Evaluation Of Genetic Diversity Research Articles

Evaluation of genetic diversity in pansy accessions (Viola spp.) using growth and flowering traits

The breeding programmes of floricultural crops lay prime stress on adding colour variability in the existing pool along with retention of other important vegetative and reproductive traits of the crop. The evaluation of accessions produced in breeding programmes of pansy in the Department of Floriculture and Landscaping, Punjab Agricultural University, Ludhiana during the year 2019-21was conducted with twenty accessions for vegetative and flowering traits. Maximum plant height was recorded in A-12 (37.4 cm), maximum plant spread in A-13 (42.1 cm) and highest number of branches in A-11 (21.6). The accession A-5 took maximum number of days (63.9days) for flowering whereas the minimum number of days for flowering (56.5 days) was taken by accession A-14. Among all the tested accessions, the maximum duration of flowering was recorded in A-5 (96.1 days). Amongst the pansy accessions, A-11 was maximum flower producing (91.1), while A-3 produced the largest flowers (4.8cm) and flower from A-20 had longest stalk (11 cm). Correlation analysis further showed that the number of flowers per plant was affected by plant vegetative traits (plant height,spread and number of branches). Cluster analysis based on morphological data divided the accessions into three groups. These variations might help in classifying pansy for pot cultivation, bedding and exhibition purposes, which could be beneficial for breeders and growers.

Molecular diversity and genetic relationships between Carpinus betulus and C. orientalis with Inter Simple Sequence Repeat (ISSR) regions

A successful management and preservation of the natural populations depend on accurate assessment of genetic diversity. Knowing the genetic diversity within a population is important for choosing the conservation strategies for the species. The genus Carpinus belonging to Coryloideae, Betulaceae, has significant economic and ornamental importance. Determination of the taxa in the genus Carpinus in Iran is one of the most controversial issues among the researchers; for example, we can see this claim in the recent botanical literatures such as Sabeti and Browicz. However, two good species namely C. betulus L. and C. orientalis Mill. are the main species in Iran, adjacent regions and also in Europe. In general, taxonomic and biosystematics studies of the Carpinus are not known in Iran, moreover, in few cases, inter-specific hybrids and intermediate forms are recognised. A detailed molecular (ISSR) study of the Carpinus is done here with the following objectives: 1) to delimitate the species; 2) to carry out population genetic study and produce information on genetic structure, genetic variability within each population in Carpinus betulus and C. orientalis. In present study, 85 randomly collected plants from 17 geographical populations of two Carpinus species were considered. Our results indicated that ISSR markers can be used as a reliable and informative technique for evaluation of genetic diversity and relationships among Carpinus species.

Multivariate Analysis of Genetic Divergence in Amaranthus hybridus L.

Evaluation of genetic divergence among species of crop is crucial for selection process in plant breeding and for developing new and enhanced varieties with desirable characteristics. This research was done to study the genetic divergence in 10 accessions of Amaranthus hybridus so as to determine highly genetically divergent parents for high yielding hybrid. Ten accessions of Amaranthus hybridus were planted in plastic buckets with three replications. Data were recorded on nine quantitative traits and analyzed using principal component analysis and Mahanalobis D2 statistics, within and between cluster distances were calculated following the formular by Singh and Chaudhary. The analysis of variance indicated highly significant (P ˂ 0.01) variability among the 10 accessions of Amaranthus hybridus for the characters evaluated. The principal component analysis recorded 86.21% of the total variation among the 10 Amaranth accessions. The intra-cluster distances were zero in all the clusters which showed that there was no difference among the accessions within the clusters. The maximum inter-cluster distance of 97.95 was observed among accessions of clusters II and IV while minimum inter-cluster (32.05) was found between clusters III and IV. The accessions of cluster III had the highest desirable cluster mean for plant height, number of leaves and number of nodes. The accessions of cluster IV had the longest leaf length, petiole length, inflorescent height and number of seeds. Selection of accessions from divergent clusters and using them in hybridization programme could produce desirable hybrids and may lead to improvement of Amaranthus hybridus for yield and quality traits.

