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In the present study we sequenced or re-sequenced, assembled and annotated 15 mitochondrial genomes representing the 12 currently recognised taxa of Trichinella using a deep sequencing-coupled approach. We then defined and compared the gene order in individual mitochondrial genomes (∼14 to 17.7 kb), evaluated genetic differences among species/genotypes and re-assessed the relationships among these taxa using the mitochondrial nucleic acid or amino acid sequence data sets. In addition, a rich source of mitochondrial genetic markers was defined that could be used in future systematic, epidemiological and population genetic studies of Trichinella . The sequencing-bioinformatic approach employed herein should be applicable to a wide range of eukaryotic parasites. [ABSTRACT FROM AUTHOR]

Tree peony is a well-known ornamental and medicinal plant in China, as well as a new crop that has been recently demonstrated to exhibit a great potential for edible oil production. However, only limited molecular markers are currently available in this species, which hinders its genetic and breeding studies. The objective of this study was to develop expressed sequence tag (EST)-simple sequence repeat (SSR) markers based on transcriptome sequences in tree peony. A total of 4,373 EST-SSRs were identified from 3,787 unigene sequences with an average of one SSR per 9.24 kb. Di-nucleotide repeats (46.26 %) were the most abundant type followed by tri-, hexa-, tetra-, and penta-nucleotide repeats. Moreover, 788 primer pairs were synthesised, out of which 373 primer pairs (47.3 %) produced successful amplifications, and 149 primer pairs (39.9 %) were polymorphic in both parents of one mapping population. The 30 polymorphic EST-SSR markers were randomly selected to assess polymorphism further in 36 tree peony accessions, in which the polymorphism information content values ranged from 0.36 to 0.85 with a mean of 0.69, thereby indicating a high level of informativeness. Transferability studies indicated that 95.3 % EST-SSR markers were transferable to nine other Paeonia species, thereby expanding their utility. In addition, as a demonstration of utility, a genetic relationship study was performed in 56 accessions. Cluster analysis using the neighbour-joining tree method demonstrated that major clusters corresponded to known pedigree trees. Thus, these newly developed markers will be valuable in facilitating marker-assisted selection breeding in tree peony and its related species. [ABSTRACT FROM AUTHOR]

The genetic diversity and relationships among 64 tree peony (Paeonia suffruticosa) germplasm of different colors were analyzed using conserve DNA-derived polymorphism (CDDP) markers. Of 16 primers screened, 13 primers could produce unambiguous and reproducible bands. Using 13 designed CDDP primers, 152 bands were generated with an average of 11.69 bands per primer among 64 accessions, with 149 (98.03%) being polymorphic. Further, accession-specific markers were observed in eight accessions. There was a significant positive correlation between the resolving power (Rp) of each primer and the number of accessions identified (r=0.96, **P<0.01). 64 accessions were clustered by UPGMA into 5 major groups at a similarity index value of 0.69 based on the CDDP marker data. Clustering of tree peony germplasm corresponded to origins and Zhongyuan group cultivars mainly based on flower color. The results demonstrated that the CDDP marker system and designed primers were efficient for the identification and genetic relationship analysis of tree peony genotypes. It is the first time that CDDP marker targeted flower color by gene-targeted primers and successfully made tree peony accessions cluster based on flower color. The results provide useful information for the utilization of gene-targeted molecular markers on cultivar identification and genetic relationship analysis in plants. [ABSTRACT FROM AUTHOR]

Stenocereus queretaroensis is an endemic, chiropterophilous, columnar cactus of economic importance in Mexico. To investigate the effect of artificial selection on genetic diversity, inter-simple sequence repeat (ISSR) markers were used to estimate the genetic variation of wild, orchard, and backyard populations of S. queretaroensis from two regions in western Mexico. Six primers were used to generate 62 bands, of which 39 were polymorphic (62.9%). The total genetic diversity was similar in the wild (HT = 0.296) and orchard (HT = 0.291) groups, and slightly lower in the backyard group (HT = 0.281). Wild populations (FST = 0.13) were less differentiated than backyard (FST = 0.17) and orchard (FST = 0.21) populations. The wild and backyard groups were genetically closer (0.015) than the wild and orchard (0.018) groups. A Mantel test revealed a positive correlation between genetic and geographic distances (r = 0.433, p = 0.002). In conclusion, gene flow and the prevailing management system have efficiently maintained genetic diversity and facilitated inter-population differentiation in S. queretaroensis. [ABSTRACT FROM AUTHOR]

Highlights: [•] Apricot cultivars in North China maintained a high level of genetic diversity. [•] Chinese and Central Asian cultivars exhibited higher diversity parameters. [•] Cultivars grouped in agreement with their geographic origins and pedigrees. [•] Kernel-using apricot is a natural hybrid type of P. armeniaca and P. sibirica. [Copyright &y& Elsevier]

In the present study, we proposed to determine the genetic diversity and relationships between local cultivars and wild olive trees from three important olive-growing regions, i.e., Marmara, Aegean, and Mediterranean, of Turkey. This is the first known large-scale molecular study to investigate the relationships between local cultivars and wild olives from the eastern Mediterranean basin. Two hundred and four oleaster trees and 27 cultivars were sampled to represent molecular diversity. We used 11 simple sequence repeat and 13 sequence-related amplified polymorphism markers to assess genetic variations and inter-relationships among the samples. The results of the analysis showed differences in the levels of allelic composition and heterozygosity between cultivated and wild olive trees. The observation of a high proportion of a certain wild-type genetic background in the cultivars may indicate the former use of local wild trees in olive domestication in Turkey, a possible autochthonal origin of cultivars. 'Gemlik' was found to be the most common olive cultivar in the Marmara region and most of the wild olive samples from this region may be feral forms derived from cultivar seed spreading. The information obtained from this study can help to assist the management of an olive collection and sheds some light on the origin of Turkish olive cultivars. [ABSTRACT FROM AUTHOR]

