Genetic Diversity Studies Research Articles

Genetic diversity and phylogeny analysis of 3-hydroxy 3-methylglutaryl-CoA reductase gene (SmHMGR) in Danshen (Salvia miltiorrhiza Bunge)

AbstractHMGR, 3-hydroxy-3-methylglutaryl-CoA reductase, is a major rate-limiting enzyme in mevalonate (MVA) pathway for isoprenoids and subsequent tanshinone biosynthesis in the Chinese traditional bulk herbal medicine Danshen, Salvia miltiorrhiza, mainly for cardiovascular disorders. In this paper, the genomic SmHMGR genes of 38 cultivated populations of S. miltiorrhiza collected in China were for the first time sequenced to reveal the genetic diversity and phylogeny. The SmHMGR gene was shown to be intron-free, 1650~1659 bp in complete CDS with the majority being 1656 bp, and two unique populations (W-FJLY-V-1 and W-SCHY-W-1) being 1659 and 1650 bp respectively. A total of 103 SNP variation sites were detected with a variation rate of 6.22%, most of which occurred in S. miltiorrhiza f. alba population W-SCHY-W-1; a total of 25 amino acid variation sites were found, of which 19 was in W-SCHY-W-1. The same four populations, W-SCHY-W-1, V-HBAG-V-1, V-JLCC-V-1 and S-NM-V-1 could be discriminated from the remaining 34 by both the SNP fingerprints and the deduced amino acid variation sites. Other or composite DNA markers are needed for better identification. The SmHMGR gene of white flower S. miltiorrhiza f. alba population W-SCHY-W-1 is especially rich in variations and worthy of further studies. Phylogenetic trees based on both the gene and the deduced amino acid sequences showed a very similar two-clade topological structure. This research enriched the content and the genetic means for the molecular identification, genetic diversity and phylogenetic studies of the cultivated S. miltiorrhiza populations, and laid a solid foundation for further related and in-depth investigations.

Genetic Variability, Correlation and Path-Coefficient Studies in Litchi (Litchi chinensis Sonn.) for Plant Growth, Panicle and Yield Attributes

Studies were carried out in National Active Germplasm Site (NAGS) at ICAR-NRC on Litchi, Muzaffarpur, Bihar, India during 2018 and 2019 to find out the association between different characters and magnitude of association of different characters with yield (kg plant-1) in nine clones of litchi (Litchi chinensis Sonn.). Result revealed that genotypic coefficient were higher than their corresponding phenotypic ones implying an inherent relationship among them. The differences between genotypic and phenotypic coefficient of variation (PCV and GCV) were found narrow for all traits indicate least influence of environment on traits. Heritability was more than 80% for all the parameters studied except seed weight (34.90%) and TSS (73.20%). Correlation analysis quantifies only the degree of association between two characters and non-significant correlation coefficient value cannot be taken to imply absence of functional relationship between the two variables but path coefficient analysis reveals this by breaking the total correlation coefficient into components of direct and indirect effects. The number of leaflet, leaf length, leaf width, rachis length, petiole length, length of panicle, fruit weight, pulp weight, TSS, total sugar and seed weight exhibited positive correlation. Among the character studied, leaf length (1.646), TSS (0.975), length of panicle (0.900), petiole length (0.639), and number of fruit per panicle (0.601), seed weight (0.465) and pulp weight (0.370) recorded maximum positive direct effect towards yield at both the level. This study revealed that leaf length, panicle length, number of fruit per panicle and seed weight could form a selection criterion for yield improvement in litchi.

Genetic Association, Variability and Path Studies for Yield Components and Quality Traits of High Yielding Rice (Oryza sativa L.) Genotypes

