scholarly journals Development of EST-derived SSR Markers with Long-core Repeat in Olive and Their Use for Paternity Testing

2013 ◽  
Vol 138 (4) ◽  
pp. 290-296 ◽  
Author(s):  
Raúl De la Rosa ◽  
Angjelina Belaj ◽  
Antonio Muñoz-Mérida ◽  
Oswaldo Trelles ◽  
Inmaculada Ortíz-Martín ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Expressed Sequence Tag ◽  
Paternity Testing ◽  
High Level ◽  
Repeated Motifs ◽  
Expressed Sequence ◽  
Simple Sequence ◽  
Olive Breeding ◽  
Genomic Project

In the present work, a set of eight new hexa-nucleotide simple sequence repeats (SSRs) is reported in olive (Olea europaea L). These SSRs loci were generated on the basis of expressed sequence tag (EST) sequences in the frame of an olive genomic project. The markers showed a high level of polymorphism when tested on a set of cultivars used as genitors in the olive breeding program of Córdoba, Spain. The long-core repeat motif of these markers allows a wider separation among alleles, thus permitting an accurate genotyping. Besides, these markers showed comparable levels of polymorphism to di-nucleotide SSRs, the only ones so far reported in olive. Selected on the basis of their discrimination capacity, four of the eight SSRs were used to test their ability for paternity testing in a total of 81 seedlings coming from 12 crosses. The paternity testing showed that seven crosses matched the alleged paternity and the remaining five were products of illicit pollinations. These results exactly matched with previous paternity testing performed with di-nucleotide SSR markers. These results demonstrate the usefulness of the developed hexa-nucleotide repeated motifs for checking the paternity of breeding progenies and suggest their use on variability studies.

scholarly journals Novel Expressed Sequence Tag-Derived and Other Genomic Simple Sequence Repeat Markers Revealed Genetic Diversity in Ethiopian Finger Millet Landrace Populations and Cultivars

2021 ◽  
Vol 12 ◽  
Author(s):  
Haftom Brhane ◽  
Teklehaimanot Haileselassie ◽  
Kassahun Tesfaye ◽  
Cecilia Hammenhag ◽  
Rodomiro Ortiz ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Finger Millet ◽  
Expressed Sequence Tag ◽  
Gene Diversity ◽  
Geographic Regions ◽  
Landrace Accessions ◽  
Expressed Sequence ◽  
Simple Sequence

Finger millet (Eleusine coracana (L.) Geartn.) is a self-pollinating amphidiploid crop cultivated with minimal input for food and feed, as well as a source of income for small-scale farmers. To efficiently assess its genetic diversity for conservation and use in breeding programs, polymorphic DNA markers that represent its complex tetraploid genome have to be developed and used. In this study, 13 new expressed sequence tag-derived simple sequence repeat (EST-SSR) markers were developed based on publicly available finger millet ESTs. Using 10 polymorphic SSR markers (3 genomic and 7 novel EST-derived), the genetic diversity of 55 landrace accessions and 5 cultivars of finger millet representing its major growing areas in Ethiopia was assessed. In total, 26 alleles were detected across the 10 loci, and the average observed number of alleles per locus was 5.6. The polymorphic information content (PIC) of the loci ranged from 0.045 (Elco-48) to 0.71 (UGEP-66). The level of genetic diversity did not differ much between the accessions with the mean gene diversity estimates ranging only from 0.44 (accession 216054) to 0.68 (accession 237443). Similarly, a narrow range of variation was recorded at the level of regional states ranging from 0.54 (Oromia) to 0.59 (Amhara and Tigray). Interestingly, the average gene diversity of the landrace accessions (0.57) was similar to that of the cultivars (0.58). The analysis of molecular variance (AMOVA) revealed significant genetic variation both within and among accessions. The variation among the accessions accounted for 18.8% of the total variation (FST = 0.19; P < 0.001). Similarly, significant genetic variation was obtained among the geographic regions, accounting for 6.9% of the total variation (P < 0.001). The results of the cluster, principal coordinate, and population structure analyses suggest a poor correlation between the genetic makeups of finger millet landrace populations and their geographic regions of origin, which in turn suggests strong gene flow between populations within and across geographic regions. This study contributed novel EST-SSR markers for their various applications, and those that were monomorphic should be tested in more diverse finger millet genetic resources.

