Rim F Gubaev

Gubaev R., Boldyrev S., Martynova E., Chernova A., Kovalenko T., Chebanova Y., Peretyagina T., Goryunova S., Goryunov D., Mukhina Z., Ben C., Gentzbittel L., Khaitovich P., Demurin Y.

Oleic acid is a monounsaturated fatty acid increasing oil oxidative stability. High content of oleic acid is thus a valuable trait in oilseed crops. Sunflower (Helianthus annuus L.) normally accumulates linoleic acid as a major fatty acid, but a mutant expressing a high oleic phenotype form was previously obtained by chemical mutagenesis and mapped on the sunflower genome. Several studies suggest the presence of additional genes involved in the control of the high content of oleic acid, with their expression possibly depending on the genetic background. To test this hypothesis, we performed a QTL mapping of the high oleic acid trait within two independent F2 crosses involving lines with contrasting oleic acid content from the Pustovoit All-Russia Research Institute of Oil Crops (VNIIMK) collection. We applied genotyping-by-sequencing (GBS) to construct single nucleotide polymorphism-based genetic maps and performed QTL mapping using quantitative and qualitative encoding for oleic acid content. Our results support the finding that the oleic acid content in the assessed crosses is controlled by one major effect locus. However, different dominant/recessive effects of the major locus were reported for both crosses. Additionally, a possible translocation between chromosome 7 and 14 was reported in one assessed cross. We defined a set of single nucleotide polymorphism markers for each cross which could be used for marker-assisted selection.

Gubaev R., Boldyrev S., Martynova E., Chernova A., Kovalenko T., Chebanova Y., Peretyagina T., Goryunova S., Goryunov D., Mukhina Z., Ben C., Gentzbittel L., Khaitovich P., Demurin Y.

Abstract Oleic acid is a monounsaturated fatty acid increasing oil oxidative stability. High content of oleic acid is thus a valuable trait in oilseed crops. Sunflower (Helianthus annuus L.) normally accumulates linoleic acid as a major fatty acid, but a mutant expressing a high oleic phenotype form was previously obtained by chemical mutagenesis and mapped on the sunflower genome. Several studies suggest the presence of additional genes involved in the control of the high content of oleic acid, with their expression possibly depending on the genetic background. To test this hypothesis, we performed a QTL mapping of the high oleic acid trait within two independent F2 crosses involving lines with contrasting oleic acid content from the Pustovoit All-Russia Research Institute of Oil Crops (VNIIMK) collection. We applied genotyping-by-sequencing (GBS) to construct single nucleotide polymorphism-based genetic maps and performed QTL mapping using quantitative and qualitative encoding for oleic acid content. Our results support the finding that the oleic acid content in the assessed crosses is controlled by one major effect locus. However, different dominant/recessive effects of the major locus were reported for both crosses. Additionally, a possible translocation between chromosome 7 and 14 was reported in one assessed cross. We defined a set of single nucleotide polymorphism markers for each cross which could be used for marker-assisted selection.

Gubaev R., Boldyrev S., Martynova E., Chernova A., Kovalenko T., Peretyagina T., Goryunova S., Goryunov D., Mukhina Z., Ben C., Gentzbittel L., Khaitovich P., Demurin Y.

Abstract Tocopherols are antioxidants that preserve oil lipids against oxidation and serve as a natural source of vitamin E in the human diet. Compared with other major oilseeds like rapeseed and soybean, sunflower (Helianthus annuus L.) exhibits low phenotypic diversity of tocopherol composition, both in wild and cultivated accessions from germplasm collections. Two major mutations that alter tocopherol composition were identified in genetic collections, and several studies suggested additional loci controlling tocopherol composition, with their expression possibly depending on the genetic background. In the present study, we performed QTL mapping of tocopherol composition in two independent F2 crosses between lines with contrasting tocopherol composition from the Pustovoit All-Russia Research Institute of Oil Crops (VNIIMK) collection. We used genotyping-bysequencing (GBS) to construct single nucleotide polymorphism-based genetic maps, and performed QTL mapping using quantitative and qualitative encoding for phenotypic traits. Our results support the notion that the tocopherol composition in the assessed crosses is controlled by two loci. We additionally selected and validated two single nucleotide polymorphism markers for each cross which could be used for marker-assisted selection.

Chernova A.I., Gubaev R.F., Singh A., Sherbina K., Goryunova S.V., Martynova E.U., Goryunov D.V., Boldyrev S.V., Vanyushkina A.A., Anikanov N.A., Stekolshchikova E.A., Yushina E.A., Demurin Y.N., Mukhina Z.M., Gavrilova V.A., et. al.

Abstract Background Sunflower is an important oilseed crop domesticated in North America approximately 4000 years ago. During the last century, oil content in sunflower was under strong selection. Further improvement of oil properties achieved by modulating its fatty acid composition is one of the main directions in modern oilseed crop breeding. Results We searched for the genetic basis of fatty acid content variation by genotyping 601 inbred sunflower lines and assessing their lipid and fatty acid composition. Our genome-wide association analysis based on the genotypes for 15,483 SNPs and the concentrations of 23 fatty acids, including minor fatty acids, revealed significant genetic associations for eleven of them. Identified genomic regions included the loci involved in rare fatty acids variation on chromosomes 3 and 14, explaining up to 34.5% of the total variation of docosanoic acid (22:0) in sunflower oil. Conclusions This is the first large scale implementation of high-throughput lipidomic profiling to sunflower germplasm characterization. This study contributes to the genetic characterization of Russian sunflower collections, which made a substantial contribution to the development of sunflower as the oilseed crop worldwide, and provides new insights into the genetic control of oil composition that can be implemented in future studies.

Gubaev R., Gorlova L., Boldyrev S., Goryunova S., Goryunov D., Mazin P., Chernova A., Martynova E., Demurin Y., Khaitovich P.

