2.11V; Exeter Software, Setauket, NY) ( Rohlf, 2004 ) based on the unweighted pair group method with arithmetic mean cluster analysis (UPGMA). Jaccard coefficients were calculated for all pairwise comparisons among the 32 tea genotypes using the same
Salih Kafkas, Sezai Ercişli, Yıldız Doğan, Yaşar Ertürk, Ayhan Haznedar, and Remzi Sekban
Xinyi Zhang, Li Liao, Zhiyong Wang, Changjun Bai, and Jianxiu Liu
genetic distance coefficients ( Nei and Li, 1979 ) for the 86 accessions. The resulting distance matrix was used to construct a dendrogram with the unweighted pair-group method with arithmetic averages (UPGMA) ( Sneath and Sokal, 1973 ) using NTSYS
Mirko Siragusa, Fabio De Pasquale, Loredana Abbate, and Nicasio Tusa
A collection of 18 accessions of sour orange (Citrus aurantium L.) coming from Sicily and other countries was investigated by two polymerase chain reaction (PCR)-based DNA marker technologies. Ten inter-simple sequence repeat (ISSR) primers and fifteen randomly amplified polymorphic DNA (RAPD) primers were used to identify and to evaluate the genetic variability and relationship of accessions. A total of 111 ISSR and 145 RAPD amplified fragments were used to estimate the Dice's coefficient of similarity for cluster analysis using a unweighted pair-group method using an arithmetic averaging (UPGMA) algorithm. The genetic relationships identified using ISSR and RAPD markers were highly concordant, such that the correlation between ISSR and RAPD genetic distance (GD) estimates was r = 0.93. The ISSR and RAPD analysis of 18 sour orange accessions found a high grade of genetic diversity in foreign accessions, while a low variability was detected in local accessions. Sicilian accessions could be grouped in two distinct clusters, including indistinctly plants from three origin regions. Some markers could be linked to the different growing areas. The ISSR and RAPD molecular reference system seems to be suitable for a fine identification of tightly related plants and the obtained results can form the basis for future setting up of Citrus rootstock genetic improvement projects.
Marianna Hagidimitriou, Andreas Katsiotis, George Menexes, Constantinos Pontikis, and Michael Loukas
The aim of the present study was to develop a reliable reference database to discriminate between the major Greek olive (Olea europaea L.) cultivars and reveal their genetic relationships, since Greece is considered a secondary center of diversity. In order to establish genetic relationships among the 26 Greek and eight international cultivars, four amplified fragment length polymorphism (AFLP) primer pairs, 12 randomly amplified polymorphic DNA (RAPD) primers, along with measurements from 10 morphological traits, were used. A total of 576 AFLP and 113 RAPD markers were produced. Genetic similarities, estimated using the Jaccard algorithim, ranged from 0.45 to 0.83 for the AFLP data and 0.27 to 0.87 for the RAPD data. The cophenetic correlation coefficients between the genetic similarities and the unweighted pair group method of arithmetic averages (UPGMA) phenograms were 0.77 for the AFLPs, 0.81 for the RAPDs, and 0.69 for the morphological traits. However, limited clustering similarities among the phenograms derived from the three methods were observed. This was also reflected by the low correlation between the three genetic similarity matrices produced (AFLP and RAPD, r = 0.39; AFLP and morphological traits, r = 0.11; RAPD and morphological traits, r = 0.02). According to the molecular results, olive cultivars are clustered according to fruit size but not according to geographical origin. Three of the cultivars tested, `Vasilicada,' `Throumbolia', and `Lianolia Kerkiras', were found to branch distantly to the others, according to the AFLP results, and can be considered as ancient Greek cultivars.
