Detection Of DNA Polymorphisms Research Articles

Understanding the influence of applying plant extracts and microorganism culture filtrates against barley leaf rust disease

Rust fungi are devastating plant pathogens, and several Puccinia species have exerting substantial financial impacts on global barley cultivation. Fungicides are used on a large scale as an effective method for combating phytopathogenic fungi. The negative environmental impacts of fungicides are steadily escalating on a daily basis. Consequently, researchers are currently exploring alternative approaches to mitigate the use of fungicides, such as the utilization of plant extracts. This method has proven effective due to its incorporation of natural antifungal substances. Among the nine natural elicitors that were tested, the application of plant extracts on barley seedlings resulted in an increase in the incubation and latent periods of Puccinia hordei. These periods are integral components of partial and induced resistance, effectively mitigating the incidence of barley leaf rust disease by over 70% on mature plants. Similarly, the biochemical analyses demonstrated a notable augmentation in all the tested treatments’ overall phenolics and oxidative enzyme activities (peroxidase and polyphenol oxidase). Random amplified polymorphic DNA (SCoT) test serves as a viable approach for assessing the impact of plant extracts and microorganisms on barley plants. The results obtained from this study indicate that the detection of DNA polymorphism through SCoT analysis holds a significant potential powerful tool to evaluate genetic changes compared with untreated plants although some of them tested displayed high similarities at the morphological reaction.

Induction of genetic variability with gamma radiation and detection of DNA polymorphisms among radiomutants using sequence-related amplified polymorphism markers in Gaillardia pulchella Foug. plants

Induction of genetic variability with gamma radiation and detection of DNA polymorphisms among radiomutants using sequence-related amplified polymorphism markers in Gaillardia pulchella Foug. plants

Genetic diversity analysis and core collection construction for Amaranthus tricolor germplasm based on genome-wide single-nucleotide polymorphisms

• Genetic diversity among Amaranthus tricolor accessions was evaluated using genome-wide SNPs. • A set of 5638 SNPs without missing data in accessions was identified. • The population structure was analyzed among accessions. • A core collection of 105 accessions was created. The genus Amaranthus includes 60 to 70 species, some used as grain or leafy vegetable crops, others as ornamental crops. A. tricolor is used as a traditional leafy vegetable in Asia. It has a remarkably valuable nutrient composition and a high tolerance to environmental stresses but has been neglected in modern breeding. Detecting DNA polymorphisms among accessions helps in understanding the genetic diversity and population structure of germplasm collections. The genetic diversity and population structure were analysed among 465 A. tricolor accessions held by the World Vegetable Center genebank with genome-wide single-nucleotide polymorphisms (SNPs) developed by the double-digest restriction-site-associated DNA sequencing method. We found a total of 10 509 SNPs among the accessions and identified a set of 5638 SNPs without missing data in 440 accessions. This marker set was used to verify the species attribution of the germplasm, to analyse genetic diversity and population structure of the collection, and to create a core collection of 105 accessions representing the genetic diversity of 377 source accessions. This core collection is available for research and breeding (World Vegetable Center: info@worldveg.org). The SNP data generated here will contribute to exploring genetic loci related to economically and agronomically important traits in this species.

Genetic Structure of Pinus Populations in the Urals

The sustainable use and conservation of forest resources must be carried out with a detailed study of the main forest-forming plant species. Coniferous forests form the basis of boreal forest ecosystems and are of great economic importance. Representatives of forest-forming boreal coniferous species are species of the genus Pinus, including Siberian pine (Pinus sibirica Du Tour) and Scots pine (Pinus sylvestris L.), which are valuable and widely used woody plant species. The purpose of this research was to conduct an extended study of genetic diversity, genetic structure, and differentiation of P. sibirica and P. sylvestris populations under the conditions of their habitat in the Middle and Northern Urals. We studied twelve populations of two Pinus species using the inter-simple sequence repeat (ISSR)-based DNA polymorphism detection PCR method. Populations are characterized by relatively high levels of genetic diversity (P. sylvestris: He = 0.163; ne = 1.270; I = 0.249; P. sibirica: He = 0.148; ne = 1.248; I = 0.225). Analysis of the intrapopulation genetic structure reveals that the studied populations are highly differentiated (P. sylvestris: GST = 0.362; P. sibirica: GST = 0.460). The interpopulation component comprised 36% and 46% of the total genetic diversity for P. sylvestris and P. sibirica, respectively. Using various algorithms to determine the spatial genetic structure, it was determined that P. sylvestris populations form two groups according to their location at a certain altitude above sea level. P. sibirica populations form two clusters, with an additional subdivision of the two populations into subclusters identified. The data obtained during the study may be useful for further research as well as for conservation management planning and related forestry practices aimed at preserving the genetic resources of valuable forest plant species.

