The genus Allium is distributed worldwide and includes about 80 North American species, with at least 13 occurring in Utah. Our study focuses on the population dynamics of three Allium species native to Utah; Allium acuminatum, A. brandegei, and A. passeyi. In conjunction with our studies of life history, growth characteristics, demographics, and habitat, we are interested in determining the levels of genetic variation in these species. This study examines amplified fragment length polymorphism (AFLP) within and among five Allium acuminatum, four A. brandegei, and three A. passeyi populations native to Utah. These species have contrasting abundance and distribution. The study populations were selected along an elevation gradient to represent within-species habitat differences. About 10–20 plants from each of the 12 populations were genotyped using six AFLP primer combinations, which detect DNA variation within and among all three species. These data will be used to compare levels of genetic variation and isolation among populations and species.
Nathan C. Phillips, Steve R. Larson, and Daniel T. Drost
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.
Chalita Sriladda, Heidi A. Kratsch, Steven R. Larson, Thomas A. Monaco, FenAnn Shen, and Roger K. Kjelgren
hybrid plants. Leaf samples were dried in 28-200 mesh silica gel (Fisher Scientific, Pittsburgh, PA). DNA was extracted with the Dneasy 96 Plant Kit (QAIGEN, Valencia, CA). Amplified fragment length polymorphisms (AFLPs) were assayed to fingerprint the
C. Thomas Chao* and Pachanoor S. Devanand
Acreages of `Nules' Clementine and `Afourer' mandarin have increased rapidly in California. One way to produce seedless mandarins is using Navel oranges or Satsuma mandarins as buffer to prevent cross-pollination. In order to determine the number of necessary buffer rows or spacing to prevent cross-pollination, we used AFLP markers to determine the pollen parentages of `Nules' and `Afourer' seedlings from two sites. The AFLP markers were able to identify Clementine as pollen parents of 26.6% (25/94) of the `Afourer' seedlings from one site. The pollen of Clementine was able to travel across minimum of 32 rows to pollinate `Afourer' mandarins. We found 12.73% (14/110) of the `Afourer' seedlings at the east side of the site were progenies of `Minneola' tangelo. Pollen of `Minneola' was able to travel across minimum 94 rows to pollinate `Afourer' mandarins. 12.73% (14/110) of the `Afourer' seedlings at the east end of the site were progenies of Clementine. Pollen of Clementine was able to travel minimum 54 rows to pollinate the `Afourer' mandarin at the east end of the site. The AFLP markers also identified `Afourer' mandarin as pollen parents of almost all `Nules' seedlings (98.63%, 72/73) at a second site. The pollen of `Afourer' was able to travel across minimum of 74 acres of empty ground from the east or minimum of 91 rows of Navel (128 acres) from the north to pollinate `Nules' Clementine. The results showed how far can compatible pollens traveled to cause seeds in mandarins in California. The implication from the results in seedless mandarin production in California is discussed.
Ying Wang, Gregory L. Reighard, Desmond R. Layne, Albert G. Abbott, and Hongwen Huang
Pawpaw (Asimina triloba) produces the largest fruit native to the United States. Six linkage groups were identified for A. triloba using the interspecific cross [PPF1-5 (A. triloba) × RET (A. reticulata Shuttlw. ex Chapman)], covering 206 centimorgans (cM). A total of 134 dominant amplification fragment length polymorphism (AFLP) markers (37 polymorphic and 97 monomorphic) were employed for estimating the genetic diversity of eight wild populations and 31 cultivars and advanced selections. For the wild populations, the percentage of polymorphic loci over all populations was 28.1% for dominant markers and Nei's genetic diversity (He) were 0.077 estimated by 134 dominant markers. Genetic diversity and the percentage of polymorphic loci estimated using only polymorphic dominant AFLPs were 0.245 and 79%, respectively, which are comparable with other plant species having the same characteristics. Estimated genetic diversity within populations accounted for 81.3% of the total genetic diversity. For cultivars and advanced selections, genetic diversity estimated by 134 dominant markers was similar to that of wild pawpaw populations (He = 0.071). Thirty-one cultivars and advanced selections were delineated by as few as nine polymorphic AFLP dominant loci. Genetic relationships among wild populations, cultivars and advanced selections were further examined by unweighted pair group method with arithmetic mean (UPGMA) of Nei's unbiased genetic distance. The genetic diversity estimated for wild populations using the clustered polymorphic markers was lower than the result estimated using the nonclustered polymorphic markers. Therefore, this study indicates that the number of sampled genomic regions, instead of the number of markers, plays an important role for the genetic diversity estimates.
