Evaluation Of Genetic Diversity Research Articles

Biochemical Properties of Superior Persian Walnut Genotypes Originated from Southwest of Iran

Evaluation of genetic diversity and identification of superior genotypes is a fundamental stepin walnut breeding programs. In addition, information on biochemical properties of superiorgenotypes can help walnut breeders to release commercial varieties with high kernel quality.To gain more information on superior genotypes, a walnut population located in southwest ofIran was morphologically evaluated from 2010 to 2016. Based on important walnut breedingtraits, nine superior walnut genotypes were selected from a total of 612 tested genotypes.These genotypes were characterized by high yield, moderate to late-leafing, lateral bearing,thin shell and large nuts with light and extra-light kernel color. Biochemical traits of theselected superior genotypes were evaluated for two consecutive years (2017 and 2018) and ahigh variation was observed among genotypes in respect of oil, protein and total phenolcontents. Oil, protein and phenol contents of walnut kernels ranged between 57.9 to 69.6%,13.0 to18.1% and 46.6 to 61.5 mg GAE g-1, respectively. Polyunsaturated fatty acids (PUFA),monounsaturated fatty acids (MUFA) and saturated fatty acids (SFA) constituted on average63.8%, 26.7% and 9.7% of fatty acid content, respectively. There was a negative correlationbetween some phenological traits and oil and protein contents. Lateral bearing genotypes haddarker kernels with higher amounts of saturated fatty acids. In general, the selected walnutgenotypes not only are superior in various aspects of phenotypic characteristics, but also havehigh kernel quality and nutritional value which can be used as a source of desirable genes forfuture walnut breeding programs.

Evaluation of genetic diversity and development of core collection of onion

Onion (Allium cepa L.) is a bulbous crop, grown in three different seasons viz. kharif, late kharif and rabi in India. ICAR-Directorate of Onion and Garlic Research being the National Active Germplasm Site (NAGS), holds a vast collection of onion accessions collected from different parts of the country. Being a highly crosspollinated crop, onion collection depicts tremendous variation at phenotypic, biochemical and molecular level. Handling of more number of accessions becomes difficult for evaluation, hence formulation of core group become pre-requisite. Addressing this, Power Core software has been used to constitute a seasonwise core group using mean data of 24 important traits. Total 131, 150 and 237 onion accessions were used to formulate core group where 27, 35 and 38 accessions were constituted in the core for kharif, late kharif and rabi seasons, respectively. The formulated core was validated using mean difference percentage (MD%), variance difference percentage (VD%), coincidence rate percentage (CR%) where MD% for all the three sets ranged between 7 to 11%, VD% between 25 to 46% and CR% between 94 to 96%. Scattered diagram of Principal Component Analysis (PCA) for core and entire collection showed core group which represented the entire collection. Further correlation strength among traits for entire and core group was found to be similar. This characterization and formulated group accessions will be helpful for further critical analysis and identifying trait-specific accessions.

Evaluation of genetic diversity and origin of song ma village dogs in Vietnam

Evaluation of genetic diversity and origin of song ma village dogs in Vietnam

Evaluation of Genetic Diversity in Barley Landraces through Agro-Morphological and Biochemical Characterization

| Genetic diversity can be investigated through different methods such as morphological traits, biochemical (SDS PAGE) and molecular markers. The present work was conducted on the basis of morphological and biochemical characterization in order to estimate the genetic diversity among the barley landraces; to explore significant variation which can be used in breeding programs. For this purpose, 40 barley landraces were collected from Dir Lower and Swat, districts of KP, Pakistan. A total of 18 traits were recorded, 10 qualitative characters including spike density, awn barbs, glume awn, lemma type and awn color, length of the rechilla hairs, lemma color, auricle pigmentation, photoperiod sensitivity and stem pigmentation. Variation was observed in these qualitative traits through frequency distribution. In quantitative traits maximum variation was found for plant height ranging from 36cm to 50cm, days to flowering range from 130 to 133 days), while 100 seed weight ranged from 36 to 86 g and plant biomass range from 50 to 199.5 g per plant. SDS-PAGE analyses of total seed storage protein resulted in a total of 18 polymorphic bands. Total genetic diversity on the basis of total seed storage protein analysis was 17.5%. In Band, the 14 total genetic diversity was (0.60%) followed by Band 16 (0.58%) and Band 17 (0.55%). Similarly, Band 3 showed diversity, while Band 8, 4 and 5 indicated 0.45, 0.38 and 0.35%, respectively. A cluster dendrogram tree was constructed which was divided into two linkage and further divided into seven clusters. The variation was found among the clusters. The information obtained from the study is useful in planning further crop improvement.

