Effects of ZnO nanoparticles and its bulk form on growth, antioxidant defense system and expression of oxidative stress related genes in Hordeum vulgare L

A comparative analysis of physio-biochemical indices and transcriptional activity of oxidative stress genes in barley (Hordeum vulgare L.) seedlings after 7-days exposure to bulk- and nano-ZnO (300 and 2000 mg/L) was carried out. A dose-dependent reduction in the length and weight of roots and shoots, as well as a significant accumulation of Zn in plant parts, was shown. Alterations in the shape and size of organelles, cytoplasmic vacuolization, and chloroplast and mitochondrial disorganization were also revealed. These processes are particularly pronounced when H. vulgare is exposed to the higher concentrations of nano-ZnO. The study of the antioxidant defense system revealed mainly an increase in the level of reduced glutathione and the activities of superoxide dismutase (SOD), catalase (CAT), glutathione reductase (GR), and glutathione S-transferase (GST). The increases in activity, by 4-fold and 3-fold, was found for glutathione transferase in the roots when exposed to 2000 mg/L bulk- and nano-ZnO, respectively. The study of transcriptional activity demonstrated that in the roots under the influence of bulk- and nano-ZnO, along with Mn-SOD, Fe-SOD is highly expressed, mainly associated with the protection of chloroplasts. Analysis of the Cat 1 and Cat 2 gene expression showed that the main contribution to the increase in catalase activity in treated H. vulgare is made by the CAT-1 isozyme. Generally, in response to the impact of the studied ZnO forms, the antioxidant defense system is activated in H. vulgare, which effectively prevents the progression of oxidative stress in early stages of plant ontogenesis. Nevertheless, with constant exposure to bulk- and nano-ZnO at high concentrations, such activation leads to a depletion of the plant's energy resources, which negatively affects its growth and development. The results obtained could be useful in predicting the risks associated with the further transfer of nano-ZnO to the environment.

Comparative analysis of chloroplast genomes of seven perennial Helianthus species

Sequencing and a comparative analysis of the complete chloroplast genomes of seven perennial Helianthus species were carried out. The chloroplast genomes have a typical quadripartite structure, including large and small single regions and a pair of inverted repeats. Genome sizes were between 151,152 bp and 151,289 bp. The genome of H. grosseserratus was the smallest, while that of H. microcephalus was the largest. The size variation of the chloroplast genomes is substantially due to the change in the length of simple sequence repeats (SSRs) in non-coding regions. An analysis of these SSRs revealed 35 polymorphic loci (average PIC value > 0.5) that can be used to examine ecological and evolutionary processes in wild Helianthus species. Eight divergence hotspots, including five intergenic regions (petN-psbM, clpP intron, rps3-rpl16, ndhD-ccsA, and ndhF-rpl32) and three gene regions (rbcL, ycf1, and ndhF) were also identified in Helianthus chloroplast genomes. The evolutionary selection pressure analysis revealed a strong purifying selection. Only the rbcL gene experienced efficiency of positive selection at the annual/perennial transitions. The inverted repeat (IR)/single copy (SC) boundaries were identical in all of these (Helianthus) species. In general, the comparison of the genomes revealed low levels of sequence variability (Pi = 0.00051). This indicates that the chloroplast genomes of the studied perennial species of Helianthus, in addition to purifying selection, are closely related and have a recent divergence time.

A point mutation in the photosystem I P700 chlorophyll a apoprotein A1 gene confers variegation in Helianthus annuus L