Anna L. Hale, J. Creighton Miller Jr., K. Renganayaki, Alan K. Fritz, J.J. Coombs, L.M. Frank, and D.S. Douches
The objective of this study was to differentiate six intraclonal variants of the potato (Solanum tuberosum L.) cultivar Russet Norkotah. One-hundred-twelve AFLP primer combinations producing 3755 bands and 79 microsatellite primers producing over 400 bands failed to identify any reproducible polymorphisms among the intraclonal variants and `Russet Norkotah'. The inability to detect differences between clones underscores the degree of genetic similarity between them, despite differences in phenotypic expression. This inability could be due to the tetraploid nature of the clones and/or to epigenetic differences not detected by the utilized procedures.
Luisa Monte-Corvo, Luis Goulão, and Cristina Oliveira
Inter-simple sequence repeat (ISSR) markers were used for cultivar identification and for determination of the phenetic relationships among 24 pear cultivars (Pyrus communis L.). The ability of several molecular marker systems including randomly amplified polymorphic DNA (RAPD), amplified fragment length polymorphisms (AFLP), inter-simple sequence repeats (ISSR), simple sequence repeats (SSR), and selective amplification of microsatellite polymorphic loci (SAMPL) to detect variation among clones of the most significant Portuguese cultivar, Rocha, was also investigated. Each of the eight ISSR primers tested was able to distinguish the 24 pear cultivars. The ISSR primers generated 337 markers, 79.5% of which were polymorphic. The cultivar dendrogram obtained with the ISSR marker data was very similar to that obtained with previous RAPD+AFLP analysis, confirming the genetic divergence of `Pérola', `Carvalhal' and `Lawson' from the other cultivars. Eight out of 15 apple [Malus sylvestris (L.) Mill. var domestica (Borkh.) Mansf.] SSR primers tested also amplified microsatellites in pear. None of the five molecular marker systems analyzed (with a total of 1082 markers) detected reproducible polymorphisms among the nine `Rocha' clones, in spite of the presence of clear phenotypic differences.
Jinggui Fang, Panchanoor S. Devanand, Chih Cheng T. Chao, Philip A. Roberts, and Jeff D. Ehlers
Cowpea (2n=2x=22) is a high protein, short-cycle, and essential legume food crop of the tropics, especially in the low input agricultural areas of sub-Saharan Africa, Asia, and South America. Lack of genetic diversity within breeding programs can limit long-term gains from selection. The cowpea gene pool is thought to be narrow and the genetic diversity within breeding programs could be even less diverse. Genetic relationships among 87 cowpea accessions, including 60 advanced breeding lines from six breeding programs in Africa and the United States, and 27 accessions from Africa, Asia, and South America were examined using amplified fragment length polymorphism (AFLP) markers with six near-infrared fluorescence labeled EcoR I + 3/Mse I + 3 primer sets. A total of 382 bands were scored among the accessions with 207 polymorphic bands (54.2%). Overall, the 87 cowpea accessions have narrow genetic basis and they shared minimum 86% genetic similarities. The data also show that the advanced breeding lines of different programs have higher genetic affinities with lines from the same program but not with lines from other programs. The results suggest that there is a need to incorporate additional germplasm of different genetic background into these breeding lines and to ensure the long-term genetic gains of the programs.
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.
M.J. Prado, S. Romo, M. Novo, M. Rey, M.T. Herrera, and M.V. González
We investigated the characterization of genotypes of Actinidia deliciosa (Chev.) Liang and Ferguson var. deliciosa by using isozymatic and molecular techniques [randomly amplified polymorphic DNA (RAPD), amplified fragment-length polymorphism (AFLP), standard AFLP, and modified AFLP]. Four genotypes were tested, the female cultivar `Hayward', the traditional New Zealand pollinizers `Matua' and `Tomuri', and a new pollinizer named clone A selected in a breeding program in Spain. PGI and PGM were the only isozymes that allowed us to distinguish the kiwifruit genotypes, although the accessions of `Matua' presented two different banding patterns for both isozymes. All three molecular markers differentiated between the genotypes of kiwifruit tested, although RAPD markers did not allow us to establish differences between accessions of `Matua', while both standard and modified AFLP did. These results, along with those of isozymes, support the hypothesis that the male kiwifruit genotypes present in Europe belong to different clones. None of the markers used showed differences between accessions of `Hayward', which would suggest that it is a uniform cultivar. On the other hand, clone A was a seedling derived from `Hayward' and an unknown pollinizer. The results obtained using AFLP markers strongly suggest that `Tomuri' may have been the male parent of clone A. A specific protocol for kiwifruit characterization based on a modified AFLP technique is also presented, that gave rise to the highest percentage of polymorphism while scoring the lowest number of bands. This, together with the technical features of modified AFLP markers, make them very useful for identifying propagated kiwifruit plant material in commercial nurseries.