Evaluation of Genetic Diversity at GDF9 and BMP4 Gene by Polymerase Chain Reaction-Single Strand Conformation Polymorphism (PCR-SSCP) in Indian Goats

Genetic diversity of three Indian goat breeds namely Barbari, Sirohi and Black Bengal goats (Capra hircus) was evaluated using Polymerase Chain Reaction-Single Strand Conformation Polymorphism (PCR-SSCP) method to detect polymorphism in two candidate genes (GDF9 and BMP4) in a sample of 90 goats with 30 goats of each breed. Both of the studied loci were polymorphic, having three variants for GDF9 and two variants for BMP4, in the studied population. Polymorphic information content (PIC) criterion revealed an intermediate polymorphism for all analysed phenotypic groups for Barbari, Sirohi and Black Bengal goats. Effective allele number criterion also revealed equally diverse nature of these genes. This preliminary study provides insight into the genetic diversity of Barbari, Sirohi and Black Bengal goats at GDF9 and BMP4 gene locus, which can be utilized for further study polymorphism and association of these polymorphic variants with traits of economic traits in future.

Evaluation of inbreeding and genetic diversity in Japanese Shorthorn cattle by pedigree analysis.

The Japanese Shorthorn is a Japanese Wagyu breed maintained at a small population size. We assessed the degree of inbreeding and genetic diversity among Japanese Shorthorn cattle using pedigree analysis. We analyzed the pedigree records of registered Japanese Shorthorn born between 1980 and 2018, after evaluating the pedigree completeness. The average of the actual inbreeding coefficients increased at the same rates annually from approximately 1.5% in 1980 to 4.2% in 2018 and was higher than the expected inbreeding coefficients over time. The effective population size based on the individual coancestry rate largely decreased from 127.8 in 1980 to 82.6 in 1999, and then remained almost constant at approximately 90. Three effective numbers of ancestors decreased over time until 1995, then remained almost constant. In particular, the effective number of founder genomes (N ge ) decreased from 43.8 in 1980 to 11.9 in 2018. The index of genetic diversity based on N ge decreased from 0.99 in 1980 to 0.96 in 2018 due to genetic drift in non‐founder generations. Changes in inbreeding and genetic diversity parameters were similar between Japanese Shorthorn and other Japanese Wagyu breeds, but the magnitude of the changes was lower in the Japanese Shorthorn.

Phylogenetic Analysis and Genetics Polymorphisms Evaluation of ROP8 and B1 Genes of Toxoplasma gondii in Livestock and Poultry Hosts of Yazd, Qom and Golestan Provinces of Iran.

Background:A high correlation is observed between specific clonal lineages and host types in toxoplasmosis. The main objectives of this study were comparing polymorphism and evolutionary analysis of the B1 and ROP8 genes, as well as the evaluation of phylogenic and Toxoplasma gondii isolates obtained from different hosts and regions.Methods:Overall 96 brain/diaphragm tissue samples of livestock and poultry from three provinces of Iran (cows: 9 from Yazd, 9 from Qom; sheep: 19 from Yazd, 7 from Qom; goats: 7 from Yazd, 4 from Qom; one camel from Yazd and 37 chickens, 2 roosters and one duck from Golestan) were tested during 2018–19. A nested PCR and PCR-PCR methods were developed with the B1 and ROP8 genes. Evaluation of genetic proximity, genetic diversity and evolutionary analysis were done using MEGA-X and DnaSP5 software. Thirty samples of both genes were sequenced (18 B1 and 12 ROP8 genes), and submitted to the GenBank (MN275903-MN275932).Results:Tajima's D index analyses showed that both genes were in the negative direction of evolution. The B1 gene was more sensitive than the ROP8 gene. The ROP8 gene showed better and more acceptable results in terms of the relationship between the host and the genotyping of the samples.Conclusion:The B1 gene was only an attractive target for rapid detection of T. gondii parasites, whereas the ROP8 gene due to a high level of polymorphism was able to isolate the three clonal lineages (type I, II and III), intertypes and even atypical strains from different isolates of T. gondii.

