scholarly journals Allelic variation of simple sequence repeats markers linked to PPV resistance in Chinese apricot

2017 ◽  
Vol 44 (No. 1) ◽  
pp. 6-13
Author(s):  
Qiu-ping Zhang ◽  
Wei-sheng Liu ◽  
Ning Liu ◽  
Yu-ping Zhang ◽  
Ming Xu
Keyword(s):  
Simple Sequence Repeats ◽  
Allelic Variation ◽  
Prunus Armeniaca ◽  
Plum Pox Virus ◽  
Germplasm Resources ◽  
Prunus Mume ◽  
Ssr Primers ◽  
Ppv Resistance ◽  
High Level ◽  
Simple Sequence

Apricot is one of the oldest fruit tree crops in China and it was spread via Armenia to other areas. There are about ten species of apricot (Subg. Armeniaca Mill.) worldwide, among which nine species are native to China. Sharka disease caused by the Plum pox virus (PPV) is widely distributed in the main producing regions of apricot. In this study, linked simple sequence repeats (SSR) primers were used to detect allele variations potentially associated with PPV resistance among Chinese apricot germplasm resources, including 52 accessions belonging to Prunus armeniaca, 7 to Prunus mandshurica, 6 to Prunus sibirica, 4 to Prunus mume, 17 to other species or types. The allelic variation at loci with PPV resistance showed that these SSR markers linked to PPV resistance kept a relatively high level of diversity in Chinese apricot. The special alleles and genotypes only found in South China cultivars might reveal new PPV resistance sources. Some famous local cultivars of Chinese apricot might be considered as candidates for PPV resistance.  

scholarly journals Development of EST-derived SSR Markers with Long-core Repeat in Olive and Their Use for Paternity Testing

2013 ◽  
Vol 138 (4) ◽  
pp. 290-296 ◽  
Author(s):  
Raúl De la Rosa ◽  
Angjelina Belaj ◽  
Antonio Muñoz-Mérida ◽  
Oswaldo Trelles ◽  
Inmaculada Ortíz-Martín ◽  
...  
Keyword(s):  
Ssr Markers ◽  
Simple Sequence Repeats ◽  
Expressed Sequence Tag ◽  
Paternity Testing ◽  
High Level ◽  
Repeated Motifs ◽  
Expressed Sequence ◽  
Simple Sequence ◽  
Olive Breeding ◽  
Genomic Project

In the present work, a set of eight new hexa-nucleotide simple sequence repeats (SSRs) is reported in olive (Olea europaea L). These SSRs loci were generated on the basis of expressed sequence tag (EST) sequences in the frame of an olive genomic project. The markers showed a high level of polymorphism when tested on a set of cultivars used as genitors in the olive breeding program of Córdoba, Spain. The long-core repeat motif of these markers allows a wider separation among alleles, thus permitting an accurate genotyping. Besides, these markers showed comparable levels of polymorphism to di-nucleotide SSRs, the only ones so far reported in olive. Selected on the basis of their discrimination capacity, four of the eight SSRs were used to test their ability for paternity testing in a total of 81 seedlings coming from 12 crosses. The paternity testing showed that seven crosses matched the alleged paternity and the remaining five were products of illicit pollinations. These results exactly matched with previous paternity testing performed with di-nucleotide SSR markers. These results demonstrate the usefulness of the developed hexa-nucleotide repeated motifs for checking the paternity of breeding progenies and suggest their use on variability studies.

scholarly journals Lemons: Diversity and Relationships with Selected Citrus Genotypes as Measured with Nuclear Genome Markers

2001 ◽  
Vol 126 (3) ◽  
pp. 309-317 ◽  
Author(s):  
O. Gulsen ◽  
M.L. Roose
Keyword(s):  
Simple Sequence Repeats ◽  
Phylogenetic Trees ◽  
Nuclear Genome ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Inter Simple Sequence Repeats ◽  
Ssr Loci ◽  
High Level ◽  
Simple Sequence

Inter-simple sequence repeats (ISSR), simple sequence repeats (SSR) and isozymes were used to measure genetic diversity and phylogenetic relationships among 95 Citrus L. accessions including 57 lemons [C. limon (L.) Burm. f.], related taxa, and three proposed ancestral species, C. maxima (Burm.) Merrill (pummelo), C. medica L. (citron), and C. reticulata Blanco (mandarin). The ancestry of lemons and several other suspected hybrids was also studied. Five isozyme and five SSR loci revealed relatively little variation among most lemons, but a high level of variation among the relatively distant Citrus taxa. Eight ISSR primers amplified a total of 103 polymorphic fragments among the 83 accessions. Similarity matrices were calculated and phylogenetic trees derived using unweighted pair-group method, arithmetic average cluster analysis. All lemons, rough lemons, and sweet lemons, as well as some other suspected hybrids, clustered with citrons. Most lemons (68%) had nearly identical marker phenotypes, suggesting they originated from a single clonal parent via a series of mutations. Citrons contributed the largest part of the lemon genome and a major part of the genomes of rough lemons, sweet lemons, and sweet limes. Bands that characterize C. reticulata and C. maxima were detected in lemons, suggesting that these taxa also contributed to the pedigree of lemon.