The sweet cherry is an important fruit species that is widespread globally. In addition to the well-known traditional and modern varieties, a myriad of landraces is present in Europe, as well as in southern Italy. This study aims to evaluate the population structure, genetic relationships, and cases of duplicate samples in a collection of 143 accessions using GBS-derived SNP markers. The genetic material under investigation includes modern commercial varieties, ancient European and American varieties, landraces, and individuals retrieved from small orchards. Some of the known varieties were genetically analyzed here for the first time. In addition, several genotypes were collected from the Basilicata region (southern Italy), an area largely unexplored for sweet cherry genetic resources. The relationships among genotypes were assessed using four different methods: allele frequency and ancestry estimation, principal component analysis, Neighbor-Joining tree, and identity-by-state estimation. The analyses returned quite congruent results and highlighted the presence of four main genetic groups, namely: (i) American varieties, (ii) the 'Germersdorfer-Ferrovia' cluster, (iii) the 'Burlat' group, and (iv) the group of Italian landraces. The main drivers of clustering were ancestry, geographical distribution, and some important traits such as self-compatibility. The sweet cherries from Basilicata, herewith examined for the first time, were mostly distributed within the group of Italian landraces, being particularly linked to the autochthonous varieties of the Campania region. However, some genotypes were outside this group, thus suggesting the introduction of genetic material from other Italian regions or from European countries. The considerable amount of American and European modern varieties analyzed are genetically very closely related, suggesting a reduced genetic basis. In addition, we highlighted the discriminating ability of SNP markers to distinguish between an original variety and its mutant. Overall, our results may be useful in defining conservation strategies for sweet cherry germplasm and developing future breeding programs to enlarge the genetic basis of commercial varieties.

The impact of extent of genetic relatedness on accuracy of genome-enabled predictions was assessed using a dairy cattle population and alternative cross-validation (CV) strategies were compared. The CV layouts consisted of training and testing sets obtained from either random allocation of individuals (RAN) or from a kernel-based clustering of individuals using the additive relationship matrix, to obtain two subsets that were as unrelated as possible (UNREL), as well as a layout based on stratification by generation (GEN). The UNREL layout decreased the average genetic relationships between training and testing animals but produced similar accuracies to the RAN design, which were about 15% higher than in the GEN setting. Results indicate that the CV structure can have an important effect on the accuracy of whole-genome predictions. However, the connection between average genetic relationships across training and testing sets and the estimated predictive ability is not straightforward, and may depend also on the kind of relatedness that exists between the two subsets and on the heritability of the trait. For high heritability traits, close relatives such as parents and full sibs make the greatest contributions to accuracy, which can be compensated by half-sibs or grandsires in the case of lack of close relatives. However, for the low heritability traits the inclusion of close relatives is crucial and including more relatives of various types in the training set tends to lead to greater accuracy. In practice, cross-validation designs should resemble the intended use of the predictive models, e.g. within or between family predictions, or within or across generation predictions, such that estimation of predictive ability is consistent with the actual application to be considered.

Highlights: [•] This is the first attempt to use Paeonia ostii as materials to develop SSR markers in Paeonia. [•] We developed 12 novel polymorphic SSR markers in tree peonies and test their cross-amplification in two herbaceous peony species (Paeonia veitchii and Paeonia lactiflora). [•] Genetic relationships among 53 accessions, including 8 species and 40 cultivars of tree peonies and 5 accessions of herbaceous species/cultivars, were studied based on the 12 polymorphic SSR markers. [ABSTRACT FROM AUTHOR]

Grevillea (Proteaceae) is native to Australia and is known as garden plant. The flowers have high diversity colors, which range over orange, yellow, pink, red and green. It is a large genus, consisted of 357 species. This genus is economically important and there are hundreds of Grevillea hybrids with beautiful color and shape of flower. Information of the genetic relationships of Grevillea hybrids is not yet available. Ten Grevillea hybrids were used in this study to evaluate the genetic relationships between hybrids and with their parents. PCR-RAPD technique was employed in this study with seven RAPD primers. The dendrogram of Grevillea hybrids was performed using Neighbor-Joining analysis based on genetic distance. The analysis revealed that 'Moonlight', 'Caloundra Gem', and Little Pink Willie' were clustered with Grevillea banksii. The three hybrids were hybrid of G. banksii and other Grevillea species. 'Superb' was closely related to 'Robyn Gordon' as they are hybrid of G. banksii and G. bipinnatifida. [ABSTRACT FROM AUTHOR]

Roses are one of the economically most important groups of ornamental plants. The internal transcribed spacers (ITS) of the nuclear ribosomal DNA and the chloroplast gene matK were used to investigate the genetic diversity and genetic relationships among Rosa germplasm including 39 wild species, 21 old garden roses, and 29 modern cultivars. Three dendrograms based on ITS and matK clustering data indicated that 1) 39 wild genotypes were consistent with their classification into botanical sections with only a few exceptions; 2) most of the wild genotypes were separated from rose cultivars. However, three sections, Synstylae, Chinenses, and Rosa, that contributed to the modern roses generally gathered together with almost all old garden and modern roses on the molecular level; and 3) the relationships between cultivated roses as inferred by ITS and matK sequences do not correlate with horticultural groups. Results demonstrated that both sequence techniques can contribute to clarifying the genetic relationships of rose accessions and germplasm conservation to enhance the ornamental and economic value of rose. [ABSTRACT FROM AUTHOR]

DArT (Diversity Array Technology) markers assessed in a large set of olive cultivars have been used to evaluate their utility for the management of the World Olive Germplasm Bank (WOGB—Córdoba) of IFAPA Centre “Alameda del Obispo” Córdoba (Spain). The coefficient of similarity of Kulczynsky (K1), which calculates the ratio between common markers relative to the number of unique markers (range 0 to ∞), was used for such purpose. Low K1 values (lower than 3.61) were obtained for the majority of the pair of cultivars (99.80% of the total). Low and similar ranges of K1 values were also found in both a seedling progeny of ‘Picual’בArbequina’ and a set of wild olives included in the study. These results may suggest that most of the WOGB—Córdoba cultivars studied probably were derived from outcrossing events. As expected, low similarity values were found among different cultivars with the same naming (homonyms). On the contrary, a total of 105 pairs (0.20%) showed K1 values above 14.58, implying thus low genetic differentiation. These high K1 values suggest the presence of potential redundant germplasm in the collection which likely includes synonyms, accumulation of somatic mutations, redundancies from prospecting surveys, and planting errors. Thus, the genetic relationships revealed by DArT markers among cultivars are of great interest for management of olive collections and could be useful to increase the performance of future breeding programs by optimizing the choice of parents in combination with phenotypic information. Finally, the transferability of DArT markers to wild olives has been confirmed. [ABSTRACT FROM AUTHOR]

