High Polymorphism Research Articles

Molecular mapping and characterization of QTLs for grain quality traits in a RIL population of US rice under high nighttime temperature stress

Elevated nighttime temperatures resulting from climate change significantly impact the rice crop worldwide. The rice (Oryza sativa L.) plant is highly sensitive to high nighttime temperature (HNT) during grain-filling (reproductive stage). HNT stress negatively affects grain quality traits and has a major impact on the value of the harvested rice crop. In addition, along with grain dimensions determining rice grain market classes, the grain appearance and quality traits determine the rice grain market value. During the last few years, there has been a major concern for rice growers and the rice industry over the prevalence of rice grains opacity and the reduction of grain dimensions affected by HNT stress. Hence, the improvement of heat-stress tolerance to maintain grain quality of the rice crop under HNT stress will bolster future rice value in the market. In this study, 185 F12-recombinant inbred lines (RILs) derived from two US rice cultivars, Cypress (HNT-tolerant) and LaGrue (HNT-sensitive) were screened for the grain quality traits grain length (GL), grain width (GW), and percent chalkiness (%chalk) under control and HNT stress conditions and evaluated to identify the genomic regions associated with the grain quality traits. In total, there were 15 QTLs identified; 6 QTLs represented under control condition explaining 3.33% to 8.27% of the phenotypic variation, with additive effects ranging from − 0.99 to 0.0267 on six chromosomes and 9 QTLs represented under HNT stress elucidating 6.39 to 51.53% of the phenotypic variation, with additive effects ranging from − 8.8 to 0.028 on nine chromosomes for GL, GW, and % chalk. These 15 QTLs were further characterized and scanned for natural genetic variation in a japonica diversity panel (JDP) to identify candidate genes for GL, GW, and %chalk. We found 6160 high impact single nucleotide polymorphisms (SNPs) characterized as such depending on their type, region, functional class, position, and proximity to the gene and/or gene features, and 149 differentially expressed genes (DEGs) in the 51 Mbp genomic region comprising of the 15 QTLs. Out of which, 11 potential candidate genes showed high impact SNP associations. Therefore, the analysis of the mapped QTLs and their genetic dissection in the US grown Japonica rice genotypes at genomic and transcriptomic levels provide deep insights into genetic variation beneficial to rice breeders and geneticists for understanding the mechanisms related to grain quality under heat stress in rice.

Genetic Relationships of 118 Castanea Specific Germplasms and Construction of Their Molecular ID Based on Morphological Characteristics and SSR Markers

To understand the genetic relationships of Castanea species, 16 phenotypic traits were measured, simple sequence repeat (SSR) markers were analyzed, and molecular identity cards (IDs) were constructed for 118 Castanea materials using fluorescent capillary electrophoresis. The coefficient of variation values of the 16 morphological traits of the test materials ranged from 11.11% to 60.38%. A total of 58 alleles were detected using six pairs of SSR core primers, with an average number of 9.7 alleles per locus. The average number of valid alleles per locus was 3.9419 and the proportion of valid alleles was 40.78%. A total of 105 genotypes were detected, and the number of genotypic species that could be amplified per primer pair ranged from 8 to 26. The mean value of the observed heterozygosity was 0.4986. The variation in the He, H, and PIC values was similar; the size of I value was approximately 2.21 times larger, and its mean number of variations was 0.7390, 0.7359, 0.6985, and 1.6015, respectively. The classification of 118 Castanea species was performed using three analytical methods: structure analysis, neighbor-joining (NJ) cluster analysis, and principal coordinate analysis (PCoA), and the results of the three methods were in high agreement. Six pairs of SSR core primers with high polymorphism and strong discriminatory properties were used to identify 118 Castanea plants, and a unique molecular ID card was constructed for each material. These results provide insight into the genetic diversity and population structure of Castanea plants and a theoretical basis for improving the phenomenon of mixed varieties and substandard plants in the Castanea plant market.