Полиморфизм ДНК собак. VI. Индивидуализирующие ампликоны

To detect DNA polymorphism in dogs and their wild relatives, a fairly simple method was used in the form of virtual amplification of certain random areas of their genomes using multiplex RAPD analysis with primers with arbitrary nucleotide sequences, which does not require prior knowledge of the sequences of nitrogenous bases of the detected DNA fragments. At the same time, information about the complete genomes of the studied species predicts the expected results, which makes it possible to reject unsuitable primers before conducting "wet" experiments. The multiplex RAPD analysis conducted in silico with 12 decameric primers, the sequences of which exclude the formation of homo- and heterodimers in PCR, showed both genomic similarities and differences between different canid species. If amplicons common to all the studied dog samples are removed from the final results of such virtual amplification, leaving only significant ones that actually act as individualizing, then it is potentially possible to DNA-cataloging each canine specimen with the probability of a random coincidence of their genomic barcodes on average one event per quadrillion.

Genetic Structure, Differentiation and Originality of Pinus sylvestris L. Populations in the East of the East European Plain

In order to carry out activities aimed at conservation and rational use of forest resources; it is necessary to study the main forest-forming plant species in detail. Scots pine (Pinus sylvestris L., Pinaceae) is mainly found in the boreal forests of Eurasia and is not so often encountered in the east of the East European Plain. The aim of the study was to study the genetic diversity, structure and differentiation of Scots pine populations in the east of the East European Plain. We studied ten populations of P. sylvestris using the Inter Simple Sequence Repeats (ISSR)-based DNA polymorphism detection method. Natural populations are demonstrated by relatively high rates of genetic diversity (He = 0.167; ne = 1.279; I = 0.253). At the same time, there is a tendency for a decrease in the genetic diversity of the studied populations of P. sylvestris from west to east. Analysis of the genetic structure shows that the studied populations are highly differentiated (GST = 0.439), the intrapopulation component accounts for about 56% of the genetic diversity. Using various algorithms for determining the spatial genetic structure, it is found that the studied populations form two groups of populations in accordance with geographic location. With the help of a genetic originality coefficient, populations with specific and typical gene pools are identified. They are recommended as sources of genetic diversity and reserves for the conservation of genetic resources of the species.

Effects Of Molecular Markers Consequences On Genotyping Errors

Genotype error can greatly reduce the power of a genetic study. For family data, genotype error can be assessed by examining marker data for non-Mendelian inconsistencies, closely linked markers for double recombination events, and consistency of duplicate genotypes. Genetic markers are widely used to determine the parentage of individuals in studies of mating systems, reproductive success, dispersals, quantitative genetic parameters and in the management of conservation populations. These markers are, however, imperfect for parentage analyses because of the presence of genotyping errors and undetectable alleles, which may cause incompatible genotypes (mismatches) between parents and offspring and thus result in false exclusions of true parentage. Highly polymorphic markers widely used in parentage analyses, such as microsatellites, are especially prone to genotyping errors. Molecular markers based on a hybridization reaction or PCR stage that detect DNA polymorphism are currently used in various fields of biology, including the study and preservation of genetic diversity, identification of individuals, phylogenetic, mapping of useful traits of quality and resistance to stress factors. , in the breeding process, biotechnology, etc. Before starting the experiment, researchers must determine what type of markers to use based on the following criteria: the variability and number of required markers, the need for their codominance, the corresponding requirements for the extracted DNA; practical - efficiency, reproducibility of analysis, the necessary appropriate technical support and cost. For a correct interpretation of the results of genotyping, one should take into account the fact that the use of any type of molecular markers is associated with a number of genotyping errors, the main ones being the loss of larger alleles, “zero” alleles, “stutter” alleles due to the peculiarities of Tag polymerase, and non-homology of amplified sequences of the same size (homoplasia). Researchers formulate defining conditions to reduce genotyping errors and reduce their impact on the final analysis. These include the quality and quantity of analyzed DNA, the level of technical capabilities and professionalism of the staff, since the human factor is defined as one of the main reasons for incorrect results; conducting pilot experiments for a comparative assessment of the theoretical and real error rate. The minimization of errors is achieved by assessing the capabilities of a particular type and screening markers; optimization of experimental methods, proper use of controls, replicates, and development of statistical approaches to identify errors. The trade-off between culling error-generating loci and increasing the potential of the retained loci to amplify the genetic signal can be different in different studies, but the main thing is that this signal is not lost for the sake of an “acceptable” level of error and the researchers develop empirical approaches to achieve the desired compromise.so that this signal is not lost for the sake of an acceptable level of error and researchers develop empirical approaches to achieve the desired compromise.so that this signal is not lost for the sake of an acceptable level of error and researchers develop empirical approaches to achieve the desired compromise.