In this work, we assess both the morphological and genetic diversity of 68 important olive cultivars from three Southern Italian regions: Calabria, Campania and Sicily. Twenty-five phenotypic traits were evaluated and 12 simple sequence repeat (SSR) markers were analysed. All SSR primers were polymorphic and reliable. The total number of alleles per locus varied from 5 to 19 with an average number of 13.1 and a mean polymorphic information content (PIC) of 0.81. These results suggested high genetic diversity within these three olive germplasm collections. Morphological traits also showed significant variability amongst cultivars. Two cases of identity were found and ten statistically significant cases of putative parent/sibling were discovered by performing a SSR-based parentage simulation analysis with CERVUS. The Mantel test indicated low but significant correlations between the morphological data and SSR allelic frequency, origin and SSR allelic frequency, and origin and morphology. Structure software allowed inference of relationships between the three olive germplasm collections and allowed us to obtain the most consistent grouping and to identify putative admixed or exchanged cultivars. Cluster and multivariate analysis, based on morphological traits, revealed geographic grouping in agreement with UPGMA dendrogram and structure analysis using SSRs. Sicilian cultivars showed a more homogenous genetic makeup, probably due to geographical isolation, whilst Calabrian and Campanian cultivars seemed to have a less distinct genetic structure, with a greater degree of intermixing. A correlation between the presence of certain SSR alleles and fruit size was also found. [ABSTRACT FROM AUTHOR]

Abstract: Nuclear ribosomal DNAs were explored to establish genetic relationships among Ficus carica cultivars and elucidate its molecular evolution. Results suggest the occurrence of haplotypic and nucleotide diversity. The neighbour-joining dendrograms show a continuous diversity that characterize local resources. Furthermore, our results demonstrated that the ITS2 spacer is seating to a larger number of substitutions than the ITS1 spacer. Sequence analysis demonstrates that the ITS2 spacer is evolving 1.12 times faster than the ITS1 one. The ratio of transition/transversion of 0.278 suggests that the 5.8S gene is evolving 2.84 and 3.20 times less rapidly than the spacers ITS1 and ITS2, respectively. Molecular evolution analysis confirmed an explicit rejection of the null hypothesis in F. carica. ITS1, ITS2 spacers and the 5.8S gene evolved under a strictly neutral model of molecular evolution. A scenario of positive selection and recent expansion of F. carica genotypes across Tunisia seems to be retained. [Copyright &y& Elsevier]

In breeding programs, the information on the relationships among the species and hybrids is important to make the correct choice of parents for hybrid production. In this study we addressed the relationship among 81 Dendrobium accessions (13 Dendrobium species, 8 commercial hybrids and 17 interspecific hybrid progenies) with 16 morphological traits. Data was analyzed using unweighted pair group method with arithmetic averages (UPGMA) cluster analysis. The results of characterization analysis revealed a high diversity between the Dendrobium accessions. Dendrobium accessions were grouped into three well-defined clusters. The first cluster consisted of 4 species, 8 commercial hybrids and 17 interspecific hybrid progenies. The second cluster consisted of 8 Dendrobium species. The third cluster comprised 1 Dendrobium species. These results indicated that the morphological characters were adequate in distinguishing between the species, commercial hybrids and interspecific hybrid progenies according to the species section and geographic origin. [ABSTRACT FROM AUTHOR]

In this study, the genetic relationships among 12 Fritillaria taxa collected from different regions of Turkey were investigated using the amplified fragment length polymorphism (AFLP) technique. Seven primer pair combinations were used for the analysis. The neighbor-joining and principal coordinate analysis methods were implemented to identify the taxonomy of the species. The analyses generated congruent results with each other and with the previous studies. The neighbor-joining analysis clustered the species into 3 groups, while the principal coordinates analysis did not support separation of the third group. The subgenera Fritillaria and Petilium diverged from each other with strong support in all analyses. The neighbor-joining tree further divided the members of subgenus Fritillaria into 2 subgroups. Statistical analysis of the data set using NTSYS 2.1 showed a very good fit between the data matrix and the cophenetic matrix for the AFLP data with an r-value of 0.91. Generating a high polymorphic band profile, this analysis presented the feasibility of using AFLP for a genetic relationship analysis of Fritillaria. This primary report on AFLP analysis of Fritillaria species could facilitate achieving a deeper understanding of genetic relationships between the species. [ABSTRACT FROM AUTHOR]

Hipparchia autonoe belongs to the family Nymphalidae ( Lepidoptera) and is designated as an endangered insect and national monument in Korea. It only inhabits a very restricted area on Mt. Halla but is widely distributed in several Asian countries including Mongolia. A previous study conducted to understand the genetic relationship between Mt. Halla and Mongolian H. autonoe for conservation purposes suffered from a limited number of samples. Therefore, we sequenced the DNA barcode region of an additional 36 H. autonoe individuals, combined them with previous data from 19 individuals, and performed phylogenetic and population genetic analyses. Furthermore, the internal transcribed spacer 2 ( ITS2) region was also sequenced from the 36 samples as a nuclear DNA marker. The existence of independent haplotypes, sequence types, and significant FST estimates ( P < 0.05) between Mt. Halla and Mongolian populations indicated hampered gene flow between the populations. Nevertheless, an absence of a reciprocal monophyletic group in Mt. Halla and Mongolian populations by cytochrome oxidase subunit I gene- and ITS2-based phylogeny suggests that the genetic isolation of the Mt. Halla population from the Mongolian populations seemed not large enough to consider them independent genetic entities. [ABSTRACT FROM AUTHOR]

Indigenous African sheep genetic resources have been classified into two main groups, fat-tailed and thin-tailed sheep. The fat-tailed sheep are the most widely distributed, being found in a large part of North Africa (from Egypt to Algeria) and in Eastern and Southern Africa (from Eritrea to South Africa). The thin-tailed sheep are present mainly in Morocco, Sudan and in West Africa. African sheep were domesticated outside Africa. They share a common ancestry with European and Asian sheep. Archaeological information supports separate introductions and dispersion histories for the African thin-tailed and fat-tailed sheep. The first sheep entered Africa via the Isthmus of Suez and/or the southern Sinai Peninsula, between 7500 and 7000 BP. They were likely of the thin-tailed type. Fat-tailed sheep entered Africa through its northeastern part and the Horn of Africa. Mitochondrial DNA analysis supports a common maternal ancestral origin for all African sheep, while autosomal and Y chromosome DNA analysis indicates a distinct genetic history for African thin-tailed and sub-Saharan fat-tailed sheep. The main ancestral population of southern African fat-tailed sheep likely originated in East Africa. Further work is needed to assess the possible dispersion of sheep from western Africa to the southern African regions. [ABSTRACT FROM AUTHOR]