AmpSeqR: an R package for amplicon deep sequencing data analysis

Amplicon sequencing (AmpSeq) is a methodology that targets specific genomic regions of interest for polymerase chain reaction (PCR) amplification so that they can be sequenced to a high depth of coverage. Amplicons are typically chosen to be highly polymorphic, usually with several highly informative, high frequency single nucleotide polymorphisms (SNPs) segregating in an amplicon of 100–200 base pair (bp). This allows high sensitivity detection and quantification of the frequency of each sequence within each sample making it suitable for applications such as low frequency somatic mosaicism detection or minor clone detection in mixed samples. AmpSeq is being increasingly applied to both biological and medical studies, in applications such as cancer, infectious diseases and brain mosaicism studies. Current bioinformatics pipelines for AmpSeq data processing lack downstream analysis, have difficulty distinguishing between true sequences and PCR sequencing errors and artifacts, and often require bioinformatic expertise. We present a new R package: AmpSeqR, designed for the processing of deep short-read amplicon sequencing data, with a focus on infectious diseases. The pipeline integrates several existing R packages combining them with newly developed functions to perform optimal filtering of reads to remove noise and improve the accuracy of the detected sequences data, permitting detection of very low frequency clones in mixed samples. The package provides useful functions including data pre-processing, amplicon sequence variants (ASVs) estimation, data post-processing, data visualization, and automatically generates a comprehensive Rmarkdown report that contains all essential results facilitating easy inclusion into reports and publications. AmpSeqR is publicly available at https://github.com/bahlolab/AmpSeqR.

Population Genetic Analysis of Phytophthora colocasiae from Taro in Japan Using SSR Markers.

Phytophthora colocasiae is an important pathogen that causes great economic losses in taro production in tropical and subtropical regions, especially in Japan. Understanding the genetic variations in P. colocasiae populations and their transmission patterns in Japan is essential for effective disease control. Here, the genetic diversity of 358 P. colocasiae isolates, including 348 from Japan, 7 from China, and 3 from Indonesia, was assessed using 11 simple sequence repeat (SSR) primer pairs with high polymorphism. The phylogenetic tree of the SSR locus showed that the isolates from Japan could be divided into 14 groups, with group A being the dominant group. Among foreign isolates, only six from mainland China were similar to those from Japan and clustered in groups B and E. Analysis of molecular variance (AMOVA), principal components analysis (PCA), and cluster analysis (K = 3) results revealed a moderate level of genetic diversity, mainly within individuals. Populations showed high heterozygosity, a lack of regional differentiation, and frequent gene flow. Analysis of mating types and ploidy levels revealed that A2 and self-fertile (SF) A2 types and tetraploids were dominant across populations. Explanations and hypotheses for the results can provide more effective strategies for disease management of taro leaf blight.

Enhanced Thermoelectric Performance of Nanostructured Cu2SnS3 (CTS) via Ag Doping

The present work aims to investigate the effect of Ag doping on the thermoelectric properties of Cu2SnS3 (CTS). Various Cu2Ag(x)Sn(1–x)S3 (0.05 ≤ x ≤ 0.25) samples were synthesized by mechanical alloying followed by spark plasma sintering, and their structural and transport properties were systematically investigated. The x = 0.15 sample presented a ∼10-fold higher power factor than the undoped CTS. Although, the x = 0.125 sample had a lower power factor than the x = 0.15 sample, owing to its lower thermal conductivity, both the samples showed the highest zT ∼ 0.8 at 723 K. This value is comparable to the best results available in the literature for earth-abundant and eco-friendly thermoelectric materials. Interestingly, the thermal conductivity of Cu2Ag(x)Sn(1–x)S3 samples increased with Ag substitution, which was further investigated using the first-principles and ab initio molecular dynamics calculations. It was observed that the incorporation of Ag into the system decreases the root mean square displacement of the other cations and anions, reducing the scattering of phonons and thereby increasing the lattice thermal conductivity. Moreover, the calculations on the formation energy have revealed the reason for the structural transformation of CTS and similar diamond-like structures toward high symmetry polymorphs by external doping. The increase in zT is directly related to the optimization of the band gap and the weighted mobility, which have been investigated experimentally and using the first principle method.