Rapeseed is the second most common oilseed crop worldwide. While the start of rapeseed breeding in Russia dates back to the middle of the 20th century, its widespread cultivation began only recently. In contrast to the world’s rapeseed genetic variation, the genetic composition of Russian rapeseed lines remained unexplored. We have addressed this question by performing genome-wide genotyping of 90 advanced rapeseed accessions provided by the All-Russian Research Institute of Oil Crops (VNIIMK). Genome-wide genetic analysis demonstrated a clear difference between Russian rapeseed varieties and the rapeseed varieties from the rest of the world, including the European ones, indicating that rapeseed breeding in Russia proceeded in its own independent direction. Hence, genetic determinants of agronomical traits might also be different in Russian rapeseed lines. To assess it, we collected the glucosinolate content data for the same 90 genotyped accessions obtained during three years and performed an association mapping of this trait. We indeed found that the loci significantly associated with glucosinolate content variation in the Russian rapeseed collection differ from those previously reported for the non-Russian rapeseed lines.

Goryunov D., Anisimova I., Gavrilova V., Chernova A., Sotnikova E., Martynova E., Boldyrev S., Ayupova A., Gubaev R., Mazin P., Gurchenko E., Shumskiy A., Petrova D., Garkusha S., Mukhina Z., et. al.

The phenomenon of cytoplasmic male sterility (CMS), consisting in the inability to produce functional pollen due to mutations in mitochondrial genome, has been described in more than 150 plant species. With the discovery of nuclear fertility restorer (Rf) genes capable of suppressing the CMS phenotype, it became possible to use the CMS-Rf genetic systems as the basis for practical utilization of heterosis effect in various crops. Seed production of sunflower hybrids all over the world is based on the extensive use of the PET1 CMS combined with the Rf1 gene. At the same time, data on Rf1 localization, sequence, and molecular basis for the CMS PET1 type restoration of fertility remain unknown. Searching for candidate genes of the Rf1 gene has great fundamental and practical value. Therefore, in this study, association mapping of fertility restorer gene for CMS PET1 in sunflower was performed. The genome-wide association study (GWAS) results made it possible to isolate a segment 7.72 Mb in length on chromosome 13, in which 21 candidates for Rf1 fertility restorer gene were identified, including 20 pentatricopeptide repeat (PPR)family genes and one Probable aldehyde dehydrogenase gene. The results will serve as a basis for further study of the genetic nature and molecular mechanisms of pollen fertility restoration in sunflower, as well as for further intensification of sunflower breeding.

Chernova A., Gubaev R., Mazin P., Goryunova S., Demurin Y., Gorlova L., Vanushkina A., Mair W., Anikanov N., Martynova E., Goryunov D., Garkusha S., Mukhina Z., Khaytovich P.

Sunflower and rapeseed are among the most important sources of vegetable oil for food and industry. The main components of vegetable oil are triglycerides (TAGs) (about 97%). Ultra- performance liquid chromatography coupled with mass spectrometry (UPLC–MS) profiling of TAGs in sunflower and rapeseed has been performed and the TAG profiles obtained for these species have been compared. It has been identified that 34 TAGs are shared by sunflower and rapeseed. It was demonstrated that TAGs 52:2, 52:5, 52:6, 54:3; 54:4, 54:7, 56:3, 56:4, and 56:5 had the highest variability levels between sunflower and rapeseed with the higher presence in rapeseed. TAGs 50:2, 52:3, 52:4, 54:5, and 54:6 also showed high variability, but were the most abundant in sunflower. Moreover, the differences in TAG composition between the winter-type and spring-type rapeseed have been revealed, which may be associated with freezing tolerance. It was shown that winter-type rapeseed seeds contain TAGs with a lower degree of saturation, while in spring-type rapeseed highly saturated lipids are the most abundant. These findings may give new insights into the cold resistance mechanisms in plants the understanding of which is especially important in terms of global climate changes.

Губаев Р.Ф., Горшков В.Ю., Гапа Л.М., Гоголева Н.Е., Ветчинкина Е.П., Гоголев Ю.В.

Gubaev R.F., Gorshkov V.Y., Gapa L.M., Gogoleva N.E., Vetchinkina E.P., Gogolev Y.V.

Modern techniques of next-generation sequencing (NGS) allow obtaining expression profile of all genes and provide an essential basis for characterizing metabolism in the organism of interest on a broad scale. An important condition for obtaining a demonstrative physiological picture using high throughput sequencing data is the availability of the genome sequence and its sufficient annotation for the target organism. However, a list of species with properly annotated genomes is limited. Transcriptome profiling is often performed in the so-called non-model organisms, which are those with unknown or poorly assembled and/or annotated genome sequences. The transcriptomes of non-model organisms are possible to investigate using algorithms of de novo assembly of the transcripts from sequences obtained as the result of RNA sequencing. A physiological interpretation of the data is difficult in this case because of the absence of annotation of the assembled transcripts and their classification by metabolic pathway and functional category. An algorithm for transcriptome profiling in non-model organisms was developed, and a transcriptome analysis was performed for the basidiomycete Lentinus edodes. The algorithm includes open access software and custom scripts and encompasses a complete analysis pipeline from the selection of cDNA reads to the functional classification of differentially expressed genes and the visualization of the results. Based on this algorithm, a comparative transcriptome analysis of the nonpigmented mycelium and brown mycelial mat was performed in L. edodes. The comparison revealed physiological differences between the two morphogenetic stages, including an induction of cell wall biogenesis, intercellular communication, ion transport, and melanization in the brown mycelial mat.

Gorshkov V., Gubaev R., Petrova O., Daminova A., Gogoleva N., Ageeva M., Parfirova O., Prokchorchik M., Nikolaichik Y., Gogolev Y.

In the present study, we have monitored the process of systemic plant colonization by the plant pathogenic bacterium Pectobacterium atrosepticum (Pba) using RNA-Seq analysis in order to compare bacterial traits under in planta and in vitro conditions and to reveal potential players that participate in switching from stealth to brute force strategy of the pathogen. Two stages of tobacco plant colonization have been assayed: i) the initial one associated with visually symptomless spread of bacteria throughout the host body via primary xylem vessels where bacterial emboli were formed (stealth strategy), and ii) the advanced stage coupled with an extensive colonization of core parenchyma and manifestation of soft rot symptoms (brute force strategy). Plant-inducible genes in Pba and potential players switching the pathogen’s behavior were revealed. Genes from the cfa locus responsible for the production of coronafacic acid displayed the strongest induction in the asymptomatic zone relative to the symptomatic one and were shown experimentally to act as the true strategy “switchers” of Pba behavior in planta. Surprisingly, cfa genes appeared to be unnecessary for establishment of the asymptomatic stage of plant colonization but were required for the transition to soft-rot-associated symptomatic stage coupled with over-induction of jasmonate-mediated pathway in the plant.