In this study, two gene fragments corresponding to the VvMYBA1 and VvMYBA2 loci were sequenced on a sample of grapes including cultivated and wild accessions originating from Tunisia, Germany and France. A total of 42 SNPs were detected in the sequenced fragments giving an average of 1 SNP every 33 bp. High level of polymorphism was observed in the samples either in cultivated or wild accessions. Pattern of nucleotide diversity indicates a non departure from neutrality expectations for wild grapevine sample for gene VvMYBA1 and VvMYBA2 and for cultivated sample for gene VvMYBA1. However, a linkage to a selective sweep was revealed for cultivated grapevine gene pool in gene VvMYBA2. A genetic structure of the studied sample according to accession taxonomic status was revealed by the UPGMA clustering with a considerable overlap. This result was confirmed by significant but low genetic differentiation values between cultivated and wild sample. The number of migrants Nm based on sequence data information between Tunisian cultivars and Tunisian wild accessions showed a low level of gene flow between those germplasms. This finding indicates that Tunisian cultivars do not derive directly from local wild populations but could mostly correspond to imported materials introduced during historical times. However, the possibility that some cultivars derived from ancestral events of local domestication or cross hybridization with native wild plants was not completely excluded for Tunisian grapevine accessions. [ABSTRACT FROM AUTHOR]

Wheat stripe rust, caused by Puccinia striiformis f. sp. tritici ( Pst ), is a crucial disease for wheat worldwide and constantly threatens wheat production in southwestern and northwestern China, where the environment is a good fit for Pst oversummering and overwintering. However, the underlying genetic dynamics of spring epidemic Pst populations across large areas of continuous planting in the southwestern and northwestern regions are poorly understood. A total of 2,103 Pst isolates were sampled in the spring of 2019 from the two agroecosystems and grouped into three horizontal spatial scales (countywide, provincial, and regional subpopulations) and two vertical spatial scales that consisted of elevational and geomorphic subpopulations. A total of 776 multilocus genotypes were identified, with the highest genetic diversity found in the northern and Sichuan populations, particularly in the Ningxia and Sichuan Basins, while the lowest genetic diversity was found in the Yunnan and Guizhou populations. Multivariate discriminant analysis of principal components (DAPC) and STRUCTURE (STRUCTURE 2.3.4) analyses revealed variation in the genotypic compositions of the molecular groups on horizontal and vertical dimensions from north to south or vice versa and from low to high or vice versa, respectively. The regional neighbor-joining tree revealed three large spatial structures consisting of the southwestern, the northwestern, and the Xinjiang regions, while the Tibetan population connected the southwestern and northwestern regions. The isolates of the Sichuan Basin were scattered over the four quartiles by principal coordinate analysis, which indicated frequent genotype interchange with others. Greater genetic differentiation was observed between the southwestern and northwestern regions. Linkage equilibrium ( P ≥  0.05) was detected on different spatial scales, suggesting that Pst populations are using sexual reproduction or mixed reproduction (sexual and clonal reproduction) in southwestern and northwestern China. IMPORTANCE Understanding the epidemiology and population genetics of plant pathogens is crucial to formulate efficient predictions of disease outbreaks and achieve sustainable integrated disease management, especially for pathogens with migratory capability. Here, this study covers the genetic homogeneity and heterogeneity of different geographical Pst populations on broad to fine spatial scales from the key epidemic regions of the two agroecosystems in China, where wheat stripe rust occurs annually. We provide knowledge of the population genetics of Pst and reveal that, for instance, there is greater genetic diversity in northwestern China, there are close genetic relationships between Yunnan and Guizhou and between Gansu-Ningxia and Qinghai, and there are effects of altitude on genetic compositions, etc. All of these findings clarify the genetic relationships and expand the insights into the population dynamics and evolutionary mechanisms of Pst in southwestern and northwestern China, providing a theoretical basis for achieving sustainable control of wheat stripe rust in key epidemic regions.

Background: The genetic differentiation of Bahrain natives is unclear because of the absence of adequate genetic studies. Aim: Eight Alu insertion polymorphisms have been analysed in Bahrainis and southern Iranians to examine the origins of Bahrainis and to determine their genetic position among wider Middle East populations. Subjects and methods: Two representative samples of 97 Bahrainis and 65 southern Iranians have been determined. Genetic relationships among populations have been estimated by a principal component plot based on the R-matrix software. Mantel tests have been used to check the statistical significance of correlation between genetic and geographic distances. Results: The results show that Bahrainis are in an intermediate genetic position between Emirians and Southern Iranians. Although a general significant correlation between genetic and geographic distances was found between the 16 populations included in the analysis, a lack of this correlation may occur in some particular situations such as the case of populations from southern Iran, United Arab Emirates (UAE) and Bahrain, separated by the Persian Gulf. Conclusion: The results support the idea that Bahrainis ancestors were mainly emigrants from Arabia and Iran. In addition the results show that the Iranian component may reach 69.2% of the current genetic pool of Bahrainis. [ABSTRACT FROM AUTHOR]

The genetic variability characterization of the accessions of the germplasm collection, using molecular markers, is being applied as a complementary strategy to the traditional approaches to redefine the plant genetic resources. In this study, we compared the informativeness and efficiency of the molecular markers RAPD, AFLP and SSR in the analysis of 94 accessions of Coffea canephora germplasm held by the breeding program of the Brazilian Agricultural Research Corporation (Embrapa), Rondônia State, Brazil. For this, we considered the marker's discriminatory power and level of polymorphism detected and also the genetic relationships and clustering (dendrogram) analysis. The RAPD marker yielded low-quality data and problems in the discrimination of some accessions, being less recommended for genetic studies of C. canephora. The SSRs had a higher level of information content and yielded high-quality data, while AFLP was the most efficient marker system because of the simultaneous detection of abundant polymorphism markers per few reactions. Our results indicate that AFLP and SSR, allies to the intrinsic characteristics of each technique, are the most suitable molecular markers for genetic studies of C. canephora. However, the choice of AFLP or SSR in the species characterization should be made in agreement with some characteristics that are discussed in this work. [ABSTRACT FROM AUTHOR]

