Dr Michael N Romanov

About Mike

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Cytogenomics in Birds

In the course of the bioinformatic support for the avian molecular cytogenetics studies, the following pivotal hypotheses were tackled to understand genome evolution in birds and other vertebrates: (1) homologous synteny blocks (HSBs) are distributed in birds in a non-random fashion, (2) specific gene ontology signatures can be observed within HSBs and evolutionary breakpoint regions (EBRs), (3) unlike mammals, EBRs represent recombination hotspots in birds, and (4) transposable elements are more frequent in EBRs. Additionally, I helped reconstruct karyotypes of hypothetical avian ancestors and even dinosaurs.

 

  1. Kretschmer R, de Souza MS, Furo IO, Romanov MN, Gunski RJ, Garnero ADV, de Freitas TRO, de Oliveira EHC, O'Connor RE, Griffin DK. Interspecies chromosome mapping in Caprimulgiformes, Piciformes, Suliformes, and Trogoniformes (Aves): Cytogenomic insight into microchromosome organization and karyotype evolution in birds. Cells. 2021;10(4):826. doi: 10.3390/cells10040826.

  2. Kiazim LG, O'Connor RE, Larkin DM, Romanov MN, Narushin VG, Brazhnik EA, Griffin DK. Comparative mapping of the macrochromosomes of eight avian species provides further insight into their phylogenetic relationships and avian karyotype evolution. Cells. 2021;10(2):362. doi: 10.3390/cells10020362.

  3. Griffin DK, O'Connor R, Romanov MN, Damas J, Farré M, Martell H, Kiazim L, Jennings R, Mandawala A, Joseph S, Fowler KE, Slack EA, Allanson E, Ferguson-Smith M, Barrett PM, Valenzuela N, Larkin DM. Jurassic spark: Mapping the genomes of birds and other dinosaurs. Comp Cytogenet. 2018;12(3):322–323. doi: 10.3897/CompCytogen.v12i3.27748.

  4. O'Connor RE, Romanov MN, Kiazim LG, Barrett PM, Farré M, Damas J, Ferguson-Smith M, Valenzuela N, Larkin DM, Griffin DK. Reconstruction of the diapsid ancestral genome permits chromosome evolution tracing in avian and non-avian dinosaurs. Nat Commun. 2018;9(1):1883. doi: 10.1038/s41467-018-04267-9.

  5. O'Connor RE, Romanov MN, Farré M, Larkin DM, Griffin DK. Gross genome evolution in the Dinosauria. Chromosome Res. 2016;24(Suppl 1):S36–S37. doi: 10.1007/s10577-016-9532-x.

  6. O'Connor RE, Damas J, Farre M, Romanov MN, Martell H, Fonseka G, Jennings R, Kiazam L, Bennett S, Ward J, Mandawala A, Joseph S, Frodsham R, Lawrie M, Archibald A, Walling GA, Fowler KE, Larkin DM, Griffin DK. Upgrading molecular cytogenetics to study reproduction and reproductive isolation in mammals, birds, and dinosaurs. Cytogenet Genome Res. 2016;148(2–3):151–152. doi: 10.1159/000446523.

  7. Griffin DK, Romanov MN, O'Connor R, Fowler KE, Larkin DM. Avian cytogenetics goes functional. In: Third Report on Chicken Genes and Chromosomes 2015, Ed. M. Schmid, J. Smith & D.W. Burt, Cytogenet Genome Res. 2015;145(2):100–105. doi: 10.1159/000430927.

