Polymorphism of PCR-based markers targeting exons, introns, promoter regions, and SSRs in maize and introns and repeat sequences in oat

Genome ◽  
2001 ◽  
Vol 44 (6) ◽  
pp. 1065-1076 ◽  
Author(s):  
J B Holland ◽  
S J Helland ◽  
N Sharopova ◽  
D C Rhyne
Keyword(s):  
Ssr Markers ◽  
Inbred Lines ◽  
Amplification Product ◽  
Promoter Regions ◽  
Repeat Sequences ◽  
Sequence Tagged Sites ◽  
Maize Genotype ◽  
Oat Cultivars ◽  
Ssr Polymorphism ◽  
Simple Sequence

Sequence databases could be efficiently exploited for development of DNA markers if it were known which gene regions reveal the most polymorphism when amplified by PCR. We developed PCR primer pairs that target specific regions of previously sequenced genes from Avena and Zea species. Primers were targeted to amplify 40 introns, 24 exons, and 23 promoter regions within 54 maize genes. We surveyed 48 maize inbred lines (previously assayed for simple-sequence repeat (SSR) polymorphism) for amplification-product polymorphism. We also developed primers to target 14 SSRs and 12 introns within 18 Avena genes, and surveyed 22 hexaploid oat cultivars and 2 diploid Avena species for amplification-product polymorphism. In maize, 67% of promoter markers, 58% of intron markers, and 13% of exon markers exhibited amplification-product polymorphisms. Among polymorphic primer pairs in maize, genotype diversity was highest for SSR markers (0.60) followed by intron markers (0.46), exon markers (0.42), and promoter markers (0.28). Among all Avena genotypes, 64% of SSR markers and 58% of intron markers revealed polymorphisms, but among the cultivars only, 21% of SSR markers and 50% of intron markers were polymorphic. Polymorphic-sequence-tagged sites for plant-breeding applications can be created easily by targeting noncoding gene regions.Key words: Avena, Zea, genetic diversity, DNA sequence.

Validation of Microsatellite Markers of Pl Resistance Genes to Downy Mildew of Sunflower

Helia ◽  
2018 ◽  
Vol 41 (68) ◽  
pp. 73-82
Author(s):  
A. Solodenko
Keyword(s):  
Downy Mildew ◽  
Ssr Markers ◽  
Resistance Genes ◽  
Microsatellite Loci ◽  
Marker Assisted Selection ◽  
Parental Line ◽  
Gene Control ◽  
Genetically Determined ◽  
Ssr Polymorphism ◽  
Simple Sequence

AbstractSimple sequence repeats (SSR) polymorphism of 34 microsatellite loci (LG1, 8 and 13) was studied in lines carrying the downy mildew resistance genes Pl and lines with no Pl. The microsatellite loci ORS328 and ORS781 were selected as markers for genes Pl6 and Pl8 in lines HA 335 and QHP-1, respectively. Markers were identified for gene PlARG in RHA 419 and some accessions of H. argophyllus. The SSR markers ORS509, ORS605, ORS610, ORS1182 and ORS1039 were proven to reliably identify the parental line carrying PlARG gene, control and select the heterozygous F1 hybrids and identify homozygous genotypes in F2 generations. Obtained results indicate the necessity of validation of the markers in various germplasm pools and breeding collections. The SSR markers that are tightly linked to Pl6, Pl8, PlARG would be useful in the sunflower breeding. PlARG homozygous F2 segregants, developed and identified with marker assisted selection in this study, are recommended for further breeding as a new source of genetically determined resistance to downy mildew.

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).

Allelic diversity of simple sequence repeats among elite inbred lines of cultivated sunflower

Genome ◽  
2002 ◽  
Vol 45 (4) ◽  
pp. 652-660 ◽  
Author(s):  
Ju-Kyung Yu ◽  
Jodie Mangor ◽  
Lucy Thompson ◽  
Keith J Edwards ◽  
Mary B Slabaugh ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Dna Sequences ◽  
Dna Markers ◽  
Allelic Diversity ◽  
Inbred Lines ◽  
Genetic Maps ◽  
Dna Polymorphisms ◽  
Tetranucleotide Repeats ◽  
The Mean ◽  
Simple Sequence

Simple sequence repeat (SSR) markers were developed for cultivated sunflower (Helianthus annuus L.) from the DNA sequences of 970 clones isolated from genomic DNA libraries enriched for (CA)n, (CT)n, (CAA)n, (CATA)n, or (GATA)n. The clones harbored 632 SSRs, of which 259 were unique. SSR markers were developed for 130 unique SSRs by designing and testing primers for 171 unique SSRs. Of the total, 74 SSR markers were polymorphic when screened for length polymorphisms among 16 elite inbred lines. The mean number of alleles per locus was 3.7 for dinucleotide, 3.6 for trinucleotide, and 9.5 for tetranucleotide repeats and the mean polymorphic information content (PIC) scores were 0.53 for dinucleotide, 0.53 for trinucleotide, and 0.83 for tetranucleotide repeats. Cluster analyses uncovered patterns of genetic diversity concordant with patterns produced by RFLP fingerprinting. SSRs were found to be slightly more polymorphic than RFLPs. Several individual SSRs were significantly more polymorphic than RFLP and other DNA markers in sunflower (20% of the polymorphic SSR markers had PIC scores ranging from 0.70 to 0.93). The newly developed SSRs greatly increase the supply of sequence-based DNA markers for DNA fingerprinting, genetic mapping, and molecular breeding in sunflower; however, several hundred additional SSR markers are needed to routinely construct complete genetic maps and saturate the genome.Key words: microsatellites, Helianthus, Compositae, DNA polymorphisms.

