Simple sequence repeat-based identification of Canadian malting barley varieties

2014 ◽  
Vol 94 (3) ◽  
pp. 485-496 ◽  
Author(s):  
Daniel J. Perry ◽  
Ursla Fernando ◽  
Sung-Jong Lee
Keyword(s):  
Simple Sequence Repeat ◽  
Pcr Primers ◽  
Variety Identification ◽  
Malting Barley ◽  
Sequence Repeat ◽  
Preparation Methods ◽  
Purity Analysis ◽  
Marker Loci ◽  
Simple Sequence ◽  
Individual Kernel

Perry, D. J., Fernando, U. and Lee, S-J. 2014. Simple sequence repeat-based identification of Canadian malting barley varieties. Can. J. Plant Sci. 94: 485–496. Practical and reliable means to identify barley varieties are required to provide assurances in segregated grain handling and for quality control in the malting and brewing industry. A set of 10 simple sequence repeat (SSR) markers was selected to differentiate among malting barley varieties grown in Canada. Modification of some PCR primers permitted assembly into two five-marker multiplexes that may be examined simultaneously using an electrophoresis-based DNA analyzer. These markers were surveyed in multiple individual kernels of each of 48 barley varieties grown in Canada, including 31 malting varieties and 17 popular feed varieties. Variation within varieties was common and three general categories of intra-variety polymorphism were recognized: (1) primary biotypes, which were characterized by a fairly even distribution of two alleles at one or more marker loci and complete mixture of allele combinations among the polymorphic loci; (2) uncommon, distinctly different variants; and (3) putative recent SSR mutations. Differentiation among varieties was complete with the exception of one pair of related six-row feed varieties (AC Rosser and AC Ranger) that was indistinguishable and one group of three very closely related two-row malting varieties (CDC Kendall, CDC PolarStar and Norman) that, on an individual-kernel basis, were only partially distinguishable using these markers. Simple, rapid individual-kernel DNA preparation methods were also developed for use in conjunction with the multiplexed markers to provide a convenient, effective and relatively inexpensive tool that may be used for barley variety identification, purity analysis or quantification of variety mixtures.

scholarly journals Use of Simple Sequence Repeat (SSR) Markers for Variety Identification of Tomato (Lycopersicon esculentum)

2006 ◽  
Vol 33 (4) ◽  
pp. 289-295 ◽  
Author(s):  
Yong-Sham Kwon ◽  
Eun-Kyung Park ◽  
Kyung-Mi Bae ◽  
Seung-In Yi ◽  
Soon-Gi Park ◽  
...  
Keyword(s):  
Lycopersicon Esculentum ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Variety Identification ◽  
Sequence Repeat ◽  
Simple Sequence

scholarly journals Length polymorphisms of simple sequence repeat DNA in soybean.

Genetics ◽  
1992 ◽  
Vol 132 (4) ◽  
pp. 1131-1139 ◽  
Author(s):  
M S Akkaya ◽  
A A Bhagwat ◽  
P B Cregan
Keyword(s):  
Genetic Markers ◽  
Simple Sequence Repeat ◽  
Pcr Amplification ◽  
Pcr Primers ◽  
F1 Hybrids ◽  
Sequence Repeat ◽  
Pcr Products ◽  
Soybean Genotypes ◽  
Ssr Loci ◽  
Simple Sequence

Abstract The objective of this work was to ascertain the presence and degree of simple sequence repeat (SSR) DNA length polymorphism in the soybean [Glycine max (L.) Merr.]. A search of GenBank revealed no (CA)n or (GT)n SSRs with n greater than 8 in soybean. In contrast, 5 (AT)n and 1 (ATT)n SSRs with n ranging from 14 to 27 were detected. Polymerase chain reaction (PCR) primers to regions flanking the six SSR loci were used in PCR amplification of DNA from 43 homozygous soybean genotypes. At three loci, amplification produced one PCR product per genotype and revealed 6, 7 and 8 product length variants (alleles) at the three loci, respectively. F1 hybrids between parents carrying different alleles produced two PCR products identical to the two parents. Codominant segregation of alleles among F2 progeny was demonstrated at each locus. A soybean DNA library was screened for the presence of (CA/GT)n SSRs. Sequencing of positive clones revealed that the longest such SSR was (CA)9. Thus, (CA)n SSRs with n of 15 or more are apparently much less common in soybean than in the human genome. In contrast to humans, (CA)n SSRs will probably not provide an abundant source of genetic markers in soybean. However, the apparent abundance of long (AT)n sequences should allow this SSR to serve as a source of highly polymorphic genetic markers in soybean.