Gavrilova V.A., Anisimova I.N., Alpatieva N.V., Porokhovinova E.A.

Background. The XRQ sunflower genome has been sequenced but not yet fully annotated, and not all candidate genes for most traits have been identified. Disclosing the relationships among traits in this study will help to understand the genetic control over phenotypic characters.Materials and methods. A set of 237 sunflower lines from VIR’s genetic collection was phenotyped for their morphological characters (plant height; branching type; shapes and sizes of the leaf, petiole, flower head, disk and ray florets; downy mildew damage rate) and genotyped with molecular markers. DNA markers were used to identify accessions carrying the Rf gene and CMS. Factor analysis was applied to structure the genetic collection.Results and discussion. The data of 2017 and 2018 were compared using the analysis of variance. The results of the latter testified to the heritability of morphological characters, as well as to the alignment and purity of lines from VIR’s genetic collection of sunflower. New data were obtained on the phenotypic diversity of sunflower and stability of its agronomic traits across the growing seasons.Conclusion. Groups of interacting characters were identified by the factor analysis: 1) plant height, and duration of the growing season phases; 2) pollen fertility restoration with CMS PET1, SCAR markers HRG02 and HRG01 of the Rf1 gene, and branching; 3) the color of ray and disk florets, and petiole shape, as well as lamina surface shape. Lines with CMS PET1 were classified into three groups differing in the systems (possibly genes) of pollen fertility restoration. The factor analysis made it possible to confirm the assumption that several Rf genes whose manifestation differed from the Rf1 gene were present in the studied sunflower lines from VIR’s genetic collection.

Schwarz A.N., Züllig T., Schicher M., Wagner F.S., Rechberger G.N.

Kefale H., You J., Zhang Y., Getahun S., Berhe M., Abbas A.A., Ojiewo C.O., Wang L.

AbstractThe multidimensional significance of metabolomics has gained increasing attention in oilseeds research and development. Sesame, peanut, soybean, sunflower, rapeseed, and perilla are the most important oilseed crops consumed as vegetable oils worldwide. However, multiple biotic and abiotic stressors affect metabolites essential for plant growth, development, and ecological adaptation, resulting in reduced productivity and quality. Stressors can result in dynamic changes in oilseed crops' overall performance, leading to changes in primary (ex: saccharides, lipids, organic acids, amino acids, vitamins, phytohormones, and nucleotides) and secondary (ex: flavonoids, alkaloids, phenolic acids, terpenoids, coumarins, and lignans) major metabolite classes. Those metabolites indicate plant physiological conditions and adaptation strategies to diverse biotic and abiotic stressors. Advancements in targeted and untargeted detection and quantification approaches and technologies aided metabolomics and crop improvement. This review seeks to clarify the metabolomics advancements, significant contributions of metabolites, and specific metabolites that accumulate in reaction to various stressors in oilseed crops. Considering the response of metabolites to multiple stress effects, we compiled comprehensive and combined metabolic biosynthesis pathways for six major classes. Understanding these essential metabolites and pathways can inform molecular breeding strategies to develop resilient oilseed cultivars. Hence, this review highlights metabolomics advancements and metabolites' potential roles in major oilseed crops' biotic and abiotic stress responses.

Kergaravat B., Kielbasa M., Chabrière É., Armengaud J., Plener L., Daudé D.

Parfirova O., Mikshina P., Petrova O., Smolobochkin A., Pashagin A., Burilov A., Gorshkov V.

Many phytopathogens’ gene products that contribute to plant–pathogen interactions remain unexplored. In one of the most harmful phytopathogenic bacterium Pectobacterium atrosepticum (Pba), phosphonate-related genes have been previously shown to be among the most upregulated following host plant colonization. However, phosphonates, compounds characterized by a carbon–phosphorus bond in their composition, have not been described in Pectobacterium species and other phytopathogenic bacteria, with the exception of Pseudomonas syringae and Pantoea ananatis. Our study aimed to determine whether Pba synthesizes extracellular phosphonates and, if so, to analyze their physiological functions. We demonstrated that Pba produces two types of extracellular phosphonates: 2-diethoxyphosphorylethanamine and phenylphosphonic acid. Notably, such structures have not been previously described among natural phosphonates. The production of Pba phosphonates was shown to be positively regulated by quorum sensing and in the presence of pectic compounds. Pba phosphonates were found to have a positive effect on Pba stress resistance and a negative effect on Pba virulence. The discovered Pba phosphonates are discussed as metabolites that enable Pba to control its “harmful properties”, thereby maintaining its ecological niche (the host plant) in a relatively functional state for an extended period.

A. Anjum N., Masood A., Umar S., A. Khan N.

A. Anjum N., Masood A., Rasheed F., Thangavel P., Umar S., A. Khan N.

Carbohydrates, lipids (mostly fats and oils), proteins, vitamins, minerals, and water are the six main classes of nutrients found in foods. After carbohydrates, oils are important source of major calories required in the human diet. Oils act as a vehicle for some of the important vitamins and possess a range of nutrients and bio-active compounds. These edible oil-yielding plants can be categorized into non-woody (herbaceous) and woody (non-herbaceous) oil-bearing plants. This chapter mainly focuses on important herbaceous edible oilseed (crop)plants such as pea(ground)nut (Arachis hypogaea L.), Indian mustard (Brassica juncea L. Czern. and Coss.), rapeseed (Brassica campestris L.) (syn. B. rapa), soybean (Glycine max L.), flaxseed (Linum usitatissimum L.), sunflower (Helianthus annuus L.), sesame (Sesamum indicum L.), safflower (Carthamus tinctorius L.), and niger (Guizotia abyssinica L.). It aims to (a) overview the key insights into the origin, botany and benefits of the mentioned herbaceous edible oilseed (crop)plants; (b) highlight the major constraints for their growth and productivity (quantitative-qualitative); (c) enlighten important mitigation-approaches for minimizing the constraints-accrued impacts; (d) briefly overview the major aims and achievements of important breeding programmes focused on these oilseed-bearing (crops)plants; and also to (e) briefly present important aspects least explored on the subject.

