Genetic Diversity Studies Research Articles

Genetic Diversity of Dominant Species Betula pendula in River Valley Forests in the Irtysh River Basin and Sustainable Conservation Measures for the Future

Biodiversity is the basis for the maintenance and functioning of ecosystems. Genetic diversity is at the heart of biodiversity, and therefore an understanding of the current state of plant genetic diversity can contribute to the future provision of sustainable ecological values and services by ecosystems. This study was conducted in the Irtysh River basin (five tributaries) with the dominant species of river valley forests, Betula pendula. Sampling points were set up at approximately 10 km intervals within each tributary using a random sampling method for genetic diversity studies based on chloroplast microsatellite molecular markers. The results indicated that (1) nine alleles were identified in 198 samples. The genetic diversity of Betula pendula was relatively rich in all tributaries (I = 0.216~0.546); genetic diversity was significantly higher in the downstream area of the basin than in the midstream and upstream areas of the basin. Genetic differentiation was at a low level in the tributaries except for the Berezek River, where genetic differentiation was high. (2) Genetic variation was mainly derived from within populations, accounting for 62% of the total genetic variation. The genetic distance was significantly positively correlated with the geographical distance (p < 0.05). The Betula pendula population structure was divided into two major groups. (3) Twelve haplotypes were identified in the basin. The dominant haplotypes in the upper tributaries were H2 and H4, while in the lower tributaries these were H1 and H3. Therefore, this paper suggests the future establishment of a germplasm resource bank for populations of the Berezek River, and the implementation of priority conservation measures for the downstream populations with higher genetic diversity, so as to realize the sustainable ecological value of the valley forests of the Betula pendula.

Clonal Evaluation and Genetic Divergence Studies in Mulberry Genotypes

Aims: This study aims to evaluate the wood quality and leaf quality traits of selected mulberry clones and assess the genetic divergence among them, providing valuable insights for the development of superior genotypes with enhanced economic value for the sericulture and agroforestry sectors.
 Study design: Twenty-one genetic resources of mulberry were collected from various regions in India and evaluated through clonal test in a Row Column Design to assess growth attributes and genetic divergence.
 Place and Duration of Study: The study was conducted in India, and the systematic progeny test and clonal evaluation were carried out in Forest College and Research Institute, Mettupalayam during 2018-2022.
 Methodology: The selected clones were evaluated for growth attributes such as plant height, diameter at breast height (DBH), volume, number of branches, leaf length, leaf width, petiole length, number of leaves, and leaf area. Genetic divergence was estimated using D2 statistics, and clustering of clones was performed using the 'GENRES' statistical package.
 Results: The study identified several clones with significantly higher growth attributes, highlighting their potential for selection in breeding and cultivation programs. Variability and heritability studies indicated that volume exhibited the highest heritability, suggesting strong genetic control and potential for improvement.
 Conclusion: Clones MI-0718, MI-0807, and MI-0845 showed superior growth performance and genetic divergence, indicating their suitability for further breeding and improvement programs. The study provides insights into the genetic variability of mulberry clones and emphasizes selecting superior clones for enhancing wood volume and overall productivity.

Agro-morphological characterization and genotypic diversity of chilli (Capsicum. frutescens) landraces of Bangladesh

Samples of 82 chilli (Capsicum spp.) genotypes grown during the Rabi season of 2016-17 were characterized based on 28 qualitative and 7 quantitative agro-morphological markers. The genotypes were collected and conserved in the Plant Genetic Resources Centre (PGRC) of the Bangladesh Agricultural Research Institute (BARI). The Chi-square (χ 2) tests and the Shannon Diversity Index (H´) were used for the genetic diversity study. All the characters under study were distributed independently except cotyledon leaf shapes and leaf pubescence density. The values of H´ of the genotypes varied widely, the maximum values being observed for the cotyledon leaf shape, leaf density, and anthocyanin leaf spot on the fruit. In contrast, the lowest values were recorded for pigmentation of node and leaf color. The estimated coefficient of variation was the highest while it was the lowest for one thousand seed weights. No variation was observed for calyx annular constriction of fruit. Analytical functions of DIVA-GIS (Geographic Information System) mapping localized the accessions into 10 districts and marked the areas of insufficient collection. Accession AMA-248 belonging to Mymensingh was almost round fruit. Accessions RAI-232 and RAI-80 belonging to Chattogram, AMA-335 belonging to Sherpur, AMA-361 belonging to Jamalpur, RAI-80 belonging to Chattogram, and AHI-01 belonging to Jhenaidah were elongated fruit. Germplasms collected from Chattogram showed the maximum variation in traits of cotyledon leaf color and stem color at the seedling transplanting age. The variation observed in different characters could be important characters in selecting parents for breeding programs.

