confirmed to advance by 31 d over 30 years of studies, ranking it as the fifth most altered among the 89 plant species investigated ( Abu-Asab et al., 2001 ). Among the neutral molecular markers, the microsatellites or simple sequence repeats (SSRs) are
Marcin Nowicki, Edward E. Schilling, Sarah L. Boggess, Logan C. Houston, Matthew L. Huff, Margaret E. Staton, Jayne A. Lampley, and Robert N. Trigiano
R.J. Schnell, C.T. Olano, J.S. Brown, A.W. Meerow, C. Cervantes-Martinez, C. Nagai, and J.C. Motamayor
Commercial production of cacao in Hawaii is increasing, and this trend is expected to continue over the next several years. The increased acreages are being planted with seedlings from introduced and uncharacterized cacao populations from at least three initial introductions of cacao into the islands. Productive seedlings have been selected from a planting at Waialua, Oahu. The parents of these selections were believed to be the population at the Hawaii Agriculture Research Center (HARC) at Kunia; however, potential parental populations also exist at Univ. of Hawaii research stations at Waimanalo and Malama Ki. Using microsatellite markers, we analyzed the potential parental populations to identify the parents and determine the genetic background for 99 productive and 50 unproductive seedlings from the Waialua site. Based on 19 polymorphic microsatellite loci the parental population was identified as trees from Waimanalo and not trees from Malama Ki or Kunia. The Kunia and Malama Ki populations were very similar with low allelic diversity (A = 1.92) and low unbiased gene diversity (Hnb) of 0.311 and 0.329, respectively, and were determined to be Trinitario in type. The Waimanalo, productive seedling, and unproductive seedling populations had much higher levels of genetic diversity with Hnb of 0.699, 0.686, and 0.686, respectively, and were determined to be upper Amazon Forastero hybridized with Trinitario in type. An additional 46 microsatellite markers were amplified and analyzed in the Waimanalo parents, productive, and unproductive seedlings for a total of 65 loci. Seventeen loci contained alleles that were significantly associated with productive seedlings as determined by Armitage's trend test. Of these, 13 loci (76.4%) co-located with previously reported quantitative trait loci for productivity traits. These markers may prove useful for marker assisted selection and demonstrate the potential of association genetic studies in perennial tree crops such as cacao.
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.
Merve Şekerli, Golnaz Komaei Koma, Jacob W. Snelling, and Shawn A. Mehlenbacher
). Simple sequence repeat (SSR) markers, also known as microsatellites, indicate that ‘Zimmerman’ is from a cross of ‘Barcelona’ and ‘Gasaway’ ( Gökirmak et al., 2009 ) and thus is the same source of resistance. The OSU hazelnut breeding program has
Emmanouil N. Tzitzikas, Antonio J. Monforte, Abdelhak Fatihi, Zacharias Kypriotakis, Tefkros A. Iacovides, Ioannis M. Ioannides, and Panagiotis Kalaitzis
PCR mix and samples were denatured at 96 °C for 2 min. Electrophoresis was performed in denaturing conditions at 50 °C in TBE (90 m m Tris–borate, 2 m m EDTA pH 8.0, and 7.5 M urea) buffer using 6% polyacrylamide gels (AA:BIS = 19:1). Microsatellite
D. Struss, M. Boritzki, R. Karle, and A.F. Iezzoni
Two rootstocks from the Giessen (GiSelA) series of dwarfing cherry (Prunus sp.) rootstocks, GiSelA (GI) 5 (syn. 148/2) and GI 6 (syn. 148/1), are becoming commercially important and five other Giessen cherry rootstocks are being evaluated for horticultural traits. Since GI 5 and GI 6 are morphologically similar, a DNA fingerprinting project was undertaken to identify molecular markers that could be used by the nursery industry to differentiate these two rootstocks. The project was extended to include six additional Giessen rootstocks of varying pedigrees. Fourteen DNA primer pairs were tested for their ability to differentiate among the eight rootstocks. None of the primer pairs could differentiate all eight rootstock selections; however, three primer pairs could differentiate all but two selections. Two primer pairs, PMS 15 and PceGA59, were identified as the most suitable for high throughput screening of GI 5 and GI 6 due to the simplicity and the size of the base pair differences among the polymorphic fragments. These results demonstrate the utility of molecular markers to differentiate the Giessen cherry rootstocks.
