Microsatellite DNA fingerprinting, differentiation, and genetic relationships of clones, cultivars, and varieties of six poplar species from three sections of the genus Populus

Genome ◽  
2002 ◽  
Vol 45 (6) ◽  
pp. 1083-1094 ◽  
Author(s):  
Muhammad H Rahman ◽  
Om P Rajora
Keyword(s):  
Resource Management ◽  
Dna Markers ◽  
Microsatellite Dna ◽  
Simple Sequence Repeat ◽  
Genetic Resource ◽  
Sequence Repeat ◽  
Genetic Fingerprinting ◽  
Microsatellite Dna Markers ◽  
The Mean ◽  
Simple Sequence

Accurate identification of Populus clones and cultivars is essential for effective selection, breeding, and genetic resource management programs. The unit of cultivation and breeding in poplars is a clone, and individual cultivars are normally represented by a single clone. Microsatellite DNA markers of 10 simple sequence repeat loci were used for genetic fingerprinting and differentiation of 96 clones/cultivars and varieties belonging to six Populus species (P. deltoides, P. nigra, P. balsamifera, P. trichocarpa, P. grandidentata, and P. maximowiczii) from three sections of the genus. All 96 clones/cultivars could be uniquely fingerprinted based on their single- or multilocus microsatellite genotypes. The five P. grandidentata clones could be differentiated based on their single-locus genotypes, while six clones of P. trichocarpa and 11 clones of P. maximowiczii could be identified by their two-locus genotypes. Twenty clones of P. deltoides and 25 clones of P. nigra could be differentiated by their multilocus genotypes employing three loci, and 29 clones of P. balsamifera required the use of multilocus genotypes at five loci for their genetic fingerprinting and differentiation. The loci PTR3, PTR5, and PTR7 were found to be the most informative for genetic fingerprinting and differentiation of the clones. The mean number of alleles per locus ranged from 2.9 in P. trichocarpa or P. grandidentata to 6.0 in P. balsamifera and 11.2 in 96 clones of the six species. The mean number of observed genotypes per locus ranged from 2.4 in P. grandidentata to 7.4 in P. balsamifera and 19.6 in 96 clones of the six species. The mean number of unique genotypes per locus ranged from 1.3 in P. grandidentata to 3.9 in P. deltoides and 8.8 in 96 clones of the six species. The power of discrimination of the microsatellite DNA markers in the 96 clones ranged from 0.726 for PTR4 to 0.939 for PTR7, with a mean of 0.832 over the 10 simple sequence repeat loci. Clones/cultivars from the same species showed higher microsatellite DNA similarities than the clones from the different species. A UPGMA cluster plot constructed from the microsatellite genotypic similarities separated the 96 clones into six major groups corresponding to their species. Populus nigra var. italica clones were genetically differentiated from the P. nigra var. nigra clones. Microsatellite DNA markers could be useful in genetic fingerprinting, identification, classification, certification, and registration of clones, clultivars, and varieties as well as genetic resource management and protection of plant breeders' rights in Populus.Key words: Populus, simple sequence repeat markers, clonal identification, genetic fingerprinting, clone–cultivar relationships.

scholarly journals Microsatellite DNA markers in Populus tremuloides

Genome ◽  
2000 ◽  
Vol 43 (2) ◽  
pp. 293-297 ◽  
Author(s):  
Muhammad H Rahman ◽  
S Dayanandan ◽  
Om P Rajora
Keyword(s):  
Populus Tremuloides ◽  
Dna Markers ◽  
Microsatellite Dna ◽  
Simple Sequence Repeat ◽  
Mendelian Inheritance ◽  
Inheritance Pattern ◽  
Sequence Repeat ◽  
Microsatellite Dna Markers ◽  
Ssr Loci ◽  
Simple Sequence

Markers for eight new microsatellite DNA or simple sequence repeat (SSR) loci were developed and characterized in trembling aspen (Populus tremuloides) from a partial genomic library. Informativeness of these microsatellite DNA markers was examined by determining polymorphisms in 38 P. tremuloides individuals. Inheritance of selected markers was tested in progenies of controlled crosses. Six characterized SSR loci were of dinucleotide repeats (two perfect and four imperfect), and one each of trinucleotide and tetranucleotide repeats. The monomorphic SSR locus (PTR15) was of a compound imperfect dinucleotide repeat. The primers of one highly polymorphic SSR locus (PTR7) amplified two loci, and alleles could not be assigned to a specific locus. At the other six polymorphic loci, 25 alleles were detected in 38 P. tremuloides individuals; the number of alleles ranged from 2 to 7, with an average of 4.2 alleles per locus, and the observed heterozygosity ranged from 0.05 to 0.61, with an average of 0.36 per locus. The two perfect dinucleotide and one trinucleotide microsatellite DNA loci were the most informative. Microsatellite DNA variants of four SSR loci characterized previously followed a single-locus Mendelian inheritance pattern, whereas those of PTR7 from the present study showed a two-locus Mendelian inheritance pattern in controlled crosses. The microsatellite DNA markers developed and reported here could be used for assisting various genetic, breeding, biotechnology, genome mapping, conservation, and sustainable forest management programs in poplars. Key words: poplar, microsatellites, genetic mapping, simple sequence repeat (SSR) markers, DNA fingerprinting.