Even a point mutation in the psaA gene mediates chlorophyll deficiency. The role of the plastid signal may perform the redox state of the compounds on the acceptor-side of PSI. Two extranuclear variegated mutants of sunflower, Var1 and Var33, were investigated. The yellow sectors of both mutants were characterized by an extremely low chlorophyll and carotenoid content, as well as poorly developed, unstacked thylakoid membranes. A full-genome sequencing of the cpDNA revealed mutations in the psaA gene in both Var1 and Var33. The cpDNA from the yellow sectors of Var1 differs from those in the wild type by only a single, non-synonymous substitution (Gly734Glu) in the psaA gene, which encodes a subunit of photosystem (PS) I. In the cpDNA from the yellow sectors of Var33, the single-nucleotide insertion in the psaA gene was revealed, leading to frameshift at the 580 amino acid position. Analysis of the photosynthetic electron transport demonstrated an inhibition of the PSI and PSII activities in the yellow tissues of the mutant plants. It has been suggested that mutations in the psaA gene of both Var1 and Var33 led to the disruption of PSI. Due to the non-functional PSI, photosynthetic electron transport is blocked, which, in turn, leads to photodamage of PSII. These data are confirmed by immunoblotting analysis, which showed a significant reduction in PsbA in the yellow leaf sectors, but not PsaA. The expression of chloroplast and nuclear genes encoding the PSI subunits (psaA, psaB, and PSAN), the PSII subunits (psbA, psbB, and PSBW), the antenna proteins (LHCA1, LHCB1, and LHCB4), the ribulose 1.5-bisphosphate carboxylase subunits (rbcL and RbcS), and enzymes of chlorophyll biosynthesis were down-regulated in the yellow leaf tissue. The extremely reduced transcriptional activity of the two protochlorophyllide oxidoreductase (POR) genes involved in chlorophyll biosynthesis is noteworthy. The disruption of NADPH synthesis, due to the non-functional PSI, probably led to a significant reduction in NADPH-protochlorophyllide oxidoreductase in the yellow sectors of Var1 and Var33. A dramatic decrease in chlorophyllide was shown in the yellow sectors. A reduction in NADPH-protochlorophyllide oxidoreductase, along with photodegradation, has been suggested as a result of chlorophyll deficiency.

Effects of bulk and nano-ZnO particles on functioning of photosynthetic apparatus in barley (Hordeum vulgare L.)

The functioning of the photosynthetic apparatus in barley (Hordeum vulgare L.) after 7-days of exposure to bulk (b-ZnO) and nanosized ZnO (n-ZnO) (300, 2000, and 10,000 mg/l) has been investigated. An impact on the amount of chlorophylls, photosynthetic efficiency, as well as the zinc accumulation in chloroplasts was demonstrated. Violation of the chloroplast fine structure was revealed. These changes were generally more pronounced with n-ZnO exposure, especially at high concentrations. For instance, the chlorophyll deficiency under 10,000 mg/l b-ZnO treatment was 31% and with exposure to 10,000 mg/l n-ZnO, the chlorophyll deficiency was already 52%. The expression analysis of the photosynthetic genes revealed their different sensitivity to b-ZnO and n-ZnO exposure. The genes encoding subunits of photosystem II (PSII) and, to a slightly lesser extent, photosystem I (PSI) showed the highest suppression of transcriptional levels. The mRNA levels of the subunits of cytochrome-b₆f, NADH dehydrogenase, ribulose-1,5-bisphosphate carboxylase and ATP synthase, which, in addition to linear electron flow (LEF), participate in cyclic electron flow (CEF) and autotrophic CO₂ fixation, were more stable or increased under b-ZnO and n-ZnO treatments. At the same time, CEF was increased. It was assumed that under the action of b-ZnO and n-ZnO, the processes of LEF are disrupted, and CEF is activated. This allows the plant to prevent photo-oxidation and compensate for the lack of ATP for the CO₂ fixation process, thereby ensuring the stability of photosynthetic function in the initial stages of stress factor exposure. The study of photosynthetic structures of crops is important from the point of view of understanding the risks of reducing the production potential and the level of food security due to the growing use of nanoparticles in agriculture.

Genome-wide analysis of genetic diversity and artificial selection in Large White pigs in Russia

Breeding practices adopted at different farms are aimed at maximizing the profitability of pig farming. In this work, we have analyzed the genetic diversity of Large White pigs in Russia. We compared genomes of historic and modern Large White Russian breeds using 271 pig samples. We have identified 120 candidate regions associated with the differentiation of modern and historic pigs and analyzed genomic differences between the modern farms. The identified genes were associated with height, fitness, conformation, reproductive performance, and meat quality.

Data on the polymorphic sites in the chloroplast genomes of seven perennial Helianthus species

Data present the chloroplast genome sequences of seven wild perennial Helianthus species obtained by using the Illumina HiSeq and NextSeq platforms. Datasets not included in the primary publication [1] are a source for further evolutionary studies. In particular, the annotated chloroplast genomes and datasets of single nucleotide polymorphisms (SNP), simple sequence repeats (SSR), insertion and deletion polymorphisms (INDEL) for H. tuberosus, H. salicifolius, H. pauciflorus, H. microcephalis, H. hirsutus, H. strumosus, and H. grosseserratus are presented. The raw reads are available in Figshare (https://doi.org/10.6084/m9.figshare.12600155). The complete chloroplast genome sequences for the seven perennial Helianthus species are available on GenBank NCBI under the accessions MT302562.1 - MT302568.1; the remaining data are provided in this article.