  8. Zhang G, Li C, Li Q, Li B, Larkin DM, Lee C, Storz JF, Antunes A, Greenwold MJ, Meredith RW, Ödeen A, Cui J, Zhou Q, Xu L, Pan H, Wang Z, Jin L, Zhang P, Hu H, Yang W, Hu J, Xiao J, Yang Z, Liu Y, Xie Q, Yu H, Lian J, Wen P, Zhang F, Li H, Zeng Y, Xiong Z, Liu S, Zhou L, Huang Z, An N, Wang J, Zheng Q, Xiong Y, Wang G, Wang B, Wang J, Fan Y, da Fonseca RR, Alfaro-Núñez A, Schubert M, Orlando L, Mourier T, Howard JT, Ganapathy G, Pfenning A, Whitney O, Rivas MV, Hara E, Smith J, Farré M, Narayan J, Slavov G, Romanov MN, Borges R, Machado JP, Khan I, Springer MS, Gatesy J, Hoffmann FG, Opazo JC, Håstad O, Sawyer RH, Kim H, Kim KW, Kim HJ, Cho S, Li N, Huang Y, Bruford MW, Zhan X, Dixon A, Bertelsen MF, Derryberry E, Warren W, Wilson RK, Li S, Ray DA, Green RE, O'Brien SJ, Griffin D, Johnson WE, Haussler D, Ryder OA, Willerslev E, Graves GR, Alström P, Fjeldså J, Mindell DP, Edwards SV, Braun EL, Rahbek C, Burt DW, Houde P, Zhang Y, Yang H, Wang J; Avian Genome Consortium, Jarvis ED, Gilbert MT, Wang J. Comparative genomics reveals insights into avian genome evolution and adaptation. Science. 2014;346(6215):1311–1320. doi: 10.1126/science.1251385.

  9. Zhang G, Li B, Li C, Gilbert MT, Jarvis ED, Wang J; Avian Genome Consortium. Comparative genomic data of the Avian Phylogenomics Project. Gigascience. 2014;3(1):26. doi: 10.1186/2047-217X-3-26.

  10. Romanov MN, Farré M, Lithgow PE, Fowler KE, Skinner BM, O'Connor R, Fonseka G, Backström N, Matsuda Y, Nishida C, Houde P, Jarvis ED, Ellegren H, Burt DW, Larkin DM, Griffin DK. Reconstruction of gross avian genome structure, organization and evolution suggests that the chicken lineage most closely resembles the dinosaur avian ancestor. BMC Genomics. 2014;15(1):1060. doi: 10.1186/1471-2164-15-1060.

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Avian ancestral karyotype [from Kretschmer & al. 2021 (Cells)]

Biodiversity and Genomic Selection in Farm Animals

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Genetic relationships between the Russian White (RW) and White Cornish (WC) chickens [from Abdelmanova & al. 2021 (Biology)]

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Stallions used in a GWAS for frozen-thawed sperm motility [from Nikitkina & al. 2022 (Anim Biosci)]

 

To ensure the sustainability of local and regional agricultural production systems, conservation and molecular genetic characterization of biodiversity among domestic animal and poultry breeds utilized for food production are two of the main goals. Since the initial publication of the chicken reference genome sequence, genomic tools and resources for study linked to livestock industry have been developed and greatly enriched to facilitate further research relevant to the conservation of the potential of genetic resources and genomic selection. These objectives were set for a project run in 2016–2020 at the Farm Animal Genomics Lab in Pushkin–St Petersburg, Russia, led by Mike.

  1. Nikitkina EV, Dementieva NV, Shcherbakov YS, Atroshchenko MM, Kudinov AA, Samoylov OI, Pozovnikova MV, Dysin AP, Krutikova AA, Musidray AA, Mitrofanova OV, Plemyashov KV, Griffin DK, Romanov MN. Genome-wide association study for frozen-thawed sperm motility in stallions across various horse breeds. Anim Biosci. 2022 Mar 3. doi: 10.5713/ab.21.0504.

  2. Larkina TA, Barkova OY, Peglivanyan GK, Mitrofanova OV, Dementieva NV, Stanishevskaya OI, Vakhrameev AB, Makarova AV, Shcherbakov YS, Pozovnikova MV, Brazhnik EA, Griffin DK, Romanov MN. Evolutionary subdivision of domestic chickens: Implications for local breeds as assessed by phenotype and genotype in comparison to commercial and fancy breeds. Agriculture. 2021;11(10):914. doi: 10.3390/agriculture11100914.