Translational genomics from sorghum (Sorghum bicolor) to sugarcane (Saccharum spp.) for bioenergy breeding

AbstractLarge‐scale evaluation of genetic diversity in crops with large and complex genomes benefits from the selective enrichment of relevant genomic regions prior to sequencing. Given the complexity of the sugarcane (Saccharum spp.) genome and the limited exploration of quantitative trait loci (QTL) for important energy traits, we used comparative genomics with the related diploid crop sorghum (Sorghum bicolor) to mine for regions associated with bioenergy production. Twenty‐one meta‐QTL (mQTL) were identified after surveying 286 QTL from 24 different studies using the Sorghum QTL Atlas. Comparative genomics revealed that at least 35% of genes located within QTL can be found in highly conserved sorghum/sugarcane collinear chromosome blocks. Additionally, a targeted candidate search identified 200 genes known for their involvement in sugar and cell wall metabolism. For a subset of these sorghum genes, we evaluated sugarcane gene copy number, sequence identity, and homoeolog expression in target tissues. This work is an initial step towards targeting and resequencing sugarcane orthologous genomic regions to discover single nucleotide polymorphisms (SNPs) as a resource for genomics‐assisted breeding.

Evaluation of genetic diversity of ginseng fruit color germplasm resources: based on SSR analysis

Illumina Xten was employed for shallow sequencing of Panax ginseng(ginseng) samples, MISA for screening of SSR loci, and Primer 3 for primer design. Polymorphic primers were screened from 180 primers. From the successfully amplified polymorphic primers, 15 primers which featured clear peak shape, good polymorphism, and ease of statistics were selected and used to evaluate the genetic diversity and germplasm resources of 36 ginseng accessions with different fruit colors from Jilin province. The results showed that red-fruit ginseng population had high genetic diversity with the average number of alleles(N_a) of 1.031 and haploid genetic diversity(h) of 0.172. The neighbor-joining cluster analysis demonstrated that the germplasms of red-fruit and yellow-fruit ginseng populations were obviously intermixed, and pick-fruit ginseng germplasms clustered into a single clade. The results of STRUCTURE analysis showed high proportion of single genotype in pick-fruit ginseng germplasm and abundant genotypes in red-fruit and yellow-fruit ginseng germplasms with obvious germplasm mixing. AMOVA revealed that genetic variation occurred mainly within populations(62.00%, P<0.001), and rarely among populations(39%, P<0.001), but homogenization was obvious among different populations. In summary, pink-fruit ginseng population may contain rare genotypes, which is the basis for breeding of high-quality high-yield, and multi-resistance varieties, genetic improvement of varieties, and sustainable development and utilization of ginseng germplasm resources.

Determining selection criteria in finger millet (Eleusine coracana) genotypes using multivariate analysis

Finger millet [Eleusine coracana (L.) Gaertn.] grows in upland rainfed conditions customarily at disadvantageousregions of the country. Evaluation of genetic diversity and the choice of parents is the crucial step to augmenting the desired improvement of crops towards grain and fodder yield. In the present study, 31 finger millet genotypes were studied for genetic diversity employing cluster and principal component analysis (PCA) at G. B. Pant Universityof Agriculture and Technology (GBPUA&T), Pantnagar during 2018 and 2019. Mahalanobis D2 statistics revealedseven clusters where cluster I represented 24 genotypes, cluster II with two genotypes, and the remaining clusterswith a single genotype each. The maximum inter-cluster distance was observed between clusters III and VII (49.783)followed by III and IV (46.737) indicating more diversity between clusters. Five PCs accounted for 77.50% of totalgenetic variability using PCA. Furthermore, two diverse and complementary parents (PKPS4 and F20) were identifiedthat possessed complement traits, viz. bold seed, high mean for single head weight, grain yield, harvest index, number of finger/spike (PKPS4), and number of tillers/plant (F20). Therefore, PKPS4 and F20 genotypes could be considered as donor parents for different traits to increase grain yield in finger millet.

