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Coat Color Allele and Mtdna Haplotype Distributions in Russian Cat 2 Populations: a Citizen-Science Research

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Coat Color Allele and Mtdna Haplotype Distributions in Russian Cat 2 Populations: a Citizen-Science Research bioRxiv preprint doi: https://doi.org/10.1101/165555; this version posted July 21, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 1 Coat color allele and mtDNA haplotype distributions in Russian cat 2 populations: a citizen-science research 3 4 Olga O. Zaytseva1,2^ & Yakov A. Tsepilov1,2^*, Ekaterina S. Yudayeva7, Artem 5 Kasianov4, Ivan V. Kulakovskiy4,5, Maria Logacheva6, Daria Belayeva7, Anna A. Gracheva7, 6 Ksenia Homenko7, Anastasia Knyazeva7, Ekaterina Kolesnikova7, Daria Nikolayeva7, 7 Mariana R. Bevova3, Pavel M. Borodin1,2 & Yurii S. Aulchenko1,2 8 9 1Institute of Cytology and Genetics SD RAS, Novosibirsk, Russia, 630090 10 2Novosibirsk State University, Novosibirsk, Russia, 630090 11 3European Research Institute for the Biology of Ageing, University of Groningen, 12 University Medical Center Groningen, 9713 AV Groningen, The Netherlands 13 4Vavilov Institute of General Genetics, Russian Academy of Sciences, Moscow, Russia, 14 119991 15 5Engelhardt Institute of Molecular Biology, Russian Academy of Sciences, Moscow, 16 Russia, 119991 17 6Moscow State University, Moscow, Russia, 119991 18 7Summer School for Molecular and Theoretical Biology, Pushino, Russia, 142290 19 20 ^These authors contributed to work equally 21 *Correspondence to: 22 Yakov A. Tsepilov 23 Institute of Cytology and Genetics SB RAS, 630090 Novosibirsk, Russia 24 [email protected] 25 26 Key words: domestic cats, coat color, mitotypes, Russian populations 27 2017 Cats manuscript page 1 bioRxiv preprint doi: https://doi.org/10.1101/165555; this version posted July 21, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 28 Abstract 29 This work has started as a project for the summer school in molecular and theoretical 30 biology. Efficient teaching and learning modern methods of molecular biology and population 31 genetics in a two-week study course for high school students needs an attractive subject. We 32 chose phylogeography of the domestic cat as the subject of our project because 1) everybody 33 likes cats; 2) cats are polymorphic for several coat color mutations, which can be easily detected 34 by street survey or in the photographs; 3) samples for DNA extraction are easy to collect without 35 posing ethical and biosafety problems; 4) rich background information of geographical 36 distribution of coat color alleles and variation in mtDNA is available; 5) phylogeography of cat 37 population in Russia is poorly studied and therefore new data collected in this large territory 38 may shed a light on the global cat distribution and on the origin of the fancy breeds. 39 During the project students studied coat color and mitotype distribution across Russian 40 random bred cats. The basics of field (observations of natural cat populations, hair collection), 41 formal (inheritance of coat colors), mathematical population (allele frequency distributions and 42 their comparisons, building phylogenetic trees, multidimensional scaling), and molecular 43 (DNA extraction and amplification, quality control of DNA sequencing data) genetics were 44 covered. 45 We scored coat color phenotypes in 1182 cats and sequenced mtDNA control region 46 from hair samples of 38 cats from 18 geographical sites. Analysis of coat color alleles 47 frequencies and mitotype distribution confirmed relative homogeneity of gene pools of Russian 48 cat populations, indicating their recent origin. We found several unique mitotypes and 49 demonstrated that OL1 mitotype, previously found only in Siberian fancy breed, was present in 50 random bred cats from several Russian cities. This contributes to the discussion on the origin 51 of the Siberian breed of cats, and supports the view that Siberians is a recent breed created in 52 the 1980s by breeding of selected representatives of the random bred population. 53 2017 Cats manuscript page 2 bioRxiv preprint doi: https://doi.org/10.1101/165555; this version posted July 21, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 54 Introduction 55 For some obscure reasons cats attract so much attention of humans that anything 56 connected to cats has an extremely high memetic fitness [1]. Thus, all other factors being equal 57 the audience would much better understand scientific facts and methodology illustrated by cats 58 rather than Drosophila. Fortunately, the domestic cat as a species is very polymorphic for easily 59 visible Mendelian traits such as coat color and texture [2]. They provide textbook examples of 60 genetic phenomena such as complete and incomplete dominance (non-agouti and piebald spot 61 correspondingly), epistasis and pleiotropy (dominant white), X-linked inheritance and X 62 chromosome inactivation (Orange). This makes domestic cat an ideal subject for teaching 63 genetics [2,3]. 