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

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

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Evaluation of the Genetic Diversity and Differentiation of Black Locust (Robinia pseudoacacia L.) Based on Genomic and Expressed Sequence Tag-Simple Sequence Repeats

International Journal of Molecular Sciences ◽

10.3390/ijms19092492 ◽

2018 ◽

Vol 19 (9) ◽

pp. 2492 ◽

Cited By ~ 2

Author(s):

Qi Guo ◽

Xiuyu Li ◽

Shuhong Yang ◽

Zhiheng Yang ◽

Yuhan Sun ◽

...

Keyword(s):

Genetic Diversity ◽

Simple Sequence Repeats ◽

Expressed Sequence Tag ◽

Black Locust ◽

Robinia Pseudoacacia ◽

Ex Situ ◽

Ssr Primers ◽

Robinia Pseudoacacia L ◽

Expressed Sequence ◽

Simple Sequence

Understanding the genetic diversity and differentiation of the genetic resources of a species is important for the effective use and protection of forest tree resources. Ex situ development is a common method for the protection of genetic diversity and an essential resource for users who require ready access to a species’ germplasm. In this study, we collected seeds of black locust (Robinia pseudoacacia L.) from 19 provenances, covering most of its natural distribution; we randomly selected 367 tender leaves with well-grown and different maternal strains from this group for further analysis. Forty-eight simple sequence repeat (SSR) primers were successfully selected from 91 pairs of SSR primers using native-deformation polyacrylamide gel electrophoresis. In addition, we identified identical genotypes among all individuals and evaluated the quality of the markers. From this, 35 loci were confirmed for analyses of genetic diversity and differentiation of the black locust provenances, which contained 28 expressed sequence tag-derived simple sequence repeats (EST-SSRs) and 7 genomic DNA-derived simple sequence repeats (G-SSRs). We observed high genetic diversity among the native black locust provenances, from which Wright’s fixation index and molecular variance suggested that a majority of the genetic differentiation variation could be attributed to within-provenance differences. The genetic distance and identity results indicated that geographic distance was not a dominating factor influencing the distribution of black locust. This is the first study to evaluate provenance genetic variation in native black locust samples using two types of SSR markers, which provides a comprehensive theoretical basis for ex situ conservation and utilization of genetic resources, with an emphasis on breeding applications.

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Simple Sequence Repeats (SSR) Marker Screening Related to Orange Fleshed Sweet Potato F1 Genotype Resistance against Scab (Sphaceloma batatas Saw.)

KnE Life Sciences ◽

10.18502/kls.v2i6.1050 ◽

2017 ◽

Vol 2 (6) ◽

pp. 279

Author(s):

Nurfitriani Rista ◽

Fitri Widiantini ◽

Anna Aina Roosdab ◽

Endah Yulia ◽

Agung Karuniawanb

Keyword(s):

Molecular Markers ◽

Sweet Potato ◽

Ssr Markers ◽

Simple Sequence Repeats ◽

Pcr Analysis ◽

Resistant Variety ◽

Resistant Varieties ◽

Ssr Primers ◽

Orange Fleshed Sweet Potato ◽

Simple Sequence

Orange fleshed sweet potato contains high beta carotene as vitamin A precursor. However, its production is limited by the presence of scab disease caused by Sphaceloma batatas Saw. The disease is able to cause yield loss up to 60%. Best controlling method is using resistant varieties. However, the development of resistant varieties are involving long procedures which is time consuming. The long procedure of resistance varieties selection can be shorted cut using molecular markers such as SSR (Simple Sequence Repeats). Specific SSR markers for sweet potato resistance against scab has not been found. This study aimed to screen SSR molecular markers which were related to resistance to scab. The study used 5 resistant genotypes, 5 susceptible genotypes, and 6 SSR primers. PCR analysis showed that those SSR primers were polymorphic. Furthermore, the biplot analysis result demonstrated that several markers allele were related to plant resistance against scab. This finding indicated that these particular SSR markers can be used in sweet potato breeding program as marker assisted selection to develop resistant variety against scab disease. Keywords: Sphaceloma batatas; orange fleshed sweet potato; SSR markers.

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

Horticultural Science ◽

10.17221/278/2015-hortsci ◽

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.

