Marker Technology Research Articles

Augmented reality marker technology as a means of geometric literacy development: efficiency and cognitive load

Introduction. The introduction of augmented reality technology into the educational process as an optimal means for visualizing three-dimensional objects opens up prospects for solving the problem of low geometric literacy, which has been detected over a number of years according to the results of the exam, GIA and PISA. One of the insufficiently studied pedagogical aspects of the use of educational AR tools is the volume of cognitive load on students in the learning process. The purpose of this study is to find out whether the use of three-dimensional AR-visualization can increase the effectiveness of training in solving geometric problems and reduce extraneous cognitive load and increase the relevant. Materials and methods. The study was organized according to the scheme of a training experiment using the control and experimental groups with measurements of the skills of solving geometric problems "before and after". The subjects were 40 first-year students of the Far Eastern Federal University, studying in the program of the pedagogical bachelor's degree in the humanities. For the diagnosis of perceived cognitive load, we used the translated into Russian and modified questionnaire of cognitive load CSL by Lepping et al., which includes three subscales – internal, extraneous and relevant cognitive loads. Primary results were analyzed using the apparatus of descriptive statistics, the Kolmogorov-Smirnov Z-test and T-tests for two independent samples and for paired samples Research results. The results showed that training using a three-dimensional AR-visualization leads to a higher growth in the results of solving geometric problems than training using three-dimensional visualization of the model on the plane (Т = -3,00**,р=0,008). It was also found that AR-mixing positively affects the volume of cognitive load in students, allowing you to reduce the extraneous load (t = - 2,04*, p=0,04) and increase the relevant релевантную (t = 2,75**, p=0,009). Conclusions. The data identified in the study contribute to scientific justifications of the methods of teaching mathematical disciplines, the development of educational AR applications, as well as to deepening the understanding of the cognitive-psychological mechanisms of the learning process

Genomic characterization of Puccinia triticina using molecular marker technology.

Leaf rust, caused by Puccinia triticina, is the most common rust disease of wheat. The fungus is an obligate parasite capable of producing infectious urediniospores. To study the genetic structure of the leaf rust population 20 RAPD primers were evaluated on 15 isolates samples collected in Pakistan. A total of 105 RAPD fragments were amplified with an average of 7 fragments per primer. The number of amplified fragments varied from 1 to 12. GL Decamer L-07 and GL Decamer L-01 amplified the highest number of bands (twelve) and primer GL Decamer A-03 amplified the lowest number of bands i.e one. Results showed that almost all investigated isolates were genetically different that confirms high genetic diversity within the leaf rust population. Rust spores can follow the migration pattern in short and long distances to neighbor areas. Results indicated that the greatest variability was revealed by 74.9% of genetic differentiation within leaf rust populations. These results suggested that each population was not completely identical and high gene flow has occurred among the leaf rust population of different areas. The highest differentiation and genetic distance among the Pakistani leaf rust populations were detected between the leaf rust population in NARC isolate (NARC-4) and AARI-11and the highest similarity was observed between NARC isolates (NARC-4) and (NARC-5). The present study showed the leaf rust population in Pakistan is highly dynamic and variable.

Molecular characterization of mutant lines of Ayvalik olive cultivar obtained by chemical mutation

This research was carried out with the aim to detect the mutagenic effect of three different doses (15, 20 and 25 mM) of Ethyl Methane Sulphonate on the Ayval?k olive cultivar (Olea europaea L.), to detect the variation and to identify whether individuals are genetically different from Ayval?k olive cultivar using molecular marker technologies. 23 mutant lines were screened using 28 SSR markers and a total of 138 alleles were detected and the number of alleles per primer ranged from 2 to 9 with an average of 4.9 alleles per primer. The polymorphism information content (PIC) value was changed between 0.4-0.98. The genetic similarity between Ayval?k olive cultivar and mutant lines was found between 5.5% and 78%. The mutant lines 15mM-12, 15mM-11 and 25mM-3 were found similar to Ayval?k cultivars at the rate of 78, 63 and 55%, respectively. Whereas, 20mM-5, 15mM-4 and 15mM-15 mutant lines were found distant to Ayval?k cultivar at the rate of 5.5, 5.6 and 8% genetic similarity, respectively. Ethyl Methane Sulphonate was successfully used in this study to extend the genetic diversity of the Ayval?k olive cultivar. Mutants might be screened for agricultural and quality traits and promising lines might be registered.