A field study was conducted during Kharif, 2017 (July–October) to evaluate seventy-one diverse genotypes for variability with regards to yield, yield components and quality traits in addition to correlation and path studies at Regional Agricultural Research station, Warangal, Telangana State, India. Estimates of variability, heritability and genetic advance as percent of mean were noted for all the traits, which revealed that high PCV (28.56%) and GCV (24.37%) values were recorded by grain yield plant-1, panicle density (28.47% and 20.06%). volume expansion ratio, filled seeds panicle-1. panicle weight, head rice recovery, plant height and days to 50% flowering which indicated selection for these traits will be effective, while high heritability coupled with genetic advance as percent of mean was recorded by days to 50% flowering (97.8% and 23.7%), kernel length after cooking (95% and 32.4%) and test weight (93.0% and 52%) respectively and these characters could be improved through selection. Hulling recovery recorded low genetic advance as percent of mean. Significant positive association was observed for grain yield plant-1 with days to 50% flowering, plant height, effective tillers, panicle density, panicle weight, filled seeds panicle-1, test weight, hulling percent, milling percent, head rice recovery and kernel length suggesting importance should be given to these characters, during selection. Path analysis showed that filled seeds panicle-1 (1.702) followed by kernel elongation ratio, panicle weight, milling percent and water uptake had direct effect of these traits on grain yield indicated their importance in determining the complex character and therefore should be kept in mind while practicing selection aimed at improving the grain yield.

DNA fingerprinting: an overview on genetic diversity studies in the botanical taxa of Indian Bamboo

DNA fingerprinting: an overview on genetic diversity studies in the botanical taxa of Indian Bamboo

Assessing the Genetic Divergence of Onion (Allium Cepa L.) through Morpho-Physiological and Molecular Markers

Onion is one of the most widely cultivated high-value vegetables on the globe. The study of variability and genetic divergence in this crop will facilitate judicious parent selection for future breeding. The present study incorporated 20 onion genotypes to determine the genetic variability and diversity through morpho-physiological and molecular markers. The genotypes were tested for two consecutive years to determine the effects on yield-attributing and bulb-quality traits. Diversity at a molecular level with 31 simple sequence repeat (SSR) markers was determined. Adequate genetic variability existed among the genotypes, with a predominance of additive gene action regarding the inheritance of most of the characteristics. Principal component (PC) analysis detected seven PCs contributing to more than 87% of the genetic diversity in the genotypes. Total yield (kg/plot), Grade ‘C’ bulb (equatorial diameter of the bulb between 3.5 and 4.5 cm), individual bulb weight (g) and phenol content were detected as characteristics positively associated with the first two PCs. A total of 16 primers were amplified, and they produced 32 alleles in the genotypes. Genetic diversity at the morphological and molecular levels indicated moderate diversity among the tested genotypes, with the dissolution of the genotypes into six and three clusters, respectively. The present study on onion facilitates the selection of diverse parents that can generate desirable segregants in future breeding programmes.

Estimation of genetic variability and correlation studies in chickpea (Cicer arietinum L.) germplasm suited to Estern plain zone of Uttar Pradesh

A set of thirty genotypes of chickpea were evaluated for studying of estimation of genetic variability and correlation studies in elite chickpea (Cicer arietinum L.) germplasm suited to eastern plain zone of Uttar Pradesh. The experiment was conducted in a Randomized Block Design with three replications during the Rabi season, 2020-21 at Naini Agriculture Institute, Naini. Analysis of variance showed significant differences among genotypes for all 11 characters. High GCV and PCV in chickpea germplasm were observed for No. of effective pods per plant, no. of pods per plant, seed yield per plant, biological yield per plant, no. of secondary branches per plant and seed index. High estimate of heritability coupled with high genetic advance as per cent of mean was recorded for no. of effective pods per plant, no. of pods per plant, biological yield per plant, seed index, seed yield per plant , no. of primary branches per plant , no. of secondary branches per plant. Phenotypic and genotypic correlation co-efficients of 11characters revealed that seed yield per plant exhibited positive and highly significant correlation at both the levels with days to 50% flowering, plant height, no. of primary branches per plant, no. of secondary branches per plant, no. of pods per plant, no. of effective pods per plant, biological yield per plant and harvest index. Path analysis revealed that direct effect of biological yield per plant, harvest index and no. of pods per plant were of high magnitude. The high positive association of other characters with seed yield per plant (g) was also due to high indirect effect through these characters. This indicated that seed yield was mainly a product of direct and indirect effects of above three characters.

Genetic variability and correlation studies in chickpea (Cicer arietinum L.)

