scholarly journals Characterization and Development of Genomic SSRs in Pecan (Carya illinoinensis)

Forests ◽  
2020 ◽  
Vol 11 (1) ◽  
pp. 61 ◽  
Author(s):  
Chengcai Zhang ◽  
Xiaohua Yao ◽  
Huadong Ren ◽  
Jun Chang ◽  
Jun Wu ◽  
...  
Keyword(s):  
Genetic Study ◽  
Polymorphic Information Content ◽  
Genetic Research ◽  
Geographic Origin ◽  
Pcr Amplification ◽  
Genetic Studies ◽  
New Development ◽  
Ssr Loci ◽  
Simple Sequence

Research Highlights: The distribution of simple sequence repeat (SSR) motifs in two draft genomes of pecan was evaluated. Sixty-six SSR loci were validated by PCR amplification in pecan. Twenty-two new development markers can be used for genetic study in genus Carya. Background and Objectives: Pecan has good nutritional and health benefits and is an important crop worldwide. However, the genetic research in this species is insufficient. One of the main reasons for this is the lack of enough accurate, convenient, and economical molecular markers. Among different marker types, SSR loci are enormously useful in genetic studies. However, the number of SSRs in C. illinoinensis (Wangenh.) K. Koch is limited. Materials and Methods: The distribution of SSR motifs in the pecan genome was analyzed. Then, the primers for each SSR were designed. To evaluate their availability, 74 SSR loci were randomly selected and amplified in pecan. Finally, 22 new SSRs and eight former ones were picked to evaluate the genetic diversity in 60 pecan genotypes and to determine their transferability in other Carya species. Results: 145,714 and 143,041 SSR motifs were obtained from two draft genomes of ‘87MX3-2’ and ‘Pawnee’, respectively. In total, 9145 candidate primers were obtained. Sixty-six (89.19%) primers amplified the target products. Among the 30 SSRs, 29 loci showed polymorphism in 60 pecan genotypes. The polymorphic information content (PIC) values ranged from 0.012 to 0.906. In total, 26, 25, and 22 SSRs can be used in C. cathayensis Sarg., C. dabieshanensis W. C. Cheng & R. H. Chang, and C. hunanensis W.C. Liu, respectively. Finally, the dendrogram of all individuals was constructed. The results agree with the geographic origin of the four species and the pedigree relationships between different pecan cultivars. Conclusions: The characterization of SSRs in the pecan genome and the new SSRs will promote the progress of genetic study and breeding in pecan, as well as other species of genus Carya.

scholarly journals Diversity Among a Wide Asian Collection of Bitter Gourd Landraces and their Genetic Relationships with Commercial Hybrid Cultivars

2016 ◽  
Vol 141 (5) ◽  
pp. 475-484 ◽  
Author(s):  
Narinder P.S. Dhillon ◽  
Supannika Sanguansil ◽  
Roland Schafleitner ◽  
Yen-Wei Wang ◽  
James D. McCreight
Keyword(s):  
Genetic Relationships ◽  
Geographic Origin ◽  
Bitter Gourd ◽  
Breeding Lines ◽  
Ssr Loci ◽  
Geographical Group ◽  
Dark Green ◽  
High Level ◽  
Simple Sequence

We report here the genetic characterization of bitter gourd (Momordica charantia) based on polymorphisms of 50 simple sequence repeat (SSR) loci in 114 accessions that included landraces, breeding lines, and commercial open-pollinated and F1 hybrid cultivars widely grown in Asia. Neighbor-joining tree analysis revealed a high level of genetic variability in the collection. The 114 accessions formed three subpopulations represented by five clusters. Distribution of accessions across the five clusters reflected their geographic origin to a large extent. South Asian accessions originating from India, Bangladesh, and Pakistan were more closely related to each other than to any other geographical group. Likewise, southeast Asian accessions that originated from Cambodia, Vietnam, Indonesia, and Philippines were grouped together. Accessions that originated from Taiwan were genetically distinct and grouped separately. A landrace from Laos was genetically close to the accessions from Thailand and genetically distinct from the rest of the accessions. White-fruited genotypes were genetically distinct from green- and dark green–fruited genotypes. Low- and medium-bitter accessions were more similar to each other than to the high-bitter genotypes. Accessions with cylindrical fruit were genetically distinct from those with spindle or elongated fruit. Commercial cultivars in each cluster were closely related, which indicated a narrowing of the bitter gourd genetic base in Asia in response to market demands for uniformity and yield. Use of diverse germplasm resources in bitter gourd breeding will help in sustainable breeding and production.

