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Assessment of molecular markers and marker-assisted selection for drought tolerance in barley(Hordeum vulgare L.)

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Journal of Integrative Agriculture 2024年第1期23卷 20-38页

作者： Akmaral Baidyussen Gulmira Khassanova Maral Utebayev Satyvaldy Jatayev Rystay Kushanova Sholpan Khalbayeva Aigul Amangeldiyeva Raushan Yerzhebayeva KulpashBulatova Carly Schramm Peter Anderson Colin L.d.Jenkins Kathleen LSoole yuri Shavrukov Faculty of Agronomy S.Seifullin Kazakh AgroTechnical Research UniversityAstana 010000Kazakhstan A.I.Barayev Research and Production Centre of Grain Farming Shortandy 021601Kazakhstan Kazakh Research Institute of Agriculture and Plant Growing AlmalybakAlmaty District 040909Kazakhstan College of Science and Engineering Biological SciencesFlinders UniversityAdelaideSA 5042Australia

This review updates the present status of the field of molecular markers and marker-assisted selection(MAS),using the example of drought tolerance in *** accuracy of selected quantitative trait loci(QTLs),candidate genes and suggested markers was assessed in the barley genome *** common strategies are described for molecular marker development,candidate gene identification and verification,and their possible applications in MAS to improve the grain yield and yield components in barley under drought *** strategies are based on the following five principles:(1)Molecular markers are designated as genomic‘tags’,and their‘prediction’is strongly dependent on their distance from a candidate gene on genetic or physical maps;(2)plants react differently under favourable and stressful conditions or depending on their stage of development;(3)each candidate gene must be verified by confirming its expression in the relevant conditions,e.g.,drought;(4)the molecular marker identified must be validated for MAS for tolerance to drought stress and improved grain yield;and(5)the small number of molecular markers realized for MAS in breeding,from among the many studies targeting candidate genes,can be explained by the complex nature of drought stress,and multiple stress-responsive genes in each barley genotype that are expressed differentially depending on many other factors.

关键词： barley candidate genes drought tolerance gene verification via expression grain yield marker-assisted selection(MAS) molecular markers quantitative trait loci(QTLs) strategy for MAS

Large-scale genome-wide SNP analysis reveals the rugged(and ragged)landscape of global ancestry,phylogeny,and demographic history in chicken breeds

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Journal of Zhejiang University-Science B(Biomedicine & Biotechnology) 2024年第4期25卷 324-340页

作者： Natalia V.dEMENTIEVA yuri S.shcherbakov Olga I.STANISHEVSKAYA Anatoly B.VAKHRAMEEV Tatiana A.LARKINA Artem P.dYSIN Olga A.NIKOLAEVA Anna E.RYABOVA Anastasiia I.AZOVTSEVA Olga V.MITROFANOVA Grigoriy K.PEGLIVANYAN Natalia R.REINBACH darren K.GRIFFIN Michael N.ROMANOV Russian Research Institute of Farm Animal Genetics and Breeding-Branch of the L.K.Ernst Federal Research Centre for Animal Husbandry.Pushkin St.Petersburg196601Russia School of Biosciences University of KentCanterburyCT27NJUK L.K.Ernst Federal Research Center for Animal Husbandry DubrovitsyPodolskMoscow Oblast142132Russia

The worldwide chicken gene pool encompasses a remarkable,but shrinking,number of divergently selected breeds of diverse *** study was a large-scale genome-wide analysis of the landscape of the complex molecular architecture,genetic variability,and detailed structure among 49 *** populations represent a significant sample of the world's chicken breeds from Europe(Russia,Czech Republic,France,Spain,UK,etc.),Asia(China),North America(USA),and Oceania(Australia).Based on the results of breed genotyping using the Illumina 60K single nucleotide polymorphism(SNP)chip,a bioinformatic analysis was carried *** included the calculation of heterozygosity/homozygosity statistics,inbreeding coefficients,and effective population *** also included assessment of linkage disequilibrium and construction of phylogenetic *** multidimensional scaling,principal component analysis,and AdMIXTURE-assisted global ancestry analysis,we explored the genetic structure of populations and subpopulations in each *** overall 49-population phylogeny analysis was also performed,and a refined evolutionary model of chicken breed formation was proposed,which included egg,meat,dual-purpose types,and ambiguous *** a large-scale survey of genetic resources in poultry farming using modern genomic methods is of great interest both from the viewpoint of a general understanding of the genetics of the domestic chicken and for the further development of genomic technologies and approaches in poultry *** general,whole genome SNP genotyping of promising chicken breeds from the worldwide gene pool will promote the further development of modern genomic science as applied to poultry.

