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Article

iPBS-Retrotransposon Markers in the Analysis of Genetic Diversity among Common Bean (Phaseolus vulgaris L.) Germplasm from Türkiye

by
Kamil Haliloğlu
1,2,
Aras Türkoğlu
3,*,
Halil Ibrahim Öztürk
4,
Güller Özkan
5,
Erdal Elkoca
6 and
Peter Poczai
7,8,*
1
Department of Field Crops, Faculty of Agriculture, Ataturk University, Erzurum 25240, Türkiye
2
Department of Biology, Faculty of Science, Cankiri Karatekin University, Çankırı 18200, Türkiye
3
Department of Field Crops, Faculty of Agriculture, Necmettin Erbakan University, Konya 42310, Türkiye
4
Health Services Vocational School, Binali Yıldırım University, Erzincan 24100, Türkiye
5
Department of Biology, Faculty of Science, Ankara University, Ankara 06100, Türkiye
6
Department of Herbal and Animal Production, Ibrahim Çeçen University, Ağrı 04100, Türkiye
7
Botany Unit, Finnish Museum of Natural History, University of Helsinki, P.O. Box 7, FI-00014 Helsinki, Finland
8
Institute of Advanced Studies Kőszeg (iASK), 9731 Kőszeg, Hungary
*
Authors to whom correspondence should be addressed.
Genes 2022, 13(7), 1147; https://doi.org/10.3390/genes13071147
Submission received: 5 June 2022 / Revised: 22 June 2022 / Accepted: 23 June 2022 / Published: 25 June 2022
(This article belongs to the Special Issue Genetic Diversity, Conservation and Utilization of Plant Genetic Resources)
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Abstract

:
Beans are legumes that play extremely important roles in human nutrition, serving as good sources of protein, vitamins, minerals, and antioxidants. In this study, we tried to elucidate the genetic diversity and population structure of 40 Turkish bean (Phaseolus vulgaris L.) local varieties and 5 commercial cultivars collected from 8 different locations in Erzurum-Ispir by using inter-primary binding site (iPBS) retrotransposon markers. For molecular characterization, the 26 most polymorphic iPBS primers were used; 52 bands per primer and 1350 bands in total were recorded. The mean polymorphism information content was 0.331. Various diversity indices, such as the mean effective allele number (0.706), mean Shannon’s information index (0.546), and gene diversity (0.361) revealed the presence of sufficient genetic diversity in the germplasm examined. Molecular analysis of variance (AMOVA) revealed that 67% of variation in bean germplasm was due to differences within populations. In addition, population structure analysis exposed all local and commercial bean varieties from five sub-populations. Expected heterozygosity values ranged between 0.1567 (the fourth sub-population) and 0.3210 (first sub-population), with an average value of 0.2103. In contrary, population differentiation measurement (Fst) was identified as 0.0062 for the first sub-population, 0.6372 for the fourth subpopulations. This is the first study to investigate the genetic diversity and population structure of bean germplasm in Erzurum-Ispir region using the iPBS-retrotransposon marker system. Overall, the current results showed that iPBS markers could be used consistently to elucidate the genetic diversity of local and commercial bean varieties and potentially be included in future studies examining diversity in a larger collection of local and commercial bean varieties from different regions.