Delen Y., Mural R.V., Palali‐Delen S., Xu G., Schnable J.C., Dweikat I., Yang J.

AbstractSunflower (Helianthus annuus L.) plays an essential role in meeting the demand for edible oil worldwide. The yield of sunflower seeds encompasses several component traits, including the disc diameter. Over three consecutive years, 2019, 2020, and 2022, we assessed phenotypic variation in disc diameter across a diverse set of sunflower accessions (N = 342) in replicated field trials. Upon aggregating the phenotypic data from multiple years, we estimated the broad sense heritability (H2) of the disc diameter trait to be 0.88. A subset of N = 274 accessions was genotyped by using the tunable genotyping‐by‐sequencing (tGBS) method, resulting in 226,779 high‐quality SNPs. Using these SNPs and the disc diameter phenotype, we conducted a genome‐wide association study (GWAS) employing two statistical approaches: the mixed linear model (MLM) and the fixed and random model circulating probability unification (farmCPU). The MLM and farmCPU GWAS approaches identified 106 and 8 significant SNPs located close to 53 and 21 genes, respectively. The MLM analysis identified two significant peaks: a prominent signal on chromosome 10 and a relatively weaker signal on chromosome 16, both of which were also detected by farmCPU. The genetic loci associated with disc diameter, as well as the related candidate genes, present promising avenues for further functional validation and serve as a basis for sunflower oil yield improvement.

Nawaz M.A., Pamirsky I.E., Golokhvast K.S.

Abstract Bioinformatics has become an interdisciplinary subject due to its universal role in molecular biology research. The current status of Russia’s bioinformatics research in Russia is not known. Here, we review the history of bioinformatics in Russia, present the current landscape, and highlight future directions and challenges. Bioinformatics research in Russia is driven by four major industries: information technology, pharmaceuticals, biotechnology, and agriculture. Over the past three decades, despite a delayed start, the field has gained momentum, especially in protein and nucleic acid research. Dedicated and shared centers for genomics, proteomics, and bioinformatics are active in different regions of Russia. Present-day bioinformatics in Russia is characterized by research issues related to genetics, metagenomics, OMICs, medical informatics, computational biology, environmental informatics, and structural bioinformatics. Notable developments are in the fields of software (tools, algorithms, and pipelines), use of high computation power (e.g. by the Siberian Supercomputer Center), and large-scale sequencing projects (the sequencing of 100 000 human genomes). Government funding is increasing, policies are being changed, and a National Genomic Information Database is being established. An increased focus on eukaryotic genome sequencing, the development of a common place for developers and researchers to share tools and data, and the use of biological modeling, machine learning, and biostatistics are key areas for future focus. Universities and research institutes have started to implement bioinformatics modules. A critical mass of bioinformaticians is essential to catch up with the global pace in the discipline.

Hashemi S.E., Nezhad N.M., Mohammadi-Nejad G., Ebrahimi F., Fakheri B.A.

Safflower oil with high oleic is an important source of oil due to its oxidative stability and nutritional value as well as its industrial benefits. Identification of molecular markers associated with oil quality traits may aid in genotype selection in breeding efforts of safflower. To determine the genetic basis of seed oil, oleic acid, and linoleic acid content in safflower seeds, a recombinant inbred population was developed from a cross between Goldasht (low oleic line) and Mex 22–191 (high oleic line) by individual self-pollinated plants in each generation (from F2 to F9). Fatty acid components were detected by gas chromatography and subsequently analyzed by QTL analysis. The high variability in fatty acid composition was demonstrated and the first high-oleic safflower genotype was generated. A new linkage map with 69 AFLP and 45 ISSR polymorphic markers was made, covering 1472,441 cM of the safflower genome. A total of 63 individual QTLs and 238 epistatic QTLs, related to oil quality, were detected in 14 genomic regions. Some major QTLs with phenotypic variation greater than 10% were identified for the measured traits. These results demonstrate that major QTL may play an important role in increase the oleic acid of the genetic material used. Furthermore, the larger number of minor QTLs and epistatic QTLs, both of which have additive effects, indicates that the expression of these traits is also influenced by interactions between multiple genes. Our results provide additional genetic resources that can be used to precisely breed these traits in the future.

Delen Y., Palali-Delen S., Xu G., Neji M., Yang J., Dweikat I.

The sunflower (Helianthus annuus L.) is one of the most essential oil crops in the world. Several component traits, including flowering time, plant height, stem diameter, seed weight, and kernel weight, determine sunflower seed and oil yield. Although the genetic mechanisms governing the variation of these yield-related traits have been studied using various approaches, genome-wide association studies (GWAS) have not been widely applied to sunflowers. In this study, a set of 342 sunflower accessions was evaluated in 2019 and 2020 using an incomplete randomized block design, and GWAS was conducted utilizing two complementary approaches: the mixed linear model (MLM) and the fixed and random model circulating probability unification (farmCPU) model by fitting 226,779 high-quality SNPs. As a result, GWAS identified a number of trait-associated SNPs. Those SNPs were located close to several genes that may serve as a basis for further molecular characterization and provide promising targets for sunflower yield improvement.

Kuznetsova G.N., Polyakova R.S.