Background and Aims The genus Arachis contains 80 described species. Section Arachis is of particular interest because it includes cultivated peanut, an allotetraploid, and closely related wild species, most of which are diploids. This study aimed to analyse the genetic relationships of multiple accessions of section Arachis species using two complementary methods. Microsatellites allowed the analysis of inter- and intraspecific variability. Intron sequences from single-copy genes allowed phylogenetic analysis including the separation of the allotetraploid genome components. Methods Intron sequences and microsatellite markers were used to reconstruct phylogenetic relationships in section Arachis through maximum parsimony and genetic distance analyses. Key Results Although high intraspecific variability was evident, there was good support for most species. However, some problems were revealed, notably a probable polyphyletic origin for A. kuhlmannii. The validity of the genome groups was well supported. The F, K and D genomes grouped close to the A genome group. The 2n = 18 species grouped closer to the B genome group. The phylogenetic tree based on the intron data strongly indicated that A. duranensis and A. ipaënsis are the ancestors of A. hypogaea and A. monticola. Intron nucleotide substitutions allowed the ages of divergences of the main genome groups to be estimated at a relatively recent 2·3–2·9 million years ago. This age and the number of species described indicate a much higher speciation rate for section Arachis than for legumes in general. Conclusions The analyses revealed relationships between the species and genome groups and showed a generally high level of intraspecific genetic diversity. The improved knowledge of species relationships should facilitate the utilization of wild species for peanut improvement. The estimates of speciation rates in section Arachis are high, but not unprecedented. We suggest these high rates may be linked to the peculiar reproductive biology of Arachis. [ABSTRACT FROM AUTHOR]

Information on genetic diversity of different commercial coffee cultivars grown in India during the last 90 years is scarce. In the present study, the genetic diversity of selected coffee cultivars, along with some advanced breeding lines, was evaluated using random amplified polymorphic DNA (RAPD), inter-simple sequence repeat (ISSR), and sequence-related amplified polymorphism (SRAP) markers. The average polymorphism information content (PIC) or the genetic diversity of ISSR primers (0.365) was higher than that for both RAPD (0.222) and SRAP primers (0.346). The average resolving power (Rp) of SRAP primers (13.29) was slightly lower than that of RAPD (13.60) but higher than that of ISSR primers (11.23). The genetic similarity among various cultivars using Jaccard's similarity coefficients ranged from 0.74 to 0.99 using RAPD, 0.48 to 0.94 using SRAP marker, and 0.57 to 0.95 using ISSR systems. Based on the marker analysis, all 24 coffee cultivars were clustered into two major groups, of which one is represented by cultivars belonging to C. arabica and the other group represented by C. canephora. Of the three marker systems used, the SRAP marker system was more informative and amplified several cultivar-specific fragments. The use of molecular markers can speed up genetic improvement of coffee cultivars. [ABSTRACT FROM AUTHOR]

The objective of this study was to exploit the molecular and morphological variability present in Malus domestica to clarify the confused characterization of apple plantations in the Azores. Most Azorean apples are grown in orchards. They are usually given a local name, and sometimes the same name is used for different cultivars and varieties which share morphology and should be known by different names. Two-hundred samples of apples cultivated in the Azores were analyzed by use of ten microsatellites. The total number of alleles per locus ranged from 10 to 24, with a mean of 15.2. Heterozygosity was high, reflecting the high variability of the samples. Expected heterozygosity varied within a narrow range, from 0.74 to 0.88, whereas observed heterozygosity ranged from 0.41 to 0.98. The high genetic variability contributed to the high discriminating power, which ranged between 0.84 and 0.93. These microsatellites were used to unambiguously discriminate most of the tested apple cultivars on the basis of their allelic profiles. The rooted UPGMA tree organized most of the samples into thirteen main clusters, often with high bootstrap values. We identified 60 synonyms and 32 homonyms among the samples. Moreover, it was possible to relate each individual to its originating population and detect likely parent-offspring groups. [ABSTRACT FROM AUTHOR]

Random amplified polymorphic DNA (RAPD) markers were used to determine genetic relationships among Velezia L. species from Turkey. A total of 432 amplified bands were obtained using 14 RAPD primers. The polymorphism in RAPD markers was high (98.61%) and was sufficient to distinguisheach species. The degree of band-sharing was used for evaluating the genetic similarity between species and for constructing a dendrogram by the unweighted pair group method with arithmetic mean (UPGMA). Genetic relationships among the species were found to be fully consistent with those obtained by the use of morphological characters. Data obtained from our study demonstrated that the RAPD technique could be successfully used for the determination of genetic relationships among Velezia species and for species identification. Furthermore, it can be efficiently employed in future studies to provide preliminary data for conservation of endangered Velezia species. [ABSTRACT FROM AUTHOR]

Georgia plume, Elliottia racemosa (Ericaceae), is a small tree endemic only to the state of Georgia, where it is listed as a threatened species, Information about genetic relatedness is critical for establishing approaches for safeguarding, reintroduction and conservation of this rare species, The genetic relationships among and within selected georgia plume populations were evaluated using random amplified polymorphic DNA (RAPD) in conjuction with site visits at which time a census and GPS survey were conducted. Populations ranges from those containing eight to over 1000 individuals with most populations containing few plants (less than 50 individuals). With one exception, small populations with less than 50 individuals had more genetic similarity than populations with greater numbers of plants. Two protected populations containing large numbers of individuals were sampled extensively. Genetic similarity of individuals was not associated with plant proximity within a population. The small number of individuals and geographic isolation characteristic of many populations were associated with high within-population genetic similarity. Conservation priorities should be given to preserving as many different populations as possible to retain the genetic diversity of the species. Whether the narrow genetic variation found in some populations may be contributing to lack of sexual reproduction in the wild is an area for further study. [ABSTRACT FROM AUTHOR]

