Genetic Distance Estimates Research Articles

Microsatellite based genetic diversity and population structure of nine indigenous Chinese domestic goats

Determination of genetic diversity and population structure plays an important role in supporting genetic improvement programs and future conservation plans. In this study, 352 individuals representing nine Chinese indigenous goat populations distributed in China were genotyped at 15 microsatellite loci. The mean number of alleles (MNA) per breed ranged from 3.867 (Matou goat, MT) to 5.400 (Ujumqin white goat, UW), the expected heterozygosity (He) varied from 0.482 (Hainan black goat, HNB) to 0.659 (UW). Allelic diversity and heterozygosity measures in the studied populations were much lower than Chinese Cashmere and meat type goats. Global F statistics revealed 9.8% of total variance explained among breeds while 90.2% of variance was due to diversities within breeds. Three major population clusters were observed broadly conforming to geographical locations of different goat populations. Three-dimensional scatterplot derived from three largest principal components supported the observed phylogeny based on genetic distance estimations. Goats from Northern China and Island region were distinct while strong admixture was observed among goat populations from Central China. The study revealed market orientation and geographical distances among populations might have contributed to the genetic structure and population sub-division among Chinese indigenous goats. Our study provided a new insight into understanding the genetic diversity and structure of Chinese indigenous goat breeds, and will be helpful to determine the strategies for breeding and conservation programs.

Review of chromosome races in blind mole rats (SpalaxandNannospalax)

The blind mole rats (Spalacinae) reveal fascinating chromosomal variation, resulting from complex karyotype re-arrangements. This variation occurs between species, between populations of single species (polytypy) and within populations (polymorphism). This article reviews the current knowledge on blind mole rats' karyotypes and their variation. A special attention is paid to differentiation of the karyotype within a species and the patterns of chromosomal variation, which result in evolution of distinct chromosomal races (cytotypes). The chromosome races are defined as a group of geographically contiguous or recently separated populations which share a similar chromosome complement by descent. The present review indicated the existence of 73 distinct chromosome races recorded in blind mole rats classified within the genus Nannospalax, along with the seven species recognized within the genus Spalax. In total, 12 distinct diploid numbers of chromosomes were reported (2n = 36-62); and variation in chromosome morphologies was observed between populations with the same number of chromosomes (NF = 62-124). The blind mole rats classified in the genus Spalax revealed rather uniform karyotype both between and within the recognized species. Considering the traditional species classified in the Nannospalax genus, 25 races can be distinguished within N. leucodon, 28 races within N. xanthodon and 20 races within N. ehrenbergi. Hybrids between the races are found only exceptionally and they seem to be almost absent in extensive areas (Europe, Turkey). This fact indicates that chromosomal evolution in blind mole rats may be related to speciation processes. The definitive phylogenetic and taxonomic conclusions can be derived only after application of reliable molecular markers and setting of estimates of genetic distances and gene flow between populations.

Rice Chloroplast Genome Variation Architecture and Phylogenetic Dissection in Diverse Oryza Species Assessed by Whole-Genome Resequencing.

BackgroundChloroplast genome variations have been detected, despite its overall conserved structure, which has been valuable for plant population genetics and evolutionary studies. Here, we described chloroplast variation architecture of 383 rice accessions from diverse regions and different ecotypes, in order to mine the rice chloroplast genome variation architecture and phylogenetic.ResultsA total of 3677 variations across the chloroplast genome were identified with an average density of 27.33 per kb, in which wild rice showing a higher variation density than cultivated groups. Chloroplast genome nucleotide diversity investigation indicated a high degree of diversity in wild rice than in cultivated rice. Genetic distance estimation revealed that African rice showed a low level of breeding and connectivity with the Asian rice, suggesting the big distinction of them. Population structure and principal component analysis revealed the existence of clear clustering of African and Asian rice, as well as the indica and japonica in Asian cultivated rice. Phylogenetic analysis based on maximum likelihood and Bayesian inference methods and the population splits test suggested and supported the independent origins of indica and japonica within Asian cultivated rice. In addition, the African cultivated rice was thought to be domesticated differently from Asian cultivated rice.ConclusionsThe chloroplast genome variation architecture in Asian and African rice are different, as well as within Asian or African rice. Wild rice and cultivated rice also have distinct nucleotide diversity or genetic distance. In chloroplast level, the independent origins of indica and japonica within Asian cultivated rice were suggested and the African cultivated rice was thought to be domesticated differently from Asian cultivated rice. These results will provide more candidate evidence for the further rice chloroplast genomic and evolution studies.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-016-0129-y) contains supplementary material, which is available to authorized users.