Analysis of Genetic Variability and Heritability in Brinjal (Solanum melongena L.) Genotypes

Analysis on “Study of genetic variability and heritability in brinjal (Solanum melongena L.) genotypes” was carried out at the experimental field of Division of Vegetable Science, FOH, SKUAST, Kashmir Shalimar during kharif season 2021 in Randomised Complete Block Design with three replications. The experimental material comprised of forty genotypes. Analysis of variance revealed that mean sum of squares due to genotypes for all the characters were highly significant, revealing significant variation among all the genotypes for all the traits under study. The phenotypic coefficients of variation were found to be higher than the corresponding genotypic coefficients of variation. The phenotypic coefficient of variation (PCV) and genotypic coefficient of variation (GCV) in present experienment were high for the traits; average fruit weight (43.69% and 43.69%), total anthocyanin content (39.10 % and 39.10%), ascorbic acid (31.73 % and 31.73) and dry matter (42.31% and 42.29). Heritability in broad sense was found to be high for all traits under study (greater than 70 per cent). Highest genetic advance as percentage of mean was recorded in average fruit weight (90) followed by dry matter (87.11) and total anthocyanin content (80.55).

Genetic Variability Studies in Sweet Sorghum (Sorghum bicolor l.) Genotypes for Sugar and Biomass Related Traits

Sorghum bicolor (L. Moench) is an important crop in the semi-arid tropics of Africa and Southern Asia. Sweet sorghum is characterized by more rapid growth, higher biomass production, wider adaptation and greater potential for ethanol production. The present study was conducted to evaluate 33 sweet sorghum genotypes including two check varieties for different yield and sugar related traits. Analysis of variance revealed the presence of significant difference for all characters under the study. The genetic variability study revealed the presence of greater phenotypic co-efficient of variation (PCV) than genotypic co-efficient of variation (GCV) for most of the characters indicating the presence of the environmental effect. Stem girth, nodes per plant, biomass weight, cane weight, juice content and total soluble solids, total sugars were recorded high PCV and GCV. Plant height and cane height recorded moderate PCV and GCV. Except for plant height at 30 days after sowing (DAS) all other characters plant height at 60 DAS, plant height at 90 DAS, cane height, nodes per plant, stem girth, biomass weight, cane weight, total biomass yield, juice yield, total soluble solids, total sugars, total reducing sugars and total non-reducing sugars showed high heritability estimates coupled with high genetic advance as percent of mean suggesting that, these characters are under the control of additive genes and phenotypic selection will be effective for these traits.

The genetic diversity of Oncomelania hupensis robertsoni, intermediate hosts of Schistosoma japonicum in hilly regions of China, using microsatellite markers