Evaluation of Genetic Diversity of Solanum tuberosum L. Cultivars by the Physiological and Biochemical Characteristics under Postharvest Conditions

Evaluation of Genetic Diversity of Solanum tuberosum L. Cultivars by the Physiological and Biochemical Characteristics under Postharvest Conditions

Evaluation of genetic diversity of Cantaloupe landraces based on the internal transcriptional spacer regions (ITS1, 4)

ABSTRACT Cantaloupe (Cucumis melo L.) landraces have highly genetic diversity so that it is important to evaluate such distances for future breeding projects. Internal transcribed spacer regions (ITS1 and ITS4 regions) capability was used to evaluate genetic diversity of cantaloupe landraces and to identity genetic diversity among cantaloupe landraces. After DNA extraction from leaf tissue at the 4-true leaf stage and DNA quantification and qualification based on spectrophotometer and agarose gel electrophoresis, electrophoretic bands were sequenced. The sequence quality was assessed and compared with the ClustalW method. Phylogenetic relationship dendrograms were plotted based on genetic distance. Melon landraces could not be separated based on geographical location. The ITS1 region was more separable and diverse than the ITS4 region and was able to differentiate landraces related to the Hirmand region in a separate dendrogram. The numerical value (dN/dS) in ITS1 and ITS4 were 0.658 and 0.450, respectively, indicating pure selection had occurred in the gene and did not cause any important changes. The ITS region is not suitable to investigate intraspecific genetic diversity.

The chloroplast genome sequence and phylogenetic analysis of Apocynum venetum L.

Apocynum venetum L. (Apocynaceae) is valuable for its medicinal compounds and fiber content. Native A. venetum populations are threatened and require protection. Wild A. venetum resources are limited relative to market demand and a poor understanding of the composition of A. venetum at the molecular level. The chloroplast genome contains genetic markers for phylogenetic analysis, genetic diversity evaluation, and molecular identification. In this study, the entire genome of the A. venetum chloroplast was sequenced and analyzed. The A. venetum cp genome is 150,878 bp, with a pair of inverted repeat regions (IRA and IRB). Each inverted repeat region is 25,810 bp, which consist of large (LSC, 81,951 bp) and small (SSC, 17,307 bp) single copy areas. The genome-wide GC content was 38.35%, LSC made up 36.49%, SSC made up 32.41%, and IR made up 43.3%. The A. venetum chloroplast genome encodes 131 genes, including 86 protein-coding genes, eight ribosomal RNA genes, and 37 transfer RNA genes. This study identified the unique characteristics of the A. venetum chloroplast genome, which will help formulate effective conservation and management strategies as well as molecular identification approaches for this important medicinal plant.

NHX-Type Na+/H+ Antiporter Gene Expression Under Different Salt Levels and Allelic Diversity of HvNHX in Wild and Cultivated Barleys.

Salinity tolerance is a multifaceted trait attributed to various mechanisms. Wild barley is highly specialized to grow under severe environmental conditions of Tibet and is well-known for its diverse germplasm with high tolerance to abiotic stresses. The present study focused on determining the profile of the expression of isoforms of the HvNHX gene in 36 wild and two cultivated barley under salt stress. Our findings revealed that in leaves and roots, expression of HvNHX1 and HvNHX3 in XZ16 and CM72 was upregulated at all times as compared with sensitive ones. The HvNHX2 and HvNHX4 isoforms were also induced by salt stress, although not to the same extent as HvNHX1 and HvNHX3. Gene expression analysis revealed that HvNHX1 and HvNHX3 are the candidate genes that could have the function of regulators of ions by sequestration of Na+ in the vacuole. HvNHX1 and HvNHX3 showed a wide range of sequence variations in an amplicon, identified via single-nucleotide polymorphisms (SNPs). Evaluation of the sequencing data of 38 barley genotypes, including Tibetan wild and cultivated varieties, showed polymorphisms, including SNPs, and small insertion and deletion (INDEL) sites in the targeted genes HvNHX1 and HvNHX3. Comprehensive analysis of the results revealed that Tibetan wild barley has distinctive alleles of HvNHX1 and HvNHX3 which confer tolerance to salinity. Furthermore, less sodium accumulation was observed in the root of XZ16 than the other genotypes as visualized by CoroNa-Green, a sodium-specific fluorophore. XZ16 is the tolerant genotype, showing least reduction of root and leaf dry weight under moderate (150 mM) and severe (300 mM) NaCl stress. Evaluation of genetic variation and identification of salt tolerance mechanism in wild barley could be promoting approaches to unravel the novel alleles involved in salinity tolerance.

