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Plant Biology at Belyaev Conference – 2017
BMC Plant Biology volume 17, Article number: 257 (2017)
This thematic issue of BMC Plant Biology continues the series of BioMed Central special post-conference issues presenting materials from the conferences on bioinformatics and systems biology collectively known as BGRS\SB (Bioinformatics of Genome Regulation and Structure\Systems Biology) held in Novosibirsk. It contains the papers discussed at the international conference “Belyaev Readings - 2017” (BR-2017) (http://conf.bionet.nsc.ru/belyaev100/en) and Young Scientists School “Systems Biology and Bioinformatics - 2017” (SBB-2017) (http://conf.bionet.nsc.ru/sbb2017/en/).
The year 2017 marks the 100-th anniversary since birth of Full Member of the USSR Academy of Sciences, Professor Dmitry K. Belyaev (1917–1985), an outstanding scientist, evolutionist and geneticist. In view of this memorable date, the Institute of Cytology and Genetics of the Siberian Branch of the Russian Academy of Sciences (ICG SB RAS) held the international Belyaev Conference on Genetics and Evolution (Novosibirsk, August 7-10, 2017).
The memorial Belyaev conference-2017 continued traditions of BGRS\SB and PlantGen conference series comprising several science sections including Plant Biology. Over the last two decades, since 1998, the BGRS/SB series gained a reputation as a prime meeting venue in Russia for biologists, computer scientists, mathematicians and biochemists working in the interdisciplinary systems biology field, now focusing more on computational plant biology.
The section on Plant Biology at Belyaev Conference-2017 was dedicated to genomic and post-genomic approaches to analysis of the organization of the plant genomes, the development of sequencing and genotyping applications for plants, with special emphasis to important crop cultivars.
Plant-Gen-2017 event in Almaty, Kazakhstan (http://primerdigital.com/PlantGen2017/en/) gathered both the international scientists and the Committee members of Plant Biology section of the Belyaev Conference-2017 from Novosibirsk, thus joining the research efforts two largest post-Soviet countries and ensuring the exchange of expertise in plant genetics. BMC Plant Biology published special thematic issue presenting materials of PlantGen-2017 event (https://bmcplantbiol.biomedcentral.com/articles/supplements/volume-17-supplement-1).
Previously published special issues of BMC Plant Biology and BMC Evol Biol covered the proceeding of BGRS\SB-2016 conference and SBB-2015 School in Novosibirsk [1,2,3,4] as well as BGRS\SB-2014 event (https://bmcgenomics.biomedcentral.com/articles/supplements/volume-15-supplement-12).
In 2017, “Vavilov Journal of Selection and Breeding” published a series of memoirs publications about Prof. Belyaev (http://vavilov.elpub.ru/jour/issue/view/32/showToc). The article by V.K. Shumny  tells the history of Belyaev’s life, while other publications discuss importance of Belyaev’s work on the theory of evolution and domestication. The material on plant biology discussed at Belyaev conference-2017 were in part published in Russian at next issue of “Vavilov Journal of Selection and Breeding” (http://vavilov.elpub.ru/jour/issue/view/33/showToc).
Current issue extends the line of breakthrough publications on a variety of agricultural crops, including potato, flax and wheat, as well as highlights the area of pathogen resistance in plants.
Olesya Y. Shoeva and co-authors  systematically reviewed the environmental factors affecting anthocyanin biosynthesis pathway genes in plants. In various plants, relative strengths of selective pressure differ, with genes of dicots undergoing stronger pressure than in monocots, and in pollinator-dependent plants more than that in pollinator-independent species. This observation highlights an important role of insects-dependent pollination in the evolution of the anthocyanin biosynthesis gene network.
The research topics of next few papers consider agriculturally important features of higher plants. Wheat morphotypes with altered spike morphology associated with the development of supernumerary spikelets present an important genetic resource for studies on genetic regulation of inflorescence development.
Oxana B. Dobrovolskaya and colleagues  characterized diploid and tetraploid wheat lines of various non-standard spike morphotypes, which allowed for identification of a new mutant allele of the WHEAT FRIZZY PANICLE (WFZP) gene that determines spike branching in diploid wheat Ttiticum monococcum L. Supernumerary spikelets mutants represent an important genetic tool for research on the development of the wheat spikelet and for identification of genes that control meristem activities. Authors show that FRIZZY PANICLE and SHAM RAMIFICATION2 genes independently regulate differentiation of floral meristems in wheat.
Alexey A. Dmitriev and co-authors  considered pathogen resistance in flax (Linum usitatissimum L.), a crop plant used for fiber and oil production. Using high-throughput sequencing, the genes involved in the early defense response of flax against the fungus Fusarium oxysporum were identified. The changes in the expression of pathogenesis-related genes and genes involved in ROS production or related to cell wall biogenesis are reported.