BackgroundThe elimination of schistosomiasis remains a challenging task, with current measures primarily focused on the monitoring and control of Oncomelania hupensis (O. hupensis) snail, the sole intermediate host of Schistosome japonicum. Given the emerging, re-emerging, and persistent habitats of snails, understanding their genetic diversity might be essential for their successful monitoring and control. The aims of this study were to analyze the genetic diversity of Oncomelania hupensis robertsoni (O. h. robertsoni) using microsatellite DNA markers; and validate the applicability of previously identified microsatellite loci for O. hupensis in hilly regions.MethodsA total of 17 populations of O. h. robertsoni from Yunnan Province in China were selected for analysis of genetic diversity using six microsatellite DNA polymorphic loci (P82, P84, T4-22, T5-11, T5-13, and T6-27).ResultsThe number of alleles among populations ranged from 0 to 19, with an average of 5. The average ranges of expected (He) and observed (Ho) heterozygosity within populations were 0.506 to 0.761 and 0.443 to 0.792, respectively. The average fixation index within the population ranged from – 0.801 to 0.211. The average polymorphic information content (PIC) within the population ranged from 0.411 to 0.757, appearing to be polymorphic for all loci (all PIC > 0.5), except for P28 and P48. A total of 68 loci showed significant deviations from Hardy-Weinberg equilibrium (P < 0.05), and pairwise Fst values ranged from 0.051 to 0.379. The analysis of molecular variance indicated that 88% of the variation occurred within snail populations, whereas 12% occurred among snail populations. Phylogenetic trees and principal coordinate analysis revealed two distinct clusters within the snail population, corresponding to “Yunnan North” and “Yunnan South”.ConclusionsO. h. robertsoni exhibited a relatively high level of genetic differentiation, with variation chiefly existing within snail populations. All snail in this region could be separated into two clusters. The microsatellite loci P82 and P84 might not be suitable for classification studies of O. hupensis in hilly regions. These findings provided important information for the monitoring and control of snail, and for further genetic diversity studies on snail populations.Graphical

Genetic Attributes for Selection and Assessment of Yield Enhancement in Paddy (Oryza sativa L.)

The present investigation was conducted in the Agricultural and Horticultural Research Station, Kathalagere. The experiment comprised sixty-seven advanced breeding lines of paddy. The experiment was conducted in three replications with 4mx3m of plot size. The observations are recorded on days to fifty per cent flowering, Days to maturity, Plant Height(cm), Panicles per sqm, Grain yield per plot(kg) and Grain yield per hectare (Kg). The data is subjected to analysis for genetic variability and diversity parameters (Key factors of plant breeding). Higher Genetic coefficient of variability (GCV) and Phenotypic coefficient of variability (PCV) are Days to fifty per cent flowering, Days to maturity, Plant height(cm), Panicles per square meter and grain yield per plot (Kgs) should be considered at the time of selecting the genotypes/varieties/breeding lines for progressing and prospering in the yield and yield contribution towards the varietal performance. Genetic diversity studies proved that the traits viz., days to 50 per cent flowering, Days to maturity, Panicles per square meter, Plant height and Grain yield per plot are prompt traits that contributed maximum divergence to the genotypes. Some clusters are composed of superior genotypes that may contribute to the several crossing studies to improve through transgressive segregants with high genetic yield potential and early maturity.

Genetic variability and association study of SSR markers for yield and powdery mildew disease in pea (Pisum sativum)

Makhyatmubi, one of the most popular local varieties of field pea (Pisum sativum L.) in Manipur has morpho- physiological bottlenecks such as tall nature and high susceptibility to fungus Erysiphe pisi causing powdery mildew disease. Therefore, an experiment was conducted during winter (rabi) seasons of 2018–19 and 2020–21 at College of Post-Graduate Studies in Agricultural Sciences (Central Agricultural University, Imphal, Manipur), Umiam, Meghalaya to generate genetic variability by hybridization of Makhyatmubi with Prakash variety which is a well-known powdery mildew resistant variety in India and possesses several contrasting characters. Fruitful heterosis was estimated with highest record in number of pods per plant (114.75%) and seed yield per plant (108.04%). These two characters also showed high PCV, GCV, heritability and GAM. Number of pods per plant (0.95) was found to have highest positive significant correlation with seed yield per plant. MP-5 and MP-119 recorded superior performance in several characters under study. For the association study of simple sequence repeats (SSR) markers, easily scorable polymorphic markers were selected for surveying association with the traits. Results revealed that SSR marker AA122 may be associated with seed yield and number of pods per plant while marker AA136 with number of seeds per pod. A5 marker was found to be associated with the powdery mildew disease. Hence, it can be employed for marker assisted selection (MAS) to identify and select pea genotypes exhibit resistance to powdery mildew disease.

