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Genetic Diversity and Population Differentiation of Calanthe Tsoongiana, a Rare and Endemic Orchid in China

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Genetic Diversity and Population Differentiation of Calanthe Tsoongiana, a Rare and Endemic Orchid in China Int. J. Mol. Sci. 2013, 14, 20399-20413; doi:10.3390/ijms141020399 OPEN ACCESS International Journal of Molecular Sciences ISSN 1422-0067 www.mdpi.com/journal/ijms Article Genetic Diversity and Population Differentiation of Calanthe tsoongiana, a Rare and Endemic Orchid in China Xin Qian, Cai-xia Wang and Min Tian * Research Institution of Subtropical Forestry, Chinese Academy of Forestry, 73, Daqiao Road, Fuyang 311400, Zhejiang, China; E-Mails: [email protected] (X.Q.); [email protected] (C.W.) * Author to whom correspondence should be addressed; E-Mail: [email protected] or [email protected]; Tel./Fax: +86-571-6310-5077. Received: 20 August 2013; in revised form: 24 September 2013 / Accepted: 25 September 2013 / Published: 14 October 2013 Abstract: Calanthe tsoongiana is a rare terrestrial orchid endemic to China, and this species has experienced severe habitat loss and fragmentation. Inter-simple sequence repeat (ISSR) markers were employed to assess the genetic diversity and differentiation of six populations of C. tsoongiana. Based on 124 discernible fragments yielded by eleven selected primers, high genetic diversity was revealed at the species level; however, genetic diversity at the population level was relatively low. High-level genetic differentiation among populations was detected based on analysis of molecular variance (AMOVA), indicating potential limited gene flow. No significant relationship was observed between genetic and geographic distances among the sampled populations. These results suggested that restricted gene flow might be due to habitat fragmentation and reduced population size as a result of human activities. Based on the findings, several conservation strategies were proposed for the preservation of this threatened species. Keywords: Calanthe tsoongiana; genetic diversity; ISSR; conservation; Orchidaceae 1. Introduction Orchidaceae is one of the largest families of flowering plants, with approximately 25,000 species comprising up to 10% of all angiosperms, including five subfamilies and about 870 genera [1]. More than any other plant family, however, Orchidaceae has a large proportion of threatened species that only survive in specific environments and may be particularly susceptible to habitat fragmentation and Int. J. Mol. Sci. 2013, 14 20400 deterioration caused by human activities, such as over-collection, due to their ornamental and medicinal value [1]. Therefore, worldwide orchid populations are often small and isolated and have increasingly been a major subject of conservation concern. The orchid genus, Calanthe R. Br., is widely distributed in tropical, subtropical and warm temperate regions from Africa to Asia and the Pacific Islands. It is characterized by distichous plicate leaves, basal or lateral inflorescences, pseudobulbous or cane-like stems made up of several internodes, similar petals and sepals, normally spurred lips and possession of eight pollinia [2]. This genus contains approximately 171 species worldwide, 40 of which inhabit China [2]. Calanthe tsoongiana T. Tang et F.T. Wang is a rare perennial orchid endemic to China and is mainly distributed in Fujian, Guizhou, Hunan, Jiangxi and Zhejiang provinces [3]. They usually grow in forest margins and rocky slopes at elevations of 300 to 1500 m [3]. The habitat range and population size of C. tsoongiana has declined acutely during the last several decades, due to climatic change, agriculture, urbanization, silviculture and mass collection for horticultural use and sale. Many populations recorded previously have disappeared, and current distributions are highly fragmented and isolated. Recently, this species has been listed as a national second class protection species in China [4]. Except for its taxonomic and morphologic characteristics, however, this species has been poorly studied. To date, nothing is known about its within-population or its intra-specific genetic diversity and population structure among the distribution areas. Comprehensive knowledge on genetic diversity and population structure is essential for species conservation, as it reflects the status and survival potential of populations [5]. The maintenance of genetic diversity is very important for the long-term survival of a species, because loss of genetic variation within populations may significantly decrease adaptability to environmental change and increase extinction risk [6]. Disappearance of an individual population will remove any unique biological traits that it possesses and may ultimately lead to species extinction [6]. George et al. [7] suggested that examining the patterns and levels of genetic diversity within and structuring among populations can help in understanding evolutionary mechanisms, such as genetic drift and mutation operating at the population and species level and can serve as an