Detecting DNA polymorphism and genetic diversity in a wide pistachio germplasm by RAPD markers

Assessing the genetic diversity in the population is the prerequisite to start and develop plant breeding projects. Pistacia vera is considered as a commercial species of Pistacia genus. In Iran, Pistachio export is in the second place in terms of non-oil exports and in the first place among horticultural crops. Therefore, we collected and analyzed 11 pistachio genotype (Pistacia vera), from two provinces of Iran regions. Our aims were 1) to assess genetic diversity among some of Irainian pistachio cultivars 2) is there a correlation between species genetic and geographical distance? 3) Genetic structure of populations and taxa. We showed significant differences in quantitative morphological characters in plant species. Akbari cultivars depicted unbiased expected heterozygosity (UHe) in the range of 0.028. Shannon information was high (0.49) in Seifadini cultivars. Akbari cultivars howed the lowest value, 0.029. The observed number of alleles (Na) ranged from 0.261 to 2.700 in Shahpasand cultivars and Kalehghoochi cultivars. The effective number of alleles (Ne) was in the range of 1.021-1.800 for Akbari cultivars and Moosaabadi cultivars .Gene flow (Nm) was relatively low (0.38) in pistachio cultivars. The Mantel test showed correlation (r = 0.33, p=0.0001) between genetic and geographical distances. We reported high genetic diversity, which clearly shows the among some of Irainian pistachio cultivars can adapt to changing environments since high genetic diversity is linked to species adaptability. Present results highlighted the utility of RAPD markers and morphometry methods to investigate genetic diversity in pistachio cultivars.

Полиморфизм ДНК собак (Canis familiaris L.). II. RAPD-анализ

A rather simple method of detecting DNA polymorphism in dogs in the form of amplification of random fragments of the genome using RAPD analysis with primers with arbitrary nucleotide sequences, which does not require prior knowledge of the sequences of nitrogenous bases of the detected DNA fragments, is considered. However, information about the complete genomes of the investigating species of organisms and, dogs in particular, allows with a preliminary in silico RAPD analysis to predict the expected results for each primer and their multiplex composition, which makes it possible at this stage to reject unsuitable primers before conducting "wet" experiments. In the case of known genomes of a number of related organisms for example in this case dogs, the multiplex RAPD analysis conducted in silico with six decameric primers, the sequences of which exclude the formation of homo- and heterodimers in PCR showed both genomic similarities and differences between different breeds, as well as with their wild relative gray wolf. Multiplex in silico RAPD analysis is a virtual PCR and if amplicons common to all studied organisms are removed from such amplification, leaving only significant ones, then this tool in the form of the ABCDNA_GS program created by us can be used to establish phylogenetic kinship, especially of those organisms whose genomes are highly collinear, which is just typical of the genomes of different dog breeds.

Determination of Genetic Relations among Tomato Accessions in Sulaymaniyah Region through ISSRs Markers Genetic Relations in Tomato Accessions

The goal of this study was to examine the genetic difference among thirty two tomato accessions (Solanum lycopersicum L.) grown in Sulaymaniyah using ISSR molecular markers technique. The results of ISSR markers revealed 65 amplified fragments, 50 of them were polymorphic from using 15 primers. Fifteen ISSR markers used to detect DNA polymorphism gave polymorphism percentage for each primer range between 50–100% with an average polymorphism percentage reaching 75.61%. ISSR6 and Sola 11 gave the highest polymorphism percentage was 100%, while 3F, Sola 5 and Sola 12 did not give any amplification. The mean of PIC (Polymorphic Information Content) value was 0.50 for ISSR markers. The similarity matrix was obtained by using Jaccard’s coefficients, based on polymorphic bands and dendrogram constituted through UPGMA cluster analysis. The dendrogram revealed 4 main groups. Genetic similarity (GS) ranged from 0.261 to 0.941 within studied accessions. The highest similarity was 0.941 for the genotype pairs G7 and G16. However, the lowest similarity index was 0.261 among G15-G24 and G15-G26. Tomato accessions were determined by two populations according to STRUCTURE analysis. The ISSR marker system ensured useful information in describing genetic diversity among tomato accessions collected from different geographical around Sulaymaniyah province.