Genetic variability, correlation and path analysis studies for yield traits in stable mutant lines of black aromatic rice of Manipur

Genetic variability, correlation and path analysis studies for yield traits in stable mutant lines of black aromatic rice of Manipur

Population Structure and Genomic Characterisation of the Ashanti Dwarf Pig of Ghana.

There is still limited information on the genomic structure and genetic diversity of African pigs. Genetic diversity studies can contribute significantly to the genetic improvement and conservation of African pigs. This study presents a genetic diversity analysis and population structure of pig breeds in Ghana, with a focus on the Ashanti Dwarf pig (ADP), an indigenous pig breed of Ghana. A total of 167 pigs sampled in Ghana and populations consisting of Ashanti Dwarf pigs (n = 106), exotics (mostly European pigs) (n = 11), crosses (between indigenous and exotic breeds) (n = 44), and unknown breeds (nondescript) (n = 6) were genotyped using Porcine SNP60K BeadChip. Moderate heterozygosity levels, ranging from 0.28 for Ashanti Dwarf pigs to 0.31 for exotic pigs (mostly European pigs), were observed. Principal component analysis of the pig populations within Ghana resulted in two distinct clusters of pigs: (i) Northern and (ii) Southern regional clusters. The PCA based on breed also resulted in four clusters: (i) ADPs; (ii) exotics (iii) crossbreeds between ADP and exotics; (iv) unknown breed types. The PCA demonstrated that the clustering was influenced by genetics, geographical location, production systems, and practices. ADMIXTURE-based analysis also showed that the populations within Ghana are admixed. FST analysis revealed SNPs associated with QTLs for traits such as disease resilience and growth among ADP populations within the different regional and ecological zones of Ghana.

A Community-Curated DokuWiki Resource on Diagnostics, Diversity, Pathogenicity, and Genetic Control of Xanthomonads.

Xanthomonads, including Xanthomonas and Xylella species, constitute a large and significant group of economically and ecologically important plant pathogens. Up-to-date knowledge of these pathogens and their hosts is essential for the development of suitable control measures. Traditional review articles or book chapters have inherent limitations, including static content and rapid obsolescence. To address these challenges, we have developed a Web-based knowledge platform dedicated to xanthomonads, inspired by the concept of living systematic reviews. This platform offers a dynamic resource that encompasses bacterial virulence factors, plant resistance genes, and tools for diagnostics and genetic diversity studies. Our goal is to facilitate access for newcomers to the field, provide continuing education opportunities for students, assist plant protection services with diagnostics, provide valuable information to breeders on sources of resistance and breeding targets, and offer comprehensive expert knowledge to other stakeholders interested in plant-pathogenic xanthomonads. This resource is available for queries and updates at https://euroxanth.ipn.pt. [Formula: see text] Copyright © 2024 The Author(s). This is an open access article distributed under the CC BY-NC-ND 4.0 International license.

Refining the genomic profiles of North African sheep breeds through meta-analysis of worldwide genomic SNP data.

The development of reproducible tools for the rapid genotyping of thousands of genetic markers (SNPs) has promoted cross border collaboration in the study of sheep genetic diversity on a global scale. In this study, we collected a comprehensive dataset of 239 African and Eurasian sheep breeds genotyped at 37,638 filtered SNP markers, with the aim of understanding the genetic structure of 22 North African (NA) sheep breeds within a global context. We revealed asubstantial enrichment of the gene pool between the north and south shores of the Mediterranean Sea, which corroborates the importance of the maritime route in the history of livestock. The genetic structure of North African breeds mirrors the differential composition of genetic backgrounds following the breed history. Indeed, Maghrebin sheep stocks constitute a geographically and historically coherent unit with any breed-level genetic distinctness among them due to considerable gene flow. We detected a broad east-west pattern describing the most important trend in NA fat-tailed populations, exhibited by the genetic closeness of Egyptian and Libyan fat-tailed sheep to Middle Eastern breeds rather than Maghrebin ones. A Bayesian FST scan analysis revealed a set of genes with potentially key adaptive roles in lipid metabolism (BMP2, PDGFD VEGFA, TBX15, and WARS2), coat pigmentation (SOX10, PICK1, PDGFRA, MC1R, and MTIF) and horn morphology RXFP2) in Tunisian sheep. The local ancestry method detected a Merino signature in Tunisian Noire de Thibar sheep near the SULF1gene introgressed by Merino's European breeds. This study will contribute to the general picture of worldwide sheep genetic diversity.

