UPGMA Research Articles

Identity, pathogenicity and genetic diversity of Lasiodiplodia associated with stem-end rot of avocado in China.

Stem-end rot (SER) causes brown necrotic lesions in the pulp near the base of the fruit pedicel and is one of the most devastating postharvest diseases of avocados in all avocado growing regions of the world. China's avocado industry is growing very rapidly, and the planting area is expanding, but little is known about the pathogens and genetic diversity of avocado SER. To determine the causal agents of SER, avocado fruits were sampled from the main avocado-producing areas in China during 2020 and 2021. Fungal isolates were obtained from SER symptomatic avocado fruits and identified by morphology combined with phylogenetic analysis of internal transcribed spacer (ITS), translation elongation factor 1-α (EF1-α) and β-tubulin (TUB2) gene sequences. All 101 isolates belonged to Lasiodiplodia spp., and four Lasiodiplodia species were identified, namely L. pseudotheobromae (59.41%), L. theobromae (24.75%), L. mahajangana (7.92%), L. euphorbiaceicola (1.98%), and six others are classified as Lasiodiplodia sp. (5.94%). There were only slight morphological differences in colonies and conidia of these four species of Lasiodiplodia. The pathogenicity tests showed symptoms of SER, and the 92.08% of the isolates exhibited a high level of virulence on avocado (disease index > 70), related to the disease severity on avocado fruit. All tested isolates grew well under conditions from 23 to 33℃. There was a significant difference in mycelial growth between the four species of Lasiodiplodia after treatment with high temperature or low temperature. L. pseudotheobromae growth was the fastest at 13 to 18℃, but was the lowest at 38℃ (P < 0.05). Red pigment could be produced by all tested isolates after culturing for 7 days at 38℃. The mycelial growth rate was the fastest on PDA medium, and the slowest on OMA medium but promoted spore formation (P < 0.05). In addition, was determined the genetic diversity of Lasiodiplodia pathogenic species associated with SER collected from avocado, mango, guava and soursop fruits was determined. A total of 74 isolates were clustered into 4 main ISSR groups by unweighted pair-group method with arithmetic mean (UPGMA) analysis, and the classification of this group was related to the host. Extensive diversity was detected in the Lasiodiplodia populations. The diverse geographical origins and host species significantly influenced the population differentiation, and most of the genetic variation occurred within populations (P < 0.001). This is the first study to identify the major pathogens of avocado SER in China and to survey their occurrence, pathogenicity and include a comparative analysis of genetic diversity with Lasiodiplodia spp. causing SER on other fruit hosts. Collectively, the Lasiodiplodia species complex affecting avocado showed high pathogenicity and diversity, while L. pseudotheobromae was the most frequently isolated species in China. The results of this study provide insights into the aspects of epidemic of SER disease caused by Lasiodiplodia species, which will help in developing strategies for the management and control of stem end-rot in avocado.

Genetic diversity of Sinapis arvensis L. (wild mustard) in Türkiye determined by microsatellite markers

Wild mustard (Sinapis arvensis L.) is a self-fertilizing weed species that exerts negative impacts on wheat production and herbicides are intensively used to manage it. Cross-fertilization may lead to genetic differentiation in this species. Therefore, this study investigated genetic diversity among wild mustard populations collected from wheat fields across various regions in Türkiye. Genetic variation was evaluated using 5 simple sequence repeat (SSR) markers in populations collected from 30 different locations. Populations were analyzed using UPGMA (unweighted pair group method with arithmetic mean) and principal component analysis (PCA). The mean genetic diversity (GD) and polymorphism information content (PIC) values were 0.752 and 0.844, respectively. High genetic variability was recorded among populations within geographic locations. The populations were categorized into two major groups by UPGMA. There was no apparent geographic isolation among tested populations, which displayed a high degree of variability. The primary source of this variability is thought to be the adaptability of wild mustard seeds dispersed through various methods across diverse locations. Despite being a predominantly self-pollinating species, wild mustard may also employ some cross-pollination mechanisms. In conclusion, SSR markers proved useful in determining genetic diversity in outcrossing species, especially where no prior genotypic information is available. The study suggests that genetic diversity is maintained in wild mustard populations even with rotational farming practices and intensive use of herbicides.

An Intra-Hospital Spread of Colistin-Resistant K. pneumoniae Isolates-Epidemiological, Clinical, and Genetic Analysis.