Salih Kafkas, Hakan Ozkan, Bekir Erol Ak, Izzet Acar, Halit Seyfettin Atli, and Sonay Koyuncu
There are limited numbers of pistachio (Pistacia vera L.) cultivars in the world and their phenotypic appearance and productivity are variable. Understanding such variation would facilitate their use in cultivar breeding programs. Therefore, in this study, 69 pistachio cultivars and genotypes originating from seven countries were characterized by randomly amplified polymorphic DNA (RAPD), inter-simple sequence repeats (ISSR), and amplified fragment-length polymorphism (AFLP) markers. The results showed that all three marker systems were able to reveal variability between pistachio cultivars and genotypes. The correlation coefficients for genetic distances were statistically significant among all three molecular marker types. The correlation between RAPD and AFLP data was the highest (r = 0.73) and the value between RAPD and ISSR data was the lowest (r = 0.58). AFLP proved to be the best technique among them. ISSR and AFLP assays were reliable and produced reproducible bands. ISSR was preferred over RAPD, especially when financial investment and technical knowledge are limited. The constructed unweighted pair group method with arithmetic averages (UPGMA) dendrogram obtained from combined data separated the genotypes into two main clusters: one cluster (“Iranian”) included genotypes originating from Iran and the second cluster (“Mediterranean”) contained most other genotypes. The “Mediterranean” cluster further divided into three subclusters: one (“Siirt”) consisted of the cultivars Siirt and Hacireso with a few other selections; the second subcluster (“Turkish”) included Turkish cultivars; and the third subcluster contained Syrian, Italian, and the remaining cultivars. The closeness of the clusters was “Iranian” - “Siirt” - “Turkish”/“Syrian.” These findings reveal a new understanding in the diffusion of pistachio cultivation from its center of origin, the Iranian-Caspian region, via southeastern Turkey to Syria, the Mediterranean region of Europe, and northern Africa.
Fei-Yun Zhuang, Jin-Feng Chen, Jack E. Staub, and Chun-Tao Qian
The current Cucumis taxonomic classification places C. hystrix Chakr. in subgen. Cucumis based on its morphological similarities to cucumber (C. sativus L., 2n = 14). However, the chromosome number of C. hystrix was identified as 2n = 24, the same number as in subgen. Melo. Cucumis hystrix is therefore considered the first wild Cucumis species of Asiatic origin possessing 12 basic chromosomes. Thus, any research regarding its biosystematics would challenge the basic chromosome number and geographic location theories that govern the current taxonomic system. The production of the amphidiploid species (Cucumis ×hytivus Chen and Kirkbride, 2n = 38) obtained from the cross between C. hystrix and C. sativus and subsequent chromosome doubling would provide an effective means of investigating the relationship between Cucumis species with two different basic chromosome numbers. Thus, RAPD markers were used to study the taxonomic placement of C. hystrix and its interspecific hybrid with cucumber. Of the 220 arbitrary primers screened, 31 were used for analysis where 402 (96.3%) fragments were polymorphic among the germplasm examined. A UPGMA-based cluster analysis partitioned 31 accessions into two main groups [C. sativus (CS) and C. melo (CM)]. Under the similarity coefficient threshold of 0.23, these two groups can be further divided into five clusters with C. hystrix, C. ×hytivus, and C. sativus as separate clusters in the CS group. A modified taxonomic system is proposed based on these results and findings of a previous chloroplast DNA analysis with the genus Cucumis containing subgen. Cucumis with three species and subgen. Melo with six series.
Jernej Jakse, William Martin, John McCallum, and Michael J. Havey
The commercial production of onion (Allium cepa L.) inbreds, hybrids, and open-pollinated (OP) cultivars would benefit from a robust set of molecular markers that confidently distinguish among elite germplasms. Large-scale DNA sequencing has revealed that single nucleotide polymorphisms (SNPs), short insertion-deletion (indel) events, and simple sequence repeats (SSRs) are relatively abundant classes of codominant DNA markers. We identified 398 SNPs, indels, and SSRs among 35 elite onion ulations and observed that all populations could be distinguished. Phylogenetic analyses of simple-matching and Jaccard's coefficients for SSRs produced essentially identical trees and relationships were consistent with known pedigrees and previous marker evaluations. The SSRs revealed that elite germplasms from specific companies or breeding programs were often closely related. In contrast, phylogenetic analyses of SNPs and indels did not reveal clear relationships among elite onion populations and there was no agreement among trees generated using SNPs and indels vs. SSRs. This discrepancy was likely due to SNPs and indels occurring among amplicons from duplicated regions (paralogs) of the onion genome. Nevertheless, these PCR-based markers will be useful in the quality control of inbred, hybrid, and OP onion seed lots.