The present investigation on genetic variability and correlation studies in chickpea (Cicer arietinum L.) were carried out with 25 genotypes in a Randomized Block Design with three replications and observations were recorded on five randomly selected plants for 13 characters to study the amount of genetic variability, correlation, heritability at field experimentation center, department of genetics and plant breeding, Sam Higginbottom university of agriculture, technology and sciences, Prayagraj during Rabi-2019-2020. a detailed analysis of the results on per se performances revealed PHULE-G-5 followed by ICC-244263, RVG-202 and NEC-799, CSQ-512. Found superior for seed yield over the check (PUSA-362). Higher estimates of phenotypic and genotypic co-efficient of variation were observed for number of primary branches and number of pods per plant. High heritability was observed in number of primary branches number of seeds per plant. High genetic advance and genetic advance has percentage mean was observed in harvest index. High estimates of phenotypic correlation and genotypic correlation were recorded for test weight and biological yield per plant maximum positive direct effect were observed in test weight by biological yield, number of pods per plant and harvest index.

Genetic variability studies in brown sarson (Brassica rapa L.) genotypes for yield and yield attributing traits under temperate conditions of Kashmir

The present study was carried out with 57 genotypes of brown sarson ( Brassica rapa L.) during Rabi 2019-2020. Estimation of the genetic variability, heritability, genetic advance and correlation analysis in the set of 57 B . rapa lines revealed that all the characters exhibited large amount of variability. The high amount of PCV and GCV along with high values of broad sense of heritability and genetic advance was found, no. of seeds per siliqua, no. of siliqua per plant followed by seed weight. The association analysis showed that the no. of seeds per siliqua, siliqua length, no. of siliqua per plant and seed weight had significant positive correlation with seed yield plot-1. The difference between PCV and GCV were observed low for all the traits. The genetic variability present in the set of breeding material shall not only provide a basis for selection but also provided some valuable information regarding selection of diverse parents to be used in the hybridization programme.Hence, In the present study, significant amount of differences were observed in the studied genotypes for all characteristics which give an insight into the existence of genetic variation in the available genotypes and thus, there is a great scope for selection and further improvement of Brassica rapa L. in terms of quality and quantity.

Conflicting nuclear and mitogenome phylogenies reveal ancient mitochondrial replacement between two North American species of collared lemmings (Dicrostonyx groenlandicus, D. hudsonius)

Collared lemmings (Dicrostonyx) are cold adapted rodents, keystone animals in the tundra communities and the model taxa in studies of Arctic genetic diversity and Quaternary paleontology. We examined mitochondrial and nuclear genomic variation to reconstruct phylogenetic relationships among the Eurasian D. torquatus and North American D. groenlandicus, D. hudsonius and evaluate biogeographic hypothesis of the two colonization events of North America from Eurasia based on morphological variation in dental traits. The nuclear and mitogenome phylogenies support reciprocal monophyly of each species but reveal conflicting relationships among species. The mitogenome tree likely reflects ancient mitochondrial replacement between currently isolated D. groenlandicus and D. hudsonius. The nuclear genome phylogeny reveals species cladogenesis and supports the hypothesis that D. hudsonius with primitive and distinct molar morphology represents a relic of the first migration event from Eurasia to North America. Species widely distributed in the North American Arctic, D. groenlandicus, with advanced dental morphology originated from a later colonization event across the Bering Land Bridge. This study shows ancient mitochondrial capture between two Arctic species and emphasizes the importance of multilocus approaches for phylogenetic inference.

Analysis of genetic diversity in Prunus sibirica L. in inner Mongolia using SCoT molecular markers

Population genetic diversity contributes to the protection and utilization of germplasm resources, especially via genetic breeding. In the present study, start codon targeted polymorphism (SCoT) molecular markers were used to study the genetic diversity of 278 individuals from 10 Prunus sibirica L. populations in Inner Mongolia. A total of 289 polymorphic bands were amplified with 23 SCoT primers, showing a polymorphism percentage of 98.87% and an average of 12.6 polymorphic bands per primer. The SCoT21, SCoT32, and SCoT53 primers amplified up to 17 bands, and the polymorphism percentage was 100%. The minimum number of bands amplified by SCoT25 was 9, and the polymorphism percentage was 90%. Therefore, SCoT molecular markers were shown to be highly polymorphic and suitable for genetic diversity studies of P. sibirica in Inner Mongolia. The analysis of molecular variance showed that 39% of the observed genetic differentiation occurred among populations and 61% occurred within populations, indicating that the genetic differentiation within populations was greater than that among populations. The results of the unweighted pair-group method with an arithmetic cluster analysis, principal coordinate analysis and STRUCTURE analysis were basically the same and divided the 278 individuals from the 10 populations into 2 groups. The results indicated that the efficient SCoT molecular marker-based genetic diversity analysis of P. sibirica in Inner Mongolia can provide a reference for P. sibirica variety breeding and resource development.