Background and Objective: Klebsiella pneumoniae appears to be a significant problem due to its ability to accumulate antibiotic-resistance genes. After 2013, alarming colistin resistance rates among carbapenem-resistant K. pneumoniae have been reported in the Balkans. The study aims to perform an epidemiological, clinical, and genetic analysis of a local outbreak of COLr CR-Kp. Material and Methods: All carbapenem-resistant and colistin-resistant K. pneumoniae isolates observed among patients in the ICU unit of Military Medical Academy, Sofia, from 1 January to 31 October 2023, were included. The results were analyzed according to the EUCAST criteria. All isolates were screened for blaVIM, blaIMP, blaKPC, blaNDM, and blaOXA-48. Genetic similarity was determined using the Dice coefficient as a similarity measure and the unweighted pair group method with arithmetic mean (UPGMA). mgrB genes and plasmid-mediated colistin resistance determinants (mcr-1, mcr-2, mcr-3, mcr-4, and mcr-5) were investigated. Results: There was a total of 379 multidrug-resistant K. pneumoniae isolates, 88% of which were carbapenem-resistant. Of these, there were nine (2.7%) colistin-resistant isolates in six patients. A time and space cluster for five patients was found. Epidemiology typing showed that two isolates belonged to clone A (pts. 1, 5) and the rest to clone B (pts. 2-4) with 69% similarity. Clone A isolates were coproducers of blaNDM-like and blaOXA-48-like and had mgrB-mediated colistin resistance (40%). Clone B isolates had only blaOXA-48-like and intact mgrB genes. All isolates were negative for mcr-1, -2, -3, -4, and -5 genes. Conclusions: The study describes a within-hospital spread of two clones of COLr CR-Kp with a 60% mortality rate. Clone A isolates were coproducers of NDM-like and OXA-48-like enzymes and had mgrB-mediated colistin resistance. Clone B isolates had only OXA-48-like enzymes and intact mgrB genes. No plasmid-mediated resistance was found. The extremely high mortality rate and limited treatment options warrant strict measures to prevent outbreaks.

Multivariate data analysis for semen quality in two frog species

Despite the growing body of research on frog reproduction and semen quality, studies employing statistical methods and analyses are scarce. The present study aimed to examine the use of exploratory multivariate data analysis for evaluating the seminal quality of frogs, determining a possible hierarchy among frog species based on semen characteristics, and identifying the most effective clustering strategy. Data on the seminal quality of the butter frog (Leptodactylus ocellatus, native specie) were collected from seven samples, and for the bullfrog (Lithobates catesbeianus, exotic specie), five samples were used, all derived from a literature review. Four distinct clustering strategies were tested: Single Linkage, Unweighted Pair Group Method with Arithmetic Mean (UPGMA), Complete Linkage, and Ward’s method. Exploratory multivariate data analysis could effectively evaluate frog seminal quality, allowing the classification of frog species (both native and exotic) based on semen. Among the tested strategies, UPGMA emerged as the most suitable grouping method.

Genetic variation among Brassica rapa subsp. rapa genotypes growing in Malatya/Türkiye

AbstractIn this study, the genetic variation of 18 Brassica rapa subsp. rapa genotypes grown in Malatya was determined using the inter simple sequence repeat - polymerase chain reaciton (ISSR-PCR). Using nine ISSR primers, a total of 73 bands were obtained and the polymorphism rate was 91.78%. The mean polymorphism information content value was determined as 0.3319. The mean gene diversity (H) value was determined as 0.4276. The mean major allele frequency value was determined as 0.6531. Similarity index values were determined to be between 0.0928 and 1.0924. The unweighted pair group method with arithmetic mean (UPGMA) dendrogram consisted of two groups. Principal component analysis analysis and UPGMA dendrogram were compatible. In addition, the groups in the phylogenetic trees were partially compatible with geographical distribution. Our results suggest that ISSR-PCR analysis is a suitable approach for breeding Brassica rapa subsp. rapa genotypes and developing different cultivars.

