scholarly journals New Insight into Wild Red Raspberry Populations using Simple Sequence Repeat Markers

2009 ◽  
Vol 134 (1) ◽  
pp. 109-119 ◽  
Author(s):  
Julie Graham ◽  
Mary Woodhead ◽  
Kay Smith ◽  
Joanne Russell ◽  
Bruce Marshall ◽  
...  
Keyword(s):  
Population Differentiation ◽  
Simple Sequence Repeat ◽  
Rubus Idaeus ◽  
Small Scale ◽  
Climate Change Scenarios ◽  
Sequence Repeat ◽  
Red Raspberry ◽  
In The Wild ◽  
Simple Sequence ◽  
Significant Population Differentiation

Scottish wild red raspberry (Rubus idaeus) plants at 12 sites were re-examined 10 years after initial studies had been carried out to examine the decline in population size and to address an earlier finding that demonstrated significant population differentiation over a small scale. Ten simple sequence repeat (SSR) loci were screened on the plants and a total of 80 alleles were detected, half of which were unique to a particular population, with all populations containing unique SSR alleles. Only 18 of the 80 alleles present in the wild were found in cultivated raspberries, highlighting the genetic diversity available for future breeding. This finding makes the decline in population number observed a concern, as this unique diversity is being eroded, primarily due to human impact. An additional 17 unique alleles were identified in the cultivars that were not present in the wild individuals studied. Gene flow into one lowland site was identified by the gain of one new allele into progeny at the site, but three alleles were also lost from parents to progeny. SSR markers were used to estimate the levels of outcrossing in wild red raspberry for the first time, and confirmed that the populations studied were outcrossing, intermating populations. The nonsignificant global F IS value indicates that red raspberry is an outbreeder (global F IS = −0.117), but significant population differentiation was observed [global F ST = 0.348 (P < 0.001)]. Diversity in this crop's wild relative and the population differentiation observed may have use in the future for breeding aimed at addressing climate change scenarios, and consideration should be given to means of conserving the diversity revealed by these studies.

scholarly journals Identification of Expressed Sequence Tag-simple Sequence Repeat Markers from the De Novo Transcriptome Sequence of Red Raspberry (Rubus idaeus L.)

HortScience ◽  
2017 ◽  
Vol 52 (4) ◽  
pp. 554-559
Author(s):  
Jianfeng Liu ◽  
Bowen Yang ◽  
Yuetong Ming ◽  
Yuchu Zhang ◽  
Yunqing Cheng
Keyword(s):  
Simple Sequence Repeat ◽  
Expressed Sequence Tag ◽  
De Novo ◽  
Rubus Idaeus ◽  
Group Method ◽  
Sequence Repeat ◽  
Red Raspberry ◽  
De Novo Transcriptome ◽  
Dinucleotide Repeats ◽  
Simple Sequence

Rubus idaeus has remarkable economic and cultural value. Developing efficient simple sequence repeat (SSR) markers is necessary for the molecular breeding of red raspberry. In this study, SSR mining was performed using the de novo transcriptome sequence of R. idaeus. In total, 14,210 SSR sequences were identified from 11,158 SSR-containing unigenes. In all the SSR sequences, mononucleotide, dinucleotide, and trinucleotide repeats were the most common, and their number and percentage were 1323 (9.31%), 6752 (47.52%), and 4897 (34.46%), respectively. Of the mononucleotide and dinucleotide repeats, A/T, AG/CT, AT/AT, and AC/GT were more abundant and accounted for 9.09%, 37.82%, 6.51%, and 3.14% of the total repeat number, respectively. In the trinucleotide, tetranucleotide, pentanucleotide, and hexanucleotide repeats, the nucleotide (NT) patterns AAG/CTT, AAAG/CTTT, AAAAG/CTTTT, and AAGAGG/CCTCTT were the most frequent, and accounted for 14.11%, 0.38%, 0.57%, and 0.23% of the total SSRs, respectively. Of the 480 SSR-containing unigenes with gene ontology (GO) annotation, the classification results showed that they were mainly involved in binding, catalytic, and transporter molecular functions. Most of the 3441 SSR-containing unigenes with the Kyoto Encyclopedia of Genes and Genomes (KEGG) annotation were involved in the following top five pathways: metabolic, RNA transport, spliceosome, protein processing in the endoplasmic reticulum, and mRNA surveillance. Thirty pairs of primers derived from the red raspberry transcriptome were randomly selected to assess their polymorphism by using 15 red raspberry germplasms, in which the polymorphism information content (PIC) values ranged from 0.50 to 0.86, with a mean of 0.73, thereby indicating a high level of polymorphism. The unweighted pair group method with arithmetic mean clustering results indicated that the thirty pairs of primers could precisely distinguish the germplasms. This study reveals the SSR distribution characteristics of red raspberry and provides a scientific basis for further genetic diversity studies and genetic linkage map construction for this species.