Study of genetic diversity and principal component analysis under limited irrigation in durum wheat (Triticum durum L.)

Drought is one of the major environmental factors affecting the yield and plant architecture of durum wheat. Days to heading, days to maturity, number of grains per spike, spike length, peduncle length, number of effective tillers per meter, plant height, protein content, sedimentation value, chlorophyll content, canopy temperature after 5 days and 15 days of anthesis like morphological, biochemical, physiological traits were measure in this study. In the current study, ten clusters of forty different durum wheat genotypes were formed, with the highest distance between clusters 6 and 10 (D2 = 373.85) followed by clusters 9 and 10 (D2 = 331.09). A total of around 73.82 percent of the overall variation seen across the forty durum wheat genotypes was explained by five main components, each having an eigenvalue ranging from 1.21 to 4.93. Different clusters 6, 9, and 10 include genotypes with particular characteristics. These genotypes may produce desirable genetic recombinants that help breeders create drought-tolerant cultivars. The PC1, PC2, PC3, PC4, and PC5 involve characters of major economic traits viz., plant height, number of grains per spike, spike length, peduncle length, 1000 grain weight, chlorophyll content, biological yield per plot, grain yield per plot, canopy temperature after 5 and 15 days of anthesis. The results of the entire experiment showed that the genotypes of durum wheat evaluated under limited irrigation circumstances had a sufficient amount of variability and diversity.

Development of microsatellite markers in Pterodon pubescens and transferability to Pterodon emarginatus, two Brazilian plant species with medicinal potential

Abstract Pterodon pubescens and P. emarginatus (Leguminosae) are native medicinal plants of Brazil. Extractivism due to its therapeutic properties threatens populations of both species. Studies of genetic diversity is a way to reason the use and promote conservation. We developed microsatellite markers for P. pubescens and transferred them to P. emarginatus to further genetic diversity investigation of these species. From genomic sequences of P. pubescens, obtained via the Illumina MiSeq platform, it was possible to identify 6,514 microsatellite regions, to design 5,419 primer pairs, and to test 30 markers amplification. We provide 26 polymorphic microsatellite markers, 10 of which were genotyped in 48 individuals per species. The number of alleles per locus range from 3 to 16, with high average genetic diversity ( P. pubescens HE = 0.753; P. emarginatus HE = 0.691). The genotyped markers have a high paternity exclusion probability (Q values greater than 0.99) and low probability of identity, indicating that set of loci is capable of individual discriminating in P. pubescens and P. emarginatus. Microsatellite markers provided in this study are a tool for population genetics studies and conservation of the two species and can be applied to closely related non-model species.

Genetic diversity and correlation between morphological traits of pequi fruits (Caryocar brasiliense Camb.) with and without thorns at the endocarp

Morphological characteristics of pequi fruits (Caryocar brasiliense) allows us to obtain information for the conservation, breeding, and detect genetic variability. Thus, the aims of this research were to characterize the genetic diversity of Caryocar brasiliense that produce fruits with and without thorn at the endocarp; determine the important characters in the study of genetic diversity, and to estimate phenotypic and genotypic correlations. 80 fruits with thorns and 90 fruits without thorns were evaluated. Data were used for analysis: Euclidian distance as a measure of dissimilarity and the Tocher method for delimitation of groups; Principal Component Analysis, and genotypic and phenotypic correlations. Genetic dissimilarity of C. brasiliense ranged from 0.066 (B6-D6) to 0.908 (A14-B3). Tocher method allowed dividing the matrices into three groups, the dendrogram into five groups, and the principal components allowed the distribution in 8 groups. We observed 15 significant correlations for characters of fruit with thorns and 31 correlations for characters of fruit without thorns. The weight of the fruit (with thorns) and the pyrene yield (without thorns) are relevant correlations for production. The groupings generated allowed the classification of the matrices into distinct sets. Allowed the identification of potential producers plants that could be used in breeding programs.