The Evolutionary History and Genetic Diversity of Kinkajous, Potos flavus (Carnivora, Procyonidae)

The genus Potos (Procyonidae) is currently recognized as a monotypic genus comprising the single species Potos flavus, the kinkajou. Kinkajous are widely distributed throughout forested habitats of tropical Central and South America, extending from eastern Brazil across central Bolivia, eastern Peru, northern Ecuador, Guianas, Suriname, Venezuela, Colombia, and then through Central America and into western Mexico. The taxonomic history of the species is complex, with seven or eight subspecies historically recognized to acknowledge the phenotypic variation among populations. In this study, the systematics and the evolutionary history of Potos flavus were investigated based on the mitochondrial gene cytochrome b, including specimens from a large range of localities, covering most of the distribution of the species, from central Middle America (Costa Rica and Panama) through South America (Ecuador, Peru, Bolivia, Brazil, Guyana, and French Guiana). Analyses of 30 Potos flavus sequences showed 27 haplotypes that were grouped in five main clades in all phylogenetic analyses. These clades suggested a high geographic structure with specimens from (1) Costa Rica, (2) Guianas and North Brazil, (3) North Peru, (4) Ecuador and Panama, (5a) interfluves Branco-Negro rivers in the Brazilian Amazon, (5b) Eastern Atlantic Forest, (5c) Amazonian lowlands east Negro river including Bolivia, Peru, and West Brazil. Each of these clades differs from 4.5 % to 9.3 % in their genetic distance estimates, which suggests that the specific status of some of these lineages should be reconsidered. Divergence dating and biogeographic analysis suggested that crown Potos diversified in the Miocene-Pliocene in South America, and geographic barriers, such as savannas and rivers, may have played a significant role in the kinkajou diversification.

Genetic characterization of Ocimum genus using flow cytometry and inter-simple sequence repeat markers

The taxonomy of the Ocimum genus is difficult and still unclear, mainly due to the existence of numerous, morphologically similar species, varieties and forms, many synonymous names, together with the occurrence of the interspecific hybridization, polyploidy, aneuploidy and other changes in the genome structure, which makes the identification as well as characterization of the Ocimum species/varieties very problematical. Molecular identification by estimation of genome size and ISSR markers proved to be effective in the Ocimum species and cytotypes identification, and in establishing a relationship between them. Genome size estimation revealed that Ocimum species possessed very small, small and intermediate genomes. Furthermore, within one species different values of genome size occurred, which indicated the presence of polyploids and aneuploids. Among O. americanum accessions three different values of genome size we detected: 2.3, 4.4 and 7.4pg/2C, while within O. basilicum accessions most of the genotypes possessed genome with 4.4–4.9pg/2C DNA content and two accessions, from India and Iran, with 7.3 and 7.4pg/2C, respectively. Similarly, in O.×citriodorum genomes with 4.6, 6.9 and 7.5pg/2C DNA content were observed. Very small genomes were detected in O. campechianum (1.2pg/2C) and in O. gratissimum (1.8–2.3pg/2C), while small genome in O. selloi (3.1pg/2C). Within O. tenuiflorum accessions with 0.9, 1.9 and 4.5pg/2C DNA content were identified. Genome size estimation allowed to distinguish some species and cytotypes, and can be used as a first step in species identification. However, more precise and detailed characterization was provided by ISSR markers. Using one of the following primers (GACA)4T, (AG)8YA and (CA)6AC, it was possible to identify species, cytotypes, and also some varieties/cultivars. The relationships within tested accessions reflected by genetic distance estimation and dendrogram construction revealed the existence of three main clusters and one accession (O.×citriodorum, USA) being not clustered to any of the created groups. The first cluster grouped all accessions of O. basilicum and two of O.×citriodorum, the second cluster–all accessions of O. americanum, O. tenuiflorum with small genome size and one accession of O.×citriodorum. The third cluster was the most diversified since it contained O. gratissimum, O. campechianum, O. selloi and O. tenuiflorum (accessions with very small genomes). The identification system composed of flow cytometry and ISSR-PCR techniques demonstrated to be useful for genotypes in the Ocimum genus.

