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Kobe University Repository : Kernel The Eurasian Steppe is an important goat propagation route: A タイトル phylogeographic analysis using mitochondrial DNA and Y-chromosome Title sequences of Kazakhstani goats Tabata, Risa / Kawaguchi, Fuki / Sasazaki, Shinji / Yamamoto, Yoshio / 著者 Bakhtin, Meirat / Kazymbet, Polat / Meldevekob, Alykhan / Suleimenov, Author(s) Maratbek Z. / Nishibori, Masahide / Mannen, Hideyuki 掲載誌・巻号・ページ Animal Science Journal,90(3):317-322 Citation 刊行日 2019-03 Issue date 資源タイプ Journal Article / 学術雑誌論文 Resource Type 版区分 author Resource Version © 2018 Japanese Society of Animal Science. This is the peer reviewed version of the following article: [Animal Science Journal, 90(3):317-322, 権利 2019], which has been published in final form at Rights https://doi.org/10.1111/asj.13144. This article may be used for non- commercial purposes in accordance with Wiley Terms and Conditions for Use of Self-Archived Versions. DOI 10.1111/asj.13144 JaLCDOI URL http://www.lib.kobe-u.ac.jp/handle_kernel/90005796 PDF issue: 2021-09-23 1 1 The Eurasian Steppe is an important goat propagation route: a 2 phylogeographic analysis using mitochondrial DNA and Y-chromosome 3 sequences of Kazakhstani goats 4 5 Risa TABATA,1 Fuki KAWAGUCHI,1 Shinji SASAZAKI,1 Yoshio YAMAMOTO,2 6 Meirat BAKHTIN,3 Polat KAZYMBET,3 Alykhan MELDEVEKOB,4 Maratbek Z. 7 SULEIMENOV,4 Masahide NISHIBORI,2 and Hideyuki MANNEN1,* 8 9 1Laboratory of Animal Breeding and Genetics, Graduate School of Agricultural 10 Science, Kobe University, Nada, Kobe 657-8501, Japan, 2Graduate School of 11 Biosphere Science, Hiroshima University, Higashi-Hiroshima 739-8528, Japan, 12 3Astana Medical University, Radiobiology Scientific Center, Astana 010000, 13 Kazakhstan, 4Institute of Zoology, Almaty 050060, Kazakhstan 14 15 *Correspondence: Hideyuki Mannen, Graduate School of Agricultural Science, 16 Kobe University, Nada, Kobe 657-8501, Japan. (E-mail: [email protected]) 17 TEL: +81-78-803-5803, FAX: +81-78-803-5803 18 19 Running title: Genetic diversity of Kazakhstan goat 20 21 2 1 Abstract 2 Goats (Capra hircus) were domesticated in the Fertile Crescent and propagated 3 all over the world. The Silk Road through the Eurasian Steppe belt is a possible 4 propagation route for domestic goats to Central Asia. Kazakhstan is in close 5 geographical proximity to domestication centers and covers the majority of the 6 Eurasian Steppe belt. In this study, we examined the genetic diversity and 7 phylogeographic structure of Kazakhstani goats. The mtDNA sequences of 141 8 Kazakhstani goats were categorized into haplogroups A, C, and D, of which 9 haplogroup A was predominant (97%), whereas haplogroups C and D were 10 detected at low frequencies (1.4% each). The Kazakhstani haplotypes C were 11 then categorized into Asian mtDNA type. Sequence analysis of the SRY gene on 12 the Y-chromosome in 67 male Kazakhstani goats revealed two haplotypes: Y1A 13 (64%) and Y2A (36%). Analysis of the distribution of mtDNA haplogroups and 14 SRY haplotypes from Eurasia and Africa demonstrated genetic similarity among 15 animals from Kazakhstan, Mongolia, and Northwest China located on the 16 Eurasian Steppe belt. These phylogeographic results suggested that the 17 Eurasian Steppe belt was an important propagation route for goats to Central 18 Asia. 19 20 Key words 21 Capra hircus, Eurasian Steppe, propagation route, mtDNA D-loop, SRY gene 3 1 Introduction 2 Domestic goats (Capra hircus) have been raised for multiple purposes, including 3 for their milk, meat, skin, and fiber. Archaeological evidence indicates that goat 4 domestication occurred in the Fertile Crescent over 10,000 years ago (Zeder & 5 Hesse, 2000; Luikart et al., 2006; Naderi et al., 2008). Because of their high 6 tolerance of harsh environments, goats are one of the most important livestock in 7 the world. Approximately 500–600 goat breeds have been reported worldwide 8 (FAOSTAT, http://www.fap.org/faostat), and most of these are native breeds, 9 which are well adapted to their environments but have not been sufficiently 10 improved. Genetic information from these native breeds would shed light on the 11 origins of domestication, their genetic relationships, environmental adaptation, 12 and propagation history. 