Neocinnamomum plants are evergreen shrubs or small trees belonging to the Neocinnamomeae tribe of the Lauraceae family. Their seeds are rich in fatty acids, and their leaves are often used in traditional Chinese medicine. Presently, only a few studies have been performed on Neocinnamomum plants; therefore, the genome-based phylogeny among Neocinnamomum species has not been determined, which limits the germplasm innovation of this genus. In this study, by the Illumina (next-generation sequencing) and third-generation sequencing technologies, the whole genomes of seven Neocinnamomum species samples were sequenced, their nuclear DNA (nrDNA) sequences were assembled and characterized, and their phylogeny was reconstructed. The results revealed four hypervariable regions (i.e. transcribed spacer regions) in the nrDNA sequences, among which the highest degree of variation was observed in the external transcribed spacer (ETS) region localized behind the 26S gene. A total of 27 insertions/deletions and 184 single-nucleotide polymorphisms, both localized mainly in the ETS and internal transcribed spacer regions, were identified. Phylogenetic trees were constructed based on the nrDNA sequences using the maximum likelihood (ML) and Bayesian inference (BI) methods with Caryodaphnopsis henryi as the outgroup. The ML tree divided the seven Neocinnamomum species into four clades. Clade I consisted of Neocinnamomum caudatum var. macrocarpum and Neocinnamomum caudatum, clade II included Neocinnamomum delavayi and Neocinnamomum mekongense, clade III included Neocinnamomum fargesii and a branch species of N. delavayi and clade IV included Neocinnamomum lecomtei, constituting a monophyletic and basal group. The BI tree shared the same topological structure as the ML tree, and all the support values of the BI tree were one except for that of one Neocinnamomum species (0.98). The results of this study provide new evidence regarding the phylogenetic evolution of the Neocinnamomum plants.

Proso millet occurs both as a crop and a weed in North America. In 1970, an olive-black seeded biotype called ‘wild proso millet’ was found as an aggressive weed in row crops in Minnesota and Wisconsin and has since spread over a large area. We used Random Amplified Polymorphic DNA (RAPD) to assess genetic relationships among biotypes, measure genetic variation within wild proso millet across its range, and detect hybridization between wild proso millet and crop biotypes of proso millet. We found 97 RAPD genotypes among 398 individuals: 69 wild proso millet genotypes, 26 crop and crop-like weed genotypes, and two hybrid genotypes. Five RAPD markers consistently differentiated wild proso millet from crop cultivars and crop-like weeds. About 10% of the genotypes had at least one marker of the other type, suggesting possible hybridization between wild proso millet and crop biotypes. Most genotypes occurred in only one or two of the over 100 populations tested. The most widespread wild proso millet genotype occurred in 12 populations distributed in North Dakota, Minnesota, Illinois, and Wisconsin. More genetic variation exists among populations of wild proso millet than expected for a plant that presumably experienced a severe genetic bottleneck only 20 generations ago. Hypermutation rates and crossing between wild proso millet and crop cultivars could not account for the degree of genetic variation found in wild proso millet. The pattern of genetic variation among wild proso millet populations suggests multiple introductions of wild proso millet to North America.

Genetic diversity of 30 common vetch (Vicia sativa L.) lines and cultivars obtained from various resources or collected from natural flora of Turkey was evaluated by using 55 sequence-related amplified polymorphism (SRAP) and five inter-simple sequence repeat (ISSR) primer sets, and their nuclear DNA contents were determined by flow cytometer. A total of 188 polymorphic loci were detected, with an average of 3.62 loci per primer. The percentage of polymorphic loci was 82.1%. The polymorphism information content values ranged from 0.12 to 0.96, with an average of 0.63. The genetic distance coefficients were in the range of 0.112–0.627. Cluster analysis revealed that the 27 lines and three cultivars could be divided into two main groups. No polyploidy was detected within any vetch lines tested while significant (P< 0.0001) nuclear DNA content differences were determined. The present study revealed that fast and accurate fingerprinting analysis could be done using SRAP and ISSR markers, which indicated existing significant variation among common vetch lines and cultivars.

Jatropha curcas (jatropha) is an important non-edible oilseed crop with potential as a raw material for biofuel production. Although J. curcas has 30–35% oil content in its seeds, it has low seed yield ( < 2 ton/ha) and thus cannot become an economically viable crop. However, jatropha has many related species and genera such as J. integerrima, J. multifida, J. podagrica and Ricinus communis that are suitable for interspecific and intergeneric hybridization. The desirable features that can be obtained from these species are high number of inflorescences from J.integerrima, large fruit size from J. multifida, high oil content from J. podagrica and raceme-type inflorescence from R. communis. We were initially successful in producing hybrids between J. curcas and these related species. Hybridity was confirmed using expressed sequence tag (EST)–simple sequence repeat markers developed from the J. curcas EST database.

Anatolia (Asia Minor) is considered to be the cradle of viticulture, but wild grape accessions from this region have not been subjected to any genetic analysis. We present the first genetic characterization of wild grapes (Vitis vinifera subsp. sylvestris) from this region. Using 15 nuclear microsatellites, we genotyped 84 wild grape accessions collected from three Anatolian locations. The unweighted pair group method with arithmetic mean analysis revealed four genetic clusters that partially separated Anatolian wild grape populations. In general, accessions from geographically closer locations showed higher genetic similarities than those from more distant locations. In some cases, accessions from one population showed close genetic relationships to accessions from a different population. The genetic diversity between natural populations from both ends of the Mediterranean basin has shown higher genetic diversity in the Anatolian Peninsula than peripheral populations, suggesting that this area could be one centre of diversity of the species. The genetic relationship between wild and cultivated grapevine from Anatolian Peninsula indicated a clear separation between them. However, we cannot discarded a local genetic contribution. Overall, this study reveals useful information for management and potential utilization of Anatolian wild grape germplasm.