The current study was carried out on the experimental fields of SES, a branch of VNIIMK in 2021–2023. The purpose was to estimate spring rape varieties and hybrids of various ecological and geographical origins based on the main economically valuable traits, to identify the most productive and adapted to the conditions of Western Siberia. The objects of the study were 16 varieties and hybrids of domestic and foreign breeding. The variety ‘Yubileiny’ and the hybrid ‘Ozorno’ were used as a standard. There was established that environmental testing of spring rape varieties and hybrids made it possible to identify significant differences in the main economically valuable traits. In the conditions of Western Siberia, among the rape varieties, the maximum productivity over three years of study was demonstrated by the varieties ‘Yarky’ (2.50 t/ha), ‘Sibiryak 60’ (2.43 t/ha) and ‘55region’ (2.42 t/ha), and among the hybrids ‘PR46X75’ (2.68 t/ha) and ‘Salsa KL’ (2.57 t/ha) were the best according to this indicator. The highest seed productivity was obtained in 2021 and ranged from 2.51 to 3.29 t/ha for varieties and from 3.02 to 3.52 t/ha for hybrids. High oil content in seeds was noted under the conditions of 2022 in such varieties as ‘Granit’, ‘55region’, ‘Yarkiy’, ‘Amulet’, ‘Geros’ and amounted to 51.2–52.6 %. With a short vegetation period of up to 85 days, the varieties ‘Amulet’, ‘Ruyan’, ‘Erebus’ and ‘Forpost KL’ were identified as early maturing varieties. Middle maturing varieties with a vegetation period of 88–90 days included ‘Granit’, ‘Yarkiy’, ‘Prometey’ and ‘Geros’. The plant height varied from 80 to 101 cm for hybrids and from 88 to 120 cm for rape varieties. The trait ‘1000-seed weight’ varied from 3.6 to 4.2 g. The varieties ‘55region’, ‘Sibiryak 60’, ‘Yarkiy’, ‘Amulet’, ‘Prometey’ and ‘Forpost KL’ were of greatest interest for practical breeding according to the complex of economically valuable traits in the southern forest-steppe of Western Siberia.

Moroldo M., Blanchet N., Duruflé H., Bernillon S., Berton T., Fernandez O., Gibon Y., Moing A., Langlade N.B.

Abstract Background Abiotic stresses in plants include all the environmental conditions that significantly reduce yields, like drought and heat. One of the most significant effects they exert at the cellular level is the accumulation of reactive oxygen species, which cause extensive damage. Plants possess two mechanisms to counter these molecules, i.e. detoxifying enzymes and non-enzymatic antioxidants, which include many classes of specialized metabolites. Sunflower, the fourth global oilseed, is considered moderately drought resistant. Abiotic stress tolerance in this crop has been studied using many approaches, but the control of specialized metabolites in this context remains poorly understood. Here, we performed the first genome-wide association study using abiotic stress-related specialized metabolites as molecular phenotypes in sunflower. After analyzing leaf specialized metabolites of 450 hybrids using liquid chromatography-mass spectrometry, we selected a subset of these compounds based on their association with previously known abiotic stress-related quantitative trait loci. Eventually, we characterized these molecules and their associated genes. Results We putatively annotated 30 compounds which co-localized with abiotic stress-related quantitative trait loci and which were associated to seven most likely candidate genes. A large proportion of these compounds were potential antioxidants, which was in agreement with the role of specialized metabolites in abiotic stresses. The seven associated most likely candidate genes, instead, mainly belonged to cytochromes P450 and glycosyltransferases, two large superfamilies which catalyze greatly diverse reactions and create a wide variety of chemical modifications. This was consistent with the high plasticity of specialized metabolism in plants. Conclusions This is the first characterization of the genetic control of abiotic stress-related specialized metabolites in sunflower. By providing hints concerning the importance of antioxidant molecules in this biological context, and by highlighting some of the potential molecular mechanisms underlying their biosynthesis, it could pave the way for novel applications in breeding. Although further analyses will be required to better understand this topic, studying how antioxidants contribute to the tolerance to abiotic stresses in sunflower appears as a promising area of research.

Tendiuk N., Diakonova A., Petrova O., Mukhametzyanov T., Makshakova O., Gorshkov V.

Svx proteins are virulence factors secreted by phytopathogenic bacteria of the Pectobacterium genus into the host plant cell wall. Svx-encoding genes are present in almost all species of the soft rot Pectobacteriaceae (Pectobacterium and Dickeya genera). The Svx of P. atrosepticum (Pba) has been shown to be a gluzincin metallopeptidase that presumably targets plant extensins, proteins that contribute to plant cell wall rigidity and participate in cell signaling. However, the particular “output” of the Pba Svx action in terms of plant-pathogen interactions and plant immune responses remained unknown. The Svx proteins are largely unexplored in Dickeya species, even though some of them have genes encoding two Svx homologs. Therefore, our study aims to compare the structural and catalytic properties of the Svx proteins of Pba and D. solani (Dso) and to test the phytoimmune properties of these proteins. Two assayed Dso Svx proteins, similar to Pba Svx, were gluzincin metallopeptidases with conservative tertiary structures. The two domains of the Svx proteins form electronegative clefts where the active centers of the peptidase domains are located. All three assayed Svx proteins possessed phytoimmunosuppressory properties and induced ethylene-mediated plant susceptible responses that play a decisive role in Pba-caused disease.

Narayana M., Premnath A.

Sunflower is an important oilseed crop. Worldwide, it ranks fifth in cultivation among oilseed crops. Sunflower oil is preferred for domestic consumption as well as for cooking due to its nutritional quality. The sunflower oil quality is decided based on the proportion of various fatty acids and tocopherols. Recent breeding efforts in sunflower require a special focus on altering the oil quality. Breeding of new sunflower genotypes for food and nonfood industries assures a bright future for sunflower. Recent developments in molecular techniques helped to understand the genetic architecture of sunflower traits and the changes that happened during domestication. The availability of the sunflower genome sequence made a real breakthrough in sunflower molecular biology. This sequence could be effectively used to locate QTLs associated with various traits. It may help to understand the metabolic pathways of various quality traits. It may also help to replace SSR markers with SNPs. The valorization of the nutritional aspects of sunflower would throw the limelight in the realization of oil sustainability and enhance the circular economy in the global oilseed market.

Gubaev R., Boldyrev S., Martynova E., Chernova A., Kovalenko T., Peretyagina T., Goryunova S., Goryunov D., Mukhina Z., Ben C., Gentzbittel L., Khaitovich P., Demurin Y.

Abstract Tocopherols are antioxidants that preserve oil lipids against oxidation and serve as a natural source of vitamin E in the human diet. Compared with other major oilseeds like rapeseed and soybean, sunflower (Helianthus annuus L.) exhibits low phenotypic diversity of tocopherol composition, both in wild and cultivated accessions from germplasm collections. Two major mutations that alter tocopherol composition were identified in genetic collections, and several studies suggested additional loci controlling tocopherol composition, with their expression possibly depending on the genetic background. In the present study, we performed QTL mapping of tocopherol composition in two independent F2 crosses between lines with contrasting tocopherol composition from the Pustovoit All-Russia Research Institute of Oil Crops (VNIIMK) collection. We used genotyping-bysequencing (GBS) to construct single nucleotide polymorphism-based genetic maps, and performed QTL mapping using quantitative and qualitative encoding for phenotypic traits. Our results support the notion that the tocopherol composition in the assessed crosses is controlled by two loci. We additionally selected and validated two single nucleotide polymorphism markers for each cross which could be used for marker-assisted selection.