Genome-wide identification and annotation of SNPs and their mapping in candidate genes related to milk production and fertility traits in Badri cattle

This study was conducted in Badri cattle using a double digest restriction-site associated DNA sequencing approach. The study aimed to identify and annotate high confidence single nucleotide polymorphisms (SNPs) and their mapping in candidate genes related to production and fertility in dairy cattle. A total of 7,168,552 genome-wide SNPs were initially identified in Badri cattle by alignment with theBos indicusreference genome. After filtration of SNPs, 65,483 high confidence SNPs were retained and further used for downstream analysis. Annotation of high confidence SNPs revealed 99.197% SNPs had modifier impact, 0.326% SNPs were low impact, 0.036% were high impact, and 0.441% were moderate impact SNPs. Most SNPs in Badri cattle were found in intergenic, transcript and intronic regions. The candidate genes for milk production PRKCE, ABCG2, GHR, EPS8, CAST and NRXN1 were found to harbour maximum high confidence variants. Among candidate genes for fertility in cattle, ATP2B1, SOX5, WDR27, ARHGAP12, CACNA1D, ANKRD6, GRIA3, ZNF521 and CAST822 have maximum high confidence variants mapped in them. The SNPs found mapped in the candidate genes will be important genetic tools in the search for phenotype-modifying nucleotide changes and will aid in formulating relevant genetic improvement programmes for dairy cattle.

Diversity analysis of guava (Psidium guajava) germplasm collection

Guava (Psidium guajava L.) is one of the commercially important cultivated fruit crops in India. Guava ranks fifthin production share of fruit crops in the country. During 2014-15, India produced 36.68 lakh tonnes of guava from anarea of 2.68 lakh ha with 13.7 t/ha productivity. In the present investigation, a total 33 genotypes including 6 speciesof Psidium and 28 genotypes of Psidium guajava were characterized using 39 SSR markers. All accessions are beingcultivated at IARI research farm, Pusa campus, New Delhi. Samples were collected from research farm to determinethe overall diversity and to assess the similarity among genotypes using molecular markers. Out of 39 primers 26were reproducible. A total of 64 alleles were produced by 26 primers and number of alleles per locus variedfrom 1 (mPgCIR01, mPgCIR18 and mPgCIR19) to 5 (mPgCIR256) with mean value of 2.34. Gene diversity rangedfrom 0.0377 to 0.6681 with a mean value of 0.2766. Highest gene diversity was observed for primer mPgCIR256(0.6681) and lowest for primer mPgCIR24 (0.0377). SSR primer mPgCIR256 was most informative with high rateof polymorphism as well as number of alleles. Phenotypic correlation indicated the correlated traits with dependentyield trait. PCA and cluster analysis showed a significant phenotypic and genetic diversity among existing cultivars.All accessions were grouped into two major groups and under each group four sub groups. Maximum diversity wasfound in leaf traits, viz. leaf length, leaf breadth, petiole and petiole length. Genetic distance and the dissimilarity matrixshowed three major clusters on the basis of genetic similarity. All these accessions were grouped in to three clusters,viz. A, B and C. While cluster A includes only cultivars, cluster B includes all species except P. friedrichsthalianum.This indicates that, the diversity among and between species is at cluster level. Genetic diversity analysis amongPsidium species showed that P. guajava had more similarity with Psidium guienensis compared to other species.Present investigation indicated the presence of substantial diversity among guava species which can be utilized forfuture guava improvement programmes

Comparison of genetic diversity and phylogenetic structure of BRCA1 gene of some domestic and wild sheep breeds in different countries

BRCA1 gene plays an important role in DNA damage repair, cell cycle, and transcription process regulation; hence it’s called gate keeper. The current research aims to perform bioinformatics analyzes of the BRCA1 gene of different breeds of domestic and wild sheep from 49 breeds in 14 countries using the NCBI genome database. The desired sequences were aligned using MEGA11 software and a phylogenetic tree was drawn by Neighbor-Joining method. The number of mutations, nucleotide diversity, and haploid diversity were also analyzed using Dnaspv5 software. The analyses showed 296 polymorphisms, which led to the creation of 45 different haplotypes with a haplotype diversity of 0.035. Nucleotide diversity and average nucleotide differences among breeds were estimated as 0.259 and 0.052, respectively. The average genetic distance within the population of countries was calculated as 0.052. The amount of sequence conservation in this research was 0.313 on average, which indicates the high polymorphism of this gene and the emergence of new proteins. Tajima’s D value in Tajima’s neutrality test was −2.421, which was significant (p < 0.05). One of the reasons for the high genetic diversity in Iran’s wild sheep population is the existence of forests and open environments, which prevent genetic drift and reduce inbreeding.