Use of Electrocatalysis for Differentiating DNA Polymorphisms and Enhancing the Sensitivity of Electrochemical Nucleic Acid-Based Sensors with Covalent Redox Tags-Part II.

Single-nucleotide polymorphisms (SNPs), insertion/deletion (indel) polymorphisms, and DNA methylation are the most frequent types of genetic variations. As such, DNA polymorphisms play significant roles in genetic mapping and diagnostics. Thus, analytical methods enabling DNA polymorphism detection will provide an invaluable means for early disease diagnosis. However, no single electrochemical nucleic acid-based sensor has achieved the detection of the three major polymorphisms (SNPs, indel polymorphisms, and DNA methylation) with sufficient specificity and sensitivity. In response, we explore the utilization of a catalytic reaction between methylene blue (MB) covalently linked to surface-bound nucleic acid and freely diffusing ferricyanide (Fe(CN)63-) to improve specificity and sensitivity of DNA polymorphism detection. We find that the dynamics of the nucleic acid tether is an additional rate-limiting factor for the electrocatalytic reaction, in addition to the more traditional kinetic and excess factors. Our proof-of-concept experiments demonstrate that the use of electrocatalysis enables differentiation of the three polymorphisms when target sequences are present at 10 nM. We hypothesize that this ability is a result of the distinct dynamics of the DNA probe with each respective polymorphism. In addition to the specificity the sensor displays, the sensor achieves a 20 pM limit of detection. We believe that the electrocatalysis between nucleic acid-tethered MB and Fe(CN)63- is highly promising for electrochemical nucleic acid-based sensors to achieve better specificity and sensitivity.

Efficient mutation induction using heavy-ion beam irradiation and simple genomic screening with random primers in taro (Colocasia esculenta L. Schott)

Progress in conventional breeding methods for taro (Colocasia esculenta L. Schott) via crossing has been limited, and suitable genetic materials for the development of new cultivars are scarce as most commercial taro cultivars are either non-flowering or rarely flowering triploids. In an attempt to advance taro breeding, we performed mutational breeding by heavy-ion beam irradiation of multiple shoots of ‘Chiba maru’ cultivar. Using 2–10 Gy neon and carbon ion beams, we achieved a plant survival rate of more than 90 % and used 94 surviving plants for genomic screening. To efficiently detect DNA polymorphisms induced by ion beam irradiation in young plants, we used five sets of 15-mer randomly amplified polymorphic DNA and arbitrarily primed-polymerase chain reaction random primers based on retrotransposon sequences for genomic screening. Two plants had polymorphic DNA bands, and the specific DNA patterns were maintained in all leaves. In one of these plants, which lacked somatic mosaicism (Cm10), the polymorphic patterns were maintained in the leaves and cormels of clones propagated from daughter cormels. Ion beam irradiation of multiple taro shoots could thus generate mutants that can be developed as new cultivars; the resulting novel polymorphic patterns would facilitate inter- and intra-cultivar identification.

Detection of dna polymorphism of transgenic wheat plants with proline metabolism heterologous genes

Detection of dna polymorphism of transgenic wheat plants with proline metabolism heterologous genes

Sensitivity of Seeds to Chemical Mutagens, Detection of DNA Polymorphisms and Agro-Metrical Traits in M1 Generation of Coffee (Coffea arabica L.)

Coffee (Coffea Arabica L.) is threatened by biotic and abiotic stresses. Nevertheless, the breeding of Arabica coffee is restricted due to its low genetic diversity. Crop improvement via mutagenesis represents an alternative for increasing genetic variability and facilitating breeding. In this sense, coffee seeds cv. Catuai were treated for 8 h with a solution of sodium azide (NaN3) (0, 50, 75, 100, and 125 mM) and ethyl methane sulfonate (EMS) (0, 80, 160, 240, 320, and 400 mM). The genetic variability induced in coffee plants after mutagenic treatment with sodium azide was determined by RAPD and AFLP analyses. As the concentration of applied NaN3 and EMS increased, the germination, seedling height, and root length decreased. The LD50 values for NaN3 and EMS were between 50-75 mM and 160-240 mM, respectively. For the 12 RAPD primers evaluated, a total of 46 fragments were obtained of which 34 were polymorphic bands (74%). The amplification with six AFLP selective primer combinations allowed the identification of 36 polymorphisms (17.8%). The analysis revealed that both NaN3 and EMS induced variability within the DNA regions amplified with AFLP and RAPD markers. Finally, under field conditions, significant differences were noticed with respect to plant height, number of nodes in the orthotropic stem, and number of branches of the M1 mutant (NaN3-treated) plants compared to the non-mutant plants. Optimal conditions for NaN3 and EMS mutagenesis using seeds were determined and the optimized conditions have been used to generate a NaN3 mutant M1 coffee var. Catuai population.

