scholarly journals Development, Linkage Mapping, and Use of Microsatellites in Bermudagrass

2010 ◽  
Vol 135 (6) ◽  
pp. 511-520 ◽  
Author(s):  
Karen R. Harris-Shultz ◽  
Brian M. Schwartz ◽  
Wayne W. Hanna ◽  
Jeff A. Brady
Keyword(s):  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Linkage Mapping ◽  
Genetic Maps ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Marker Data ◽  
Genetic Linkage Maps ◽  
Expressed Sequence ◽  
Simple Sequence

Genetic linkage maps of bermudagrass (Cynodon spp.) species using 118 triploid individuals derived from a cross of T89 [C. dactylon (2n = 4x = 36)] and T574 [C. transvaalensis (2n = 2x = 18)] were enriched with expressed sequence tags-derived simple sequence repeat (EST-SSR) markers. Primers were developed from 53 ESTs containing SSRs producing 75 segregating markers from which 28 could be mapped to the T89 and T574 genetic maps. With the addition of previously generated marker data, 26 T89 linkage groups and eight T574 linkage groups were formed using a log-of-odds (LOD) value of 4.0. The T89 and T574 linkage maps spanned 1055 cM and 311.1 cM and include 125 and 36 single-dose amplified fragments (SDAFs), respectively. Many of the SDAFs displayed disomic segregation and thus T89 may be a segmental allotetraploid or an allotetraploid. The additional EST-SSR markers add value to the maps by increasing marker density and provide markers that can be easily transferred to other bermudagrass populations. Furthermore, EST-SSRs can be immediately used to assess genetic diversity, identify non-mutated cultivars of bermudagrass, confirm pedigrees, and differentiate contaminants from cultivars derived from ‘Tifgreen’.

scholarly journals VfODB: a comprehensive database of ESTs, EST-SSRs, mtSSRs, microRNA-target markers and genetic maps in Vicia faba

AoB Plants ◽  
2020 ◽  
Vol 12 (6) ◽  
Author(s):  
Morad M Mokhtar ◽  
Ebtissam H A Hussein ◽  
Salah El-Din S El-Assal ◽  
Mohamed A M Atia
Keyword(s):  
Vicia Faba ◽  
Faba Bean ◽  
Expressed Sequence Tags ◽  
Genetic Linkage ◽  
Genetic Maps ◽  
Linkage Maps ◽  
Microrna Target ◽  
Genetic Linkage Maps ◽  
Expressed Sequence ◽  
Simple Sequence

Abstract Faba bean (Vicia faba) is an essential food and fodder legume crop worldwide due to its high content of proteins and fibres. Molecular markers tools represent an invaluable tool for faba bean breeders towards rapid crop improvement. Although there have historically been few V. faba genome resources available, several transcriptomes and mitochondrial genome sequence data have been released. These data in addition to previously developed genetic linkage maps represent a great resource for developing functional markers and maps that can accelerate the faba bean breeding programmes. Here, we present the Vicia faba Omics database (VfODB) as a comprehensive database integrating germplasm information, expressed sequence tags (ESTs), expressed sequence tags-simple sequence repeats (EST-SSRs), and mitochondrial-simple sequence repeats (mtSSRs), microRNA-target markers and genetic maps in faba bean. In addition, KEGG pathway-based markers and functional maps are integrated as a novel class of annotation-based markers/maps. Collectively, we developed 31 536 EST markers, 9071 EST-SSR markers and 3023 microRNA-target markers based on V. faba RefTrans V2 mining. By mapping 7940 EST and 2282 EST-SSR markers against the KEGG pathways database we successfully developed 107 functional maps. Also, 40 mtSSR markers were developed based on mitochondrial genome mining. On the data curation level, we retrieved 3461 markers representing 12 types of markers (CAPS, EST, EST-SSR, Gene marker, INDEL, Isozyme, ISSR, RAPD, SCAR, RGA, SNP and SSR), which mapped across 18 V. faba genetic linkage maps. VfODB provides two user-friendly tools to identify, classify SSR motifs and in silico amplify their targets. VfODB can serve as a powerful database and helpful platform for faba bean research community as well as breeders interested in Genomics-Assisted Breeding.

