The development of next-generation sequencing technologies has provided new opportunities for genotyping various organisms, including plants. Genotyping by sequencing (GBS) is used to identify ...genetic variability more rapidly, and is more cost-effective than whole-genome sequencing. GBS has demonstrated its reliability and flexibility for a number of plant species and populations. It has been applied to genetic mapping, molecular marker discovery, genomic selection, genetic diversity studies, variety identification, conservation biology and evolutionary studies. However, reduction in sequencing time and cost has led to the need to develop efficient bioinformatics analyses for an ever-expanding amount of sequenced data. Bioinformatics pipelines for GBS data analysis serve the purpose. Due to the similarity of data processing steps, existing pipelines are mainly characterised by a combination of software packages specifically selected either to process data for certain organisms or to process data from any organisms. However, despite the usage of efficient software packages, these pipelines have some disadvantages. For example, there is a lack of process automation (in some pipelines, each step must be started manually), which significantly reduces the performance of the analysis. In the majority of pipelines, there is no possibility of automatic installation of all necessary software packages; for most of them, it is also impossible to switch off unnecessary or completed steps. In the present work, we have developed a GBS-DP bioinformatics pipeline for GBS data analysis. The pipeline can be applied for various species. The pipeline is implemented using the Snakemake workflow engine. This implementation allows fully automating the process of calculation and installation of the necessary software packages. Our pipeline is able to perform analysis of large datasets (more than 400 samples).
Genomic selection is a technology that allows for the determination of the genetic value of varieties of agricultural plants and animal breeds, based on information about genotypes and phenotypes. ...The measured breeding value (BV) for varieties and breeds in relation to the target trait allows breeding stages to be thoroughly planned and the parent forms suitable for crossing to be chosen. In this work, the BLUP method was used to assess the breeding value of 149 Russian varieties and introgression lines (4 measurements for each variety or line, 596 phenotypic points) of spring wheat according to the content of seven chemical elements in the grain – K, Ca, Mg, Mn, Fe, Zn, Cu. The quality of the evaluation of breeding values was assessed using cross-validation, when the sample was randomly divided into five parts, one of which was chosen as a test population. The following average values of the Pearson correlation were obtained for predicting the concentration of trace elements: K – 0.67, Ca – 0.61, Mg – 0.4, Mn – 0.5, Fe – 0.38, Zn – 0.46, Cu – 0.48. Out of the 35 models studied, the p-value was below the nominal significant threshold (p-value < 0.05) for 28 models. For 11 models, the p-value was significant after correction for multiple testing (p-value < 0.001). For Ca and K, four out of five models and for Mn two out of five models had a p-value below the threshold adjusted for multiple testing. For 30 varieties that showed the best varietal values for Ca, K and Mn, the average breeding value was 296.43, 785.11 and 4.87 mg/kg higher, respectively, than the average breeding value of the population. The results obtained show the relevance of the application of genomic selection models even in such limited-size samples. The models for K, Ca and Mn are suitable for assessing the breeding value of Russian wheat varieties based on these characteristics.
Infections, Pandemics, and Sleep Disorders Kolokolov, O. V.; Salina, E. A.; Yudina, V. V. ...
Neuroscience and behavioral physiology,
2022/3, Letnik:
52, Številka:
3
Journal Article
Recenzirano
Odprti dostop
Studies of the neurological symptoms and signs associated with the acute and late phases of infectious diseases are important in pandemic conditions. The novel coronavirus infection (COVID-19) ...pandemic has increased the number of patients with sleeplessness, this being an adverse prognostic factor for infections. This review addresses the factors and mechanisms of sleep impairments and their relationship with inflammation and immune system dysfunction in infectious diseases. In particular, impairments to the functioning of the melatoninergic system are discussed as the cause of sleeplessness during pandemics. The relevance of developing measures for rehabilitating patients, particularly use of Sonnovan to restore normal sleep, which plays a fundamental role in supporting people’s mental and physical health, is emphasized.
