054 Characterization of Malus hupehensis (Tea Crabapple) with DNA Simple Sequence Repeats

Simple sequence repeats (SSRs) are highly polymorphic regions of DNA that can be used for the molecular characterization of apple (Malus) germplasm. SSR markers are sufficiently variable to distinguish between individual plants in wild Malus species. In this study, accessions of Malus hupehensis were screened for fragment length variation in PCR amplified simple sequence repeat regions of DNA. The fragment length phenotype produced by five SSR primer pairs showed no variation between two lineages of M. hupehensis collected in the Changjiang (Yangtse) River valley. One lineage was collected by E.H. Wilson in 1908 near the city of Ichang, Hubei Province. The second lineage was collected by cooperators at China's Southwest Agricultural University (SWAU) in 1997 near the city of Chongqing (Chungking). M. hupehensis Plant Introduction No. 588760 from the National Plant Germplasm System lacks provenance, but displays a fragment length phenotype identical to both the Wilson and SWAU lineages. The spread of a clone may be aided by asexual reproduction through seed, which is not uncommon in polyploid apples. Two seedlings each of 15 maternal trees from the SWAU lineage were assayed for ploidy level by flow cytometry. The DNA content per nucleus for all SWAU progeny fell within the range for triploids, 2.19 to 2.68 pg DNA/nucleus. It appears that plant explorers in China separated by almost 90 years have succeeded in sampling a single clonal lineage of M. hupehensis.

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Molecular Identification of Malus hupehensis (Tea Crabapple) Accessions Using Simple Sequence Repeats

HortScience ◽

10.21273/hortsci.36.5.961 ◽

2001 ◽

Vol 36 (5) ◽

pp. 961-966 ◽

Cited By ~ 7

Author(s):

Laura L. Benson ◽

Warren F. Lamboy ◽

Richard H. Zimmerman

Keyword(s):

Simple Sequence Repeats ◽

Germplasm Conservation ◽

The United States ◽

Ex Situ ◽

Ploidy Levels ◽

Plant Germplasm ◽

Malus Hupehensis ◽

National Plant Germplasm System ◽

Simple Sequence ◽

The U.S

The U.S. National Plant Germplasm System (NPGS) currently holds 36 separate accessions of the `Yichang' clone of Malus hupehensis (Pamp.) Rehd. The `Yichang' clone originally entered the United States in 1908 as seed collected for the Arnold Arboretum by E.H. Wilson near Yichang, Hubei Province, China. The original description of M. hupehensis omits fruit characters, and botanists frequently augment these omissions with descriptions of the `Yichang' clone. Apomixis occurs in Malus, including M. hupehensis, and is strongly associated with elevated ploidy levels. Simple sequence repeats (SSRs) were used to characterize 65 accessions of M. hupehensis. To check for polyploidy, a set of M. hupehensis accessions was evaluated with flow cytometry. The simple sequence repeat phenotypes and ploidy information revealed the `Yichang' clone under various accession names in arboreta. It was neither known nor suspected that the U.S. National Plant Germplasm System held many duplicate accessions of the `Yichang' clone prior to their molecular characterization. Germplasm conservation decisions for Malus species can benefit from an increased knowledge of the genetic variation or lack thereof in naturalized populations and ex situ collections.

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DNA Fingerprinting and Characterization of some Egyptian Date Palm Cultivars Using Simple Sequence Repeats (SSRs)

Journal of Plant Production Sciences ◽

10.21608/jpps.2015.7402 ◽

2015 ◽

Vol 3 (1) ◽

pp. 31-41

Author(s):

Mohammed Hussein ◽

Samah Sabry ◽

Manal Eid

Keyword(s):

Dna Fingerprinting ◽

Simple Sequence Repeats ◽

Date Palm ◽

Simple Sequence

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Genetic Diversity and Characterization of a Core Collection of Malus Germplasm Using Simple Sequence Repeats (SSRs)

Plant Molecular Biology Reporter ◽

10.1007/s11105-011-0399-x ◽

2011 ◽

Vol 30 (4) ◽

pp. 827-837 ◽

Cited By ~ 35

Author(s):

Sarah M. Potts ◽

Yuepeng Han ◽

M. Awais Khan ◽

Mosbah M. Kushad ◽

A. Lane Rayburn ◽

...

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeats ◽

Core Collection ◽

Simple Sequence

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SIMPLE SEQUENCE REPEATS (SSRS) FOR DIVERSITY CHARACTERIZATION OF GUAVA (PSIDIUM GUAJAVA L.)

Acta Horticulturae ◽

10.17660/actahortic.2010.849.17 ◽

2010 ◽

pp. 155-162 ◽

Cited By ~ 3

Author(s):

J. Valdés-Infante ◽

N.N. Rodríguez ◽

B. Velásquez ◽

D. Rivero ◽

F. Martínez ◽

...

Keyword(s):

Simple Sequence Repeats ◽

Psidium Guajava ◽

Simple Sequence

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Characterization of Simple Sequence Repeats (SSRs) in Ciliated Protists Inferred by Comparative Genomics

Microorganisms ◽

10.3390/microorganisms8050662 ◽

2020 ◽

Vol 8 (5) ◽

pp. 662 ◽

Cited By ~ 1

Author(s):

Yuan Li ◽

Xiao Chen ◽

Kun Wu ◽

Jiao Pan ◽

Hongan Long ◽

...

Keyword(s):

Simple Sequence Repeats ◽

Evolutionary History ◽

Rapid Evolution ◽

Genome Diversity ◽

Unicellular Eukaryotes ◽

Genome Wide ◽

Species Analysis ◽

Simple Sequence ◽

High Diversity

Simple sequence repeats (SSRs) are prevalent in the genomes of all organisms. They are widely used as genetic markers, and are insertion/deletion mutation hotspots, which directly influence genome evolution. However, little is known about such important genomic components in ciliated protists, a large group of unicellular eukaryotes with extremely long evolutionary history and genome diversity. With recent publications of multiple ciliate genomes, we start to get a chance to explore perfect SSRs with motif size 1–100 bp and at least three motif repeats in nine species of two ciliate classes, Oligohymenophorea and Spirotrichea. We found that homopolymers are the most prevalent SSRs in these A/T-rich species, with AAA (lysine, charged amino acid; also seen as an SSR with one-adenine motif repeated three times) being the codons repeated at the highest frequencies in coding SSR regions, consistent with the widespread alveolin proteins rich in lysine repeats as found in Tetrahymena. Micronuclear SSRs are universally more abundant than the macronuclear ones of the same motif-size, except for the 8-bp-motif SSRs in extensively fragmented chromosomes. Both the abundance and A/T content of SSRs decrease as motif-size increases, while the abundance is positively correlated with the A/T content of the genome. Also, smaller genomes have lower proportions of coding SSRs out of all SSRs in Paramecium species. This genome-wide and cross-species analysis reveals the high diversity of SSRs and reflects the rapid evolution of these simple repetitive elements in ciliate genomes.

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