scholarly journals Developing Microsatellite DNA Markers in Pecan

2003 ◽  
Vol 128 (3) ◽  
pp. 374-380 ◽  
Author(s):  
L.J. Grauke ◽  
Muhammad J. Iqbal ◽  
Avutu S. Reddy ◽  
Tommy E. Thompson
Keyword(s):  
Dna Markers ◽  
Microsatellite Dna ◽  
Southern Hybridization ◽  
Genomic Library ◽  
Carya Illinoinensis ◽  
Enriched Library ◽  
Microsatellite Dna Markers ◽  
Ssr Primers ◽  
Nucleotide Repeats ◽  
Simple Sequence

A microsatellite-enriched library was developed from `Halbert', a native pecan [Carya illinoinensis (Wangenh.) K. Koch] selection from Coleman County, Texas. A genomic library enriched for simple sequence repeats (SSR) containing 6144 clones was archived in 384 well plates for screening. In total, 439 clones were identified after Southern hybridization using di- and tri-nucleotide repeats as probes. In total, 125 positive clones were sequenced and primers were designed for 24 repeats. The SSR markers chosen for analysis include di-(CT and GA) and tri-nucleotide repeats (CTT, GAA and GAT). Of the 24 primer pairs tested, 19 successfully amplified microsatellites from `Halbert'. DNA was isolated from 48 pecan and hickory accessions selected to strategically represent the genetic diversity of the National Clonal Germplasm Repository (NCGR) Carya collections. The 19 SSR primers that produced good amplification products in `Halbert' were used to evaluate the collection, with 11 revealing polymorphism. The number of fragments amplified with different primer combinations ranged from 4 to 32 in the 48 genotypes tested. Evaluation of the data confirms the utility of the microsatellites in delimiting known relationships.

Mapping of digested and undigested random amplified microsatellite polymorphisms in barley

Genome ◽  
1995 ◽  
Vol 38 (5) ◽  
pp. 991-998 ◽  
Author(s):  
Jörg Becker ◽  
Manfred Heun
Keyword(s):  
Simple Sequence Repeats ◽  
Dna Markers ◽  
Simple Sequence Repeat ◽  
Sequence Data ◽  
Linkage Maps ◽  
Sequence Repeat ◽  
Rflp Map ◽  
Alternative Approach ◽  
Microsatellite Mapping ◽  
Simple Sequence

The broad use of microsatellites as a tool for constructing linkage maps in plants has been limited by the need for sequence data to detect the underlying simple sequence repeats. Therefore, random amplified microsatellite polymorphisms (RAMPs) were studied as an alternative approach for barley mapping. Labelled (GA)n simple sequence repeat primers were combined with RAPD primers of different length and sequence to generate RAMPs. To get additional polymorphisms (called dRAMPs), the obtained products were also analysed after digestion with MseI. There were 0–11 polymorphisms found per primer combination. Sixty RAMPs/dRAMPs identifying 40 new loci were mapped onto a barley RFLP map. The new DNA markers are found on all chromosomes and they increased the length of the barley map by 174 cM to a total of 1270 cM. Interestingly, the RAMPs/dRAMPs caused stretching effects in genome areas where stretching was also observed for AFLPs.Key words: barley, microsatellite, mapping, RAMP, RFLP.

Analysis of the polymorphism of expressed sequencetag-Simple sequence repeat in quail

2016 ◽  
Author(s):  
Jun Yan Bai ◽  
You Zhi Pang ◽  
Yan Xia Qi ◽  
Xiao Hui Zhang ◽  
Yin Xian Yun
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Genetic Improvement ◽  
Melanin Synthesis ◽  
Sequence Repeat ◽  
Average Heterozygosity ◽  
Information Contents ◽  
The Mean ◽  
Simple Sequence

Aiming at accelerating the application of molecular markers in the genetic improvement of quails, six EST-SSR markers were successfully developed using a bioinformatics method. Polymorphisms of three quail populations (Chinese yellow, China black and Korean quail) were detected. The results showed that there were 2-6 alleles in six EST-SSR markers. The mean polymorphism information contents of Chinese yellow , China blackand Korean quail were 0.5451, 0.4962 and 0.4937, respectively. The average heterozygosity values were 0.6134, 0.5759 and 0.5613. Among the six EST-SSR markers, three were highly polymorphicand the others were moderately polymorphic. The newly-developed six EST-SSR markers may be used to determine the genetic diversity of quails. The six EST-SSR markers identified were related to carbohydrate metabolism and melanin synthesis, but the specific mechanisms need to be further analyzed.