Dependence of maize yield on hydrothermal factors in various agro-climatic zones of the Rostov region of Russia in the context of climate change

Trends in mean monthly temperature and precipitation during the growing season and their effects on the maize yield were analyzed at the Zimovnikovsky (Zim) and Rostov (Ros) state variety plots (SVPs), located in different agro-climatic zones of the Rostov region. For these two SVPs, in the period of 1975-2019, the Mann-Kendall test showed a statistically significant increase (p < 0.05) in mean temperature (0.70 and 0.52 °C/decade) and a trend of decreased total precipitation (- 14.81 and - 10.40 mm/decade) during the maize growing season. The dependence of the maize yield on hydrothermal factors was estimated for the period of 2011-2019 using the Pearson correlation coefficient (p < 0.05). The mean temperature in September at Zim negatively (r =  - 0.78), and in June at Ros positively (r = 0.77) correlated with yield, which explained, according to the value of the coefficient of determination (R²), up to 60.7% and 58.7%, respectively, of the interannual variability of the maize yield. The precipitation in July at the Zim and Ros positively correlated (r = 0.75 and r = 0.71) with yield and explained up to 55.9% and 50.6%, respectively, of the interannual variability of the maize yield. The total amount of precipitation during the growing season at Zim was the dominant factor, explaining up to 75.7% of the interannual variability of maize yield. The continuation of the observed climatic trends during the growing season could lead in the next decade to both a decrease in the maize yield by an average of 0.25 t/ha at Zim and an increase in the maize yield by an average of 0.42 t/ha at Ros.

Evaluation of genetic differentiation and search for candidate genes for reproductive traits in pigs

OBJECTIVE

The use of molecular genetic methods in pig breeding can significantly increase the efficiency of breeding and breeding work. We applied the Fst (fixsacion index) method, the main focus of the work was on the search for common options related to the number of born piglets and the weight of born piglets, since today the urgent task is to prevent a decrease in the weight of piglets at birth while maintaining high fertility of sows.

METHODS

One approach is to scan the genome, followed by an assessment of Fst and identification of selectively selected regions. We chose Large White sows (n = 237) with the same conditions of keeping and feeding. The data were collected from the sows across three farrowing. For genotyping, we used GeneSeek GGP Porcine HD Genomic Profiler v1, which included 68,516 single nucleotide polymorphisms evenly distributed with an average spacing of 25 kb (Illumina Inc, San Diego, CA, USA).

RESULTS

Based on the results of the Fst analysis, 724 variants representing selection signals for the signs BALWT, BALWT1, NBA, and TNB (weight of piglets born alive, average weight of the 1st piglets born alive, total number born alive, total number born). At the same time, 18 common variants have been identified that are potential markers for both the number of piglets at birth and the weight of piglets at birth, which is extremely important for breeding work to improve reproductive characteristics in sows.

CONCLUSION

Оur work resulted in identification of variants associated with the reproductive characteristics of pigs. Moreover, we identified, variants which are potential markers for both the number of piglets at birth and the weight of piglets at birth, which is extremely important for breeding work to improve reproductive performance in sows.

Spatiotemporal shifts in humidification zones: assessing climate impact on bioclimatic landscapes

Climate change is a global problem that is accompanied by the significant changes in humidification conditions in many regions all over the world. The study examined spatiotemporal changes in humidification zones in southern Russia in the period 1961-2020. Humidification zones were determined in accordance with the classification of the Selyaninov hydrothermal coefficient. During the research period, a significant increase in average annual temperatures was noted for the region (+ 0.31 °C/decade) and generally positive, but insignificant, dynamics of annual precipitation (+ 4.80 mm/decade). These changes were accompanied by a significant shift in the humidification zones. Despite some periods of decline, the territories of semi-desert and desert zones, as well as dry steppes, have significantly expanded from the east of the region to the west in the last decade. The expansion of these zones was primarily due to a reduction in the area of the more humid steppe zone, with a lesser contribution from the forest-steppe zone. Overall, during the study period, the area of semi-desert and desert zone expanded by an average of + 5.505 thou km2/decade. The zone of the Taiga and deciduous forests has not undergone significant changes. The results obtained indicate arid warming and a general deterioration in humidification conditions in most of southern Russia in the period 1961-2020. According to calculations, further warming, other things being equal, can lead to an even greater expansion of the semi-desert and desert bioclimatic zone, which can provoke a number of socio-economic and environmental problems, especially in the eastern part of the region.