1. Introduction

It has been reported that the rate of disappearance of plant species has increased in recent years and it is thought that the rate of genetic erosion of plant species will increase in the coming years [1]. To minimize genetic erosion in agriculture and to ensure sustainability in this field, many strategies have been developed for the protection of germplasm [2]. Germplasm refers to living tissues that are used in plant breeding studies and have a very important place for the conservation of plant genetic resources. One of the important tools in which plant germplasm is preserved is plant gene banks. These gene banks contain different plant germplasms such as seeds, pollen, in vitro. These gene banks are extremely important as they reflect the genetic diversity of both cultivated plants and their wild relatives [3]. Genetic variation information is crucial to GenBank management and breeding studies. This information assists in the creation of seed collections and facilitates the use of desired local varieties in breeding programs [4]. Knowledge of the genetic diversity between native species and improved varieties is crucial to supporting plant breeding programs so that breeders can take advantage of existing local varieties adapted to the climatic conditions of particular regions [5].
Bean (Phaseolus vulgaris L.) is one of the most valuable herbal products in the world due to its nutritional properties, benefits to human health and economic importance [1]. Beans are an important product that is widely grown and distributed in almost every region of the world [2]. Beans show wide variation phenotypically, biochemically, and genotypically, and are comprised of independent and differentiated gene pools, forming gene centers in Central America and the Andes Mountains [6]. The contributions of these two gene pools can generally be distinguished by seed size and certain other morphological characteristics. The seeds of the Mesoamerican local varieties are small or medium in size, while those of the Andean local varieties are larger [7]. The first bean cultivars corresponding to the small-grained Mesoamerican local varieties s were identified in Spain, Portugal, and South America in the early 16th century. Beans first came to Europe in the 16th-17th centuries [3]. It is reported that it reached Turkey from Europe in the 17th century [8]. Turkey is not the homeland of the bean, but several studies have indicated the existence of wide variation among local bean local varieties in Turkey [9]. The characterization of local varieties provides an opportunity to determine genetic diversity and to identify new variations that can be used in various breeding programs [10,11,12,13,14].
Genetic diversity studies have been carried out with bean varieties in many parts of Turkey. However, these studies are not yet enough. Such diversity studies can support breeding activities by both farmers and plant breeders. It is also crucial to the conservation and sustainable use of the plant genetic resources needed to meet future food-security demands [15].
Various morphological, chemical, biochemical, and molecular markers are widely used to characterize bean genetic diversity [16]. The development of molecular markers changed the fate of breeding studies and allowed these studies to accelerate. Molecular markers provide direct estimation of genetic variation at the DNA level, reducing the interference of environmental variation and being unaffected by the environment [17]. Molecular markers with different properties have been developed with studies by scientific communities. Various methods have used molecular markers, including amplified fragment length polymorphisms (AFLPs) [18], random amplified polymorphic DNA (RAPD) [19], sequence characterized amplified region (SCAR) [20], single nucleotide polymorphism (SNP) [21], inter simple-sequence repeat (ISSR) [4], simple-sequence repeats (SSR) [22], and expressed sequence tag (EST) [23], all to assess the genetic diversity and associations among several Phaseolus species.
Moreover, among them, retrotransposons are genetic elements capable of forming major components of most eukaryotic genomes, constituting 50–90% of the plant genome. Retrotransposons are divided into two: long terminal repeat (LTR) and non-LTR retrotransposons. LTR-retrotransposons are more common in plants than the other group [24]. Due to limitations in both LTR and non-LTR retrotransposons, inter primer binding site (iPBS) retrotransposons have been developed as a universal marker used in the characterization of both animal and plant species [25]. iPBS markers are the dominant markers and have become a preferred marker in genetic diversity assessment in recent years due to their universality [26]. The universality of the iPBS-retrotransposon marker has been proven and molecular characterization and phylogenetic studies are available for these markers, also in beans [8,24,26]. In our previous studies [26] and in the studies of other researchers [8,9], it has been observed that retrotransposon markers are quite efficient for genetic diversity studies in terms of the total number of amplified and polymorphic bands. The local varieties evaluated so far represent only a small subset of the available resources. In addition, a comprehensive study has not yet been conducted to measure the genetic diversity of bean germplasm in Türkiye. Previous studies [7,8,9,20,26] allow the investigation of the genetic diversity of local bean varieties collected from a very narrow geographical region in Türkiye. There are no previous studies to reveal bean genetic diversity and population structure in Erzurum-Ispir district in the Northeastern Anatolia region of Türkiye using iPBS markers. Therefore, we here investigate the genetic diversity and population structure local bean varieties collected from the district of Ispir, using the iPBS marker system. It is necessary to identify, define, and use genetic resources for the continuity of breeding studies. We expect that our findings here will assist in the use, improvement, and preservation of local varieties that are well adapted to the changing environment.

2. Materials and Methods

2.1. Plant Materials

In this study, 45 Turkish bean (Phaseolus vulgaris L.) local varieties were used as plant material. The names and gathering places of the regional varieties are presented in Table 1 and Figure 1. Bean local varieties were collected in cultivated fields in form eight different Ispir districts of Erzurum in the Northeastern Anatolia region of Türkiye. The plants were grown for tissue sampling in the greenhouse of Atatürk University, Department of Field Crops, Faculty of Agriculture.

2.2. DNA Isolation and Quantification

Young leaves of beans (P. vulgaris L.) approximately 15-day-old plants were ground in liquid nitrogen at the molecular biology and genetics laboratory of Ataturk University. The collective DNA of 45 individuals per participation was then prepared, using the DNA extraction method of Zeinalzadehtabrizi et al. [27], with modifications. The DNA quality was determined by electrophoresis, using agarose gel at 0.8% concentration. A NanoDrop ND-1000 UV/Vi’s spectrophotometer device (Thermo Fisher Scientific Company, Waltham, MA, USA) was used to determine the DNA concentrations. The final DNA concentration was selected for the iPBS analysis. The DNA samples for which the concentrations were determined were stored at –20 °C for PCR (polymerase chain reactions) after further dilution.

2.3. PCR and iPBS Marker Analyses

Genetic diversity analyses were performed with iPBS primers available from Sigma Aldrich (Castle Hill, NSW, Australia). In the present study, 26 iPBS primers developed by Kalendar et al. [28] were used (Table 2). PCR Amplification was performed in a thermos cycler (SensoQuest Labcycler) and were conducted in 10 µL reaction mixture comprising 25 ng template DNA, 0.5 U Taq polymerase, 0.25 mM dNTP, 1 µM (20 pmol) primer, 1X buffer; 2 mM MgCl2. The PCR thermal cycling profile is as follow; initial denaturation for 3 min at 95 °C, 38 cycles of 95 °C for 60 s, 50–60 °C for 60 s, 72 °C for 120 s and final extension at 72 °C for 10 min [29]. All PCR amplification products were resolved in agarose gel at 3% concentration at 200 V for 105 min. Finally, gels were visualized under UV light and photographed by digital camera (Model Nikon Coolpix500).