Zsolt Galli, Gábor Halász, Erzsébet Kiss, László Heszky, and Judit Dobránszki
A collection of 66 commercial apple (Malus ×domestica Borkh.) cultivars was screened with six previously described SSR (Simple Sequence Repeat) markers for molecular identification. In total, 55 polymorphic alleles were detected at the 6 SSR loci (average 9.2 alleles per locus) and the polymorphism information content (PIC) averaged 0.72. Successful differentiation of all apple genotypes except for somatic mutants was accomplished by using only four (CH03g07, CH04e03, CH05d11, and CH05e03) SSR markers. Sport mutants proved to be indistinguishable from each other and their progenitors. The cumulative probability of obtaining an identical SSR profile for two randomly chosen apple genotypes was 1.79 × 10–4, which confirms the high potential of simple sequence repeats (SSRs) for cultivar identification.
Thomas M. Davis, Laura M. DiMeglio, Ronghui Yang, Sarah M.N. Styan, and Kim S. Lewers
The cultivated strawberry, Fragaria ×ananassa Duchesne ex Rozier, originated via hybridization between octoploids F. chiloensis (L.) Mill. and F. virginiana Mill. These three octoploid species are thought to share a putative genome composition of AAA`A'BBB`B'. Diploid F. vesca L., is considered to have donated the A genome. Current attention to the development of a diploid model system for strawberry genomics warrants the assessment of simple sequence repeat (SSR) marker transferability between the octoploid and diploid species in Fragaria L. In the present study, 23 SSR primer pairs derived from F. ×ananassa `Earliglow' by genomic library screening were evaluated for their utility in six diploid Fragaria species, including eight representatives of F. vesca, four of F. viridis Weston, and one each of F. nubicola (Hook. f.) Lindl. ex Lacaita, F. mandshurica Staudt, F. iinumae Makino, and F. nilgerrensis Schltdl. ex J. Gay. SSR primer pair functionality, as measured by amplification success rate (= 100% - failure rate) in each species, was ranked (from highest to lowest) as follows: F. vesca (98.4%) > F. iinumae (93.8%) = F. nubicola (93.8%) > F. mandshurica (87.5%) > F. nilgerrensis (75%) > F. viridis (73.4%). The extent to which these octoploid-derived SSR primer pairs generated markers that could be added to the F. vesca linkage map also was assessed. Of the 13 F. ×ananassa SSR markers that segregated codominantly in the F. vesca mapping population, 11 were assigned to linkage groups based upon close linkages to previously mapped loci. These markers were distributed over six of the seven F. vesca linkage groups, and can serve as anchor loci defining these six groups for purposes of comparative mapping between F. vesca and F. ×ananassa.
Minou Hemmat, Norman F. Weeden, Patrick J. Conner, and Susan K. Brown
The columnar mutation `Wijcik McIntosh' has attracted much attention because of its compact growth habit, which is compatible with high-density plantings. Using bulked segregant analysis, we identified several randomly amplified polymorphic DNA (RAPD) markers that displayed a close linkage with the columnar locus (Co). The RAPD marker that displayed the closest linkage was end sequenced to develop a sequence tagged site for rapidly screening segregating populations. A simple sequence repeat (SSR) of (GA)17 was identified within the DNA fragment. Four allelic forms, including an apparent null allele, could be distinguished among the cultivars tested. The null allele displayed close linkage with Co in two progenies, and we used this marker to identify the location of the gene on the apple linkage map.
Nahla Bassil, Kim Hummer, and Joseph Postman
Simple Sequence Repeat (SSR) markers developed in apple and pear were used to determine genetic relationships among heritage apple and pear cultivars from Portugal's Azore Islands, and to develop identity fingerprints for European and Asian pear accessions at the USDA–ARS National Clonal Germplasm Repository (NCGR). We used 11 SSR markers (six from apple and five from pear) to examine 18 heritage apple and 9 heritage pear cultivars from the Azores. Eight additional Portuguese and economically important cultivars of apple and eight of pear were used as standards. Cluster analysis separated the apple and pear accessions into two distinct groups. Among apple genotypes, 12 unique accessions and five groups of synonyms were identified, while, in pear, seven unique genotypes and three pairs of synonyms were found. None of the accessions obtained from the Azores corresponded to widely grown standard Portuguese apple or pear cultivars. To examine 144 NCGR pear accessions, we used nine polymorphic SSR loci that were developed from GenBank sequences. Cluster analysis identified five sets of synonyms (four in P. communis L. and one in P. ussuriensis Maxim.) and four pairs of homonyms (three in P. communis and one in P. pyrifolia Burm. f. Nakai), and confirmed three clonal sets. Morphological evaluations and additional SSR markers will be used to confirm these results, and to genetically document the identities of pear genotypes. SSR markers will greatly assist the management of ex situ pome fruit germplasm collections by helping to eliminate duplicate accessions and expanding the genetic diversity represented.