The Evolution of DNA Typing in Agri-Food Chain

Background: DNA typing has revolutionised not only diagnostics and forensics but also how we can analyse food. A number of techniques have been successfully applied for DNA analysis of plant-derived food however, unlike forensics, no method has become universally employed. Methods: A keyword-based search was performed using the ISI-Web of Science database to look for research articles on DNA testing in agri-food chain. After screening and eligibility check, the systematic review was performed focusing on the techniques used to detect DNA polymorphisms. Results: The collection and summarization of the eligible peer-reviewed empirical evidence indicated that PCR-based methods are the predominant technical approach for DNA testing in agri-food chain. Simple Sequences Repeats are the preferred DNA molecular markers. In recent years, DNA-sequencing is expanding, with the DNA barcoding representing the most popular option for species identification. Hypothesis-free NGS approaches are limited. Conclusions: The choice of the approach is mainly dictated by the aim of the genetic analysis (e.g. to distinguish plant species or varieties) and the need of quantitative information, more than the features of the food product or beverages. The importance of new technologies (e.g. NGS-based) is growing but their use remains narrow compared to the diagnostic sector.

Molecular characterization and genetic diversity in some Egyptian wheat (Triticum aestivum L.) using microsatellite markers

Wheat (Triticum aestivum L.) is the most important and strategic cereal crop in Egypt and has many bread wheat varieties. Seventeen Egyptian bread wheat varieties used in this study with a set of sixteen wheat microsatellite markers to examine their utility in detecting DNA polymorphism, estimating genetic diversity and identifying genotypes. A total of 190 alleles were detected at 16 loci using 16 microsatellite primer pairs. The number of allele per locus ranged from 8 to 20, with an average of 11.875. The polymorphic information content (PIC) and marker index (MI) average values were 0.8669, 0.8530 respectively. The (GA) n microsatellites were the highest polymorphic (20 alleles). The Jaccard's Coefficient for genetic similarity was ranged from 0.524 to 0.109 with average of 0.375. A dendrogram was prepared based on similarity matrix using UPGMA algorithm, divided the cultivars into two major clusters. The results proved the microsatellite markers utility in detecting polymorphism due to the discrimination of cultivars and estimating genetic diversity.

Genetic diversity analysis based on sequence-related amplified polymorphism (SRAP) reveals the genetic background of Xinan tree peony group cultivars from different geographical provenances

The Xinan tree peony cultivar group, one of four Chinese peony cultivar groups, is distributed sparsely throughout Southwest China. This study aimed to characterize its genetic diversity and its genetic relationships with other peony groups. A total of 96 specimens from seven groups of different geographical provenances were collected and their genetic similarity was analyzed based on sequence-related amplified polymorphism molecular markers. Twenty primer pairs were selected to detect DNA polymorphisms. A total of 868 bands were generated with an average of 43.4 bands per primer pair and 98.39% polymorphic ratio. The genetic similarity coefficient varied from 0.5081 to 0.9173. The closest phylogenetic relationship was found between hybrids 2 and 3 of Paeonia rockii, while the farthest genetic relationship was between P. lutea and P. suffruticosa ‘Bangningzi’. Among the 20 Xinan samples the genetic similarity coefficient ranged from 0.6351 to 0.8710, revealing slight genetic variation. The 96 cultivars clustered into five branches at the genetic similarity coefficient of 0.6419. The results revealed that the Xinan group has a closer relationship with Japanese, French and American groups. Additionally, these results show that the phylogenetic relationships of different tree peony germplasms correspond to their origins and are primarily related with flower color.

