Introduction
The genus Pyrus (pears), belonging to the Rosaceae family, represents one of the most widespread fruits with significant economic and health values. Pear species have been used worldwide for more than two millennia as nutritious food, folk medicine and ornamental plants in landscaping (Hong et al., Reference Hong, Lansky, Kang and Yang2021; Simionca Mărcășan et al., Reference Simionca Mărcășan, Pop, Somsai, Oltean, Popa, Sestras, Militaru, Botu and Sestras2023). The genus Pyrus, comprising deciduous species, demonstrates relatively an easy adaptation to environmental stresses, including drought and salinity (Tatari et al., Reference Tatari, Jafari, Shirmardi and Mohamadi2020; Dbara et al., Reference Dbara, Boussetta, Hafi and Mars2021). Pears are broadly categorized into two main types: The European and Western pears, represented by P. communis L., and P. pyrifolia (Burm.) Nak., respectively. The genus exhibits a rich diversity, consisting of a minimum of 22 primary species and 10 naturally occurring interspecific hybrid taxa. It is also known for hosting over 5000 subspecies or accessions worldwide (Li et al., Reference Li, Li, Wang, Gao, Simmonds and Preedy2016; Hong et al., Reference Hong, Lansky, Kang and Yang2021). However, due to inclination of the species towards hybridization, establishing a precise count of pear species remains challenging (Wolko et al., Reference Wolko, Antkowiak, Lenartowicz and Bocianowski2010).
Widely distributed across temperate regions of Europe, Asia, and North Africa, the genus Pyrus boasts a cultivation history spanning over 3000 years. Many species are believed to have originated in East Asia and have been cultivated in regions such as China, Japan and Korea. Notable centres of diversity extend beyond East Asia to include the Mediterranean, Georgia and Central Asia. The cultivation of pears in Europe dates back to at least 1000 BC (Aldasoro et al., Reference Aldasoro, Aedo and Muñoz Garmendia1996; Bell et al., Reference Bell, Quamme, Layne, Skirvin, Janick and Moore1996).
According to the Food and Agriculture Organization of the United Nations, P. communis is the second most produced and consumed pome fruit around the world (FAOSTAT, 2018). Although cultivars of the species are economically valuable throughout the World, the wild populations of cultivated pears are primarily distributed in Europe and the Caucasus. In support, fossils of P. communis leaves have been discovered in eastern Georgia, Azerbaijan and Türkiye during the Cretaceous or Palaeocene, predating the Tertiary period (Rubzov, Reference Rubzov1944; Zeven and Zhukovsky, Reference Zeven and Zhukovsky1975).
Türkiye is one of the world's leading pear-producing countries, along with China, the European Union, the United States of America and Argentina (USDA Foreign Agricultural Service, 2023). There is a diverse array of pear genetic resources, encompassing several taxa, with some being endemic, including P. anatolica Browicz, P. serikensis Güner & Duman and P. yaltirikii Browicz. The rich tapestry of local pear cultivars encompasses approximately 500 varieties, displaying considerable diversity in fruit size, shape, colour and texture. Notably, some of these cultivars exhibit resistance to fire blight, contributing to the overall resilience and adaptability of pear cultivation in the region (Muminjanov and Karagöz, Reference Muminjanov and Karagöz2018). The country, particularly the lower Caucasus, stands out as a unique region where pear species have been cultivated for over 2000 years, harbouring wild genetic resources of cultivated pears (Kaya et al., Reference Kaya, Kun and Güner1997). Specifically, the Çoruh River basin in the Artvin province, situated in northeastern Türkiye and part of the lower Caucasus Mountain regions, has wild populations of cultivated pears. The rugged terrains and deep canyons contribute to the isolation of many villages or settlements, compelling them to be agriculturally self-sufficient (Çakmakçı et al., Reference Çakmakçı, Aslantaş, Erdoğan and Erdoğan2017). Wild resources of Pyrus exhibit notable characteristics such as cold resistance, drought resistance, disease resistance and saline–alkali tolerance (Li et al., Reference Li, Li, Wang, Gao, Simmonds and Preedy2016; Hong et al., Reference Hong, Lansky, Kang and Yang2021). These attributes make them valuable resources for screening high-quality rootstocks and molecular breeding purposes (Liu et al., Reference Liu, Song, Liu, Zhang, Sun, Zhang and Wu2015). The diverse and complex nature of the genus Pyrus sets the stage for a comprehensive exploration of its genetic resources and conservation implications. The genetic resources of pear are generally conserved in clonally established or seedling-based gene banks around the world (Kocsisne et al., Reference Kocsisne, Bolla, Anhalt-Bruderl, Forneck, Taller and Kocsis2020). The dispersion of the cultivars is facilitated mainly by the agricultural cultivation, mostly via seedlings and grafting on traditional varieties bred locally by farmers (Davarynejad and Davarynejad, Reference Davarynejad and Davarynejad2004). These ex situ conservation programmes are important to maintain the existing genetic diversity in cultivated pears, but they do not allow evolutionary process to be continued. Assessing the magnitude and pattern of genetic diversity is crucial for the future utilization and maintenance of village pear cultivars (hereafter referred to as cultivars) which are kinds of landraces that are discovered, propagated and maintained by village farmers.