scholarly journals Comparison of RAPD, ISSR and SSR markers in assessing genetic diversity among rye (Secale cereale L.) inbred lines

2010 ◽  
Vol 62 (1) ◽  
pp. 107-115 ◽  
Author(s):  
Beata Myśków ◽  
Paweł Milczarski ◽  
Piotr Masojć
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Secale Cereale ◽  
Simple Sequence Repeats ◽  
Random Amplified Polymorphic Dna ◽  
Correlation Coefficients ◽  
Inbred Lines ◽  
Winter Rye ◽  
Dna Primers ◽  
Simple Sequence

Comparison of RAPD, ISSR and SSR markers in assessing genetic diversity among rye (Secale cereale L.) inbred lines Forty eight inbred lines of winter rye, of various origin and pedigree, were analysed using 19 RAPD (random amplified polymorphic DNA) primers, 8 ISSR (inter-simple sequence repeats) primers and 13 SSR (simple sequence repeats) primer pairs. On the basis of particular marker types, there were created three separate dendrograms and one combined similarity tree, prepared on account of the whole data. Correlation coefficients for individual technique based on genetic similarity matrices were not significant. By comparing the GS data obtained on the basis of singular methods with collective matrix, it was observed that the highest correlation rate was for ISSR method (r=0.68). The utility of each marker technique was compared by using marker index MI. Diversity detecting index (DDT) was suggested in the paper, which may prove helpful in planning and comparing researches on phenetic relationships.

scholarly journals Application of simple sequence repeat (SSR) markers for molecular diversity and heterozygosity analysis in maize inbred lines

2009 ◽  
Vol 16 (2) ◽  
pp. 57-62 ◽  
Author(s):  
Afaf I. Shehata ◽  
Haila A. Al-Ghethar ◽  
Ali A. Al-Homaidan
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Molecular Diversity ◽  
Inbred Lines ◽  
Sequence Repeat ◽  
Maize Inbred Lines ◽  
Simple Sequence

scholarly journals The newly developed genomic-SSR markers uncover the genetic characteristics and relationships of olive accessions

PeerJ ◽  
2020 ◽  
Vol 8 ◽  
pp. e8573 ◽  
Author(s):  
Danyang Li ◽  
Cui Long ◽  
Xiaoming Pang ◽  
Delu Ning ◽  
Tao Wu ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Trinucleotide Repeat ◽  
Principal Coordinate Analysis ◽  
Clonal Variation ◽  
Dna Fingerprints ◽  
Genetic Characteristics ◽  
Repeat Sequences ◽  
Genomic Ssr ◽  
Olive Cultivars ◽  
Simple Sequence

Background Olive (Olea europaea L.) is an important oil and fruit crop worldwide, owning a rich germplasm with a large number of cultivars. Simple sequence repeats (SSRs) are excellent markers and have been used for the identification of olive cultivars. However, the limited number of SSR markers and the occurrence of confusion on the names of cultivars, as well as the possible appearance of clonal variation make it difficult to identify cultivars and interpret relationships among olive cultivars. Method SSR markers were designed based on trinucleotide repeat sequences by screening the whole genome of olive, and the polymorphic SSR markers were developed that were applied to the identification of 53 olive accessions. The genetic characteristics and relationships of these olive accessions were evaluated based on the developed SSR markers. Results Twenty-one highly polymorphic genomic-SSR markers were developed, covering most chromosomes of olive. These SSR markers could well distinguish all 53 olive accessions, confirming their effectiveness. DNA fingerprints of the 53 olive accessions were constructed based on the 21 SSR markers. The dendrogram clearly divided the tested accessions into two main groups, which was also supported by the results of principal coordinate analysis. A total of 31 private alleles were detected in 15 olive accessions, which reflected the genetic diversity within 53 olive accessions to some extent. Six homonymy cases were also clarified by genetic analysis. These results suggest that the newly developed olive SSR markers are informative for the exploitation, preservation and breeding of olive.

LEGITIMACY OF PROGENIES USING SSR MARKERS AS CONTROLLING SYSTEM AND EARLIER SELECTION IN THE OIL PALM NURSERY (Elaeis guineensis JACQ.)