Establishment of an effective set of simple sequence repeat markers for sunflower variety identification and diversity assessment

2005 ◽  
Vol 83 (1) ◽  
pp. 66-72 ◽  
Author(s):  
L S Zhang ◽  
V Le Clerc ◽  
S Li ◽  
D Zhang
Keyword(s):  
Genetic Diversity ◽  
Helianthus Annuus ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Inbred Lines ◽  
Variety Identification ◽  
Large Set ◽  
Sequence Repeat ◽  
Diversity Assessment ◽  
Simple Sequence

The objective of this study was to identify an efficient set of simple sequence repeat (SSR) markers for sunflower (Helianthus annuus L.) variety fingerprinting, relying on semi-automated analysis conditions. Based on criteria such as quality of amplification products, co-dominant and single locus, 78 SSR markers were selected and used to assess the genetic variability among a large set of 124 sunflower inbred lines, including 67 female maintainers (M lines) and 57 male restorers (R lines). They revealed a total of 276 alleles across the 124 elite inbred lines, with a mean of 3.5 alleles per SSR locus. The polymorphism index content per locus varied from 0.06 to 0.81, with an average of 0.51. Relationships among the inbred lines were studied using estimations of Rogers' distances. The great majority of the distance estimates ranged between 0.4 and 0.6, but distances between some pairs of lines were less than 0.1. The genetic diversity value was similar within each subset of R and M lines and low, but significant differentiation was found (GST = 0.049) between the two pools. The selected set of SSRs proved to be useful both for sunflower fingerprinting and genetic diversity assessment.Key words: genetic diversity, genotyping, Helianthus annuus, multiplex PCR, simple sequence repeats (SSR).

scholarly journals Identification of hepatocarcinogen-resistance genes in DBA/2 mice.

Genetics ◽  
1995 ◽  
Vol 139 (1) ◽  
pp. 387-395 ◽  
Author(s):  
G H Lee ◽  
L M Bennett ◽  
R A Carabeo ◽  
N R Drinkwater
Keyword(s):  
Resistance Genes ◽  
Liver Tumor ◽  
Recombinant Inbred ◽  
Simple Sequence Repeat ◽  
Liver Tumors ◽  
Inbred Strains ◽  
Sequence Repeat ◽  
Backcross Population ◽  
Marker Loci ◽  
Simple Sequence

Abstract Male DBA/2J mice are approximately 20-fold more susceptible than male C57BL/6J mice to hepatocarcinogenesis induced by perinatal treatment with N,N-diethylnitrosamine (DEN). In order to elucidate the genetic control of hepatocarcinogenesis in DBA/2J mice, male BXD recombinant inbred, D2B6F1 x B6 backcross, and D2B6F2 intercross mice were treated at 12 days of age with DEN and liver tumors were enumerated at 32 weeks. Interestingly, the distribution of mean tumor multiplicities among BXD recombinant inbred strains indicated that hepatocarcinogen-sensitive DBA/2 mice carry multiple genes with opposing effects on the susceptibility to liver tumor induction. By analyzing D2B6F1 x B6 backcross and D2B6F2 intercross mice for their liver tumor multiplicity phenotypes and for their genotypes at simple sequence repeat marker loci, we mapped two resistance genes carried by DBA/2J mice, designated Hcr1 and -2, to chromosomes 4 and 10, respectively. Hcr1 and Hcr2 resolved the genetic variance in the backcross population well, indicating that these resistance loci are the major determinants of the variance in the backcross population. Although our collection of 100 simple sequence repeat markers allowed linkage analysis for approximately 95% of the genome, we failed to map any sensitivity alleles for DBA/2J mice. Thus, it is likely that the susceptibility of DBA/2J mice is the consequence of the combined effects of multiple sensitivity loci.

scholarly journals Simple sequence repeat marker loci discovery using SSR primer

2004 ◽  
Vol 20 (9) ◽  
pp. 1475-1476 ◽  
Author(s):  
A. J. Robinson ◽  
C. G. Love ◽  
J. Batley ◽  
G. Barker ◽  
D. Edwards
Keyword(s):  
Simple Sequence Repeat Marker ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Marker Loci ◽  
Simple Sequence

