.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
Daofeng Liu, Jing Ma, Jianfeng Yang, Tien V. Nguyen, Huamin Liu, Renwei Huang, Shunzhao Sui and Mingyang Li
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
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
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
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
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
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
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
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.
Michael J. Havey and Yul-Kyun Ahn
Garlic (Allium sativum) is cultivated worldwide and appreciated for its culinary uses. In spite of primarily being asexually propagated, garlic shows great morphological variation and adaptability to diverse production environments. Molecular markers and phenotypic characteristics have been used to assess the genetic diversity among garlics. In this study, we undertook transcriptome sequencing from a single garlic plant to identify molecular markers in expressed regions of the garlic genome. Garlic sequences were assembled and selected if they were similar to monomorphic sequences from a doubled haploid (DH) of onion (Allium cepa). Single nucleotide polymorphisms (SNPs) and insertion–deletion (indel) events were identified in 4355 independent garlic assemblies. A sample of the indels was verified using the original complementary DNA (cDNA) library and genomics DNAs from diverse garlics, and segregations confirmed by sexual progenies of garlic. These molecular markers from the garlic transcriptome should be useful for estimates of genetic diversity, identification and removal of duplicate accessions from germplasm collections, and the development of a detailed genetic map of this important vegetable crop.