Single-nucleotide-polymorphism (SNP) is the most abundant genetic variation among individuals within a species. SNPs can be used as markers for gene discovery and for assessment of biodiversity. We established a practical strategy for discovering candidate SNPs in fruiting-mei (Prunusmume Sieb. et Zucc.), a non-model tree fruit, from amplified-fragment-length-polymorphism (AFLP) fragments. Eighty-one of the 150 chosen bands from 10 cultivars of fruiting-mei were successfully re-amplified and 67 of these re-amplified PCR products yielded 13 groups of reliable sequences. The sequencing results from both directions of 23 randomly selected PCR products using the corresponding selective primers showed that all the purified fragments from the gels were EcoR I-EcoR I fragments. The sequence alignment of 13 groups of sequence yielded 95 SNPs from a total of 5252 bp, averaging one SNP every 55 bp. Among these SNPs, 73 were heterozygous in the loci of some individual cultivars. The SNPs distribution were: 58% transition, 40% transversion, and 2% InDels. There were also one di-nucleotide polymorphism and one tetra-nucleotide deletion. The procedure of SNP isolation from AFLP fragments can be useful for transferring AFLP markers into sequence-tagged-site markers.
Jinggui Fang, Pachanoor S. Devanand and ChihCheng T. Chao
Chih-Cheng T. Chao, Dan E. Parfitt, Louise Ferguson, Craig Kallsen and Joe Maranto
Trunk cross-sectional area from a population of 6192 pistachio trees was used to estimate tree growth from 1995 to 1997. The narrow-sense heritabilities of trunk cross-sectional area were near zero across multiple locations based on analyses of progenies from 20 half-sib families. However, within individual location, there were values from 0.20 to 0.56 for 1995, 1996, and 1997, respectively. Broad-sense heritability estimates were considerably higher, from 0.36 to 0.64 at multiple locations and 0.51 to 1.35 for individual locations. These results suggest that dominance and significant interaction effects, epistatic and genotype by environment, were important. Breeding strategies should emphasize selection of superior parents based on individual performance, and parents should be selected in the environment in which the progeny are intended to be used.
Dan E. Parfitt, Chih-Cheng T. Chao, Craig Kallsen, Joe Maranto and Louise Ferguson
A pistachio breeding program was initiated in 1989 to develop new cultivars for the California industry. The program was begun with an initial set of 1940 progeny from 78 crosses. In 1990, an additional 5470 seedlings were produced from 176 controlled crosses. Progeny were planted at Winters, Calif., Kearney Agr. Center, and a plot near Bakersfield in a randomized block design with crosses as treatments. Fifty-three, 962, and 2943 genotypes flowered in 1994, 1995, and 1996, respectively. Data on flowering, flowering date, sex, tree size as measured by trunk cross-section area, and disease status were collected on all trees in the breeding program at the three field locations. Nuts were collected and evaluated for number of nuts/tree, % splits, % blanks, wet and dry weight, kernel weight, and volume. Heritability estimates for nut characters, tree size, and Alternaria resistance were ranged from 0.30 to 0.76. Several parents were identified that apparently provide a high level of resistance to Alternaria. Relationships among various nut parameters and the relationship of tree size to flowering and parentage were also investigated and evaluated statistically. Replicated advanced selection trials will be established in 1997.
Jianjun Chen, Richard J. Henny, Pachanoor S. Devanand and Chih-Cheng T. Chao
Peace lily (Spathiphyllum Schott) is one of the most popular tropical ornamental foliage plants and is used worldwide for interiorscaping. However, little information is available on the genetic relationships of cultivars. Using amplified fragment length polymorphism (AFLP) markers with near-infrared fluorescence-labeled primers, this study analyzed genetic relatedness of 63 commercial cultivars and breeding lines. Forty-eight EcoRI + 2/MseI + 3 primer set combinations were initially screened, from which six primer sets were selected and used in this investigation. All cultivars were clearly differentiated by their AFLP fingerprints, and the relationships were analyzed using the unweighted pair-group method of arithmetic average cluster analysis (UPGMA). The 63 cultivars were divided into four clusters. All commercial cultivars or breeding lines resulted from crosses of some of the cultivars, a total of 45, were positioned in cluster I with Jaccard's similarity coefficients between 0.61 and 0.88. There was only one cultivar in cluster II. Cluster III contained 16 cultivars; they are either species or breeding lines generated from interspecific hybridization. Cluster IV had one unknown species. This study provides genetic evidence as to why cultivars from cluster I and III are not readily crossable because the Jaccard's similarity coefficient between the two clusters was only 0.35. Results also indicate that commercial cultivars are genetically close. Strategies for increasing genetic diversity of cultivated peace lily should be sought for future breeding efforts.
