The genus Allium contains about 500 species, several of which have been cultivated for millennia. Despite its long history of cultivation and its worldwide economic importance, little is known phylogenetically about Allium. Identification of the likely progenitor of A. cepa (the bulb onion) will focus future collection efforts on wild germplasm that may be useful in the genetic improvement of the bulb onion. Several classification schemes based on morphological characteristics have been proposed for A. cepa and its presumed closest relatives. None of these schemes has been definitive. Nuclear restriction fragment length polymorphisms (RFLPs) were identified among Allium species in sections Cepa and Phyllodolon. These were used to unbiasedly estimate phylogenetic relationships.
James M. Bradeen and Michael J. Havey
Michael J. Havey
PstI-genomic and cDNA clones revealing mapped restriction fragment-length polymorphisms (RFLP) in cucumber (Cucumis sativus L.) were sequenced in order to ensure that these clones remain available and to determine if any clones showing genetic linkage in cucumber are physically linked in Arabidopsis thaliana. Sequence comparisons using translated searches revealed that 80% of the cucumber cDNA clones showed significant (≤e-20) similarities to Arabidopsis expressed sequence tags (ESTs) or genomic sequences, as opposed to relatively few (32%) of the cucumber genomic clones. Two clones revealing RFLPs linked at 2 cM in cucumber showed significant (≤e-20) similarities to sequences separated by 347,616 basepairs on chromosome 4 of Arabidopsis.
Genyi Li and Carlos F. Quiros
DNA samples from 21 cultivars of celery (Apium graveolens L. var. dulce) were subjected to amplified fragment length polymorphism (AFLP) analysis. The most informative adapter combination was EcoRI-TaqI. All cultivars could be distinguished from each other by their unique fingerprints based on 73 markers. The program NTSYS grouped the cultivars in three main clusters according to their origin. The groupings observed agreed, with a few exceptions, with those expected by historical accounts and previous analyses based on biochemical and ramdomly amplified polymorphic DNA (RAPD) markers.
Ram K. Birhman, Sylvain R. Rivard, and Mario Cappadocia
Using restriction fragment length polymorphism (RFLP) analysis, the genetic architecture of some anther-culture-derived S. chacoense Bitt. plants was studied, and their origins were elucidated. Our RFLP analyses showed that 1) several plants, even of different ploidy but otherwise genetically identical (clones), can be regenerated from callus originating from a single microspore and, conversely, that 2) some plants regenerated from single callus can have different genetic constitutions and, therefore, must have originated from two different microspore. These findings imply that previous anther culture efficiency estimates might have to be reconsidered.
A. Belaj, I. Trujillo, R. de la Rosa, L. Rallo, and M.J. Giménez
Random amplified polymorphic DNA (RAPD) analysis was performed on the main Mediterranean cultivars of olive (Olea europaea L.) from the Germplasm Bank of the Centro de Investigación y Formación Agraria “Alameda del Obispo” in Cordoba, Spain. One hundred and ninety reproducible amplification fragments were identified using 46 random primers followed by agarose gel electrophoresis. Some 63.2% of the amplification products were polymorphic, with an average of 2.6 RAPD markers obtained for each primer. The combination of polymorphic markers resulted in 244 banding patterns. The high degree of polymorphism detected made identification of all the cultivars (51) possible by combining the RAPD banding patterns of just only four primers: OPA-01, OPK-08, OPX-01, and OPX-03. Cultivar-specific RAPD markers and banding patterns were also found. A dendrogram based on unweighted pair-group method cluster analysis was constructed using a similarity matrix derived from the RAPD amplification products generated by the 46 primers. Three major groups of cultivars could be distinguished by RAPD analysis: 1) cultivars from east and northeast Spain, 2) Turkish, Syrian, and Tunisian cultivars, and 3) the majority of common olive cultivars in Spain. The dendrogram thus showed a good correlation between the banding patterns of olive cultivars and their geographic origin. A higher level of polymorphism was observed when polyacrylamide gel electrophoresis was used to separate the amplification products. Thus, adequate use of RAPD technology offers a valuable tool to distinguish between olive cultivars.