The invasive Asian green mussel Perna viridis in South Africa: all that is green is not viridis

The Asian green mussel Perna viridis is an invasive Indo-Pacific species recently reported from South African harbours. To verify the invasion, a phylogenetic (and morphological) analysis of green-shelled mussels (n = 39), found in six South African harbours, was conducted using the mitochondrial cytochrome c oxidase subunit I gene (COI). Estimates of genetic distances using the neighbour-joining analysis identified P. viridis only from Durban Harbour. All other green mussels were more than 3.2% divergent from P. viridis and were identified as green-shelled variants of indigenous P. perna. The only reliable morphological differences distinguishing the two species were the poorly developed mantle papillae and the wavy pallial line in P. viridis. The confirmed occurrence of P. viridis in a South African harbour suggests that there is a possible threat of the species becoming established and then spreading onto the open coast and competing with indigenous P. perna.

Characterization of rare migratory cattle and evaluation of its phylogeny using short-tandem-repeat-based markers

ABSTRACTBovine-specific microsatellite markers were used to assess the genetic variation in Belahi cattle. Both within-breed (Belahi) and between-breed (Sahiwal, Gir, Tharparkar, Rathi, Nagori, Mewati, Kankrej and Belahi breeds) diversity indices were estimated. Sixteen microsatellite loci were polymorphic with more than five alleles per locus. Mean allelic diversity was 9.31, with a total of 149 alleles. Polymorphism information content varied from 0.31 (TGLA227) to 0.87 (CSSM33) with an average of 0.71. Estimate of Nei’s gene diversity was 0.72 ± 0.15. The observed and expected heterozygosity at different loci were 0.69 ± 0.17 and 0.71 ± 0.15 and varied from 0.30 (TGLA227) to 0.88 (TGLA122) and 0.32 (TGLA227) to 0.88 (CSSM33), respectively. Within-population inbreeding estimates (FIS) for Belahi cattle was 0.0337, indicating an average deficiency of 3.37%. Belahi cattle revealed the presence of genetic diversity within population and there was no significant heterozygosity excess indicating the absence of genetic bottleneck in the recent past. Global FST estimates demonstrated that 85% of the total variation was contributed by within-breed genetic differentiation, while 15% genetic variation was present across different breeds. Nei’s standard genetic distance estimates among the studied milch breeds varied from 0.27 (Tharparkar and Rathi) to 0.51 (Tharparkar and Sahiwal), whereas in studied dual-purpose breeds, it varied from 0.07 (Kankrej and Mewati) to 0.90 (Belahi and Mewati). Unweighted Pair Group Method with Arithmetic Mean based phylogenetic tree constructed from the Nei’s genetic distances revealed that Sahiwal and Belahi cattle were grouped together in one cluster. However, Kankrej and Mewati were found to be closely related breeds.