2.4. Data Scoring and Analysis

The PCR was performed in three replicates for each primer to verify the band pattern consistency. The DNA bands were scored, using TotalLab TL120 software (TotalLab Ltd., Gosforth, Newcastle upon Tyne, UK). For the iPBS amplification products, a band is scored “1” or absent “0” for each locus. Only clear, strong bands were scored, while faint, weak bands were ignored. The Numerical Taxonomy and Multivariate Analysis System for personal computer (NTSYSpc) V.2.0 programs based on the Dice similarity matrix [30] were used to determine the genetic similarities between the varieties. A UPGMA (Unweighted Pair-Group Method with Arithmetic mean) dendrogram was created with the NTSYSpc V.2.0 program. In addition, molecular variance (AMOVA) and PCoA (Principal Coordinate Analysis) analysis were performed using the Genalex 6.5 program [31]. A PIC (Polymorphism Information Content value) was used to assess the diversity of each iPBS marker [32]. The POPGEN v.1.32 program was used to determine the effective number of allele (ne), Nei genetic diversity (h), and Shannon’s information index (I) [33]. The Structure v.2.3.4 program was used to determine the genetic structures of the varieties [34,35]. Evanno’s ∆K [36] and Structure Harvester [37] methods were used to estimate the most expected K value. Using this method, Markov chain Monte Carlo (MCMC) posterior probabilities were estimated. The MCMC chains were run with a 10,000-iteration burn-in period, followed by 100,000 iterations using a model allowing for admixture and correlated allele frequencies. Principal coordinate analysis (PCoA) was performed with the GenALEx 6.5 program [38].

3. Results

3.1. Polymorphism Revealed by iPBS Primers

Sufficiently clear and scoreable bands were obtained from all primers included in the study. With these 26 primers, 1350 visible and scoreable bands were generated. The number of alleles in the primers varied between 23 (iPBS 2077 and 2383) and 80 (iPBS 2274) (Mean 37.14). When the analysis was performed with the iPBS markers, the PIC varied between 0.151 (iPBS 2298) and 0.495 (iPBS 2383) (Mean 0.331). Major allele frequency ranged from 0.528 (iPBS-2383) to 0.888 (iPBS-2298). The mean major allele frequency was 0.706 (Table 3).

3.2. Genetic Diversity

The number of effective alleles (ne), genetic diversity of Nei (h) and Shannon’s information index (I) value of the bean varieties is presented in Table 4. The greatest ne (1.720), h (0.419), and I (0.609) values were observed in variety G36. The lowest ne (1.470), h (0.320), and I (0.500) values were observed in variety G27. The mean ne, h, and I value were calculated as 1.566, 0.361, and 0.546, respectively.

3.3. Heterozygosity and Diversity of Varieties

The summary statistics for nine populations (na: Observed number of alleles, ne: effective number of alleles, I: shannon’s information index, He: expected heterozygosity, uHe: and unbiased expected heterozygosity are listed in Table 5. We determined that the He value ranged from 0.173 (Av) to 0.052 (Kt) (Mean 0.110), while the uHe value ranged from 0.104 (Kt) to 0.208 (Av) (Mean 0.149). The I value among the nine populations ranged from 0.072 (Kt) to 0.286 (Iov) (Mean 0.161). The Percentage of Polymorphic Loci (PPL) for bean was lowest at 10.38% and 13.21%. Among the nine populations of bean, the PPL value ranged from 10.38% (Mv) to 84.30% (Ic) (Mean 28.05%). The h values of the nine bean populations are presented in Table 6. Among the nine populations of bean from Ispir, the smallest h values observed were in Av/Uv (0.068), while the greatest were observed in Ic/Kv (0.232).

3.4. Principal Coordinate Analysis (PCoA) and Dendrogram Generated from 26 iPBS Markers

The unweighted pair-group method with arithmetic mean (UPGMA) dendrogram placed the 45-bean variety into three clusters. There were only 18 (40%), 14 (31.11%) and 13 (28.88%) varieties in the first to three clusteres, respectively (Figure 2). Cluster I contained 18 bean varieties including G36, G45, G44, G43, G42, G41, G40, G39, G38, G37, G35, G34, G33, G32, G30, G31, G29 and G28. Group II contained 14 bean varieties including G27, G26, G25, G24, G23, G22, G21, G20, G19, G18, G16, G15, G17 and G14. In addition, the third subcluster contained 13 bean varieties including G13, G12, G11, G10, G9, G8, G7, G4, G6, G5, G3, G2, and G1. Principal coordinate analysis (PCoA) spatially showed the relative h values between the varieties, revealing three distinct groups. All local varieties collected from Öztoprak Village of Ispir center and one local variety (G26) from Ağilere village are on the upper right, 2 varieties (G25, G27) from Ispir-Center, Maden village, Yeşilyurt and Ağıldere villages are on the lower left. The commercial varieties on the left of the axis and the varieties belonging to other locations are scattered in various parts of the diagram. The result showed the grouping pattern of the PCoA analysis corresponded with cluster analysis (Figure 3). The percentage of genetic diversity explained by each of the three main coordinates of the basic coordinate analysis was determined as 32.34, 6.35 and 5.23, respectively, and these first three components explained 43.92% of the diversity (Table 7). The group I contained G6, G8, G14, G7, G3, G9, G12, G13, G26, G1, G11, G4, G5, G2, G10, G15, G18, G27, G19, G16, G17, G21, G24, G20, G25, G22 and G23 where all of them consisted of Ispir-Öztoprak Village, Ağildere Village, Ispir-Center and Maden Village. The varieties within this group showed higher variation and were scattered over a larger area. The group II comprised of G41 (commercial variety) and G34 (Ulubel village). The third group was composed of all other accessions including G37, G42, G36, G45, G38, G44, G43, G40, G31, G33, G39, G32, G29, G35, G28 and G30. The results showed that G45, G44, G42, G37 and G 36 belong to groups II and III. AMOVA (Analysis of Molecular Variance) was used to detect the total variation and showed that the variation within populations was 67% and that between populations was 33% (Table 8).