Population structure and genetic diversity have been assessed by using several different marker techniques as biochemical, morphological and DNA based ones (Kajiura et al., Reference Kajiura, Nakajima, Sakai, Kotani and Oogaki1985; Chevreau et al., Reference Chevreau, Leuliette and Gallet1997; Iketani et al., Reference Iketani, Manabe, Matsuta, Akihama and Hayashi1998; Kim et al., Reference Kim, Lee, Han, Ryu and Lee2000; Monte-Corvo et al., Reference Monte-Corvo, Cabrita, Oliveira and Leitão2000; Yamamoto et al., Reference Yamamoto, Kimura, Sawamura, Kotobuki, Ban, Hayashi and Matsuta2001, Reference Yamamoto, Kimura, Shoda, Band, Hayashi and Matsuta2002a, Reference Yamamoto, Kimura, Sawamura, Manabe, Kotobuki, Hayashi, Ban and Matsuta2002b; Kimura et al., Reference Kimura, Shi, Shoda, Kotobuki, Matsuda, Hayashi, Ban, Yoshiyuki and Yamamoto2002; Teng et al., Reference Teng, Tanabe, Tamura and Itai2002; Paganova, Reference Paganova2003; Elshihy et al., Reference Elshihy, Sharaf and Muzher2004; Wolko et al., Reference Wolko, Antkowiak, Lenartowicz and Bocianowski2010; Bao et al., Reference Bao, Chen, Zhang, Cao, Yamamoto and Teng2007; Brini et al., Reference Brini, Mars and Hormaza2008). Simple sequence repeat (SSR) markers, among the other marker techniques, have been used to characterize pear germplasm in Türkiye (Akcay et al., Reference Akçay, Burak, Kazan, Yüksel, Mutaf, Bakir, Ayanoglu and Ergül2014; Öztürk and Demirsoy, Reference Öztürk and Demirsoy2015; Bozhüyük and Aslantaş, Reference Bozhüyük and Aslantaş2020; Kaymak and Pinar, Reference Kaymak and Pinar2020). As of now, no study has been conducted to assess the genetic structure of village pear cultivar genotypes in Türkiye. Several studies, which focused on sampling country-wide popular pear cultivars, reported that pear germplasm displays an intermixed population structure from different regions of Türkiye (Akçay et al., Reference Akçay, Burak, Kazan, Yüksel, Mutaf, Bakir, Ayanoglu and Ergül2014; Öztürk and Demirsoy, Reference Öztürk and Demirsoy2015; Bozhüyük and Aslantaş, Reference Bozhüyük and Aslantaş2020; Kaymak and Pinar, Reference Kaymak and Pinar2020). However, there is a lack of information regarding the genetic diversity of village pear cultivar populations (hereafter referred to as populations). Additionally, there is a need to understand how the practices of local farmers impact the genetic diversity and structure of the pear gene pool, particularly among and within village pear cultivar populations located in village territories.
Selected pear cultivars from wild populations of P. communis are extensively distributed clonally by grafting on compatible rootstocks throughout Türkiye to maintain genotypes with economically valuable fruit characteristics. Thus, the genetic information obtained from the populations in the Artvin province, situated in the lower Caucasus, would be highly valuable for future pear breeding programmes. We employed eleven microsatellite markers to screen the cultivars preserved by local village farmers in the Çoruh River basin in order to evaluate their genetic composition for conservation. The acquired information regarding the genetic diversity and structure of village pear cultivar populations could provide valuable insights for both in situ and ex situ pear conservation programmes. This research endeavours to fill the current knowledge gap by presenting a comprehensive analysis of the genetic diversity of the populations. Thus, findings advance our comprehension of the genetic structuring in traditional pear cultivars within the specified region.