scholarly journals Characterization of a Suite of 40 EST-derived Microsatellite Markers For Use in Sitka Spruce (Picea sitchensis (Bong.) Carr)

2007 ◽  
Vol 56 (1-6) ◽  
pp. 138-141 ◽  
Author(s):  
S. W. A’Hara ◽  
J. E. Cottrell
Keyword(s):  
Pcr Amplification ◽  
Pcr Primers ◽  
Sitka Spruce ◽  
Mendelian Inheritance ◽  
Picea Sitchensis ◽  
Genetic Population ◽  
Genetic Studies ◽  
Polymorphic Microsatellite ◽  
Simple Sequence

Abstract This paper describes 40 novel, data-mined, polymorphic microsatellite loci for use in a QTL association study in Sitka spruce. Publicly available EST sequences of Picea in Genbank were searched in silico for simple sequence repeat (SSR) motifs, principally dinucleotide microsatellites, and PCR primers were designed to flank these regions. PCR amplification was carried out in the progeny of a full-sib family to test simple Mendelian inheritance. For further characterization, the amplification products of Sitka spruce material from unrelated trees were assessed to determine the potential of these loci for population genetic studies. These polymorphic markers therefore represent a valuable tool-kit both for establishing a molecular map of this species and for Picea genetic population studies.

scholarly journals Development and characterization of fifteen polymorphic microsatellite loci in Bryconamericus aff. iheringii (Teleostei: Characidae) and cross-amplification in related Characidae species

2018 ◽  
Vol 16 (1) ◽  
Author(s):  
Caroline Apolinário-Silva ◽  
Dhiego G. Ferreira ◽  
Analiza F. Cavenagh ◽  
Nícollas G. O. Aprígio ◽  
Bruno A. Galindo ◽  
...  
Keyword(s):  
Information Content ◽  
Microsatellite Loci ◽  
Polymorphic Information Content ◽  
Neotropical Fish ◽  
Genetic Studies ◽  
Cross Amplification ◽  
Abstract Data ◽  
Polymorphic Microsatellite

ABSTRACT Data on 15 novel microsatellite loci from the Neotropical fish Bryconamericus aff. iheringii are presented here. Analyses of 32 individuals from four different streams revealed 192 different alleles, ranging from four to 32 alleles per locus (mean of 12.8 per locus). Observed and expected heterozygosities ranged from 0.094 to 0.813 and 0.205 to 0.952, respectively. These loci showed high polymorphic information content and will be a resource for genetic studies of B. aff. iheringii. Furthermore, several loci also amplified other small Neotropical Characidae (Piabarchus stramineus and Piabina argentea) and should be useful for these species.

scholarly journals Molecular characterization of Trypanosoma cruzi Mexican strains and their behavior in the mouse experimental model

2011 ◽  
Vol 44 (6) ◽  
pp. 684-690 ◽  
Author(s):  
César Gómez-Hernández ◽  
Karine Rezende-Oliveira ◽  
Gabriel Antônio Nogueira Nascentes ◽  
Lara Rocha Batista ◽  
Henrique Borges Kappel ◽  
...  
Keyword(s):  
Trypanosoma Cruzi ◽  
Chagas Disease ◽  
Random Amplified Polymorphic Dna ◽  
Geographic Origin ◽  
Pcr Amplification ◽  
Biological Characterization ◽  
Long Time ◽  
Intergenic Regions ◽  
Mexican Strains