HYBRID PURITY ANALYSIS OF RICE USING MICRO SATELLITE MARKERS

Rice is the staple food crop which can fight against hunger and poverty in most of the developing nations. Hybrids perform better than the traditional verities in both yield and quality aspects. But the main problem lies in the genetic purity of the hybrids. In this study, molecular test was conducted and compared with the grow out test to assess the genetic purity of the rice hybrid, JGLH1 at Seed Research and Technology Centre, Professor Jayashankar Telangana State Agricultural University (PJTSAU), Hyderabad. JGLH1 and its parents were used as materials, using SSR molecular marker technology, to select primers and identify genetic purity according to its polymorphism. The SSR marker, XA 21 was amplified on the DNA extracted from the rice hybrid, JGLH1, and its parents, CMS 64A and JBR7. The amplification of marker was conducted on the DNA of 20 hybrid leaves and 1 leaf from each parent, separately. The marker was amplified at 650 bp in the parent, CMS-64A, and 730bp in JBR7, and amplified at both the base pairs in their F1 progeny, JGLH1. This confirms the hybridity of the rice hybrid JGLH1. The marker was unveiled in all the 20 leaves of the hybrid rice sample ensuring the purity of the seed lot. The grow out test results also showed 100% purity without any deviations. It concludes that molecular marker, XA 21 is effective in hybrid purity evaluation of the rice hybrid, JGLH 1.

Evaluation and comparison of population genetics software in Rabari Tribe of Gujarat population

BackgroundToday, when forensic experts talk about quantifiable hereditary traits, they do not just depend on the assessment and examination of DNA profiles but also relate them to the population structures. The use of high-throughput molecular marker technologies and advanced statistical and software tools have improved the accuracy of human genetic diversity analysis in many populations with limited time and resources. The present study aimed to investigate the genomic diversity in Gujarat’s Rabari population, using 20 autosomal genetic markers.Numerous bio-statistical software programs are available for the interpretation of population data in forensics. These statistics deal with the measurement of uncertainty and also provides a probability of a random match. The present paper aims to provide a practical guide to the analysis of population genetics data. Three statistical software packages named Cervus, Genepop, and Fstat are compared and contrasted. The comparison is performed on the profiles obtained from fifty unrelated blood samples of healthy male individuals. DNA was extracted using the organic extraction method, 20 autosomal STR loci were amplified using PowerPlex 21 kit (Promega, Madison, WI, USA) and detected on 3100 Genetic Analyser (Life Technologies Corporation, Carlsbad, CA, USA).ResultsA total of 170 alleles were observed in the Rabari Tribe of Gujarat population, and allele frequencies ranged from 0.010 to 0.480. The highest allele frequency detected was 0.480 for allele 9 at locus TH01. Based on heterozygosity and the polymorphism information content, FGA may be considered as the most informative markers. Both the combined power of discrimination (CPD) and the combined power of exclusion (CPE) for the 20 analyzed loci were higher than 0.999999. The combined match probability (CPM) for all 20 loci was 2.5 × 10−22.ConclusionsWith respect to the results, the 20 STR loci are highly polymorphic and discriminating in the Gujarat population and could be used for forensic practice and population genetics studies. However, Fstat demonstrated better genetic software for analysis of the demographic structure of a specific or set of populations.

Nomenclatural standards and genetic passports of potato cultivars bred in the A.G. Lorkh All-Russian Research Institute of Potato Farming

