Interest of phenomic prediction as an alternative to genomic prediction in grapevine

Phenomic prediction has been defined as an alternative to genomic prediction by using spectra instead of molecular markers. A reflectance spectrum reflects the biochemical composition within a tissue, under genetic determinism. Thus, a relationship matrix built from spectra could potentially capture genetic signal. This new methodology has been successfully applied in several cereal species but little is known so far about its interest in perennial species. Besides, phenomic prediction has only been tested for a restricted set of traits, mainly related to yield or phenology. This study aims at applying phenomic prediction for the first time in grapevine, using spectra collected on two tissues and over two consecutive years, on two populations and for 15 traits. First, we characterized the genetic signal in spectra and under which condition it could be maximized, then phenomic predictive ability was compared to genomic predictive ability. We found that the co-inertia between spectra and genomic data was stable across tissues or years, but variable across populations, with co-inertia around 0.3 and 0.6 for diversity panel and half-diallel populations, respectively. Differences between populations were also observed for predictive ability of phenomic prediction, with an average of 0.27 for the diversity panel and 0.35 for the half-diallel. For both populations, there was a correlation across traits between predictive ability of genomic and phenomic prediction, with a slope around 1 and an intercept of -0.2, thus suggesting that phenomic prediction could be applied for any trait.

The origin and evolution of a two-component system of paralogous genes encoding the centromeric histone CENH3 in cereals

Background The cereal family Poaceae is one of the largest and most diverse angiosperm families. The central component of centromere specification and function is the centromere-specific histone H3 (CENH3). Some cereal species (maize, rice) have one copy of the gene encoding this protein, while some (wheat, barley, rye) have two. We applied a homology-based approach to sequenced cereal genomes, in order to finally trace the mutual evolution of the structure of the CENH3 genes and the nearby regions in various tribes. Results We have established that the syntenic group or the CENH3 locus with the CENH3 gene and the boundaries defined by the CDPK2 and bZIP genes first appeared around 50 Mya in a common ancestor of the subfamilies Bambusoideae, Oryzoideae and Pooideae. This locus came to Pooideae with one copy of CENH3 in the most ancient tribes Nardeae and Meliceae. The βCENH3 gene as a part of the locus appeared in the tribes Stipeae and Brachypodieae around 35–40 Mya. The duplication was accompanied by changes in the exon-intron structure. Purifying selection acts mostly on αCENH3s, while βCENH3s form more heterogeneous structures, in which clade-specific amino acid motifs are present. In barley species, the βCENH3 gene assumed an inverted orientation relative to αCENH3 and the CDPK2 gene was substituted with LHCB-l. As the evolution and domestication of plant species went on, the locus was growing in size due to an increasing distance between αCENH3 and βCENH3 because of a massive insertion of the main LTR-containing retrotransposon superfamilies, gypsy and copia, without any evolutionary preference on either of them. A comparison of the molecular structure of the locus in the A, B and D subgenomes of the hexaploid wheat T. aestivum showed that invasion by mobile elements and concomitant rearrangements took place in an independent way even in evolutionarily close species. Conclusions The CENH3 duplication in cereals was accompanied by changes in the exon-intron structure of the βCENH3 paralog. The observed general tendency towards the expansion of the CENH3 locus reveals an amazing diversity of ways in which different species implement the scenario described in this paper.

Biological and agronomic characterization of bread wheat (Triticum aes-tivum L.) and barley (Hordeum vulgare L.) cultivated in the region of Constantine, Algeria

The biological and agronomic characterization of cereals constitutes a pre-liminary and essential step for the assessment of genetic diversity state which must be valued, exploited and known in a clear and complete manner in order to be able to exploit them in improvement and adaptation programs of cereals. In this context, our study was carried out during the 2018/2019 agricultural campaign on the experimental site of the technical institute of field crops ITGC of El Khroub (Constantine, Algeria). Its objective was to char-acterize the biological and agronomic diversity in two cereal species, bread wheat (Triticum aestivum L.) and barley (Hordeum vulgare L.) by evaluating many pheno-morphological, physiological and biochemical characters as well as production traits (agronomic traits). The correlation coefficients analysis between traits indicates that the short and early heading varieties which accumulate less proline are more productive than varieties which are charac-terized by long straw and late heading in both species. However, it has been noted that barley varieties reach heading before bread wheat varieties. In addition, it shows that the grain yield is positively correlated with these com-ponents, in particular with the number of seeds per ear, the number of ears per square meter, and with the following parameters: the surface of the flag leaf and its content of chlorophyll pigments, the totality of the ear character-istics such as the length of the ear neck. These results lead us to say that an indirect selection via these crops can be beneficial for the production and improvement programs of cereals.