INTRODUCTION: For a long time, the importance of Chagas disease in Mexico, where many regarded it as an exotic malady, was questioned. Considering the great genetic diversity among isolates of Trypanosoma cruzi, the importance of this biological characterization, and the paucity of information on the clinical and biological aspects of Chagas disease in Mexico, this study aimed to identify the molecular and biological characterization of Trypanosoma cruzi isolates from different endemic areas of this country, especially of the State of Jalisco. METHODS: Eight Mexican Trypanosoma cruzi strains were biologically and genetically characterized (PCR specific for Trypanosoma cruzi, multiplex-PCR, amplification of space no transcript of the genes of the mini-exon, amplification of polymorphic regions of the mini-exon, classification by amplification of intergenic regions of the spliced leader genes, RAPD - (random amplified polymorphic DNA). RESULTS: Two profiles of parasitaemia were observed, patent (peak parasitaemia of 4.6×10(6) to 10(7) parasites/mL) and subpatent. In addition, all isolates were able to infect 100% of the animals. The isolates mainly displayed tropism for striated (cardiac and skeletal) muscle. PCR amplification of the mini-exon gene classified the eight strains as TcI. The RAPD technique revealed intraspecies variation among isolates, distinguishing strains isolated from humans and triatomines and according to geographic origin. CONCLUSIONS: The Mexican T. cruzi strains are myotrophic and belong to group TcI.

scholarly journals Genome-Wide Characterization of Simple Sequence Repeat (SSR) Loci in Chinese Jujube and Jujube SSR Primer Transferability

PLoS ONE ◽  
2015 ◽  
Vol 10 (5) ◽  
pp. e0127812 ◽  
Author(s):  
Jing Xiao ◽  
Jin Zhao ◽  
Mengjun Liu ◽  
Ping Liu ◽  
Li Dai ◽  
...  
Keyword(s):  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Chinese Jujube ◽  
Genome Wide ◽  
Ssr Loci ◽  
Simple Sequence

Data Mining for Simple Sequence Repeats in Expressed Sequence Tags from Japanese Flounder (Paralichthys olivaceus)

2013 ◽  
Vol 765-767 ◽  
pp. 274-277
Author(s):  
Song Bo Chen ◽  
Xin Lu Xie ◽  
Gong Li ◽  
Hai Jin Liu
Keyword(s):  
Genome Mapping ◽  
Average Distance ◽  
Paralichthys Olivaceus ◽  
Japanese Flounder ◽  
Genetic Studies ◽  
Dominant Type ◽  
The Public ◽  
Ssr Loci ◽  
Expressed Sequence ◽  
Simple Sequence

Based on ESTs of Japanese flounder (Paralichthys olivaceus) in the public database, EST-SSR makers were developed after mining and evaluating SSRs in them by bioinformatics methods. 5 927 non-redundant ESTs of Japanese flounder were screened and 390 SSRs were mined out. The frequency of these EST-SSRs was 7.95% and the average distance of distribution was 7.9 kb in non-redundant ESTs. The dinucleotide repest motif was dominant type (59.02%) with repeat motif AC being the most common (16.91%). The distribution of trinucleotide, tetranucleotide and hexanucleotide repeats were dispersive. 30 primer pairs for EST-SSRs were designed, 27 primer pairs showed the amplification, and 17 primer pairs showed polymorphisms, the rates of polymorphic EST-SSRs were 62.96% with the alleles per locus ranging from 2 to 6 (mean 3.5). The observed (HO) and expected (HE) heterozygosities of these EST-SSRs were 0.280.92 and 0.31550.8033, respectively. Two EST-SSR loci significantly deviated from the HardyWeinberg equilibrium (HWE) expectation, and theremaining 15 loci were in HWE. These new EST-SSR markers would provide sufficient polymorphism for population genetic studies and genome mapping of Japanese flounder.

