Development of expressed sequence tag simple sequence repeat (EST-SSR) markers and genetic resource analysis of tea oil plants (Camellia spp.)

2022 ◽  
Author(s):  
Bin Dong ◽  
Zheng Deng ◽  
Wen Liu ◽  
Fazal Rehman ◽  
Tae-Jin Yang ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Genetic Resource ◽  
Expressed Sequence Tag ◽  
Sequence Repeat ◽  
Resource Analysis ◽  
Expressed Sequence ◽  
Simple Sequence

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 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 Impact of Plant Breeding on the Genetic Diversity of Cultivated Strawberry as Revealed by Expressed Sequence Tag-derived Simple Sequence Repeat Markers

2009 ◽  
Vol 134 (3) ◽  
pp. 337-347 ◽  
Author(s):  
David Jesús Gil-Ariza ◽  
Iraida Amaya ◽  
José Manuel López-Aranda ◽  
José Federico Sánchez-Sevilla ◽  
Miguel Ángel Botella ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Expressed Sequence Tag ◽  
Natural Populations ◽  
Group Method ◽  
Sequence Repeat ◽  
Expressed Sequence ◽  
Simple Sequence ◽  
Strawberry Cultivars

Unlike other important crops analyzed so far for genetic diversity and population structure, the brief history and particularities of the genetics of the cultivated strawberry (Fragaria ×ananassa Duchesne) have limited its genetic characterization. The genomic composition and the pattern of inheritance have not been fully elucidated, although a number of studies have suggested a highly diploidized genome. In this study, the similarity relationships and structure of 92 selected strawberry cultivars with widely diverse origins have been established using simple sequence repeat (SSR) markers derived from expressed sequence tags (EST-SSR markers). Genetic analysis performed by the unweighted pair group method with arithmetic mean clustering revealed a distribution according to both date of cultivar release and breeding for a specific climatic adaptation. Additionally, a model-based clustering approach identified three populations among the strawberry cultivars with an overall FST value of 0.15 to 0.16. Both analyses support a limited differentiation of modern cultivars, most probably as a consequence of the methodology of strawberry breeding. Interestingly, the collection of strawberry cultivars here analyzed showed comparable genetic differentiation to that observed in natural populations of Fragaria chiloensis (L.) Mill., one of its wild ancestors. Our results suggest that breeding has produced a small but significant reduction on the genetic diversity of F. ×ananassa. The panel of 10 EST-SSRs described in this work provided an extremely low probability of confusion (less than 10−11), offering an efficient and accurate method for cultivar identification.

Characterization of expressed sequence tag-derived simple sequence repeat markers for 17 Linum species

Botany ◽  
2010 ◽  
Vol 88 (5) ◽  
pp. 537-543 ◽  
Author(s):  
Yong-Bi Fu ◽  
Gregory W. Peterson
Keyword(s):  
Simple Sequence Repeat ◽  
Expressed Sequence Tag ◽  
Sequence Repeat ◽  
Simple Sequence Repeat Markers ◽  
Linum Usitatissimum L ◽  
Evolutionary Studies ◽  
Expressed Sequence ◽  
Simple Sequence ◽  
Cultivated Flax

One major challenge in genetic and evolutionary studies of wild flax species is the lack of informative molecular markers. A set of 100 informative expressed sequence tag-derived simple sequence repeat (EST-SSR) primer pairs developed in cultivated flax ( Linum usitatissimum L.) were characterized on 35 Linum accessions representing 17 Linum species for their transferability to other Linum species. Ninety-nine primer pairs displayed scorable polymorphisms across 35 Linum samples and generated 627 bands likely from 121 loci. About 50% of the detected bands occurred only in three or fewer samples. A total of 393 bands, likely from 116 loci, were detected by 97 primer pairs in Linum bienne Mill. samples, but only up to 60 bands, likely from up to 39 loci, were revealed by 6 to 37 primer pairs in the samples of the other 15 Linum species. The L. bienne samples displayed 23.7% more EST-SSR variation than the L. usitatissimum samples. These characterized EST-SSR markers should be useful for future genetic diversity and evolutionary studies of Linum species, particularly for the progenitor of cultivated flax.

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