Stem rust in recent years has acquired an epiphytotic character, causing significant economic damage for wheat production in some parts of Western Siberia. On the basis of a race composition study of ...the stem rust populations collected in 2016-2017 in Omsk region and Altai Krai, 13 pathotypes in Omsk population and 10 in Altai population were identified. The race differentiation of stem rust using a tester set of 20 North American Sr genes differentiator lines was carried out. The genes of stem rust pathotypes of the Omsk population are avirulent only to the resistance gene Sr31, Altai isolates are avirulent not only to Sr31, but also to Sr24, and Sr30. A low frequency of virulence (10-25 %) of the Omsk population pathotypes was found for Sr11, Sr24, Sr30, and for Altai population - Sr7b, Sr9b, Sr11, SrTmp, which are ineffective in Omsk region. Field evaluations of resistance to stem rust were made in 2016-2018 in Omsk region in the varieties and spring wheat lines from three different sources. The first set included 58 lines and spring bread wheat varieties with identified Sr genes - the so-called trap nursery (ISRTN - International Stem Rust Trap Nursery). The second set included spring wheat lines from the Arsenal collection, that were previously selected according to a complex of economically valuable traits, with genes for resistance to stem rust, including genes introgressed into the common wheat genome from wild cereal species. The third set included spring bread wheat varieties created in the Omsk State Agrarian University within the framework of a shuttle breeding program, with a synthetic wheat with the Ae. tauschii genome in their pedigrees. It was established that the resistance genes Sr31, Sr40, Sr2 complex are effective against stem rust in the conditions of Western Siberia. The following sources with effective Sr genes were selected: (Benno)/6*LMPG-6 DK42, Seri 82, Cham 10, Bacanora (Sr31), RL 6087 Dyck (Sr40), Amigo (Sr24, 1RS-Am), Siouxland (Sr24, Sr31), Roughrider (Sr6, Sr36), Sisson (Sr6, Sr31, Sr36), and Fleming (Sr6, Sr24, Sr36, 1RS-Am), Pavon 76 (Sr2 complex) from the ISRTN nursery; No. 1 BC1F2 (96 × 113) × 145 × 113 (Sr2, Sr36, Sr44), No. 14а F3 (96 × 113) × 145 (Sr36, Sr44), No. 19 BC2F3 (96 × 113) × 113 (Sr2, Sr36, Sr44), and No. 20 F3 (96 × 113) × 145 (Sr2, Sr36, Sr40, Sr44) from the Arsenal collection; and the Omsk State Agrarian University varieties Element 22 (Sr31, Sr35), Lutescens 27-12, Lutescens 87-12 (Sr23, Sr36), Lutescens 70-13, and Lutescens 87-13 (Sr23, Sr31, Sr36). These sources are recommended for inclusion in the breeding process for developing stem rust resistant varieties in the region.
Crop pangenomes Pronozin, A. Yu; Bragina, M. K.; Salina, E. A.
Vavilovskiĭ zhurnal genetiki i selekt͡s︡ii,
02/2021, Letnik:
25, Številka:
1
Journal Article
Recenzirano
Odprti dostop
Progress in genome sequencing, assembly and analysis allows for a deeper study of agricultural plants’ chromosome structures, gene identif ication and annotation. The published genomes of ...agricultural plants proved to be a valuable tool for studing gene functions and for marker-assisted and genomic selection. However, large structural genome changes, including gene copy number variations (CNVs) and gene presence/absence variations (PAVs), prevail in crops. These genomic variations play an important role in the functional set of genes and the gene composition in individuals of the same species and provide the genetic determination of the agronomically important crops properties. A high degree of genomic variation observed indicates that single reference genomes do not represent the diversity within a species, leading to the pangenome concept. The pangenome represents information about all genes in a taxon: those that are common to all taxon members and those that are variable and are partially or completely specif ic for particular individuals. Pangenome sequencing and analysis technologies provide a large-scale study of genomic variation and resources for an evolutionary research, functional genomics and crop breeding. This review provides an analysis of agricultural plants’ pangenome studies. Pangenome structural features, methods and programs for bioinformatic analysis of pangenomic data are described.