Distinctive foliar features and volatile profiles in three Ambrosia species (Asteraceae).

Ambrosia species differ both in their trichome types and in metabolic profiles of leaf volatiles. The current study provides tools for easier taxonomic identification of ragweed species. The genus Ambrosia (Asteraceae) includes some of the most noxious allergenic invasive weeds in the world. Due to high polymorphism in this genus, identification of species is often difficult. This study focuses on microscopic investigation of foliar features and GC-MS identification of the main leaf volatile components of three Ambrosia species currently found in Israel-invasive species Ambrosia confertiflora and A. tenuifolia, and transient A. grayi. A. confertiflora and A. tenuifolia have three trichome types: non-glandular trichomes, capitate glandular trichomes and linear glandular trichomes. Their non-glandular trichomes and capitate trichomes have distinct structures and can serve as taxonomic characters. A. grayi (the least successful invader) has only very dense covering trichomes. All three Ambrosia species have secretory structures in their leaf midrib. A. confertiflora, the most problematic invasive plant in Israel, had a ten times higher volatiles content than the other two species. In A. confertiflora, the most abundant volatiles were chrysanthenone (25.5%), borneol (18%), germacrene D and (E)-caryophyllene (both around 12%). In A. tenuifolia, the most abundant volatiles were β-myrcene (32.9%), (2E)-hexenal (13%) and 1,8-cineole (11.7%). In A. grayi, the most abundant volatiles were β-myrcene (17.9%), germacrene D (17.8%) and limonene (14%). The three examined species have distinct trichome types and metabolic profiles. Non-glandular trichomes show structural diversification between species and are a good descriptive character. Considering the anthropocentric significance of this highly problematic genus, the current study provides tools for easier identification of ragweed species.

Population genetic characteristics of Aedes aegypti in 2019 and 2020 under the distinct circumstances of dengue outbreak and the COVID-19 pandemic in Yunnan Province, China.

Introduction: Since Aedes aegypti invaded Yunnan Province in 2002, its total population has continued to expand. Shi et al. used microsatellite and mitochondrial molecular markers to study the Ae. aegypti populations in Yunnan Province in 2015 and 2016, found that it showed high genetic diversity and genetic structure. However, there are few studies on the population genetic characteristics of Ae. aegypti in Yunnan Province under different levels of human intervention. This study mainly used two common types of molecular markers to analyze the genetic characteristics of Ae. aegypti, revealing the influence of different input, prevention and control pressures on the genetic diversity and structure of this species. Understanding the genetic characteristics of Ae. aegypti populations and clarifying the diversity, spread status, and source of invasion are essential for the prevention, control and elimination of this disease vector. Methods: We analyzed the genetic diversity and genetic structure of 22 populations sampled in Yunnan Province in 2019 and 17 populations sampled in 2020 through nine microsatellite loci and COI and ND4 fragments of mitochondrial DNA. In 2019, a total of 22 natural populations were obtained, each containing 30 samples, a total of 660 samples. In 2020, a total of 17 natural populations were obtained. Similarly, each population had 30 samples, and a total of 510 samples were obtained. Results: Analysis of Ae. aegypti populations in 2019 and 2020 based on microsatellite markers revealed 67 and 72 alleles, respectively. The average allelic richness of the populations in 2019 was 3.659, while that in 2020 was 3.965. The HWE analysis of the 22 populations sampled in 2019 revealed significant departure only in the QSH-2 population. The 17 populations sampled in 2020 were all in HWE. The average polymorphic information content (PIC) values were 0.546 and 0.545, respectively, showing high polymorphism. The average observed heterozygosity of the 2019 and 2020 populations was 0.538 and 0.514, respectively, and the expected average heterozygosity was 0.517 and 0.519, showing high genetic diversity in all mosquito populations. By analyzing the COI and ND4 fragments in the mitochondrial DNA of Ae. aegypti, the populations sampled in 2019 had a total of 10 COI haplotypes and 17 ND4 haplotypes. A total of 20 COI haplotypes were found in the populations sampled in 2020, and a total of 24 ND4 haplotypes were obtained. STRUCTURE, UPGMA and DAPC cluster analyses and a network diagram constructed based on COI and ND4 fragments showed that the populations of Ae. aegypti in Yunnan Province sampled in 2019 and 2020 could be divided into two clusters. At the beginning of 2020, due to the impact of COVID-19, the flow of goods between the port areas of Yunnan Province and neighboring countries was reduced, and the sterilization was more effective when goods enter the customs, leading to different immigration pressures on Ae. aegypti population in Yunnan Province between 2019 and 2020, the source populations of the 2019 and 2020 populations changed. Mantel test is generally used to detect the correlation between genetic distance and geographical distance, the analysis indicated that population geographic distance and genetic distance had a moderately significant correlation in 2019 and 2020 (2019: p < 0.05 R2 = 0.4807, 2020: p < 0.05 R2 = 0.4233). Conclusion: Ae. aegypti in Yunnan Province maintains a high degree of genetic diversity. Human interference is one reason for the changes in the genetic characteristics of this disease vector.

