جستجوی مقالات مرتبط با کلیدواژه "marker" در نشریات گروه "کشاورزی"

The genome-wide association study (GWAS) is a powerful approach to identify genomic regions associated with fertility traits that explain a significant portion of the genetic variance associated with these traits and identify the relevant causal mutations. Evaluating the correlation between each genotyped marker and trait is an essential strategy for GWAS studies that examine the effects of all markers by considering their possible interactions, environmental factors, and even mutual effects between markers. Recently, machine learning methods have been introduced to genomic topics, and the basis of these methods is different from the common methods of genomic evaluation. The machine learning method is used to estimate the genomic breeding values of the candidate animals by considering the training data (genotypic and phenotypic information of the reference population). One of the key advantages of this method is the ability to analyze large data. Machine learning is a branch of artificial intelligence whose goal is to achieve machines that can extract knowledge (learning) from the environment. A variety of machine learning methods (random forest, boosting, and deep learning) are used to model genetic variance and environmental factors, study gene networks, GWAS, study epistasis effects, and genomic evaluation. Random forest is one of the machine learning methods that has been successfully used in various fields of science. This research was conducted to identify markers and genes related to reproductive traits such as calving interval (CI), days open (DO), daughter pregnancy rate (DPR), and age at first calving (AFC) in Iranian Holstein dairy cattle. These traits have already been investigated with the ssGBLUP method and using a smaller sample size. However, in the present research, by using more genotyped animals, a random forest algorithm was used to identify markers and genes related to reproductive traits.
The records used in this research were provided by the National Animal Breeding Center and Promotion of Animal Products of Iran and included AFC, DO, CI, and DPR related to the genotyped bulls' daughters. In this research, the pedigree information of 2774183 animals was used. The genotypic information of the markers related to 2419 Holstein bulls was used. Genomic data quality control was performed using factors such as the number of genotyped SNPs per animal (ACR), the number of genotyped animals per SNP (CR), Hardy-Weinberg equilibrium (HWE), and minor allele Frequency (MAF). When filtering genomic data, the markers whose MAF was less than 5% were removed, and then the samples whose genotyped frequency was less than 90% were identified and removed. Then, the markers whose genotyping rate was less than 95% in the samples were identified and removed. Finally, the SNPs that deviated from the HWE test (P<10-6) were excluded from the analysis as a measure of genotyping error. To control the quality of genomic data, PLINK 1.9 software was used. Then Ranfog software was used in the Linux environment to perform analysis through random forest algorithm.
By using the random forest algorithm, a total of 21 important SNPs were observed, then important fertility trait candidate genes were identified by the gene ontology method, and 62 genes were within 250 Kb of these SNPs. The most significant SNP was observed for AFC. The main SNP for AFC is in ARS-BFGL-NGS-22647 BTA3, for CI is in ARS-BFGL-NGS-114194 (BTA11), for DO is in BTA-74076 -no-rs (BTA5), and for DPR is in ARS-BFGL-NGS-32553 (BTA26). The researchers, who studied fertility traits in Nellore cattle using machine learning methods, identified MPZL1 and CD247 genes on chromosome number 3 and this gene was associated with age at first calving. Many pathways of cell biology affect the performance of reproductive traits. Research has reported the relationship between the CD247 gene and pathways of biology, including cell development and function. Research has shown that the IFFO2 gene plays an important role in the molecular structure of cells, as well as in the mechanism of blastocyst formation, embryos, and the length of gestation in cattle. In a study conducted on the mouse population on the structure of the flagellum and the sperm maturation process, the role of the ALDH4A1 gene in the sperm maturation process was reported. The association of the RPS6KC1 gene with pregnancy rate and antral follicle number in Nellore heifers has been reported. The KAT2B gene is a transcriptional activator that plays an essential role in regulating the correction of histone acetylation and plays an important role in improving carcass quality, muscle and fat development, and metabolism in native Chinese cattle. In addition, they play a key role in regulating biological processes and are related to cell growth, metabolism and immune system function.
  According to the objectives of this research, new information on markers and candidate genes related to reproductive traits in Iranian Holstein dairy cattle was reported. The markers and candidate genes identified in the present research can be used in genomic selection to improve the reproductive traits of Holstein dairy cattle.