Evaluation of Genetic Variations of Mangifera sp. in Southern Vietnam

Evaluation of Genetic Variations of Mangifera sp. in Southern Vietnam

Evaluation of Genetic Diversity in Three Diospyros Species, Collected from Different Regions in Iran, Using ISSR and SCoT Molecular Markers

ABSTRACT The Diospyros genus contains approximately 400 to 500 species, among which D. kaki is cultivated as the edible persimmon. Knowledge about the genetic diversity of Diospyros genotypes is of high significance for breeding programs. In this research, the genetic diversity of 57 Diospyros genotypes collected from different regions of Iran was evaluated using inter simple sequence repeats (ISSR) and start codon targeted (SCoT) markers. Seven ISSR and 10 SCoT markers produced a total of 42 and 75 fragments with the averages of 6 and 7.5 fragments per primer, respectively. The average polymorphism information content (PIC) for ISSR markers was 0.3 and for SCoT markers was 0.36. The average marker index (MI) for ISSR and SCoT markers were 1.81 and 1.79, respectively. Cluster analysis based on Jaccard’s genetic similarity coefficient and UPGMA method classified 57 Diospyros genotypes into four main groups based on ISSR and SCoT markers. However, the clustering pattern based on the combination of ISSR and SCoT markers data separated the species genotypes better than each marker alone. Accordingly, groups 1 and 2 contained all D. kaki genotypes, both encompassing various subgroups, group 3 included D. lotus and group 4 included D. virginiana genotypes. Genotype distribution visualized with principal coordinate analysis (PCoA) was in accordance with the cluster analysis. Based on our results Iran is a rich source of Diospyrus germplasm, and a combination of ISSR and SCoT markers can be used as an accurate technique for evaluating genetic diversity among the Diospyros genotypes.

Determination of Genetic Diversity and Similarity among Methicillin Resistant Staphylococcus aureus strains by RAPD-PCR

Purpose: The aim of this study was to determine the genetic diversity and genetic similarity of Methicillin Resistant S.aureus (MRSA) strains isolated from clinical samples. Material and Methods: Thirty-two MRSA strains were identified by conventional methods. Methicillin resistance of strains were determined by PCR using the mecA gene primers. These strains were genetically typed by RAPD PCR using primers OLP-11 and OLP-13. Bionumerics V7.5 (Applied Maths) program was used for analysis and dendograms were generated by unweighted pair group method with arithmetic averages (UPGMA). Results: All strains were confirmed as MRSA by PCR. Many different bands from 400 bp to 1000 bp were detected by RAPD PCR and five clusters (1-5) with OLP-11 and four clusters (1-4) were formed with OLP-13. In RAPD PCR performed with OLP-11 and OLP-13 primers, 80% (cluster 3-5) and 86% (cluster 1-4) similarities were found, respectively. MRSA strains isolated from wound samples were found to be more genetically similar to each other, with at least one in each cluster. Conclusion: RAPD PCR was found to be an effective method for the evaluation of genetic similarity and genetic diversity of MRSA strains.

Evaluation of Genetic Variation in Indian mustard (Brassica Juncea L Czern and Coss) Using Multivariate Techniques

A set of 310 lines of Indian mustard (Brassica juncea L Czern and Coss) were analysed for cluster and principal component analysis (PCA). PCA identified four principal components which explained 65.13% of total variability among the 310 genotypes. Hierarchical cluster analysis grouped 310 genotypes into 3 clusters. Cluster1 included maximum number of 155 genotypes and clusters 3 had the lowest number of 43 genotypes. The grouping pattern of genotypes obtained by cluster analysis and PCA plots was almost similar.