Genetic Diversity and Population Structure Analysis in the Chinese Endemic Species Michelia crassipes Based on SSR Markers

Michelia crassipes Y. W. Law (Magnoliaceae) is endemic to China and is the only species with purple flowers in the genus Michelia. It is commonly used as an important parent for flower color improvement and hybrid breeding. M. crassipes is recognized as an endangered plant. An urgent need exists to explore the genetic diversity of M. crassipes to efficiently select hybrid parents and develop efficient conservation strategies. In this study, a total of 128 samples were selected from seven natural populations of M. crassipes to explore their genetic diversity and structure. A total of 14 microsatellite (SSR) markers with high polymorphism and repeatability were developed, and 218 alleles were detected. This study mainly revealed three results: (1) The parameters of expected heterozygosity (He = 0.536) and mean Shannon’s information index (I = 1.121) revealed moderately high levels of genetic diversity for the M. crassipes natural population; (2) The genetic differentiation coefficient (Fst = 0.108) showed that there was a low level of genetic differentiation, and AMOVA indicated that genetic variation existed mainly within populations and that there was frequent gene exchange between populations; and (3) The population genetic structure analysis showed that seven natural populations originated from two ancestral groups, and the Mantel test revealed that genetic and geographical distances between populations were significantly correlated. Our study is the first to explore the genetic diversity and structure of the M. crassipes natural population, which provides an important reference for the collection, conservation and utilization of Michelia crassipes germplasm resources.

The development of the novel 22 X- indel multiplex system for forensic genetics

InDel (Insertions/deletion) markers have been used as an alternative, or as a complementary marker system, to STR markers in human identification due to their advantages such as low mutation rates, no stutter, and potential small amplicon sizes. In forensic sciences, sex chromosomes are widely used in forensic genetics for specific cases. For example, the relationship between father and daughter can be determined by using X-InDels. In this study, we developed a novel 22 X-InDel multiplex system that was identified by two separate assays with fluorescence amplification and capillary electrophoresis detection technology. We chose 22 X-InDel markers based on the following criteria: mean heterozygosity over 30% in Europeans; minimum of 250 Kb differences between each InDel loci; and an amplicon length that was less than 300 bp. We performed an optimization and validation study of 22 X-InDel systems under the following parameters: analytical threshold, sensitivity, precision and accuracy, stochastic threshold, repeatability, and reproducibility. We evaluated the allele frequency of this multiplex system in the Turkish population, and then the population comparisons were carried out on data from 1000 Genome populations (Europe, Africa, America, South Asia, and East Asia). The sensitivity test showed a complete genotyping profile with DNA concentrations as low as 0.5 ng. The heterozygosity ratio of 22 X-InDel loci was determined as 0.4690 and the discrimination power was defined as 0.99. The results show that the new 22 X-InDel multiplex system provides high polymorphism information, and it is a reproducible, accurate, sensitive, and robust system that could be used as an additional tool for kinship testing.