Desempenho agronômico e estimativa da diversidade genética entre linhagens de soja baseada em caracteres quantitativos

ABSTRACT Although soybean is one of the most important agricultural commodities in the world, it has been losing genetic diversity in recent decades, due to the intense breeding process and reproduction method. Thus, the objective of this study was to evaluate the agronomic performance and estimate the genetic diversity among inbred lines, and identify promising crossings. A total of 66 soybean genotypes were evaluated, 61 of which were pre-commercial lines, and five commercial cultivars (AS3797, DESAFIO, M7110, M7739, M8210) as controls. The experimental design consisted of randomized blocks with three replicates. The distance matrix between the inbred lines was calculated by Mahalanobis distance and grouping by the unweighted pair group method with arithmetic mean (UPGMA). The maximum distance was 1,776.26 between cultivar M7110 and the G23 inbred line, and the minimum 1.50 between inbred lines G13 and G36, with an average distance of 364.40, demonstrating genetic diversity. The traits that contributed most to genetic divergence were number of days to flowering (66.7%) and physiological maturation (28.55%). Inbred lines G60 (higher grain yield), G51 and G33 (lower physiological maturation) and cultivar M7110 (greater divergence) stood out. Four groups were formed, with G1 having the highest grain yield and fewest days to flowering and physiological maturation. The indicated crossings are between G60, G57, CD2728, M7110, G33 and G32 (group G1) and G47 (group G4).

Assessing the Genetic Diversity of Parents for Developing Hybrids Through Morphological and Molecular Markers in Rice (Oryza sativa L.)

The advancement of hybrid technology plays a crucial role in addressing yield plateau and diminishing resources in rice cultivating regions. The knowledge of genetic diversity among parental lines is a prerequisite for effective hybrid breeding program. In the current study, a set of 66 parental lines was studied for diversity based on both morphological characters and microsatellite SSR markers. The genetic variability parameters unveiled that number of productive tillers per plant, single plant yield and hundred grain weight exhibited additive gene action. Mahalanobis D2 statistics grouped the genotypes into ten clusters based on yield and grain traits. The principal component analysis identified four PCs with eigen value more than one accounting for 71.28% of cumulative variance. The polymorphic SSR markers produced 122 alleles among which the marker RM474 recorded the highest values for Polymorphic Information Content (0.83) and heterozygosity index (0.85). The genotypes were assembled in seven clusters based on jaccard distances using the Unweighted Pair Group method with Arithmetic Mean (UPGMA). The population structure divided the entire population into 3 subpopulations. In both clustering, there was difference in the assembling of genotypes, but, good performing genotypes identified through PCA were positioned in different clusters in both approaches. The genotypes CBSN 495 and CBSN 494 located in different clusters were identified as the potential restorers for high yielding and short duration hybrids. The hybridization among CRR Dhan 310, CRR Dhan 315, IR64 DRT, CB 17135 and WGL 347 can be performed to develop climate smart varieties with improved nutrition.

Investigation of genetic diversity among autochthonous grape cultivars grown in Türkiye using molecular primers

AbstractGrape is a type of fruit widely grown globally and in Türkiye thanks to its importance in human nutrition and diversity of usage areas. Türkiye has a long history of grape cultivation, and the genetic diversity of local grapes grown in some regions has still not been revealed. This study showed the genetic diversity between 60 local grape genotypes selected from north Central Anatolia and nine reference grape cultivars;10 inter simple sequence repeats (ISSR) and 7 inter-primer binding site (IPBS) retrotransposon primers were used. The mean values of genetic diversity indices in ISSR and IPBS retrotransposon primers were calculated as expected allelic frequency (p) 0.476/0.195, observed allelic frequency (q) 0.524/0.805, number of effective alleles (Ne) 1.326/1.378, Shannon’s information index (I) 0.308/0.367, expected heterozygosity (He) 0.199/0.232 and unbiased expected heterozygosity (uHe) 0.201/0.234, respectively. Unweighted pair group method with arithmetic mean (UPGMA) and model-based STRUCTURE analysis divided the studied germplasm into two groups. However, local genotypes were not grouped per the regions where they grew. As a result of the analysis of molecular variance (AMOVA) analysis, the inter-population variation was determined to be 11%, and the intra-population variation was determined to be 89%. The mean genetic differentiation value (Fst) between populations was 0.303. The results showed that ISSR and IPBS retrotransposon primers effectively explained the genetic diversity.