Material and methods
Plant material and DNA extraction
Leaf tissues from 63 village pear (P. communis) cultivars (pear landraces) used in this study were collected from six villages in Artvin Province: Camili, Meydancık, Veliköy, Meşeli, Aşağı Koyunlu and Kirazlı. These pear cultivars were discovered in the wild pear populations in the past, propagated and maintained clonally by the village farmers to date. These cultivars could be considered as landraces being highly heterozygous, harbouring adaptive gene complexes, and adapting to the local climate. The villages, in which cultivars were sampled, were selected due to their remote locations and presence of traditional farming practices for maintaining pear cultivars. Especially, the Camili village located in the Camili Biosphere Reserve (with a 27,152-hectare area) where introduction of non-native plant and animal species are forbidden. Sample size ranged from 6 cultivars in Meşeli to 14 in Camili villages. Additionally, leaf samples from 15 unique genotypes (these are also village pear cultivars) were obtained from a special pear clone collection, referred to as the Sample Collection Garden (SCC). The SCC was a collection of cultivars and set up as ex situ conservation site by a family from the Dalkırmaz village under the guidance of the Artvin Directorate of Food, Agriculture and Livestock (Fig. 1). Since the Panta genotypes are used as a compatible root stock in grafting practices by villagers, six wild P. communis genotypes named by locals as ‘Panta’, with one genotype sampled from a forest land near each village, were also included in the study. Here after, this will be referred as wild Panta root stock population. The locations of the villages are depicted in Fig. 1, and geographic information about the sample locations can be found in online Supplementary Table S1. Except for the Panta genotypes, the remaining 78 genotypes are cultivated clonally and maintained as village pear cultivars by local village farmers. The Panta genotypes serve as rootstocks for grafting scions of village pear cultivars. The sampled cultivars were grouped based on village locations and treated as village pear cultivar populations in the analysis of population genetic diversity parameters.
Figure 1. The locations of the eight sampled village pear (Pyrus communis L.) cultivar populations from the Çoruh river basin (Artvin province) in northeastern Türkiye.
During sampling, green, fresh leaves of village pear cultivars were collected and stored in silica gel-filled bags until DNA extraction. Initially, dried leaves in silica gel bags were crushed in a mortar with liquid nitrogen to obtain tissue powder. The tissue powder from all samples was stored at −80°C. For DNA extraction, an altered version of the CTAB (cetyltrimethylammonium bromide) protocol was utilized (Doyle and Doyle, Reference Doyle and Doyle1987) (see online Supplementary methods). The purity of the extracted DNA was quantified by measuring their OD values at 230, 260 and 280 nm using a NanoDrop Spectrophotometer (NanoDrop 2000, Thermo Scientific, USA).
PCR amplification of microsatellites
Out of 19 microsatellite loci which were previously developed for Pyrus and Malus species (Gianfranceschi et al., Reference Gianfranceschi, Seglias, Tarchini, Komjanc and Gessler1998; Yamamoto et al., Reference Yamamoto, Kimura, Shoda, Band, Hayashi and Matsuta2002a, Reference Yamamoto, Kimura, Sawamura, Manabe, Kotobuki, Hayashi, Ban and Matsuta2002b; Nishitani et al., Reference Nishitani, Terakami, Sawamura, Takada and Yamamoto2009), eleven of them were selected based on their polymorphism rates to assess the genetic diversity of the populations. Eight of the 19 microsatellite loci could not be amplified successfully in polymerase chain reaction (PCR) conditions despite of subjecting to extensive optimization experiments. Among the amplified loci, KU10, Bgt23b, NH013a, NB113a, TsuEnh008, NH007b and NH008b were primarily developed for Pyrus species (Yamamoto et al., Reference Yamamoto, Kimura, Shoda, Band, Hayashi and Matsuta2002a, Reference Yamamoto, Kimura, Sawamura, Manabe, Kotobuki, Hayashi, Ban and Matsuta2002b, Reference Yamamoto, Kimura, Shoda, Imai, Saito, Sawamura, Kotobuki, Hayashi and Matsuta2002c; Nishitani et al., Reference Nishitani, Terakami, Sawamura, Takada and Yamamoto2009), while CH03G06, CH02B10, CH02F06 and CH01F02 were specific to Malus species (Gianfranceschi et al., Reference Gianfranceschi, Seglias, Tarchini, Komjanc and Gessler1998; Liebhard et al., Reference Liebhard, Gianfranceschi, Koller, Ryder, Tarchini, Van de Weg and Gessler2002) (online Supplementary Table S2).