3.5. Population Genetic Structure Analysis for iPBS Markers

To understand the population structure among the 45 bean varieties, we divided each entry into corresponding subgroups using the model-based approach in the STRUCTURE software. The ∆K value is used to calculate the optimum K value. The result of genetic structure analysis suggests that the greatest value of K was calculated as 5 (red [A], green [B], blue [C], yellow [D], pink [E]) (membership probability < 0.8) (Figure 4). At K = 5, group I included 1 variety containing G36 mixed with yellow and pink groups. Group II contained 7 varieties including G22, G23, G26, G25, G24, G20, G19. Group III included 12 varieties counting G8, G9, G11, G6, G3, G4, G7, G5, G10, G2 and G12. Group IV included 6 varieties counting G42, G41, G40, G38, and G43. Group V contains 4 varieties including G29, G30, G28 and G31. Furthermore, G21, G17, G16, G18, G27, G13, G14, G15, G1, G39, G44, G44, G37, G32, G33, G34 and G35 were placed in mixed groups (40.00%; membership probability < 0.8). The F-statistic (FST) value was determined as 0.0002, 0.4371, 0.4061, 0.6372, and 0.5440 in the first to fifth subpopulations, respectively. Likewise, the expected heterozygosity values (He) were determined as 0.3210, 0.1858, 0.1947, 0.1567, and 0.1907 in the first to fifth subpopulations, respectively (Table 9 and Table 10).

4. Discussion

Determining the genetic diversity levels of the germplasm of a plant species is essential for the designing and structuring of plant breeding programs [39]. Molecular markers such as iPBS for determining the genetic diversity and associations of varieties and accessions play important roles in targeted parental selection independent of environmental influences. Along with a role of retrotransposons in the diversification of genetic material, retrotransposon activation is reported to be one of the key factors involved in host adaptation to environmental changes [40]. In our study, polymorphic iPBS markers enabled the identification of bean (P. vulgaris L.) species at the molecular level. This provided important information about the genetic associations between these varieties. The information produced by the iPBS marker system suggests that it can be used effectively for diversity studies and genetic analysis in bean varieties. Using this marker system, other researchers have successfully examined similar bean species in genetic diversity studies [6,8,24]. The genetic diversity observed in our study is higher than in similar studies performed on Turkish beans, using different molecular markers [7]. This result clearly indicates that iPBS retrotransposons are highly polymorphic markers. The PIC value is a crucial piece of information that scores the efficacy of polymorphic loci and indicates the discriminatory power of a primer [41]. In our study the PIC varied between 0.151 (iPBS 2298) and 0.495 (iPBS 2383) (Mean 0.331). In a similar study of beans in which iPBS markers were used, PIC values were reported between 0.19 and 0.42 (Mean 0.33) [26]. The results are different to those of [8], who found PIC values between 0.65 and 0.93 (Mean 0.80) in their study with iPBS retrotransposons in beans. The results of the researchers differed, probably due to the varieties being different, while other researchers used fewer markers.
The mean number of effective alleles (ne), genetic diversity of Nei (h) and Shannon’s information index (I) value of the bean varieties were calculated as 1.566, 0.361, and 0.546, respectively. [42], in their study using iPBS markers in peas, reported I values between 0.24 and 0.58 (Mean 0.39). The mean PIC value (0.73) obtained in this study was higher than the studies performed on iPBS markers and guava (0.24) [43] and grape (0.44) [44]. According to the comparison, it can be said that the iPBS primers used in this study of beans are more suitable. The maximum number of effective alleles is always desirable as they indicate the presence of greater genetic variation. Moreover, Shannon’s index of knowledge is an important criterion for understanding variation, as it distinguishes genetic variation in a population combining abundance and uniformity. In a study to explore the genetic diversity and population structure of scarlet eggplant with iPBS markers, the average polymorphism information content was found to be 0.363. The mean effective number of alleles, mean Shannon’s information index and gene diversity values were reported as 1.298, 0.300 and 0.187, respectively [45]. The results differed, probably due to the plant species and the various locations studied. Knowledge of the genetic variation between populations of a plant species is crucial to breeding and conservation [46]. Population-specific traits within each bean strain or variety can also be used to optimize crossbreeding studies.
The population structure identified in this study was consistent with distance-based clustering from principal coordinate analysis (PCoA). In our study, we showed that intraspecific crosses, especially those between the Ic/Kv (0.232), Yy/Ky (0.229), and Kt/Ic (0.222) populations, may produce stronger hybrids, due to their greater genetic distance. We also performed PCoA analysis to examine the genetic associations between bean varieties. In the first three axes, PCoA analysis explained 43.92% of the total variation. In PCoA analysis, cluster analysis data obtained from this matrix are generally considered reliable when the axes explain 25% or more of the total variation [47]. PCoA is a widely used method for assessing genetic diversity based on quantitative and qualitative traits that scales distance data to multidimensional planes to characterize diversity. However, the grouping based on population structure seems to be more accurate, as it could precisely differentiate the bean varieties. Molecular analysis of variance (AMOVA) revealed the presence of high variation within bean varieties, with the percentage of total variance being 67%. It has been stated that higher variations in varieties may be due to reasons such as selection, adaptation, gene flow, genetic drift, variation in ecotypes and pollination method [48].
The findings showed that the bean varieties were divided into five groups according to their genetic structures. Varieties accumulate several living mutations throughout the evolutionary process, which form the basis of genetic diversity. Moreover, recombination, random drift, natural selection, such forces shape the genetic makeup of populations. In the recent past, understanding population structure has become a feature of great interest, as it can be helpful in selecting various parents and mapping sign-trait relationships. As a tool, analysis of population structure can predict similarity levels between individuals, subpopulations, and contributions. When samples are plotted with different geographic origins, analysis of population structure shows the pattern of geographic distribution among populations [49]. In a similar study [9] reported that 67 bean varieties were divided into four subpopulations (K = 4). In a study by [50], SSR markers were used to determine the genetic diversity in 149 dry bean varieties, and the varieties were divided into three subpopulations (K = 3) according to genetic structure analysis. The markers used in the study are primarily effective in grouping the genotypes [17].