SSR-Primer Generator: A Tool for Finding Simple Sequence Repeats and Designing SSR-Primers

2011 ◽  
Vol 9 (4) ◽  
pp. 189-193
Author(s):  
Chang-Pyo Hong ◽  
Su-Ryun Choi ◽  
Yong-Pyo Lim
Keyword(s):  
Simple Sequence Repeats ◽  
Ssr Primers ◽  
Simple Sequence

scholarly journals Genome-Wide Characterization and Linkage Mapping of Simple Sequence Repeats in Mei (Prunus mume Sieb. et Zucc.)

PLoS ONE ◽  
2013 ◽  
Vol 8 (3) ◽  
pp. e59562 ◽  
Author(s):  
Lidan Sun ◽  
Weiru Yang ◽  
Qixiang Zhang ◽  
Tangren Cheng ◽  
Huitang Pan ◽  
...  
Keyword(s):  
Simple Sequence Repeats ◽  
Linkage Mapping ◽  
Prunus Mume ◽  
Genome Wide ◽  
Simple Sequence

scholarly journals DNA Fingerprinting of Tetraploid Cherry Germplasm Using Simple Sequence Repeats

2001 ◽  
Vol 126 (2) ◽  
pp. 205-209 ◽  
Author(s):  
Claudio Cantini ◽  
Amy F. Iezzoni ◽  
Warren F. Lamboy ◽  
Manuela Boritzki ◽  
Darush Struss
Keyword(s):  
Simple Sequence Repeats ◽  
Agricultural Research ◽  
Gene Diversity ◽  
Sour Cherry ◽  
Department Of Agriculture ◽  
Global Database ◽  
Usda Agricultural Research ◽  
The Individual ◽  
High Level ◽  
Simple Sequence

The U.S. Department of Agriculture (USDA), Agricultural Research Service (ARS) tetraploid cherry (Prunus L. sp.) collection at Geneva, N.Y., contains ≈75 accessions of sour cherry (P. cerasus L.), ground cherry (P. fruticosa Pall.), and their hybrids. Accurate and unambiguous identification of these accessions is essential for germplasm preservation and use. Simple sequence repeats (SSRs) are currently the markers of choice for germplasm fingerprinting because they characteristically display high levels of polymorphism. Recently SSR primer pairs from sweet cherry (P. avium L.), sour cherry, and peach [(P. persica L. Batsch (Peach Group)] have been reported. Ten SSR primer pairs were tested on 59 tetraploid cherry accessions to determine if they could differentiate among the accessions. Scorable SSR fragments were produced with all primer-accession combinations. The cherry accessions exhibited high levels of polymorphism with 4 to 16 different putative alleles amplified per primer pair. Most of the putative alleles were rare with frequencies <0.05. Heterozygosity values ranged from 0.679 to 1.00, while gene diversity values ranged from 0.655 to 0.906. The primer pairs differentiated all but two of the 59 cherry accessions. Based upon the ability of the SSR data to differentiate the cherry accessions and the high level of gene diversity, we propose that all the tetraploid cherry accessions in the USDA/ARS collection be fingerprinted to provide a mechanism to verify the identity of the individual accessions. The fingerprinting data are available on the World Wide Web (http://www.ars-grin.gov/gen/cherry.html) so that other curators and scientists working with cherry can verify identities and novel types in their collections and contribute to a global database.

scholarly journals Cost-Effective and Time-Efficient Molecular Assisted Selection for Ppv Resistance in Apricot Based on ParPMC2 Allele-Specific PCR

Agronomy ◽  
2020 ◽  
Vol 10 (9) ◽  
pp. 1292 ◽  
Author(s):  
Ángela Polo-Oltra ◽  
Carlos Romero ◽  
Inmaculada López ◽  
María Luisa Badenes ◽  
Elena Zuriaga
Keyword(s):  
Woody Species ◽  
Cost Effective ◽  
Prunus Armeniaca ◽  
Host Susceptibility ◽  
Limiting Factor ◽  
Plum Pox Virus ◽  
Breeding Programs ◽  
Specific Pcr ◽  
Allele Specific ◽  
Ppv Resistance