Increasing grain yield and improving the quality of bread are among the most important goals of wheat breeding programs in Iran. Understanding the genetic control of traits and finding molecular or morphological markers associated with them are also prerequisites for any genetic engineering program. In this study, 100 progenies of a 10 × 10 diallel cross were used to analyse the genetics of grain yield and bakery values using STS markers associated with HMWG subunits. This research was carried out during 2018 and 2019 cropping season at Gorgan University of Agricultural Sciences and Natural Resources experimental fields. In the first year, 10 wheat cultivars, including Gonbad, Morvarid, Kalate, Ehsan, Sirvan, Baharan, Chamran2, Shush, Mehrgan and Brat collected from different geographical regions of Iran were planted and crossed in the field. In the second year, the parents and crosses were planted in the form of a randomized complete block design with three replications. The grain yield, number of spikes per plant, number of seeds per spike, seed weight, days to emergence and plant height were recorded. The results of this study indicated significant genetic differences between the parents. Narrow-sense heritability analysis revealed that the crossing of cultivars is the best breeding method to enhance seed yield, number of spikes per plant and days to emergence. Also, to improve the number of seeds per spike, seed weight and plant height, classical breeding methods may offer higher efficiency. Marvarid and Gonbad were ranked 1st and 2nd, respectively with respect to general combining abilities for grain yield, attributed to their positive and significant general combining ability effects. The highest specific combining ability was observed for Ehsan×Gonbad, Marvarid×Chamran 2 and Shush×Sirvan crosses. The results of molecular markers analysis showed that the STS markers were able to identify the difference in the baking value of cultivars. The quality score of the cultivars ranged 6 and 10 and to this end, Kalate and Brat were the top cultivars. Therefore, due to superiority in terms of both quantity and quality for yield, these cultivars can be used as parents with desirable genes for future breeding programs. Overall, the STS markers employed in this study proved to be valuable markers for enhancing the genetic background of bread wheat, particularly when employing marker-assisted selection for bakery value.

 Water deficit stress is a serious threat to food security worldwide. Association mapping is a suitable method to identify the location of quantitative traits based on linkage disequilibrium, which is highly effective in describing complex genetic traits. This study aimed to evaluate the population structure and the SNP markers association morphological traits of spring wheat genotypes under water deficit stress conditions.

In this research, genome-wide association mapping was done for 111 spring wheat genotypes. Phenotyping evaluation was done in the form of a simple lattice design with two replications in the agricultural year 2020-2021 under non stress and water deficit stress conditions in the experimental field of Gachsaran Rain-fed Agricultural Research Station in Iran. Genotyping of the samples was done using SNP markers (15 K SNP array) in Trait-Genetic company in Germany. Each genotype was evaluated using 15 thousand SNP markers. The obtained SNP data were filtered in terms of MAF indices (minor allele frequency) and missing data (Missing data >10%). From each of the 21 pairs of bread wheat homologous chromosomes, seven SNP markers with no missing data and with suitable distribution were selected (147 markers in total) to determine the structure of the studied population (Q matrix) using STRUCTURE 2.3 software and the number of groups (K) was identified. The studied traits were flag leaf area, number of nodes, first internode length, number of tiller per plant, number of fertile tillers per plant, number of infertile tiller per plant, and spike weight. Genome-wide association mapping using TASSEL 5.0 software and the general linear model (GLM) method with Q matrix and decomposition into principal components with more than 80% justification (PCA) with 52 components was used.

The results of the analysis of variance showed that there was an acceptable genetic variation in terms of all studied traits and also the reaction of genotypes was different in facing water deficit stress.
In the water deficit stress condition, chromosome 2A had the maximum significant correlation with 39 and chromosome 5A had the minimum association marker with the trait with four. In the of water stress conditions, three bread wheat genomes (A, B, and D) accounted for 53, 36, and 11% of the frequency of marker-trait association, respectively. A and D genomes of bread wheat under water deficit stress conditions ratio to non-stress conditions assigned a more prominent role for the examined traits. In total in the non-stress and water deficit stress condition 180 and 111 marker trait association (MTA) were identified respectively. In the water deficit stress conditions, the number of correlations with markers for flag leaf area, first internode length, tiller of number per plant, and spike weight were 17, 24, 10 and 19, respectively. In the water deficit stress condition, the frequency of significant marker association more significant than in non-stress condition for traits of first internode and fertile tiller of number per plant. Three bread wheat genomes showed an unequal contribution for the studied traits in terms of the number of identified marker-trait associations (MTA). Also, genome A had a significant contribution to grain yield under water stress conditions with 74% of significant correlations between the marker and the spike weight trait.