关键词： Chicken genome diversity Single nucleotide polymorphism(SNP)analysis Gene pool Global ancestry Phylogeny demographic history

Recovery of Brachiopod and Ammonoid Faunas Following the End-Permian Crisis:Additional Evidence from the Lower Triassic of the Russian Far East and Kazakhstan

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Journal of Earth Science 2014年第1期25卷 1-44页

作者： yuri d Zakharov Alexander M Popov Far Eastern Geological Institute Far Eastern BranchRussian Academy of Sciences

After the End-Permian mass extinction, ammonoids reached levels of taxonomic diver- sity higher than in the Changhsingian by the dienerian Substage of the Induan. However, brachiopods exhibit a prolonged delay in recovery, and their taxonomic diversity had not recovered to Late Permian levels even by the Olenekian. The differential patterns of recovery between these two clades may reflect fundamental differences in physiology and behavior. Brachiopods were benthic organisms that were dependent on specific trophic sources, and their general reduction in size during the Early Triassic may have been a response to a relative paucity of food resources. In contrast, ammonoids were sluggish- nektic organisms that utilized a wider range of trophic sources and that suffered no comparable size decrease during the Early Triassic. Brachiopods may have been at a disadvantage also due to vulner- abilities associated with their larval stage, during which they had to locate a suitable substrate for set- tlement. In contrast, ammonoids had no larval stage and juveniles may have been dispersed widely into favorable habitats. These factors may account for differences in the relative success of ammonoids and brachiopods at high-latitude regions following the End-Permian mass extinction： ammonoids success- fully reeolonized the Boreal region during the Early Triassic whereas brachiopods did not.

关键词： Lower Triassic South Primorye Kazakhstan brachiopod ammonoid biotic recovery.

Nitrogen and Carbon Isotope data of Olenekian to Anisian deposits from Kamenushka/South Primorye, Far-Eastern Russia and Their Palaeoenvironmental Significance

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Journal of Earth Science 2018年第4期29卷 837-853页

作者： yuri d Zakharov Micha Horacek Alexander M Popov Liana G Bondarenko Far Eastern Geological Institute of Russian Academy of Sciences (Far Eastern Branch) Stoletiya Prospect 159 Vladivostok 690022 Russia BLT Wieselburg Research Center HBLFA Francisco-Josephinum Wieselburg 3250 Austria Institute of Lithospheric Research Vienna University Vienna 1090 Austria

The Kamenushka Formation, exposed in the northern part of South Primorye （Kamennshka-1 and Kamenushka-2 sections）, is one of the few localities in the world with richly fossiliferous Lower-Upper Olenekian sedimentary successions. Lower to Middle Triassic ammonoid-, brachiopod- and conodont-bearing silty-clayey deposits of the Kamenushka-1 and Kamenushka-2 sections have been isotope-geochemically investigated in detail. As a result, these sections, together with the previously investigated Abrek Section, exposed in the southern part of South Primorye, provide almost complete ^15Non- and ^13Corg- records for the Lower Triassic of this region. Nine N- isotope intervals and the five negative C-isotope excursions, reflecting, apparently, unstable climatic and hydrological conditions, have been distinguished in the Lower Triassic of South Primorye. On the basis of the new C-isotope data the Mesohedenstroemia bosphorensis Zone （upper part）, Shimanskyites shimanskyi and Neocolumbites insignis zones of South Primorye are correlated now with the Lower Smithian part of the Yinkeng Formation, the Upper Smithian part of the Helongshan Formation and the Middle Spathian part of the Nanlinghu Formation in South China, respectively, as has been observed in the Abrek, Kamenushka-2, West Pingdingshan and Majiashan sections.

关键词： Triassic N- and C-isotopes palaeoclimatology bio- and chemostratigraphy Pri- morye Russia.

Unique Marine Olenekian-Anisian Boundary Section from South Primorye, Russian Far East

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Journal of China University of Geosciences 2005年第3期16卷 219-230页

作者： yuri d Zakharov Alexander M Popov Galina I Buryi Far Eastern Geological Institute Russian Academy of Sciences (Far Eastern Branch) Stoletiya Prospect 159 Vladivostok 690022 RussiaFar Eastern Geological Institute Russian Academy of Sciences (Far Eastern Branch) Stoletiya Prospect 159 Vladivostok 690022 Russia Far Eastern Geological Institute Russian Academy of Sciences (Far Eastern Branch) Stoletiya Prospect 159 Vladivostok 690022 Russia

