scholarly journals Genetic analysis of citron (Citrus medica L.) using simple sequence repeats and single nucleotide polymorphisms

2015 ◽  
Vol 195 ◽  
pp. 124-137 ◽  
Author(s):  
Chandrika Ramadugu ◽  
Manjunath L. Keremane ◽  
Xulan Hu ◽  
David Karp ◽  
Claire T. Federici ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Genetic Analysis ◽  
Simple Sequence Repeats ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Citrus Medica ◽  
Simple Sequence

scholarly journals Single Nucleotide Polymorphisms, Indels, and Simple Sequence Repeats for Onion Cultivar Identification

2005 ◽  
Vol 130 (6) ◽  
pp. 912-917 ◽  
Author(s):  
Jernej Jakse ◽  
William Martin ◽  
John McCallum ◽  
Michael J. Havey
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Simple Sequence Repeats ◽  
Large Scale ◽  
Phylogenetic Analyses ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Onion Seed ◽  
Onion Cultivar ◽  
Simple Sequence

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.

scholarly journals Segregations for Onion Bulb Colors Reveal That Red Is Controlled by at Least Three Loci

2008 ◽  
Vol 133 (1) ◽  
pp. 42-47 ◽  
Author(s):  
Anil Khar ◽  
Jernej Jakse ◽  
Michael J. Havey
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Allium Cepa ◽  
Simple Sequence Repeats ◽  
Regulatory Genes ◽  
Nucleotide Polymorphisms ◽  
Anthocyanidin Synthase ◽  
Single Nucleotide ◽  
The Family ◽  
Simple Sequence ◽  
Bulb Color

Onion (Allium cepa L.) bulb color is controlled by at least five major loci (I, C, G, L, and R) and seedcoat color by one locus (B). The authors developed families segregating for bulb and seedcoat colors, simple sequence repeats (SSRs), and single nucleotide polymorphisms (SNPs) in genomic amplicons of dihydroflavonol 4-reductase (DFR) and anthocyanidin synthase (ANS). The B and C loci were linked to SSRs on chromosomes 1 and 6 respectively. For all of three families, SNPs in DFR cosegregated with the R locus conditioning red bulb color. In the family from B2246 × B11159, red bulbs versus yellow bulbs were controlled by DFR and a locus (L2) linked at 6.3 cM to ANS. The authors propose that yellow bulb onions have been independently selected numerous times and that yellow populations carry independent mutations in structural or regulatory genes controlling the production of red bulb color in onion.

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