(SSR) or microsatellite markers ( Che et al., 2003 ; Levi et al., 2001b , 2012 ; Mujaju et al., 2010 ; Nantoumé et al., 2013 ; Ocal et al., 2014 ; Uluturk et al., 2011 ). Microsatellite markers are currently the marker of choice for genetic
Jacob Mashilo, Hussein Shimelis, Alfred Odindo, and Beyene Amelework
Dilson A. Bisognin and David S. Douches
An understanding of the genetic relationship within potato germplasm is important to establish a broad genetic base for breeding purposes. The objective of this study was to assess the genetic diversity of potato (Solanum tuberosum subsp. tuberosum Hawkes) germplasm that can be used in the development of cultivars with resistance to late blight caused by Phytophthora infestans (Mont.) de Bary. Thirty-three diploid and 27 tetraploid late blight resistant potato clones were evaluated for their genetic diversity based on 11 isozyme loci and nine microsatellites. A total of 35 allozymes and 42 polymorphic microsatellite fragments was scored for presence or absence. The germplasm was clustered based on the matrix of genetic similarities and the unweighted pair group means analysis of the isozyme and microsatellite data, which were used to construct a dendrogram using NTSYS-pc version 1.7. Twenty-three allozymes and DNA fragments were unique to the wild species. The diploid Solanum species S. berthaultii Hawkes and S. microdontum Bitter formed two distinct phenetic groups. Within S. microdontum, three subgroups were observed. The tetraploid germplasm formed another group, with S. sucrense Hawkes in one subgroup and the cultivated potato and Russian hybrids in another subgroup. Based upon the genetic diversity and the level of late blight resistance, S. microdontum and S. sucrense offer the best choice for strong late blight resistance from genetically diverse sources. This potato germplasm with reported late blight resistance should be introgressed into the potato gene pool to broaden the genetic base to achieve stronger and more durable resistance.
Gerald S. Dangl, Keith Woeste, Mallikarjuna K. Aradhya, Anne Koehmstedt, Chuck Simon, Daniel Potter, Charles A. Leslie, and Gale McGranahan
One hundred and forty-seven primer pairs originally designed to amplify microsatellites, also known as simple sequence repeats (SSR), in black walnut (Juglans nigra L.) were screened for utility in persian walnut (J. regia L.). Based on scorability and number of informative polymorphisms, the best 14 loci were selected to analyze a diverse group of 47 persian walnut accessions and one J. hindsii (Jepson) Jepson ex R.E. Sm × J. regia hybrid (Paradox) rootstock. Among the 48 accessions, there were 44 unique multi-locus profiles; the accessions with identical profiles appeared to be synonyms. The pairwise genetic distance based on proportion of shared alleles was calculated for all accessions and a UPGMA (unweighted pair group method with arithmetic mean) dendrogram constructed. The results agree well with what is known about the pedigree and/or origins of the genotypes. The SSR markers distinguished pairs of closely related cultivars and should be able to uniquely characterize all walnut cultivars with the exception of budsports. They provide a more powerful and reliable system for the molecular characterization of walnut germplasm than those previously tested. These markers have numerous applications for the walnut industry, including cultivar identification, verification of pedigrees for cultivar and rootstock breeding programs, paternity analysis, and understanding the genetic diversity of germplasm collections.