Joseph J. King, James M. Bradeen, and Michael J. Havey
Nuclear RFLPs were used to estimate relationships among 14 elite commercial inbreds of bulb onion (Allium cepa) from Holland, Japan, and the United States. Variability for known alleles at 75 RFLP loci and 194 polymorphic fragments revealed by 69 anonymous cDNA probes and a clone of alliinase were scored to yield genetically characterized and uncharacterized data sets, respectively. The inbred onion populations possessed more than two alleles at 20 of 43 (46%) codominant RFLP loci. Relationships among the inbreds were estimated by cluster analysis of simple-matching (genetically characterized data) and Jaccard (genetically uncharacterized data) coefficients using the unweighted pair group method and agreed with known pedigrees. RFLPs confidently distinguished among elite inbreds within and between specific market classes. RFLP profiles for virtual hybrids were computer-generated by combining gametic arrays among inbreds of the same market class and analyzed as described above. Allelic and genetically uncharacterized RFLPs confidently distinguished among these hybrids, even though heterozygosity for many markers produced a majority of monomorphic fragments. We randomly sampled decreasing numbers of RFLPs from the complete data sets and calculated simple-matching and Jaccard distances, noting the numbers of probes that were unable to distinguish any two inbreds or hybrids. As few as 10 polymorphic probe-enzyme combinations distinguished among all the inbreds and samples of 20 genetically characterized or 10 genetically uncharacterized clones distinguished all the virtual hybrids. This study demonstrated that the previously reported few RFLPs observed among open-pollinated (OP) onion populations were due to the highly heterozygous nature of the OP population.
Marilyn L. Warburton and Fredrick A. Bliss
Previous studies of peach germplasm using pedigree information and isozyme polymorphism data have shown limited diversity in the U.S. gene pool. To further investigate the genetic diversity among peach cultivars grown in different regions of the United States, 94 RAPD markers were used to estimate the genetic distances among 136 cultivars. Of the 12 clusters formed in a dendrogram, the 90 U.S. cultivars and breeding lines and most of those from Europe and Latin America grouped to only three clusters, while the 23 peach entries from India, Pakistan, Russia, Okinawa, and China, as well as the almond cultivar used as an outgroup, were distributed among the other nine clusters. Therefore, the genetic diversity within temperate U.S. peach germplasm is quite limited, and to expand the variability, additional germplasm should be obtained, especially from Asia. Comparison of genetic similarity based on inbreeding coefficients with similarity coefficients based on the RAPD data produced a correlation of 0.395, which is comparable to values in similar investigations in other crops. Thus, similar conclusions can be drawn from these two sources of information. RAPD data are useful particularly when pedigree information is incomplete, there has been substantial selection within breeding populations, and a high proportion of alleles are identical in state but not by descent.
Mohammed Aziz Elhoumaizi, Panchanoor S. Devanand, Jinggui Fang, and Chih-Cheng T. Chao
We studied 66 `Medjool' date palm (Phoenix dactylifera L.) accessions from Morocco, six varieties of dates from Egypt, and four `Medjool' accessions and one `Deglet Noor' accession from California to investigate the hypothesis that `Medjool' is a landrace variety in Morocco. We used four sets of fluorescent-labeled amplified fragment length polymorphism (AFLP) markers to examine these accessions. A total of 402 bands were generated, of which 217 were polymorphic (54.0%). The 66 `Medjool' accessions from Morocco shared a minimum of 79% genetic similarity. These results support the hypothesis that `Medjool' is a landrace variety in Morocco and it is not genetically uniform. `Medjool' is the first confirmed landrace variety of date palm in the world. This finding raises the possibility that other date palms may be landrace varieties in different growing areas. Confirmation of a landrace variety in date palm has significant implication for future date palm germplasm collection and preservation. The mechanism(s) generating the genetic variation within `Medjool' accessions remains unknown. One possibility is that spontaneous genetic changes could occur frequently within vegetative tissues like offshoots under high temperature and drought stress.