Genetic fingerprint and diversity evaluation of halophilic Bacillus species by RAPD-PCR.

Random amplified polymorphic DNA-PCR (RAPD-PCR) is a technique successfully used to generate characteristic fingerprints of different bacteria. Bacillus is a genus that includes heterogeneous species, thus a combination of different techniques is essential for their identification. Here we used RAPD-PCR methodology to distinguish among genetically similar strains and to evaluate the genetic diversity of Bacillus species from the Salar del Hombre Muerto, in the Northwest of Argentina. The RAPD-PCR used allowed obtaining different amplification profiles for each Bacillus species and strains. By comparing the fingerprint profiles, we could observe that some of the salt flat isolates showed similar profiles than identified strains. As expected, the bacilli group isolated revealed a wide heterogeneity. RAPD-PCR was found to be a quick and reliable technique to evaluate the diversity of Bacillus strain and was successfully applied to characterize the genetic diversity present in the Salar del Hombre Muerto.

Molecular characterization and core collection evaluation of Manihot esculenta Crantz

Cassava is one of the most important subsistence crops in tropical regions. It is necessary to preserve and to know the genetic diversity existent for the adequate use of genetic resources. The evaluation of genetic diversity among genotypes results in information about potential parents in breeding programs, allows duplicates identification, and facilitates germplasm exchange between research institutions. The objective of this study was to characterize the genetic diversity of cassava accessions of North Brazil region. A total of 106 accessions were analyzed using ten microsatellite markers. The genetic parameters estimated were: expected heterozygosity (HE), observed heterozygosity (HO) and polymorphic information content (PIC). Clustering was performed using the UPGMA and Neighbor-Joining (NJ) method. Bayesian analysis, analysis of principal coordinates and identification of a core collection were also used. The ten loci amplified 8,40 alleles on average. The average heterozygosity estimates were: HE = 0.71, HO = 0.58 and PIC = 0.72. Genetic distances ranged from 0.158 to 0.908. Six (5,66%) accesses were redundant. Clustering and dispersion analysis didn’t differentiate bitter from sweet cassava, and there wasn’t correlation between groups and collect origin. The core collection consisted of 22 individuals that represented 94% of total allelic diversity and 20,75% of the base collection. The results indicate high dissimilarity between the accessions and allowed the detection of redundant genotypes, showing the use of genetic markers as informative tools for the management of collections.

Evaluation of Genetic Diversity of QPM, Provit-A, and Elite Maize Inbreds Resistant to Downy Mildew Disease Using Simple Sequence Repeats

<p>Functional maize tends to be more susceptible to major maize diseases, particularly Downy mildew. Among the functional maize are Quality Protein Maize (QPM) and Provit A maize. The presence of higher amino acid and beta carotene in functional maize might have caused these types of maize more susceptible to Downy mildew disease. The objective of the research was to identify the heterotic pairs among maize inbreds i.e. QPM, Provit A, and local maize varieties resistant to Downy mildew disease using Simple Sequence Repeats (SSR) marker. The research was conducted from April to July 2017 at the Molecular Biology Laboratory of Indonesian Cereals Research Institute. A total of five QPM inbreds, 15 Provit A inbreds, and 11 Downy mildew resistant local varieties of maize were used in the experiment using 34 SSR markers. Results indicated that among 34 SSR locus analysed, variation of allele lengths ranged from 74 bp to 500 bp. A total of 125 alleles ranging from two to nine alleles per locus with an average of 3.68 alleles were generated. The data indicated wide genetic variations among characters. DNA band profile showed that nc130 marker produced the highest PIC (over 0.83) and allele value (8.00). Genetic distance analysis found a total of 21 heterotic genotypes with genetic distance exceeds 0.65. </p>