scholarly journals Simple Sequence Repeat (SSR) Markers for Raspberry and Blackberry

HortScience ◽  
2004 ◽  
Vol 39 (4) ◽  
pp. 785D-785 ◽  
Author(s):  
Kim S. Lewers* ◽  
Eric T. Stafne ◽  
John R. Clark ◽  
Courtney A. Weber ◽  
Julie Graham
Keyword(s):  
Molecular Markers ◽  
Simple Sequence Repeat ◽  
Mapping Population ◽  
Black Raspberry ◽  
Sequence Repeat ◽  
Red Raspberry ◽  
Simple Sequence Repeat Markers ◽  
Cultivar Development ◽  
Pcr Product ◽  
Simple Sequence

Some raspberry and blackberry breeders are interested in using molecular markers to assist with selection. Simple Sequence Repeat markers (SSRs) have many advantages, and SSRs developed from one species can sometimes be used with related species. Six SSRs derived from the weed R. alceifolius, and 74 SSRs from R. idaeus red raspberry `Glen Moy' were tested on R. idaeus red raspberry selection NY322 from Cornell Univ., R. occidentalis `Jewel' black raspberry, Rubus spp. blackberry `Arapaho', and blackberry selection APF-12 from the Univ. of Arkansas. The two raspberry genotypes are parents of an interspecific mapping population segregating for primocane fruiting and other traits. The two blackberry genotypes are parents of a population segregating for primocane fruiting and thornlessness. Of the six R. alceifolius SSRs, two amplified a product from all genotypes. Of the 74 red raspberry SSRs, 56 (74%) amplified a product from NY322, 39 (53%) amplified a product from `Jewel', and 24 (32%) amplified a product from blackberry. Of the 56 SSRs that amplified a product from NY322, 17 failed to amplify a product from `Jewel' and, therefore, detected polymorphisms between the parents of this mapping population. Twice as many detected polymorphisms of this type between blackberry and red raspberry, since 33 SSRs amplified a product from NY322, but neither of the blackberry genotypes. Differences in PCR product sizes from these genotypes reveal additional polymorphisms. Rubus is among the most diverse genera in the plant kingdom, so it is not surprising that only 19 of the 74 raspberry-derived SSRs amplified a product from all four of the genotypes tested. These SSRs will be useful in interspecific mapping and cultivar development.

A taxonomic appraisal of the Chatham Islands flax (Phormium tenax) using morphological and DNA fingerprint data

2010 ◽  
Vol 23 (5) ◽  
pp. 371 ◽  
Author(s):  
R. D. Smissen ◽  
P. B. Heenan
Keyword(s):  
New Zealand ◽  
Simple Sequence Repeat ◽  
Fragment Length Polymorphism ◽  
The Other ◽  
Dna Fingerprint ◽  
Sequence Repeat ◽  
In The Wild ◽  
The 19Th Century ◽  
Simple Sequence ◽  
Fingerprint Data

A range of leaf forms of Phormium tenax J.R.Forst. & G.Forst. can be observed in the wild on the Chatham Island archipelago. At one extreme are plants with more or less upright leaves, similar to those observed in New Zealand P. tenax, and at the other extreme there are plants with floppy leaves. The upright-leaved form is found more or less throughout the archipelago, whereas the floppy-leaved form is concentrated in the southern part of Chatham Island, Pitt Island, and on the other southern islands (e.g. South East and Mangere islands). Analysis of amplified fragment length polymorphism (AFLP) and simple-sequence-repeat (SSR) variation, and comparison with a diverse sampling of New Zealand Phormium suggested that both Chatham Islands forms are indigenous and part of a common gene pool. We found no evidence of hybridism with Phormium introduced from New Zealand. Floppy-leaved forms are therefore linked to typical upright leaved P. tenax through upright-leaved plants with bent tips, and do not require taxonomic recognition. AFLP and SSR data both support the view that a plant collected from Ranui Cove, Auckland Island, is descended from Chatham Islands material, and was most likely introduced there by Ngāti Mutunga and Moriori settlers during the 19th century.

scholarly journals Simple Sequence Repeat (SSR) Markers for Genetic Mapping of Raspberry and Blackberry

