Genetic diversity and structure of Pinus dabeshanensis revealed by expressed sequence tag-simple sequence repeat (EST-SSR) markers

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.

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

Frontiers in Plant Science ◽

10.3389/fpls.2021.735610 ◽

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.

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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 ◽

10.21273/hortsci.51.3.227 ◽

2016 ◽

Vol 51 (3) ◽

pp. 227-231 ◽

Cited By ~ 1

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.

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

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.133.6.810 ◽

2008 ◽

Vol 133 (6) ◽

pp. 810-818 ◽

Cited By ~ 33

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.

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Characterization of novel developed expressed sequence tag (EST)-derived simple sequence repeat (SSR) markers and their application in diversity analysis of eggplant

AFRICAN JOURNAL OF BIOTECHNOLOGY ◽

10.5897/ajb11.1029 ◽

2011 ◽

Vol 10 (45) ◽

pp. 9023-9031 ◽

Cited By ~ 5

Author(s):

Ge Haiyan ◽

Li Huaizhi ◽

Liu Yang ◽

Li Xiang ◽

Chen Huoying

Keyword(s):

Ssr Markers ◽

Simple Sequence Repeat ◽

Expressed Sequence Tag ◽

Diversity Analysis ◽

Sequence Repeat ◽

Expressed Sequence ◽

Simple Sequence

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Development and characterization of EST-derived simple sequence repeat (SSR) markers for pasture grass endophytes

Genome ◽

10.1139/g03-001 ◽

2003 ◽

Vol 46 (2) ◽

pp. 277-290 ◽

Cited By ~ 33

Author(s):

Eline van Zijll de Jong ◽

Kathryn M Guthridge ◽

German C Spangenberg ◽

John W Forster

Keyword(s):

Genetic Diversity ◽

Ssr Markers ◽

Expressed Sequence Tags ◽

Simple Sequence Repeat ◽

Fragment Length Polymorphism ◽

Sequence Repeat ◽

Pasture Grass ◽

Ssr Loci ◽

Expressed Sequence ◽

Simple Sequence

Fungal endophytes of the genus Neotyphodium are common in temperate pasture grass species and confer both beneficial and deleterious agronomic characteristics to their hosts. The aim of this study was to develop molecular markers based on simple sequence repeat (SSR) loci for the identification and assessment of genetic diversity among Neotyphodium endophytes in grasses. Expressed sequence tags (ESTs) from both Neptyphodium coenophialum and Neotyphodium lolii were examined, and unique SSR loci were identified in 9.7% of the N. coenophialum sequences and 6.3% of the N. lolii sequences. A variety of SSRs were present, although perfect trinucleotide repeat arrays were the most common. Primers were designed to 50 SSR loci from N. coenophialum and 57 SSR loci from N. lolii and were evaluated using 20 Neotyphodium and Epichloë isolates. A high proportion of the N. coenophialum and N. lolii primers produced amplification products from the majority of isolates and most of these primers detected genetic variation. SSR markers from both N. coenophialum and N. lolii detected high levels of polymorphism between Neotyphodium and Epichloë species, and low levels of polymorphism within N. coenophialum and N. lolii. SSR markers may be used in appropriate combinations to discriminate between species. Comparison with amplified fragment length polymorphism (AFLP) data demonstrated that the SSR markers were informative for the assessment of genetic variation within and between endophyte species. These markers may be used to identify endophyte taxa and to evaluate intraspecific population diversity, which may be correlated with variation for endophyte-derived agronomic traits.Key words: Neotyphodium, simple sequence repeats, expressed sequence tags, amplified fragment length polymorphism, genetic diversity.

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

Journal of the American Society for Horticultural Science ◽

10.21273/jashs.133.6.794 ◽

2008 ◽

Vol 133 (6) ◽

pp. 794-800 ◽

Cited By ~ 7

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.

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