2018 ◽  
Vol 25 (1) ◽  
pp. 21-30
Author(s):  
Rokhana Faizah ◽  
Sri Wening ◽  
Abdul Razak Purba
Keyword(s):  
Dna Fingerprinting ◽  
Ssr Markers ◽  
Oil Palm ◽  
Dna Markers ◽  
Elaeis Guineensis ◽  
Gene Marker ◽  
Controlling System ◽  
Crossing Probability ◽  
Simple Sequence

Information of legitimacy of oil palm progenies is important to guaranty the quality and to control commercial seeds procedures. A true and legitimate cross will produce progeny which has a combination of their parent's allele. The information could be obtained early in the nursery stage through DNA fingerprinting analysis. Simple Sequence Repeats (SSR) is one of DNA markers used for DNA fingerprinting, since the marker system has advantages to acquire information of allele per individual in population and efficiency diverse allele of progeny and their parents. The aim of the research is to obtain legitimacy of 12 progenies analyzing in the oil palm nursery stage. Thirteen SSR markers were used to analyze 12 crossings number of oil palm. The genotypes data by alleles of SSR inferred and quantified using Gene Marker® Software version 2.4.0 Soft Genetics® LLC and analyzed based on Mendel's Law of Segregation. The result showed based on heredity pattern of progeny and their parent's allele that progenies H were indicated genetically derived from their known parents while progenies from A and G indicated as illegitimate crossing. Probability value for legitimacy of progenies of 9 other crosses has 0.031 and 0.5. Legitimacy analysis of progeny using SSR markers could be used to control the quality of crossing material and earlier selection in the oil palm nursery.

scholarly journals Genotyping of Peach and Nectarine Cultivars with SSR and SRAP Molecular Markers

2004 ◽  
Vol 129 (2) ◽  
pp. 204-210 ◽  
Author(s):  
Riaz Ahmad ◽  
Dan Potter ◽  
Stephen M. Southwick
Keyword(s):  
Molecular Markers ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Sweet Cherry ◽  
Prunus Persica ◽  
Sequence Repeat ◽  
Srap Markers ◽  
Upgma Cluster Analysis ◽  
Commercially Important ◽  
Simple Sequence

Simple sequence repeat (SSR) and sequence related amplified polymorphism (SRAP) molecular markers were evaluated for detecting intraspecific variation in 38 commercially important peach and nectarine (Prunus persica) cultivars. Out of the 20 SSR primer pairs 17 were previously developed in sweet cherry and three in peach. The number of putative alleles revealed by SSR primer pairs ranged from one to five showing a low level of genetic variability among these cultivars. The average number of alleles per locus was 2.2. About 76% of cherry primers produced amplification products in peach and nectarine, showing a congeneric relationship within Prunus species. Only nine cultivars out of the 38 cultivars could be uniquely identified by the SSR markers. For SRAP, the number of fragments produced was highly variable, ranging from 10 to 33 with an average of 21.8 per primer combination. Ten primer combinations resulted in 49 polymorphic fragments in this closely related set of peaches and nectarines. Thirty out of the 38 peach and nectarine cultivars were identified by unique SRAP fingerprints. UPGMA Cluster analysis based on the SSR and SRAP polymorphic fragments was performed; the relationships inferred are discussed with reference to the pomological characteristics and pedigree of these cultivars. The results indicated that SSR and SRAP markers can be used to distinguish the genetically very close peach and nectarine cultivars as a complement to traditional pomological studies. However, for fingerprinting, SRAP markers appear to be much more effective, quicker and less expensive to develop than are SSR markers.

scholarly journals Assessment of the Genetic Diversity of Rice Germplasms Characterized by Black-Purple and Red Pericarp Color Using Simple Sequence Repeat Markers

Plants ◽  
2019 ◽  
Vol 8 (11) ◽  
pp. 471
Author(s):  
Jae-Ryoung Park ◽  
Won-Tae Yang ◽  
Yong-Sham Kwon ◽  
Hyeon-Nam Kim ◽  
Kyung-Min Kim ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Germplasm Collection ◽  
Group Method ◽  
Sequence Repeat ◽  
Rice Varieties ◽  
Red Pericarp ◽  
Simple Sequence ◽  
Colored Rice

The assessment of the genetic diversity within germplasm collections can be accomplished using simple sequence repeat (SSR) markers and association mapping techniques. The present study was conducted to evaluate the genetic diversity of a colored rice germplasm collection containing 376 black-purple rice samples and 172 red pericarp samples, conserved by Dong-A University. There were 600 pairs of SSR primers screened against 11 rice varieties. Sixteen informative primer pairs were selected, having high polymorphism information content (PIC) values, which were then used to assess the genetic diversity within the collection. A total of 409 polymorphic amplified fragments were obtained using the 16 SSR markers. The number of alleles per locus ranged from 11 to 47, with an average of 25.6. The average PIC value was 0.913, ranging from 0.855 to 0.964. Four hundred and nine SSR loci were used to calculate Jaccard’s distance coefficients, using the unweighted pair-group method with arithmetic mean cluster analysis. These accessions were separated into several distinctive groups corresponding to their morphology. The results provided valuable information for the colored rice breeding program and showed the importance of protecting germplasm resources and the molecular markers that can be derived from them.

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