Targetting microsatellites (SSRs) in genetic linkage maps of bread wheat

2001 ◽  
Vol 52 (12) ◽  
pp. 1143 ◽  
Author(s):  
M. J. Hayden ◽  
S. Khatkar ◽  
P. J. Sharp
Keyword(s):  
Bread Wheat ◽  
Ssr Markers ◽  
Genetic Linkage ◽  
Linkage Maps ◽  
Linkage Groups ◽  
Intraspecific Polymorphism ◽  
Chromosomal Origin ◽  
Genetic Linkage Maps ◽  
Genomic Regions ◽  
Simple Sequence

The construction of genetic linkage maps from intraspecific crosses of bread wheat is slow and difficult due to very limited levels of polymorphism, which hinder the assignment of linkage groups to chromosomes and leave large genomic regions without markers. Simple sequence repeats (SSRs) reveal a higher incidence of polymorphism and are more informative than any other DNA marker, and are therefore considered a marker of choice for self-pollinating crops with little intraspecific polymorphism. However, the availability of SSRs in bread wheat is still limited. In this study, selectively amplified microsatellite (SAM) analysis was used to develop informative SSR markers to assist in the construction of an intraspecific wheat map. Three markers were developed for under-represented regions in the genetic map, and 7 for unassigned linkage groups. The latter SSRs permitted the chromosomal origin of 4 unassigned linkage groups to be determined. These results demonstrate the utility of SAM analysis for the targetted development of informative SSR markers to genomic regions of interest, and assignment of linkage groups to chromosomes. Furthermore, SAM analysis facilitates the development of markers for relatively short (<11) dinucleotide repeat sequences, a class of SSRs generally inaccessible to traditional hybridisation-based methods used to develop these markers.

Transferability of cereal EST-SSR markers to ryegrass

Genome ◽  
2009 ◽  
Vol 52 (5) ◽  
pp. 431-437 ◽  
Author(s):  
Sung-Chur Sim ◽  
Ju-Kyung Yu ◽  
Young-ki Jo ◽  
Mark E. Sorrells ◽  
Geunhwa Jung
Keyword(s):  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
High Rate ◽  
Linkage Groups ◽  
Flanking Sequences ◽  
Systematic Development ◽  
Reference Sequences ◽  
High Degree ◽  
Expressed Sequence ◽  
Simple Sequence

A large number of expressed sequence tags (ESTs) in public databases have provided an opportunity for the systematic development of simple sequence repeat (SSR) markers. EST-SSRs derived from conserved coding sequences show considerable cross-species transferability in related species. In the present study, we assessed the utility of cereal EST-SSRs in ryegrass ( Lolium spp.). A total of 165 cereal EST-SSRs were tested; a high rate of transferability (57%) and polymorphism (67% of functional EST-SSRs) was demonstrated between cereals and ryegrass. A total of 46 segregating loci derived from 37 EST-SSRs were mapped on an existing ryegrass genetic map. The mapped loci were uniformly distributed across all seven linkage groups without significant clustering at the distal regions of linkage groups. Sequences of ryegrass amplicons generated by randomly selected 16 EST-SSRs were aligned with reference sequences of cereal EST-SSRs. The SSR motifs and repeat lengths of the cereal EST-SSR markers were different from the majority of ryegrass amplicons. Furthermore, a majority of EST-SSRs amplified different flanking sequences of SSRs in ryegrass than the original cereal sequences. Our results suggest that the high degree of cereal EST-SSR transferability to ryegrass can be a useful enhancement to the molecular database of PCR-based markers but sequence analysis is essential before transferring genetic information using comparative mapping.

Development of EST-SSR markers and genetic diversity analysis among three Artemia species from different geographic populations

Crustaceana ◽  
2019 ◽  
Vol 92 (7) ◽  
pp. 841-851
Author(s):  
Xuekai Han ◽  
Ruyi Xu ◽  
Yuyu Zheng ◽  
Meirong Gao ◽  
Liying Sui
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Polymorphic Information Content ◽  
Diversity Analysis ◽  
Food Items ◽  
Geographical Populations ◽  
Geographic Populations ◽  
Expressed Sequence ◽  
Simple Sequence

Abstract Artemia is one of the most important live food items used in larviculture. In order to study the genetic diversity of Artemia in China, 170 novel simple sequence repeats (SSR) markers were identified from expressed sequence tags (ESTs) of the transcriptome library of Artemia parthenogenetica. Of these, 8 microsatellite loci were developed to characterize three geographical populations of Artemia. The results showed the expected and observed heterozygosity varied from 0.43 to 0.50 and from 0.59 to 0.64, respectively. The PIC (polymorphic information content) ranged from 0.37 to 0.45. These observations indicated that the Yuncheng population has the highest genetic diversity, whereas the Shuanghu population has the lowest. The Fst value (genetic differentiation coefficient) indicated that the three populations are highly differentiated. Genetic identity analyses revealed that the Yuncheng and Shuanghu populations have the closest relationship. The SSR markers described here will serve as a valuable tool for further studies in population and conservation genetics on Artemia.