Zhengwang Jiang, Feiyan Tang, Hongwen Huang, Hongju Hu, and Qiliang Chen
, M. Olivieri, A. 1993 PCR-amplified microsatellites as markers in plant genetics Plant J. 3 175 182 Nei, M. Tajima, F. Tateno, Y. 1983 Accuracy of estimated phylogenetic trees from molecular data J. Mol. Evol. 19 153 170 Peakall, R. Smouse, P.E. 2001
Xiu Cai Fan, Hai Sheng Sun, Ying Zhang, Jian Fu Jiang, Min Li, and Chong Huai Liu
been used in genetic diversity analyses of the Chinese wild grape resources. Liu et al. (2012a) reported on the relationship of 15 Chinese wild grape species based on the 10 microsatellite markers and 12 SRAP combinations. Fan et al. (2015) assessed
Riaz Ahmad, Miki Okada, Jeffrey L. Firestone, Chris R. Mallek, and Marie Jasieniuk
We isolated and characterized microsatellite loci in the ornamental pampas grass Cortaderia selloana (Schult. & Schult. f.) Asch. & Graebn. for purposes of identifying cultivars and assessing genetic relationships among cultivars. Small insert genomic libraries were enriched for dinucleotide (CT)n and (CA)n repeats. Ninety clones were sequenced of which 76% contained at least one microsatellite with a basic motif greater than six repeat units. Nine primer pairs amplified 10 polymorphic and putatively disomic loci, and were used to genotype 88 individuals representing 17 named cultivars and four selections. In total, 93 alleles were detected with a maximum of two to 19 per locus. Effective number of alleles varied from 1.3 to 9.5. Observed heterozygosity ranged from 0.07 to 0.81. The 10 microsatellite loci distinguished the majority of pampas grass cultivars. An unweighted pair group method with arithmetic mean (UPGMA) cluster analysis, based on proportion of shared alleles among individuals, revealed groups of cultivars corresponding to origin and morphological characteristics. With few exceptions, individuals of a single cultivar clustered together with moderate to strong bootstrap support (greater than 50%). Interestingly, `Pumila' from Europe and the United States formed separate clusters indicating independent origins. A large, diverse cluster with low bootstrap support consisted of selections and cultivars sold as seed, rather than potted or bare-root clonal plants. Primers designed for C. selloana amplified microsatellite loci in other Cortaderia Stapf species concordant with phylogenetic relationships among the species. Cross-amplification was 100% in C. jubata (Lemoine ex Carrière) Stapf; 77% in C. pilosa (d'Urv.) Hack. and C. rudiuscula Stapf; 66% in C. fulvida (Buch.) Zotov; and 55% in C. richardii (Endl.) Zotov and C. toetoe Zotov.
Innocenzo Muzzalupo, Nicola Lombardo, Aldo Musacchio, Maria Elena Noce, Giuseppe Pellegrino, Enzo Perri, and Ashif Sajjad
Genetic diversity studies using microsatelite analysis were carried out in a set of 39 accessions of Olea europaea L., corresponding to the majority of the regional autochthon germplasm in Apulia. Samples of olive leaves were harvested from plants growing in the olive germplasm collection of the Consiglio per la Ricerca e Sperimentazione in Agricoltura (C.R.A.) - Istituto Sperimentale per l'Olivicoltura at Rende in Cosenza Italy. Herein, we evaluated the extent to which microsatellite analysis using electrophoresis was capable of identifying traditional olive cultivars. In addition, the DNA sequence of all amplicons was determined and the number of repeat units was established for each sample. Using five loci, electrophoretic analysis identified 24 genotype profiles, while DNA sequence analysis detected 28 different genotype profiles, identifying 54% of cultivars. The remaining 46% were composed of seven different accession groups containing genetically indistinguishable cultivars, which are presumably synonyms. This study demonstrates the utility of microsatellite markers for management of olive germplasm and points out the high level of polymorphisms in microsatellite repeats when coupled with DNA sequence analysis. The establishment of genetic relationships among cultivars in the Apulian germplasm collection allows for the construction of a molecular database that can be used to establish the genetic relationships between known and unknown cultivars.
Hua Wang, Dong Pei, Rui-sheng Gu, and Bao-qing Wang
microsatellite primers selected from an earlier study in Juglans nigra L. ( Woeste et al., 2002 ) ( Table 2 ). SSR reaction was conducted according to the protocol of Victory et al. (2006) with some modifications. Amplification reaction was performed in a 15
Jason D. Zurn, Katie A. Carter, Melinda H. Yin, Margaret Worthington, John R. Clark, Chad E. Finn, and Nahla Bassil
to 3 ng·μL −1 . Pedigree validation using the 6-SSR fingerprinting set. The populations were evaluated with the 6-SSR fingerprinting developed by Bassil et al. (2016) ( Table 2 ). Polymerase chain reaction (PCR) was conducted using a microsatellite
Marcin Nowicki, Edward E. Schilling, Sarah L. Boggess, Logan C. Houston, Matthew L. Huff, Margaret E. Staton, Jayne A. Lampley, and Robert N. Trigiano
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