 Finally, the MTAs identified in the present study can be used in the development of wheat breeding programs under water deficit conditions especially gene pyramiding or marker-assisted selection.

Fenugreek (Trigonella foenum-graecum L.) as an important aromatic and medicinal plant is a rich source of the Diosgenin and Trigonelline. Genetic diversity analysis using reliable methods provides useful information for the crop breeding programs and conservation of genetic resource. In the present study, 40 Fenugreek genotypes were evaluated for genotypic diversity using two gene-targeted markers. Seven SCoT and ten CBDP primers amplified 78 and 93 fragments in which 65 and 78 were polymorphic, respectively. The average of polymorphism information content (PIC) for SCoT and CBDP Primers were 0.37 and 0.29 respectively, that showed a higher resolving power of SCoTs than CBDPs. The dendrogram generated using the UPGMA algorithm based on Dice distance coefficient, classified all 40 investigated samples into four main groups. Furthermore, these results were confirmed by principal coordinate analysis (PCoA). Analysis of molecular variance (AMOVA) showed a higher distribution of genetic diversity within populations (66%), than between them (34%). Among all five investigated populations, the highest values of diversity indexes such as number of effective alleles (1.54), Shannon’s index (0.46) and Nei’s gene diversity (0.31) were estimated for population IV indicating the higher variation within this population than others. These results showed a high amounts of genetic variation among tested genotypes, which can be used in breeding programs. Moreover, the results revealed that these two gene-targeted markers are suitable and reliable techniques for DNA fingerprinting and genetic diversity investigations.

Production of high-quality seeds to stabilize crop yield is an important challenge for breeders. One of the most important answers to this challenge is to clarify the molecular mechanisms associated with seed vigor characteristics. Functional proteins of Cupin superfamily are among the molecules in signaling pathway. Previous research has shown that in maize, a storage protein similar to the functional Cupin superfamily protein called ZmGLP is effective in seed germination. However, in the previous experiments, suitable indicators were not used to assess seed vigor and its relationship with field establishment. So, it is needed to study the performance of ZmGLP in predicting field emergence to complete the previous research.

An experiment was performed on 14 samples of commercial inbred maize lines. In this experiment, in addition to the laboratory evaluation of seed germination, field indices of physiological seed quality including the percentage of seedling emergence in the field, time to 50% seedling emergence, time to 90% seedling emergence, seedling dry weight, seedling height and coefficient of variation of seedling height was also assessed. In the polymerase chain reaction, two pairs of primers (CF / CR primers and IDF / IDR primers) were used to identify the DNA sequence of the Cupin.

The results show that the seeds were different in terms of physiological quality. The lowest percentage of germination in laboratory was related to K1264/1, while the lowest physiological quality of seeds in field indices was observed in K1263/17. The molecular test confirmed the presence of the desired allele at the InDel9 site of vigor-related genes in the three samples of B73, K1264/1, and K1264/5-1, but no amplification band of the InDel9 site was observed in all K1263/17 seed samples. Due to the fact that line K1264/1, which had the lowest germination percentage in the laboratory, had an amplification band at this related site to vigor, it is not enough to rely on the results of the laboratory germination test to investigate the relationship between this gene and seed vigor. The field emergence test and seed vigor test that have a good prediction of field emergence must be used in these studies.

According to the results of this experiment, molecular tests with functional markers based on Indel9 can be used to accelerate the evaluation of vigor, especially when the breeder is breeding a new line or hybrid. It is a useful, rapid, and effective molecular method to predict seed emergence in the field and screen the lines to ensure the genetic strength of the germination of the lines, especially in the temperate germplasms of corn. Finally, it is necessary to determine the threshold of low vigor during seed quality investigation in different cultivars, and relationship between the presence or absence InDel9 site should be considered in future research.