PCRs were carried out using 5× HOT FIREPol® Blend Master Mix Ready to Load (Solis BioDyne, Tartu, Estonia) as a PCR reaction mixture. The PCR mix included 5 μl of PCR mix, 0.5 μl fluorescently labelled forward primer, 0.5 μl reverse primer, and 5 μl template DNA (20 ng/μl). The PCR cycles were set for 4 min at 94°C for denaturation, followed by 30 cycles of 94°C for 40 s, 30 s at the annealing temperature (Ta), and 2 min at 72°C, with a final extension at 72°C for 10 min. The PCR products were run on 3% agarose gels at 100 V for 45 min in electrophoresis. The bands were visualized under UV light (Vilber Lourmat, France), considering bands of a low-range DNA ladder (Fermentas, Generuler, EU).
Data collection and analysis
Fluorescently labelled PCR product analysis was conducted by BM Labosis Company (Çankaya, Ankara). The resulting electropherograms were manually checked, and allele sizes were scored using Peak Scanner Software 2.0 (Applied Biosystems Inc., Foster City, CA, USA). The collected data were utilized for investigating genetic diversity and characterization by Genepop (Raymond and Rousset, Reference Raymond and Rousset1995; Rousset, Reference Rousset2008), and the poppr package in R (Kamwar et al., Reference Kamwar, Tabima and Grünwald2014). Population genetics parameters were calculated using GenAlEx (Peakall and Smouse, Reference Peakall and Smouse2012), null alleles were checked using Micro-Checker (Van Oosterhout et al., Reference Van Oosterhout, Hutchinson, Wills and Shipley2004), and population structure was revealed by STRUCTURE software (Pritchard et al., Reference Pritchard, Stephens and Donnelly2000). More detailed information on the written scripts and software parameters can be found in Coban (Reference Çoban2019).
Results
Microsatellite marker selection
Eleven microsatellite loci were found to be suitable for further analysis based on their high level of polymorphism rate (online Supplementary Table S2). These loci are informative markers for genetic diversity analysis as they exhibit a large proportion of individuals within the population with different alleles at these SSR loci. No null alleles were identified. The linkage disequilibrium (LD) analysis, conducted using the poppr package (Kamwar et al., Reference Kamwar, Tabima and Grünwald2014), revealed no significant LD between the studied loci (online Supplementary Fig. S1). Two out of the ten cultivars from the Meydancık population were found to be identical clones. Therefore, one of the clones was removed from the data used in further analysis.
Genetic diversity analysis
The average allele number per locus was found to be 12. While KU10 had the highest mean number of different alleles (Na) and effective alleles (Ne) values (9.38 and 6.65, respectively), the CH02B10 loci had the lowest Na and Ne values (5.00 and 2.68, respectively). Observed (Ho) and expected heterozygosity (He) ranged from 0.55 in TsuEnh008 to 0.97 in CH01F02 and from 0.62 in CH02B10 to 0.84 in KU10, respectively. An excess of heterozygosity was observed in NB113a, CH03G06, CH02B10 and CH01F02 loci. The remaining of the eleven loci had positive fixation indices. The high number of positive indices indicates that the studied populations included a high number of homozygote genotypes. Polymorphic information content (PIC) values of the loci ranged between 0.62 and 0.88 with an average of 0.75, indicating that the microsatellite loci used in the study are highly informative. The inbreeding coefficient (FIS), genetic differentiation (FST), and number of migrants (Nm) were estimated as 0.03, 0.06 and 4.17, respectively (Table 1).
Table 1. Descriptive statistics for the studied microsatellite loci
N, Mean number of individuals with amplification; Na, Mean number of different alleles; Ne, Mean number of effective alleles; Ar, Allelic richness; PIC, Polymorphic information content; Ho, Observed heterozygosity; He, Expected heterozygosity; F IS, Inbreeding coefficient within individuals; F IT, Inbreeding coefficient within total population; F ST, Genetic differentiation within total population.