In order to preserve the genetic diversity of cultivars, it is recommended to develop documentation approaches through the registration of cultivar nomenclatural standards in accordance with the International Code of Nomenclature for Cultivated Plants. The N.I Vavilov Institute of Plant Genetic Resources keeps developing this approach along with the DNA marker technologies: SSR genotyping and molecular screening with DNA markers of genes controlling valuable traits. In 2018, VIR, together with the leading national centre for potato breeding – the A.G. Lorkh All-Russian Scientific-Research Institute of Potato Farming (now the A.G. Lorkh Russian Potato Research Center), initiated the preparation of nomenclatural standards for potato cultivars bred both at the A.G. Lorkh institute and in co-authorship with other breeding institutions. This paper presents 30 nomenclatural standards which are maintained in the Nomenclature standard fund of the Herbarium of cultivated plants and their wild relatives and weeds (VIR Herbarium, WIR). Also, the paper presents genetic passports of the mentioned 30 cultivars, developed using DNA samples extracted from the plant material of nomenclatural standards. Genetic passports include information about the polymorphism of the 8 chromosome-specific microsatellites and data on the results of molecular screening with 15 markers of 11 genes conferring resistance to the most dangerous pathogens and pests: potato viruses Y and X, late blight and potato cyst nematodes. A comparison of SSR-profiles of nomenclatural standards with those of 66 cultivar samples obtained from various sources made it possible to verify authenticity and homogeneity of the latter.

Molecular Genetics, Genomics and Biotechnology in Crop Plant Breeding, Series II

This second volume of this series of Special Issues provides research papers and reviews on the use of molecular marker technologies, genomics selection, site-directed mutagenesis, gene-discovery by genome-wide association studies and biotechnology in important grain crops, tubers, fruit bearing shrub and small fruit crops [...]

A proline metabolism selection system and its application to the engineering of lipid biosynthesis in Chinese hamster ovary cells

Chinese hamster ovary (CHO) cells are the leading mammalian cell host employed to produce complex secreted recombinant biotherapeutics such as monoclonal antibodies (mAbs). Metabolic selection marker technologies (e.g. glutamine synthetase (GS) or dihydrofolate reductase (DHFR)) are routinely employed to generate such recombinant mammalian cell lines. Here we describe the development of a selection marker system based on the metabolic requirement of CHO cells to produce proline, and that uses pyrroline-5-carboxylase synthetase (P5CS) to complement this auxotrophy. Firstly, we showed the system can be used to generate cells that have growth kinetics in proline-free medium similar to those of the parent CHO cell line, CHOK1SV GS-KO™ grown in proline-containing medium. As we have previously described how engineering lipid metabolism can be harnessed to enhance recombinant protein productivity in CHO cells, we then used the P5CS selection system to re-engineer lipid metabolism by over-expression of either sterol regulatory element binding protein 1 (SREBF1) or stearoyl CoA desaturase 1 (SCD1). The cells with re-engineered proline and lipid metabolism showed consistent growth and P5CS, SCD1 and SREBF1 expression across 100 cell generations. Finally, we show that the P5CS and GS selection systems can be used together. A GS vector containing the light and heavy chains for a mAb was super-transfected into a CHOK1SV GS-KO™ host over-expressing SCD1 from a P5CS vector. The resulting stable transfectant pools achieved a higher concentration at harvest for a model difficult to express mAb than the CHOK1SV GS-KO™ host. This demonstrates that the P5CS and GS selection systems can be used concomitantly to enable CHO cell line genetic engineering and recombinant protein expression.

Genetic Diversity, Chemical Components, and Property of Biomass Paris polyphylla var. yunnanensis.

Paris polyphylla var. yunnanensis is a kind of biomass resource, which has important medicinal and economical values with a huge market. This review article aims to summarize the recent development of biomass P. polyphylla var. yunnanensis. The genetic diversity and chemical components of biomass P. polyphylla var. yunnanensis were reviewed based on the literature. Both the genetic diversity and genetic structure of biomass P. polyphylla var. yunnanensis were compared by using molecular marker technologies. All the extraction processes, harvest time, and drying methods on the chemical components were summarized in detail. The differences of arbuscular mycorrhizal fungi on the infection rate, diosgenin content, microorganisms, enzyme activities, rhizospheric environment, and endogenous hormones were discussed. This review article is beneficial for the applications of biomass P. polyphylla var. yunnanensis as a biomass resource in the biomedical field.

Molecular Breeding Strategy and Challenges Towards Improvement of Downy Mildew Resistance in Cauliflower (Brassica oleracea var. botrytis L.).