Characterization of anatomical characters of Peperomia (Piperaceae) from Asia for taxonomy

Abstract The flowers of Peperomia (Piperaceae) are simple, minute, and unique structures within the angiosperms consisting of a rounded bract, two stamens and an ovary, but generally lack taxonomic value at species level. Because of this, morphological characters of vegetative parts have been mainly used for species level taxonomy. There is a need to supplement these vegetative characters with anatomical characters. We selected 17 native Thai species representatives of South East Asian Peperomia to investigate the utility of vegetative anatomical characters for species delimitation, taxon identification, and classification. Stem, petiole, and leaf anatomical characters were studied using standard microscopic techniques. The anatomical characters demonstrated high diversity and supported species identification. Unweighted Pair Group Method with Arithmetic Mean (UPGMA) culstering, Principal Coordinates analysis (PCoA), and Principal Component Anaysis (PCA) were used to investigate patterns in the multivariate anatomical data and identify groupings of value to species classification. Four broad groupings were retrieved and some subgroupings identified. The most important characters that differentiated the species in the multivariate analysis included stem shape (roundness and ridges), petiole indumentum and trichome type, vascular bundle pattern and number, stem pith cavity, mucilage canals, and stem cortex sclerenchyma. These data were further used to prepare anatomical descriptions at generic and species levels and to provide a key to species.

Heavy metal and genetic diversity studies in three populations of Snail (Achatina achatina Linnaeus, 1758) from Southwest, Nigeria.

Environmental pollutants may often alter the genetic components of natural populations. In this study, heavy metals and genetic diversity in land snail (Achatina achatina) from three populations of south-western Nigeria were investigated, using the Atomic Absorption Spectrometry and DNA Sequencing technology respectively. Metal analysis revealed that the snails accumulated lead (Pb) and nickel (Ni) in high concentrations in two of the three states, while cadmium (Cd) was the least detected. Editing and alignment of the sequences of all snail accessions generated a range of 384bp to 419 bp. Analysis of Molecular Variance (AMOVA) in all 18 accessions was low at only 16%. The query coverage (QC) ranged between 96% and 100%, with 14 (77.8%) of the 18 accessions showing 100% identity. Pairwise comparison of the accessions studied also showed a high genetic similarity. The unweighted pair group method with arithmetic mean (UPGMA) generated two main clusters. Cluster I was unique and contain one sample (AaOy06) while the other cluster are very closely related and can be further sub-divided into sub-clusters. The similarity index of between the clusters is 0.5357. The close similarity among the accessions may be due to the geographical proximity of the three states. The uniqueness of accession AaOy06 in comparison to other accessions might be due to the negative influence of heavy metal, particularly lead. The determination of evolutionary relationships among snail populations may be useful towards the breeding efforts of the species in Nigeria.

Genetic diversity analysis of commercial Arabica coffee in Nepal using Molecular markers

Coffee is an established plant for its flavor and has high commercial use. In Nepal, the popularity of coffee is increasing for its high economic value. However, its diversity and the status of its genetic mapping have not been studied in Nepal. In the present study, the genetic diversity of 28 coffee accessions was assessed by using twenty-four SSR markers with the aim of studying the variation of coffee in accord with the genetic markers from a molecular approach. With the use of DNA extraction and marker selection for its amplification using PCR tools, a total of 81 loci from SSR were identified. Of all SSR 63.22% showed for mean polymorphism. The mean polymorphic information content of SSR was 0.38, which showed low genetic diversity of SSR markers among Coffea genotypes. On the basis of the SSR marker, the unweighted pair group method with arithmetic mean (UPGMA) dendrogram constructed showed a similar group of distribution among 28 accessions, which was further supported by a principle coordinate analysis scatter plot. The phylogenetic relationships among the accessions were assessed by SSR marker, which also showed low diversity in coffee genotypes. Our study demonstrated the use of SSR markers in diversity analysis as the data were informative and highly reproducible for evaluating relationships among coffee cultivars in Nepal. The use of more markers systems and a high genotype pool would have been beneficial in accessing more accurately. Regardless, the information from the phylogenetic relationship study could be useful for breeding, varietal improvement, and for conservation programs.

Assessment of Simple Sequence Repeat (SSR) Markers Derived from Whole-Genome Sequence (WGS) of Mungbean (Vigna radiata L. Wilczek): Cross-Species Transferability and Population Genetic Studies in Vigna Species

