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.

scholarly journals The application of high resolution melting in the analysis of simple sequence repeat and single nucleotide polymorphism markers in a pea (Pisum sativum L.) population

2014 ◽  
Vol 50 (No. 2) ◽  
pp. 151-156 ◽  
Author(s):  
M. Knopkiewicz ◽  
M. Gawłowska ◽  
W. Święcicki
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
High Resolution Melting ◽  
Melting Curve ◽  
Sequence Repeat ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Pisum Sativum L ◽  
Pcr Product ◽  
Simple Sequence

The aim of this study was to verify the high resolution melting (HRM) method in the analysis of single nucleotide polymorphism (SNP) and simple sequence repeat (SSR) markers in pea (Pisum sativum L.). A recombinant inbred line population, Carneval × MP1401, was tested for three SNP and 103 SSR markers. HRM analysis was conducted on a LightScanner 96 instrument with LC Green dye. The melting curve shape permitted two polymorphic genotypes to be distinguished. The results were confirmed by gel electrophoresis. Three SSR markers were sequenced and analysed by the melting prediction software. The results confirmed the presence of one polymerase chain reaction (PCR) product with two melting domains. Sequence tagged site (STS) markers produced specific products: Psat_EST_00189_01_1 (300 bp), Pis_GEN_18_2_1 (400 bp), Pis_GEN_7_1-2_1 (600 bp). Amplicons contained one, four and seven single nucleotide polymorphisms, respectively. Melting curve differences enabled the population genotyping except for Psat_EST_00189_01_1 where resolution was too low. Primers for Psat_EST_00189_01_1 were redesigned to obtain a shorter (100 bp) PCR product which increased the resolution. The number of SNPs and amplicon length are crucial for HRM resolution. The HRM method is fast and has a high throughput. The melting analysis of 96 samples takes less than 10 min. Agarose gel analysis confirmed the reliability of HRM, which eliminates laborious post-PCR analysis.

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.

Development of simple sequence repeat markers for bermudagrass from its expressed sequence tag sequences and preexisting sorghum SSR markers

2010 ◽  
Vol 29 (1) ◽  
pp. 23-30 ◽  
Author(s):  
Chengcheng Tan ◽  
Yanqi Wu ◽  
Charles M. Taliaferro ◽  
Michael P. Anderson ◽  
Chuck Tauer ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Expressed Sequence Tag ◽  
Sequence Repeat ◽  
Simple Sequence Repeat Markers ◽  
Expressed Sequence ◽  
Simple Sequence

scholarly journals Genetic Diversity, Population Structure, and Parentage Analysis of Croatian Grapevine Germplasm

Genes ◽  
2020 ◽  
Vol 11 (7) ◽  
pp. 737
Author(s):  
Maja Žulj Mihaljević ◽  
Edi Maletić ◽  
Darko Preiner ◽  
Goran Zdunić ◽  
Marijan Bubola ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Single Nucleotide Polymorphism ◽  
Simple Sequence Repeat ◽  
Genetic Erosion ◽  
Parentage Analysis ◽  
Snp Markers ◽  
Sequence Repeat ◽  
Nucleotide Polymorphism ◽  
Single Nucleotide ◽  
Simple Sequence

Croatian viticulture was most extensive at the beginning of the 20th century, when about 400 varieties were in use. Autochthonous varieties are the result of spontaneous hybridization from the pre-phylloxera era and are still cultivated today on about 35 % of vineyard area, while some exist only in repositories. We present what is the most comprehensive genetic analysis of all major Croatian national repositories, with a large number of microsatellite, or simple sequence repeat (SSR) markers, and it is also the first study to apply single nucleotide polymorphism (SNP) markers. After 212 accessions were fingerprinted, 95 were classified as unique to Croatian germplasm. Genetic diversity of Croatian germplasm is rather high considering its size. SNP markers proved useful for fingerprinting but less informative and practical than SSRs. Analysis of the genetic structure showed that Croatian germplasm is predominantly part of the Balkan grape gene pool. A high number of admixed varieties and synonyms is a consequence of complex pedigrees and migrations. Parentage analysis confirmed 24 full parentages, as well as 113 half-kinships. Unexpectedly, several key genitors could not be detected within the present Croatian germplasm. The low number of reconstructed parentages (19%) points to severe genetic erosion and stresses the importance of germplasm repositories.

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