Metabolic Changes in Seed Embryos of Hypoxia-Tolerant Rice and Hypoxia-Sensitive Barley at the Onset of Germination

Rice (Oryza sativa L.) and barley (Hordeum vulgare L.) are the cereal species differing in tolerance to oxygen deficiency. To understand metabolic differences determining the sensitivity to low oxygen, we germinated rice and barley seeds and studied changes in the levels of reactive oxygen species (ROS) and reactive nitrogen species (RNS), activities of the enzymes involved in their scavenging, and measured cell damage parameters. The results show that alcohol dehydrogenase activity was higher in rice than in barley embryos providing efficient anaerobic fermentation. Nitric oxide (NO) levels were also higher in rice embryos indicating higher NO turnover. Both fermentation and NO turnover can explain higher ATP/ADP ratio values in rice embryos as compared to barley. Rice embryos were characterized by higher activity of S-nitrosoglutathione reductase than in barley and a higher level of free thiols in proteins. The activities of antioxidant enzymes (superoxide dismutase, ascorbate peroxidase, monodehydroascorbate reductase, dehydroascorbate reductase) in imbibed embryos were higher in rice than in barley, which corresponded to the reduced levels of ROS, malonic dialdehyde and electrolyte leakage. The observed differences in metabolic changes in embryos of the two cereal species differing in tolerance to hypoxia can partly explain the adaptation of rice to low oxygen environments.

Economic efficiency of creation and use of long-term hayfields on dry lands of the Non-Chernozem zone

In order to accelerate the implementation of improved technologies, taking into account the requirements of a market economy, the economic assessment of the creation and use of long-term haymaking was carried out according to five technological systems of management, using the methodology approved by the Russian Academy of Agricultural Sciences (1995). On long-term haymaking (75 years of life) over the past 28 years, productivity in extensive low-cost management systems amounted to 1.9-3.9 thousand fodder. units / ha, conditionally net income 11.7-13.2 thousand rubles / ha, with a production profitability of 52-174%. In intensive technological systems, the productivity of long-term haymaking increased to 3.4-4.5 thousand fodder. units / ha, conditionally net income from 11.9 to 16.2 thousand rubles / ha, with a production profitability of 56-60%. Extensive management systems can be used on farms with limited material and technical resources. Capital costs for the creation of long-term haymaking during the development period (2 years) amounted to 32.5 thousand rubles / ha, which paid off in 1.4-3.0 years, the annual production costs for five technological systems - 6.6-28, 3 thousand rubles per year, 40-75% of them were hay bales, with a feed unit cost of 3.5-6.4 rubles. The creation of long-term hayfields on the basis of self-renewing cereal species of phytocenosis allows saving material resources for re-planting herbage by 8-10 times, providing animals with high-quality hay, and reducing the volume of concentrates in the winter stall period.

Expression of Two Rye CENH3 Variants and Their Loading into Centromeres

Gene duplication and the preservation of both copies during evolution is an intriguing evolutionary phenomenon. Their preservation is related to the function they perform. The central component of centromere specification and function is the centromere-specific histone H3 (CENH3). Some cereal species (maize, rice) have one copy of the gene encoding this protein, while some (wheat, barley, rye) have two. Therefore, they represent a good model for a comparative study of the functional activity of the duplicated CENH3 genes and their protein products. We determined the organization of the CENH3 locus in rye (Secale cereale L.) and identified the functional motifs in the vicinity of the CENH3 genes. We compared the expression of these genes at different stages of plant development and the loading of their products, the CENH3 proteins, into nucleosomes during mitosis and meiosis. Using extended chromatin fibers, we revealed patterns of loading CENH3proteinsinto polynucleosomal domains in centromeric chromatin. Our results indicate no sign of neofunctionalization, subfunctionalization or specialization in the gene copies. The influence of negative selection on the coding part of the genes led them to preserve their conserved function. The advantage of having two functional genes appears as the gene-dosage effect.