Genetic structure and diversity of Glehnia littoralis, an endangered medicinal plant in China

The medicinal plant Glehnia littoralis has become increasingly endangered in China. To assist in the formulation of conservation strategies for this species, we assessed the genetic diversity of G. littoralis with a total of 172 samples from 10 populations using SRAP markers. The results showed that Nei's gene diversity (H) per locus ranged from 0.04 to 0.2504, with an average of 0.245, and that Shannon's information index (I) ranged from 0.233 to 0.6253, averaging 0.5516 at the population level. The total genetic diversity (Ht) was 0.2471, and 66.5% (Hs = 0.1643) of the total genetic variation was attributed to within-population diversity (P < 0.05), with the rest (33.5%) due to differences between populations (Gst = 0.3353), indicating that gene flow was restricted among populations (Nm = 0.9911). AMOVA also suggested that the main source of variation was within populations (77.8%), whereas 22.2% of differentiation was found among populations. Estimates of genetic distance were not correlated with geographic distance according to a Mantel test (r = 0.0792, P = 0.329). These results show that high levels of genetic variation are present within and among populations. The endangered status of this species is likely due to the destruction of the habitats of the wild populations, rather than a loss of genetic diversity.

A high-dimensional linkage analysis model for characterizing crossover interference.

Linkage analysis has played an important role in understanding genome structure and evolution. However, two-point linkage analysis widely used for genetic map construction can rarely chart a detailed picture of genome organization because it fails to identify the dependence of crossovers distributed along the length of a chromosome, a phenomenon known as crossover interference. Multi-point analysis, proven to be more advantageous in gene ordering and genetic distance estimation for dominant markers than two-point analysis, is equipped with a capacity to discern and quantify crossover interference. Here, we review a statistical model for four-point analysis, which, beyond three-point analysis, can characterize crossover interference that takes place not only between two adjacent chromosomal intervals, but also over multiple successive intervals. This procedure provides an analytical tool to elucidate the detailed landscape of crossover interference over the genome and further infer the evolution of genome structure and organization.

Genetic variation in sorghum as revealed by phenotypic and SSR markers: implications for combining ability and heterosis for grain yield

AbstractHybrid breeding relies on selection of genetically unrelated and complementary parents for key traits. The objective of this study was to examine genetic variation and identify unique sorghum genotypes using phenotypic and simple sequence repeat (SSR) markers and to determine their relationships with combining ability and heterosis for grain yield. A total of 32 landraces and four cytoplasmic male sterile (CMS) lines were phenotyped using 25 agro-morphological traits and genotyped with 30 polymorphic SSR markers. The landraces were crossed with four CMS lines using a line × tester mating design. The 128 hybrids, 36 parentals and four check varieties were field-evaluated using a 12 × 14 alpha lattice design with three replications. General combining ability (GCA), specific combining ability (SCA) and heterosis for grain yield were determined. Genetic distance estimates ranged from 0.39 to 0.60 and 0.50 to 0.79, based on phenotypic and SSR markers, respectively. Landraces 72572, 75454, 200654, 239175, 239208, 244735A and 242039B and CMS lines ICSA 743 and ICSA 756 displayed positive and significant GCA effects for grain yield. Based on the SCA effects of yield, lines were classified into three heterotic groups aligned to the different cytoplasmic systems of testers. Lines with high GCA effects rendered hybrids with highly significant SCA effects with high mid-parent heterosis (MPH) for grain yield. Both marker systems were effective in demarcating sorghum genotypes that provided desirable cross-combinations with high combining ability effects and MPH for grain yield. The selected genotypes are recommended as potential parents for sorghum hybrid breeding in moisture stress environments.

Robust Estimation of Evolutionary Distances with Information Theory.

Methods for measuring genetic distances in phylogenetics are known to be sensitive to the evolutionary model assumed. However, there is a lack of established methodology to accommodate the trade-off between incorporating sufficient biological reality and avoiding model overfitting. In addition, as traditional methods measure distances based on the observed number of substitutions, their tend to underestimate distances between diverged sequences due to backward and parallel substitutions. Various techniques were proposed to correct this, but they lack the robustness against sequences that are distantly related and of unequal base frequencies. In this article, we present a novel genetic distance estimate based on information theory that overcomes the above two hurdles. Instead of examining the observed number of substitutions, this method estimates genetic distances using Shannon's mutual information. This naturally provides an effective framework for balancing model complexity and goodness of fit. Our distance estimate is shown to be approximately linear to elapsed time and hence is less sensitive to the divergence of sequence data and compositional biased sequences. Using extensive simulation data, we show that our method 1) consistently reconstructs more accurate phylogeny topologies than existing methods, 2) is robust in extreme conditions such as diverged phylogenies, unequal base frequencies data, and heterogeneous mutation patterns, and 3) scales well with large phylogenies.