Evaluation of Genetic Diversity and Identification of <i>Huperzia</i> Species Collected in Some Different Areas in Vietnam by Molecular Markers

The objective of this study was to evaluate genetic diversity of 35 Huperzia samples collected from the different ecological areas in Vietnam by using rbcL markers. The results revealed that the samples were genetically diverse in high genetic similarity which ranged from 98.0 to 99.0%, respectively. Based on the Genbank data in comparison, it was ascertained that only one sample (BK3) is a member of H.phlegmarioides group, and others belonged H. squarrosa group as divided into two main groups by phylogenetic tree analyses. It suggests that some Huperzia samples may plausibly descend from the same origin, evolution and arising relations. This study has provided useful information for further identifying the high-quality genetic plant sources for propagation, development and conservation of the high-valued medicinal materials of Huperzia plants in this country.

Genetic variability in peppers accessions based on morphological, biochemical and molecular traits

The evaluation of genetic diversity among the accessions of a germplasm collection results in information about promising materials suitable for breeding programs. Thus, the goal of this work was to characterize Capsicum baccatum accessions from different Brazilian regions, based on morphological, biochemical and molecular traits, aiming to support chili pepper breeding programs. The fruits were morphologically characterized based on fruit length, diameter, fresh mass and pericarp thickness, and biochemically analyzed for their content in ascorbic and phenolic acids, flavonoid and antioxidant activity by 2,2-diphenyl-1-picrylhydrazyl radical (DPPH•) and ferric reducing antioxidant power (FRAP) assays. All phenotypic traits showed significant differences among the chili pepper accessions, indicating a wide variability. The fruits were also characterized using amplified fragment length polymorphism (AFLP) molecular markers. The combination of six AFLP primers resulted in 1117 bands, 1033 of which were polymorphic. Divergence between accessions was estimated by the Ward’s hierarchical agglomerative clustering method, resulting in three and two clusters for fruit phenotypic traits and molecular data, respectively. In Bayesian analysis, molecular data also clustered the accessions in two groups. There was no association between the phenotypic descriptors and AFLP markers, indicating that both characterizations are important to better understand the genetic variability. Furthermore, it was not possible to group the accessions solely based on their origin for neither phenotypic descriptors and AFLP markers. The accessions G1, G5, G6, and G20 showed interesting characteristics and can be used in breeding programs, aiming the development of Capsicum spp. cultivars with desirable morphological and biochemical traits.

Evaluation of Genetic Diversity and Identification of <i>Huperzia</i> Species Collected in Some Different Areas in Vietnam by Molecular Markers

The objective of this study was to evaluate genetic diversity of 35 Huperzia samples collected from the different ecological areas in Vietnam by using rbcL markers. The results revealed that the samples were genetically diverse in high genetic similarity which ranged from 98.0 to 99.0%, respectively. Based on the Genbank data in comparison, it was ascertained that only one sample (BK3) is a member of H.phlegmarioides group, and others belonged H. squarrosa group as divided into two main groups by phylogenetic tree analyses. It suggests that some Huperzia samples may plausibly descend from the same origin, evolution and arising relations. This study has provided useful information for further identifying the high-quality genetic plant sources for propagation, development and conservation of the high-valued medicinal materials of Huperzia plants in this country.

RAPD-based evaluation of genetic diversity among populations of the Iranian endemic species Rhabdosciadium aucheri Boiss. (Apiaceae).