Regarding population-wise descriptive statistics, Na ranged between 8.09 and 5.36. The Veliköy population had the highest Na (8.09), and the wild Panta root stock population had the lowest Na (5.36). Ne varied between 4.03 and 5.57 with a mean of 4.74. Similarly, Veliköy had the highest Ne value (5.57), and the wild Panta root stock population had the lowest Ne value (4.04). The number of private alleles for the studied populations varied between 1 in Meşeli, Meydancık, and Veliköy to 4 in Camili population. The SCC had two private alleles (Table 2).
Table 2. Genetic diversity parameters for the village pear cultivar populations
N, Number of individuals; Na, Mean number of different alleles; Ne, Mean number of effective alleles; Pa, Number of private alleles; Ho, Observed heterozygosity; He, Expected heterozygosity; F, Fixation index.
The average observed heterozygosity was calculated as 0.74, and the expected heterozygosity was 0.76. Observed heterozygosity ranged between 0.77 (Veliköy population) and 0.64 (wild Panta root stock population), while expected heterozygosity varied from 0.81 (Veliköy) to 0.71 (wild Panta root stock population). As expected, the SCC, serving as an ex situ conservation site, had the second-highest observed heterozygosity. Out of the eight populations, observed heterozygosity was only slightly higher than expected heterozygosity in the A. Koyunlu population, with an FIS value of −0.02. The highest inbreeding was observed in the wild Panta root stock population with an FIS value of 0.10 (Table 2).
Genetic structure and differentiation
The pairwise number of migrants ranged from 3.42 to 10.65. Therefore, FST values varied between populations. It was the lowest between Camili and Kirazlı (0.02), while it was the highest between the wild Panta root stock population and Meşeli population (0.07, Table 3). A principal coordinate analysis was performed based on the pairwise FST values (Fig. 2) and found that 95% of the total variation is explained by the first three axes, with 48, 36 and 11%.
Table 3. Pairwise FST values (below diagonal) and number of migrants (above diagonal) between the studied village pear cultivar populations
Figure 2. Principal coordinate analysis based on Nei's distance of studied village pear (Pyrus communis L.) cultivar populations.
Pairwise FST values and the principal coordinate analysis showed that wild Panta root stock population and Meydancık population are the most distinct ones among the pairwise village pear cultivar population comparisons. Two Structure analyses were performed, with and without locality information of the populations. However, in both cases, delta K was estimated as 2. Akkoyunlu, Camili, Kirazlı, Meşeli, Meydancık, Veliköy populations and SCC were clustered into two groups with changing membership values, not related to their original locations of the populations. The members of the wild Panta root stock population were only found in Cluster 1, which also included several members of Camili and Kirazlı populations. The members of the populations clustered into the Cluster 1 with membership values ranging between 40% and 85.7%. The Cluster 2 included cultivars mainly from SCC, Meşeli and Meydancık populations, though there were also some cultivars from other populations (Fig. 3).
Figure 3. STRUCTURE clustering of village pear (Pyrus communis L.) cultivar populations sampled from the Çoruh river basin (Artvin province) in northeastern Türkiye. Each colour represents a different genetic cluster.
Discussion
This study has yielded valuable insights into the magnitude and structure of genetic diversity within village pear cultivar populations in Türkiye, including wild Panta root stock population. The outcomes of genetic diversity and structure analyses highlight the substantial genetic diversity and high admixture present in the populations, indicative of the practices employed by local farmers. These findings underscore the dynamic interplay between human cultivation practices (such as clonal material exchanges among village farmers and clonal propagation of pear cultivars) and the genetic composition of pear populations in the region, shedding light on the intricate patterns of diversity and gene flow that shape the landscape of pear cultivation in this geographic area.