Study of genetic diversity in Mungbean

An experiment was conducted to study heritability in broad sense, association effects, direct and indirect effect of yield attributing traits on yield among 12 green gram genotypes. ISSR markers were also used to study the genetic diversity present in the studied genotypes at molecular level. Analysis of variance for RBD indicated presence of significant amount of genetic diversity among the genotypes for all the traits. Phenotypic coefficient of variation was higher than Genotypic coefficient of variation. Path coefficient revealed that most of the yield attributing traits viz., days to 75 percent flowering, duration of reproductive phase, days to maturity, number of secondary branches per plant, number of clusters per plant, grain per pod, pod density and number of seed per pod, traits had positive direct effect on yield per plant. Two clusters were obtained from Mahalobinis D2 statistics. Traits viz., number of pods per plant, plant height, 1000-seed weight and yield per plant showed high heritability with high genetic advance.

Inter-primer binding site (iPBS) retrotransposon markers provide insights into thegenetic diversity and population structure of carrots (Daucus, Apiaceae)

Studies of genetic diversity and population structure are essential as an initial step in conservation and breeding programs for modern crops. Carrot (Daucus spp.) is among the ten most important vegetables worldwide, however, its genetic structure and phylogenetic relationships are not totally deciphered. Here, we explored the utility of 21 inter-primer binding site (iPBS) retrotransposon markers to determine the genetic diversity and population structure of 38 accessions of Daucus and one accession of a related genus. The manual scoring revealed 309 bands based on their presence/absence. The dendrogram based on the UPGMA clustering algorithm and a principal coordinate analysis (PCoA) indicated the presence of four clusters. The Daucus species with 2n = 18 chromosome (subclade A´) separated from the other two species D. pusillus and D. muricatus, which were positioned into two individual clusters. The other clade includes the Daucus from the B group. It was also noticed that few accessions were intermixed amongst clusters. Different genetic diversity parameters were estimated based on the four clusters (populations) defined by STRUCTURE software, demonstrating that clusters 3 and 4 possessed the lowest and highest diversity values, respectively. AMOVA showed variation between and within clusters of 41.85% and 58.15%, respectively. The highest population divergence (Fst) was observed between clusters 2 and 3 (0.579), on the other hand, clusters 1 and 4 depicted the lowest Fst with 0.160. Our research highlighted that iPBS markers were successful and effective to study Daucus genetic diversity. These results will contribute to the genetic improvement of carrots and sustainable management of its diversity.

Genetic diversity study of Chrysoperla carnea (Neuroptera: Chrysopidae) populations via molecular markers

The objective of this study was to determine the genetic diversity among Chrysoperla carnea samples collected from different locations of Iran (including, East-Azerbaijan, West-Azerbaijan, Isfahan, Kerman, Kermanshah, Lorestan, Mazandaran, Gilan, Hormozgan and Hamedan provinces) using the Inter simple sequence repeat (ISSR) and mitochondrial (Cytochrome Oxidase I - COI) molecular markers in 2016-2018. The results showed that a total of 64 bands were produced by ten primers of ISSR markers which among them 43 bands were polymorphic. The highest and lowest polymorphic percentages belonged to primer UBC-809 (88.88%) and primer UBC-886 (33.33%), respectively. The results of cluster analysis based on ISSR marker data divided the samples into three separate clusters. This grouping was also confirmed by analysis of molecular variance. According to the results of the analysis of molecular variance diversity within and among groups was about 84% and 16%, respectively. In the present study five haplotypes were obtained. The first haplotype (H1) was common in all populations which can be considered as the ancestral haplotype, the other haplotypes have been evolved from it. The novelty of this study is that we report the first time genetic diversity analysis of family Chrysopidae using ISSR and CO1 markers covering more than ten provinces and thirty cities of Iran with a full picture of its genetic diversity. Genetic distance matrix based on Jaccard index indicated low genetic distance of populations. The results showed that ISSR and CO1 markers have high efficiency in study of genetic diversity in the family Chrysopidae.

Study of Genetic Variability, Character Association and Genetic Diversity Analysis for Quantitative Traits in Winged Bean (Psophocarpus Tetragonolobus L)

Study of Genetic Variability, Character Association and Genetic Diversity Analysis for Quantitative Traits in Winged Bean (Psophocarpus Tetragonolobus L)

Development of anthocyanin markers: gene mapping, genomic analysis and genetic diversity studies in Ipomoea species.