Vessel diameter polymorphism determines vulnerability-to-embolism curve shape

Summary Sherwin Carlquist proposed several functional interpretations for vessel diameter, including that narrow vessels were hydraulically “safe” while wide diameter vessels were more vulnerable to embolism. He applied these ideas both across species and biomes, and within xylem tissue, where function of growth ring types was inferred from vessel diameter polymorphisms (occurrence of differing vessel diameter classes within a tissue). Following on Carlquist’s ideas, we were interested in evaluating if vessel diameter polymorphism could be linked to vulnerability-to-embolism curve shape. Vulnerability curves were fit with a model that included a continuous shape term (alpha). We predicted that high variation in vessel diameter would result in lower alpha (more r-shaped) curves whereas low variation would produce higher alpha (more s-shaped) curves, with potential for intermediate curve types. Our findings support Carlquist’s functional interpretations of vessel diameter. Vessel diameter polymorphism was strongly correlated to vulnerability curve shape. Homogeneous vessel diameters were associated with more s-shaped curves. As vessel diameter polymorphism increased, alpha declined and curves became more linear. High polymorphism was associated with r-shaped curves. There was no relationship between vessel length and curve shape. Vessel diameter was strongly correlated with a common estimate of embolism resistance (P50), with wider diameter vessels associated with increased vulnerability. Vulnerability curves show enormous variety in shape and scale, and both parameters are likely critical in understanding and predicting plant function. Carlquist’s ecological anatomy data, predictions, and functional inferences will continue to be valuable as we expand our understanding of structure–function links in plant anatomy.

Microsatellite Genome-Wide Database Development for the Commercial Blackhead Seabream (Acanthopagrus schlegelii)

Simple sequence repeats (SSRs), the markers with the highest polymorphism and co-dominance degrees, offer a crucial genetic research resource. Limited SSR markers in blackhead seabream have been reported. The availability of the blackhead seabream genome assembly provided the opportunity to carry out genome-wide identification for all microsatellite markers, and bioinformatic analyses open the way for developing a microsatellite genome-wide database in blackhead seabream. In this study, a total of 412,381 SSRs were identified in the 688.08 Mb genome by Krait software. Whole-genome sequences (10×) of 42 samples were aligned against the reference genome and genotyped using the HipSTR tools by comparing and counting repeat number variation across the SSR loci. A total of 156,086 SSRs with a 2-4 bp repeat were genotyped by HipSTR tools, which accounted for 55.78% of the 2-4 bp SSRs in the reference genome. High accuracy of genotyping was observed by comparing HipSTR tools and PCR amplification. A set of 109,131 loci with a number of alleles ≥ 3 and with a number of genotyped individuals ≥ 6 were reserved to constitute the polymorphic SSR database. Fifty-one polymorphic SSR loci were identified through PCR amplification. This strategy to develop polymorphic SSR markers not only obtained a large set of polymorphic SSRs but also eliminated the need for laborious experimental screening. SSR markers developed in this study may facilitate blackhead seabream research, which lays a certain foundation for further gene tagging and genetic linkage analysis, such as marker-assisted selection, genetic mapping, as well as comparative genomic analysis.

Phylogenomics reveals within species diversification but incongruence with color phenotypes in widespread orchid bees (Hymenoptera: Apidae: Euglossini)

AbstractColoration is an important phenotypic trait for taxonomic studies and has been widely used for identifying insect species and populations. However, coloration can be a poor diagnostic character for insect species that exhibit high polymorphism in this trait, which can lead to over-splitting of taxonomic units. In orchid bees, color variation has been interpreted by different taxonomists as either polymorphism associated with Müllerian mimicry complexes or diagnostic traits for species identification. Despite this uncertainty, integrative approaches that incorporate multiple independent datasets to test the validity of hair coloration as a character that identifies independent evolutionary units have not been used. Here, we use phylogenomic data from Ultraconserved Elements (UCEs) to explore whether color phenotypes in the widespread orchid bee species complexes Eulaema meriana and Eulaema bombiformis (Hymenoptera: Apidae: Euglossini) correspond to independent lineages or polymorphic trait variation within species. We find that lineages within both species are structured according to geography and that color morphs are generally unassociated with evolutionarily independent groups except for populations located in the Atlantic Forest of Brazil. We conclude that there is compelling evidence that E. atleticana and E. niveofasciata are subspecies of E. meriana and E. bombiformis, respectively, and not different species as previously suggested. Therefore, we recognize Eulaema meriana atleticanacomb. n. and Eulaema bombiformis niveofasciatacomb. n. and discuss their morphological characteristics. We make recommendations on the use of color traits for orchid bee taxonomy and discuss the significance of subspecies as evolutionary units relevant for conservation efforts.

