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Study on Inter-Taxon Population Structure and Diversity Variation Of Annals of Agricultural Sciences xxx (xxxx) xxx–xxx HOSTED BY Contents lists available at ScienceDirect Annals of Agricultural Sciences journal homepage: www.elsevier.com/locate/aoas Study on inter-taxon population structure and diversity variation of hosta inferring from trnG-trnS regional cpDNA ⁎ Hasan Mehraja,c, , Subarna Sharmaa,c, Kouhei Ohnishib, Kazuhiko Shimasakic a The United Graduate School of Agricultural Sciences, Ehime University, Ehime 790-8556, Japan b Research Institute of Molecular Genetics, Kochi University, B200 Monobe, Nankoku, Kochi 783-8502, Japan c Laboratory of Vegetable and Floricultural Science, Faculty of Agriculture and Marine Science, Kochi University, Kochi 783-8502, Japan ARTICLE INFO ABSTRACT Keywords: Diversity studies are now a key tool in genetic conservation work. The perennial herb genus Hosta showed a Giboshi complex radiation of numerous species in mountains and riversides around the Shikoku Island, Japan. The Plantain lily purpose of this study was to evaluate trnS-trnG regional genetic structure and the genetic divergence within hosta Shikoku Island taxa populations in this area. We sequenced trnS-trnG regional (chloroplast DNA) cpDNA in 81 populations Taxa comprising 399 individuals of 11 Hosta taxa collected from Shikoku area. The different numbers of haplotypes Haplotype network were found in different taxon. The divergences of population of Hosta genus and individual taxon were shown in Phylogenetic tree NJ phylogenetic tree. The highest number of haplotypes (14) was found in H. longipes var. gracillima. H. sie- boldiana and H. kiyosumiensis populations showed the maximum haplotype diversity (1.0), and H. alismifolia showed maximum nucleotide diversity (π: 0.012). The genetic structures of the H. tardiva with H. kikutii var. caput-avis (FST divergence: 52.7%) and H. sieboldiana with H. tardiva (FST divergence: 52.2%) populations were greatly differentiated from each other (FST value: > 0.15 to 0.25). We found maximum evolutionary divergence (0.009) between H. alismifolia and H. kikutii var. polyneuron populations. The significant negative neutrality test values are the evidence of expansion of the total population. H. sieboldiana and H. kiyosumiensis are more widely distributed than other taxa. H. sieboldiana, H. alismifolia, H. longipes var. gracillima and H. kikutii var. polyneuron showed the excessive low frequency variants. Introduction 1976). H. shikokiana had already been placed on the endangered species list in this area (Schmid, 1991). Among the habitats around Shikoku, Genus Hosta, a member of the Asparagaceae family, is a shade-tol- hosta plants show numerous numbers of taxa with phenotypic varia- erant perennial garden plant. It is also known as plantain lily (giboshi in tions which has not been studied yet at genetical level. Hosta plants are Japan). It is preferred by gardeners for its striking foliage, and creation frequently found in this area; but a number of taxa are placed under the of a landscape focal point. Islands are unique but have not been pro- list of extinction. It may be caused by the continuous changes of allelic tected from human activities. Evolutionary processes works differently frequency through adaptation to locality that resulted from selection