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Lidia Lozano, Ignasi Iglesias, Diego Micheletti, Michela Troggio, Satish Kumar, Richard K. Volz, Andrew C. Allan, David Chagné, and Susan E. Gardiner

traits are difficult to assess. In recent years, the application of SNP markers has gained much attention in both the scientific and plant breeding communities ( Rafalski, 2002 ). SNPs are abundant and evenly distributed throughout the genomes of most

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Luwbia Aranda, Timothy G. Porch, Mark J. Bassett, Laura Lara, and Perry B. Cregan

the advent of the common bean genome sequence, SNP markers, and tools such as mutagenesis populations and TILLING ( Porch et al., 2009 ), novel methods are available for identifying genes of interest. Although the genetics of Cl have been studied

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Xingbo Wu and Lisa W. Alexander

goals of this research were to apply genotyping-by-sequencing to discover SNPs for bigleaf hydrangea cultivars, investigate the genetic diversity and population structure of H. macrophylla cultivars, and determine the disputed taxonomic classification

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Hsuan Chen, Jason D. Lattier, Kelly Vining, and Ryan N. Contreras

. Genotyping-by-sequencing (GBS) is a promising option to generate high-density markers for minor crops such as lilac. GBS is a fast and cost-effective molecular tool that can generate large numbers of single-nucleotide polymorphism (SNP) markers based on next

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Christina H. Hagerty, Alfonso Cuesta-Marcos, Perry Cregan, Qijian Song, Phil McClean, and James R. Myers

containing 5398 SNP markers. Access to the Illumina chip was provided through the Bean Coordinated Agriculture Project ( Bean CAP, 2012 ). SNP genotyping was conducted at the USDA-ARS, Soybean Genomics and Improvement Laboratory, Beltsville, MD, on the

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Jinggui Fang, Tal Twito, Zhen Zhang, and Chih Cheng T. Chao

The genetic relationship among 50 fruiting-mei (Prunus mume Sieb. et Zucc.) cultivars from China and Japan was investigated using 767 amplified fragment length polymorphism (AFLP) and 103 single nucleotide polymorphism (SNP) markers. The polymorphism among the cultivars was 69.77% based on EcoR I + Mse I AFLP primer pairs. The sequence alignment of 11 group sequences derived from 50 samples yielded 103 SNPs with a total length of 3683-bp genomic sequences. Among these SNPs, 73 were heterozygous in the loci of different cultivars. The SNP distribution were: 58% transition, 40% transversion, and 2% InDels. There was also one tri-nucleotide deletion. Both AFLP and SNP allowed the evaluation of genetic diversity of these 50 fruiting-mei cultivars; however, the two derived cladograms have some differences: 1) all the cultivars formed two sub-clusters (1A and 1B) within cladogram based on AFLP polymorphisms, and there were three sub-clusters (2A, 2B and 2C) formed in the cladogram based on SNP polymorphisms; and 2) most cultivars from G-F, Y-H-S regions and Japan are grouped in cluster 1A and 18 (78.26%) out of 23 cultivars from J-Z origin are grouped in cluster 1B in the cladogram generated based on AFLP polymorphisms. The results show cultivars from Japan are clustered within cultivars from China and supports the hypothesis that fruitingmei in Japan was introduced from China in the past. Cultivars from J-Z region of China have higher genetic similarities. Cultivars from G-F and Y-S-H regions have lower genetic similarities and suggest more germplasm exchanges in the past.

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Gennaro Fazio, Jack E. Staub, and Sang Min Chung

Highly polymorphic microsatellites or simple sequence repeat (SSR), along with sequence characterized amplified region (SCAR) and single nucleotide polymorphisms (SNP), markers are reliable, cost-effective, and amenable for large scale analyses. Molecular polymorhisms are relatively rare in cucumber (Cucumis sativus L.) (3% to 8%). Therefore, experiments were designed to develop SSR, SCAR and SNP markers, and optimize reaction conditions for PCR. A set of 110 SSR markers was constructed using a unique, strategically applied methodology that included the GeneTrapper (Life Technologies, Gaithersburg, Md.) kit to select plasmids harboring microsatellites. Of these markers, 58 (52%) contained dinucleotide repeats (CT, CA, TA), 21 (19%) possessed trinucleotide repeats (CTT, ATT, ACC, GCA), 3 (2.7%) contained tetranucleotide repeats (TGCG, TTAA, TAAA), 4 (3.6%) enclosed pentanucleotide repeat (ATTTT, GTTTT, GGGTC, AGCCC), 3 (2.7%) contained hexanucleotide repeats (CCCAAA, TAAAAA, GCTGGC) and 21 possessed composite repeats. Four SCARs (L18-3 SCAR, AT1-2 SCAR, N6-A SCAR, and N6-B SCAR) and two PCR markers based on SNPs (L18-2H19 A and B) that are tightly linked to multiple lateral branching (i.e., a yield component) were also developed. The SNP markers were developed from otherwise monomorphic SCAR markers, producing genetically variable amplicons. The markers L18-3 SCAR and AT1-2 SCAR were codominant. A three-primer strategy was devised to develop a codominant SCAR from a sequence containing a transposable element, and a new codominant SCAR product was detected by annealing temperature gradient (ATG) PCR. The use of a marker among laboratories can be enhanced by methodological optimization of the PCR. The utility of the primers developed was optimized by ATG-PCR to increase reliability and facilitate technology transfer. This array of markers substantially increases the pool of genetic markers available for genetic investigation in Cucumis.

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Gennaro Fazio, Yizhen Wan, Dariusz Kviklys, Leticia Romero, Richard Adams, David Strickland, and Terence Robinson

polymorphism (SNP) loci resolved using the International RosBREED SNP Consortium (IRSC) Infinium ® II (Illumina, San Diego, CA) array developed through the RosBREED project ( Chagné et al., 2012 ; Iezzoni, 2010 ) and used to genotype an M.27 × MM.106 apple

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Youngjae Oh, Jason D. Zurn, Nahla Bassil, Patrick P. Edger, Steven J. Knapp, Vance M. Whitaker, and Seonghee Lee

® single nucleotide polymorphism (SNP) array ( Bassil et al., 2015 ), developed as part of the first RosBREED project, has been used as a high-throughput genotyping tool for QTL discovery in numerous strawberry programs worldwide ( Anciro et al., 2018

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Karen R. Harris, Kai-Shu Ling, W. Patrick Wechter, and Amnon Levi

polymorphism (SNP) at base pair 190. The primers used were designated ZYRP-80-F (5′TGTAAAACGACGGCCAGTAGAGCGAGATGCAACGAGAG-3′) and ZYRP-216-R (5′-ACGCTTCTGTCGCTCAGAGT-3′). The ZYRP SCAR was amplified and fluorescently labeled in a final reaction volume of 10 μL