Natural Occurrence of Alternaria Fungi and Associated Mycotoxins in Small-Grain Cereals from The Urals and West Siberia Regions of Russia

Alternaria fungi dominate the grain microbiota in many regions of the world; therefore, the detection of species that are able to produce mycotoxins has received much attention. A total of 178 grain samples of wheat, barley and oat obtained from the Urals and West Siberia regions of Russia in 2017–2019 were included in the study. Grain contamination with Alternaria fungi belonging to sections Alternaria and Infectoriae was analysed using qPCR with specific primers. The occurrence of four mycotoxins produced by Alternaria, AOH, AME, TEN, and TeA, was defined by HPLC-MS/MS. Alternaria DNA was found in all analysed grain samples. The prevalence of DNA of Alternaria sect. Alternaria fungi (range 53 × 10−4–21,731 × 10−4 pg/ng) over the DNA of Alternaria sect. Infectoriae (range 11 × 10−4‒4237 × 10−4 pg/ng) in the grain samples was revealed. Sixty-two percent of grain samples were contaminated by at least two Alternaria mycotoxins. The combination of TEN and TeA was found most often. Eight percent of grain samples were contaminated by all four mycotoxins, and only 3% of samples were free from the analysed secondary toxic metabolites. The amounts varied in a range of 2–53 µg/kg for AOH, 3–56 µg/kg for AME, 3–131 µg/kg for TEN and 9–15,000 µg/kg for TeA. To our knowledge, a new global maximum level of natural contamination of wheat grain with TeA was detected. A positive correlation between the amount of DNA from Alternaria sect. Alternaria and TeA was observed. The significant effects of cereal species and geographic origin of samples on the amounts of DNA and mycotoxins of Alternaria spp. in grain were revealed. Barley was the most heavily contaminated with fungi belonging to both sections. The content of AOH in oat grain was, on average, higher than that found in wheat and barley. The content of TEN in the grain of barley was lower than that in wheat and similar to that in oat. The content of TeA did not depend on the cereal crop. The effect of weather conditions (summer temperature and rainfall) on the final fungal and mycotoxin contamination of grain was discussed. The frequent co-occurrence of different Alternaria fungi and their mycotoxins in grain indicates the need for further studies investigating this issue.

Effectiveness of herbicides against annual weeds (weed vegetation) on tomatoes

Agrocenoses of cultivated plants are more or less overgrown with unwanted weeds, which complicate and complicate the care of plants and harvesting. The purpose of our research was to assess the impact of modern herbicides on the infestation (clogging) of tomato seedlings with annual weeds and the productivity of cultivated plants in the natural and climatic conditions of the Republic of Kalmykia. It was revealed that the main weeds of tomato plantings for all the years of research from annual dicotyledonous species were-white mar, bindweed buckwheat, bird mountaineer, southern salt grass; less common - bedstraw tenacious, nightshade black, hibiscus triplet and others. Annual cereal species were more often represented by common oatmeal, blue and green bristles, and less often by barn grass. The introduction of herbicides Unimark, WDG and Lapis Lazuli, LP (loose powder) before planting seedlings did not have a negative effect on the survival rate of seedlings; it was 94-96% of the planned density of standing plants. It was found (established) that the use of herbicides in the planting of tomato seedlings restrained the increase in the number of annual grass weeds by 30-75%, annual dicotyledonous-by 70-90%. The introduction of preparations before planting seedlings was the most effective. The decrease in the number of annual weeds had a positive effect on the growth, development and productivity of tomato plants: there was an increase in the number of leaves by 10.4-16.5%, the mass of leaves (leaf weight) – by 11.8-21.2%, the area of the leaf surface – by 8.9-16.2%, the number of set fruits – by 18.9-23.8%, the average weight (mass) of a mature fruit – by 7.5-11.3%. The increase in the yield (the yield gain) of tomato fruits was in the range from 21.6 to 28.4%. The studied herbicides did not have a significant effect on the quality indicators of tomato fruits.