Chernova A.I., Gubaev R.F., Singh A., Sherbina K., Goryunova S.V., Martynova E.U., Goryunov D.V., Boldyrev S.V., Vanyushkina A.A., Anikanov N.A., Stekolshchikova E.A., Yushina E.A., Demurin Y.N., Mukhina Z.M., Gavrilova V.A., et. al.

Abstract Background Sunflower is an important oilseed crop domesticated in North America approximately 4000 years ago. During the last century, oil content in sunflower was under strong selection. Further improvement of oil properties achieved by modulating its fatty acid composition is one of the main directions in modern oilseed crop breeding. Results We searched for the genetic basis of fatty acid content variation by genotyping 601 inbred sunflower lines and assessing their lipid and fatty acid composition. Our genome-wide association analysis based on the genotypes for 15,483 SNPs and the concentrations of 23 fatty acids, including minor fatty acids, revealed significant genetic associations for eleven of them. Identified genomic regions included the loci involved in rare fatty acids variation on chromosomes 3 and 14, explaining up to 34.5% of the total variation of docosanoic acid (22:0) in sunflower oil. Conclusions This is the first large scale implementation of high-throughput lipidomic profiling to sunflower germplasm characterization. This study contributes to the genetic characterization of Russian sunflower collections, which made a substantial contribution to the development of sunflower as the oilseed crop worldwide, and provides new insights into the genetic control of oil composition that can be implemented in future studies.

Sui M., Jing Y., Li H., Zhan Y., Luo J., Teng W., Qiu L., Zheng H., Li W., Zhao X., Han Y.

Tocopherol (Toc) occurs in soybean seeds and is extracted together with the soybean oil. Toc is utilized as an antioxidant in food and an additive in animal feed. A total of 180 representative accessions and 144 recombinant inbred lines (RILs) from the cross of ‘Hefeng 25’ and ‘OAC Bayfield’ were selected to evaluate individuals and total Toc concentrations in soybean seeds. The 180 soybean samples were sequenced by the approach of Specific Locus Amplified Fragment Sequencing (SLAF-seq). A total of 22,611 single nucleotide polymorphisms (SNPs) were developed. Nineteen quantitative trait nucleotides (QTNs) were identified associated with individual or total-Toc based on genome-wide association analysis (GWAS). Among them, three QTNs located near known QTLs, and 16 were novel. Eighteen QTLs and nine eQTLs were also detected by linkage mapping. The QTN rs9337368 on Chr.02 was co-localized according to the linkage mapping of the RILs and genome-wide association analysis, and regarded as a stable locus for mining the candidate genes in association with Toc. A total of 42 candidate genes near the 200 kbp flanking region of this identified locus were found. Upon a gene-based association, 11 SNPs from 5 genes out of the 42 candidates were detected. Expression levels analysis of 5 candidate genes revealed that two genes were significantly related to Toc content. The identified loci, along with the candidate genes, might be valuable for increasing the Toc concentration in soybean seeds and improving the nutritional value of soybean oil.

Gubaev R., Gorlova L., Boldyrev S., Goryunova S., Goryunov D., Mazin P., Chernova A., Martynova E., Demurin Y., Khaitovich P.

Rapeseed is the second most common oilseed crop worldwide. While the start of rapeseed breeding in Russia dates back to the middle of the 20th century, its widespread cultivation began only recently. In contrast to the world’s rapeseed genetic variation, the genetic composition of Russian rapeseed lines remained unexplored. We have addressed this question by performing genome-wide genotyping of 90 advanced rapeseed accessions provided by the All-Russian Research Institute of Oil Crops (VNIIMK). Genome-wide genetic analysis demonstrated a clear difference between Russian rapeseed varieties and the rapeseed varieties from the rest of the world, including the European ones, indicating that rapeseed breeding in Russia proceeded in its own independent direction. Hence, genetic determinants of agronomical traits might also be different in Russian rapeseed lines. To assess it, we collected the glucosinolate content data for the same 90 genotyped accessions obtained during three years and performed an association mapping of this trait. We indeed found that the loci significantly associated with glucosinolate content variation in the Russian rapeseed collection differ from those previously reported for the non-Russian rapeseed lines.

Terzić S., Boniface M., Marek L., Alvarez D., Baumann K., Gavrilova V., Joita-Pacureanu M., Sujatha M., Valkova D., Velasco L., Hulke B.S., Jocić S., Langlade N., Muños S., Rieseberg L., et. al.

Modern breeding of sunflower (Helianthus annuus L.), which started 100 years ago, increased the number and the diversity of cultivated forms. In addition, for more than 50 years, wild sunflower and otherHelianthusspecies have been collected in North America where they all originated. Collections of both cultivated and wild forms are maintained in gene banks in many countries where sunflower is an important crop, with some specificity according to the availability of germplasm and to local research and breeding programmes. Cultivated material includes land races, open pollinated varieties, synthetics and inbred lines. The majority of wild accessions are ecotypes of wildHelianthus annuus, but also 52 other species ofHelianthusand a few related genera. The activities of three gene banks, in USA, France and Serbia, are described in detail, supplemented by data from seven other countries. Past and future uses of the genetic resources for environmental adaptation and breeding are discussed in relation to genomic and improved phenotypic knowledge of the cultivated and wild accessions available in the gene banks.

Liu S., Huang H., Yi X., Zhang Y., Yang Q., Zhang C., Fan C., Zhou Y.