Cross-species amplification and characterization of microsatellite loci in Pinus mugo Turra

Biologia ◽  
2013 ◽  
Vol 68 (4) ◽  
Author(s):  
Konrad Celiński ◽  
Ewa Pawlaczyk ◽  
Aleksandra Wojnicka-Półtorak ◽  
Ewa Chudzińska ◽  
Wiesław Prus-Głowacki
Keyword(s):  
Microsatellite Markers ◽  
Polymorphic Information Content ◽  
Pinus Mugo ◽  
Genetic Studies ◽  
Transfer Rates ◽  
Isolation And Characterization ◽  
Nuclear Microsatellite ◽  
European Mountain ◽  
High Level

AbstractPinus mugo (dwarf mountain pine) is an important component of European mountain ecosystems. However, little is known about the present genetic structure and population differentiation of this species at the DNA level, possibly due to a lack of nuclear microsatellite markers (SSR) developed for Pinus mugo. Therefore in this study we transferred microsatellite markers originally developed for Pinus sylvestris and Pinus taeda to Pinus mugo. This cross-species amplification approach is much faster and less expensive than isolation and characterization of new microsatellite markers. The transfer rates from the source species to Pinus mugo were moderately low (26%). There were no differences in microsatellite repeat motifs between the source species and Pinus mugo. Nuclear microsatellite markers successfully transferred to Pinus mugo can be applied to various genetic studies on this species, due to the high level of their polymorphism and high value of polymorphic information content.

scholarly journals Development of microsatellite markers for the genetic analysis of Magnaporthe grisea

2000 ◽  
Vol 23 (4) ◽  
pp. 753-762 ◽  
Author(s):  
Claudio Brondani ◽  
Rosana Pereira Vianello Brondani ◽  
Lucas da Ressurreição Garrido ◽  
Márcio Elias Ferreira
Keyword(s):  
Magnaporthe Grisea ◽  
Pcr Amplification ◽  
Polymorphism Analysis ◽  
Single Spore ◽  
Genetic Studies ◽  
Central Brazil ◽  
Dna Library ◽  
Ssr Loci ◽  
Genomic Dna Library ◽  
Microsatellite Alleles

An AG microsatellite-enriched genomic DNA library was constructed for Magnaporthe grisea (anamorph Pyricularia grisea), the causal agent of rice blast. Seventy-two DNA clones containing microsatellite repeats were isolated and sequenced in order to develop a series of new PCR-based molecular markers to be used in genetic studies of the fungus. Twenty-four of these clones were selected to design primer pairs for the PCR amplification of microsatellite alleles. Single spore cultures of M. grisea isolated from rice and wheat in Brazil, Colombia and China were genotyped at three microsatellite loci. Isolates from southern Brazil were predominantly monomorphic at the tested SSR loci, indicating a low level of genetic variability in these samples. However, seven alleles were observed at the MGM-1 locus in isolates from Central Brazil and at least nine alleles were detected at the same locus in a sample of Colombian isolates. Polymorphism analysis at SSR loci is a simple and direct approach for estimating the genetic diversity of M. grisea isolates and a powerful tool for studying M. grisea genetics.

Familial Bipolar Disorder: Preliminary Results from the Otago Familial Bipolar Genetic Study

1998 ◽  
Vol 32 (6) ◽  
pp. 823-829 ◽  
Author(s):  
Liza K. Edmonds ◽  
Barbara J. Mosley ◽  
Anita J. Admiraal ◽  
Robin J. Olds ◽  
Sarah E. Romans ◽  
...  
Keyword(s):  
Bipolar Disorder ◽  
New Zealand ◽  
Panic Disorder ◽  
Genetic Study ◽  
Suicidal Behaviour ◽  
Age Of Onset ◽  
Genetic Research ◽  
Genetic Studies ◽  
Compulsive Disorder ◽  
First Degree Relatives