Comprehensive evaluation and economic analysis in some barley genotypes under soil salinity

Abstract. Mariey SA, El-Bialy MA, Khedr RA, Mohamed EN, Meleha AMI, Khatab IA. 2023. Comprehensive evaluation and economic analysis in some barley genotypes under soil salinity. Asian J Agric 7: 20-33. Soil salinity is one of the abiotic stresses that cause a significant reduction in barley production. Understanding the phenotypic and genetic diversity among Barley genotypes is necessary to improve barley salt tolerance. Herne comprehensive sets of morph-physiological, grain quality traits and Simple Sequence Repeat (SSR) markers combined with economic analysis were done to determine the phenotypic and genetic variation of eight barley genotypes under salinity stress during seasons 2019/2020 and 2020/2021. High genetic variation was observed among studied genotypes for all measured traits. Salinization caused a significant increase in (Sodium content, soluble carbohydrate content, and crude protein content %) in sensitive genotypes (Giza 132 and line 1). SSRs markers generated clear patterns with high polymorphism with 31 alleles by an average of 2.07 alleles per locus. Out of 15 SSR markers, nine (Bmac 0209, Bmag 0011, Bmag 125, Bmac 0871, Bmag 770, Bmac 701, Bmag 0387, Bmac316, and Bmag 0009) were highly useful in distinguishing tolerant and sensitive Barley genotypes. Soil salinity decreased the benefit-cost ratio for Giza 123,136 and 137, which appear beneficial as salt-tolerant cultivars. Those cultivars had low reductions for almost studied traits and had the highest grain yield production due to increasing the farmer's income under salt affect area.

Correlation between High Myopia Susceptibility and Polymorphisms of RASGRF1 Gene among College Students in Zhejiang.

The aim of the study is to analyze the correlation between high myopia susceptibility and Ras protein-specific guanine nucleotide-releasing factor-1(RASGRF1) gene polymorphism among college students in Zhejiang. A stratified whole-group sampling method was used to select 218 cases of college students in Zhejiang who met the inclusion and exclusion criteria from January, 2019, to December, 2021, and they were divided into 77 cases (154 eyes) in the high myopia group and 141 cases (282 eyes) in the medium-low myopia group according to the degree of myopia, and 109 cases of college volunteers without myopia from the same period of medical examination in the region were included in the control group. The single nucleotide polymorphisms (SNPs) located in functional regions were selected by searching the literature and genetic databases, and the base sequences of rs939658, rs4778879, and rs8033417 loci were obtained by genotyping candidate SNPs using multiplex ligase detection reaction technique. The cardinality test was used to compare the differences in genotype frequency distribution of each locus of the RASGRF1 gene between the high myopia group and the low to moderate myopia group and the control group. The genotype frequencies and allele frequencies of the RASGRF1 gene rs939658 locus in the high myopia group compared with the moderate-low myopia group and the control group were not statistically significant (P > 0.05). The genotype frequencies and allele frequencies of the rs4778879 locus of the RASGRF1 gene were compared among the three groups, and the differences were not statistically significant (P > 0.05). The genotype frequency and allele frequency of the rs8033417 locus of the RASGRF1 gene differed significantly among the three groups (P < 0.05). The polymorphism of the rs8033417 locus of the RASGRF1 gene was significantly correlated with the susceptibility of high myopia among college students in Zhejiang.

VARIABILITY OF AMPLIFIED PROFILES GENERATED BY BBAP IN AVENA SATIVA L.