Detection of genomic regions associated malformations in newborn piglets: a machine-learning approach

Background

A significant proportion of perinatal losses in pigs occurs due to congenital malformations. The purpose of this study is the identification of genomic loci associated with fetal malformations in piglets.

Methods

The malformations were divided into two groups: associated with limb defects (piglet splay leg) and associated with other congenital anomalies found in newborn piglets. 148 Landrace and 170 Large White piglets were selected for the study. A genome-wide association study based on the gradient boosting machine algorithm was performed to identify markers associated with congenital anomalies and piglet splay leg.

Results

Forty-nine SNPs (23 SNPs in Landrace pigs and 26 SNPs in Large White) were associated with congenital anomalies, 22 of which were localized in genes. A total of 156 SNPs (28 SNPs in Landrace; 128 in Large White) were identified for piglet splay leg, of which 79 SNPs were localized in genes. We have demonstrated that the gradient boosting machine algorithm can identify SNPs and their combinations associated with significant selection indicators of studied malformations and productive characteristics.

Data availability

Genotyping and phenotyping data are available at http://www.compubioverne.group/data-and-software/.

PSIX-24 Genome-wide association mapping for additive and dominance effects in pig fertility

The aim of the work was to conduct GWAS for Total Number Born (TNB) based on the Gradient Boosting Machine (GBM) algorithm, taking into account additive and dominance effects. The study population consisted of 218 Landrace sows. DNA samples were genotyped using GGP HD Porcine. After filtering, 40358 SNPs are left for further analysis. The target variable is the Total Number Born estimated from the third farrow. To assess the additive (model A) and dominant (model D), the coding 0/1/2 and 0/1/0 were used, respectively. Based on the test results, the top 50 SNPs were selected for each of the models in accordance with the relative importance. Of the top 50 SNPs determined by model D, 36 SNPs were identified based on model A (of which 14 SNPs were included in the top of model A). However, the top 14 SNPs for Model D showed relative importance = 0 for Model A. The genes identified in Models A and D are responsible for Molecular functions: binding (GO: 0005488), catalytic activity (GO: 0003824), and transcriptional regulator activity (GO: 0140110); Biological process: cellular process (GO: 0009987), biological regulation (GO: 0065007), metabolic process (GO: 0008152); Cellular component: part of a cell (GO: 0044464) and a cell (GO: 0005623). Further research will allow a more detailed study of the genetic electrical energy of fertility traits in pigs. The results showed that the dominance effects has additional value for genomic effects that control pig fertility. This research was performed with financial support from the Russian Science Foundation (RSF) 19-76-10012.

Origin of CMS-PET1 cytotype in cultivated sunflower: A new insight

The vast majority of commercial sunflower hybrids worldwide are produced using cytoplasmic male sterility (CMS) of the PET1 type, resulting from the interspecific hybridization of Helianthus petiolaris with Helianthus annuus. Due to the fact that CMS-PET1 was not previously detected in wild sunflower, it was believed that this cytotype could arise during interspecific hybridization and is specific solely for cultivated sunflower. In this study, the open reading frame, orfH522, associated with the CMS-PET1 phenotype, was revealed for the first time in the 3'-flanking region of the mitochondrial atpA gene in wild H. annuus. An analysis of whole genome data from 1089 accessions showed that the frequency of occurrence of CMS-orfH522 in wild H. annuus populations is 3.58%, while in wild H. petiolaris populations, it is 1.26%. In general, the analysis demonstrated that PET1-CMS is a natural cytotype of H. annuus, and the appearance of the CMS phenotype in cultivated sunflowers is associated with the loss of stabilizing nuclear genes of fertility restorers, which occurred during interspecific hybridization. These data can explain the patterns of differential cytoplasmic and nuclear introgression occurring in wild sunflower and are useful for further evolutionary studies.

PSIX-23 Correlation between VRTN and PPARD gene variants and the phenotypic manifestation of productive traits and the hind limbs conformation in pigs

