scholarly journals Development of Simple Sequence Repeat (SSR) Markers of Sesame (Sesamum indicum) from a Genome Survey

Molecules ◽  
2014 ◽  
Vol 19 (4) ◽  
pp. 5150-5162 ◽  
Author(s):  
Xin Wei ◽  
Linhai Wang ◽  
Yanxin Zhang ◽  
Xiaoqiong Qi ◽  
Xiaoling Wang ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Sesamum Indicum ◽  
Sequence Repeat ◽  
Genome Survey ◽  
A Genome ◽  
Simple Sequence

scholarly journals Development of simple sequence repeat (SSR) markers from a genome survey of Chinese bayberry (Myrica rubra)

BMC Genomics ◽  
2012 ◽  
Vol 13 (1) ◽  
pp. 201 ◽  
Author(s):  
Yun Jiao ◽  
Hui-min Jia ◽  
Xiong-wei Li ◽  
Ming-liang Chai ◽  
Hui-juan Jia ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Chinese Bayberry ◽  
Myrica Rubra ◽  
Genome Survey ◽  
A Genome ◽  
Simple Sequence

scholarly journals Genome survey sequencing and characterization of simple sequence repeat (SSR) markers in Platostoma palustre (Blume) A.J.Paton (Chinese mesona)

2022 ◽  
Vol 12 (1) ◽  
Author(s):  
Zhao Zheng ◽  
Nannan Zhang ◽  
Zhenghui Huang ◽  
Qiaoying Zeng ◽  
Yonghong Huang ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Genetic Similarity ◽  
Genetic Improvement ◽  
Similarity Coefficient ◽  
Sequence Repeat ◽  
Genome Survey ◽  
Simple Sequence ◽  
Genome Survey Sequencing

AbstractPlatostoma palustre (Blume) A.J.Paton is an annual herbaceous persistent plant of the Labiatae family. However, there is a lack of genomic data for this plant, which severely restricts its genetic improvement. In this study, we performed genome survey sequencing of P. palustre and developed simple sequence repeat (SSR) markers based on the resulting sequence. K-mer analysis revealed that the assembled genome size was approximately 1.21 Gb. A total of 15,498 SSR motifs were identified and characterized in this study; among them, dinucleotide, and hexanucleotide repeats had the highest and lowest, respectively. Among the dinucleotide repeat motifs, AT/TA repeat motifs were the most abundant, and GC/CG repeat motifs were rather rare, accounting for 44.28% and 0.63%, respectively. Genetic similarity coefficient analysis by the UPMGA methods clustered 12 clones, of P. palustre and related species into two subgroups. These results provide helpful information for further research on P. palustre resources and variety improvements.

scholarly journals Application of Simple Sequence Repeat (SSR) Markers for the Discrimination of Korean and Chinese Sesame (Sesamum indicum L.) Accessions

2014 ◽  
Vol 2 (1) ◽  
pp. 80-87 ◽  
Author(s):  
Jong-Hyun Park ◽  
Sundan Suresh ◽  
Xiang-Min Piao ◽  
Gyu Taek Cho ◽  
Sok-Young Lee ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Sesamum Indicum ◽  
Sequence Repeat ◽  
Simple Sequence

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.

scholarly journals Grass Hosts Harbor More Diverse Isolates of Puccinia striiformis Than Cereal Crops

2016 ◽  
Vol 106 (4) ◽  
pp. 362-371 ◽  
Author(s):  
P. Cheng ◽  
X. M. Chen ◽  
D. R. See
Keyword(s):  
Ssr Markers ◽  
Stripe Rust ◽  
Simple Sequence Repeat ◽  
Puccinia Striiformis ◽  
The United States ◽  
Grass Species ◽  
Cereal Crops ◽  
Sequence Repeat ◽  
Grass Hosts ◽  
Simple Sequence

Puccinia striiformis causes stripe rust on cereal crops and many grass species. However, it is not clear whether the stripe rust populations on grasses are able to infect cereal crops and how closely they are related to each other. In this study, 103 isolates collected from wheat, barley, triticale, rye, and grasses in the United States were characterized by virulence tests and simple sequence repeat (SSR) markers. Of 69 pathotypes identified, 41 were virulent on some differentials of wheat only, 10 were virulent on some differentials of barley only, and 18 were virulent on some differentials of both wheat and barley. These pathotypes were clustered into three groups: group one containing isolates from wheat, triticale, rye, and grasses; group two isolates were from barley and grasses; and group three isolates were from grasses and wheat. SSR markers identified 44 multilocus genotypes (MLGs) and clustered them into three major molecular groups (MG) with MLGs in MG3 further classified into three subgroups. Isolates from cereal crops were present in one or more of the major or subgroups, but not all, whereas grass isolates were present in all of the major and subgroups. The results indicate that grasses harbor more diverse isolates of P. striiformis than the cereals.

scholarly journals Use of simple sequence repeat (SSR) markers for screening blue disease resistance in cotton germplasm exchange

2015 ◽  
Vol 14 (41) ◽  
pp. 2871-2875 ◽  
Author(s):  
Faustine Christopher ◽  
Vieira Hoffmann Lucia ◽  
Ismail Tibazarwa Flora ◽  
Lukonge Everina
Keyword(s):  
Disease Resistance ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Germplasm Exchange ◽  
Simple Sequence
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