The loci utilized in this study are informative and well-suited for conducting genetic diversity analysis in pear genetic resources. Regarding the suitability of microsatellite loci for the genetic characterization of cultivars, both the Ar and PIC values of the loci were observed to be higher than the critical values of 0.3 and 0.5, respectively. Consistent with previous studies (Yamamoto et al., Reference Yamamoto, Kimura, Sawamura, Kotobuki, Ban, Hayashi and Matsuta2001; Bao et al., Reference Bao, Chen, Zhang, Cao, Yamamoto and Teng2007; Brini et al., Reference Brini, Mars and Hormaza2008; Sharifani et al., Reference Sharifani, Kimura, Yamamoto and Nishtani2017; Erfani-Moghadam and Zarei, Reference Erfani-Moghadam and Zarei2018), high expected heterozygosities were identified for the studied loci, ranging between 0.62 and 0.84 for CH02B10 and KU10 loci, respectively. Notably, NH007b, TsuEnh008, NH013a, NH008b, Bgt23b and CH02F06 loci exhibited relatively higher FST values. As a result, the differentiation of populations is mainly influenced by these markers, which identify unique cultivars and rare alleles that vary significantly in frequency between different populations. This variability allows populations to be differentiated on the basis of their genetic profiles. Consequently, these markers can be effectively used as valuable tools for establishing in situ or ex situ conservation programmes. Conservation efforts can prioritize the preservation of the genetic diversity captured by these markers, ensuring the maintenance of distinct populations within each village.
All populations exhibited high observed and expected heterozygosity values, with these values being of comparable magnitude within each population. Generally, He values were found to be greater than Ho values. The plausible explanation for the elevated observed heterozygosity values lies in the admixture of populations over the years. This admixture was driven by considerations of horticultural factors such as fruit size, colour, taste, softness and growth performance, as such selections practiced by village farmers. It appears that cultivars with heterozygote superiorities, selected for their desirable cultivation traits and dispersal, have been propagated and consistently distributed in the villages where the populations originated in the Artvin province of north-eastern Türkiye.
The overall estimated FST values suggest that genetic differences among the studied populations are low, indicating that P. communis is likely cultivated and dispersed through human activities. The extensive years of human involvement in pear propagation and dispersal through seeds or clonal materials are expected to contribute to the decrease in genetic differentiation among pear genetic resources, primarily due to the high level of gene flow. This is substantiated by estimated low pairwise FST values, ranging between 0.02 and 0.06 among the populations. Additionally, the presence of a high number of migrants in the populations further supports the influence of gene flow in minimizing genetic differentiation among them. Vegetatively growing pear species, facilitated by practices like grafting as well as pollination occurring over long distances could also play a role in gene flow between populations (Culley and Hardiman, Reference Culley and Hardiman2009; Hardiman and Culley, Reference Hardiman and Culley2010; Zheng et al., Reference Zheng, Cai, Potter, Postman, Liu and Teng2014; Reim et al., Reference Reim, Proft, Heinz, Lochschmidt, Höfer, Tröber and Wolf2017).
The difference between pairwise FST values suggests that wild Panta root stock population is the genetically most distant group. Within the wild Panta root stock population, a high level of inbreeding was observed. The high level of inbreeding in the wild Panta root stock population may be attributed to the utilization of a limited number of Panta genotypes as rootstock among the six villages and consequences of mating among genetically similar genotypes within the population in the past. The observed level of inbreeding could be influenced by genetic isolation, population structure, mating patterns and demographic history. These factors may result in a decrease in genetic diversity and an increase in homozygosity within the population. This could potentially compromise the population's long-term viability and adaptability. Similar to the FST results, despite its lower sample size, the wild Panta root stock population exhibited a high number of private alleles that set it apart from the populations. These exclusive alleles hold significant value in identifying genotypes suitable for graft-compatible root stock, making them valuable candidates for future pear breeding programmes. Therefore, it is crucial to conserve these graft-compatible wild Panta root stock genotypes through a clonal orchard as part of an ex situ programme. This conservation effort can be easily achieved by transferring the graft-compatible wild Panta root stock genotypes to the SCC which already exists in the region as an ex situ programme. Furthermore, the SCC ex situ programme could be enhanced further by screening wild P. Communis trees located in the forests of the villages for compatible rootstocks using the private alleles identified in the wild Panta root stock population.
Both Structure analyses, conducted with and without prior information on population locations, reveal that genotypes of the populations in the Artvin Çoruh River Basin appear to have originated from two distinct gene pools. One gene pool is associated with Meydancık village, while the other is linked to Camili village, located in the Camili Biosphere Reserve. With the exception of the members of the wild Panta root stock population, cultivars from the populations did not consistently cluster into the same group. Some members grouped into the Cluster 1 alongside the wild Panta root stock population, while others were assigned to the Cluster 2. The population structure analysis indicates that the studied populations are highly admixed. This outcome is not unexpected, given that valuable pear cultivars within the region could be easily disseminated through clonal means, considering the remoteness of the region. Similar results have been reported by others (Liu et al., Reference Liu, Song, Liu, Zhang, Sun, Zhang and Wu2015; Zurn et al., Reference Zurn, Nyberg, Montanari, Postman, Neale and Bassil2020). Hybridization is a common phenomenon in Pyrus, even with other species such as Malus. Intergeneric hybridization has been facilitated between Pyrus and Malus, allowing for the incorporation of valuable traits from diverse gene pools. Given the high hybridization potential of pears combined with efficient human assisted dispersal mechanism, it is expected to observe high admixture among populations (Morimoto et al., Reference Morimoto, Narazaki, Okabe, Zhang, Nishumura and Itai2024).