Identification of pleiotropic loci mediating structural and non-structural carbohydrate accumulation within the sorghum bioenergy association panel using high-throughput markers.

Molecular characterization of diverse germplasm can contribute to breeding programs by increasing genetic gain for sorghum [Sorghum bicolor (L.) Moench] improvement. Identifying novel marker-trait associations and candidate genes enriches the existing genomic resources and can improve bioenergy-related traits using genomic-assisted breeding. In the current scenario, identifying the genetic loci underlying biomass and carbon partitioning is vital for ongoing efforts to maximize each carbon sink's yield for bioenergy production. Here, we have processed a high-density genomic marker (22 466 550) data based on whole-genome sequencing (WGS) using a set of 365 accessions from the bioenergy association panel (BAP), which includes ~19.7 million (19 744 726) single nucleotide polymorphism (SNPs) and 2.7 million (~2 721 824) insertion deletions (indels). A set of high-quality filtered SNP (~5.48 million) derived markers facilitated the assessment of population structure, genetic diversity, and genome-wide association studies (GWAS) for various traits related to biomass and its composition using the BAP. The phenotypic traits for GWAS included seed color (SC), plant height (PH), days to harvest (DTH), fresh weight (FW), dry weight (DW), brix content % (BRX), neutral detergent fiber (NDF), acid detergent fiber (ADF), non-fibrous carbohydrate (NFC), and lignin content. Several novel loci and candidate genes were identified for bioenergy-related traits, and some well-characterized genes for plant height (Dw1 and Dw2) and the YELLOW SEED1 locus (Y1) were validated. We further performed a multi-variate adaptive shrinkage analysis to identify pleiotropic QTL, which resulted in several shared marker-trait associations among bioenergy and compositional traits. Significant marker-trait associations with pleiotropic effects can be used to develop molecular markers for trait improvement using a marker-assisted breeding approach. Significant nucleotide diversity and heterozygosity were observed between photoperiod-sensitive and insensitive individuals of the panel. This diverse bioenergy panel with genomic resources will provide an excellent opportunity for further genetic studies, including selecting parental lines for superior hybrid development to improve biomass-related traits in sorghum.

A dataset of genetic diversity studies in the China Seas

Genetic diversity, a fundamental aspect of biodiversity, greatly influences the ecological and evolutionary characteristics of populations and species. Compiling genetic data is crucial as the initial step in comprehending and applying genetic resources; however, regional collating work is still insufficient, especially in marine ecosystems. Here, by conducting a thorough literature search and quality-control procedures, we provide a dataset of genetic diversity studies on marine species in the China Seas. The final dataset comprised a total of 746 studies (encompassing 840 data sets and 3658 populations) across 343 species from 1998 to 2022. For each data set, information including publication year, publication language, studied species, belonged taxonomic group, applied molecular markers, and sampling strategies (number of populations, total number of individuals, etc.) was collated to analyse the scope, strengths, and omissions of these works. This dataset offers a comprehensive overview of genetic diversity studies in the China Seas, which may help to adjust future research focuses, promote conservation and macrogenetics studies in this region, and also facilitate regional cooperation.

Conservation genomics of wolves: The global impact of RK Wayne's research.