  3. Abdelmanova AS, Dotsev AV, Romanov MN, Stanishevskaya OI, Gladyr EA, Rodionov AN, Vetokh AN, Volkova NA, Fedorova ES, Gusev IV, Griffin DK, Brem G, Zinovieva NA. Unveiling comparative genomic trajectories of selection and key candidate genes in egg-type Russian White and meat-type White Cornish chickens. Biology. 2021;10(9):876. doi: 10.3390/biology10090876.

  4. Romanov MN, Zinovieva NA, Griffin DK. British sheep breeds as a part of world sheep gene pool landscape: Looking into genomic applications. Animals. 2021;11(4):994. doi: 10.3390/ani11040994.

  5. Dementieva NV, Mitrofanova OV, Dysin AP, Kudinov AA, Stanishevskaya OI, Larkina TA, Plemyashov KV, Griffin DK, Romanov MN, Smaragdov MG. Assessing the effects of rare alleles and linkage disequilibrium on estimates of genetic diversity in the chicken populations. Animal. 2021;15(3):100171. doi: 10.1016/j.animal.2021.100171.

  6. Dementieva NV, Kudinov AA, Larkina TA, Mitrofanova OV, Dysin AP, Terletsky VP, Tyshchenko VI, Griffin DK, Romanov MN. Genetic variability in local and imported germplasm chicken populations as revealed by analyzing runs of homozygosity. Animals. 2020;10(10):1887. doi: 10.3390/ani10101887.

  7. Dementieva NV, Fedorova ES, Krutikova AA, Mitrofanova OV, Stanishevskaya OI, Pleshanov NV, Smaragdov MG, Kudinov AA, Terletsky VP, Romanov MN. Genetic variability of indels in the prolactin and dopamine receptor D2 genes and their association with the yield of allanto-amniotic fluid in Russian White laying hens. Tarim Bilim Derg: J Agric Sci. 2020;26(3):373–379. doi: 10.15832/ankutbd.483561.

  8. Kudinov AA, Dementieva NV, Mitrofanova OV, Stanishevskaya OI, Fedorova ES, Larkina TA, Mishina AI, Plemyashov KV, Griffin DK, Romanov MN. Genome-wide association studies targeting the yield of extraembryonic fluid and production traits in Russian White chickens. BMC Genomics. 2019 Apr 4;20(1):270. doi: 10.1186/s12864-019-5605-5.

  9. Dementeva NV, Kudinov AA, Mitrofanova OV, Stanishevskaya OL, Fedorova ES, Romanov MN. Genome-wide association study of reproductive traits in a gene pool breed of the Russian White chickens. Reprod Domest Anim. 2018;53(Suppl 2):123–124. doi: 10.1111/rda.13300.

  10. Dementeva NV, Romanov MN, Kudinov AA, Mitrofanova OV, Stanishevskaya OI, Terletsky VP, Fedorova ES, Nikitkina EV, Plemyashov KV. Studying the structure of a gene pool population of the Russian White chicken breed by genome-wide SNP scan. Sel’skokhozyaistvennaya Biol. [Agric Biol.]. 2017;52(6):1166–1174. doi: 10.15389/agrobiology.2017.6.1166eng.

  11. Moiseyeva IG, Sevastyanova AA, Aleksandrov AV, Vakhrameev AB, Romanov MN, Dmitriev YI, Semenova SK, Sulimova GE. [Orloff chicken breed: history, current status and studies]. Izv Timiryazev S-Kh Akad [Proc Timiryazev Agric Acad.]. 2016;Issue 1:78–96.

 

In modern practical research on poultry, high-performance molecular genetic and genomic technologies are widely exploited. By utilizing efficient feed compositions and a variety of feed additives, it is possible to produce the highest production of eggs and egg products thanks to the genetic potential of commercial laying hens. Studying the mechanisms of how feed preparations affect the microorganisms of birds requires the use of molecular genetic technology for the characterization of the gut microbiota and the expression of essential genes for productivity and resistance.