Mapping of simple sequence repeat (SSR) DNA markers in diploid and tetraploid alfalfa

2000 ◽  
Vol 101 (1-2) ◽  
pp. 165-172 ◽  
Author(s):  
N. Diwan ◽  
J. H. Bouton ◽  
G. Kochert ◽  
P. B. Cregan
Keyword(s):  
Dna Markers ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Simple Sequence

scholarly journals Simple Sequence Repeat Markers Reveal Genetic Diversity Within and among Landrace Collections of Citron and Dessert Watermelon from South Africa

2016 ◽  
Vol 141 (6) ◽  
pp. 598-608 ◽  
Author(s):  
Jacob Mashilo ◽  
Hussein Shimelis ◽  
Alfred Odindo ◽  
Beyene Amelework
Keyword(s):  
South Africa ◽  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Polymorphic Information Content ◽  
Citrullus Lanatus ◽  
Sequence Repeat ◽  
Simple Sequence Repeat Markers ◽  
The Mean ◽  
Two Populations ◽  
Simple Sequence

Genetic diversity analysis is fundamental for effective breeding and genetic conservation. The objective of this study was to determine the genetic diversity present among dessert watermelon (Citrullus lanatus var. lanatus) and citron watermelon (C. lanatus var. citroides) landraces widely grown in South Africa and to select genetically diverse and complimentary genotypes for strategic breeding or conservation. Thirty-one dessert watermelon and 34 citron watermelon landraces were genotyped using 10 polymorphic simple sequence repeat markers. The number of alleles detected per marker ranged from 2 to 23 alleles, with a mean of 13.5 alleles. A total of 135 putative alleles were amplified from sampled watermelon populations. Number of effective alleles ranged from 1.99 to 10.88 alleles with a mean of 5.83 alleles. The mean observed and expected heterozygosity were 0.50 and 0.79, respectively. The mean polymorphic information content was 0.79. Cluster and principal coordinate analyses grouped the two watermelon populations into two separate clusters. The two populations were genetically differentiated with low gene flow, suggesting the presence of high genetic differences between the two populations. Overall, the study established the existence of considerable genetic diversity among South African grown dessert and citron watermelon landraces. Unique dessert watermelon landraces such as SWM-39, SWM-24, SWM-01, SWM-40, SWM-18, SWM-36, and SWM-26; and citron watermelon genotypes including WWM-24, WWM-37, WWM-28, WWM-34, WWM-02, WWM-22, WWM-50, and WWM-36 were selected based on their high dissimilarity index. These could be useful for breeding and systematic conservation.

Genetic diversity analysis of yam cultivars (Dioscorea rotundata Poir.) in Benin using simple sequence repeat (SSR) markers

2007 ◽  
Vol 5 (02) ◽  
pp. 71-81 ◽  
Author(s):  
Serge Tostain ◽  
Clément Agbangla ◽  
Nora Scarcelli ◽  
Cédric Mariac ◽  
Ogoubi Daïnou ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Management Practices ◽  
Genetic Relationships ◽  
Sequence Repeat ◽  
Dioscorea Rotundata ◽  
Tuber Crop ◽  
The Mean ◽  
Simple Sequence

Guinea yam (Dioscorea rotundataPoir.) is a dioecious vegetatively propagated tuber crop. It is widely cultivated by traditional techniques in West Africa, its area of origin. The genetic diversity of 146 accessions from Benin was analysed using 10 polymorphic simple sequence repeat (SSR) nuclear markers and agromorphological traits. An average of 8.4 alleles per locus was detected. The mean heterozygosity was 0.57 and the mean polymorphism information content (PIC) for polymorphic markers was 0.51. Some cultivars (23%) were found to have an identical genotype for the 10 markers. The structure of the genetic diversity observed in Benin is the result of farmers' crop management practices and their know-how. The cultivar diversity had a geographical component. We also noted major differentiation between early and late cultivars, with higher diversity in the early ones. Cultivars from northern Benin and early cultivars had the greatest allelic richness. SSR markers proved to be powerful tools for fingerprinting each cultivar and analysing their genetic relationships. The results of this study could be useful for defining a strategy for the conservation of genetic diversity in yams.

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