Highlights:

1- The feasibility of using molecular markers to determine the seed vigor of corn lines in the field was studied and optimized for the first time.
2- The results of physiological quality assessment of seeds in the field for the studies related to the relationship between molecular markers and seed vigor were exploited for the first time.
3- The Indel9 site and molecular markers related to seed vigor in the field were introduced.

Grape is one of the most important horticultural products in the world and in Iran and has a high genetic diversity. Determining the level of genetic diversity is the first step in plant breeding programs. Knowledge of genetic diversity, in addition to providing information on evolutionary and phylogenetic relationships, genetic mapping, ecological and environmental adaptations, and ultimately selecting the right parents for breeding programs, will reduce the time and cost of breeding projects. This study was performed to investigate the genetic diversity of 69 cultivars and promising genotypes of Russian grapevines with three Iranian commercial grapevine cultivars using 15 microsatellite markers (ISSR). Polymerase chain reaction (PCR) samples were electrophoresed in 1.3% agarose gel. Cluster analysis with the UPGMA method was used based on the Jaccard coefficient after assigning one and zero to the presence or absence of a band in each primer for each genotype. The highest percentage of polymorphisms (100%) was related to UBC-823, UBC-825, UBC-841, UBC-846, UBC-855, and UBC-873 primers, and the lowest (66.7%) was related to UBC-817 primer. The highest and lowest levels of the polymorphic content index were observed in UBC-825 (0.487) and UBC-856 (0.216) primers, respectively. The highest and lowest levels of marker index were 2.718 and 0.904 related to UBC-889 and UBC-817 primers, respectively. The highest and lowest values of the effective multiplex ratio index were 7 and 1.33 for UBC-841 and UBC-817 primers, respectively. The highest and lowest resolving power were 8.11 and 2 for UBC-877 and UBC-841 primers, respectively. The UBC-815 and UBC-834 primers had no clear and concise bands. Overall, 73 bands were obtained from the 13 primers of the ISSR DNA marker which 64 bands were polymorphic and the total polymorphism was 88.1%. The highest and lowest numbers of bands were eight and two bands for UBC-826 and UBC-817 primers, respectively. The cluster analysis was performed by the UPGMA method based on Jaccard's coefficient of similarity, which led to the classification of 72 grape varieties with a similarity value of 0.12 to 0.89 in seven different groups. In the present study, high diversity was observed among the studied grapevine cultivars. This indicates the different geographical origins of the cultivars and genotypes under study.