Plum pox virus (PPV) is the most important limiting factor for apricot (Prunus armeniaca L.) production worldwide, and development of resistant cultivars has been proven to be the best solution in the long-term. However, just like in other woody species, apricot breeding is highly time and space demanding, and this is particularly true for PPV resistance phenotyping. Therefore, marker-assisted selection (MAS) may be very helpful to speed up breeding programs. Tightly linked ParPMC1 and ParPMC2, meprin and TRAF-C homology (MATH)-domain-containing genes have been proposed as host susceptibility genes required for PPV infection. Contribution of additional genes to PPV resistance cannot be discarded, but all available studies undoubtedly show a strong correlation between ParPMC2-resistant alleles (ParPMC2res) and PPV resistance. The ParPMC2res allele was shown to carry a 5-bp deletion (ParPMC2-del) within the second exon that has been characterized as a molecular marker suitable for MAS (PMC2). Based on this finding, we propose here a method for PPV resistance selection in apricot by combining high-throughput DNA extraction of 384 samples in 2 working days and the allele-specific genotyping of PMC2 on agarose gel. Moreover, the PMC2 genotype has been determined by PCR or by using whole-genome sequences (WGS) in 175 apricot accessions. These results were complemented with phenotypic and/or genotypic data available in the literature to reach a total of 325 apricot accessions. As a whole, we conclude that this is a time-efficient, cost-effective and straightforward method for PPV resistance screening that can be highly useful for apricot breeding programs.

scholarly journals Resistance to Plum Pox Virus (Dideron Isolate RB3.30) in a Group of California Almonds and Transfer of Resistance to Peach

2004 ◽  
Vol 129 (4) ◽  
pp. 544-548 ◽  
Author(s):  
P. Martínez-Gómez ◽  
M. Rubio ◽  
F. Dicenta ◽  
T.M. Gradziel
Keyword(s):  
Prunus Persica ◽  
Prunus Avium ◽  
Sour Cherry ◽  
Prunus Armeniaca ◽  
Pcr Analysis ◽  
Plum Pox Virus ◽  
Rt Pcr ◽  
Resistance Transfer ◽  
High Level ◽  
Peach Rootstocks

Sharka [(plum pox virus (PPV)] mainly affects Prunus species, including apricot (Prunus armeniaca L.), peach (Prunus persica L.), plum (Prunus salicina Lindl., Prunus domestica L.), and, to a lesser degree, sweet (Prunus avium L.) and sour cherry (Prunus cerasus L.). Level of resistance to a Dideron isolate of PPV in seven California almond [P. dulcis (Miller) D.A. Webb], five processing peach cultivars, and two peach rootstocks was evaluated. In addition, almond and peach selections resulting from interspecific almond × peach hybridization and subsequent gene introgression were tested. Evaluations were conducted in controlled facilities after grafting the test genotypes onto inoculated GF305 peach rootstocks. Leaves were evaluated for PPV symptoms during three consecutive cycles of growth. ELISA-DASI and RT-PCR analysis were also employed to verify the presence or absence of PPV. Peach cultivars and rootstocks showed sharka symptoms and were ELISA-DASI or RT-PCR positive for some growth cycles, indicating their susceptibility to PPV. Almond cultivars and almond × peach hybrids did not show symptoms and were ELISA-DASI and RT-PCR negative, demonstrating resistance to PPV. Two (almond × peach) F2 selections as well as two of three backcrossed peach selections also showed a resistant behavior against the PPV-D isolate. Results demonstrate a high level of resistance in almond and indicate potential for PPV resistance transfer to commercial peach cultivars.

scholarly journals Genetic Diversity of Iraqi Date Palms Revealed By Microsatellite Polymorphism

2011 ◽  
Vol 136 (4) ◽  
pp. 282-287 ◽  
Author(s):  
Hussam S.M. Khierallah ◽  
Saleh M. Bader ◽  
Michael Baum ◽  
Alladin Hamwieh
Keyword(s):  
Genetic Diversity ◽  
Date Palm ◽  
Phoenix Dactylifera ◽  
Principal Coordinate Analysis ◽  
Group Method ◽  
Arithmetic Average ◽  
Pair Group ◽  
Ssr Primers ◽  
High Level ◽  
Simple Sequence