13 Previous molecular studies using mtDNA D-loop region were performed 14 to investigate the origin and genetic relationship of goats (Luikart et al., 2001; 15 Mannen, Nagata & Tsuji, 2001; Sultana, Mannen & Tsuji 2003; Joshi et al., 2004; 16 Chen et al., 2005; Fernandez et al., 2006; Naderi et al., 2007; Lin et al., 2012). 17 These studies revealed six highly divergent lineages of goat mtDNA (haplogroups 18 A–G). Haplogroup A is distributed worldwide (Naderi et al., 2007), whereas most 19 animals in haplogroup B are primarily found in South and Southeast Asia, with 20 their frequency tending to increase southeastward (Lin et al., 2012). Haplogroup 21 C is found in Asia and Europe with low frequencies, and the minor haplogroups 4 1 D, F, and G are observed in Asia, Sicily, and the Near East and northern Africa, 2 respectively, at low frequencies (Naderi et al., 2007). These lineages are believed 3 to have diverged prior to goat domestication (Luikart et al., 2001). 4 In addition, genetic variations on the Y-chromosome are useful for 5 understanding paternal genetic diversity. Previous studies using SRY 3′UTR 6 sequences (Canon et al., 2006; Pereira et al., 2008; Pereira et al., 2009; Waki et 7 al., 2015) identified four major SRY haplotypes worldwide (Y1A, Y1B, Y2A, and 8 Y2B). The haplotypes Y1A and Y2A are found worldwide at high frequencies, 9 whereas the haplotypes Y1B and Y2B are found specifically in Europe and 10 Southeast Asia, respectively. 11 Goat domestication likely occurred at several sites in the Fertile Crescent 12 (Zeder & Hesse, 2000; Luikart et al., 2006; Naderi et al., 2008). From this center 13 of domestication, many domesticated animals were propagated to Asia via the 14 Silk Road, which was a series of ancient trade routes, including the Oasis Road, 15 Sea Road, and Steppe Route (Eurasian Steppe belt). Nozawa (1991), Pereira & 16 Amorim (2010), and Porter et al. (2016) also suggested that the Eurasian Steppe 17 belt was a possible propagation route for goats, which are capable of adapting to 18 the harsh environment of the Steppe. Kazakhstan and Mongolia occupy the 19 majority of the Eurasian Steppe belt, and Kazakhstan in particular is in close 20 geographical proximity to the goat domestication center and covers most of the 21 Eurasian Steppe belt. Therefore, it is likely that Kazakhstani goats were 5 1 introduced to this region at an early stage of goat expansion, and their genetic 2 information could provide important information toward understanding their 3 propagation to Asia. Therefore, the objective of this study was to characterize the 4 genetic diversity and the genetic relationships among countries and 5 understanding the history of goat propagation in the Eurasian Steppe belt using 6 mitochondrial and Y-chromosomal sequences of Kazakhstani goats. 7 8 Materials and Methods 9 Ethical Conditions 10 All procedures in the present study were performed according to the Research 11 Guidelines for Kobe University. 12 13 Animals 14 We collected blood samples from 145 native goats from five regions in 15 Kazakhstan: central (Astana city, n = 55), north (Aktobe and West Kazakhstan 16 state, n = 31), southeast (Almaty state, n = 20), south (South Kazakhstan state, 17 n = 20), and west (Mangystau state, n = 19). These geographic locations are 18 shown in Figure 1. Genomic DNA was extracted from fresh blood using a 19 standard phenol-chloroform method. 