2005 ◽  
Vol 130 (5) ◽  
pp. 722-728 ◽  
Author(s):  
Eric T. Stafne ◽  
John R. Clark ◽  
Courtney A. Weber ◽  
Julie Graham ◽  
Kim S. Lewers
Keyword(s):  
Molecular Markers ◽  
Genetic Mapping ◽  
Ssr Markers ◽  
Simple Sequence Repeat ◽  
Genetic Maps ◽  
Black Raspberry ◽  
Sequence Repeat ◽  
Red Raspberry ◽  
Simple Sequence ◽  
Mapping Populations

Interest in molecular markers and genetic maps is growing among researchers developing new cultivars of Rubus L. (raspberry and blackberry). Several traits of interest fail to express in seedlings or reliably in some environments and are candidates for marker-assisted selection. A growing number of simple sequence repeat (SSR) molecular markers derived from Rubus and Fragaria L. (strawberry) are available for use with Rubus mapping populations. The objectives of this study were to test 142 of these SSR markers to screen raspberry and blackberry parental genotypes for potential use in existing mapping populations that segregate for traits of interest, determine the extent of inter-species and inter-genera transferability with amplification, and determine the level of polymorphism among the parents. Up to 32 of the SSR primer pairs tested may be useful for genetic mapping in both the blackberry population and at least one of the raspberry populations. The maximum number of SSR primer pairs found useable for mapping was 60 for the raspberry population and 45 for the blackberry population. Acquisition of many more nucleotide sequences from red raspberry, black raspberry, and blackberry are required to develop useful molecular markers and genetic maps for these species. Rubus, family Rosaceae, is a highly diverse genus that contains hundreds of heterozygous species. The family is one of the most agronomically important plant families in temperate regions of the world, although they also occur in tropical and arctic regions as well. The most important commercial subgenus of Rubus is Idaeobatus Focke, the raspberries, which are primarily diploids. This subgenus contains the european red raspberry R. idaeus ssp. idaeus L., as well as the american black raspberry R. occidentalis L. and the american red raspberry R. idaeus ssp. strigosus Michx. Interspecific hybridization of these, and other raspberry species, has led to greater genetic diversity and allowed for the introgression of superior traits such as large fruit size, fruit firmness and quality, disease resistance, and winter hardiness.

Chloroplast DNA variability in wild and cultivated rice (Oryza spp.) revealed by polymorphic chloroplast simple sequence repeats

Genome ◽  
1997 ◽  
Vol 40 (1) ◽  
pp. 104-110 ◽  
Author(s):  
J. Provan ◽  
G. Corbett ◽  
W. Powell ◽  
J. W. McNicol
Keyword(s):  
Simple Sequence Repeats ◽  
Wild Rice ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Cultivated Rice ◽  
Chloroplast Markers ◽  
Chloroplast Genomes ◽  
In The Wild ◽  
Wild Accessions ◽  
Simple Sequence

Short mononucleotide repeats analogous to nuclear microsatellites or simple sequence repeats (SSRs) have been identified in chloroplast genomes. Primers flanking mononucleotide repeats in the fully sequenced rice chloroplast genome have been used in conjunction with PCR to amplify genomic DNA from 42 wild rice accessions. The amplification products exhibited length polymorphism, which allowed the levels of chloroplast variability detected to be quantified. Seven primer pairs that amplified products from different regions of the rice chloroplast were used, five of which also amplified polymorphic products in cultivated rice (Oryza sativa). Diversity values ranged from 0.5224 ± 0.0845 (SE) to 0.8298 ± 0.0085 in the wild accessions, which was higher than that detected in the O. sativa accessions. Both intra- and inter-specific polymorphism was detected, and the extent of chloroplast genomic differentiation based on chloroplast simple sequence repeat (cpSSR) assays was quantified using the RST statistic. Primers designed to amplify cpSSRs in O. sativa can also be used to generate polymorphic chloroplast markers in related taxa. The potential of using cpSSR to trace the origin of rice polyploid species is discussed.Key words: rice, chloroplast, simple sequence repeat, microsatellites.