Cauliflower (Brassica oleracea var. botrytis L.) is one of the important, nutritious and healthy vegetable crops grown and consumed worldwide. But its production is constrained by several destructive fungal diseases and most importantly, downy mildew leading to severe yield and quality losses. For sustainable cauliflower production, developing resistant varieties/hybrids with durable resistance against broad-spectrum of pathogens is the best strategy for a long term and reliable solution. Identification of novel resistant resources, knowledge of the genetics of resistance, mapping and cloning of resistance QTLs and identification of candidate genes would facilitate molecular breeding for disease resistance in cauliflower. Advent of next-generation sequencing technologies (NGS) and publishing of draft genome sequence of cauliflower has opened the flood gate for new possibilities to develop enormous amount of genomic resources leading to mapping and cloning of resistance QTLs. In cauliflower, several molecular breeding approaches such as QTL mapping, marker-assisted backcrossing, gene pyramiding have been carried out to develop new resistant cultivars. Marker-assisted selection (MAS) would be beneficial in improving the precision in the selection of improved cultivars against multiple pathogens. This comprehensive review emphasizes the fascinating recent advances made in the application of molecular breeding approach for resistance against an important pathogen; Downy Mildew (Hyaloperonospora parasitica) affecting cauliflower and Brassica oleracea crops and highlights the QTLs identified imparting resistance against this pathogen. We have also emphasized the critical research areas as future perspectives to bridge the gap between availability of genomic resources and its utility in identifying resistance genes/QTLs to breed downy mildew resistant cultivars. Additionally, we have also discussed the challenges and the way forward to realize the full potential of molecular breeding for downy mildew resistance by integrating marker technology with conventional breeding in the post-genomics era. All this information will undoubtedly provide new insights to the researchers in formulating future breeding strategies in cauliflower to develop durable resistant cultivars against the major pathogens in general and downy mildew in particular.

Evidence for interspecific hybridization in bryophytes during pre-molecular and molecular eras

Interspecific hybridization had been long recognized as a widespread evolutionary process in vascular plants. In the present review, we summarize knowledge concerning studies of interspecific hybridization in bryophytes before and after the advent of molecular methods. The available data indicate that hybridization is an important evolutionary phenomenon among bryophytes. Evidence for hybridization events before the molecular era is mainly based on studies of intermediacy of parental morphology. The recent molecular marker technology has revolutionized studies of hybridization, generating new insights into the genetic and evolutionary consequences of homoploid and allopolyploid speciation. The current molecular approaches support the prevalence of allopolyploidy in bryophytes. However, we anticipate that homoploid hybridization is under-reported. Finally, we suggest some directions for future studies of hybrid speciation among bryophytes.

Scenario of Plant Breeding in Nepal and Its Application in Rice

Rice, the number one staple food crop of Nepal, contributes nearly 20% to the agricultural gross domestic product, almost 7% to gross domestic product, and supplies with 40% of the food calorie consumption of Nepalese people. Despite of increasing production, the national demand of rice cannot be fulfilled, and billions of rupees are spent yearly for importing rice from India. This article reviews history, recent scenario, prospects, and importance of rice breeding research in Nepal for self-sufficiency. Though plant breeding inception point in Nepal was 1951, the systematic research in rice was started from 1972 after the establishment of the National Rice Research Program. Introduction and evaluation of high yielding exotic germplasm of rice was the initial rice breeding activities. After analysing several foreign materials, CH-45 variety of rice was first recommended in 1959. Nepal Agriculture Research Council (NARC), the leading organisation for rice varietal improvement to date, has been doing rice research activities such as germplasm conservation, exchange, varietal development, verification of technologies, and knowledge updates in collaboration with various organizations. International Rice Research Institute (IRRI), since 1966, has been playing an important role in Nepal’s rice research. Major plant breeding achievements are introduction of exotic materials and their evaluation, local landraces identification, collection and analysis, crossing of local landraces with exotic genetic materials, heterosis breeding, tissue culture technology, genetic marker technology, and National Genebank. RAPD and SSR, DNA-based markers, are mostly used for diversity appraisal and selecting desirable genotypes. Integration of advanced tools such as genetic engineering, bioinformatics, protoplast fusion, and SNP markers could not be still applied in rice research and development. Hence, emphasis should be given to improve the capacity and abilities of the rice scientists and should release more short duration, drought, and submergence-tolerant rice varieties by optimum utilisation of local landraces combining modern and conventional breeding.