Renewal of wild grapevine (Vitis vinifera L. subsp. sylvestris (Gmelin) Hegi) populations through sexual pathway: Some Italian case studies

Wild Euro-Asiatic grapevine (Vitis vinifera L. subsp. sylvestris (Gmelin) Hegi) is an opportunistic liana with reproductive patterns characterized both by vegetative propagation and sexual reproduction. Vegetative propagation would ensure a rapid vine regeneration and land colonization, while sexual reproduction would assure genetic recombination and chromosome re-assortment crucial for evolution and survival of the species. The aim of this study was the analysis of the parentage relationships within and between fourteen Italian wild grapevine populations, in order to characterize the natural mating system of this taxon. Beside parentage relationship analyses, the estimation of genetic diversity, genetic distance and genetic differentiation were assessed. The populations showed a good extent of genetic diversity and low levels of genetic distance and isolation between them, indicating gene flow among sites. This result was supported by parentage relationships between different populations. Nevertheless, populations from North Italy showed the lowest genetic diversity, while internal relatedness and inbreeding estimation values were higher than the populations from Central and Southern Italy. One of the northern populations resulted particularly high in inbreeding intensity. The parentage relationship analysis pointed out in all sites a, sometimes active, sexual reproduction within populations. Seed dispersal by frugivorous vectors among neighbouring sites seemed less frequent and depending on specific environmental circumstances.

Genetic diversity in sorghum mini-core and elite rainy and post-rainy genotypes of India

Knowledge on genetic diversity is necessary to determine the relationships among the genotypes, which allow the selection of individual accessions for crop breeding programmes. The present study aimed at assessing the extent and pattern of genetic diversity within a set of 251 sorghum genotypes using SSR markers. A total of 393 alleles were detected from the 251 genotypes, with the number of alleles ranging from 2 (Xcup11) to 24 (Sb5-206) and an average of 10.07 alleles per primer pair. Pairwise Wright's FSTstatistic and Nei's genetic distance estimates revealed that the race and geographical origin were responsible for the pattern of diversity and structure in the genetic materials. In addition, the analysis also revealed high genetic differentiation between the rainy and post-rainy sorghum groups. Narrow diversity was observed among the different working groups in the rainy (restorers and varieties) and post-rainy (varieties and advanced breeding lines) sorghum groups. Neighbour-joining and STRUCTURE analysis also classified 44 elite lines broadly into two distinct groups (rainy and post-rainy). However, limited diversity within the rainy and post-rainy sorghum groups warranted an urgent need for the utilization of diverse germplasm accessions for broadening the genetic base of the Indian breeding programme. The diverse germplasm accessions identified from the mini-core accessions for utilization in breeding programmes are discussed.

Resolving patterns of population genetic and phylogeographic structure to inform control and eradication initiatives for brown rats Rattus norvegicus on South Georgia

Summary The control and eradication of invasive species is a common management strategy to protect or restore native biodiversity. On South Georgia in the Southern Ocean, the brown rat Rattus norvegicus was brought onto the island with the onset of whaling and sealing activity in the 1800s and has had a significant detrimental impact on key bird species of conservation concern. Efforts to eradicate rats from South Georgia using poisoned bait are ongoing. Despite the South Georgia rat eradication programme being the geographically largest and most ambitious eradication initiative to date, its success is facilitated by the potential that rat populations are effectively isolated by glacial barriers. This allows for localized eradication effort at manageable scales, leading to sequential eradication of individual populations with minimal risk of incursion from neighbouring areas. Here, we use the levels of population genetic divergence estimated from 299 single nucleotide polymorphism (SNP) loci and DNA sequence variation across 993 base pairs of the mitochondrial DNA cytochrome B locus to examine whether rat populations from nine glacially isolated areas on South Georgia are genetically distinct and so can be treated as independent eradication units. Bayesian clustering of individuals based on SNP similarity identified seven different genetic groups, which were confirmed using analyses based on pairwise genetic distance estimates and ordination of individuals using principal coordinate analysis. From a management perspective, these seven groups represent individual targets in baiting operations. Two mtDNA haplotypes were resolved across South Georgia, with a distinct geographical separation between the north‐western and south‐eastern populations. Approximate Bayesian computation (ABC) was used to identify that this divergence was a consequence of two separate historical colonization events. Synthesis and applications. We illustrate that molecular markers are a valuable tool in species management and pest eradication given that the spatial distribution of genetic diversity can: (i) identify demographically and genetically independent populations on which local eradication effort can be focussed, (ii) distinguish between incomplete eradication and immigration in situations where individuals remain after eradication has been attempted and (iii) identify the source of migrants when dispersal occurs over large spatial scales.