5. Conclusions

There are many tools for determining and revealing genetic diversity in plant breeding. However, in plant breeding programs, it is extremely important to know the genetic distance of the varieties that are not clearly defined are unknown in the germplasm. Although classical breeding studies have reached the desired rate in many plant species and varieties, molecular markers provide very important information in breeding programs in genotypes development studies. In addition, the determination of distance and proximity conditions between varieties by performing genetic analyses contributes to the creation of new populations and to obtaining high-yielding varieties with heterosis. Therefore, evaluation of the genetic diversity of local bean varieties is needed for the conservation and breeding of this genetic material. Molecular markers and genetic diversity studies provide the useful information that is so critically needed about population structure. More informative molecular markers, such as iPBS, are being increasingly used in the study of bean genetic diversity, and their power cannot be underestimated. In conclusion, we used the iPBS retrotransposon marker system to generate pre-breeding data that could potentially be applied to the identification of common bean (P. vulgaris L.) genetic re-sources, conservation, and selection of suitable parents to provide greater genetic diversity for use in breeding programs. We showed here that the iPBS marker system is a powerful and easy method for detecting variation among bean varieties. The current findings reveal the diversity in local bean varieties collected from Erzurum-Ispir and will provide a basis for subsequent bean breeding programs, as well as integrity in bean identification studies. According to the information obtained in the study, it was determined that the genetically most distant cultivars were the G1 and G36 local varieties. With future studies, it is thought that these varieties can be used in breeding and hybridization studies, taking into account their agro-morphological characteristics, their resistance to biotic and abiotic conditions.

Author Contributions

K.H. and A.T., concept; K.H. and A.T., design; K.H., E.E. and P.P., resources; E.E., materials; A.T., H.I.Ö. and G.Ö., data collection and/or processing; P.P., data validation; A.T. analysis and/or interpretation; A.T. and H.I.Ö., literature search; A.T., writing; K.H. and P.P., critical reviews; P.P., project administration and funding acquisition. All authors have read and agreed to the published version of the manuscript.

Funding

PP expresses his gratitude for the support of the iASK Research Grant. The authors thank the Helsinki University Library for supporting open-access publication.

Institutional Review Board Statement

Not applicable.

Informed Consent Statement

Not applicable.

Data Availability Statement

Data are contained within the article.

Acknowledgments

Open access funding provided by University of Helsinki, as well as we are very grateful to The Scientific and Technological Research Council of Turkiye (TUBITAK) for generous financial support (Project no 115O260).

Conflicts of Interest

The authors have no conflict of interest to declare.