Rhabosciadium aucheri is an Iranian endemic herbaceous species that grows in the west, center, and south regions of Iran. In the present study, genetic variation of 70 individuals belonging to seven natural populations of four provinces was investigated using Random Amplified Polymorphic DNA (RAPD) markers. Ten out of twenty-two RAPD primers employed in this study, generated 110 highly amplified and reproducible loci and a mean of 11.1 bands per primer and 48.13% of polymorphism was obtained. According to our results, the primer OPA10 presented the highest effective number of alleles, Shannon's index, and genetic diversity. The highest value of genetic identity (0.916) was determined between Hamadan, Nahavand and Hamadan, Alvand Mts. populations and the highest genetic distance (0.277) was observed between Hamadan, Asadabad and Kurdistan, Qorveh populations. Therefore, there is an obvious correlation between genetic diversity and geographical distribution. PCA was obtained based on RAPD molecular data and Neighbor Joining (NJ) dendrogram was provided successively. Similar results were attained employing UPGMA and Neighbor Joining dendrograms, supported by PCA ordination plot. Overall, almost moderate level of polymorphism was obtained by RAPD molecular markers at the population level that shows a reasonable amount of intraspecific variability. The reason might be due to the low level of gene flow between populations that could give rise to high genetic differentiation.

Phylogenetic Analysis and Molecular Diversity of Capsicum Based on rDNA-ITS Region

The genus Capsicum is comprised of 5 domesticated and more than 30 wild species. The region of nuclear ribosomal DNA internal transcribed spacers (rDNA-ITS) has widely been used for species identification, but has rarely been used in Capsicum. In this study, the evaluation of genetic diversity and a phylogenetic analysis were conducted using rDNA-ITS of 28 Capsicum accessions, including five domesticated and two wild species. We surveyed six conventional keys of domesticated species and another five traits in Capsicum accessions. Specific morphological characteristics were found in C. annuum, C. baccatum, and C.pubescens. Three subclones of each accession were sequenced, and rDNA-ITS polymorphisms were detected in all accessions excluding C. annuum, suggesting that incomplete concerted evolution occurred in rDNA-ITS of Capsicum. The genetic diversity was evaluated using nucleotide polymorphism and diversity. C. annuum had the lowest genetic diversity of all species in this study. The phylogenetic tree formed a species-specific clade for C. annuum, C. baccatum, and C. pubescens. The C. chinense clade existed in the C. frutescens clade, implying that it was a cultivated variant of C. frutescens. C. chacoense likely belonged to the C. baccatum complex according to its morphologic and genetic features. This study indicated that the rDNA-ITS region can be used for simple identification of domesticated Capsicum species.

AFLP Markers for Genetic Diversity Evaluation of Pomegranate (Punica granatum L.) in Duhok Province, Kurdistan Region – Iraq

In this work, 15 pomegranate (Punica granatum L.) cultivars collected throughout Duhok Province in Kurdistan-Iraq were characterized using ten AFLP primer combinations. A high degree of genetic diversity was found among tested cultivars. The total scored number of amplified fragments was 435 of which 374 were polymorphic. The rate of polymorphism varied ranging 40 to 100% with an average percentage of 86.64. The UPGMA clustering analysis based on these data revealed three main groups and that cultivars were not grouped by their geographical distribution. All calculated genetic parameters including PIC, RP, EMR and MI mean results were 0.2974, 45.66, 22.79 and 6.872 respectively, further revealed that pomegranate varieties/cultivars in this region have a rich genetic diversity. The findings showed that a molecular characterization was necessary in order to have a reliable result to evaluate and determine relationships between pomegranate genotypes.

SSR-based evaluation of genetic diversity in populations of Agriophyllum squarrosum L. and Agriophyllum minus Fisch. & Mey. collected in South-East Kazakhstan.