64 Because of a high level of Mendelian variation and mostly random breeding, cat is a 65 good model species for the studies in population genetics and gene geography. J.B.S.Holdane 66 was the first scientist to notice this [4]. In 1940s he put forward a very simple but powerful 67 research program which later resulted in hundreds of surveys of coat color allele frequencies in 68 cat populations all over the globe [4] and finally in detailed genogeographic map and phylogeny 69 of local cat populations [5–8]. The results of a relatively recent microsatellite-based study [9] 70 were in a good agreement with the results of coat color based studies. All these studies 71 demonstrated a subdivision of the domestic cat into four distinct phylogeographic groups: 72 Asian, Mediterranean, West European, and East African. North American cats consistently 73 grouped with cats from Western Europe, suggesting European settlers probably brought cats to 74 the New World and the cat's time in America has been too brief for significant genetic 75 differentiation. 76 As Darwin pointed out in the Origin of Species “cats, from their nocturnal rambling 77 habits, cannot be matched, and, although so much valued by women and children, we hardly 78 ever see a distinct breed kept up; such breeds as we do sometimes see are almost always 79 imported from some other country” [10]. This remains mostly true even now. Eighty five 80 percent of fancy cat breeds recognized by international associations were established in the past 81 75 years on basis of so-called natural breeds (local forms) and many of them are based on 82 single-gene variants. Molecular genetic analysis indicates rather close resemblance between 83 modern breeds derived from the local forms and random bred populations at the localities of 2017 Cats manuscript page 3 bioRxiv preprint doi: https://doi.org/10.1101/165555; this version posted July 21, 2017. The copyright holder for this preprint (which was not certified by peer review) is the author/funder, who has granted bioRxiv a license to display the preprint in perpetuity. It is made available under aCC-BY-NC-ND 4.0 International license. 84 their origin [11]. 85 The molecular population genetics of fancy breeds and random bred populations was 86 investigated with use of micro-satellite markers [9], and, more recently, sequencing of the 87 mitochondrial DNA [12–14]. The studies of cat mtDNA [13,15,16] generated a comprehensive 88 database of mtDNA control region (CR) mitotypes. The database included data on 1394 cats, 89 of which 1027 were random bred cats from 25 distinct world-wide populations. Analysis of the 90 database revealed 12 universal mitotypes with a frequency of >1% in the combined population 91 set. However, most of the 12 mitotypes can be collapsed into two major mitotypes, A and D, as 92 others are different from these by three mutations at most. 93 Russia is an interesting area in terms of cat phylogeography. It borders with three of 94 four defined phylogeographic area and it is a likely source of at least two breeds: Russian blue 95 and Siberian. There were several surveys of coat color gene frequencies in Russian populations. 96 They indicated a relative homogeneity of genetic profiles of the cat populations across whole 97 country and their resemblance to Mediterranean profile. A substantial contribution of West 98 European cat populations was detected in sea port populations of St. Petersburg, Vladivostok 99 and Petropavlovsk-Kamchatsky and their neighbors [17–20]. 100 However, many Russian sites, which are interesting from the point of view of 101 phylogeography and cat and human population dynamics have not been examined yet. A 102 variability of mtDNA haplotype of the Russian cats remains totally unknown. 103 In our project we aimed to characterize coat color allele frequency and mitotypes of the 104 control region of mtDNA in random bred cats of several Russian cities. This study started as a 105 two-week project at Summer School in Molecular and Theoretical Biology 106 (https://dynastybioschooleng.wordpress.com/) organized by NGO Dynasty Foundation and 107 held in Academic city of Pushchino, Russia in 2013. The school program was oriented towards 108 high school students. It was designed to integrate participants into research process in 109 laboratories alongside with professional scientists with a possibility of obtaining novel results 110 of scientific value. We chose gene geography of the domestic cat as the study subject because 111 coat color genotypes can be easily detected by street survey or from photographs.
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