Reproduction is one of the most important economic traits in sheep with within and between-breeds variation. Reproductive traits normally show low to medium heritability and therefore response to conventional selection methods is not satisfactory for these traits. Considering the genetic information of the genetic variants underlying reproduction variability could efficiently increase the selection efficacy. Genome-wide association studies (GWAS) have been used to identify associations between genotypes and phenotypes as well as candidate genes for economically important traits. Statistical power in GWAS is mostly affected by sample size. The low sample size is hence a main obstacle in GWAS. Combining multiple data sets of different studies for joint (mega) GWAS provides an opportunity to increase the sample size required for GWAS. This study was performed to identify genomic regions affecting litter size in sheep using the mega-analysis of GWAS.
Multi-population joint GWAS was performed using genotypic and phenotypic data of six sheep breeds retrieved from the database. Quality control was performed using the Plink software. The markers or individuals were removed from the further study based on the following criteria: (1) unknown chromosomal or physical location, call rate <0.95, missing genotype frequency >0.05, minor allele frequency (MAF) < 0.05, and a P-value for Hardy–Weinberg equilibrium test less than 10-6. Before analysis, imputation of missing genotypes for combined data set was implemented by LD-kNNi method. Mega-analysis was performed using a mixed linear model in TASSEL software considering kinship and population structure (top five components of principal component analysis (PCA)) as confounding effects. The quantile–quantile (Q–Q) plot was visualized by plotting the distribution of obtained vs. expected log10 (P-value). The association results along the genome and the significant SNPs were visualized in the Manhattan plot. To account for multiple test problem and identify the genome-wide and chromosome-wide significance level, Bonferroni test was used based on the number of independent SNPs obtained from pairwise linkage disequilibrium analysis. After GWAS analysis, the 300 bp sequence upstream and downstream of the significant SNP was explored to identify the adjacent candidate genes using Ovis aries_v4.0 (UCSC).
In the present study, we implemented a mega GWAS using six different sheep breed data to identify the genetic mechanisms responsible for litter size in sheep. After quality control, 305 animals and 351,615 SNP markers with a mean MAF of 0.33 were kept for further analysis. The results of the mega-analysis identified one marker on chromosome 21 at the genome-wide level and 10 markers at the chromosome-wide level on chromosomes 1, 2, 3, 14, 17, and 22. The quantile–quantile plot that features the total distribution of the observed P-values (−log10 P-values) of quality passed SNPs vs. the expected values, showed the effective control for confounding effects. Many of the significant SNPs identified in this study were located in or very adjacent to known genes (OPCML, GULP1, RBP4, MMP2, and LPCAT2) that have been already reported for their contribution to fertility and pregnancy success. It has been reported that OPCML is more consistently expressed in cells lining the uterus, oviduct, and rete ovarii. OPCML has been reported as a tumor suppressor protein that is frequently inactivated in epithelial ovarian cancer. It has been reported that the RBP4 gene is expressed during the period of fast elongation of the pig blastocyst which is a crucial period for the survival of the embryos. Also, it has been suggested that RBP4 has the main contribution in uterine and conceptus physiology during the establishment of pregnancy and therefore can be considered as a candidate gene for litter size. MMP2 has an essential function during ovulation and pregnancy through extracellular matrix (ECM) components degradation and therefore enabling cell migration and angiogenesis.
Comparison of the results of this study with previous reports showed that the mega-analysis of GWAS, compared to the meta-analysis already reported for GWAS results, had comparable power in identifying genomic regions influencing litter size in sheep but identified fewer genomic regions than individual GWAS for each breed. No previously reported major genes controlling litter size in sheep were identified using our mega GWAS. The results of our research are suggested for further investigations in identifying causal genetic variants or genomic regions underlying the litter size variation in sheep and can be used to understand the genetic mechanism controlling this trait.

Persian black cumin is one of the most important endemic plants to Iran. Its seed is used in the daily diet of Iranians and also has medicinal properties and aromatic compounds. Unfortunately, there is little information about its genome and molecular markers. In this study, the transcriptome of Iranian black cumin was sequenced in the granulation stage and after extracting the microsatellites (SSR markers) related to this growth stage, their interpretation was done. After RNA extraction, the inflorescences and stems were sequenced. Sequencing depth and length were 6 GB and 150 bp pair-end, respectively. Sequencing data were analyzed using different softwares. De-novo assembly of Persian black cumin was performed by Trinity software. Microsatellite markers were extracted using MISA software. Finally, the functional interpretation of the microsatellite-containing sequences was performed by the WEGO database. The GC content of different samples was 47 to 50%. 8389 microsatellite markers were obtained from 45146 unigenes. At least 11% of unigenes contained microsatellites. A/T and AG/CT nucleotides had the highest percentage of microsatellite markers. Among the three nucleotide repeats, ATC/ATG and AAG/CTT had the highest frequency of microsatellites. The results of functional interpretation showed that unigenes containing microsatellite markers cover a wide range of biological activities of Persian black cumin and the genes involved in seed development and growth have a high level of expression. This study is the first report of microsatellite markers of Persian black cumin. The results of the present study can be useful in finding different markers for breeding programs and developing cultivars with different goals.

The main goal of genome-wide association study (GWAS) is to identify genes associated with a specific trait. In this mapping method, researchers compare the whole genomic DNA sequence of people in the community to find single nucleotide differences between them. Identifying and mapping effective genes in response to drought stress, in addition to understanding the molecular and physiological mechanisms, can provide breeders with a better understanding of the genetic structure of population and the genetic control of stress and it’s breeding in the studied population. In this experiment, the mapping genes controlling important agronomic traits of bread wheat under two non-stress and drought stress conditions using genome wide association analysis method was performed. The objective of the experiment was to analyze QTLs related to the response to water deficit and to identify markers related to some important and effective traits in bread wheat.