20 [Figure 1] 21 6 1 Sequencing 2 We sequenced the hypervariable segment I (HVI) of the mitochondrial D-loop 3 from bp 15,707 to 16,187 (481bp) based on the goat mtDNA reference sequence 4 (Accession No. AF533441.1) in 145 goats from Kazakhstan. Polymerase chain 5 reaction was performed according to a previously described method (Sultana, 6 Mannen & Tsuji, 2003). Standard double-strand DNA sequencing was performed 7 using 20 ng of the amplified product using BigDye® Terminator version 3.1 Cycle 8 Sequencing Kit (Applied Biosystems, Tokyo, Japan), a primer with sequence 5′- 9 TACCCACACAAACGCCAACACC-3′, and an ABI PRISM® 3100 Genetic 10 Analyzer (Applied Biosystems, Tokyo, Japan). 11 We additionally sequenced the SRY 3′UTR region (478 bp) of 67 male 12 Kazakhstani goats, covering nucleotide position bp 2,568 to 3,045 based on the 13 goat SRY reference sequence (Accession No. D82963). This region was 14 amplified and sequenced according to a previously published method (Waki et 15 al., 2015). 16 17 Data analysis 18 Sequence alignment of HVI was performed using MEGA 7.0.14 (Kumar et al., 19 2016). To investigate the genetic relationships between mtDNA sequences, an 20 unrooted neighbor-joining phylogenetic tree (Saitou & Nei, 1987) was constructed 21 using the Tamura–Nei distance method (Tamura & Nei, 1993), including 22 7 1 reference haplotypes from six mtDNA haplogroups in goats selected by Naderi et 2 al. (2007). The distance computation and phylogenetic tree construction were 3 also conducted in MEGA 7.0.14, as was the estimation of the average number of 4 nucleotide differences in each geographic region. Median-joining was used to 5 construct a network (Bandelt, Forster & Röhl, 1999) in NETWORK 5.0.0.1, in 6 which all mutations were equally weighted. To investigate the differences 7 within/among populations, analysis of molecular variance (AMOVA) was 8 conducted using ARLEQUIN 3.5.2.2 (Excoffier & Lischer, 2010). 9 To analyze the distribution of the mtDNA haplogroups in Eurasia and 10 Africa, we used mtDNA data of 4,000 individuals from the DDBJ database (Table 11 S1). In addition, to investigate regional differentiation within haplogroup A, we 12 included 20 European, 20 Middle-Eastern, and 20 Eurasian Steppe goat 13 sequences (Table S2).
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  • The Paternal and Maternal Genetic History Of

    The Paternal and Maternal Genetic History Of

    The paternal and maternal genetic history of Vietnamese populations Enrico Macholdt, Leonardo Arias, Nguyen Thuy Duong, Nguyen Dang Ton, Nguyen Van Phong, Roland Schröder, Brigitte Pakendorf, Nong Van Hai, Mark Stoneking To cite this version: Enrico Macholdt, Leonardo Arias, Nguyen Thuy Duong, Nguyen Dang Ton, Nguyen Van Phong, et al.. The paternal and maternal genetic history of Vietnamese populations. European Journal of Human Genetics, Nature Publishing Group, 2020, 28 (5), pp.636-645. 10.1038/s41431-019-0557-4. hal-02559765 HAL Id: hal-02559765 https://hal.archives-ouvertes.fr/hal-02559765 Submitted on 30 Apr 2020 HAL is a multi-disciplinary open access L’archive ouverte pluridisciplinaire HAL, est archive for the deposit and dissemination of sci- destinée au dépôt et à la diffusion de documents entific research documents, whether they are pub- scientifiques de niveau recherche, publiés ou non, lished or not. The documents may come from émanant des établissements d’enseignement et de teaching and research institutions in France or recherche français ou étrangers, des laboratoires abroad, or from public or private research centers. publics ou privés. European Journal of Human Genetics (2020) 28:636–645 https://doi.org/10.1038/s41431-019-0557-4 ARTICLE The paternal and maternal genetic history of Vietnamese populations 1 1 2 2 2 Enrico Macholdt ● Leonardo Arias ● Nguyen Thuy Duong ● Nguyen Dang Ton ● Nguyen Van Phong ● 1 3 2 1 Roland Schröder ● Brigitte Pakendorf ● Nong Van Hai ● Mark Stoneking Received: 13 June 2019 / Revised: 14 October 2019 / Accepted: 17 November 2019 / Published online: 11 December 2019 © The Author(s) 2019.