in any island thus results faster species variation in an island archipe- potency, quantity of gene flow, efficient population size (Andre et al., lago than on the larger continuous landmass of a larger continent. Hosta 2011) and ecological factors as well (Pilot et al., 2006). Neutrality tests has approximately 43 species which was originated in Japan, Korea and are generally indicated the abuses of mutation equilibrium flow caused China (Schmid, 1991). Fujita (1976) identified 18 species and 7 vari- by selection or alter in population size (Tajima, 1989; Fu and Li, 1993) eties of the Hosta genus in Japan. The Japanese archipelago has many and Fu’s test is done for the past population expansion (Fu, 1997). FST islands; Hokkaido, Honshu, Shikoku, and Kyushu are the main four matrix provides the insights the genetic structure variation (Holsinger (Millien-Parra and Jaeger, 1999). Hosta taxa are widely distributed and Weir, 2009) and searches the associations between allele fre- throughout all of these four islands in Japan. Though Shikoku is the quencies with particular habitats (Bierne et al., 2011). smallest among these major islands, but it is a major center for the Molecular markers have been used as effective and dominant tools distribution of genus Hosta. Shikoku is considered as the home of some for inference of the current and previous demographic progression of taxa, including H. shikokiana and H. kikutii var. polyneuron (Fujita, plant species (Maki et al., 2008). Genetic structure, diversity, and Peer review under responsibility of Faculty of Agriculture, Ain-Shams University. ⁎ Corresponding author at: Laboratory of Vegetable and Floricultural Science, Faculty of Agriculture and Marine Science, Kochi University, Kochi 783-8502, Japan. E-mail addresses: [email protected] (H. Mehraj), [email protected] (S. Sharma), [email protected] (K. Ohnishi), [email protected] (K. Shimasaki). https://doi.org/10.1016/j.aoas.2017.12.003 Received 26 February 2017; Received in revised form 7 December 2017; Accepted 8 December 2017 0570-1783/ 2017Production and hosting by Elsevier B.V. on behalf of Faculty of Agriculture, Ain Shams University. This is an open access article under the CC BY-NC-ND license (http://creativecommons.org/licenses/BY-NC-ND/4.0/). Please cite this article as: Mehraj, H., Annals of Agricultural Sciences (2017), https://doi.org/10.1016/j.aoas.2017.12.003 H. Mehraj et al. Annals of Agricultural Sciences xxx (xxxx) xxx–xxx Table 1 Hosta genus sample collection locality around Shikoku, Japan with geographical data and accession number. Pcode NInd Locality N E Accession number Hosta sieboldiana A1 3 Shiozuka highland roadside, Tairano, Yamashiro-cho, Miyoshi-shi, Tokushima 33.9900 133.8800 LC152207 A2 5 Shiozuka highland roadside, Tairano, Yamashiro-cho, Miyoshi-shi, Tokushima 33.9300 133.8500 LC152208 A3 3 Yamashiro-cho, Miyoshi-shi, Tokushima 34.0500 134.5200 LC152209 A4 6 Yamashiro-cho, Miyoshi-shi, Tokushima 34.0700 134.5200 LC152210 Hosta alismifolia B1 12 Itachino, Nankoku-shi, Kochi 33.5600 133.6300 LC152211 B2 2 Mihara-mura, Hata-gun, Kochi 32.8800 132.9100 LC152212 B3 3 Sakawa-cho, Takaoka-gun, Kochi 33.5200 133.2200 LC152213 B4 5 Sakawa-cho, Takaoka-gun, Kochi 33.5000 133.2300 LC152214 B5 6 Sakawa-cho, Takaoka-gun, Kochi 33.5100 133.2300 LC152215 B6 5 Koda, Kochi-shi, Kochi 33.5200 133.5100 LC152216 B7 4 Koda, Kochi-shi, Kochi 