Abstract: Sixteen pairs of EST-SSR primers developed from apricot (Prunus armeniaca L) and 11 pairs from fruiting-mei (Prunus mume) were employed in PCR amplification for analysis of genetic relationships and identification of 54 flowering-mei accessions. The results show that 14 pairs of apricot and 11 pairs of fruiting-mei EST-SSR primers had clear amplification products in flowering-mei, among which 8 apricot and 9 fruiting-mei EST-SSR primer pairs could amplify polymorphic bands and a total of 65 alleles, were detected from all the 54 flowering-mei accessions. The ratio of polymorphic bands amplified by the 8 apricot and 9 fruiting-mei EST-SSR primers 59.1% and 72.1%, respectively, indicating that the levels of polymorphism from fruiting-mei EST-SSR primers were relatively high. Analysis of genetic relationships of all the 54 accessions by the polymorphic SSR markers showed that EST-SSR markers could clearly separate flowering-mei accessions and the clustering pattern of most cultivars was in accordance with their pedigree information. In addition, a manual cultivar identification diagram (MCID) of the 54 cultivars was constructed using polymorphic bands from the DNA fingerprints. To the best of our knowledge, this new strategy is by far the most efficient and workable in identifying plant varieties using EST-SSR markers. This MCID strategy could separate all the cultivars from each other, with the polymorphic bands employed for identifying the cultivars and the corresponding primers being marked in the correct position on the MCID. This flowering-mei MCID can provide the information needed to separate any of the 54 important cultivars studied here, which is of benefit to flowering-mei cultivar identification for cultivar-right-protection and the general flowering-mei industry in China. [Copyright &y& Elsevier]

Abstract: The phylogenetic relationships among seven wild species and 25 loquat cultivars of genus Eriobotrya were studied by comparing sequences of the internal transcribed spacer (ITS) region. The length of ITS1 region of Eriobotrya was 223bp and the lengths of ITS2 were ranged from 201bp to 203bp. The G+C contents varied from 64.1% to 65.5% in ITS1 and from 68.5% to 72.1% in ITS2. The aligned sequences were analyzed by neighbor-joining (NJ) and maximum parsimony (MP) methods. The ITS1 spacer region comprised 223 characters, of which 44 were variable sites and 34 were parsimony informative sites. The NJ tree had very similar topology to the MP tree. E. malipoensis and E. seguinii had only one different character in ITS2 region and both of them could be the most primitive species of Eriobotrya genus. ITS2 evolved much faster and had more parsimony informative sites than ITS1. ITS2 presented much more precise information about the phylogenetic relationships. Based on ITS2 regions, the evolution order of the studied taxa in this paper could be concluded, which was E. bengalensis f. angustifolia, E. prinoides var. dadunensis, E. prinoides (E. bengalensis), E. dayaoshanensis and E. japonica Lindl. [Copyright &y& Elsevier]

Abstract: Nucleotide variation in 8 diploid Pseudoroegneria species was characterized using two single copy nuclear genes, the second largest subunit of RNA polymerase II (RPB2) and the translation elongation factor G (EF-G), and one chloroplast TrnD/T intergenic region. Among the Pseudoroegneria species studied, the estimates of nucleotide diversity (π) ranged from 0.04577 (RPB2) and 0.00183 (TrnD/T) for Pseudoroegneria tauri to 0.10667 (RPB2), 0.06174 (EF-G) and 0.03743 (TrnD/T) for Pseudoroegneria spicata. The highest nucleotide diversity of the RPB2 data set was found for P. spicata among the taxa analyzed. Our phylogenetic analyses separated the accessions of P. spicata into several groups, with 7 accessions of P. spicata forming a highly supported subclade (BS = 100%, PP = 1.00). The phylogenetic analysis also suggests that P. spicata, Pseudoroegneria gracillima and Pseudoroegneria stipifolia have a closer relationship than the other species within Pseudoroegneria. Pseudoroegneria libanotica and P. tauri were also found to exhibit a high level of sequence homology, however, only nuclear gene data (RPB2 and EF-G) clearly indicated the differentiation between the P. libanotica + P. tauri group with other St genome species. [Copyright &y& Elsevier]

Woad (Isatis tinctoria L.) was introduced in Europe in ancient times to produce indigo, a natural blue pigment used mainly for dyestuff. This species was cultivated in Portugal until the beginning of the 20th century, especially in the inner North and South. A set of nine inter-simple sequence repeat (ISSR) markers generated 177 reproducible fragments, of which 171 were polymorphic. The mean number of fragments/accession was 111, ranging between 100 (Portugal-Coimbra) and 124 (Poland). The total polymorphism observed was 0.3272, the average polymorphism was 0.1784 and the gene differentiation between accessions was 0.4546. Polymorphism ranged between 53.8% (Austria) and 73.1% (Belgium). The genetic relationship among woad accessions was obtained with unweighted pair group method with arithmetic mean dendrogram based on a molecular marker, clearly clustering the woad accessions according to their geographic origin. The genetic diversity observed in this collection shows that there is a considerable potential for its improvement and that ISSR could be used to evaluate intra- and inter-accession similarities in I. tinctoria species. [ABSTRACT FROM AUTHOR]

Three molecular marker systems, RAPD (random amplified polymorphic DNA), ISSR (inter-simple sequence repeat) and SRAP (sequence related amplified polymorphism), were employed for identification and genetic relationship between five indigenous coffee species from India and cultivated species Coffea canephora. A total of 304, 140 and 234 bands were detected by 22 RAPD, 12 ISSR and 20 SRAP primer combinations, among which 95%, 91.3% and 96.1% bands were polymorphic respectively. The average PIC of SRAP primers (0.82) was higher than RAPD primers (0.78) but lesser than that of ISSR primers (0.83) where as the average RP of SRAP primers (8.3) is higher than ISSR primers (8.2) but less than RAPD primers (10.3). Some of the RAPD and SRAP primers were able to distinguish all the indigenous coffee species independently. The genetic similarity among the species ranged from 0.34 to 0.75 using RAPD, 0.30 to 0.69 using ISSR and 0.23 to 0.63 using SRAP marker systems. Based on the marker analysis, all the six species were clustered in to two major groups. The results demonstrated that these three marker systems could be useful for identification and genetic diversity analysis of indigenous coffee species and provide an important input in to conservation biology. [ABSTRACT FROM AUTHOR]