The anthocyanins are pigments responsible for a wide range of colours in plants, from blue, red and purple, play essential biological roles as well as their genes are evolutionarily conserved. Purple sweet potatoes have anthocyanins as the predominant colour, even though they are present in orange roots masked by carotenoids. Several studies have focused on molecular aspects of anthocyanin genes, mainly in wild Ipomoea species, although the structure and segregation analysis of those genes in sweet potato hexaploid species are still unknown. Based on an "exon-primed intron-crossing" (EPIC) approach, fourteen pairs of primers were designed, on five structural anthocyanin genes as candidates. The strategy exploits the Intron Length Polymorphism (ILP) from Candidate Genes (CG), resulting in 93% of successful markers giving scorable and reproducible alleles. The results allowed to define partial structure and sequence of the introns and exons from the selected CG, and to determine patterns of sequence variation. The evaluation of marker dosage and allelic segregations in an Ipomoea batatas (L.) Lam mapping population identified several alleles for linkage analysis. The study validated the utility of ILP-CG markers for genetic diversity and conservation applicability and a successful amplification gradient across wild Ipomoea species validated their transferability.

Mitochondrial diversity and population structure of grass carp (Ctenopharyngodon idella) in the Pearl River after anthropogenic release

The grass carp Ctenopharyngodon idella is a commercially relevant carp species with a long-term artificial release history in China. To date, several genetic diversity studies have been performed on the Yangtze River C. idella populations, but similar reports were sparse for the Pearl River populations. Here, our study explored the genetic diversity patterns and population structure of the Pearl River C. idella populations after human intervention using two mitochondrial loci. Phylogenetic analyses demonstrated that grass carp populations in the Pearl River exhibited two maternal genetic lineages. Haplotype networks demonstrated that most main Pearl River haplotypes were shared with those of the Yangtze River samples. No genetic structure was detected among the Pearl populations and low level of population differentiation was observed between individual Yangtze River populations and the Pearl River populations. These findings might be attributed to the high dispersal ability of grass carp, as well as anthropogenic release. Moreover, the nucleotide diversity of the Pearl River populations was higher than that of the Yangtze River, indicating that artificial release programs might have significant effects on the genetic diversity of the Pearl River populations. Taken together, our findings demonstrated artificial release programs may have influenced the Pearl River grass carp populations and provide important knowledge that may guide the future management of grass carp in the Pearl River.

Anti-androgenic potential of the fruit extracts of certain Egyptian Sabal species and their genetic variability studies: a metabolomic-molecular modeling approach.

This work aimed to evaluate the anti-androgenic activity of S. blackburniana Glazebrook, S. causiarum (O. F. Cook) Becc, and S. palmetto (Walter) Lodd. Ex Schult fruit extracts in rats using Hershberger assay. Furthermore, to annotate secondary metabolites using LC-HRMS technique, to investigate underlying mechanisms responsible for 5-α-reductase inhibitory activity in silico and to compare cytotoxic effects in vitro against human prostatic stromal myofibroblast (WPMY-1) and human benign prostatic hyperplasia (BPH-1) cell lines using MTT, 3-[4,5-dimethylthiazol-2-yl]-2,5-diphenyltetrazolium bromide (spectrophotometrically). The results showed significant anti-androgenic implications with varying degrees, markedly decreased sex organ weights, reduction in testosterone and increase in LH and FSH serum levels. Genetic diversity study ensured the correct genotype and revealed outperformance of SCoT compared with CBDP markers to interpret polymorphism among selected species. S. blackburniana exhibited selective cytotoxic activity against BPH-1 compared to finasteride. Molecular docking of 59 dereplicated metabolites belonging to various chemical classes revealed that helasaoussazine, pinoresinol and tetra-O-caffeoylquinic acid are the top inhibitors of 5-α-reductase-2. Our study provides an insight into the anti-androgenic activity of selected species of EgyptianSabal supported by docking study for the first time, demonstrates safety toward liver and kidney and highlights a new potential therapeutic candidate for anti-androgenic related disease such as benign prostatic hyperplasia.