To show paleontological characteristics of the Olenekian-Anislan boundary beds in the Russian Far East, a review of new data on the Upper Olenekian and Lower Anisian biostratigraphy of South Primorye is given on the basis of five sections： Golyi Cape, Petrovka River, Zhitkov Peninsula, Tchernyschew Bay and Atlasov Cape, using new ammonoid, brachiopod and conodont findings. The most representative ammonoid assemblage at the base of the Anisian was discovered in the Ussuriphyllites amurensis Zone （10.6 m thick） of the Atlasov Cape Section： Parasageceras sp. nov., Prionitidae gen. et sp. nov. , Ussuriphyllites amurensis （Kiparisova）（dominant）, Megaphyllites atlasoviensis Zakharov, Leiophyllites praematurus Kiparisova, Leiophyllites sp. , Ussurites sp. , Paradanubites sp. indet., Paracrochordiceras sp. nov., Prohungarites popowi Kiparisova, Arctohungarites primoriensis Zakharov, A. solimani （Toula）, Salterites sp. indet. （gigantic shell）, and Tropigastrites sublachontanus Zakharov. Conodonts Neospathodus cf. homeri （Bender） were found in the lower part of the Ussuriphyllites amurensis Zone of the Atlasov Cape. The Atlasov Cape seems to be one of the very promising sections of the Russian Far East for detailed investigation of the Olenekian-Anisian boundary.

关键词： South Primorye Triassic Olenekian-Anisian boundary ammonoid conodont

Significance of Caucasian Sections for Working out Carbon-Isotope Standard for Upper Permian and Lower Triassic (Induan) and Their Correlation with the Permian of North-Eastern Russia

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Journal of China University of Geosciences 2005年第2期16卷 141-151页

作者： yuri d Zakharov Alexander S Biakov Aymon Baud Heinz Kozur Far Eastern Geological Institute Russian Academy of Sciences (Far Eastern Branch) Vladivostok 690022 Russia North-East Interdisciplinary Scientific Research InstituteRussian Academy of Sciences (Far Eastern Branch)Magadan 685000 RussiaMusee de GeologieBFSH2-UNI 1015 Lausanne Switzerland Rézsü u. 83H-1029 Budapest Hungary

data obtained on conodont distribution in the Permian-Triassic Sovetashen Section of Transcaucasia provide further limitations on the age of the carbon-isotopic anomalies discovered by Baud et al. (1989). The significance of Caucasian sections for working out the carbon-isotope standard for the Upper Permian and Lower Triassic (Induan) is shown. Original data on carbon-isotope composition of bivalve and brachiopod shells from Permian sediments of North-Eastern Russia (Omolon and Okhotsk areas) have been obtained, which may be used for their correlation.

关键词： Armenia North-Eastern Russia Permian Triassic conodonts ammonoids bivalves brachiopods isotopic composition paleotemperatures correlation

A NUMERICAL METHOd FOR THE SIMULATION OF FREE SURFACE FLOWS OF VISCOPLASTIC FLUId IN 3d

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Journal of Computational Mathematics 2011年第6期29卷 605-622页

作者： Kirill d. Nikitin Maxim A. Olshanskii Kirill M. Terekhov yuri V. Vassilevski Institute of Numerical Mathematics Russian Academy of Sciences Moscow Russia department of Mechanics and Mathematics Moscow State University Moscow Russia

In this paper we study a numerical method for the simulation of free surface flows of viscoplastic （Herschel-Bulkley） fluids. The approach is based on the level set method for capturing the free surface evolution and on locally refined and dynamically adapted octree cartesian staggered grids for the discretization of fluid and level set equations. A regu- larized model is applied to handle the non-differentiability of the constitutive relations. We consider an extension of the stable approximation of the Newtonian flow equations on staggered grid to approximate the viscoplastic model and level-set equations if the free boundary evolves and the mesh is dynamically refined or coarsened. The numerical method is first validated for a Newtonian case. In this case, the convergence of numerical solutions is observed towards experimental data when the mesh is refined. Further we compute several 3d viscoplastic Herschel-Bulkley fluid flows over incline planes for the dam-break problem. The qualitative comparison of numerical solutions is done versus experimental investigations. Another numerical example is given by computing the freely oscillating viscoplastic droplet, where the motion of fluid is driven by the surface tension forces. Altogether the considered techniques and algorithms （the level-set method, compact discretizations on dynamically adapted octree cartesian grids, regularization, and the surface tension forces approximation） result in efficient approach to modeling viscoplastic free-surface flows in possibly complex 3d geometries.

关键词： Free surface flows Viscoplastic fluid Adaptive mesh refinement Oetree meshes.