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Genes 13 01147 g001 550
Figure 1. Locations where local bean varieties were collected (Table 1; 1: Öztoprak village, 2: Ispir Center, 3: Yeşilyurt, 4: Maden Village, 5: Elmalı District Ağıldere village, 6: Ulubel village, 7: Kirazlı village, 8: Köprübaşı town. Commercial cultivars are not shown on the map).
Figure 1. Locations where local bean varieties were collected (Table 1; 1: Öztoprak village, 2: Ispir Center, 3: Yeşilyurt, 4: Maden Village, 5: Elmalı District Ağıldere village, 6: Ulubel village, 7: Kirazlı village, 8: Köprübaşı town. Commercial cultivars are not shown on the map).
Genes 13 01147 g001
Genes 13 01147 g002 550
Figure 2. Dendrogram of 45-bean varieties generated with data from 26 inter primer binding site (iPBS) primers.
Figure 2. Dendrogram of 45-bean varieties generated with data from 26 inter primer binding site (iPBS) primers.
Genes 13 01147 g002
Genes 13 01147 g003 550
Figure 3. Principal coordinates analysis (PCoA) calculated from the pooled data of twenty-six inter-primer binding site (iPBS) primers in 45 bean varieties.
Figure 3. Principal coordinates analysis (PCoA) calculated from the pooled data of twenty-six inter-primer binding site (iPBS) primers in 45 bean varieties.
Genes 13 01147 g003
Genes 13 01147 g004 550
Figure 4. Genetic structure of varieties according to iPBS data (the bean varieties given in K = 5 (Figure 5) are presented in Table 9).
Figure 4. Genetic structure of varieties according to iPBS data (the bean varieties given in K = 5 (Figure 5) are presented in Table 9).
Genes 13 01147 g004
Genes 13 01147 g005 550
Figure 5. Line graphs from the mixture model of Ln P (D) and ∆K for bean populations (a); average value of the Ln P (D) statistics generated by the structure at each value of K (b); DK.
Figure 5. Line graphs from the mixture model of Ln P (D) and ∆K for bean populations (a); average value of the Ln P (D) statistics generated by the structure at each value of K (b); DK.
Genes 13 01147 g005
Table
Table 1. List of beans (P. vulgaris L.) local varieties and commercial cultivars collected from the Erzurum-Ispir district in Türkiye.
Table 1. List of beans (P. vulgaris L.) local varieties and commercial cultivars collected from the Erzurum-Ispir district in Türkiye.
VarietyCollected LocationLatitudeLongitudeAltitude (m)
G1Ispir- Öztoprak village40.51841.0521431
G2Ispir- Öztoprak village40.51841.0521431
G3Ispir- Öztoprak village40.51841.0521431
G4Ispir- Öztoprak village40.51841.0521431
G5Ispir- Öztoprak village40.51841.0521431
G6Ispir- Öztoprak village40.51841.0521431
G7Ispir- Öztoprak village40.51841.0521431
G8Ispir- Öztoprak village40.51841.0521431
G9Ispir- Öztoprak village40.51841.0521431
G10Ispir- Öztoprak village40.51841.0521431
G11Ispir- Öztoprak village40.51841.0521431
G12Ispir- Öztoprak village40.51841.0521431
G13Ispir- Öztoprak village40.51841.0521431
G14Ispir- Öztoprak village40.51841.0521431
G15Ispir-center40.48541.0021264
G16Ispir-center40.46840.9831168
G17Ispir-center40.46840.9831168
G18Yeşilyurt40.51841.0691549
G19Yeşilyurt40.51841.0691549
G20Yeşilyurt40.51841.0691549
G21Maden village40.43540.8511226
G22Maden village40.43540.8511226
G23Maden village40.43540.8511226
G24Maden village40.43540.8511226
G25Ağıldere village40.40140.8341470
G26Ağıldere village40.40140.8341470
G27Ağıldere village40.40140.8341470
G28Ağıldere village40.40140.8341470
G29Ağıldere village40.40140.8341470
G30Ağıldere village40.40140.8341470
G31Ulubel village40.41840.8681424
G32Ulubel village40.41840.8681424
G33Ulubel village40.41840.8681424
G34Ulubel village40.41840.8681424
G35Ulubel village40.41840.8681424
G36Ulubel village40.41840.8681424
G37Kirazlı village40.43640.8871220
G38Kirazlı village40.43640.8871220
G39Köprübaşı town40.43440.8191286
G40Köprübaşı town40.43440.8191286
G41Aras-98Commercial cultivars
G42Elkoca-05
G43Göynük-98
G44Karacaşehir-90
G45Yakutiye-98
Table
Table 2. List of 26 iPBS-retrotransposon primers with their sequence used to elucidate genetic diversity among 45 common bean varieties.