Implementing molecular marker technology in forage improvement

2003 ◽  
pp. 229-238
Author(s):  
M. Faville ◽  
B. Barrett ◽  
A. Griffiths ◽  
M. Schreiber ◽  
C. Mercer ◽  
...  
Keyword(s):  
Quantitative Trait Locus ◽  
Genetic Variation ◽  
White Clover ◽  
Simple Sequence Repeat ◽  
Sequence Repeat ◽  
Linkage Groups ◽  
Seedling Vigour ◽  
Genome Map ◽  
Trait Locus ◽  
Simple Sequence

Accelerated improvement of two cornerstones of New Zealand's pastoral industries, per ennial ryegrass (Lolium perenne L.) and white clover (Trifolium repens L.), may be realised through the application of markerassisted selection (MAS) strategies to enhance traditional plant breeding programmes. Genome maps constructed using molecular markers represent the enabling technology for such strategies and we have assembled maps for each species using EST-SSR markers - simple sequence repeat (SSR) markers developed from expressed sequence tags (ESTs) representing genes. A comprehensive map of the white clover genome has been completed, with 464 EST-SSR and genomic SSR marker loci spanning 1125 cM in total, distributed across 16 linkage groups. These have been further classified into eight pairs of linkage groups, representing contributions from the diploid progenitors of this tetraploid species. In perennial ryegrass a genome map based exclusively on EST-SSR loci was constructed, with 130 loci currently mapped to seven linkage groups and covering a distance of 391 cM. This map continues to be expanded with the addition of ESTSSR loci, and markers are being concurrently transferred to other populations segregating for economically significant traits. We have initiated gene discovery through quantitative trait locus (QTL) analysis in both species, and the efficacy of the white clover map for this purpose was demonstrated with the initial identification of multiple QTL controlling seed yield and seedling vigour. One QTL on linkage group D2 accounts for 25.9% of the genetic variation for seed yield, and a putative QTL accounting for 12.7% of the genetic variation for seedling vigour was detected on linkage group E1. The application of MAS to forage breeding based on recurrent selection is discussed. Keywords: genome map, marker-assisted selection, perennial ryegrass, QTL, quantitative trait locus, SSR, simple sequence repeat, white clover

Genetic diversity of Symplocos paniculata of Hunan province revealed by inter-simple sequence repeat (ISSR)

2019 ◽  
Vol 51 (5) ◽  
Author(s):  
Huifang Cao ◽  
Qiang Lin ◽  
Peiwang Li ◽  
Jingzhen Chen ◽  
Changzhu Li ◽  
...  
Keyword(s):  
Genetic Diversity ◽  
Simple Sequence Repeat ◽  
Inter Simple Sequence Repeat ◽  
Hunan Province ◽  
Sequence Repeat ◽  
Simple Sequence

Mapping Unequal Crossing over Hotspot Region of Simple Sequence Repeat in Maize

2009 ◽  
Vol 35 (5) ◽  
pp. 958-961
Author(s):  
Ji-Hua TANG ◽  
Xi-Qing MA ◽  
Wen-Tao TENG ◽  
Jian-Bing YAN ◽  
Jing-Rui DAI ◽  
...  
Keyword(s):  
Simple Sequence Repeat ◽  
Crossing Over ◽  
Sequence Repeat ◽  
Unequal Crossing Over ◽  
Simple Sequence

scholarly journals A Simple Sequence Repeat-Based Linkage Map of Barley

Genetics ◽  
2000 ◽  
Vol 156 (4) ◽  
pp. 1997-2005 ◽  
Author(s):  
L Ramsay ◽  
M Macaulay ◽  
S degli Ivanissevich ◽  
K MacLean ◽  
L Cardle ◽  
...  
Keyword(s):  
Simple Sequence Repeat ◽  
Interspecific Cross ◽  
Hordeum Spontaneum ◽  
Doubled Haploid Population ◽  
Sequence Repeat ◽  
Genomic Libraries ◽  
Barley Cultivars ◽  
Multiple Loci ◽  
Marker Distribution ◽  
Simple Sequence

AbstractA total of 568 new simple sequence repeat (SSR)-based markers for barley have been developed from a combination of database sequences and small insert genomic libraries enriched for a range of short simple sequence repeats. Analysis of the SSRs on 16 barley cultivars revealed variable levels of informativeness but no obvious correlation was found with SSR repeat length, motif type, or map position. Of the 568 SSRs developed, 242 were genetically mapped, 216 with 37 previously published SSRs in a single doubled-haploid population derived from the F1 of an interspecific cross between the cultivar Lina and Hordeum spontaneum Canada Park and 26 SSRs in two other mapping populations. A total of 27 SSRs amplified multiple loci. Centromeric clustering of markers was observed in the main mapping population; however, the clustering severity was reduced in intraspecific crosses, supporting the notion that the observed marker distribution was largely a genetical effect. The mapped SSRs provide a framework for rapidly assigning chromosomal designations and polarity in future mapping programs in barley and a convenient alternative to RFLP for aligning information derived from different populations. A list of the 242 primer pairs that amplify mapped SSRs from total barley genomic DNA is presented.

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