The article by Alex V. Kochetov et al.  dissects major nematode resistance genes in the potato by comparative analysis of root transcriptomes of Solanum phureja genotypes with contrasting resistance to Globodera rostochiensis. It was shown earlier that nucleotide-binding site-leucine-rich repeat (NBS-LRR) genes compose the largest plant resistance gene family, accounting for about 80% of known resistance genes. Combination of transcriptomic analysis with data on predicted potato NBS-LRR-encoding genes considerably improved the results. Authors discussed candidate genes that provide S. phureja with strong resistance to the potato golden cyst nematode.
Saule Abugalieva and colleagues  performed taxonomic reassessment of the specimens of Allium subgenus Reticulatobulbosa collected in Central Asia according to the sequences of internally transcribes spacers and matK markers. Their analysis robustly confirmed the monophyletic origin of the Allium species. The study contributes to taxonomy clarification in Allium.
The article by Maria D. Logacheva et al.  discusses evolutionary events which shaped up the plastomes of polypod ferns (Polypodiales). Сhloroplast genomes (plastomes) of land plants are generally conserved, having slow rate of the sequence and structure evolution. The authors characterized plastid genomes of three species of Dryopteris, which is one of the largest fern genera, and performed comparative analysis of their chloroplast DNA enriched with available plastomes of Polypodiales, the most species-rich group of ferns. The authors argue that Inverted Repeats of Polypodiales plastomes are dynamic genetic system being constantly re-shuffled by gene loss, duplication and putative lateral transfer from mitochondria.
Ćilerdžić and colleagues  discuss the degradation of lignin by fungal enzymes. Structural component of plant biomass, lignocellulose, is the most abundant renewable resource in nature. Its delignification is critically dependent on white-rot fungi owing to their strong ligninolytic enzyme system. The authors consider the differences in ligninolytic potential of the fungal species and shortlist best candidates for engineering for a variety of biotechnological processes involving biotransformation of lignocellulose residues/wastes.
At the end of this Special Issue, two articles on the novel techniques for genetic analysis in plants are presented.
Satyvaldy Jatayev and co-authors  provided scientific community with an improve plant genotyping technique. Widespread introduction of both low- and high-throughput SNP-based genotyping systems formed a cornucopia of potential applications. In their paper, Jatayev et al. showcase cost-efficiency of Amplifluor-like (Amplification with fluorescence) system for SNP genotyping of plant genomes.
Finally, Bykova et al.  presented chip-based SNPs phenotyping of the resistance to spot blotch in barley. Spot blotch, caused by Cochliobolus sativus, is one of the most widespread and harmful diseases in barley. The study utilized 50 K Illumina Infinium iSELECT assay and spring barley core collection to identify three genomic loci conferring seedling resistance to two C. sativus.
We hope that that the readership of BMC Plant Biology would find this collection of papers interesting and useful.
Orlov YL, Baranova AV, Salina EA. Computational plant bioscience at BGRS\SB-2016: introductory note. BMC Plant Biol. 2016;16(Suppl 3):243. 10.1186/s12870-016-0923-0.
Baranova AV, Orlov YL. The papers presented at 7th young scientists school “systems biology and bioinformatics” (SBB’15): introductory note. BMC Genet. 2016;17(Suppl 1):20. 10.1186/s12863-015-0326-5.
Orlov YL, Hofestädt RM, Kolchanov NA. Introductory note for BGRS\SB-2014 special issue. J Bioinform Comput Biol. 2015;13(1):1502001. 10.1142/S0219720015020011.
Baranova AV, Orlov YL. Evolutionary biology at BGRS\SB-2016. BMC Evol Biol. 2017;17(Suppl 1):21. 10.1186/s12862-016-0869-8.
Shumny VK. To the centenary of the birth of outstanding evolutionist Dmitri Konstantinovich Belyaev. Vavilovskii Zhurnal Genetiki i Selektsii. 2017;21(4):387–91. 10.18699/VJ17.256. (In Russian).
Shoeva OY, Glagoleva AY, Khlestkina E.K. The factors affecting selective pressure on anthocyanin biosynthesis pathway genes in monocot and dicot plants. BMC Plant Biol. 2017;17(Suppl 2):S2 (this issue).
Dobrovolskaya OB, Amagai Y, Popova KI, Dresvyannikova AE, Martinek P, Krasnikov AA, Watanabe N. Genes wheat FRIZZY PANICLE and SHAM RAMIFICATION2 independently regulate differentiation of floral meristems in wheat. BMC Plant Biol. 2017;17(Suppl 2):S3 (this issue).
Dmitriev AA, Krasnov GS, Rozhmina TA, Novakovskiy RO, Snezhkina AV, Fedorova MS, Yurkevich OY, Muravenko OV, Bolsheva NL, Kudryavtseva AV, Melnikova NV. Differential gene expression in response to Fusarium oxysporum in resistant and susceptible genotypes of flax (Linum usitatissimum L.). BMC Plant Biol. 2017;17(Suppl 2):S4 (this issue).