Avena sativa L. is a very common specie for human consumption that provide different health benefits. As a dual purpose crop, oat provide a source of protein, fiber and minerals. Here, homologs of Bet v 1 allergen genes were used as DNA markers to analyse their utilization for genomic variability of oat varieties. The presence of Bet v 1 homologues in seven oat varieties were examined and their length polymorphism was analysed. Bet v 1 based amplified profile – BBAP- was used to obtain the polymorphic profiles for the used oat varieties by a combination of specific and degenerated primer pair. This method was reported to be universal in plants for screening of variability of coding regions. Using the primer pair Bet v 1 forward and degenerated Bet v 1 reverse 49 amplicons were amplified in a total. The length of the amplicons varied from 265 base pairs to 1929 base pairs. All analysed oat varieties generated unique amplicons, but there was not a size of amplicon that all cultivars shared. Constructed dendrogram based on hierarchical cluster analysis using UPGMA algorithm grouped the analysed varieties genotypes into three main clusters – Black Beauty and Zvolen varieties, Valentín and Earl and Vendelín varieties and Floron and Dagles varieties. BBAP technique provide a high polymorphism in the Bet v 1 isoforms present in oat and all of the analysed varieties were distinguished what showed the utility of this marker technique for analysis of genetic diversity and genotype identification of oat varieties.

S-Locus Genotyping in Japanese Plum by High Throughput Sequencing Using a Synthetic S-Loci Reference Sequence.

Self-incompatibility in Prunus species is governed by a single locus consisting of two highly multi-allelic and tightly linked genes, one coding for an F-box protein-i.e., SFB in Prunus- controlling the pollen specificity and one coding for an S-RNase gene controlling the pistil specificity. Genotyping the allelic combination in a fruit tree species is an essential procedure both for cross-based breeding and for establishing pollination requirements. Gel-based PCR techniques using primer pairs designed from conserved regions and spanning polymorphic intronic regions are traditionally used for this task. However, with the great advance of massive sequencing techniques and the lowering of sequencing costs, new genotyping-by-sequencing procedures are emerging. The alignment of resequenced individuals to reference genomes, commonly used for polymorphism detection, yields little or no coverage in the S-locus region due to high polymorphism between different alleles within the same species, and cannot be used for this purpose. Using the available sequences of Japanese plum S-loci concatenated in a rosary-like structure as synthetic reference sequence, we describe a procedure to accurately genotype resequenced individuals that allowed the analysis of the S-genotype in 88 Japanese plum cultivars, 74 of them are reported for the first time. In addition to unraveling two new S-alleles from published reference genomes, we identified at least two S-alleles in 74 cultivars. According to their S-allele composition, they were assigned to 22 incompatibility groups, including nine new incompatibility groups reported here for the first time (XXVII-XXXV).

Features of the epidemiological situation with acute urogenital gonococcal infection in the Perm Region for the period from 2010 to 2021

BACKGROUND: According to WHO, more than 60 million people get sick with gonococcal infection every year. Recently, there has been a decrease in the incidence of gonorrhea in Russia. However, in addition to Neisseria gonorrhoeae, other microorganisms may also cause acute urethritis. However, there is no record of morbidity for them.&#x0D; AIM: This study analyzes the epidemiological situation of the incidence of аcute genital gonococcal infection and urethral nonspecific inflammatory diseases in the Perm Region for the period 20102021.&#x0D; MATERIALS AND METHODS: A comparative retrospective analysis of the incidence of аcute genital gonococcal infection and urogenital tract nonspecific inflammatory diseases among patients of the Perm Region was performed using the annually published data of official statistics. The data on the incidence of genital tract nonspecific inflammatory diseases were obtained from outpatient patient records of three clinics in the city of Perm. Epidemiological and statistical information processing methods were used in the work, and the Pearson coefficient was used for correlation analysis.&#x0D; RESULTS: The long-term dynamics of the incidence of аcute genital gonococcal infection among the population of the Perm Region was characterized by a pronounced downward trend. However, in recent years, the number of genital tract infections in women and men has increased. The decrease in the incidence of аcute genital gonococcal infection is most likely due to changes in the properties of N. gonorrhoeae, causing significantly more difficult laboratory diagnoses and often leading to false negative results. In addition, the high polymorphism of cultural, morphological, and biochemical properties of conditionally pathogenic microorganisms further complicates the identification stage of the isolated strains.&#x0D; CONCLUSION: As a result, against the background of a decrease in the incidence of аcute genital gonococcal infection, an increase in the incidence of genital tract nonspecific inflammatory diseases was revealed. The peculiarities of the epidemic process of аcute genital gonococcal infection and urogenital tract and the complexity of laboratory diagnostics of these conditions cause their untimely detection.