Random Priming PCR Strategies for Identification of Multilocus DNA Polymorphism in Eukaryotes

A historical review of the advent and improvement of the methods for detecting multilocus DNA polymorphism that do not require preliminary knowledge of the individual gene and complete genome sequences of eukaryotes is presented. The first group of these methods includes approaches based on the use of primers with arbitrary sequence (random priming). Another group of methods to detect DNA polymorphism is based on the use of primers that consist of short repetitive sequences having anchor nucleotides at the 5'- or 3'-ends that position the annealing sites of these primers (microsatellite priming). Another approach for revealing polymorphism that does not require knowledge of the DNA sequence is based on cleavage of total DNA by a combination of restriction endonucleases (random cleavage) accompanied by PCR amplification. Considerable attention is paid to the opportunities of using these approaches to detect DNA polymorphism in the form of converting the obtained data to digital format and creation of integrative databases for all organisms, regardless of the methods used.

Genome-Wide Discovery of DNA Polymorphisms in Mei (Prunus mume Sieb. et Zucc.), an Ornamental Woody Plant, with Contrasting Tree Architecture and their Functional Relevance for Weeping Trait

Next-generation sequencing technologies provide opportunities to ascertain the genetic basis of phenotypic differences, even in the closely related cultivars via detection of large amount of DNA polymorphisms. In this study, we performed whole-genome re-sequencing of two mei cultivars with contrasting tree architecture. 75.87 million 100 bp pair-end reads were generated, with 92 % coverage of the genome. Re-sequencing data of two former upright mei cultivars were applied for detecting DNA polymorphisms, since we were more interested in variations conferring weeping trait. Applying stringent parameters, 157,317 mutual single nucleotide polymorphisms (SNPs) and 15,064 mutual insertions-deletions (InDels) were detected and found unevenly distributed within and among the mei chromosomes, which lead to the discovery of 220 high-density, 463 low-density SNP regions together with 80 high-density InDel regions. Additionally, 322 large-effect SNPs and 433 large-effect InDels were detected, and 10.09 % of the SNPs were observed in coding regions. 5.25 % SNPs in coding regions resulted in non-synonymous changes. Ninety SNPs were chosen randomly for validation using high-resolution melt analysis. 93.3 % of the candidate SNPs contained the predicted SNPs. Pfam analysis was further conducted to better understand SNP effects on gene functions. DNA polymorphisms of two known QTL loci conferring weeping trait and their functional effect were also analyzed thoroughly. This study highlights promising functional markers for molecular breeding and a whole-genome genetic basis of weeping trait in mei.

Development and validation of allele-specific SNP/indel markers for eight yield-enhancing genes using whole-genome sequencing strategy to increase yield potential of rice, Oryza sativa L.

BackgroundRice is one of the major staple foods in the world, especially in the developing countries of Asia. Its consumption as a dietary source is also increasing in Africa. To meet the demand for rice to feed the increasing human population, increasing rice yield is essential. Improving the genetic yield potential of rice is one ideal solution. It is imperative to introduce the identified yield-enhancing gene(s) into modern rice cultivars for the rapid improvement of yield potential through marker-assisted breeding.ResultsWe report the development of PCR-gel-based markers for eight yield-related functional genes (Gn1a, OsSPL14, SCM2, Ghd7, DEP1, SPIKE, GS5, and TGW6) to introduce yield-positive alleles from the donor lines. Six rice cultivars, including three each of donor and recipient lines, respectively, were sequenced by next-generation whole-genome sequencing to detect DNA polymorphisms between the genotypes. Additionally, PCR products containing functional nucleotide polymorphism (FNP) or putative FNPs for yield-related genes were sequenced. DNA polymorphisms discriminating yield-positive alleles and non-target alleles for each gene were selected through sequence analysis and the allele-specific PCR-gel-based markers were developed. The markers were validated with our intermediate breeding lines produced from crosses between the donors and 12 elite indica rice cultivars as recipients. Automated capillary electrophoresis was tested and fluorescence-labeled SNP genotyping markers (Fluidigm SNP genotyping platform) for Gn1a, OsSPL14, Ghd7, GS5, and GS3 genes were developed for high-throughput genotyping.ConclusionsThe SNP/indel markers linked to yield related genes functioned properly in our marker-assisted breeding program with identified high yield potential lines. These markers can be utilized in local favorite rice cultivars for yield enhancement. The marker designing strategy using both next generation sequencing and Sanger sequencing methods can be used for suitable marker development of other genes associated with useful agronomic traits.Electronic supplementary materialThe online version of this article (doi:10.1186/s12284-016-0084-7) contains supplementary material, which is available to authorized users.