Study of simple sequence repeat (SSR) markers from wheat expressed sequence tags (ESTs)

2004 ◽  
Vol 109 (4) ◽  
pp. 800-805 ◽  
Author(s):  
N. Nicot ◽  
V. Chiquet ◽  
B. Gandon ◽  
L. Amilhat ◽  
F. Legeai ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Expressed Sequence ◽  
Simple Sequence

scholarly journals Development of Highly Polymorphic Expressed Sequence Tags-Simple Sequence Repeat Markers and Their Application in Analysis of Genetic Diversity of Chinese Bayberry (Morella rubra)

HortScience ◽  
2016 ◽  
Vol 51 (3) ◽  
pp. 227-231 ◽  
Author(s):  
Wenting Wang ◽  
Chao Feng ◽  
Zehuang Zhang ◽  
Liju Yan ◽  
Maomao Ding ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Simple Sequence Repeat ◽  
Mean Value ◽  
Sequence Repeat ◽  
Chinese Bayberry ◽  
Cultivated Populations ◽  
Expressed Sequence ◽  
Simple Sequence

Chinese bayberry (Morella rubra) is an economically important subtropical evergreen fruit crop native to China and other Asian countries. For facilitating cultivar discrimination and genetic diversity analysis, a total of 38 high-quality and highly polymorphic expressed sequence tags-simple sequence repeat (EST-SSR) markers, with little or no polymerase chain reaction (PCR) stutter bands, including 21 screened from those obtained previously and 17 newly developed markers, were developed. The average number of alleles (Na) per locus was 5.6, and polymorphism information content varied from 0.34 to 0.86, with a mean value of 0.57. With these markers, all 42 Chinese bayberry accessions analyzed were successfully discriminated and the phylogenetic relationship between accessions was revealed. The accessions can be separated into two groups with six subgroups. The grouping of four main cultivars in three subgroups and 12 white-fruited accessions, each with little or no anthocyanin accumulation in ripe fruit, into five subgroups suggested the preservation of broad diversity among cultivated populations. These EST-SSR markers and the findings obtained in this study can assist the discrimination of cultivars and lines and contribute to genetic and breeding studies in Chinese bayberry.

scholarly journals Study of simple sequence repeat markers from coffee expressed sequences associated to leaf miner resistance

2007 ◽  
Vol 42 (3) ◽  
pp. 377-384 ◽  
Author(s):  
Fernanda de Oliveira Pinto ◽  
Mirian Perez Maluf ◽  
Oliveiro Guerreiro-Filho
Keyword(s):  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Defense Mechanisms ◽  
Leaf Miner ◽  
Gene Transcript ◽  
Est Database ◽  
Hybrid Frequency ◽  
Ssr Loci ◽  
Expressed Sequence ◽  
Simple Sequence

The objective of this work was to identify expressed simple sequence repeats (SSR) markers associated to leaf miner resistance in coffee progenies. Identification of SSR markers was accomplished by directed searches on the Brazilian Coffee Expressed Sequence Tags (EST) database. Sequence analysis of 32 selected SSR loci showed that 65% repeats are of tetra-, 21% of tri- and 14% of dinucleotides. Also, expressed SSR are localized frequently in the 5'-UTR of gene transcript. Moreover, most of the genes containing SSR are associated with defense mechanisms. Polymorphisms were analyzed in progenies segregating for resistance to the leaf miner and corresponding to advanced generations of a Coffea arabica x Coffea racemosa hybrid. Frequency of SSR alleles was 2.1 per locus. However, no polymorphism associated with leaf miner resistance was identified. These results suggest that marker-assisted selection in coffee breeding should be performed on the initial cross, in which genetic variability is still significant.

Development and use of EST-SSR markers for assessing genetic diversity in the brown planthopper (Nilaparvata lugensStål)

2011 ◽  
Vol 102 (1) ◽  
pp. 113-122 ◽  
Author(s):  
S. Jing ◽  
B. Liu ◽  
L. Peng ◽  
X. Peng ◽  
L. Zhu ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Expressed Sequence Tags ◽  
Large Scale ◽  
Brown Planthopper ◽  
Nilaparvata Lugens ◽  
Rice Varieties ◽  
Genetics And Genomics ◽  
Expressed Sequence ◽  
Simple Sequence

AbstractTo assess genetic diversity in populations of the brown planthopper (Nilaparvata lugensStål) (Homoptera: Delphacidae), we have developed and applied microsatellite, or simple sequence repeat (SSR), markers from expressed sequence tags (ESTs). We found that the brown planthopper clusters of ESTs were rich in SSRs with unique frequencies and distributions of SSR motifs. Three hundred and fifty-one EST-SSR markers were developed and yielded clear bands from samples of four brown planthopper populations. High cross-species transferability of these markers was detected in the closely related planthopperN. muiri. The newly developed EST-SSR markers provided sufficient resolution to distinguish within and among biotypes. Analyses based on SSR data revealed host resistance-based genetic differentiation among different brown planthopper populations; the genetic diversity of populations feeding on susceptible rice varieties was lower than that of populations feeding on resistant rice varieties. This is the first large-scale development of brown planthopper SSR markers, which will be useful for future molecular genetics and genomics studies of this serious agricultural pest.

Sign in / Sign up

Export Citation Format

Share Document