Pachanoor S. Devanand, Jianjun Chen, Richard J. Henny and Chih-Cheng T. Chao
Philodendrons (Philodendron Schott) are among the most popular tropical ornamental foliage plants used for interior decoration. However, limited information is available on the genetic relationships among popular Philodendron species and cultivars. This study analyzed genetic similarity of 43 cultivars across 15 species using amplified fragment length polymorphism (AFLP) markers with near infrared fluorescence labeled primers. Forty-eight EcoR I + 2/Mse I + 3 primer set combinations were screened, from which six primer sets were selected and used in this investigation. Each selected primer set generated 96 to 130 scorable fragments. A total of 664 AFLP fragments were detected, of which 424 (64%) were polymorphic. All cultivars were clearly differentiated by their AFLP fingerprints, and the relationships were analyzed using the unweighted pair-group method of arithmetic average cluster analysis (UPGMA) and principal coordinated analysis (PCA). The 43 cultivars were divided into five clusters. Cluster I comprises eight cultivars with arborescent growth style. Cluster II has only one cultivar, `Goeldii'. There are 16 cultivars in cluster III, and most of them are self-heading interspecific hybrids originated from R.H. McColley's breeding program in Apopka, Fla. Cluster IV contains 13 cultivars that exhibit semi-vining growth style. Cluster V has five cultivars that are true vining in morphology, and they have lowest genetic similarity with philodendrons in other clusters. Cultivated philodendrons are generally genetically diverse except the self-heading hybrids in cluster III that were mainly developed using self-heading and semi-vining species as parents. Seven hybrid cultivars have Jaccard's similarity coefficients of 0.88 or higher, suggesting that future hybrid development needs to select parents with diverse genetic backgrounds.
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.
Jinggui Fang, Jianjun Chen, Richard J. Henny and Chih-Cheng T. Chao
Ornamental Ficus L. is a group of lactiferous trees, shrubs, and woody root-climbing vines that are cultivated either as landscape plants in the tropics and subtropics or as foliage plants used worldwide for interiorscaping. With the recent rapid expansion of the ornamental plant industry, more new Ficus species and cultivars have been introduced. However, no study has thus far addressed the genetic relationships of cultivated ornamental Ficus. Using amplified fragment length polymorphism (AFLP) markers with near-infrared fluorescence-labeled primers, this study analyzed the genetic relatedness of 56 commercial cultivars across 12 species. Forty-eight EcoRI + 2/MseI + 3 primer set combinations were initially screened, from which six primer sets were selected and used in this investigation. Most cultivars were differentiated by their AFLP fingerprints, and their relationships were determined using the unweighted pair-group method of arithmetic average cluster analysis. The 56 cultivars were divided into 12 clusters that correspond to 12 species, indicating that no interspecific hybrids of ornamental Ficus are in commercial production. The 12 species are genetically diverse, with Jaccard's similarity coefficients ranging from 0.21 to 0.43. However, cultivars within three species—Ficus benjamina L., Ficus elastica Roxb. Ex Hornem., and Ficus pumila L.—are genetically close. Twenty-seven of the 29 cultivars of F. benjamina and five cultivars of F. pumila had Jaccard's similarity coefficients of 0.98 or higher respectively. Nine cultivars of F. elastica shared Jaccard's coefficients higher than 0.96. These results indicate potential genetic vulnerability of these cultivars within the three species. Because there are increasing reports of invasive pests in the ornamental plant industry, strategies for conserving genetic resources and broadening genetic diversity of cultivated Ficus are discussed.
Jianjun Chen, Richard J. Henny, David J. Norman, Pachanoor S. Devanand and Chih-Cheng T. Chao
Dieffenbachia Schott is an important ornamental foliage plant genus. A total of 30 species has been recognized, but most cultivars come from or are related to a single species, D. maculata (Lodd.) G. Don. At least 11 of the cultivars are sports or somaclonal variants. As a result, the potential lack of genetic diversity in cultivated Dieffenbachia has become a concern. However, no research has been conducted to determine the genetic relatedness of the cultivars. This study analyzed the genetic similarity of 42 Dieffenbachia cultivars using amplified fragment length polymorphism (AFLP) markers. Six primer sets, selected from an initial screening of 48, generated a total of 453 scorable AFLP fragments of which 323 (71%) are polymorphic. All cultivars were clearly differentiated by their AFLP fingerprints. A dendrogram was constructed using the unweighted pair-group method of arithmetic averages, and principal coordinated analysis was carried out to show multiple dimensions of the distribution of the cultivars. The 42 cultivars were divided into three clusters; clusters I and II comprise 18 and 23 cultivars, respectively. Jaccard's similarity coefficients for cultivars in the clusters I and II varied from 0.44 to 0.95 and 0.41 to 0.87, respectively. These results indicate that broadening the genetic variability in the Dieffenbachia gene pool is needed, but the genetic similarity of many cultivars is not as close as previously thought. Additionally, Jaccard's similarity coefficients between most sports or somaclonal variants and their parents were 0.73 or lower, suggesting that accumulation of somatic mutations through tissue culture may play a role in the increased variation between some sports or variants and their parents.