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Michael J. Havey and Farhad Ghavami

of different daylength responses may represent divergent germplasm pools within the cultivated onion. Single nucleotide polymorphisms are robust, codominant genetic markers that commonly occur in the genomes of cultivated plants. In previous research

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Yuan Yu, Chunxian Chen, Ming Huang, Qibin Yu, Dongliang Du, Matthew R. Mattia and Frederick G. Gmitter Jr.

relatives analyzed by a 1536-single nucleotide polymorphism genotyping assay. Diversity and phylogenetic statistics. The software PowerMarker 3.25 ( Liu and Muse, 2005 ) was applied to calculate allele frequency, PIC, expected and observed heterozygosity ( H

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Daofeng Liu, Jing Ma, Jianfeng Yang, Tien V. Nguyen, Huamin Liu, Renwei Huang, Shunzhao Sui and Mingyang Li

.8%) and deletions (62.5%) among the indels ( Fig. 2B ). Fig. 1. Summary of putative single nucleotide polymorphisms (SNPs) and insertion/deletions (indels) in the transcriptome of wintersweet. Fig. 2. Statistics of single nucleotide polymorphisms (SNPs

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Umesh R. Rosyara, Audrey M. Sebolt, Cameron Peace and Amy F. Iezzoni

‘Bing’ as a grandparent ( Table 3 ). Table 1. Sweet cherry cultivars, selections, and wild accessions, their parents if known, coefficient of relatedness (ρ) to ‘Bing’ using single nucleotide polymorphism markers (n = 519), and S -locus genotype. z

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Limeng Xie, Patricia Klein, Kevin Crosby and John Jifon

. 1. Physical map of 1002 single-nucleotide-polymorphism markers distributed on 12 chromosomes in the Solanum lycopersicum RvT1 × S. cheesmaniae Lche4 F 2 population (n = 181). Supplemental Fig. 2. Genetic map of the Solanum lycopersicum RvT1

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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

fruit from 94 apple genotypes in a breeding population in Lleida, Spain, in 2008. Table 2. List of single-nucleotide polymorphisms (SNPs) that showed significant association with skin color traits [L* trait, a* trait, b* trait, hue angle, a*/b* trait

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Pei Xu, Tingting Hu, Yuejian Yang, Xiaohua Wu, Baogen Wang, Yonghua Liu, Dehui Qin, Jeffrey Ehlers, Timothy Close, Zhongfu Lu and Guojing Li

single nucleotide polymorphism locus 1_0643. ( Right ) A regional-magnified schematic show of soybean chromosome 6. The monogenic dominance of purple over white flower observed in our population is consistent with some previous reports from ssp

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John McCallum, Susan Thomson, Meeghan Pither-Joyce, Fernand Kenel, Andrew Clarke and Michael J. Havey

carried out using SeqScape version 2.1 (Applied Biosystems) using Genbank sequences of ESTs used in original primer design as reference sequences. Single-nucleotide polymorphism assay design. Restriction polymorphisms were identified using

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Michael J. Havey

between the two NILs using KASPar ( Duangjit et al., 2013 ). Table 1. Genotypes at the nuclear male-fertility restoration locus ( Ms ) and single nucleotide polymorphisms (SNPs) among public-sector onion inbreds. z Results and Discussion Testcrosses of the

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Jernej Jakse, William Martin, John McCallum and Michael J. Havey

The commercial production of onion (Allium cepa L.) inbreds, hybrids, and open-pollinated (OP) cultivars would benefit from a robust set of molecular markers that confidently distinguish among elite germplasms. Large-scale DNA sequencing has revealed that single nucleotide polymorphisms (SNPs), short insertion-deletion (indel) events, and simple sequence repeats (SSRs) are relatively abundant classes of codominant DNA markers. We identified 398 SNPs, indels, and SSRs among 35 elite onion ulations and observed that all populations could be distinguished. Phylogenetic analyses of simple-matching and Jaccard's coefficients for SSRs produced essentially identical trees and relationships were consistent with known pedigrees and previous marker evaluations. The SSRs revealed that elite germplasms from specific companies or breeding programs were often closely related. In contrast, phylogenetic analyses of SNPs and indels did not reveal clear relationships among elite onion populations and there was no agreement among trees generated using SNPs and indels vs. SSRs. This discrepancy was likely due to SNPs and indels occurring among amplicons from duplicated regions (paralogs) of the onion genome. Nevertheless, these PCR-based markers will be useful in the quality control of inbred, hybrid, and OP onion seed lots.