indicator of the extent of gene flow and population divergence. Among various molecular tools for genetic analysis, inter-simple sequence repeat (ISSR) is a powerful tool for conservation genetic study, due to its greater reliability and reproducibility of bands, resolution of a high number of polymorphic fragments and relatively low cost [8–10]. In addition, because no prior knowledge of target sequences is required for ISSR, this marker is especially suited to rare orchids, where few or no molecular genetic studies have been previously conducted [8,11]. Furthermore, ISSR has been used successfully for studying population genetics in several orchid species, including Piperia yadonii [7], Cymbidium goeringii [11], Tipularia discolor [12], Platanthera aquilonis [13], P. dilatata [13], P. huronensis [13], Gastrodia elata [14] and Dendrobium fimbriatum [15]. Consequently, the aim of the present study on the genetic diversity and structure of C. tsoongiana was to contribute to the pool of background genetic information and to suggest conservation schemes from a genetic perspective. Int. J. Mol. Sci. 2013, 14 20401 2. Results 2.1. Genetic Diversity of C. tsoongiana In total, 104 individuals from six C. tsoongiana populations generated 124 clear and discernible bands using eleven selected ISSR primers, of which 120 (96.8%) were polymorphic (Table 1). This indicated that the ISSR markers measured sufficient polymorphism for DNA typing in the population genetic study of C. tsoongiana. The number of fragments yielded per primer varied from eight to 14, with an average of 11.3. The size of the amplified products ranged from 100 to 2000 bp. Genetic diversity was relatively low at the population level (percentage of polymorphic loci, PPL = 50%; Nei’s gene diversity, H = 0.183; Shannon’s Information index, I = 0.271; observed number of alleles, Na = 1.500; effective number of alleles, Ne = 1.318) and shifted variably across different sites. The highest and lowest levels of genetic diversity were found in SZ (PPL = 72.6%; H = 0.284; I = 0.415) and WN (PPL = 30.7%; H = 0.119; I = 0.174), respectively. However, the natural populations of C. tsoongiana had high levels of genetic diversity at the species level (PPL = 96.8%; H = 0.398; I = 0.576; Na = 1.968; Ne = 1.720). Table 1. Genetic diversity within the populations of C. tsoongiana. Populations Na Ne H I PPL LA 1.419 (0.496) 1.286 (0.378) 0.163 (0.206) 0.239 (0.296) 41.9% RJ 1.524 (0.501) 1.314 (0.377) 0.182 (0.200) 0.273 (0.287) 52.4% SZ 1.726 (0.448) 1.504 (0.389) 0.284 (0.201) 0.415 (0.282) 72.6% TR 1.694 (0.463) 1.379 (0.360) 0.226 (0.192) 0.342 (0.271) 69.4% WN 1.307 (0.463) 1.210 (0.356) 0.119 (0.191) 0.174 (0.274) 30.7% WYS 1.331 (0.472) 1.215 (0.351) 0.122 (0.191) 0.180 (0.275) 33.1% Average 1.500 (0.474) 1.318 (0.369) 0.183 (0.197) 0.271 (0.281) 50.0% Species Level 1.968 (0.177) 1.720 (0.285) 0.398 (0.129) 0.576 (0.164) 96.8% Na: observed number of alleles; Ne: effective number of alleles; H: Nei’s gene diversity; I: Shannon’s Information index; PPL: the percentage of polymorphic loci; values in brackets are standard deviations. 2.2. Genetic Differentiation and Gene Flow in C. tsoongiana The total genetic diversity (Ht) of the species was 0.406, and the genetic diversity within populations (Hs) was 0.183. The coefficient of genetic differentiation among populations (Gst) was about 0.55, indicating that 55% of the genetic variation was among the populations and 45% was within the populations. The analysis of molecular variance (AMOVA) result (Φpt = 0.522) further revealed that a large proportion of genetic differentiation was partitioned among populations, and the differences among populations were highly significant (p = 0.001) (Table 2) [16]. These findings were consistent with the relatively low gene flow value (Nm = 0.408) obtained among populations. Int. J. Mol. Sci. 2013, 14 20402 Table 2. Analysis of molecular variance (AMOVA) for the populations of C. tsoongiana. SV d.f. SSD MSD VC TVP Φpt p (rand ≥ data) Among populations 5 1252.535 250.507 13.878 52% 0.522 0.001 Within populations 98 1246.456 12.719 12.719 48% Total 103 2498.991 26.597 100% SV: source of variation; d.f.: degree of freedom; SSD: sum of squares; MSD: mean squares; VC: variance component; TVP: total variance percentage; Φpt: the proportion of the total variance among populations. 2.3. Genetic Relationships among C. tsoongiana Populations The Nei’s genetic distance among the C. tsoongiana populations ranged from 0.229 (between LA and WYS) to 0.638 (between WN and WYS) (Table 3). The Mantel test indicated that there was no significant correlation between genetic distance and geographic distance (r = 0.088, p = 0.306) (Figure 1). The UPGMA dendrogram showed general separation of the six populations, but a few individuals from four populations (RJ, JR, SZ and TR) were cluster mixed (not shown). All 104 plants were clustered into two major groups, three populations (LA, WYS and RJ) and two individuals from SZ and two from TR formed the first group, while the second group included the remaining three populations (SZ, TR and WN).
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