Quantification of the geometric uncertainty when using implanted markers as a surrogate for lung tumor motion

Fiducial markers are used as surrogates for tumor location during radiation therapy treatment. Developments in lung fiducial marker and implantation technology have provided a means to insert markers endobronchially for tracking of lung tumors. This study quantifies the surrogacy uncertainty (SU) when using endobronchially implanted markers as a surrogate for lung tumor position. We evaluated SU for 17 patients treated in a prospective electromagnetic-guided MLC tracking trial. Tumor and markers were segmented on all phases of treatment planning 4DCTs and all frames of pretreatment kilovoltage fluoroscopy acquired from lateral and frontal views. The difference in tumor and marker position relative to end-exhale position was calculated as the SU for both imaging methods and the distributions of uncertainties analyzed. The mean (range) tumor motion amplitude in the 4DCT scan was 5.9mm (1.7-11.7mm) in the superior-inferior (SI) direction, 2.2mm (0.9-5.5mm) in the left-right (LR) direction, and 3.9mm (1.2-12.9mm) in the anterior-posterior (AP) direction. Population-based analysis indicated symmetric SU centered close to 0mm, with maximum 5th/95th percentile values over all axes of -2.0mm/2.1mm with 4DCT, and -2.3/1.3mm for fluoroscopy. There was poor correlation between the SU measured with 4DCT and that measured with fluoroscopy on a per-patient basis. We observed increasing SU with increasing surrogate motion. Based on fluoroscopy analysis, the mean (95% CI) SU was 5% (2%-8%) of the motion magnitude in the SI direction, 16% (6%-26%) of the motion magnitude in the LR direction, and 33% (23%-42%) of the motion magnitude in the AP direction. There was no dependence of SU on marker distance from the tumor. We have quantified SU due to use of implanted markers as surrogates for lung tumor motion. Population 95th percentile range are up to 2.3mm, indicating the approximate contribution of SU to total geometric uncertainty. SU was relatively small compared with the SI motion, but substantial compared with LR and AP motion. Due to uncertainty in estimations of patient-specific SU, it is recommended that population-based margins are used to account for this component of the total geometric uncertainty.

Advances in Genomics-Based Breeding of Barley: Molecular Tools and Genomic Databases

Barley is the fourth most important cereal crop and has been domesticated and cultivated for more than 10,000 years. Breeding climate-smart and stress-tolerant cultivars is considered the most suitable way to accelerate barley improvement. However, the conventional breeding framework needs to be changed to facilitate genomics-based breeding of barley. The continuous progress in genomics has opened up new avenues and tools that are promising for making barley breeding more precise and efficient. For instance, reference genome assemblies in combination with germplasm sequencing to delineate breeding have led to the development of more efficient barley cultivars. Genetic analysis, such as QTL mapping and GWAS studies using sequencing approaches, have led to the identification of molecular markers, genomic regions and novel genes associated with the agronomic traits of barley. Furthermore, SNP marker technologies and haplotype-based GWAS have become the most applied methods for supporting molecular breeding in barley. The genetic information is also used for high-efficiency gene editing by means of CRISPR-Cas9 technology, the best example of which is the cv. Golden Promise. In this review, we summarize the genomic databases that have been developed for barley and explain how the genetic resources of the reference genome, the available state-of-the-art bioinformatics tools, and the most recent assembly of a barley pan-genome will boost the genomics-based breeding for barley improvement.

The Potential Role of Transposable Elements as Molecular Markers

Molecular markers emerged as very important biotechnological tools in plant biotechnology. Molecular markers represent any gene region or DNA fragment related to the gene region in the genome. Numerous molecular marker techniques have been developed especially after the discovery of the Polymerase Chain Reaction. In agricultural biotechnology studies; they are used effectively in many areas such as physical mapping, gene discovery, labeling and genetic diversity with molecular marker technologies. Transposons can also be used as genetic markers because they cause insertional polymorphism. Transposons are DNA sequences that displace within the genome, causing permanent mutations and responsible for genome size changes. With the development of technologies, new techniques and the completion of genome studies in many species, transposon has been observed that it is found in almost every living species and a large part of the genome of many species consists of transposons. Plants are the living things with the highest percentage of transposons. Transposons are grouped as DNA transposons and retrotransposons according to their working principles. Studies are conducted to determine the relationship between retrotransposon markers and species. For this purpose, many marker methods have been developed; based on IRAP and REMAP retrotransposon insertion polymorphisms.