Glucosinolates (GSLs), whose degradation products have been shown to be increasingly important for human health and plant defence, compose important secondary metabolites found in the order Brassicales. It is highly desired to enhance pest and disease resistance by increasing the leaf GSL content while keeping the content low in seeds of Brassica napus, one of the most important oil crops worldwide. Little is known about the regulation of GSL accumulation in the leaves. We quantified the levels of 9 different GSLs and 15 related traits in the leaves of 366 accessions and found that the seed and leaf GSL content were highly correlated (r = 0.79). A total of 78 loci were associated with GSL traits, and five common and eleven tissue-specific associated loci were related to total leaf and seed GSL content. Thirty-six candidate genes were inferred to be involved in GSL biosynthesis. The candidate gene BnaA03g40190D (BnaA3.MYB28) was validated by DNA polymorphisms and gene expression analysis. This gene was responsible for high leaf/low seed GSL content and could explain 30.62% of the total leaf GSL variation in the low seed GSL panel and was not fixed during double-low rapeseed breeding. Our results provide new insights into the genetic basis of GSL variation in leaves and seeds and may facilitate the metabolic engineering of GSLs and the breeding of high leaf/low seed GSL content in B. napus.

Liu Y., Zhou X., Yan M., Wang P., Wang H., Xin Q., Yang L., Hong D., Yang G.

QTL mapping and candidate gene analysis indicate that allelic variations in BnaC2.MYB28 resulted from homeologous exchange and determine difference in seed glucosinolate content. A low seed glucosinolate content has long been an important breeding objective in rapeseed improvement. However, the molecular mechanisms underlying seed GSL content variations remain to be elucidated in allotetraploid Brassica napus. Here, we developed a double haploid population from a cross between two B. napus accessions that possess relatively low, but significantly different seed GSL contents and identified a major QTL, qGSL-C2, on chromosome C02 that explains 30.88–72.87% of the phenotypic variation observed in five environments. Using near-isogenic lines, we further delimited qGSL-C2 to a physical region of 49 kb on the B. rapa chromosome A02 which is highly homologous to the target C02 interval. Among five candidate genes, BnaC2.MYB28, a homologue of the Arabidopsis MYB28 encoding a putative R2R3-MYB-type transcription factor functioning in aliphatic methionine-derived GSL synthesis, was most likely to be the target gene underlying the QTL. Sequence analysis revealed multiple insertion/deletion and SNP variations in the genomic region between the alleles of the NILs. Furthermore, the allelic variations in BnaC2.MYB28 in the natural B. napus population were significantly associated with seed GSL content. Remarkably, the phylogenetic analysis and sequence comparison suggested that while the BnaC2.MYB28 allele from the parental line G120 was inherited from B. oleracea BolC2.MYB28, its counterpart from the other parent, 9172, most likely evolved from B. rapa BraA2.MYB28 via possible homeologous exchange. Our study promotes greater understanding of the molecular regulation of seed GSL content and provides useful molecular markers for seed GSL improvement in B. napus.

Quijano Xacur O.A.

We introduce a new distribution with support on (0,1) called unifed. It can be used as the response distribution for a GLM and it is suitable for data aggregation. We make a comparison to the beta regression. A link to an R package for working with the unifed is provided.

Kittipol V., He Z., Wang L., Doheny-Adams T., Langer S., Bancroft I.

The diverse biological activities of glucosinolate (GSL) hydrolysis products play significant biological and economical roles in the defense system and nutritional qualities of Brassica napus (oilseed rape). Yet, genomic-based study of the B. napus GSL regulatory mechanisms are scarce due to the complexity of working with polyploid species. To address these challenges, we used transcriptome-based GWAS approach, Associative Transcriptomics (AT), across a diversity panel of 288 B. napus genotypes to uncover the underlying genetic basis controlling quantitative variation of GSLs in B. napus vegetative tissues. Single nucleotide polymorphism (SNP) markers and gene expression markers (GEMs) associations identify orthologues of MYB28/HAG1 (AT5G61420), specifically the copies on chromosome A9 and C2, to be the key regulators of aliphatic GSL variation in leaves. We show that the positive correlation observed between aliphatic GSLs in seed and leaf is due to the amount synthesized, as controlled by Bna.HAG1.A9 and Bna.HAG1.C2, rather than by variation in the transport processes. In addition, AT and differential expression analysis in root tissues implicate an orthologue of MYB29/HAG3 (AT5G07690), Bna.HAG3.A3, as controlling root aromatic GSL variation. Based on the root expression data we also propose Bna.MAM3.A3 to have a role in controlling phenylalanine chain elongation for aromatic GSL biosynthesis. This work uncovers a regulator of homophenylalanine-derived aromatic GSLs and implicates the shared biosynthetic pathways between aliphatic and aromatic GSLs.

Hinckley W.E., Keymanesh K., Cordova J.A., Brusslan J.A.

Nutrient remobilization during leaf senescence nourishes the growing plant. Understanding the regulation of this process is essential for reducing our dependence on nitrogen fertilizers and increasing agricultural sustainability. Our laboratory is interested in chromatin changes that accompany the transition to leaf senescence. Previously, darker green leaves were reported for Arabidopsis thaliana hac1 mutants, defective in a gene encoding a histone acetyltransferase in the CREB-binding protein family. Here, we show that two Arabidopsis hac1 alleles display delayed age-related developmental senescence, but have normal dark-induced senescence. Using a combination of ChIP-seq for H3K9ac and RNA-seq for gene expression, we identified 43 potential HAC1 targets during age-related developmental senescence. Genetic analysis demonstrated that one of these potential targets, ERF022, is a positive regulator of leaf senescence. ERF022 is regulated additively by HAC1 and MED25, suggesting MED25 may recruit HAC1 to the ERF022 promoter to increase its expression in older leaves.

Zhu Q., King G.J., Liu X., Shan N., Borpatragohain P., Baten A., Wang P., Luo S., Zhou Q.

