complex introgression as backcrosses, F 2 s, etc. ( Hoban et al., 2009 ). For these reasons, hybrids are often difficult to distinguish by silvic characters, and identification using DNA markers is essential. Simple sequence repeat (SSR) markers exhibit
Zhan Shu, Xue Zhang, Dianqiong Yu, Sijia Xue, and Hua Wang
Ashok K. Ghosh, Lewis N. Lukens, David M. Hunter, and Judith N. Strommer
The genus Pyrus (pear) includes species and cultivars of great diversity. We have tested the feasibility of a polyacrylamide gel eletrophoresis (PAGE)-based +/– simple sequence repeat (SSR) screen as a means of defining relationships amongst pears of commercial importance in North America. The screen included 28 pear accessions, including economically important cultivars, numbered selections from breeding programs and interspecific hybrids. It relied on 18 SSR primer pairs, each of which produced polymorphic banding patterns in all the genotypes examined. Fragments were scored for presence or absence within genotypes. The results show that amplification and analysis of a small number of SSR loci enable identification of cultivars and reasonable definition of genetic relationships in North American pears. Seven primer pairs were sufficient to distinguish the 28 pear cultivars. Analyses using both distance and parsimony criteria grouped cultivars in a manner consistent with known pedigrees and sites of origin.
Luís Goulão, Luisa Monte-Corvo, and Cristina M. Oliveira
Variability of commercial plum (Prunus L. sp.) cultivars is unknown since breeding often involves intercrossing hybrids with several species but has been based on a low number of parents. Molecular markers like amplified fragment length polymorphisms (AFLP) and inter-simple sequence repeats (ISSR), which sample multiple loci simultaneously, have become increasingly popular, and were used to characterize 24 diploid and four hexaploid cultivars of plum. Seven AFLP and six ISSR primers were used, and resulted in amplification of 379 and 270 products, respectively. Unweighted pair-group method with arithmetic averages (UPGMA) dendrograms, based on similarity coefficients, reflected a clear separation between diploid and hexaploid plums. Among diploid plums, two pairs of cultivars were relatively distinct from the rest, namely `Golden Japan' and `Methley' and `Ozark Premier' and `Songold'. Furthermore, several cultivars were grouped together both with AFLP and ISSR analysis: 1) `Ambra', `Red Beaut', and `Black Beaut', 2) `Black Diamond' and `Royal Diamond', 3) `June Rose', `Santa Rosa', and `Royal Red', and iv) `Freedom', `Larry Ann', and `Queen Rosa'. Although the phenetic classification obtained by the two methods were similar (r = 0.73, for the diploid group), ISSR had a higher reproducibility and percentage of polymorphisms (87.4% vs. 62.8%) than AFLP. Methodological aspects of both markers systems are discussed. Results obtained suggest that the AFLP and ISSR approaches are valuable tools for identification of specific genotypes and analysis of phenetic relationships in plum.
Jack E. Staub, Gennaro Fazio, Thomas Horejsi, Yael Danin-Poleg, Noa Reis, and Nurit Katzir
Random amplified polymorphic DNA (RAPD) and simple sequence repeat (SSR) markers were used to characterize genetic relationships among 46 accessions in two C. melo L. subsp. melo (Cantalupensis, Inodorus) and subsp. agrestis (Conomon and Flexuosus) groups. Genetic distance (GD) estimates were made among and between accessions in four melon market classes [Galia, Ogen, Charentais, and Shipper (European and U.S. types)] of Cantalupensis, one market class of Inodorus (Cassaba and Honey Dew), one accession of Conomon, and one accession of Flexuosus by employing three GD estimators; simple matching coefficient, Jaccard's coefficient, and Nei's distance-D. Differences detected among 135 RAPD bands and 54 SSR bands (products of 17 SSR primers) were used to calculate GD. Band polymorphisms observed with 21 RAPD primers and 7 SSR primers was important in the detection of genetic differences. Estimators of GD were highly correlated (P > 0.0001; rs = 0.64 to 0.99) when comparisons were made between estimation methods within a particular marker system. Lower correlations (P > 0.001; rs = 0.17 to 0.40) were detected between marker systems using any one estimator. The GD of the Conomon and Flexuosus accessions was significantly different from the mean GD of all the market classes examined, and market classes were distinguishable from each other. Although lower coefficients of variation can be attained in the estimation of GD when using RAPDs compared to SSRs, the genetic relationships identified using these markers were generally similar. Results of RAPD marker analysis suggest that 80 marker bands were adequate for assessing the genetic variation present in the accessions examined.
Warren F. Lamboy and Christopher G. Alpha
Curators of plant genetic resources collections must preserve germplasm possessing known useful characteristics as well as material displaying general genetic diversity. In order to ensure that both types of germplasm are included in a collection, germplasm curators require three fundamental types of information about each accession: taxonomic identity, genetic identity, and genetic relationship. Because simple sequence repeat DNA fragments (SSRs) have been successfully used to determine the genetic identity of grape clones, we conducted a study to determine if SSRs would supply all three types of information for the accessions in the cold-hardy Vitis (grape) germplasm collection. SSR fragments were amplified at six different loci for 23 accessions of cold-hardy grape spanning the range of species diversity in the collection. The minimum number of different alleles found at a locus was 9; the maximum was 26. Heterozygosity values ranged between 0.565 and 0.783, while gene diversity values were in the range 0.785 to 0.944. Two hundred fifty-two pairs of plants out of a possible 253 could be distinguished by their SSR profiles. Nei's genetic identities were computed between all pairs of plants and used in a UPGMA cluster analysis. The relationships obtained did not correspond well to expected relationships based on geography and taxonomy. Four species of grapes were represented by two or more accessions in this study. No DNA fragments found at these six loci served to unambiguously distinguish one species from another. Thus, SSR fragments from the six loci studied were useful in determining genetic identity of accessions, but were not helpful in determining genetic relationships or taxonomic identities. We are searching for additional loci that are informative for these types of information. Meanwhile we highly recommend SSRs for determining genetic identity in germplasm resources collections.