Development of polymorphic SSR markers and their applicability in genetic diversity evaluation in Euptelea pleiosperma

Euptelea pleiosperma is a characteristic species of East Asian flora with both ornamental and scientific values. Based on the reduced-representation sequencing (RRS) technology of RAD-Seq, this study conducted high-throughput Illumina paired-end sequencing to find SSR marker information in the genome of E. pleiosperma, and to screen and verify polymorphism of SSR markers. We obtained 5.5G of high-quality data using RAD-Seq. The total number of contigs of the RAD tags was 299,376, with the maximum contig length of 2,062 bp and the average length of 445 bp. From these sequences, we identified 20,718 SSR loci, with a distribution density of one SSR per 6.45 kb (1/6.45 kb). Among all SSRs, dinucleotides (52.00%) were the most detected SSRs, followed by mononucleotides (21.63%). AG/CT was the dominant motif in the SSR loci, accounting for 34.8%. Primers were successfully designed for 14,593 loci, and 100 pairs of these primers were randomly selected for chemical synthesis and validated by SSR-PCR amplification in 20 individuals of E. pleiosperma. Seventy-nine primers were able to amplify the target bands. Cervus 3.0 software was used to analyze the selected 20 SSR loci with good polymorphism. For the 20 SSR markers, the number of alleles ranged from 4 to 9, and the observed heterozygosity and expected heterozygosity were from 0.35 to 0.75 and 0.541 to 0.875, respectively. The information content of polymorphic loci ranged from 0.463 to 0.848, with an average value of 0.638. Among them, there were 18 highly polymorphic loci, and 20 SSR loci did not deviate from the HardyWeinberg equilibrium. Furthermore, the 20 pairs of SSR primers were used to conduct PCoA analysis based on Nei’s genetic distance of 51 individuals from three populations. The results showed that these SSR markers could distinguish genetic differences based on different geographical locations.

Genetic Diversity and Classification of Chinese Elite Foxtail Millet [<i>Setaria italica</i> (L.) P. Beauv.] Revealed by Acid-PAGE Prolamin

Arid and semi-arid regions of China account for more than half of the country. Because of drought resistance and high nutritive value, elite foxtail millet (Setaria Italica (L.) P. Beauv.) is one of the most important cereal crops in China. Evaluation of germplasm and genetic diversity of foxtail millet is still in its infancy, but prolamin could play an important role as a protein marker. To investigate the genetic diversity and population structure of foxtail millet from different ecological zones of China, 90 accessions of foxtail millet were collected from three major ecological areas: North, Northwest, and Northeast China. The prolamin contents were examined by acid polyacrylamide gel electrophoresis (acid-PAGE). Five to twenty-two prolamin bands appeared in tested varieties, of which were polymorphic, so prolamin patterns of foxtail millet varieties can be used in variety identification and evaluation. Structure analysis identified six groups, which matches their pedigree information but not their geographic origins. This indicated a high degree (87.78%) of consistency with a phylogenetic classification based on SSR. The results showed prolamin banding patterns were an effective method for analyzing foxtail millet genetic variability.

Characterization of Some Cultivated Rice (Oryza sativa L.) Based on Phenotypic, Physicochemical and Cooking Properties

Evaluation of rice genetic diversity is an important step for character specific varietal development program. The present study characterizes 15 rice germplasm of Indian accessions on the basis of agro morphological, physicochemical and cooking parameters. The cultivars showed high degree of variations on their traits. Mean plant height of 88.96 cm, flag leaf length (26.48 cm), flag leaf width (1.17 cm), grain per panicle ( 130), panicle length (20.97 cm), days to 50% flowering (112.06 days), kernel length breadth ratio (2.65), cooked kernel length breadth ratio (3.25), linear elongation ratio (1.65). Out of 15 rice cultivars, only Sada nunia and Das nunia are aromatic rice and Sada nunia also contain awn. Plant height showed significant positive correlation with PnL and DF and significant negative correlation with GB. GL positively significantly correlates with FLL, GrWt with GL and GB, DF with MT. The cluster analysis grouped the 15 cultivars into 4 clusters with 37.5 dissimilarity coefficient. The high variability with promising traits among the cultivars expected to be significance for future rice breeding programmes.