Table 2. List of 26 iPBS-retrotransposon primers with their sequence used to elucidate genetic diversity among 45 common bean varieties.
MarkerPrimers Sequences (5′→3′)MarkerPrimers Sequences (5′→3′)
iPBS-2074GCTCTGATACCAiPBS-2377ACGAAGGGACCA
iPBS-2077CTCACGATGCCAiPBS-2378GGTCCTCATCCA
iPBS-2078GCGGAGTCGCCAiPBS-2380CAACCTGATCCA
iPBS-2079AGGTGGGCGCCAiPBS-2381GTCCATCTTCCA
iPBS-2080CAGACGGCGCCAiPBS-2383GCATGGCCTCCA
iPBS-2095GCTCGGATACCAiPBS-2384GTAATGGGTCCA
iPBS-2231ACTTGGATGCTGATACCAiPBS-2385CCATTGGGTCCA
iPBS-2270ACCTGGCGTGCCAiPBS-2386CTGATCAACCCA
iPBS-2271GGCTCGGATGCCAiPBS-2389ACATCCTTCCCA
iPBS-2274ATGGTGGGCGCCAiPBS-2390GCAACAACCCCA
iPBS-2276ACCTCTGATACCAiPBS-2391ATCTGTCAGCCA
iPBS-2278GCTCATGATACCAiPBS-2392TAGATGGTGCCA
iPBS-2298AGAAGAGCTCTGATACCAiPBS-2402TCTAAGCTCTTGATACCA
Table
Table 3. Twenty-six iPBS primers used in the detection of polymorphism among 40 local varieties and 5 commercial cultivars of beans (P. vulgaris L.).
Table 3. Twenty-six iPBS primers used in the detection of polymorphism among 40 local varieties and 5 commercial cultivars of beans (P. vulgaris L.).
MarkerNumber of AllelesMajor Allele FrequencyPIC *MarkerNumber of AllelesMajor Allele FrequencyPIC *
iPBS-2074400.6510.430iPBS-2377450.7150.309
iPBS-2077230.6530.387iPBS-2378640.8050.241
iPBS-2078710.6820.323iPBS-2380510.6780.336
iPBS-2079350.8100.226iPBS-2381570.6870.359
iPBS-2080430.7560.316iPBS-2383230.5280.495
iPBS-2095640.6910.352iPBS-2384560.7610.252
iPBS-2231520.6550.398iPBS-2385630.7280.313
iPBS-2270250.8770.153iPBS-2386640.6120.397
iPBS-2271360.6740.311iPBS-2389650.5870.396
iPBS-2274800.7430.342iPBS-2390620.6540.431
iPBS-2276420.7320.329iPBS-2391530.6680.341
iPBS-2278570.7000.338iPBS-2392470.6540.379
iPBS-2298720.8880.151iPBS-2402600.7760.292
Mean520.7060.331
* PIC: Polymorphism Information Content.
Table
Table 4. Summary statistics for mean values for beans (P. vulgaris L.) varieties assessed with 26 iBPS primers.
Table 4. Summary statistics for mean values for beans (P. vulgaris L.) varieties assessed with 26 iBPS primers.
Varietyne *h **I *Varietyne *h **I *
G11.4910.3290.511G241.5300.3470.531
G21.5380.3500.534G251.5860.3690.556
G31.5400.3510.535G261.5500.3550.540
G41.6010.3760.563G271.4700.3200.500
G51.5210.3430.526G281.6580.3970.586
G61.5680.3620.548G291.6960.4100.601
G71.6090.3790.566G301.6420.3910.580
G81.6040.3770.564G311.6880.4080.598
G91.5930.3720.560G321.5880.3700.557
G101.5910.3720.559G331.5860.3690.556
G111.5760.3650.552G341.5240.3440.528
G121.5890.3710.558G351.4760.3220.503
G131.5490.3540.539G361.7200.4190.609
G141.5680.3620.548G371.6480.3930.582
G151.5620.3600.546G381.5200.3420.526
G161.5380.3500.535G391.5670.3620.548
G171.5380.3500.534G401.5280.3450.529
G181.5700.3630.549G411.5640.3610.546
G191.4700.3200.500G421.5620.3600.546
G201.5260.3450.529G431.5860.3700.556
G211.5400.3510.535G441.5560.3580.543
G221.5140.3400.523G451.5050.3350.518
G231.5210.3420.526Mean1.5660.3610.546
* ne: Number of effective alleles; ** h: genetic diversity of Nei; * I: Shannon’s information index.
Table
Table 5. Summary statistics for 45 bean (P. vulgaris L.) varieties assessed with 26 iPBS primers.
Table 5. Summary statistics for 45 bean (P. vulgaris L.) varieties assessed with 26 iPBS primers.
PopulationnnaneIHeuHePPL (%)
Av60.9081.3050.2530.1730.20843.40
Iov141.0981.2700.2540.1650.17824.72
Ic30.5191.1660.1320.0920.13853.58
Kv20.3891.1320.0920.0660.13220.75
Kt20.3361.1040.0720.0520.10413.21
Mv40.6131.1820.1580.1070.14310.38
Uv60.7811.2180.1950.1300.15626.98
Yy30.5601.1900.1510.1060.15835.66
Com50.5741.1650.1420.0960.12023.77
Mean 0.6421.1920.1610.1100.14928.05
n: number of sample size, na: number of distinct alleles, ne: effective number of alleles, I: Shannon’s information index, He: expected heterozygosity, uHe: unbiased expected heterozygosity, PPL: percentage of polymorphic loci; Av: Ağıldere village, Iov: Ispir-Öztoprak village, Ic: Ispir-center, Kv: Kirazlı village, Kt: Köprübaşı town, Mv: Maden village, Uv: Ulubel village, Yy: Yeşilyurt, Com: Commercial variety.
Table