Variety Discrimination Power: An Appraisal Index for Loci Combination Screening Applied to Plant Variety Discrimination.

Molecular marker technology is used widely in plant variety discrimination, molecular breeding, and other fields. To lower the cost of testing and improve the efficiency of data analysis, molecular marker screening is very important. Screening usually involves two phases: the first to control loci quality and the second to reduce loci quantity. To reduce loci quantity, an appraisal index that is very sensitive to a specific scenario is necessary to select loci combinations. In this study, we focused on loci combination screening for plant variety discrimination. A loci combination appraisal index, variety discrimination power (VDP), is proposed, and three statistical methods, probability-based VDP (P-VDP), comparison-based VDP (C-VDP), and ratio-based VDP (R-VDP), are described and compared. The results using the simulated data showed that VDP was sensitive to statistical populations with convergence toward the same variety, and the total probability of discrimination power (TDP) method was effective only for partial populations. R-VDP was more sensitive to statistical populations with convergence toward various varieties than P-VDP and C-VDP, which both had the same sensitivity; TDP was not sensitive at all. With the real data, R-VDP values for sorghum, wheat, maize and rice data begin to show downward tendency when the number of loci is 20, 7, 100, 100 respectively, while in the case of P-VDP and C-VDP (which have the same results), the number is 6, 4, 9, 19 respectively and in the case of TDP, the number is 6, 4, 4, 11 respectively. For the variety threshold setting, R-VDP values of loci combinations with different numbers of loci responded evenly to different thresholds. C-VDP values responded unevenly to different thresholds, and the extent of the response increased as the number of loci decreased. All the methods gave underestimations when data were missing, with systematic errors for TDP, C-VDP, and R-VDP going from smallest to biggest. We concluded that VDP was a better loci combination appraisal index than TDP for plant variety discrimination and the three VDP methods have different applications. We developed the software called VDPtools, which can calculate the values of TDP, P-VDP, C-VDP, and R-VDP. VDPtools is publicly available at https://github.com/caurwx1/VDPtools.git.

Genome Based Research in Aquaculture

Genome -based technologies are being instigated to manipulate the structure and function of the genome and to identify the genes of interest for genetic modification of economically important species. Genome editing technologies have also been designed for genetic manipulation of aquaculture species to increase production and quality with minimum investment costs. DNA marker technologies are the most widely used genome technologies. DNA fingerprints are used to construct physical maps while genetic maps are based upon meiotic recombination. BAC fingerprinting is the commonly used method for physical mapping. Next- generation sequencers revolutionized science and allowed the de-novo whole genome sequencing. QTL mapping has made it possible to identify the genes responsible for a particular trait. Government involvement and better training of aqualturists are direly needed to reinforce the practical implications of genome- based technologies.

Bioinformatics analysis of microsatellite sites in the RNA-sequencing of <italic>Meretrix meretrix</italic>

<italic>Meretrix meretrix</italic> is one of the most important economic shellfish species in China due to rich nutrition, delicious meat and high economic value. In this study, <italic>Meretrix meretrix</italic> DNA was transcribed and sequenced by using the second generation high-throughput sequencing technique. Through the statistical analysis of different types of microsatellites in <italic>Meretrix meretrix</italic>, the distribution frequency and number of microsatellites were understood, and the SSR composition characteristics of <italic>Meretrix meretrix</italic> were clarified at the transcriptome level. It is beneficial to the research of individual identification, germplasm resource identification, biological genetic mapping and so on, and has important reference value for further using microsatellite marker technology to carry out genetic marker-assisted breeding and population genetics research. The bioinformatics method was used to analyze the distribution of microsatellite sequences in the transcriptome of <italic>Meretrix meretrix</italic>. After searching the SSR loci of <italic>Meretrix meretrix</italic>, 8 856 complete SSR loci were found. The total length of SSR was 162 416 bp, with an average length of 18.34 bp, accounting for about 0.15% of the total sequence size, including 3 001 single-base repeat sequences, 2 254 three-base repeat sequences, 2 200 four-base repeats sequence, 1 052 two-base repeats sequences, 332 five-base repeat sequences and 13 six-base repeat sequences. The SSR of <italic>Meretrix meretrix</italic> transcriptome contained 26 types of repeats, among which the most was single-base repeat sequence A / T (2 809). The second most was triple-base repeat sequence AAC / TTG (907). Four-base repeat sequence AAAC / TTTG and two-base repeat sequence AT / TA was 588 and 561, respectively, indicating that the distribution of microsatellites in the RNA-sequencing of <italic>Meretrix meretrix</italic> had a preference for A / T. The average length of SSR (integrity) of <italic>Meretrix meretrix</italic> was 18.34 bp, and the main length of microsatellite was 12-20 bp, accounting for 41%. Most of the 8 856 SSR loci in the transcriptome had moderate polymorphism potential, which meant certain value for the future development of microsatellite molecular markers. The results of this study will provide a theoretical basis for the development of microsatellite markers, population genetic diversity, genetic linkage map, identification of germplasm resources and molecular genetics and breeding of shellfish. It also has important reference value for further study of genetic marker-assisted breeding and population genetics by using microsatellite marker technology.