scholarly journals Genetic Diversity Analysis and Single-nucleotide Polymorphism Marker Development in Cultivated Bulb Onion Based on Expressed Sequence Tag–Simple Sequence Repeat Markers

2008 ◽  
Vol 133 (6) ◽  
pp. 810-818 ◽  
Author(s):  
John McCallum ◽  
Susan Thomson ◽  
Meeghan Pither-Joyce ◽  
Fernand Kenel ◽  
Andrew Clarke ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Expressed Sequence Tag ◽  
Snp Markers ◽  
Sequence Repeat ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Bulb Onion ◽  
Expressed Sequence ◽  
Simple Sequence

Bulb onion (Allium cepa L.) is a globally significant crop, but the structure of genetic variation within and among populations is poorly understood. We broadly surveyed genetic variation in a cultivated onion germplasm using simple sequence repeat (SSR) markers and sequenced regions flanking expressed sequence tag (EST)-SSRs to develop single-nucleotide polymorphism (SNP) markers. Samples from 89 inbred and open-pollinated (OP) bulb onion populations of wide geographical adaptation and four related Allium L. accessions were genotyped with 56 EST-SSR and four genomic SSR markers. Multivariate analysis of genetic distances among populations resolved long-day, short-day, and Indian populations. EST-SSR markers frequently revealed two major alleles at high frequency in OP populations. The median proportion of single-locus polymorphic loci was 0.70 in OP and landrace populations compared with 0.43 in inbred lines. Resequencing of 24 marker amplicons revealed additional SNPs in 17 (68%) and five SNP assays were developed from these, suggesting that resequencing of EST markers can readily provide SNP markers for purity testing of inbreds and other applications in Allium genetics.

Development of EST–SSR markers in castor bean (Ricinus communis L.) and their utilization for genetic purity testing of hybrids

Genome ◽  
2011 ◽  
Vol 54 (8) ◽  
pp. 684-691 ◽  
Author(s):  
B. Pranavi ◽  
G. Sitaram ◽  
K.N. Yamini ◽  
V. Dinesh Kumar
Keyword(s):  
Ssr Markers ◽  
Castor Bean ◽  
Expressed Sequence Tag ◽  
Ricinus Communis ◽  
Rapid Development ◽  
Genetic Purity ◽  
Ricinus Communis L ◽  
Purity Testing ◽  
Expressed Sequence ◽  
Simple Sequence

Expressed sequence tag (EST) databases offer opportunity for the rapid development of simple sequence repeat (SSR) markers in crops. Sequence assembly and clustering of 57 895 ESTs of castor bean resulted in the identification of 10 960 unigenes (6459 singletons and 4501 contigs) having 7429 SSRs. On an average, the unigenes contained 1 SSR for every 1.23 kb of unigene sequence. The identified SSRs mostly consisted of dinucleotide (62.4%) and trinucleotide (33.5%) repeats. The AG class was the most common among the dinucleotide motifs (68.9%), whereas the AAG class (25.9%) was predominant among the trinucleotide motifs. A total of 611 primer pairs were designed for the SSRs, having repeat length more than or equal to 20 nucleotides, of which a set of 130 markers were tested and 92 of these yielding robust amplicons were analyzed for their utility in genetic purity assessment of castor bean hybrids. Nine markers were able to detect polymorphism between the parental lines of nine commercial castor bean hybrids (DCH-32, DCH-177, DCH-519, GCH-2, GCH-4, GCH-5, GCH-6, GCH-7, and RHC-1), and their utility in genetic purity testing was demonstrated. These novel EST–SSR markers would be a valuable addition to the growing molecular marker resources that could be used in genetic improvement programmes of castor bean.