Genetic diversity in 30 date palm (Phoenix dactylifera L.) cultivars in Iraq representing 24 female and six male cultivars was investigated using 22 microsatellite [simple sequence repeat (SSR)] primers. The tested SSR markers showed a high level of polymorphism. A total of 188 alleles were detected at the 22 loci ranging from three to 21 with an average of 8.54 alleles per locus. The average of heterozygosity for all cultivars was 0.503; genetic distance among cultivars varied from 0.171 to 0.938 indicating diverse relationships. The cultivar Ghanami Akhder was highly divergent from ‘Ghnami Ahmer’, whereas ‘Jamal Al-Dean’ was very closely related to ‘Qitaz’. Unweighted pair group method arithmetic average ordered date palm cultivars into two main clusters. Principal coordinate analysis exhibited the similar clusters of cultivars as in the dendrogram.

scholarly journals UJI POLIMORPIK DAN HETEROZIGOSITAS PADA PROGENI F4 KEDELAI (Glycine max (L.) Merril) TAHAN SALIN DENGAN MENGGUNAKAN MARKA SSR (Simple Sequence Repeats)

2020 ◽  
Vol 5 (2) ◽  
Author(s):  
Evi Julianita Harahap ◽  
Rosmayanti Rosmayanti ◽  
Diana Sofia Hanafiah
Keyword(s):  
Glycine Max ◽  
Simple Sequence Repeats ◽  
Ssr Marker ◽  
Specific Primers ◽  
Allele Number ◽  
Map Construction ◽  
Expected Heterozygosity ◽  
Ssr Primers ◽  
Glycine Max L ◽  
Simple Sequence

SSR marker has some merits such as quickness, simplicity, rich polymorphism and stability, thus being widely applied in genetic diversity analysis, molecular map construction and gene mapping. the purpose of this study was to determine polymorpic test and heterozygosity in F4 soybean (Glycine max (L.) Merril) progeni saline resistant characters using SSR (Simple Sequence Repeats) markers. This research was conducted in Biomolecular Laboratory, Socfindo Seed Production Laboratory (SSPL), Kebun Bangun Bandar Village Martebing District Dolok Masihul Regency Serdang Bedagai on December-May 2017. The number of samples were used 44. The five SSR primers (QS080465, QS1101, QS1112, QS100011, and Sat_091) used were specific primers, with a band pattern that was clearly visible around one or two bands. The percentage of polymorphic primers (PLP) of these three populations is high, all populations with a PLP of 100% of the saline resistant character. The effective allele number (Ne) of  7,160 for the progeny population is lower than the number of observed alleles (Na) of 10,000 which means that many progeny individuals are homozygous. The expected heterozygosity (He) value of 0.854 in the progeny population was higher than the observed heterozygosity (Ho) value of 0.027. The overall average observed heterozygosity (Ho) was 0.009 lower than the overall expected heterozygosity (He) of 0.61. This means that each character has a low heterozygosity.Keywords: Progeny F4, soybean, SSR, saline resistant, polymorphic, heterozygosity

scholarly journals SSR based characterization of peach (Prunus persica L.) and apricot (Prunus armeniaca L.) varieties cultivated in Hungary

2018 ◽  
pp. 17-24
Author(s):  
Janka Bedő ◽  
Eren Baris ◽  
Zsolt Szani ◽  
Dezső Surányi ◽  
Erzsébet Kiss ◽  
...  
Keyword(s):  
Simple Sequence Repeat ◽  
Prunus Persica ◽  
Prunus Armeniaca ◽  
Dna Fingerprints ◽  
Informative Marker ◽  
Simple Sequence Repeat Markers ◽  
Ssr Primers ◽  
Prunus Armeniaca L ◽  
Simple Sequence

The SSR (Simple Sequence Repeat) markers allow the discrimination of the cultivars and determination its specific DNA fingerprints. The aim of this research was to evaluate fifteen apricot (Prunus armeniaca L.) and fifty-one peach (Prunus persica L.) genotypes cultivated in Hungary to obtain their DNA fingerprints in 6 SSR (Simple Sequence Repeats) loci by allele numbers and sizes. DNAs were extracted from leaves. PCR was carried out with CY-5 fluorescent labeled Prunus microsatellite markers and the products were separated on polyacrylamide gel with ALF (Automated Laser Flourometer)-Express II. According to our results, in the case of peach genotypes, all 6 SSRs were able to amplify alleles. UDP 96 005 was the most informative marker and UCDCH 17 was the least due to its monomorphic pattern. Regarding the apricot samples BPPCT 041 did not amplify any allele. In the case of P. armeniaca UDP 96 005 had the highest heterozygosity index as well and the highest number of alleles. The least informative marker was the UCDCH 17. Since the 6 SSR were not enough to discriminate the apricot and peach genotypes, it is suggested to use more SSR primers.

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