Phylogenetic Analysis of Poliovirus Sequences.

Comparative genomic sequencing is a major surveillance tool in the Polio Laboratory Network. Due to the rapid evolution of polioviruses (~1 % per year), pathways of virus transmission can be reconstructed from the pathways of genomic evolution. Here, we describe three main phylogenetic methods; estimation of genetic distances, reconstruction of a maximum-likelihood (ML) tree, and estimation of substitution rates using Bayesian Markov chain Monte Carlo (MCMC). The data set used consists of complete capsid sequences from a survey of poliovirus sequences available in GenBank.

Voice Characteristics of Some Sheep: Utilization to Estimation of genetic distance

Sound analysis has been carried out in various activities including identification and differentiation of species as well as the preparation of the taxonomy of some animals’ species because of several advantages, including no need to capture or too close to the subject observed. Analysis of voice used to differentiate and to estimate of breeds’ sheep genetic distance has not been reported. This research was conducted to study the character of a few breeds’ sheep sound and likely to be used as a predictor of genetic distance between breeds of sheep. The study was conducted in the Animal House at Indonesian Research Institute for Animal Production, Bogor. A total of 20 head adult of five sheeps (St. Croix cross / SC, Barbados Black Belly cross / BC, Local Garut/LG, Composite Garut / KG and Composites Sumatra / KS) used in this study. Call sound recorded using a digital voice recorder. Sound analysis performed by Raven Software Pro 1.3 for Windows to count as many as 24 variables sound. Analysis of variance of each variable sound was performed using PROC GLM of SAS software Ver. 9.0. It used PROC CANDISC for canonical discriminant analysis and then PROC TREE to build a dendogram. The results showed that there were variations in amplitude, energy, power and frequency variables among the five breeds of sheep. By plotting canonical, LG, KS and BC sheep were from a different group. It was concluded that the sound characteristics variables which can be used as a differentiator breeds of sheep were the third quartile frequency, center frequency, maximum frequency and the first quartile time. Dendogram showed that KG sheep was in the less accurate group. Genetic distance estimation method using voice characteristic data may be applied on sheep. Key Words : Characteristics, Call Voice, Differentiation, Genetic Distance, Sheep

Diversity assessment of drought tolerant exotic and adapted maize (Zea mays L.) inbred lines with microsatellite markers

Knowledge about the genetic diversity within a germplasm allows for a more effective and efficient use of resources for crop improvement programs. Diversity assessment of 48 tropical drought-tolerant maize inbreds, 24 each from CIMMYT and IITA, was carried out with microsatellite markers to determine the genetic divergence between the two groups of maize inbred lines. Eighty-one polymorphic SSR markers were used for the assessment. Results showed that the average number of alleles per locus was 3.7. The mean polymorphic information content (PIC) was 0.51 whereas the average modified Roger’s genetic distance (MRD) was 0.49. The mean genetic distance estimates between the CIMMYT and IITA lines were higher than the mean genetic distance among IITA lines or among CIMMYT lines. The average linkage cluster analysis separated the lines into two broad groups along institutional lines. The observed sub-groups within each main group were reflections of the relationships of the lines based on pedigree records. The F ST value of 19.5% reflects a high level of genetic differentiation between the two groups of lines. The results highlighted the presence of appreciable genetic divergence between CIMMYT and IITA lines that can be exploited for superior hybrid maize development.