The plant materials of this experiment were 121 spring bread wheat genotypes, including 111 lines obtained from local spring bread wheat varieties originating from 28 countries from five different continents and 10 spring bread wheat genotypes from Iran and Pakistan, which were evaluated under two non-stress and water deficit stress conditions in the field. Genotyping for the samples was done using SNP markers (15 K SNP array) at TraitGenetic Company in Germany, and each genotype was evaluated using a set of SNPs. To determine the population structure, 147 SNP markers with no missing data and with suitable distribution on 21 homologous chromosome pairs of bread wheat (seven markers per chromosome) were used. To determine the possible sub-populations and studying the population structure, Bayesian method and Structure software V 2.3.4 were used, and then the average fixation index (Fst) and membership matrix (Q) were calculated with the same software. Genome-wide association analysis with the general linear model (Q+PCA) method was used to identify the markers related to the studied traits under non-stress and drought stress conditions with average data in TASSEL 5.0 software.

The results of analysis of variance showed that there was an acceptable genetic diversity in terms of all the studied traits between the genotypes and reaction of the genotypes to water deficit stress was different. Based on genome-wide association mapping, in total, 511 and 469 significant marker-trait relationships were identified under non-stress and water deficit stress conditions, respectively. The most significant marker-trait association under water deficit stress was revealed for plant height, flag leaf area, peduncle length, and spike yield on chromosomes 1A, 2A, 3B, and 2A, respectively. Also, five SNP markers at positions of 113.30, 25.02, 13.90, 43.10, and 71.97 cM on chromosomes 2A, 2A, 5A, 6A, and 6B, respectively, showed the highest significant associations with flag leaf length and area, plant height, peduncle length, and spike yield under water deficit stress conditions, respectively. Multi-trait loci were also identified on chromosome 2A for flag leaf length, width and area, plant height and spike yield under water stress conditions. Finally, 21, 12, 14, 44, 92 and 14 significant marker-trait associations (QTLs) were found for flag leaf length, width and area, plant height, peduncle length and spike yield under water deficit stress conditions, respectively, using genome-wide association study.

The results of this study provided valuable information on the genetic basis of the studied traits under water deficit stress conditions, which can be used in bread wheat breeding programs, including marker assisted selection (MAS).

Capparis spinose is from Capparis genus, and Capparidaceae family includes 350 species. It is originated from Mediterranean region. Human as food uses entire parts of C. spinose as young stems, flower buds, fruit, and seed. Caper, trade name, has several species in Iran. C. spinose has a high capacity in international agriculture markets. Today, focused on Caper selection and breeding programmes in many countries in the world. Kinds of genetics analysis techniques accompanied by genetic markers based on PCR are presented to evaluate genetic variation on plant species. ISSR and Scot are dominant markers used for genetic variation evaluation in plant germplasm.

To evaluate C. spinosa population structure, which grows naturally in western Iran, collected 80 genotypes from 12 different locations.

Neutral statistical clustering of genotypes without previous knowledge of populations, using two ISSR and SCoT markers, distributed 80 genotypes in the two groups. According to the results of morphological analysis of morphological traits based on ISSR and SCoT markers, all reported markers were significant. Based on the results, 966 SCoT markers and 571 ISSR markers were identified with a significant relationship (with a probability level of 5%) with the studied traits.

Based on structure analysis, using SCot markers, collected genotypes from Kermanshah, Charmeleh, Ilam, Sarpolzohab, Ghasr Shirin, Gor Safid, Gilan, Khosravi, Naft Shahr, Somar classified in group one, and collected genotypes from Karand and Ivan classified in group two. Based on structure analysis, using ISSR markers, collected genotypes from Karand, Khosravi, Naft Shahr, and most of genotypes from Somar were classified in group one and collected genotypes from Kermanshah, Chaemeleh, Ilam, Ivan, Sapolzohab, Ghasr Shirin, Gor Safid, Gilan and little Somar genotypes classified in group two. Generally, ISSR and SCoT markers showed high genetic diversity in samples collected from western Iran. The results of correlation analysis showed that using GLM method with a combination of different markers can identify markers related to morphological traits in C. spinose.