RK Wayne has arguably been the most influential geneticist of canids, famously promoting the conservation of wolves in his homeland, the United States. His influence has been felt in other countries and regions outside the contiguous United States, where he inspired others, also including former graduate students and research fellows of his, to use modern molecular techniques to examine the evolutionary biology of canids to inform the conservation and management of wolves. In this review, we focus on the implications of Wayne's work on wolves outside the United States. He envisioned a clear future for wolf conservation research, involving the study of wolves' ecological and genetic diversity, and the description of ecotypes requiring conservation. He also documented widespread hybridization among canids and introgression of DNA from domestic dogs to wolves, a process that started dozens of thousands of years ago. His work therefore calls for innovative studies, such as examining the potential fitness benefits of introgression. Inspired by his results, for example, on the purging of deleterious alleles in small populations, wolf researchers should use novel molecular tools to challenge other conservation genetics paradigms. Overall, RK Wayne's work constitutes a call for answers, which as scientists or citizens concerned with conservation matters, we are obliged to address, as we contribute to monitoring and maintaining biodiversity during our period of dramatic transformations of the biosphere.

Genetic Diversity Study of Cinnamomum cassia Blume Using Random Amplified Polymorphic DN A Markers (RAPD)

Aims: To investigate Genetic diversity study of Cinnamomum cassia Blume in Vietnam.&#x0D; Methodology: Fresh leaves of Cinnamomum cassia Blume sample were grinded in liquid nitrogen and total genomic DNA was extracted and purified by CTAB method. The primer was amplified via the polymerase chain reaction on a Gene Amp PCR system 9700. The binary data set was utilized to compute the pairwise Jaccard similarity index and to construct the related similarity matrix. All analyses were performed by using the NTSYS-PC software application.&#x0D; Results: Twenty-four accessions of Cinnamomum cassia Blume belongs to Cinnamomum species collected from some mountainous areas of the Yenbai province, Vietnam were examined to assess genetic variation using the RAPD method. The accessions included 4 in Lucyen, 5 in Tranyen, 5 in Vanchan, 6 in Vanyen and 4 in Yenbinh. Eighty-one out of 99 bands detected by 15 selected RAPD primers were polymorphic. The average number of band/primer was 6.6, in which the polymorphic bands/primer was 5.4, corresponding to 82 %. The similarity indexes among accessions fluctuate between 0.67 to 0.91 The coefficient of estimated PIC/primer range from 0.371 to 0.883, with an average of 0.756. The hight polymophylic and similarity indexes showed large modification of genome. Grouping accessions in phylogenetic tree reflected the fact that the different areas may used the same or different cultivars of Cinnamomum cassia Blume for cultivation.&#x0D; Conclusion: Cinnamomum cassia Blume belongs to Cinnamomum species was introduced in Yenbai from multiple sources and possesses hight genetic diversity and variation and suggests that necessary to establish conservation plan, evaluation and selection of the best gene resources for commercial purposes.

A Comparative Study of Genetic Diversity and Multiplicity of Infection in Uncomplicated Plasmodium falciparum Infections in Selected Regions of Pre-Elimination and High Transmission Settings Using MSP1 and MSP2 Genes.

Understanding the genetic structure of P. falciparum population in different regions is pivotal to malaria elimination. Genetic diversity and the multiplicity of infection are indicators used for measuring malaria endemicity across different transmission settings. Therefore, this study characterized P. falciparum infections from selected areas constituting pre-elimination and high transmission settings in South Africa and Nigeria, respectively. Parasite genomic DNA was extracted from 129 participants with uncomplicated P. falciparum infections. Isolates were collected from 78 participants in South Africa (southern Africa) and 51 in Nigeria (western Africa). Allelic typing of the msp1 and msp2 genes was carried out using nested PCR. In msp1, the K1 allele (39.7%) was the most common allele among the South African isolates, while the RO33 allele (90.2%) was the most common allele among the Nigerian isolates. In the msp2 gene, FC27 and IC3D7 showed almost the same percentage distribution (44.9% and 43.6%) in the South African isolates, whereas FC27 had the highest percentage distribution (60.8%) in the Nigerian isolates. The msp2 gene showed highly distinctive genotypes, indicating high genetic diversity in the South African isolates, whereas msp1 showed high genetic diversity in the Nigerian isolates. The RO33 allelic family displayed an inverse relationship with participants' age in the Nigerian isolates. The overall multiplicity of infection (MOI) was significantly higher in Nigeria (2.87) than in South Africa (2.44) (p < 0.000 *). In addition, heterozygosity was moderately higher in South Africa (1.46) than in Nigeria (1.13). The high genetic diversity and MOI in P. falciparum that were observed in this study could provide surveillance data, on the basis of which appropriate control strategies should be adopted.