scholarly journals Verification of Mandarin and Pummelo Somatic Hybrids by Expressed Sequence Tag–Simple Sequence Repeat Marker Analysis

2008 ◽  
Vol 133 (6) ◽  
pp. 794-800 ◽  
Author(s):  
Chunxian Chen ◽  
Jude W. Grosser ◽  
Milica Ćalović ◽  
Patricia Serrano ◽  
Gemma Pasquali ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Breeding System ◽  
Simple Sequence Repeat ◽  
Expressed Sequence Tag ◽  
Somatic Hybrids ◽  
Poncirus Trifoliata ◽  
Sequence Repeat ◽  
Expressed Sequence ◽  
Simple Sequence

Somatic hybridization is a powerful tool for the genetic improvement of citrus rootstocks, and it is part of an efficient in vitro-based breeding system described here. An essential component of the system is the requirement of confirming tetraploidy and the combination of the two donor genomes. Expressed sequence tag–simple sequence repeat (EST-SSR) markers provide a means to accomplish both of these objectives, and their application to a population of pummelo [Citrus grandis (L.) Osbeck] + mandarin (C. reticulata Blanco) somatic hybrids developed for the specific purpose of providing alternative rootstocks for sour orange (Citrus aurantium L.) is detailed. Nineteen new somatic hybrids were produced from various mandarin and pummelo parents, and their ploidy level and the complementation of their nuclear genomes were confirmed using four EST-SSR markers. These markers were selected from markers previously mapped in sweet orange [C. sinensis (L.) Osbeck] and trifoliate orange [Poncirus trifoliata (L.) Raf.] and prescreened for suitable allelic polymorphism within the mandarin and pummelo lines used. After polymerase chain reaction amplification of sequences from the parents and putative hybrids, the products were separated on a genetic sequencer and visualized electronically. Additionally, EST-SSR markers identified the unexpected zygotic origin of a presumed nucellar embryogenic callus line. Integration of EST-SSR techniques for high-throughput genotyping with previously developed approaches to somatic hybrid creation increases substantially the effectiveness and efficiency of this in vitro-based breeding system for citrus rootstock improvement.

Assessment of the genetic diversity and phylogenetic relationships of a temperate bamboo collection by using transferred EST-SSR markers

Genome ◽  
2005 ◽  
Vol 48 (4) ◽  
pp. 731-737 ◽  
Author(s):  
N A Barkley ◽  
M L Newman ◽  
M L Wang ◽  
M W Hotchkiss ◽  
G A Pederson
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Phylogenetic Relationships ◽  
Expressed Sequence Tag ◽  
Genetic Distances ◽  
Group Method ◽  
Arithmetic Means ◽  
Pair Group ◽  
Expressed Sequence ◽  
Simple Sequence

Polymorphic expressed sequence tag - simple sequence repeat (EST-SSR) markers derived from major cereal crops were used to assess the genetic diversity of the USDA temperate bamboo collection consisting of 92 accessions classified in 11 separate genera and 44 species. A total of 211 bands were detected with a mean number of alleles per locus of 8.440. Phylogenetic relationships were determined by calculating genetic distances between all pairwise combinations and assessing differences in character data. The resulting dendrograms (unweighted pair group method with arithmetic means (UPGMA) and parsimony) clustered the accessions into 2 main clades, which corresponded to accessions characterized morphologically as either clumping (sympodial) or running (monopodial) bamboos. The majority of the accessions clustered according to their current taxonomic classification. These markers were also beneficial in identifying contaminated and (or) misidentified plots. Overall, these transferred markers were informative in differentiating the various bamboo accessions and determining the level of genetic variation within and among species and genera.Key words: bamboo germplasm, genetic diversity, phylogeny.

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