The development of informative polymorphic DNA markers for poorly studied genera is an important step in population analyses of living organisms, including those that play very important ecological roles in harsh environments, such as desert and semi-desert area. Examples of those poorly studied desert species are Agriophyllum squarrosum L. and Agriophyllum minus Fisch. & Mey. However, a recent RNA-sequencing project in A. squarrosum has proposed a large set of hypothetical SSR (simple sequence repeat) markers. In this work, 11 novel polymorphic SSRs were found due to the screening of 24 randomly selected SSRs for three populations of A. squarrosum and one population of A. minus. The analysis of 11 SSRs revealed 16 polymorphic loci in two Agriophyllum species, 8 polymorphic loci within three populations of A. squarrosum, and 6 polymorphic loci in the population of A. minus. Statistical analyses showed high interspecific, but relatively low intraspecific genetic diversity. The phylogenetic clusterization and population structure analysis have demonstrated a clear segregation of A. minus from A. squarrosum, as well as the separation of population 1 from populations 2 and 3 of A. squarrosum. Thus, we identified the set of novel and informative SSR markers suitable for the study of genetic diversity in Agriophyllum.

STUDIES ON VARIABILITY OF MORPHOLOGICAL CHARACTERS ON JAMUN (SYZYGIUM CUMINII SKEELS) GENOTYPES GROWING IN NORTHERN BASTAR PLATEAU REGION OF CHHATTISGARH

Surveys were undertaken for characterization and evaluation of genetic diversity of Jamun (SyzygiumcuminiiSkeels) of seedling origin for different morphological characters of tree characters and leaf characters during 2016-17 and 2017-18 in the Jamun growing in Northern Bastar Plateau region of Chhattisgarh areas. Investigations were undertaken during the entire vegetative phase to assess the distribution, range and to record the range of genetic variability of different morphological traits on the selected sixty trees. Mature leaves were plucked and analyzed for different parameters such as leaf surface and leaf glands. Results of evaluated Jamun genotypes showed wide variability for studied characteristic.

Evaluation of genetic diversity and development of core collections of industrial brewing yeast using ISSR markers.

Germplasm of industrial brewing yeast of the worldwide have a richer diversity, and various successes in improving the performance of brewing yeasts. However, they are limited in that they have relatively low odds of combining desirable traits in a correct manner. To improve germplasm resource preservation, management, and utilization efficiency. In this study, the genetic diversity of 35 industrial brewing yeasts were analyzed based upon inter simple sequence repeat (ISSR) markers, in which 151 out of 167 SSR loci (90.42%) were polymorphic between two or more strains. Three preliminary core collections were established using ISSR data, and based on three different strategies as follows: an advanced maximization (M) strategy, an allele preferred sampling (A) strategy, and a random sampling (R) strategy. Comparison of genetic parameters, including polymorphic information content, Nei's genetic diversity (H), effective allele number, observed allele number, Shannon's index (I), and principal coordinate analyses, confirmed that all the core collections accurately recapitulated the diversity of the initial germplasm. Considering the loci retention ratio and trait coverage efficiency, Core1 was considered the best core collection.

Evaluation of Genetic Diversity by DNA Barcoding of Local Lotus Populations from Thua Thien Hue Province

Background: DNA barcoding is a relatively new method of identifying plant species using short sequences of chloroplast DNA. Although there is a large number of studies using barcoding on various plant species, there are no such studies in the genus Nelumbo. Methods: Three chloroplast DNA regions (rbcL, matK, trnH-psbA) were tested for their suitability as DNA barcoding regions of thirty three lotus samples which were collected in Thua Thien Hue province, Vietnam. Universal primers were used and sequenced products were analyzed using Minimum Evolution method in the MEGA 7.0 program.Result: We did not observe high variability in nucleotide sequences within the rbcL region (0.135%). White Nelumbo, while, the most encoding matK (8.013%) and variable trnH-psbA (with different number of repeating regions TAAAA) intergenic regions was the most useful for Nelumbo barcoding. Individual application of the studied regions did not provide the expected results. None of the regions used in the study allowed the division of white and pink lotus varieties of N. nucifera specie according to the adopted classification of the genus Nelumbo. The results confirm that the use of matK, rbcL and trnH-psbA or combine all three regions together is insufficient for DNA barcoding in white and pink lotus varieties of N. nucifera specie and better discrimination within the genus Nelumbo. Our results also indicate the necessity of using a different region. All of the new sequences have been deposited in GeneBank under the following accession numbers: rbcL (MN011708 to MN068956); matK (MN011719 to MN068978) and trnH-psbA (MN011730 to MN086252).