New Findings of Latest Early Olenekian(Early Triassic)Fossils in South Primorye,Russian Far East,and Their Stratigraphical Significance

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Journal of Earth Science 2021年第3期32卷 554-572页

作者： yuri d.Zakharov Liana G.Bondarenko Alexander M.Popov Olga P.Smyshlyaeva Far Eastern Geological Institute Far Eastern BranchRussian Academy of SciencesVladivostok 690022Russia

Information on latest early Olenekian(latest Smithian)ammonoids is available apparently from only seven regions of the world,including South *** Smithian evidences on this topic are recorded from the West SMId(abbreviation from the Russian name of the quarry:"Building Materials and details"),East SMId and Golyj Cape areas in South *** provides additional information on systematic composition of latest Smithian ammonoid,as well as conodont and brachiopod assemblages from the recently identified Shimanskyites shimanskyi Zone,located between lower Olenekian Anasibirites nevolini Zone and upper Olenekian Tirolites subcassianus *** are many common ammonoid species in the Shimanskyites shimanskyi Zone and the underlying Anasibirites nevolini Zone,e.g.,Prosphingitoides sp.,Arctoceras septentrionale(diener),Churkites syskoi Zakharov et Shigeta,Submeekoceras?subhhydaspis(Kiparisova),Prionites markevichi Zakharov et Smyshlyaeva,?Anasibirites?simanenkoi Zakharov et Smyshlyaeva,Xenoceltites?subvariocostatus Zakharov et Smyshlyaeva,and Mianwaliites zimini Zakharov et *** base of the Shimanskyites shimanskyi Zone,marked by a negativeδ13Corg excursion in the Kamenushka-2 Section by our previous study,coincides with the FO(first occurrence)of ammonoids Shimanskyites shimanskyi Zakharov et Smyshlyaeva and Glyptophiceras ***(Waagen)and conodont Hindeodella budurovi *** zone is characterized additionally by some fossils common for the overlying upper Olenekian Tirolites subcassianus Zone:ammonoids of the genus Kamenushkaites,brachiopods Bittnerihyris margaritovi(Bittner)and Lepismatina *** conodont?Neogondolella?(=?Borinella)jubata *** latest Smithian ammonoids recorded from the Shimanskyites shimanskyi Zone totally consist of 30 taxa belonging to 11 families(Sageceratidae,Ussuiriidae,Aspenitidae,Paranannitidae,Arctoceratidae,Proptychitidae,?Galfetitidae,Prionitidae,?Kashmiritidae,Xenoceltitidae and Palaeophyllitidae).Th

关键词： ammonoids conodonts brachiopods biostratigraphy Smithian Russia

Short‐term and long‐term memory self‐attention network for segmentation of tumours in 3d medical images

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CAAI Transactions on Intelligence Technology 2023年第4期8卷 1524-1537页

作者： Mingwei Wen Quan Zhou Bo Tao Pavel shcherbakov Yang Xu Xuming Zhang department of Biomedical Engineering College of Life Science and TechnologyHuazhong University of Science and TechnologyWuhanChina State Key Laboratory of digital Manufacturing Equipment and Technology Huazhong University of Science and TechnologyWuhanChina Institute for Control Science Russian Academy of SciencesMoscowRussia Hubei Medical devices Quality Supervision and Test Institute WuhanChina

Tumour segmentation in medical images(especially 3d tumour segmentation)is highly challenging due to the possible similarity between tumours and adjacent tissues,occurrence of multiple tumours and variable tumour shapes and *** popular deep learning‐based segmentation algorithms generally rely on the convolutional neural network(CNN)and *** former cannot extract the global image features effectively while the latter lacks the inductive bias and involves the complicated computation for 3d volume *** existing hybrid CNN‐Transformer network can only provide the limited performance improvement or even poorer segmentation performance than the pure *** address these issues,a short‐term and long‐term memory self‐attention network is ***,a distinctive self‐attention block uses the Transformer to explore the correlation among the region features at different levels extracted by the ***,the memory structure filters and combines the above information to exclude the similar regions and detect the multiple ***,the multi‐layer reconstruction blocks will predict the tumour *** results demonstrate that our method outperforms other methods in terms of subjective visual and quantitative *** with the most competitive method,the proposed method provides dice(82.4%vs.76.6%)and Hausdorff distance 95%(Hd95)(10.66 vs.11.54 mm)on the KiTS19 as well as dice(80.2%vs.78.4%)and Hd95(9.632 vs.12.17 mm)on the LiTS.

关键词： 3d medical images convolutional neural network self‐attention network transformer tumor segmentation