We formed three samples: Landrace (L, n = 86), Large White (LW, n = 120), and Duroc pigs (D, n = 140). Three traits investigated: the mean daily gain (ADG), early maturity (DAY100) and limb condition (LEG; good/bad). The PPARD (rs80828473) and VRTN (rs343248943) genes were selected. The effects of genotypes PPARD on ADG and DAY100 were determined in Duroc by the association with these traits. Pigs D of AA, comparing to GG had better ADG by 82.3 (P = 0.01) and DAY100 by 6.5 (P = 0.05). Pigs L with the AA genotype, comparing to the GG genotype, had the best ADGs by 101.0 (P = 0.05) and DAY100 by 13.1 (P = 0.04). The effect of the PPARD in LW is unknown as AA genotype was not detected in LW. For the VRTN gene D pigs of the AG and GG genotype comparing to the AA genotype had the best ADGs by 49.1 (P = 0.03) and 56.5 (P = 0.09); DAY100 by 4.8 (P = 0.03) and 9.7 (P = 0.005). Pigs D of AA genotype (P = 0.01) had the best limbs conformation but demonstrated lower productivity. In Landrace pigs, no differences in ADG and DAY100 associated with the VRTN genotypes were found. The possible reason is the low frequency of the GG genotype in this group. Regarding to the limbs the desired genotype in pigs L is AA (P = 0.05). In Large white pigs a positive effect of the AG genotype on ADG and DAY100 was found, comparing to the AA genotype it was 100.6 g (P = 0.02) and 11.7 days. (P = 0.01). The effect of the VRTN different genotypes on the LW limbs has not been found. Research was performed with the Russian Foundation for Basic Research financial support 19-016-00068 A.

Evaluating the phytotoxicological effects of bulk and nano forms of zinc oxide on cellular respiration-related indices and differential gene expression in Hordeum vulgare L

The increasing use of nanoparticles is driving the growth of research on their effects on living organisms. However, studies on the effects of nanoparticles on cellular respiration are still limited. The remodeling of cellular-respiration-related indices in plants induced by zinc oxide nanoparticles (nnZnO) and its bulk form (blZnO) was investigated for the first time. For this purpose, barley (Hordeum vulgare L.) seedlings were grown hydroponically for one week with the addition of test compounds at concentrations of 0, 0.3, 2, and 10 mg mL-1. The results showed that a low concentration (0.3 mg mL-1) of blZnO did not cause significant changes in the respiration efficiency, ATP content, and total reactive oxygen species (ROS) content in leaf tissues. Moreover, a dose of 0.3 mg mL-1 nnZnO increased respiration efficiency in both leaves (17 %) and roots (38 %). Under the influence of blZnO and nnZnO at medium (2 mg mL-1) and high (10 mg mL-1) concentrations, a dose-dependent decrease in respiration efficiency from 28 % to 87 % was observed. Moreover, the negative effect was greater under the influence of nnZnO. The gene transcription of the subunits of the mitochondria electron transport chain (ETC) changed mainly only under the influence of nnZnO in high concentration. Expression of the ATPase subunit gene, atp1, increased slightly (by 36 %) in leaf tissue under the influence of medium and high concentrations of test compounds, whereas in the root tissues, the atp1 mRNA level decreased significantly (1.6-2.9 times) in all treatments. A dramatic decrease (1.5-2.4 times) in ATP content was also detected in the roots. Against the background of overexpression of the AOX1d1 gene, an isoform of alternative oxidase (AOX), the total ROS content in leaves decreased (with the exception of 10 mg mL-1 nnZnO). However, in the roots, where the pressure of the stress factor is higher, there was a significant increase in ROS levels, with a maximum six-fold increase under 10 mg mL-1 nnZnO. A significant decrease in transcript levels of the pentose phosphate pathway and glycolytic enzymes was also shown in the root tissues compared to leaves. Thus, the disruption of oxidative phosphorylation leads to a decrease in ATP synthesis and an increase in ROS production; concomitantly reducing the efficiency of cellular respiration.

Identifying Significant SNPs of the Total Number of Piglets Born and Their Relationship with Leg Bumps in Pigs

The aim of this study was to identify genetic variants and pathways associated with the total number of piglets born and to investigate the potential negative consequences of the intensive selection for reproductive traits, particularly the formation of bumps on the legs of pigs. We used genome-wide association analysis and methods for identifying selection signatures. As a result, 47 SNPs were identified, localized in genes that play a significant role during sow pregnancy. These genes are involved in follicle growth and development (SGC), early embryonic development (CCDC3, LRRC8C, LRFN3, TNFRSF19), endometrial receptivity and implantation (NEBL), placentation, and embryonic development (ESRRG, GHRHR, TUSC3, NBAS). Several genes are associated with disorders of the nervous system and brain development (BCL11B, CDNF, ULK4, CC2D2A, KCNK2). Additionally, six SNPs are associated with the formation of bumps on the legs of pigs. These variants include intronic variants in the CCDC3, ULK4, and MINDY4 genes, as well as intergenic variants, regulatory region variants, and variants in the exons of non-coding transcripts. The results suggest important biological pathways and genetic variants associated with sow fertility and highlight the potential negative impacts on the health and physical condition of pigs.