Objective: This paper outlines the methodologies used, and preliminary descriptive data collected, on a cohort of familial bipolar disorder (BPD) probands and first-degree relatives taking part in a descriptive and genetic study into familial BPD in New Zealand. Method: Fifity-five bipolar probands and 67 first-degree relatives were interviewed using the modified Diagnostic Interview for Genetic Studies (DIGS) and Family Interview for Genetic Studies (FIGS). Data was also collated from other sources. Blood samples were taken for DNA genomic analysis. Results: New Zealand families in which BPD segregates proved willing participants in this familial based genetic research. The methodologies used were acceptable. High rates of comorbidity were found in probands (27.3% met DSM-IV criteria for panic disorder/sub-threshold panic disorder; 12.7% for phobic disorder; 1.8% for obsessive-compulsive disorder; 9.1% for alcohol-related disorders and 7.3% for an eating disorder) and relatives (major depression 34.3%; panic disorder/sub-threshold panic disorder 12.0%; phobias 11.9% and alcohol-related disorders 11.9%). The polarity of index BPD illness was related to age of onset and frequency of comorbidity. Suicidal behaviour was common. Conclusions: Psychiatric genetic research in New Zealand families is highly feasible. Emerging trends in the familial transmission of BPD include high rates of comorbidity, illness patterns based on polarity of index episode and frequent suicidal behaviour. Such trends will be delineated further as numbers accrue, perhaps enabling identification of more homogenous phenotypic subgroups than currently produced by diagnostic schemes.

scholarly journals Development and Application of Genic Simple Sequence Repeat Markers from the Transcriptome of Loquat

2014 ◽  
Vol 139 (5) ◽  
pp. 507-517 ◽  
Author(s):  
Xiaoying Li ◽  
Hongxia Xu ◽  
Jianjun Feng ◽  
Junwei Chen
Keyword(s):  
Large Scale ◽  
Trinucleotide Repeat ◽  
Genetic Relationships ◽  
Pcr Amplification ◽  
Eriobotrya Japonica ◽  
Pcr Products ◽  
Ssr Loci ◽  
Trait Locus ◽  
High Level ◽  
Simple Sequence

Deep transcriptome sequencing allows for the acquisition of large-scale microsatellite information, and it is especially useful for genetic diversity analysis and mapping in plants without reference genome sequences. In this study, a total of 14,004 simple sequence repeats (SSRs) were mined from 10,511 unigenes screening of 63,608 nonredundant transcriptome unigenes in loquat (Eriobotrya japonica) with a frequency of 22 SSR loci distributed over 100 unigenes. Dinucleotide and trinucleotide repeat SSRs were dominant, accounting for 20.62%, and 42.1% of the total, respectively. Seventy primer pairs were designed from partial SSRs and used for polymerase chain reaction (PCR) amplification. Of these primer pairs, 54 exhibited amplification and 33 were polymorphic. The number of alleles at these loci ranged from two to 17, and the polymorphism information content values ranged from 0.24 to 0.89. We tested the transferability of 33 SSR polymorphic primer pairs in apple and pear, and the transferability rates in these two species were 90.9% and 87.9%, respectively. A high level of marker polymorphism was observed in apple [Malus ×domestica (66.7%)], whereas a low level was observed in pear [Pyrus sp. (51.5%)]. In addition, the PCR products from seven SSR primer pairs were selected for sequence analysis, and 89.2% of the fragments were found to contain SSRs. SSR motifs were conserved among loquat, apple, and pear. According to our sequencing results for real SSR loci, ≈12,490 SSR loci were present in these loquat unigenes. The cluster dendrogram showed a distinct separation into different groups for these three species, indicating that these SSR markers were useful in the evaluation of genetic relationships and diversity between and within the species of Maloideae in the Rosaceae. The results of our identified SSRs should be useful for genetic linkage map construction, quantitative trait locus mapping, and molecular marker-assisted breeding of loquat and related species.

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