Kochetov AV, Glagoleva AY, Strygina KV, Khlestkina EK, Gerasimova SV, Ibragimova SM, Shatskaya NV, Vasilyev GV, Afonnikov DA, Shmakov NA, Antonova OY, Gavrilenko TA, Khiutti A, Afanasenko OS. Differential expression of NBS-LRR encoding genes in root transcriptomes of two Solanum phureja genotypes with contrasting resistance to Globodera rostochiensis. BMC Plant Biol. 2017;17(Suppl 2):S5 (this issue).
Abugalieva S, Volkova L, Ivaschenko A, Kotuhov Y, Sakauova G, Turuspekov Y. Taxonomic reassessment of Allium subgenus Reticulatobulbosa based on ITS and matK markers. BMC Plant Biol. 2017;17(Suppl 2):S6 (this issue).
Logacheva MD, Krinitsina AA, Belenikin MS, Khafizov K, Konorov EA, Kuptsov SV, Speranskaya AS. Comparative analysis of Inverted Repeats of polypod fern (Polypodiales) plastomes reveals two hypervariable regions. BMC Plant Biol. 2017;17(Suppl 2):S7 (this issue).
Ćilerdžić J, Galić M, Vukojević J, Brčeski I, Stajić M. Potential of selected fungal species to degrade wheat straw, the most abundant plant raw material in Europe. BMC Plant Biol. 2017;17(Suppl 2):S8 (this issue).
Jatayev S, Kurishbayev A, Shvidchenko V, Turbekova A, Zotova L, Khasanova G, Serikbay D, Zhubatkanov A, Botayeva M, Zhumalin A, Soole K, Langridge P, Shavrukov Y. Advantages of Amplifluor-like SNP markers over KASP in plant genotyping. BMC Plant Biol. 2017;17(Suppl 2):S9 (this issue).
Bykova IV, Lashina NM, Efimov VM, Afanasenko OS, Khlestkina EK. Identification of barley 50k Illumina-chip SNPs associated with seedling study resistance to spot blotch. BMC Plant Biol. 2017;17(Suppl 2):S10 (this issue).
The authors acknowledge critical contribution of the Conference Chairman Academician Prof. Nikolay A. Kolchanov and unwavering support by Academician Vladimir K. Shumny, Professor Elena K. Klestkina and Alexey V. Kochetov, as well as all other members of the Organizing Committee.
The work was supported in part by ICG SB RAS budget project (0324-2016-0008), RFBR (16-54-53064) and NSFC (31611130033).
The guest editors of the special issue are grateful to the reviewers who helped in the articles editing and issue preparation: Alla Shnyreva (Moscow State University, Russia), Andrey Shcherban (ICG SB RAS, Novosibirsk, Russia), Austin J. Case (University of Minnesota, USA), Branislav Rankovic (University of Kragujevac, Serbia), Christopher A. Cullis (Case Western Reserve University, USA), Elena Kashuba (Karolinska Institute, Stockholm, Sweden), Elena K. Khlestkina (ICG SB RAS, Novosibirsk, Russia), Julio Fernandez (University of Havana, Cuba), Mathieu Deblieck (Julius Kühn-Institute, Quedlinburg, Germany), Michael K. Deyholos (University of British Columbia, Canada), Nataliya Melnikova (Engelhardt Institute of Molecular Biology RAS, Russia), Nikolai Borisjuk (Huaiyin Normal University, Huaian, China), Robert Adams (Baylor University, USA), Frank Blattner (IPK, Gatersleben, Germany), Ruiqi Zhang (Nanjing Agricultural University, Nanjing, China), Tatjana Odintsova (Moscow State University, Moscow), Varvara E. Tvorogova (St.-Petersburg State University, Russia), Vladimir Aleshin (Moscow State University, Russia), Vladimir Zhukov (All Russian Research Institute for Agricultural Microbiology, Russia), Yuri M. Konstantinov (Siberian Institute of Plant Physiology and Biochemistry, Irkutsk, Russia), Yuri Shavrukov (Flinders University, Adelaide, Australia).
About this supplement
This article has been published as part of BMC Plant Biology Volume 17 Supplement 2, 2017: Selected articles from Belyaev Conference 2017: plant biology. The full contents of the supplement are available online at https://bmcplantbiol.biomedcentral.com/articles/supplements/volume-17-supplement-2.
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Orlov, Y.L., Baranova, A.V., Chen, M. et al. Plant Biology at Belyaev Conference – 2017. BMC Plant Biol 17 (Suppl 2), 257 (2017). https://doi.org/10.1186/s12870-017-1189-x