Characterization of plant germplasm using molecular techniques is playing an increasingly important role in the management and utilization of plant genetic resources, but has its limitations in the screening of large numbers of accessions held in seed genebanks worldwide. Bulking individual plants from one accession or group to form a representative sample is a promising approach to widening the scope of a characterization, but it is not without technical problems in detecting genetic variation. This review was conducted to assess the technical pitfalls of bulking, and to evaluate the effectiveness of various bulking methods in the assessment of genetic variation and genetic relationships, and in the identification of plant germplasm. Clearly, some alleles, particularly those occurring at low frequency, may go undetected in a bulked sample, depending on the bulking methods and the molecular techniques used. As a result, genetic diversity estimates and genetic relationship inferences can be significantly biased. Germplasm identification may not be always reliable. Thus, it is imperative that the detection limit imposed by bulking be assessed for a newly initiated molecular germplasm characterization and bias be considered in interpretation of the resulting characterization data. Equally imperative is the need for continuous efforts of exploring efficient bulking procedures for the screening of large germplasm collections, particularly by the newly developed marker systems.

A total of six amplified fragment length polymorphism (AFLP) primer combinations were used to detect genetic variation of pooled DNA in a sample of 12 chicken breeds indigenous to China, and AFLP DNA fingerprinting of each chicken breed was constructed. Polymorphic bands, specific bands and genetic similarity coefficients of 12 chicken breeds were calculated from AFLP data. A total of 279 polymorphic bands were generated by the six primer combinations, giving, on average, 46.5 polymorphic markers detected per primer combination. Nine specific bands were produced in the pooled DNA of Jiuyuan black and Dongxiang black chickens. However, one specific band was produced in the pooled DNA of Wenchang and Xingyi bantam chickens. An unweighted-pair-group method using average linkages (UPGMA) cluster analysis revealed that the 12 chicken breeds could be divided into three groups. Genetic similarity coefficients and the UPGMA tree of the 12 chicken breeds were consistent with their breeding history as well as their geographical distribution. Based on AFLP DNA fingerprinting, genetic diversity, genetic relationship and identification of chicken breeds can be analysed.

We present here the first large-scale genetic characterization of grape cultivars from Transcaucasia and Anatolia. These regions where wild grapes still grow in nature have been cultivating wine and table grapes for thousands of years and are considered the cradles of viticulture. Using 12 nuclear microsatellite markers, we genotyped 116 accessions of traditional grape cultivars from Armenia, Georgia and Turkey and we detected 17 identical genotypes and six homonymy cases, mainly within each national germplasm. Neighbour-joining analysis of genetic distance showed that each germplasm could have multiple origins and although they are now separated, they might have some common ancestors. In addition, four varieties from Western Europe included as outgroups turned out to be more related to Georgian cultivars than other germplasms, suggesting a possible ancient origin in Georgia. This work represents a first step towards germplasm management of this rich ampelographic heritage.

Sinapis alba L. is a major specialty crop grown as a condiment in western Canada, but little is known about its genetic diversity. The objective of this study was to assess the level and pattern of genetic diversity in a collection of 127 S. alba accessions held at Plant Gene Resources of Canada using amplified fragment length polymorphism (AFLP) markers. Five AFLP primer pairs were applied, and 134 polymorphic bands were scored for each accession. These scored bands had frequencies of occurrence ranging from 0.02 to 0.99 with an average of 0.69. More AFLP variation was found within single (79.1%) than between (20.9%) S. alba accessions. A small degree of AFLP difference (1.7%) was observed among the accessions of various regions, while relatively large variation (9.2%) existed among the accessions of various countries. A large AFLP difference (15.6%) also existed between the yellow- and brown-seeded accessions, but only 6.2% difference was observed between the cultivar and landrace accessions. Two distinct groups of S. alba germplasm were identified on the basis of the seed colour (yellow or brown), although a few mixtures also existed. No apparent ‘duplicated’ accessions were observed. The most diverse accessions were from Italy, Spain, France and Greece. Among the most genetically distinct accessions were SA97 from Portugal, SA89 and SA88 from France, SA83 from Russia and SA57 from Italy. These findings are significant not only for managing S. alba germplasm, but also for identifying diverse germplasm that can be used by plant breeders to improve S. alba seed yield and quality parameters.

Cili (Rosa roxburghii Tratt), characterized by containing the highest vitamin C content among fruits and showing attractive senescence-retarding and cancer-preventing effects, has gained widespread interest. RAPD markers were applied to identify the seven genotypes of cili and to evaluate the genetic relationships within cili, as well as among its relatives. Sixteen arbitrary primers screened from 154 were adopted to analyse polymorphism in RAPD profiles for the 15 samples. A total of 137 RAPD bands ranging in size from 480 bp to 3.3 kb were obtained, among which 95 were polymorphic, covering 69.3% of the total bands obtained; and an average of 8.6 bands/primer was scored. The genotypes of cili and seedless cili could be identified efficiently by 14 genotype-specific bands, which were obtained from the polymorphic primers OPB-11, OPAF-16 and OPW-02. Additionally, using the unweighted pair group method with arithmetic mean, a dendrogram showing genetic relationships among the 15 samples was constructed based on cluster analysis of genetic distance. The possible origin of seedless cili and multiple-corolla cili is also discussed.