Tiantian Zhao, Wenxu Ma, Qinghua Ma, Zhen Yang, Lisong Liang, Guixi Wang, and Lujun Wang
genetic diversity and population structure of hazelnut, such as random amplified polymorphic DNA [RAPD ( Galderisi et al., 1999 ; Miaja et al., 2001 )], simple sequence repeat [SSR ( Boccacci et al., 2006 , 2008 ; Gökirmak et al., 2009 ; Gürcan et al
K.S. Lewers, S.M.N. Styan, S.C. Hokanson, and N.V. Bassil
Although simple sequence repeat (SSR) markers have been developed for species in the closely related genera Fragaria L. (strawberry) and Rubus L. (raspberry and blackberry), the number of SSRs available is insufficient for genetic mapping. Our objective was to use and compare multiple approaches for developing additional SSRs for Fragaria and Rubus. The approaches included: the development of SSRs from GenBank sequences from species of varied relatedness to Fragaria and Rubus and identified with two different data-mining methods (BLAST and SSRIT); the evaluation of some previously published SSRs designed from related species; and the development of SSRs from a genomic library made from F. ×ananassa Duschene ex Rozier `Earliglow'. When an SSR was developed from a known gene sequence, the location of the repeat in the gene was determined to evaluate the effect on amplification and polymorphism detection. Cross-generic amplification between closely related Fragaria and Rubus as well as transference from species of varied relatedness to Fragaria and Rubus also was evaluated and indicated limited transference within the subfamily Rosoideae. However, development of SSRs for Fragaria and Rubus from Rosa L. (rose) and Rosaceae genera outside Rosoideae was not efficient enough to be practical for new map development. SSRIT was superior to BLAST for identifying GenBank sequences containing repeats. SSRs developed from repeats found in either the 5′UTR (80% polymorphic) or 3′UTR (85% polymorphic) were most likely to detect polymorphisms, compared with those developed from coding regions (30%). SSRs developed from the genomic library were only slightly superior to GenBank-derived SSRs in their ability to detect polymorphisms.
Pei Xu, Tingting Hu, Yuejian Yang, Xiaohua Wu, Baogen Wang, Yonghua Liu, Dehui Qin, Jeffrey Ehlers, Timothy Close, Zhongfu Lu, and Guojing Li
reference genetic map (the ‘ZZ’ map), which is enriched with expressed sequence tag (EST)-derived SNPs and SSR markers ( Xu et al., 2011 ). Materials and Methods Plant materials included ‘ZN016’, a landrace of asparagus bean originating from southern China
Kentaro Kitahara, Shogo Matsumoto, Toshiya Yamamoto, Junichi Soejima, Tetsuya Kimura, Hiromitsu Komatsu, and Kazuyuki Abe
As the parents of the some of the apple cultivars were unknown and others were uncertain, we investigated the parent-offspring relationships of eight apple cultivars by S-RNase analysis and SSR markers. The paternal parent of `Hida' was identified as `Golden Delicious', not the previously mentioned `Orin'. It was indicated that `Ryoka No Kisetsu' and `Korin' showing identical SSR genotype are likely sports of `Fuji'. `Fuji', rather than `Toko', seemed to be a maternal parent of `Kotoku', but was not a paternal parent of `Orei', `Starking Delicious', `Nero 26', `Empire', or `Aori 3'. Previously mentioned `Mutsu', `Indo', and `Shin Indo' were excluded as paternal parents of `Hokuto'. `Tsugaru' and `Jonathan' and were identified as the respective paternal parents of three cultivars described as having unknown paternal parents, i.e., `Aika No Kaori', `Yoko', and `Tsugaru'.
Deqiu Fang, Robert R. Krueger, and Mikeal L. Roose
ISSR markers were analyzed to study phylogenetic relationships among 46 Citrus L. accessions representing 35 species. A dendrogram based on the unweighted pair-group method, arithmetic average cluster analysis was constructed using a similarity matrix derived from 642 polymorphic ISSR fragments generated by 10 primers. These 46 accessions could be classified into five major groups: 1) C. indica Tan.; 2) C. maxima (Burm.) Merrill; 3) lemon [C. limon (L.) Burm.] or lime [C. aurantifolia (Christm.) Swingle] type accessions; 4) C. halimii B. C. Stone; and 5) sour orange (C. aurantium L.), mandarins and their hybrids. Group 5 was further divided into three subgroups. Although some previous work had grouped it with mandarins, C. indica appeared to be a distinct genotype or species that was not close to mandarins. C. tachibana Tan. grouped closely to mandarins. C. vulgaris Risso was not related to sour orange but was similar to accessions usually classified in the lime or lemon group. Sour orange and its hybrids, C. nippokoreana Tan., C. hanayu Hort. ex Shirai, C. sudachi Hort. ex Shirai, and C. yuko Hort. ex Tan. had close phylogenetic relationships with mandarins. Although the mandarin accessions studied were divergent in morphology, the genetic distances among them were relatively small. Relationships among these Citrus accessions revealed by ISSR markers were generally in agreement with previous taxonomic classifications.