The results of the population structure analysis and the population genetics parameters indicate that the studied populations are highly admixed. Artificial selection during pear cultivation has contributed to an increased genetic distance between the wild Panta root stock population and cultivar populations in the region. These findings shed light on the intricate dynamics of genetic diversity of the populations through gene flow, hybridization and village farmer practices, providing valuable insights into the evolutionary processes shaping the genetic landscape of P. communis in the region. The geography of the Çoruh River basin in the Artvin province, combined with traditional cultivation practices, significantly facilitates the exchange of genes among various village pear cultivars. This dynamic gene exchange makes this area be with a promising potential of pear genetic resources for establishing in situ conservation site. To preserve village pear cultivars in north-eastern Türkiye, in situ conservation on-farm by using the Camili population could be practiced since it exhibits the highest number of private alleles. Furthermore, the Camili village located in the Camili Biosphere Reserve is convenient place for in situ conservation due to its high protection status. The reserve includes two nature conservation sites where strict regulations are in practice for preventing the introduction of non-native plant and animal species to the reserve area (UNESCO, 2023). Thus, the Camili Biosphere Reserve in which Camili village located is the right place for active management and safeguarding of the village pear cultivar genetic resources as in situ in the Çoruh river basin.
Conclusions
This study has furnished crucial insights into the magnitude and structure of genetic diversity within the village pear cultivar populations, including the wild Panta root stock population. The findings from genetic diversity and structure analyses underscore that populations maintain elevated genetic diversity and significant admixture due to the practices employed by local farmers. The pear genetic resources in the Çoruh River basin appear to have originated from two distinct gene pools, specifically the Meydancık and Camili populations. Furthermore, genetic diversity statistics and structure analysis indicate that the Sample Collection Garden did not fully capture the existing genetic diversity in the village pear cultivar populations in the Çoruh river basin. To enhance the Sample Collection Garden's representation of genetic diversity, it is recommended to incorporate new pear cultivars from the populations and graft-compatible genotypes from the wild Panta root stock population. This inclusion should consider the presence of private alleles and amount of heterozygosities. In situ genetic conservation of cultivars of the species emerges as crucial for sustaining genetic diversity and facilitating breeding efforts, especially considering the likelihood of increasing anthropogenic pressures (such as the replacement of traditional varieties with genetically improved ones) and climatic factors in the future.
To maintain the genetic diversity and allow evolution to progress which are necessary to provide genetic resources for future pear breeding programmes, the Camili village population should be considered as an in situ genetic reserve. The Camili village population is located within the Camili UNESCO Biosphere Reserve where plant and animal genetic resource uses in the reserve are already strictly regulated, but special efforts for design and management plan need to be devoted to conservation of the pear genetic resources in the area.
Supplementary material
The supplementary material for this article can be found at https://doi.org/10.1017/S1479262124000455
Acknowledgements
The authors are grateful to the farmers and Artvin Directorate of Food, Agriculture and Livestock in Dalkırmaz village for their collaboration during field sampling. The manuscript is based on the study which was the master thesis of Abdulbaki Çoban (<https://tez.yok.gov.tr/UlusalTezMerkezi/giris.jsp>, thesis number:548099). Also, we thank the editor, associate editor and anonymous reviewers of the journal for their constructive comments and critics.
Author contributions
Abdulbaki Çoban carried out the laboratory work and wrote the first draft of the manuscript. Funda Ö. Değirmenci and Asiye Uluğ helped to Mr. Çoban in the lab works, data analysis of the study. Mevlüde Alev Ateş, Emrah Yüksel and Özgür Eminağaoğlu involved in sampling and cultivar identifications. Zeki Kaya designed the experiment, provided the lab facilities, reviewed and edited the manuscript.
Competing interests
The authors declare that they have no conflicts of interest.