A framework linkage map of perennial ryegrass based on SSR markers

Genome ◽  
2006 ◽  
Vol 49 (4) ◽  
pp. 354-364 ◽  
Author(s):  
G P Gill ◽  
P L Wilcox ◽  
D J Whittaker ◽  
R A Winz ◽  
P Bickerstaff ◽  
...  
Keyword(s):  
Linkage Map ◽  
Ssr Markers ◽  
Lolium Perenne ◽  
Perennial Ryegrass ◽  
Simple Sequence Repeat ◽  
Ssr Marker ◽  
Sequence Repeat ◽  
Linkage Groups ◽  
Marker Loci ◽  
Simple Sequence

A moderate-density linkage map for Lolium perenne L. has been constructed based on 376 simple sequence repeat (SSR) markers. Approximately one third (124) of the SSR markers were developed from GeneThresher® libraries that preferentially select genomic DNA clones from the gene-rich unmethylated portion of the genome. The remaining SSR marker loci were generated from either SSR-enriched genomic libraries (247) or ESTs (5). Forty-five percent of the GeneThresher SSRs were associated with an expressed gene. Unlike EST-derived SSR markers, GeneThresher SSRs were often associated with genes expressed at a low level, such as transcription factors. The map constructed here fulfills 2 definitions of a "framework map". Firstly, it is composed of codominant markers to ensure map transferability either within or among species. Secondly, it was constructed to achieve a level of statistical confidence in the support-for-order of marker loci. The map consists of 81 framework SSR markers spread over 7 linkage groups, the same as the haploid chromosome number. Most of the remaining 295 SSR markers have been placed into their most likely interval on the framework map. Nine RFLP markers and 1 SSR marker from another map constructed using the same pedigree were also incorporated to extend genome coverage at the terminal ends of 5 linkage groups. The final map provides a robust framework with which to conduct investigations into the genetic architecture of trait variation in this commercially important grass species.Key words: Framework map, perennial ryegrass, SSR, simple sequence repeat, GeneThresher, Lolium perenne.

Implementing molecular marker technology in forage improvement

2003 ◽  
pp. 229-238
Author(s):  
M. Faville ◽  
B. Barrett ◽  
A. Griffiths ◽  
M. Schreiber ◽  
C. Mercer ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Genetic Variation ◽  
White Clover ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Linkage Groups ◽  
Seedling Vigour ◽  
Genome Map ◽  
Trait Locus ◽  
Simple Sequence

Accelerated improvement of two cornerstones of New Zealand's pastoral industries, per ennial ryegrass (Lolium perenne L.) and white clover (Trifolium repens L.), may be realised through the application of markerassisted selection (MAS) strategies to enhance traditional plant breeding programmes. Genome maps constructed using molecular markers represent the enabling technology for such strategies and we have assembled maps for each species using EST-SSR markers - simple sequence repeat (SSR) markers developed from expressed sequence tags (ESTs) representing genes. A comprehensive map of the white clover genome has been completed, with 464 EST-SSR and genomic SSR marker loci spanning 1125 cM in total, distributed across 16 linkage groups. These have been further classified into eight pairs of linkage groups, representing contributions from the diploid progenitors of this tetraploid species. In perennial ryegrass a genome map based exclusively on EST-SSR loci was constructed, with 130 loci currently mapped to seven linkage groups and covering a distance of 391 cM. This map continues to be expanded with the addition of ESTSSR loci, and markers are being concurrently transferred to other populations segregating for economically significant traits. We have initiated gene discovery through quantitative trait locus (QTL) analysis in both species, and the efficacy of the white clover map for this purpose was demonstrated with the initial identification of multiple QTL controlling seed yield and seedling vigour. One QTL on linkage group D2 accounts for 25.9% of the genetic variation for seed yield, and a putative QTL accounting for 12.7% of the genetic variation for seedling vigour was detected on linkage group E1. The application of MAS to forage breeding based on recurrent selection is discussed. Keywords: genome map, marker-assisted selection, perennial ryegrass, QTL, quantitative trait locus, SSR, simple sequence repeat, white clover

Genetic diversity of Symplocos paniculata of Hunan province revealed by inter-simple sequence repeat (ISSR)

2019 ◽  
Vol 51 (5) ◽  
Author(s):  
Huifang Cao ◽  
Qiang Lin ◽  
Peiwang Li ◽  
Jingzhen Chen ◽  
Changzhu Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Hunan Province ◽  
Sequence Repeat ◽  
Simple Sequence
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