Abstract: Multilocus enzyme electrophoresis (MEE) and DNA sequencing of the mitochondrial cytochrome c oxidase subunit 1 (CO1) gene were used to genetically compare four species of echinostomes of human health importance. Fixed genetic differences among adults of Echinostoma revolutum, Echinostoma malayanum, Echinoparyphium recurvatum and Hypoderaeum conoideum were detected at 51–75% of the enzyme loci examined, while interspecific differences in CO1 sequence were detected at 16–32 (8–16%) of the 205 alignment positions. The results of the MEE analyses also revealed fixed genetic differences between E. revolutum from Thailand and Lao PDR at five (19%) of 27 loci, which could either represent genetic variation between geographically separated populations of a single species, or the existence of a cryptic (i.e. genetically distinct but morphologically similar) species. However, there was no support for the existence of cryptic species within E. revolutum based on the CO1 sequence between the two geographical areas sampled. Genetic variation in CO1 sequence was also detected among E. malayanum from three different species of snail intermediate host. Separate phylogenetic analyses of the MEE and DNA sequence data revealed that the two species of Echinostoma (E. revolutum and E. malayanum) did not form a monophyletic clade. These results, together with the large number of morphologically similar species with inadequate descriptions, poor specific diagnoses and extensive synonymy, suggest that the morphological characters used for species taxonomy of echinostomes in South-East Asia should be reconsidered according to the concordance of biology, morphology and molecular classification. [Copyright &y& Elsevier]

Abstract: A full-length complementary DNA (cDNA; designated Hc-stp-1) encoding a serine/threonine phosphatase (Hc-STP-1) was isolated from Haemonchus contortus, a strongylid nematode parasite of small ruminants. Hc-stp-1 was shown to be transcribed in males of both adults and fourth-stage larvae, but not in females, early larval stages or eggs. The full-length gene (2854bp) contained ten exons and nine introns, and encoded a cDNA of 951bp. Comparisons of the conceptually translated protein (316 amino acids, estimated at ∼35kDa) with serine/threonine phosphatases (STPs) from other organisms revealed the presence of the conserved motif LRGNHE. Structural analysis, by comparative modelling, confirmed strict conservation of residues and features involved in catalytic activity, and variation in the ligand-binding interface. Phylogenetic analysis of amino acid sequence data revealed that Hc-STP-1 clustered with STPs from other nematodes (including Caenorhabditis elegans, Trichostrongylus vitrinus, Oesophagostomum dentatum, Ascaris suum and Brugia malayi) to the exclusion of STPs from other organisms. The protein was inferred to be most closely related to the PP1 class of STPs of C. elegans, within a group containing STPs encoded, amongst others, by the genes gsp-3 and gsp-4 in this free-living nematode. The functions of proteins GSP-3 and GSP-4 are known to be central to spermatogenesis and other male-specific processes in C. elegans. The findings from the present and previous studies support the proposal that Hc-stp-1 and its product play a significant role in reproductive and/or developmental processes in maturing or adult male H. contortus. [Copyright &y& Elsevier]

The objective of this work was to estimate the genetic and phenotypic correlations among fertility traits of 317 Holstein Friesian and Brown Swiss cows. Cows were born and reared under subtropical conditions, during a 20-year period (1986 to 2006), and were daughters of 116 sires and 199 dams. The study was carried out in Las Margaritas research station, in Hueytamalco, Puebla, México, which belongs to the Instituto Nacional de Investigaciones Forestales, Agrícolas y Pecuarias (INIFAP). Fertility traits studied were: days to first service after calving (DFS), calving interval (CI), days open (DO), number of services per conception (NSC) and conception rate at first service (CR). Genetic correlations were estimated with a two-trait animal model (bivariate analysis), which included individual additive genetic effect as a sole random effect. Main fixed effects were: calving year, calving season and breed of cow. Analyses were carried out with restricted maximum likelihood, using an algorithm free of derivatives. In general, fertility traits were favorably and strongly correlated genetically. Estimates of genetic correlations for DFS-CI, DFS-DO, DFS-NSC, CI-DO, CI-NSC, and DO-NSC were positive (0,89, 0,89, 0,25, 0,90, 0,59 and 0,97, respectively), while all estimates of genetic correlations that included conception rate to first service (DFS-CR, CI-CR, DO-CR, NSC-CR) were negative (-0,45, -0,62, -0,72, -0,85). The high estimates of genetic correlations between CI and DFS or DO indicate that selection for less DFS or DO would reduce CI. [ABSTRACT FROM AUTHOR]

The genetic diversity of 11 bread and durum wheat varieties was estimated using germination characteristic and molecular analysis. The phenotypic data showed highly significant differences between cultivars for germination speed, germination percentage, seedling length, fresh weight, and dry weight. Simple sequence repeats (SSRs) were used to examine the genomic diversity of wheat (Triticum aestivum L. and Triticum durum L.). Eleven wheat varieties of diverse origins were analyzed with 12 selected SSRs to provide uniform and maximum genome coverage. A total of 18 bread wheat and 20 durum wheat polymorphic allelic variants were detected, ranging from 1 to 4 per locus with an average of 1.5 and 1.7, respectively. Genetic similarities calculated from SSR data ranged from 0.286 to 1 for bread wheat and 0.333 to 0.818 for durum wheat. Unweighted pair group method with arithmetic mean (UPGMA) analysis based on genetic distance estimates produced 2 loose groupings that were generally consistent with available pedigree information. Cham 6 and Cham 4 were closely related. Their genetic relationship was confirmed by the facts that they share a common ancestor and that they were clustered together. A wide range of genomic diversity was observed among all the genotypes, indicating them as prime candidates for selective breeding for specific traits and broadening the genetic base. [ABSTRACT FROM AUTHOR]