Development of a 76k Alpaca (Vicugna pacos) Single Nucleotide Polymorphisms (SNPs) Microarray.

Small farm producers’ sustenance depends on their alpaca herds and the production of fiber. Genetic improvement of fiber characteristics would increase their economic benefits and quality of life. The incorporation of molecular marker technology could overcome current limitations for the implementation of genetic improvement programs. Hence, the aim of this project was the generation of an alpaca single nucleotide polymorphism (SNP) microarray. A sample of 150 Huacaya alpacas from four farms, two each in Puno and Cerro de Pasco were used for SNP discovery by genotyping by sequencing (GBS). Reduced representation libraries, two per animal, were produced after DNA digestion with ApeK1 and double digestion with Pst1-Msp1. Ten alpaca genomes, sequenced at depths between 12× to 30×, and the VicPac3.1 reference genome were used for read alignments. Bioinformatics analysis discovered 76,508 SNPs included in the microarray. Candidate genes SNPs (302) for fiber quality and color are also included. The microarray SNPs cover 90.5% of the genome length with a density of about 39 ± 2.51 SNPs/Mb of DNA at an average interval of 26.45 ± 18.57 kbp. The performance was evaluated by genotyping 30 family trios and comparing them to their pedigrees, as well as comparing microarray to GBS genotypes. Concordance values of 0.93 and 0.94 for ApeK1 and Pst1-Msp1 generated SNPs were observed. Similarly, 290 fiber quality and color candidate gene SNPs were validated. Availability of this microarray will facilitate genome-wide association studies, marker-assisted selection and, in time, genomic selection.

Study on Sparganium stoloniferum from different regions in China based on appearance characters and ISSR markers

Based on the characteristics and ISSR molecular marker technology, the study is aimed to compare and perform genetic diversity analysis on Sparganium stoloniferum from 7 regions. Molecular identification method was established for S. stoloniferum from Hunan province. Differences among Sparganii Rhizoma samples from seven habitats were analyzed via measuring weight, length, width and thickness of them. Genetic diversity of S. stoloniferum from 7 regions was analyzed by screening out primers amplifying clear band and showing rich polymorphism, then a cultivars dendrogram was built. The target primer was screened out, and the specific band was sequenced. Nine ISSR primers were selected to amplified clear band, rich polymorphism. A total of 73 bands were amplified by nine ISSR primers selected from 27 ISSR primers. On average, each primer produced 8.0 bands. A total of 38 bands were polymorphic, which occupied 52.8% of all bands. The cultivars dendrogram showed the genetic similarity was 0.54-0.94. Genetic similarity coefficient of S. stoloniferum from Jiangsu province, Anhui province and Jiangxi province was big, indicating the differences among them were slight on genetic level. S. stoloniferum from Hunan province is quite different from samples from the other six habitats on appea-rance and genetic level. A specific band(327 bp) in S. stoloniferum from Hunan province was obtained via ISSR-857 primer, and was sequenced. According BLASTn database, there were few sequences similar to the gene fragment and had little correlation with the growth process of plant. ISSR molecular marker technology provides a new idea for the identification of S. stoloniferum. This result confirmed the particularity of S. stoloniferum from ancient Jingzhou.