Tolerance to preharvest sprouting and yield of wheat genotypes from different breeding programs

Abstract:The objective of this work was to characterize the performance of elite wheat genotypes from different Brazilian breeding programs for traits associated with grain yield and preharvest sprouting. The study was conducted in 2010 and 2011 in the municipality of Capão do Leão, in the state of Rio Grande do Sul, Brazil, in a randomized complete block design with three replicates. Thirty-three wheat genotypes were evaluated for traits related to preharvest sprouting and grain yield. The estimate of genetic distance was used to predict potential combinations for selection of plants with high grain yield and tolerance to preharvest sprouting. The combined analysis of sprouted grains and falling number shows that the TBIO Alvorada, TBIO Mestre, Frontana, Fundacep Raízes, Fundacep Cristalino, and BRS Guamirim genotypes are tolerant to preharvest sprouting. Combinations of TBIO Alvorada and TBIO Mestre with Fundacep Cristalino show high potential for recovering superior genotypes for high grain yield and tolerance to preharvest sprouting.

Genetic diversity of Iranian melon cultigens revealed by AFLP markers

Iran is a part of the secondary centre of origin of melons, and therefore, there is a wealth of genetic variation of these species in this country. The Amplified Fragment Length Polymorphism (AFLP) marker was applied to investigate the genetic variations among five major Iranian melon cultigens (Cucumis melo) and ‘Ananasi’ as a general well-known cultivar. Ten primer pairs were used on 90 individuals producing 318 polymorphic fragments, with an average of 31.8 fragments per primer combination. The polymorphism rates ranged from 80 to 100%. The genetic similarities among accessions were calculated according to Dice’s Similarity Index and used to construct a dendrogram based on the Unweighted Pair Group Method with Arithmetic Average (UPGMA). The genetic distance estimates based on AFLPs ranged from 0.29 to 0.63, with a mean of 47±0.3. Iranian melon genotypes and the ‘Ananasi’ cultivar were considered as two separate groups on the cluster analysis. The principal coordinate analysis showed a separate allocation of the melon cultivar groups. The results demonstrated a wide diversity of Iranian melon cultigens. The high number of alleles and the high expected genetic diversity detected with the AFLP marker indicated that the Iranian melon cultigens had distinctive characteristics and were an important genetic diversity pool, which made them a valuable source of breeding materials.

Genetic diversity and distribution patterns of Ecuadorian capuli (Prunus serotina)

Prunus serotina subsp. capuli (Cav.) is an arboreal species with promising economic prospects in the timber, health-food and neutraceutical markets. Despite its cultural and commercial significance, limited information exists with regards to the degree of genetic variation and ecological history of P. serotina in Ecuador. The main objective of this study was to evaluate the degree of genetic diversity and population structure of Ecuadorian P. serotina, as a preliminary step towards understanding the distribution history of this species in Ecuador and establishing germplasm conservation programs. P. serotina samples (217, representing 8 provinces from the Ecuadorian highlands) were characterized using 8 heterologous SSR markers derived from related Prunus species. Expected heterozygosity across samples (He = 0.71) reveals a moderate level of genetic diversity for Ecuadorian P. serotina. Nevertheless, simple allele-count analysis indicates that Ecuadorian capuli has a narrower degree of allelic richness relative to collections from the species’ center of origin in North America. Furthermore, pairwise F statistics (0.0069 ≤ Fst ≤ 0.0319) and Nei genetic distance estimates (0.02 ≤ Ds ≤ 0.09) indicate minimal population differentiation within Ecuadorian capuli. However, Bayesian population structure analysis suggests a subtle genetic contrast between germplasm from the Northern and Southern highlands. Certainly, it is of interest to analyze whether this underlying genetic differentiation between the Northern- and Southern-Highland groups is also manifested in morphological, agronomic or other phenotypic characters that could indicate adaptive differences to divergent agro-ecosystems.