Evaluation of Genetic Parameters for Yield and its Attributing Traits in Green gram [Vigna radiata (L.) Wilczek

A study was conducted employing twelve quantitative traits viz., days to 50% flowering, days to maturity, plant height(cm), number of branches per plant, number of clusters per plant, number of pods per cluster, pod length(cm), number of seeds per pod, 100 seed weight(g), harvest index, biological yield per plant and seed yield per plant (g) on 40 green gram genotypes with the intent to uncover the genetic variability, heritability and genetic advance. Significant variance was found for each characteristic when using simple descriptive statistics. High PCV and GCV estimates was noticed for number of pods per plant, seed yield per plant, number of cluster per plant and number of pods per cluster. Days to 50% flowering, plant height, number of branches per plant, number of clusters per plant, number of pods per plant, pod length, number of seeds per pod, 100 seed weight, biological yield per plant and seed yield per plant showed high heritability with high genetic advancement based on a study of genetic variability, suggesting that additive gene action predominates. It will be beneficial to select for these traits.

Primer Design and in Silico PCR for Detection Microsatellite Locus on Cassava (Manihot esculenta) as an Early Study of Genetic Diversity of Gluten Free Food Crops

Food allergy is a hypersensitive reaction of the body to certain substances that should not be harmful. One of the basic ingredients of foods that are reported to contain allergens is wheat. The type of allergen in wheat is found in gluten, which produces the protein gliadin. The protein gliadin is thought to be the cause of allergic reactions, especially in children and people who have celiac disease. Local food ingredients such as cassava can be used as alternative raw materials for gluten-free food products. The genetic diversity test of cassava is needed to determine the genetic variation of the cassava population and the ability to adapt to natural surroundings. Study of genetic diversity of a plant population can be analyzed by DNA fingerprinting technique using microsatellite molecular markers in the PCR method. Primer selection is a crucial stage because the position of the primer attachment will determine the success of the amplification process. Primer design and in silico PCR assay were carried out as a preliminary study to design the right primer to attach to a specific template. The method used digitally with the help of the NCBI Pick Primer page and FastPCR software for PCR stimulation, knowing the position of the primer attachment, precisely determining the primer and the length of the resulting amplicon. The results obtained in the form of 5 pairs of primer sequences attached to the microsatellite polymorphic locus. The length of the amplicon produced in each primer was 167 bp, 195 bp, 155 bp, 161 bp and 112 bp. The basis of primer selection consists of the length of the primary base, the TM value (melting temperature), the percentage of GC amount and the possibility of the formation of dimers between primers.

Isolation and characterisation of 17 microsatellite DNA loci from RAD reduced-representation genomes for Asian warty newts, genus Paramesotriton (Caudata: Salamandridae).

Asian warty newts, genus Paramesotriton, are endemic to southern China and northern Vietnam. Despite the achievements in biodiversity, molecular systematics and biogeography of species in this genus, population genetic diversity studies are lacking due to the lack of economical and available genetic markers. In this study, we developed 17 highly polymorphic microsatellite loci from RAD simplified genomic data for the Asian warty newts, genus Paramesotriton and successfully completed cross-species amplification tests on 20 samples of four species of Paramesotriton. These microsatellite markers can be used as important tools to study population genetic structure, levels of gene flow, population differentiation, mating systems and landscape genetics within the genus Paramesotriton and, thus, to make scientific conservation decisions and actions for the conservation of these rare and endangered amphibians.