnetic recovery of surface-modified MPs (Stage 3). The method was optimised for four different soil types (loam, high­carbon loamy sand, sandy loam and high-clay sandy loam) spiked with different MP types (polyethylene, polyethylene terephthalate, and polytetrafluoroethylene) of different particle sizes (63 µm to 2 mm) as well as polyethylene fibres (2-4 mm). The optimised method achieved average recoveries of 96% for fibres and 92% for particles in loam, 91% for fibres and 87% for particles in high­carbon loamy sand, 96% for fibres and 89% for particles in sandy loam, and 97% for fibres and 94% for particles in high-clay sandy loam. These were significantly higher than recoveries achieved by DS, particularly for fibres and high-density MPs (p < 0.05). To demonstrate the practical application of the HGMS method, it was applied to a farm soil sample, and high-density MP particles were only recovered by HGMS. Furthermore, this study showed that HGMS can recover fibre-aggregate complexes. This improved extraction method will provide better estimates of MP quantities in future studies focused on monitoring the prevalence of MPs in soils.

Root canal configuration and the prevalence of C-shaped canals in mandibular second molars in an Iranian population.

A total of 139 extracted mandibular second molars were injected with India ink and demineralized. They were made clear and transparent with methyl salicylate, and the anatomy of their canals was studied. It was found that 86.3% of mandibular second molars had two roots, 9.3% had one root, and 4.3% had three roots. Ninety percent of the mesial roots of the mandibular second molars with two roots had two canals (predominantly with a type II or III configuration), and 77.5% of the distal roots of these teeth had one canal (predominantly with a type I configuration). Among the mandibular second molars, 7.2% had C-shaped canals and these configurations were seen mostly in single-rooted mandibular second molars. The results of this study indicate that mandibular second molar teeth have many variations in the number of roots and the morphology of their canals. Therefore it should not be assumed that all mandibular second molar teeth have two roots and three canals.