33.5100 133.5100 LC152217 Hosta sieboldii C1 6 Otoyo-cho, Nagaoka-gun, Kochi 33.4147 133.4130 LC152218 C2 4 Yoshiuno Otsu, Tsuno-cho, Takaoka-gun, Kochi 33.2726 133.0170 LC152219 C3 5 Yoshiuno Otsu, Tsuno-cho, Takaoka-gun, Kochi 33.2715 133.0140 LC152220 C4 5 Yoshiuno Otsu, Tsuno-cho, Takaoka-gun, Kochi 33.2735 133.0370 LC152221 C5 5 Nagatake, Kamo, Sakawa-cho, Takaoka-gun, Kochi 33.3060 133.1940 LC152222 C6 4 Higashi Iya, Higashimiyoshi-cho, Miyoshi-gun, Tokushima 34.0870 134.5586 LC152223 C7 6 Sedo (Akutagawa), Tosa-cho, Tosa-gun, Kochi 33.7100 133.4100 LC152224 Hosta longissima D1 4 Kochi kada (Warei shrine), Ino-cho, Agawa-gun, Kochi 33.5358 133.5141 LC152225 D2 6 Kochi koda dais, Kochi-shi, Kochi 33.5339 133.0879 LC152226 D3 2 Tengu highland, Tsuno-cho, Takaoka-gun, Kochi 33.4707 132.9780 LC152227 Hosta tardiva E1 5 Sedo, Tosa-cho, Tosa-gun, Kochi 33.3902 133.2584 LC152228 E2 7 Higashiishihara, Tosa-cho, Tosa-gun, Kochi 33.4145 133.2773 LC152229 E3 6 Higashiishihara, Tosa-cho, Tosa-gun, Kochi 33.4029 133.2695 LC152230 E4 5 Higashiishihara, Tosa-cho, Tosa-gun, Kochi 33.4168 133.2789 LC152231 E5 4 Nishiyamagumi, Sakawa-cho, Takaoka-gun, Kochi 33.2853 133.1540 LC152232 E6 4 Oishi, Motoyama-cho, Nagaoka-gun, Kochi 33.4517 133.3550 LC152233 E7 8 Itachino, Nankoku-shi, Kochi 33.5637 133.3749 LC152234 E8 4 Itachino, Nankoku-shi, Kochi 33.5648 133.3749 LC152235 E9 5 Itachino, Nankoku-shi, Kochi 33.5666 133.3748 LC152236 E10 4 Kochi koda dais, Kochi-shi, Kochi 33.5308 133.5250 LC152237 Hosta longipes var. gracillima F1 5 Tosayama-mura, Kochi-shi, Kochi 33.3758 133.2981 LC152238 F2 3 Tosayama-mura, Kochi-shi, Kochi 33.3799 133.2965 LC152239 F3 6 Kagamiogachi, Kochi-shi, Kochi 33.5789 133.4730 LC152240 F4 4 Kagamiogachi, Kochi-shi, Kochi 33.5798 133.4730 LC152241 F5 5 Kagamikariyama, Kochi-shi, Kochi 33.5994 133.4704 LC152242 F6 6 Kagamikariyama, Kochi-shi, Kochi 33.5994 133.4707 LC152243 F7 1 Kuroson valley, Shimanto-shi, Kochi 33.1317 132.8970 LC152244 F8 3 Kuroson valley, Shimanto-shi, Kochi 33.1389 132.8910 LC152245 F9 6 Nametoko valley, Uwajima-shi, Ehime 33.1275 132.4840 LC152246 F10 3 Kankakedori, Shodoshima-cho, Shozu-gun, Kagawa 34.5173 134.3201 LC152247 F11 4 Kozukushi-cho, Sukumo-shi, Kochi 32.9407 132.7510 LC152248 F12 4 Kozukushi-cho, Sukumo-shi, Kochi 32.8307 132.7610 LC152249 F13 9 Onaro, Shimanto-cho, Takaoka-gun, Kochi 33.2309 132.9831 LC152250 F14 7 Shimotsui, Shimanto-cho, Takaoka-gun, Kochi 33.2996 132.9449 LC152251 F15 4 Shimotsui, Shimanto-cho, Takaoka-gun, Kochi 33.2936 132.9559 LC152252 F16 8 Hashikami, Hashikami-cho, Sukumo-shi, Kochi 33.0400 132.7200 LC152253 Hosta nakaiana G1 4 Hongawa-Erimon, Ino-cho, Agawa-gun, Kochi 33.7269 133.2398 LC152254 G2 2 Omorikawa valley, Hongawa, Ino-cho, Agawa-gun, Kochi 33.4248 133.1780 LC152255 G3 2 Omorikawa valley, Hongawa, Ino-cho, Agawa-gun, Kochi 33.4136 133.1810 LC152256 Hosta kikutii var. caput-avis H1 5 Tosayamahirose, Kochi-shi, Kochi 33.4734 133.3520 LC152257 H2 5 Tosayamahirose, Kochi-shi, Kochi 33.4634 133.3620 LC152258 H3 7 Hibihara, Tosayamahirose, Kochi-shi, Kochi 33.4791 133.3830 LC152259 H4 3 Hibihara, Tosayamahirose, Kochi-shi, Kochi 33.4841 133.3530 LC152260 H5 6 Tosayama, Kochi-shi, Kochi 33.3816 133.3031 LC152261 H6 4 Hibihara, Tosayamahirose, Kochi-shi, Kochi 33.5324 133.7682 LC152262 Hosta kikutii var.
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