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Fidelity of Sugarcane Crosses Assessed with SSR Markers

Agronomy ◽

10.3390/agronomy10030386 ◽

2020 ◽

Vol 10 (3) ◽

pp. 386

Author(s):

James Todd ◽

Yong-Bao Pan ◽

Deborah Boykin

Keyword(s):

Water Treatment ◽

Ssr Markers ◽

Simple Sequence Repeats ◽

Field Evaluation ◽

Hot Water ◽

Control Measures ◽

Hot Water Treatment ◽

Maternal Parent ◽

Ssr Primers ◽

Simple Sequence

Sugarcane (Saccharum hybrids spp.) is a wind-pollinated species that bears very small yet complete flowers. During crossing, a lack of pollen control (trimming off dehisced florets and hot water treatment) may result in both self-pollination (selfs) and unintentional pollination from stray pollen (off-types). Due to this uncertainty, it is important to estimate the percentage of intentional paternal hybridizations to better understand and possibly improve the crossing process. In this study, six pairs of simple sequence repeats (SSR) primers were used to assess the fidelity of 343 bi-parental crosses made at three U.S. breeding stations in 2002, 2003, 2004, 2005, and 2006. By comparing the SSR fingerprints between the two parents and 20 random progenies, three types of progenies were identified, namely, hybrids, selfs, and off-types. Hybrids had only SSR fingerprints found in either parent; selfs had only SSR fingerprints of the maternal parent; and off-types had SSR fingerprints that were not found in either parent. The fidelity of the 343 crosses fluctuated from 100% hybrids to 100% off-types. Multinomial analysis indicated that the ratio of hybrids from intentional hybridization to selfs and off-types fluctuated by year and location. Selfing rates (−30.5%) and off-type rates (−9.2%) were lower in crosses from which superior progenies were selected and advanced through 10-year field evaluation and testing, but off-type rates were not significant indicating that selfing may reduce advancement rates more than the off-types. Hot water treatment reduced off-types by 27% and selfing by 20%. This research demonstrates the utility of SSR markers for measuring hybridization rates and highlights the importance of pollen control measures through trimming and hot water treatment of sugarcane flowers.

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Polymorphism revealed by simple sequence repeats

Trends in Plant Science ◽

10.1016/s1360-1385(96)86898-0 ◽

1996 ◽

Vol 1 (7) ◽

pp. 215-222 ◽

Cited By ~ 528

Author(s):

W POWELL ◽

G MACHRAY ◽

J PROVAN

Keyword(s):

Simple Sequence Repeats ◽

Simple Sequence

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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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Implications of genome simple sequence repeats signature in 98 Polyomaviridae species

3 Biotech ◽

10.1007/s13205-020-02583-w ◽

2021 ◽

Vol 11 (1) ◽

Author(s):

Rezwanuzzaman Laskar ◽

Md Gulam Jilani ◽

Safdar Ali

Keyword(s):

Simple Sequence Repeats ◽

Simple Sequence

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Cross-species microsatellite amplification in Vasconcellea and related genera and their use in germplasm classification

Genome ◽

10.1139/g06-035 ◽

2006 ◽

Vol 49 (7) ◽

pp. 786-798 ◽

Cited By ~ 13

Author(s):

T Kyndt ◽

B Van Droogenbroeck ◽

A Haegeman ◽

I Roldán-Ruiz ◽

G Gheysen

Keyword(s):

Population Genetics ◽

Chloroplast Microsatellites ◽

Microsatellite Data ◽

Chloroplast Microsatellite ◽

Diversity Assessment ◽

Ssr Primers ◽

Polymorphism Rate ◽

Nuclear Ssr ◽

Simple Sequence ◽

Future Population

To generate inexpensive and efficient DNA markers for addressing a number of population genetics problems and identification of wild hybrids in Vasconcellea, we have evaluated the use of simple sequence repeat (SSR) primers previously developed for other species. A set of 103 Vasconcellea accessions and some individuals of the related genera Carica and Jacaratia were analyzed with 10 primer pairs directing amplification of chloroplast microsatellites in Nicotiana tabacum and 9 nuclear SSR primer pairs recently identified in Vasconcellea × heilbornii. Heterologous amplification of chloroplast SSRs was successful for 8 of the 10 loci, of which 6 showed polymorphism. Seven of the 9 nuclear SSR primer pairs were useful in Vasconcellea and often also in Jacaratia and Carica, all revealing polymorphism. Exclusive haplotypes for each described taxon were identified based on chloroplast microsatellite data. Clustering based on separate nuclear and chloroplast data resulted in a clear grouping per taxon, but only low resolution was obtained above species level. The codominancy of nuclear SSRs and the general high polymorphism rate of SSR markers will make them more useful in future population genetics studies and diversity assessment in conservation programs.Key words: Carica, Jacaratia, Vasconcellea, simple sequence repeats, cross-species amplification, classification, interspecific hybrids.

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