The study of genetic improvement and the recognition of traits that have played a role in it are important in assessing the effectiveness of breeding methods used in the past as well as defining new goals in breeding projects in the future. The aim of this study was to estimate the amount of genetic improvement and awareness of the level of variation in barley cultivars that were released in Iran between 1951 and 2013.

This study was conducted in Gorgan University of Agricultural Sciences and Natural Resources during the years 2017 to 2018. The evaluated materials were compromised a sample of 21 barley cultivars released in the period 1951 to 2013 in Iran. In the field section, the cultivars were planted in a randomized complete block design with three replications to evaluate plant variables including per plot, plant height, number of spikes, number of seeds per spike, spike length, number of tillers, 1000-seed weight and days to maturity. ISSR markers were used to evaluate the diversity and grouping of cultivars. Initially, 23 ISSR random primers were used, from which seven primers with high polymorphism were selected for final evaluation and marker production.

Analysis of variance revealed significant differences between cultivars for grain yield, grain weight, number of spikes, number of grains per spike, number of tillers, spike length and stem length. Of the studied traits, effects of breeding were considerable and significant for grain yield and tiller number. Cluster analysis of the morphological data by dividing barley cultivars into three groups (released from 2011 onwards), middle (released between 2011 and 1961) and old (released between 1951 to 1961) confirmed the achievement of genetic improvement. The Nei and Shannon indexes for ISSR markers also indicated significant genetic diversity among the studied cultivars. Based on the PIC values, primers 15, 18, and 23 will be useful for identifying parents to produce segregating populations or for marker assisted selection.

Among the studied decades, the cultivars of the seventh decade (2011 to 2013) had the highest grain yield and among them two cultivars Zahak and Nik were the best. The results showed that the average progress of barley cultivars during seven decades of breeding was approximately equal to 3.7 kg per year.

Regarding the importance of aquaculture industry development, it is necessary to focus on inbreeding in artificial propagation to prevent genetic diversity reduction and problems arising from low genetic variation. Indeed, lack of facilities and the rules related to the responsible transportation of live aquatic animals, and carelessness on health- diseases control in farms has led to some diseases outbreaks which have imposed high costs for farmers, including huge losses or cure. Therefore, it is required to identify the species and population traits before initiating any culturing or breeding programs and evaluate them with molecular genetic methods to synchronizing study with biological characteristics such as reproductive potential, growth rate, and mortality. Achieving broodstocks and fry owning genetically relatedness is a principal issue in each hatchery. This article tries to discuss the significance of genetic diversity assessment by microsatellite marker for broodstocks' genetic relatedness, with an emphasis on Asian sea bass.Keywords: diversity, pedigree, Asian sea bass, marker

Durum wheat (Triticum turgidum) with an average annual production of 40 million tons, is the tenth most important and common crop grown worldwide. The aim of this study was to analysis the genetic diversity and population structure of durum wheat genotypes for knowledge and apply in future genomic studies using SilicoDArT markers generated by DarTseq.

The DNA of 94 durum wheat genotypes were extracted by CTAB method from fresh leaves. The quality and quantity of extracted DNA were measured using spectrophotometer and adjusted to 50 ng / μl. The DNA samples were processed at Diversity Array Technology Pty, Ltd, Australia (https://www.diversityarrays.com) for DArTseq analyses using genotyping by sequencing Platform. Genetic diversity and population structure analysis were performed on the remaining 7882 markers using: Power Markerv.3.25, DARwinver 5.0, STRUCTURE2.1., GenAlexv. 6.41 and Rv3.2.3 software.