 

  1. Kochish II, Romanov MN, Posyabin SV, Myasnikova OV, Korenyuga MV, Motin MS. [The effect of the prebiotic Vetelact on the gut microbiota of chickens of the parent herd]. Russ. J. "Problems of Veterinary Sanitation, Hygiene and Ecology". 2021;No. 2(38):152–156. doi: 10.36871/vet.san.hyg.ecol.202102008.

  2. Laptev GY, Yildirim EA, Ilina LA, Filippova VA, Kochish II, Gorfunkel EP, Dubrovin AV, Brazhnik EA, Narushin VG, Novikova NI, Novikova OB, Dunyashev TP, Smolensky VI, Surai PF, Griffin DK, Romanov MN. Effects of essential oils-based supplement and Salmonella infection on gene expression, blood parameters, cecal microbiome, and egg production in laying hens. Animals. 2021;11(2):360. doi: 10.3390/ani11020360.

  3. Narushin VG, Laptev GY, Yildirim EA, Ilina LA, Filippova VA, Kochish II, Gorfunkel EP, Dubrovin AV, Novikova NI, Novikova OB, Dunyashev TP, Smolensky VI, Surai PF, Bondarenko YuV, Griffin DK, Romanov MN. Modelling effects of phytobiotic administration on coherent responses to Salmonella infection in laying hens. Ital J Anim Sci. 2020;19(1):282–287. doi: 10.1080/1828051X.2020.1733445.

  4. Surai PF, Kochish II, Romanov MN, Griffin DK. Nutritional modulation of the antioxidant capacities in poultry: the case of vitamin E. Poult Sci. 2019;98(9):4030–4041. doi: 10.3382/ps/pez072.

  5. Laptev GY, Filippova VA, Kochish II, Yildirim EA, Ilina LA, Dubrovin AV, Brazhnik EA, Novikova NI, Novikova OB, Dmitrieva ME, Smolensky VI, Surai PF, Griffin DK, Romanov MN. Examination of the expression of immunity genes and bacterial profiles in the caecum of growing chickens infected with Salmonella Enteritidis and fed a phytobiotic. Animals. 2019;9(9):615. doi: 10.3390/ani9090615.

  6. Nikonov I, Romanov MN, Kochish II, Surai P. Determination of microbiocoenoses in the intestine of the Hisex Brown hens in ontogenesis. Worlds Poult Sci J. 2018;Suppl:337.

  7. Nikonov IN, Il'ina LA, Kochish II, Romanov MN, Podobed LI, Laptev GY, Panin AN, Smolenskij VI, Suraj PF. [Changing the intestinal microbiota of chickens in ontogenesis]. Ukr J Ecol. 2017;7(4):492–499. doi: 10.15421/2017_150.

  8. Barkova OY, Laptev GY, Kochish II, Romanov MN, Shevkhuzhev AF. Overview of genes associated with egg productivity and resistance of domestic hen. Res J Pharm Biol Chem Sci. 2017;8(6):638–644.

  9. Nikonov IN, Kochish II, Ilyina LA, Romanov MN, Shevhuzhev AF. Microbiota in the intestines of cross chick Lohmann Brown in ontogeny. Res J Pharm Biol Chem Sci. 2017;8(6):645–654.

  10. Laptev GY, Ilyina LA, Nikonov IN, Kochish II, Romanov MN, Smolensky VI, Panin AN, Yildirim EA, Novikova NI, Filippova VA, Dubrovin AV. [Determination of intestinal microbiocenoses of chickens of the Hisex breed by the T-RFLP method in ontogenesis]. Acta Nat. 2017;9(SI 1):33.