Rapeseed oil (canola, Brassica napus L.) is an important healthy vegetable oil throughout the world, the nutritional and economical value of which largely depends on its seed fatty acid composition. In this study, based on 201,187 SNP markers developed from the SLAF-seq (specific locus amplified fragment sequencing), a genome wide association study of four important fatty acid content traits (erucic acid, oleic acid, linoleic acid and linolenic acid) in a panel of 300 inbred lines of rapeseed in two environments (JXAU and JXRIS) was carried out. A total of 148 SNP loci significantly associated with these traits were detected by MLM model analysis respectively, and 30 SNP loci on A08 and C03 chromosomes were detected in three traits of erucic acid, oleic acid and linoleic acid contents simultaneously. Furthermore, 108 highly favorable alleles for increasing oleic acid and linoleic acid content, also for decreasing erucic acid content simultaneously were observed. By a basic local alignment search tool (BLAST) search with in a distance of 100 Kb around these significantly SNP-trait associations, we identified 20 orthologs of the functional candidate genes related to fatty acid biosynthesis, including the known vital fatty acid biosynthesis genes of BnaA.FAE1 and BnaC. FAE1 on the A08 and C03 chromosomes, and other potential candidate genes involving in the fatty acid biosynthesis pathway, such as the orthologs genes of FAD2, LACS09, KCS17, CER4, TT16 and ACBP5. This study lays a basis for uncovering the genetic variations and the improvement of fatty acid composition in B. napus.

Negro S.S., Millet E.J., Madur D., Bauland C., Combes V., Welcker C., Tardieu F., Charcosset A., Nicolas S.D.

Single Nucleotide Polymorphism (SNP) array and re-sequencing technologies have different properties (e.g. calling rate, minor allele frequency profile) and drawbacks (e.g. ascertainment bias). This lead us to study their complementarity and the consequences of using them separately or combined in diversity analyses and Genome-Wide Association Studies (GWAS). We performed GWAS on three traits (grain yield, plant height and male flowering time) measured in 22 environments on a panel of 247 F1 hybrids obtained by crossing 247 diverse dent maize inbred lines with a same flint line. The 247 lines were genotyped using three genotyping technologies (Genotyping-By-Sequencing, Illumina Infinium 50 K and Affymetrix Axiom 600 K arrays). The effects of ascertainment bias of the 50 K and 600 K arrays were negligible for deciphering global genetic trends of diversity and for estimating relatedness in this panel. We developed an original approach based on linkage disequilibrium (LD) extent in order to determine whether SNPs significantly associated with a trait and that are physically linked should be considered as a single Quantitative Trait Locus (QTL) or several independent QTLs. Using this approach, we showed that the combination of the three technologies, which have different SNP distributions and densities, allowed us to detect more QTLs (gain in power) and potentially refine the localization of the causal polymorphisms (gain in resolution). Conceptually different technologies are complementary for detecting QTLs by tagging different haplotypes in association studies. Considering LD, marker density and the combination of different technologies (SNP-arrays and re-sequencing), the genotypic data available were most likely enough to well represent polymorphisms in the centromeric regions, whereas using more markers would be beneficial for telomeric regions.

Jan H.U., Guan M., Yao M., Liu W., Wei D., Abbadi A., Zheng M., He X., Chen H., Guan C., Nichols R.A., Snowdon R.J., Hua W., Qian L.

Combining ability is crucial for parent selection in crop hybrid breeding. Many studies have attempted to provide reliable and quick methods to identify genome regions in parental lines correlating with improved hybrid performance. The local haplotype patterns surrounding densely spaced DNA markers include a large amount of genetic information, and analysis of the relationships between haplotypes and hybrid performance can provide insight into the underlying genome regions which might contribute to enhancing combining ability. Here, we generated 24,403 single-copy, genome-wide SNP loci and calculated the general combining ability (GCA) of 950 hybrids from a diverse panel of 475 pollinators of spring-type canola inbred lines crossed with two testers for days to flowering (DTF) and seed glucosinolate content (GSL). We performed a genome-wide analysis of the haplotypes and detected eight and seven haplotype regions that were significantly associated with the GCA values for DTF and seed GSL, respectively. Additionally, two haplotype blocks containing orthologs of flowering time genes FLOWERING LOCUS T (FT) and FLOWERING LOCUS C (FLC) on chromosome A02 showed additive epistatic interactions influencing flowering time. Moreover, two homoeologous haplotype regions on chromosomes A02 and C02 corresponded to major quantitative trait loci (QTL) for GSL which showed additive effects related to reduction of seed GSL in F1 hybrids. Our study showed that haplotype analysis has the potential to substantially improve the efficiency of hybrid breeding programs.

Vinnichek L., Pogorelova E., Dergunov A.

Abstract According to FAO estimates, the world food products markets still remain fairly balanced, which is due to sufficient stocks of wheat and corn and the recovery of oilseeds production. The value of oilseeds in the national economy is almost impossible to overestimate, since their food and non-food role in the world is constantly increasing. Vegetable oils obtained from oilseeds form the basis of human nutrition, they are widely used in various types of industry. The increasing role of oilseeds is also due to their use as a raw material for the production of biodiesel. The paper additionally considers the specificity of the market oilseeds. The main regions are the producers of individual oilseeds and major oilseeds in the world. The analysis of the production of major oilseeds, their production structure and global trends, which allowed to determine the main factors influencing the market of oilseeds. The composition of the countries-exporters and importers in the market of oil seeds and their share is given. The vector in the development of the world oilseed market and the role of alternative oilseeds on it are also reviewed in the paper.

Goryunova S.V., Goryunov D.V., Chernova A.I., Martynova E.U., Dmitriev A.E., Boldyrev S.V., Ayupova A.F., Mazin P.V., Gurchenko E.A., Pavlova A.S., Petrova D.A., Chebanova Y.V., Gorlova L.A., Garkusha S.V., Mukhina Z.M., et. al.

Abstract Publicly supported collections of cultivated germplasm are one of the key sources of new genes for crop improvement. VNIIMK is the leading organization in oil and essential oil crop breeding and seed growing in the Russian Federation with more than a century-long history. Sunflower varieties created by V.S. Pustovoit at VNIIMK became the basis for the development of the modern sunflower varieties worldwide. In the present study, 186 sunflower lines from the VNIIMK collection were characterized based on their genotype and general morphological and phenological economically-important traits. Additionally, for 99 sunflower lines fatty acid content, seed oil content, seed husk content, 100-seed weight, and seed number in the head were determined. Sequencing of RAD-libraries and the subsequent analysis have identified 65,553 variants including SNPs and indels. LD analysis revealed substantial variability across the genome. The longest LD blocks (>5,000 Kb) were found in the linkage groups 1, 5, and 17. The analysis revealed significant genetic and phenotypic diversity of the VNIIMK sunflower collection. Novel significant associations with linolenic acid content in the seeds were found on LGs 8, 9, and 17.