The ways of improving and stabilization the productivity of pasture reclamation and forage plantations in the agricultural landscapes of the Lower Volga region

The goal of the research is the development of effective methods of stabilization and determining ways to increase productive productivity in natural and designed agrocenosis. It is necessary to choose the promising composition of the pasture reclamation and forage plantations, taking into account their seasonality and the optimal seizures of the seizure of phytomass. The objects of research chosen pasture phytocenoses of the Astrakhan Volga region, the northern part of the Harabali district, the Burley plot (47° 33' N.; 47° 16' E), and vegetative sites of the hydrological complex of the Federal research center of agroecology of the Russian Academy of Sciences, Volgograd (48 ° 65' N., 44 ° 44' E.). Ecological and biological features of the dominant forage shrubs of Eurotia Ceratoides L. and Kochia Prostrata L. Schrad, Artemisia Lercheana Web., and the herbs of the Poaceae family studied according to generally accepted techniques. As a result of research, it was found that in the vegetative sites with a black soil soil substrate, the best conditions for the growth and development of herbage with the average productivity of the green mass of 1.1 t / ha for vegetation are formed, where more than 70% of the phytomass shape Poaceae. The smallest average productivity is marked on the light-chestnut soup substrate "Spring-Summer" pasture – 0.73 t / ha. Conclusion. The use of pastures is different, so the composition of agrocenoses must be chosen based on the season of operation, optimizing the load on the pasture. At the moment, the maximum adapted composition of the pasture reclamation and forage plantations, promising to create multi-tiered communities. The presented assortment serves as a stable source of additional and stable animal feed on the pasture, while at the same time rendering a positive phytomeliorative effect. The design of pasture agrocenoses allows to achieve productivity of at least 0.73 t / ha. In the structure of their phytomass, cereal species dominate, and shrubs and semi-stares perform a stabilizing role, contributing to the acceleration of the processes for the restoration of degraded pasture phytocenoses.

Impact of lead on the amount of chlorophyll and carotenoids in the leaves of Triticum durum and T. aestivum, Hordeum vulgare and Avena sativa

Lead is one of the most dangerous pollutants to both the environment and humans. It causes structural changes in photosynthetic apparatus and reduced biosynthesis of chlorophyll pigments inhibits carbon metabolism. The aim of our study was to determine the dynamics of photosynthetic pigments in leaves of wheat (Triticum durum and T. aestivum), barley (Hordeum vulgare) and oats (Avena sativa) at different lead acetate, Pb(CH3COO)2 levels: 0, 0.15, 0.30 and 0.60 g/L. The results of this research indicate that these concentrations significantly affected chlorophyll content of H. vulgare and A. sativa as compared to T. durum and T. aestivum. Analysis of variance showed that lead concentration and interaction between cereal species had a significant effect on all chlorophyll characteristics at 0.1% probability and on carotenoids contents at 1% significance. Lead acetate in 0.3 and 0.6 g/L concentrations had a highly significant effect on chlorophyll a, b and carotenoids in H. vulgare seedlings, its carotenoid contents increased from 0.002 mg/g FW at 0 g/L to 0.107 mg/g FW at 0.6 g/L, whereas its chlorophyll content decreased under heavy metal stress, corresponding to the concentration of the metal ion. Carotenoids of A. sativa were not affected compared to Chl a and Chl b, while higher concentrations significantly increased chlorophyll contents of the seedlings from 1.384 mg/g FW of total chlorophyll at 0 g/L to 1.883 mg/g FW at 0.6 g/L. The increased amount of carotenoids was indicative of the formation of free radicals in plants under heavy metal stress, while decreased levels of chlorophyll content were an indication of reduction in the growth of the plants leading to decrease in the yield. It is suggested that chlorophyll content can be adopted as a very useful in vivo indicator of heavy metal toxicity.