Simple Sequence Repeat Primer Sets Research Articles

Genetic variation and association mapping in the F2 population of the Perilla crop (Perilla frutescens L.) using new developed Perilla SSR markers

The transcriptome sequencing approach RNA-seq represents a powerful tool for transcriptional analysis and development of simple sequence repeat (SSR) markers for nonmodel crop. In the Perilla crop, analysis of the distribution of different repeat motifs showed that the most abundant type was dinucleotide repeats (62.0%), followed by trinucleotide repeats (35.3%), with the two together comprising 97.3% of the eSSR repeats. In this study, we developed 39 new SSR primer sets by the transcriptome sequencing approach RNA-sEq. In total, 130 alleles were detected segregating in nine Perilla accessions with an average of 3.3 alleles per locus, ranging from 125 to 360 bp. The number of alleles per locus ranged from two to six. To detect SSR markers associated with morphological characteristics of Perilla crop, 40 individuals from an F2 population of Perilla were selected for association analysis based on their leaf- and plant-related characteristics. An association analysis of 37 SSR markers and 9 leaf- and plant-related traits in the 40 individuals of the F2 population was conducted. From the analysis, we identified 12 SSR markers associated with leaf-related traits and 11 SSR markers associated with plant-related traits. Therefore, the new Perilla SSR primers described in this study could be helpful in identifying genetic diversity and genetic mapping, designating important genes/QTLs for Perilla crop breeding programs, and allowing Perilla breeders to improve leaf and plant quality through marker-assisted selection (MAS) breeding programs.

SSR markers developed using next-generation sequencing technology in pineapple, Ananas comosus (L.) Merr.

Simple sequence repeat (SSR) markers provide a reliable tool for the identification of accessions and the construction of genetic linkage maps because of their co-dominant inheritance. In the present study, we developed new SSR markers with next-generation sequencing using the Roche 454 GS FLX+ platform. Five hundred SSR primer sets were tested for the genetic identification of pineapple, including 100 each for the di-, tri-, tetra-, penta-, and hexa-nucleotide motif SSRs. In total, 160 SSR markers successfully amplified fragments and exhibited polymorphism among accessions. The SSR markers revealed the number of alleles per locus (ranging from 2 to 13), the expected heterozygosity (ranging from 0.041 to 0.823), and the observed heterozygosity (ranging from 0 to 0.875). A total of 117 SSR markers with tri- or greater nucleotide motifs were shown to be effective at facilitating accurate genotyping. Using the SSR markers, 25 accessions were distinguished genetically, with the exception of accessions ‘MD-2’ and ‘Yonekura’. The developed SSR markers could facilitate the establishment of efficient and accurate genetic identification systems and the construction of genetic linkage maps in the future.

Sources of genetic resistance in maize to Fusarium stalk rot andtheir variations at molecular level

Identifying the resistant genotypes is one of the vital strategies to control Fusarium stalk rot disease in maize. Fifty accessions of maize germplasm were evaluated for resistance to stalk rot caused by Fusarium verticillioides at the Maize and Millet Research Institute, Yousafwala, Pakistan, during the spring and autumn of 2010, and their genetic variations were also studied at the molecular level to avoid environmental effects in the Department of Medicinal Chemistry, University of Minnesota, USA. Disease severity was calculated in the field using a severity scale (SS) and direct estimation of stalk discoloration (SD) by artificial inoculation method. Both SS and SD results were highly significant (P < 0.01) in both seasons and maize accessions significantly differed in SS (P < 0.01) and SD (P < 0.01). Disease assessments based on SS and SD were significantly correlated (r = 0.983, 0.974; P < 0.01) in spring and autumn, respectively. Two genotypes, EL7 and Y11, showed highly resistant response in both growing seasons. Variations among the lines were also exploited by using 14 simple sequence repeat primer sets. A total of 535 alleles were amplified with an average of 10.7 alleles per genotype. The highest number of alleles per locus was seen with the xp-umc1186 primer, exhibiting 128 alleles with an average of 2.5 alleles per genotype. Resistance genotypes can be utilized in hybridization programs for the improvement of local high-yielding varieties.1397124194

큰느타리(Pleurotus eryngii) 품종 판별을 위한 초위성체 유래 다중 표지 개발

For development of a method for differentiation of Pleurotus eryngii cultivars, simple sequence repeats (SSR) from whole genomic DNA sequence analysis was used for genotyping and two multiplex-SSR primer sets were developed. These SSR primer sets were employed to distinguish 12 cultivars and strains. Five polymorphic markers were selected based on the genotyping results. PCR using each primer produced one to four distinct bands ranging in size from 200 to 300 bp. Polymorphism information content (PIC) values of the five markers were in the range of 0.6627 to 0.6848 with an average of 0.6775. Unweighted pairgroup method with arithmetic mean clustering analysis based on genetic distances using five SSR markers classified 12 cultivars into two clusters. Cluster I and II were comprised of four and eight cultivars, respectively. Two multiplex sets, Multi-1 (SSR312 and SSR366) and Multi-2 (SSR178 and SSR277) completely discriminated 12 cultivars and strains with 21 alleles and a PIC value of 0.9090. These results might be useful in providing an efficient method for the identification of P. eryngii cultivars with separate PCR reactions.

Simple sequence repeat (SSR) marker를 이용한 벼 품종 식별

The objective of this study was carried out to evaluate the suitability of simple sequence repeat (SSR) markers for genetic diversity assessment and identification of rice varieties. The 23 primers selected from 50 SSR primers showed polymorphisms in the 21 rice varieties. The 2 to 9 SSR alleles were detected for each locus with an average of 3.00 alleles per locus. The polymorphism information content (PIC) ranged from 0.091 to 0.839. Based on band patterns, UPGMA cluster analysis was conducted. These varieties were separated into 4 groups corresponding to rice ecotype and pedigree information and genetic distance of cluster ranging from 0.59 to 0.92. The 4 SSR primer sets (RM206, RM225, RM418, RM478) selected from 23 polymorphic primers were differentiated all the rice variety from each other by markers genotypes. These markers may be used wide range of practical application in variety identification of rice.

The use of Simple Sequence Repeats (SSRs) to identify commercially important potato (Solanum tuberosum L.) cultivars in South Africa

The morphological traits that are traditionally used to identify potato cultivars are not always reliable, especially when dealing with in vitro plants. Various molecular marker techniques have been described for cultivar identification, but the Simple Sequence Repeat (SSR) technique has certain qualities that render it highly suitable for this application. In this study five SSR primer sets were used to characterize twenty-four commercially important potato cultivars. All profiles were found to be reliable and no variation was found between clones of the same cultivar. The number of polymorphisms detected with each of the markers varied, but none of the primers yielded only monomorphic fragments. The multilocus primer, STIIKA produced unique profiles for each of the 24 primer sets. However, the complicated nature of the profiles limits its use for routine diagnostic purposes. The use of the markers STS and STU 69633 the fact that they can be analysed simultaneously on one gel, saves time and costs. The present study thus confirms that SSRs can be employed in a routine profiling system to provide highly discriminative and standardized profiles for South African potato cultivars.