Table 6. Pairwise population matrix of Nei genetic distance for nine groups of bean (P. vulgaris L.) varieties.
Table 6. Pairwise population matrix of Nei genetic distance for nine groups of bean (P. vulgaris L.) varieties.
AvComIovIcKvKtMvUvYy
Av0.000
Com0.1250.000
Iov0.1240.1790.000
Ic0.1370.2150.0810.000
Kv0.1280.0720.2090.2320.000
Kt0.1290.0710.2070.2220.0710.000
Mv0.0990.2020.1140.1090.2150.2110.000
Uv0.0680.0850.1770.2020.0810.1080.1840.000
Yy0.1190.2070.1040.0860.2290.2120.0870.1970.000
Av: Ağıldere village, Com: Commercial variety, Iov: Ispir-Öztoprak village, Ic: Ispir-center, Kv: Kirazlı village, Kt: Köprübaşı town, Mv: Maden village, Uv: Ulubel village, Yy: Yeşilyurt.
Table
Table 7. PCoA analysis of bean varieties.
Table 7. PCoA analysis of bean varieties.
Axis123
%32.346.355.23
Cum %32.3438.6943.92
Table
Table 8. AMOVA of bean varieties, using inter primer binding site (iPBS) marker.
Table 8. AMOVA of bean varieties, using inter primer binding site (iPBS) marker.
SchemeDegree of Freedom (DF)Sum of Squares (SS)Variance Component% Of Total Variancep-Value
Among Population81150.7021.43933%0.332
Within Population361554.8943.19267%0.001
Total442705.6064.631100%
Table
Table 9. Membership coefficients of five subpopulations of bean varieties.
Table 9. Membership coefficients of five subpopulations of bean varieties.
Subpopulation Subpopulation
VarietiesIIIIIIIVVVarietiesIIIIIIIVV
G10.4010.0050.5790.0040.012G240.0170.9460.0090.0250.003
G20.0590.0050.9230.0080.006G250.0210.9600.0020.0040.014
G30.0090.0020.9720.0130.004G260.0120.9680.0040.0050.011
G40.0140.0120.9700.0030.001G270.3990.5600.0100.0110.019
G50.0110.0110.9610.0110.006G280.0330.0180.0040.0070.938
G60.0080.0030.9750.0110.003G290.0040.0020.0030.0020.989
G70.0240.0020.9690.0020.002G300.0090.0040.0050.0040.979
G80.0020.0030.9930.0010.001G310.2140.0030.0050.0100.767
G90.0070.0090.9800.0030.002G320.0100.0040.0030.2570.727
G100.0070.0410.9460.0030.003G330.0110.0240.0060.2860.674
G110.0050.0100.9790.0030.003G340.0020.0020.0020.4320.561
G120.0140.0700.9090.0040.003G350.0300.0950.0060.3420.528
G130.0250.2050.7090.0310.030G360.7020.0020.0030.0460.246
G140.0130.2980.6820.0030.004G370.3780.0040.0020.5720.043
G150.0070.3200.6650.0040.004G380.0090.0060.0090.8570.118
G160.0170.6400.3360.0050.002G390.1500.0410.0050.7920.012
G170.0030.6700.3230.0020.002G400.0780.0280.0070.8700.017
G180.0140.6250.3440.0070.009G410.0090.0040.0030.9840.002
G190.0310.8490.1000.0090.012G420.0030.0010.0020.9920.002
G200.0200.8930.0810.0040.003G430.0880.0040.0640.8230.022
G210.2780.7010.0150.0030.003G440.3550.0060.0030.6310.005
G220.0030.9880.0030.0020.004G450.2460.0030.0130.7350.002
G230.0050.9840.0040.0020.004
Table
Table 10. Expected heterozygosity (He) and FST values in four squash subpopulations.
Table 10. Expected heterozygosity (He) and FST values in four squash subpopulations.
Subpopulation (K)Expected Heterozygosity (He)FST
10.32100.0002
20.18580.4371
30.19470.4061
40.15670.6372
50.19070.5440
Mean0.21030.4049
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Haliloğlu, K.; Türkoğlu, A.; Öztürk, H.I.; Özkan, G.; Elkoca, E.; Poczai, P. iPBS-Retrotransposon Markers in the Analysis of Genetic Diversity among Common Bean (Phaseolus vulgaris L.) Germplasm from Türkiye. Genes 2022, 13, 1147. https://doi.org/10.3390/genes13071147

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Haliloğlu K, Türkoğlu A, Öztürk HI, Özkan G, Elkoca E, Poczai P. iPBS-Retrotransposon Markers in the Analysis of Genetic Diversity among Common Bean (Phaseolus vulgaris L.) Germplasm from Türkiye. Genes. 2022; 13(7):1147. https://doi.org/10.3390/genes13071147

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Haliloğlu, Kamil, Aras Türkoğlu, Halil Ibrahim Öztürk, Güller Özkan, Erdal Elkoca, and Peter Poczai. 2022. "iPBS-Retrotransposon Markers in the Analysis of Genetic Diversity among Common Bean (Phaseolus vulgaris L.) Germplasm from Türkiye" Genes 13, no. 7: 1147. https://doi.org/10.3390/genes13071147

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