Soybean, Glycine max L., is one of the most important agricultural crops grown in a wide range of latitude. In this regard, in soybean breeding, it is necessary to pay attention to the set of genes ...that control the transition to the f lowering stage, which will make it possible to adapt genotypes to local growing conditions as accurately as possible. The possibilities of soybean breeding for this trait have now signif icantly expanded due to identif ication of the main genes (E1-E4, GmFT2a, GmFT5a) that control the processes of f lowering and maturation in soybean, depending on the day length. The aim of this work was to develop a panel of markers for these genes, which could be used for a rapid and eff icient genotyping of domestic soybean cultivars and selection of plant material based on sensitivity to photoperiod and the duration of vegetation. Combinations of 10 primers, both previously developed and our own, were tested to identify different alleles of the E1-E4, GmFT2a, and GmFT5a genes using 10 soybean cultivars from different maturity groups. As a result, 5 combinations of dominant and recessive alleles for the E1-E4 genes were identif ied: (1) e1-nl(e1-as)/ e2-ns/e3-tr(e3-fs)/e4; (2) e1-as/e2-ns/e3-tr/E4; (3) e1-as/e2-ns/E3-Ha/e4; (4) E1/e2-ns/e3-tr/E4; (5) e1-nl/e2-ns/E3-Ha/E4. The studied cultivars contained the most common alleles of the GmFT2a and GmFT5a genes, with the exception of the 'Cassidi' cultivar having a rare dominant allele GmFT5a-H4. The degree of earliness of cultivars positively correlated with the number of recessive genes E1-E4, which is consistent with the data of foreign authors on different sets of cultivars from Japan and North China. Thus, the developed panel of markers can be successfully used in the selection of soybean for earliness and sensitivity to photoperiod.
s
We conducted a molecular analysis of the
Vrn
-
B1
gene in two near-isogenic lines (NILs) carrying the dominant
Vrn
-
B1
S
and
Vrn
-
B1
Dm
alleles from the Saratovskaya 29 and Diamant 2 cultivars, ...respectively. These lines are characterized by different times of ear emergence. PCR analysis and subsequent sequencing of the regulatory regions of
Vrn
-
B1
revealed the full identity of the promoter region in both alleles. Simultaneously, we found significant differences in the structure of the first intron of the
Vrn
-
B1
S
allele when compared to
Vrn
-
B1
Dm
; specifically, the deletion of 0.8 kb coupled with the duplication of 0.4 kb. We suggest that these changes in intron 1 of
Vrn
-
B1
S
caused earlier ear emergence in the corresponding NIL. The unusual structure of intron 1 within the
Vrn
-
B1
S
allele was described for the first time in this study. The allele
Vrn
-
B1
Dm
was almost identical with the previously studied sequence of the
Vrn
-
B1a
allele of
T. aestivum,
Triple Dirk B. We designated the new
Vrn
-
B1
S
allele as
Vrn
-
B1c.
PCR analysis of the
Vrn
-
B1
gene in 26 spring wheat cultivars of both Russian and foreign breeding revealed that 16 of them contain the
Vrn
-
B1a
allele and 6 contain the
Vrn
-
B1c
allele
.
Other cultivars studied contained the recessive
vrn
-
B1
gene
,
except for Novosibirskaya 67. This study demonstrates that the traditional system of
Vrn
-
1
markers does not fully encompass the allelic diversity of these genes because none of the cultivars containing the
Vrn
-
B1c
allele gave a PCR product using the previously developed set of primers for identification of the
Vrn
-
B1
locus. We showed that the newly characterized
Vrn
-
B1c
allele is widely distributed among different genotypes of spring wheat. The findings indicate the impact of structural changes in the first intron of
Vrn
-
1
on the vernalization response and heading time.
Present-day wheat breeding for immunity exploits extensively closely related species from the family Triticeae as gene donors. The 2NS/2AS translocation has been introduced into the genome of the ...cultivated cereal Triticum aestivum from the wild relative T. ventricosum. It contains the Lr37, Yr17, and Sr38 genes, which support seedling resistance to the pathogens Puccinia triticina Eriks., P. striiformis West. f. sp. tritici, and P. graminis Pers. f. sp. tritici Eriks. & E. Henn, which cause brown, yellow, and stem rust of wheat, respectively. This translocation is present in the varieties Trident, Madsen, and Rendezvous grown worldwide and in the Russian varieties Morozko, Svarog, Graf, Marquis, and Homer bred in southern regions. However, the Sr38 gene has not yet been introduced into commercial varieties in West Siberia; thus, it remains of practical importance for breeding in areas where populations of P. graminis f. sp. tritici are represented by avirulent clones. The main goal of this work was to analyze the frequency of clones (a)virulent to the Sr38 gene in an extended West Siberian collection of stem rust agent isolates. In 2019-2020, 139 single pustule isolates of P. graminis f. sp. tritici were obtained on seedlings of the standard susceptible cultivar Khakasskaya in an environmentally controlled laboratory (Institute of Cytology and Genetics SB RAS) from samples of urediniospores collected on commercial and experimental bread wheat f ields in the Novosibirsk, Omsk, Altai, and Krasnoyarsk regions. By inoculating test wheat genotypes carrying Sr38 (VPM1 and Trident), variations in the purity of (a)virulent clones were detected in geographical samples of P. graminis f. sp. tritici. In general, clones avirulent to Sr38 constitute 60 % of the West Siberian fungus population, whereas not a single virulent isolate was detected in the Krasnoyarsk collection. The Russian breeding material was screened for sources of the stem rust resistance gene by using molecular markers specif ic to the 2NS/2AS translocation. A collection of hybrid lines and varieties of bread spring wheat adapted to West Siberia (Omsk SAU) was analyzed to identify accessions promising for the region. The presence of the gene was postulated by genotyping with specif ic primers (VENTRIUP-LN2) and phytopathological tests with avirulent clones of the fungus. Dominant Sr38 alleles were identif ied in Lutescens 12-18, Lutescens 81-17, Lutescens 66-16, Erythrospermum 79/07, 9-31, and 8-26. On the grounds of the composition of the West Siberian P. graminis f. sp. tritici population, the Sr38 gene can be considered a candidate for pyramiding genotypes promising for the Novosibirsk, Altai, and Krasnoyarsk regions.
