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 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 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.

scholarly journals Genotyping-by-Sequencing of Gossypium hirsutum Races and Cultivars Uncovers Novel Patterns of Genetic Relationships and Domestication Footprints

2019 ◽  
Vol 15 ◽  
pp. 117693431988994
Author(s):  
Shulin Zhang ◽  
Yaling Cai ◽  
Jinggong Guo ◽  
Kun Li ◽  
Renhai Peng ◽  
...  
Keyword(s):  
Gossypium Hirsutum ◽  
Genetic Relationships ◽  
Phylogenetic Analyses ◽  
Genotyping By Sequencing ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Breeding Programs ◽  
Association Analyses ◽  
Genome Wide ◽  
Candidate Gene Locus

Determining the genetic rearrangement and domestication footprints in Gossypium hirsutum cultivars and primitive race genotypes are essential for effective gene conservation efforts and the development of advanced breeding molecular markers for marker-assisted breeding. In this study, 94 accessions representing the 7 primitive races of G hirsutum, along with 9 G hirsutum and 12 Gossypium barbadense cultivated accessions were evaluated. The genotyping-by-sequencing (GBS) approach was employed and 146 558 single nucleotide polymorphisms (SNP) were generated. Distinct SNP signatures were identified through the combination of selection scans and association analyses. Phylogenetic analyses were also conducted, and we concluded that the Latifolium, Richmondi, and Marie-Galante race accessions were more genetically related to the G hirsutum cultivars and tend to cluster together. Fifty-four outlier SNP loci were identified by selection-scan analysis, and 3 SNPs were located in genes related to the processes of plant responding to stress conditions and confirmed through further genome-wide signals of marker-phenotype association analysis, which indicate a clear selection signature for such trait. These results identified useful candidate gene locus for cotton breeding programs.

scholarly journals DNA Melting Analysis for Detection of Single Nucleotide Polymorphisms

2001 ◽  
Vol 47 (4) ◽  
pp. 635-644 ◽  
Author(s):  
Robert H Lipsky ◽  
Chiara M Mazzanti ◽  
Joseph G Rudolph ◽  
Ke Xu ◽  
Gopal Vyas ◽  
...  
Keyword(s):  
Single Nucleotide Polymorphisms ◽  
Large Scale ◽  
Denaturing Gradient Gel Electrophoresis ◽  
Dna Melting ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Efficient System ◽  
Gradient Gel Electrophoresis ◽  
Melting Analysis ◽  
Scale Detection

Abstract Background: Several methods for detection of single nucleotide polymorphisms (SNPs; e.g., denaturing gradient gel electrophoresis and denaturing HPLC) are indirectly based on the principle of differential melting of heteroduplex DNA. We present a method for detecting SNPs that is directly based on this principle. Methods: We used a double-stranded DNA-specific fluorescent dye, SYBR Green I (SYBR) in an efficient system (PE 7700 Sequence Detector) in which DNA melting was controlled and monitored in a 96-well plate format. We measured the decrease in fluorescence intensity that accompanied DNA duplex denaturation, evaluating the effects of fragment length, dye concentration, DNA concentration, and sequence context using four naturally occurring polymorphisms (three SNPs and a single-base deletion/insertion). Results: DNA melting analysis (DM) was used successfully for variant detection, and we also discovered two previously unknown SNPs by this approach. Concentrations of DNA amplicons were readily monitored by SYBR fluorescence, and DNA amplicon concentrations were highly reproducible, with a CV of 2.6%. We readily detected differences in the melting temperature between homoduplex and heteroduplex fragments 15–167 bp in length and differing by only a single nucleotide substitution. Conclusions: The efficiency and sensitivity of DMA make it highly suitable for the large-scale detection of sequence variants.

scholarly journals Association between a Variant in MicroRNA-646 and the Susceptibility to Hepatocellular Carcinoma in a Large-Scale Population

2014 ◽  
Vol 2014 ◽  
pp. 1-7 ◽  
Author(s):  
Rui Wang ◽  
Jun Zhang ◽  
Weiru Jiang ◽  
Yanyun Ma ◽  
Wenshuai Li ◽  
...  
Keyword(s):  
Hepatocellular Carcinoma ◽  
Single Nucleotide Polymorphisms ◽  
Protective Effect ◽  
Large Scale ◽  
Cancer Development ◽  
Nucleotide Polymorphisms ◽  
Single Nucleotide ◽  
Scale Population

Background. Single-nucleotide polymorphisms in microRNAs play important roles in oncogenesis and cancer development.Objective. We aim to explore whether miR-646 rs6513497 is associated with the risk of hepatocellular carcinoma.Methods. Total 997 HCC patients and 993 cancer-free controls were enrolled in this study. Genotyping was performed using MassARRAY method.Results. Compared with the T allele of rs6513497, the G allele was associated with a significantly decreased risk of HCC (OR = 0.788, 95% CI = 0.631–0.985,P= 0.037); moreover, a more protective effect of the G allele was shown in males (OR = 0.695, 95% CI = 0.539–0.897,P= 0.005 in HCC and OR = 0.739, 95% CI = 0.562–0.972,P= 0.030 in HBV-related HCC), basically in a dominant manner (HCC: OR = 0.681, 95% CI = 0.162–0.896,P= 0.006; HBV-related HCC: OR = 0.715, 95% CI = 0.532–0.962,P= 0.027).Conclusions. Our findings support the view that the miR-646 SNP rs6513497 may contribute to the susceptibility of HCC.

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