Rice (Oryza sativa L.) Breeding among Hassawi Landrace and Egyptian Genotypes for Stem Borer (Chilo agamemnon Bles.) Resistance and Related Quantitative Traits

Rice stem borer (Chilo agamemnon Bles.) is a primary insect pest of rice and is a major limiting factor to rice production. Breeding for insect-resistant crop varieties has been an economic way of integrated pest management (IPM) as it offers a viable and ecologically acceptable approach. This study was aimed to evaluate rice genotypes for their resistance against rice stem borer. Seven parental genotypes with twenty one F1 crosses were evaluated for genotypic variation in field experiments. Analysis of variance revealed significant differences for the studied traits in almost all crosses and parents. In addition, the mean squares of parents versus their crosses were signifi- cant for stem borer resistance and other associated traits. Moreover, both general combining ability (GCA) and specific combining ability (SCA) variances were highly significant for all characters studied in the F1 generation. Based on GCA, 4 genotypes (Sakha101, Gz6903-3-4-2-1, Gz9577-4-1-1 and Hassawi) exhibited highly significant negative values for stem borer resistance (–0.53, –1.06, –0.18 and –0.49, respectively) indicating they are the best combiners for stem borer resistance. Based on SCA analysis, nine cross combinations showed highly significant negative effects for stem borer resistance. Similarly, the cross Giza178 Hassawi was the best combination with significantly highest value for early maturity. In addition, seven crosses showed highly significant negative SCA for plant height trait. On the other hand, for panicle length, number of primary branches/panicle, panicle weight and 1000-grain weight, seven, four, eight and six crosses showed highly significant positive SCA, respectively. The result further revealed that the non-additive dominance genetic variance was higher than the additive variance for all evaluated traits indicating that non-additive genetic variances have a role in their inheritance. The broad-sense heritability estimates were high for all the studied traits. The stem borer resistance was significantly correlated with panicle weight and 1000-grain weight, which also showed a highly significant correlation with grain yield/plant. Thus these traits can be effectively employed in a breeding program to confer resistance against stem borer infestation in rice. It was further supported by biplot analysis, which clustered these potentially important traits into two quadrants showing their importance in any future breeding program to control stem borer infestation. This study has contributed valuable information for evaluation of genetic diversity in the local rice germplasm and its utilization in futuristic rice genetic improvement programs.

Genetic diversity in parthenocarpic cucumber (Cucumis sativus L.) for yield and quality traits under protected cultivation

Cucumber (Cucumis sativus L.) is one of the mostimportant cucurbitaceous vegetable crops grownextensively in tropical and subtropical parts of thecountry. Cucumber is thermophilic and required optimumtemperature range between 18 0C and 24 °C. It is grownfor its tender fruits, which are consumed either raw assalad, cooked as vegetable or as pickling cucumber inits immature stage. It is a rich source of carbohydrates,Ca, P and vitamin C. The appreciable yield deficit betweenpotential and realized crop yield indicated an urgent needto develop superior hybrids having desirable yield andquality attributes. Diverse parents are expected toproduce high yielding hybrids through manifestation ofheterosis, increase the probability to obtain transgressivesegregants in F2 and in subsequent generations.

Phenotypic and Genetic Diversity Evaluation of Sengon (Falcataria moluccana (Miq.) Barneby & JW Grimes) from Solomon Provenance on Progeny Trial in Cirangsad Experimental Forest, West Java

Initial evaluation of phenotypic variability and genetic diversity was conducted on the progeny test of 2 years-old sengon from Solomon provenance, which derived from nine families of mother tree and were then planted in 4 blocks in the Cirangsad Experimental Forest. Phenotypic assessment on eight traits was conducted on 36 trees using a scoring system, while genetic diversity of 15 selected individuals which represented high and low-score phenotypic traits was analyzed using 5 selected RAPD primers. The result on phenotypic assessment showed that family 3 (57.25 points) has the highest average score of phenotypic quality and family 4 has the lowest average score (7.50 points). Furthermore, genetic analysis showed that the low-scoring sengon population had a greater mean genetic diversity (He = 0.2535) than the high-score population (He = 0.2345). The analysis of molecular variance (AMOVA) revealed a significant genetic differences (p-value < 0.001) among high and low-score populations and the dendrogram of genetic distance revealed clustering of individuals having similar superior phenotypic against those having non-superior, indicating the selection based on phenotypes in this study had succeeded in pooling the good quantitative alleles in the selected population. This evaluation results can be used as a reference in determining the best families to produce superior sengon (from Solomon provenance) offspring in the future that have desired adaptability, productivity, and diversity.