Current studies on bread wheat resistance to stem rust have two main subjects: complex analysis for resistance of bread wheat germplasm using molecular markers, field screening and laboratory tests ...against samples of different fungal populations, and searching for sources and donors of new genes and gene loci, including cultivated and wild relatives of wheat. To achieve adequate genetic control of the disease, an integral approach is important, incorporating both data on sources of resistance and relevant information on pathogenic populations existing in the region, their race composition and dynamics of virulence genes. The analysis of experimental data on field screening of bread wheat varieties from the CIMMYT nursery germplasm for stem rust resistance in the Omsk and Novosibirsk regions, together with laboratory testing of infection samples on the international set of wheat differential lines, suggests that a separate "Asian" population of Puccinia graminis f. sp. tritici exists in Western Siberia and the Altai Territory. Wheat resistance genes Sr2, Sr6Ai#2, Sr24, Sr25, Sr26, Sr31, Sr39, Sr40, Sr44, and Sr57 are of practical interest for advanced wheat breeding programs for stem rust immunity in Western Siberia. This review provides an analysis of the gene sources that remain effective against the West Siberian population of P. graminis, in order to facilitate the initial stage of selection of breeding material to develop a stable genotype by gene pyramiding. The basic requirements for conducting a phytopathological test of breeding material are presented. A list of molecular markers for the mentioned resistance genes, both widely used in marker-assisted selection and requiring verification, has been compiled.
Backgr ound.
The basic approach to the production of new common wheat genotypes involving introgressive hybridization entails a long-term process. Doubled haploid production could accelerate it. ...However, this method is not widely used in breeding programs due to its main limitation: the genotype dependence. Due to genetic differences between wheat and related species, it was assumed that alien genetic materials are different in their capacity to affect androgenesis. The effect of alien translocations on androgenesis has been shown earlier. The aim of this study was to develop a set of DH wheat lines containing a wheat-alien translocation in the genome and study the effect of alien translocations on androgenesis of anther culture in such lines.
Materials and methods
. The plant material included: the spring wheat cultivar ‘Novosibirskaya 16’, line Velut 991 carrying wheat-alien translocations 1RS.1BL from rye and 5BS.5BL-5SL from Aegilops speltoides Tausch, and four hybrid F3 generation lines (10-7, 14-8, 15-8, 15-12) from their crossing, differing in the content of alien translocations.
Results.
It was shown that parameters of androgenesis such as the number of embryo-like structures per 100 anthers, the number of albino regenerants per 100 anthers, and the number of green regenerants per 100 anthers varied depending on the line. The best -responding lines Velut 991, 10-7 and 14-8 are characterized by the presence of a 1RS.1BL wheat-rye translocation chromosome. Regeneration frequency of green plants was recorded to be 8,6%, 3,6% and 10,1% respectively. The values of the parameters for lines 15-12 (carrying 5BS.5BL-5SL translocation) and 15-8 (without translocations) did not differ significantly.
Conclusion.
Therefore, it can be concluded that the presence of the introgressive fragment of chromosome 5S did not affect the efficiency of androgenesis and the short shoulder of chromosome 1R carries genes that stimulated androgenesis in anther culture.
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