Ockyung H. Bark, Michael J. Havey, and Joe N. Corgan
Allium fistulosum L. (bunching onion) is resistant to many of the important diseases and pests of Allium cepa L. (bulb onion). Although the first interspecific hybrids were generated more than 50 years ago, there is no conclusive evidence that any desirable trait in bunching onion has been successfully transferred to bulb onion by backcrossing. We identified RFLPs in the chloroplast and nuclear genomes to assess DNA transfer from bunching to bulb onion by backcrossing an interspecific hybrid to a bulb onion. Polymorphisms in the chloroplast genome established that the interspecific hybrid and three putative backcross plants had the cytoplasm of a bunching onion. All 57 random cDNA probes detected polymorphisms between the bulb and bunching onion for at least one of two restriction enzymes. The backcross progenies always possessed the bulb-onion fragments and an excess of probes detected the bunching-onion fragments. Only one plant showed an acceptable fit to the expected 1:1 backcross ratio. Significant deviations from expected segregation ratios may be the result of abnormal meiosis in the interspecific hybrid. However, these observations could also be explained by a previously proposed nuclear-cytoplasmic interaction conditioning preferential survival in the bunching-onion cytoplasm of eggs carrying bunching-onion chromosomes.
Jaeho Yoon, Dongcheng Liu, Wonseob Song, Weisheng Liu, Aimin Zhang, and Shaohua Li
The genetic relationships among 96 peach and nectarine [Prunus persica (L.) Batsch.] genotypes and botanical varieties originating from different ecogeographical regions of China, Japan, North America, and South Korea were evaluated with 33 SSR markers screened from 108 published SSR markers developed for peach or sweet cherry (P. avium L.). The 33 SSRs detected polymorphisms among 96 genotypes and revealed a total of 283 alleles with an average of 8.6 alleles per locus. The polymorphism information content (PIC) value ranged from 0.40 (BPPCT041) to 0.98 (BPPCT009) with an average of 0.80. Unweighted pair group method average (UPGMA) cluster analysis based on Nei's genetic distances classified genotypes into six groups, corresponding to their ecogeographical origin. Group I consisted of northern Chinese and northwestern Chinese local cultivars, and was divided into two subgroups, white and yellow peaches. Group II contained mainly southern Chinese local, Japanese, and North American cultivars and can be divided into four subgroups: Japanese white, Chinese flat, North American yellow, and some Chinese local ornamental peach cultivars. Groups III, IV, and V were comprised of Chinese local ancient cultivars, and contained `Xinjiangdatianren' and `Renmiantao', Chinese dwarf cultivars, and `Fenshouxing', respectively. Group VI had only `Baishanbitao', a Chinese ornamental cultivar. Northern and northwestern Chinese local cultivars clustered together with a greater diversity than southern Chinese local cultivars, indicating that the northern and northwestern Chinese local cultivars are similar ecotypes, and southern Chinese local cultivars are a subset of the northern Chinese group. Moreover, the Japanese and North American genotypes had a close phylogenetic relationship with southern Chinese local cultivars. The taxonomic placement of P. ferganensis (Kost. et Kiab) Kov. et Kost. and the phylogenetic relationship of `Baishanbitao' with peaches are discussed.
Richard Durham, Gloria Moore, and Charles Guy
Genetic linkage analysis was performed on an interspecific backcross of citrus [Citrus grandis (L.) Osbeck cv. Thong Dee X (Thong Dee X Poncirus trifoliata (L.) Raf. cv. Pomeroy)], using restriction fragment length polymorphism (RFLP) and isozyme analysis. Sixty-five progeny were analyzed for a total of 57 segregating markers including 9 isozymes and 48 RFLPs. Significant (p = 0.05) deviation from an expected 1:1 segregation ratio was observed for 21 (37%) of the 57 loci, but this did not exclude their use in the mapping study. Linkage analysis revealed that 50 loci mapped to 12 linkage groups while 7 loci segregated independently from all other markers. The total map distance included in the 12 linkage groups was 472 cM with the mean distance between markers being 12.8 cM. This does not represent a saturation of the genome with markers; however, this work demonstrates the potential for mapping traits of economic importance in citrus.
Lili Zhou, Frank Kappel, Cheryl Hampson, Paul A. Wiersma, and Guus Bakkeren
Amplified fragment length polymorphisms (AFLPs) were used to analyze the relationships between sweet cherry (Prunus avium L.) cultivars and selections from the breeding program at the Pacific Agri-Food Research Centre in Summerland, Canada. Six pairs of preselected primers were used for the analysis of a total of 67 cultivars and selections. Scoring the absence and presence of 118 polymorphic DNA fragments produced a unique binary code for each cultivar and selection. Two phylogenetic trees were constructed using these 118 polymorphic fragments, one tree for 55 related cultivars and selections from the Summerland breeding program and the other for 23 self-incompatible cultivars of differing origins. The reliability of AFLP DNA fingerprints was confirmed by correlating relationships revealed by AFLP profiles with known genetic relationships of some sweet cherry cultivars and by a blind test for cultivar identification. Results indicate that AFLP analysis is a good technique to evaluate genetic distance and relationships in a sweet cherry breeding population.
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.