Biotechnologies to Assess Gene Expression and Microbiome in Relation to Economically Important Traits in Poultry

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International Laboratory of Molecular Genetics and Poultry Genomics, Moscow, headed by Mike

RT-PCR used for determining the number of amplified fragments of genes in bacteria, archaea, and fungi and for differential expression of chicken genes

The assessment of egg quality in poultry breeding is crucial, along with selection and genetic work. There is a need for developing non-destructive technologies and mathematical methods for evaluating the egg quality, which make it possible to accurately determine the external and internal parameters of the egg without breaking the eggshell and can serve as a basis for further research in the field of quality improvement of egg products. This is in addition to the intensive search for molecular genetic mechanisms and markers of egg quality. One of the major breakthroughs in this area made by a rather energetic triumvirate we have gathered, i.e., Narushin–Romanov–Griffin, was the creation and publishing of a universal egg shape formula that hit research press releases, mass media and social networks worldwide (Altmetric score: 355). International research group have started quoting our universal egg model as the NRG equation. As one can notice, this is consonant with “ENERGY". So, from the EGGY team we now go to the ENERGY team status.

 

  1. Narushin VG, Romanov MN, Griffin DK. Measurement of the neutral axis in avian eggs reveals which species conform to the “golden ratio.” Ann N Y Acad Sci. 2022 (accepted).

  2. Narushin VG, Romanov MN, Griffin DK. Egg-inspired engineering in the design of thin-walled shelled vessels: a theoretical approach for shell strength. Front Bioeng Biotechnol. 2022 (accepted). doi: 10.3389/fbioe.2022.995817.

  3. Narushin VG, Romanov MN, Mishra B, Griffin DK. Mathematical progression of avian egg shape with associated area and volume determinations. Ann N Y Acad Sci. 2022;1513(1):65–78. doi: 10.1111/nyas.14771.

  4. Narushin VG, Romanov MN, Griffin DK. Egg and math: introducing a universal formula for egg shape. Ann N Y Acad Sci. 2021;1505(1):169–177. doi: 10.1111/nyas.14680.

  5. Narushin VG, Chausov MG, Shevchenko LV, Pylypenko AP, Davydovych VA, Romanov MN, Griffin DK. Shell, a naturally engineered egg packaging: Estimated for strength by non-destructive testing for elastic deformation. Biosyst Eng. 2021;210:235–246. doi: 10.1016/j.biosystemseng.2021.08.023.

  6. Narushin VG, Romanov MN, Griffin DK. Non-destructive evaluation of the volumes of egg shell and interior: Theoretical approach. J Food Eng. 2021;300:110536. doi: 10.1016/j.jfoodeng.2021.110536.

  7. Narushin VG, Romanov MN, Griffin DK. Non-destructive measurement of chicken egg characteristics: Improved formulae for calculating egg volume and surface area. Biosyst Eng. 2021;201:42–49. doi: 10.1016/j.biosystemseng.2020.11.006.

  8. Narushin VG, Romanov MN, Lu G, Cugley J, Griffin DK. How oviform is the chicken egg? New mathematical insight into the old oomorphological problem. Food Control. 2021;119:107484. doi: 10.1016/j.foodcont.2020.107484.

  9. Narushin VG, Romanov MN, Griffin DK. A novel egg quality index as an alternative to Haugh unit score. J Food Eng. 2021;289:110176. doi: 10.1016/j.jfoodeng.2020.110176.

  10. Narushin VG, Romanov MN, Lu G, Cugley J, Griffin DK. Digital imaging assisted geometry of chicken eggs using Hügelschäffer's model. Biosyst Eng. 2020;197:45–55. doi: 10.1016/j.biosystemseng.2020.06.008.

  11. Narushin VG, Lu G, Cugley J, Romanov MN, Griffin DK. A 2-D imaging-assisted geometrical transformation method for non-destructive evaluation of the volume and surface area of avian eggs. Food Control. 2020;112:107112. doi: 10.1016/j.foodcont.2020.107112.

  12. Narushin VG, Bogatyr VP, Romanov MN. Relationship between hatchability and non-destructive physical measurements of chicken eggs. J Agric Sci. 2016;154(2):359–365. doi: 10.1017/S0021859615001045.

"Eggology"

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