Abstract: Genetic diversity and relationships between local cultivars and wild olive trees from three important Spanish olive-growing regions, Andalusia (South), Catalonia and Valencia (from Eastern Mediterranean Coastal area), were studied by means of eight SSR loci. Distinct allelic composition and heterozygosity levels were found in wild olive populations and cultivars. The observed patterns of genetic variation revealed: a) the independent clustering of Andalusian wild olives in a separate gene pool, b) the belonging of wild populations and most cultivars from Catalonia to another gene pool, c) the joined clustering of Andalusian and a set of Valencian cultivars in a third gene pool, and d) clustering of wild individuals from Valencia to the three different gene pools. These results suggest that wild populations of Andalusia may represent true oleasters, the ones from Catalonia may be feral forms derived from cultivar seed spreading, while the population of Valencia seems to be the most admixed one. The significant differentiation between Andalusian and most Catalonian cultivars is indicating an independent selection of olive cultivars in the two regions. The detection of a certain wild genetic background in some Catalonian and Valencian cultivars and the similarity found between wild and cultivated forms may suggest the use of local wild trees in olive domestication. The proposed scenario for the development of olive cultivars in Andalusia includes an empirical selection of outstanding local wild genotypes followed by various generations of crosses and various replanting campaigns, as well as possible introductions of ancestral cultivars. Therefore, our findings would lead us to support the hypothesis that the current diversity found in Spanish olive cultivars may be regionally differentiated and due to both, autochthonous and allochthonous origin. The information obtained in this work gives insights into the genetic resources of the main olive producing country, demonstrating that wild olive populations and local cultivars both represent potential sources of useful variability for olive breeding programs. [Copyright &y& Elsevier]

Genetic relationships in 55 accessions belonging to 14 species of Chenopodium have been studied by RAPD and DAMD markers. A UPGMA dendrogram based on 242 DNA markers divided the taxa into two main clusters. The first cluster joins all the accessions of Chenopodium quinoa with Chenopodium berlandieri subsp. nuttalliae, one Chenopodium album (4x) from Mexico and three north Indian 2x accessions of C. album. The other clusters comprises mainly 6x accessions of C. album and Chenopodium giganteum forming two subclusters. This clearly shows that C. album complex is a heterogenous assemblage and its taxonomic affinities need reassessment. Other wild species placed in the dendrogram are more or less according to their taxonomic position. [ABSTRACT FROM AUTHOR]

Genetic diversity and relationships within and among Korean, Japanese and Chinese Jilin provincial wild soybeans based on SSR makers were evaluated to enlarge genetic variation in soybeans breeding in the future. A total of 184 wild soybeans including 67 Korean, 71 Japanese and 46 Chinese Jilin provincial wild soybeans were analyzed to evaluate genetic diversity and relationships based on 23 SSR markers. Korean and Japanese wild soybeans were obtained from National Agrobiodiversity Center, Korea, and Biological Resource Center in Lotus and Gycine, Frontier Science Research Center, University of Miyazaki, Japan, respectively. Chinese wild soybeans were collected from Jilin province, China. Twenty three SSR markers generated a total of 964 alleles with an average of 41.9 alleles per marker. Number of alleles ranged from 23 (Satt635) to 56 (satt157). Genetic diversity (PIC value) of 184 wild soybeans ranged from 0.880 to 0.968 with an average of 22.2, beans was similar with an average of 13.6 per marker, respectively. PIC value for Korean, Japanese and Chinese Jilin provincial wild soybeans was similar with an average of 0.905, 0.897, and 0.850, respectively. Cluster analysis based on genetic distances estimated by SSR markers classified wild soybeans into 3 clusters. Cluster I was now sub classified, but cluster II and III were sub classified into various groups. Genetic distance evaluated by SSR markers between Korean and Japanese wild soybeans was closer than that of between Korean and Chinese Jilin provincial, and between Japanese and Chinese Jilin provincial wild soybeans. [ABSTRACT FROM AUTHOR]

Pyrolysis mass spectrometry (PyMS) is a rapid, simple, high-resolution analytical method based on thermal degradation of complex materials in a vacuum. It is widely applied to the discrimination of closely related microbial strains. Leaf samples from eight cultivars (‘Apricot Delight’, ‘Cooler Grape’, ‘Cooler Peppermint’, ‘Equator Grape’, ‘Equator Rose’, ‘Equator White’, ‘Equator White Eye’, and ‘Little Bright Eye’) of Catharanthus roseus were subjected to PyMS for spectral fingerprinting. Discriminant analysis (DA) of PyMS data enabled us to assign these cultivars to discrete clusters. A hierarchical dendrogram based on DA provided a possible relationship among them that was in general agreement with a previously reported classification of the cultivars based on DNA fingerprints. Furthermore, those belonging to the same ‘series’ were grouped into a single cluster, which previously could not be achieved through similar approaches based on Fourier transform infrared spectroscopy or 1H NMR data. Overall results suggest that chemical differences (i.e., in pyrolysate composition) among cultivars, as detected by mass spectrometry, reflect their genetic variation. [ABSTRACT FROM AUTHOR]

A total 23 morphological traits, 19 AFLP-primer combinations, 80 RAPD primers and 32 SSR primer pair were used to compare the informativeness and efficiency of random amplified polymorphic DNA (RAPD), amplified fragment length polymorphism (AFLP) and simple sequence repeat (SSR) markers in establishing genetic relationships among 29 almond cultivars and three related wild species. SSRs presented a high level of polymorphism and greater information content, as assessed by the expected hetrozygosity, compared to AFLPs and RAPDs. The lowest values of expected hetrozygosity were obtained for AFLPs; however AFLPs showed the highest efficiency, owing to their capacity to reveal large numbers of bands per reaction, which led to high values for various types of indices of diversity. All the three techniques discriminated almond genotypes very effectively, except that SSRs failed to discriminate between ‘Monagha’ and ‘Sefied’ almond genotypes. The correlation coefficients of similarity were statistically significant for all the three marker systems, but were lower for the SSR data than for RAPDs and AFLPs. For all the markers, high similarity in dendrogram topologies was obtained, although some differences were observed. All the dendrograms, including that obtained by the combined use of all the marker data, reflect relationships for most of cultivars according to their geographic diffusion. AMOVA detected more variation among cultivated and related wild species of almond within each geographic group. Bootstrap analysis revealed that the number of markers used was sufficient for reliable estimation of genetic similarity and for meaningful comparisons of marker types. [ABSTRACT FROM AUTHOR]

Genetic relationships between 61 dog breeds were investigated, using a sampling of 1514 animals and a panel of 21 microsatellite markers. Based on the results from distance-based and Bayesian methods, breed constituted the main genetic structure, while groups including genetically close breeds showed a very weak structure. Depending on the method used, between 85.7% and 98.3% of dogs could be assigned to their breed, with large variations according to the breed. However, breed heterozygosity influenced assignment results differently according to the method used. Within-breed and between-breed diversity variations when breeds were removed were highly negatively correlated ( r = −0.963, P < 0.0001), because of the genetic structure of the breed set. [ABSTRACT FROM AUTHOR]