The amount of polymorphic information content (PIC) of SilicoDArT markers ranged from 0.023 to 0.499 with an average of 0.38. The mean reproducibility and call rate of sequences in all linkage groups were above 0.98 and 0.92, respectively. The number of mapped SilicoDArT markers varied from 300 markers in the linkage group (Chr1A) to 853 markers in the linkage group (Chr7B). Chromosome size covered by SilicoDArT markers ranged from 829200 kbp in the linkage group (Chr3B) to 589293.786 kbp in the linkage group (Chr1A). The results of cluster analysis by Neighbor-Joining (NJ) method, population structure and discriminant analysis of principal components were highly consistent with each other and clearly divided the studied genotypes into four distinct groups. Genetic diversity among populations was primarily within the population (76.36 vs. 23.64%).

The relatively high number of subpopulations and the presence of high genetic diversity among and within populations were the characteristics of studied durum wheat genotypes in this study. Therefore, considering the loss of 84% genetic diversity of durum wheat during the early domestication processes, these populations can be used as a valuable resource in basic and applied research in breeding projects.

In order to identify the QTLs controlling the morphologic traits of bread wheat, 148 recombinant inbred lines of spring wheat derived from American Yecora Rojo (early maturity and dwarf as the male parent) and No.49 genotype from Sistan Baluchestan (late maturity and tall as the female parent) were studied with the parents. The studied traits included peduncle length, spike length, awn length, flag leaf length, the number of spikes, spike weight, and the number of grains in spike. In this study, linkage map was used based on 202 markers (177 SSR markers and 51 Retro transposon Markers). The map length was about 691.36 cM with the average distance of 3.42 cM in every marker pair and covered 21 chromosomes in bread wheat. QTL analysis was done based on composite interval mapping (CIM) method, and additive effects were estimated for the identified QTLs. The results of QTL analysis showed that one QTL was detected on chromosomes 7B, 5A, 3A, 4A, 3A and 3A respectively for plant height, peduncle length, spike length, awn length, flag leaf length, the number of seed per spikes; two QTL was detected on chromosomes 3A and 2D for the number of spike and seed wieght per spike; and three QTLs were detected and mapped on chromosomes 3A, 4A, and 3A for spike weight. Among the detected QTLs, QSNS3A had the highest additive effect. For spike length, spike weight, the number of grains in spike, and seed weight per spike. The negative additive effect of the mapped QTLs indicate the optimal allele inheritance to crosses in this position of No.49 parent. The phenotypic variance explained by these QTLs varied from 4.93 to 13.63. In this study, the number of QTLs found for spike traits was so limited; it can be due to the large number of small-effect QTLs, mutual effects, and environmental effects.

This study aimed to investigate the genetic diversity of different genotypes of this valuable medicinal plant under the same culture condition which can be used as an introduction to domestication, germplasm conservation, and possible cross in the future.

In this study, after preparing 20 different genotypes from all over Iran, they were cultivated in complete randomized blocks design with three replications under the same condition. After extraction of DNA, the survey of genetic diversity using 12 ISSR markers from 15 markers was conducted by polymerase chain reaction (PCR). The essential oil for each genotype was extracted by water distillation. The dry yield based on gr/m2 and essential oil content (w/w, based on dry weight) were measured. Furthermore, the correlation of molecular markers with dry yield and essential oil content from each genotype was determined using stepwise regression. 

The mean percentage of polymorphism determined in all the genotypes was 91.97. The number of polymorphic bands for each primer varied from 5 to 9 and a total of 89 replicate bands were scored, of which 82 bands showed polymorphism. The average content of primer information polymorphism (PIC) was estimated to be 0.31 and the IS1 primer showed the highest PIC (0.46). The Ni and Shannon indices for IS1 primers were 0.43 and 0.61, respectively. Cluster analysis using the Jaccard similarity coefficient and UPGMA algorithm divided the studied genotypes into four groups. The highest genetic distance was observed between Khuzestan and Qazvin genotypes with a coefficient of 0.39 and the lowest between Kerman-2 and Kerman-4 genotypes with a similarity coefficient of 0.77. Stepwise regression showed that the IS10 primer has a coefficient of 0.70 with the essential oil percentage and dry matter yield.

The results of this study showed that ISSR markers can be effectively used to study the genetic diversity of wild mint genotypes and will provide the possibility of breeding. So that, IS1 and IS10 primers were introduced as the best markers. Also, Khuzestan and Qazvin genotypes had the highest genetic distance.