The genus Vigna is pan-tropical, having more than 200 species with many desirable economically important traits. This study aimed to validate the in silico polymorphism of whole-genome-sequence-developed mungbean-specific SSR markers and their transferability among different Vigna species. The present study utilized a set of 200 SSR markers developed from the whole-genome sequence of mungbean and validated them using a diversity panel of 25 accessions that belong to 13 Vigna species. Out of 200 SSR markers, 130 markers (65%) were polymorphic across the various Vigna species, and the number of alleles amplified varied from 7 to 24. The SSR markers showed more than 90 percent transferability across the different Vigna species accessions. Utilizing allelic data, the 25 Vigna accessions were clustered into three groups using the unweighted pair group method with arithmetic mean (UPGMA). The two integral coalitions explained 50.79 and 15.42% of the total variance. The principal coordinate analysis (PCA) biplot graph and UPGMA-based neighbor-joining clustering diagram showed a similar pattern of Vigna accession distribution. A population structure assessment grouped the cultivated and wild species accessions into two sub-populations based upon a maximum delta K value of 144.79, which drew a sharp peak at K = 2. The estimated marker parameters, such as the polymorphic information content (0.09–0.84), marker index (0.091–3.342), and effective multiplex ratio (1.0–4.0), suggested their adequacy for several genetic studies, such as parental selection, hybrid testing, genetic mapping, and marker-aided breeding programs, for the genetic enhancement of species belonging to the Vigna genus.

The effect of clustering algorithms on question answering

Question answering (QA) is one of the essential fields in information retrieval where specific answers are provided instead of large documents. The relations among questions and answers are determined using natural language processing techniques while clustering algorithms can be helpful in improving the effectiveness of result retrieval by reducing the amount of required comparisons for a specific question or answer. In this work, we introduce a clustering-based approach for a QA system. This approach groups related questions into clusters using different clustering algorithms, specifies the appropriate answer using similarity methods between the answers and the generated clusters, and then assigns answers to their most related questions. Different clustering algorithms, such as k-means, spherical k-means, single-linkage hierarchical clustering (SLHA), unweighted pair group method with arithmetic mean (UPGMA), expectation–maximization (EM), and clustering Arabic documents based on bond energy (CADBE), are tested. The effectiveness of a clustering algorithm is investigated with respect to certain factors, including number of clusters, text representation, similarity measure between answers and clusters, and similarity measure between answers and questions in a selected cluster. In addition, a comprehensive ranking system is introduced to evaluate the performance of clustering algorithms. Evaluation is performed using the Dataset of Arabic Why Question Answering System (DAWQAS) and the Multilingual Question Answering (MLQA) dataset. Results show that CADBE achieves the highest accuracy and the first rank, followed by SLHA and UPGMA, while spherical k-means has the lowest rank. The performance of clustering algorithms for MLQA dataset is affected by its characteristics, such as short questions, long and varied answers, and diverse subject domains. Unigram and bigram intersection measures perform well in most cases. Term frequency inverse document frequency representation outperforms word embedding in DAWQAS. Overall, the experiments provide insights into the performance of clustering algorithms in QA systems.

Yield potency assessment and characters association of promising lines of mustard (Brassica rapa L.) in southern region of Bangladesh

Mustard (&lt;em&gt;Brassica spp&lt;/em&gt;.) is a major oilseed crop and the world’s third largest source of vegetable oil. During the rabi season of 2022–2023, the experiment was carried out at the Regional Agricultural Research Station, Bangladesh Agricultural Research Institute (BARI), Barishal to evaluate the performance of 12 genotypes of &lt;em&gt;Brassica rapa&lt;/em&gt; L., including the check variety BARI Sarisha-14. The experiment was conducted under randomized complete block design (RCBD) design with three replications. Analysis of variance demonstrated that a highly significant (p ≤ 0.01) differences for the traits viz., plant height, no. of primary branches, no. of secondary branches, and no. of seeds per siliqua whereas no. of siliqua per plant, 1000 seeds weight, yield kg per hectare had significant difference at p ≤ 0.05. Among the examined accessions, the unweighted pair group method with arithmetic mean (UPGMA) cluster analysis identified four different clusters. Cluster II (28.91%) with only one accession had the highest average yield, followed by Cluster I (26.25%) and Cluster IV (22.68%) with the best agronomic features. Furthermore, we observed 1.6% and 11.93% greater (+) mean yield compared to the grand mean yield (1502.33 kg ha&lt;sup&gt;−1&lt;/sup&gt;) for cluster I and cluster II, respectively. Correlation analysis examine the positive and highly significant association among the yield with its related traits. Principal component analysis (PCA) revealed the total proportion of variation 54.86% for PC1 and 16.89% for PC2. The genotypes BC-100614(8)-7 gave 7.20% higher yield over the check variety. Considering the statistical results, maturity period, yield and yield contributing characters of &lt;em&gt;Brassica rapa &lt;/em&gt;L. genotypes BC-100614(8)-7 (1681 kg ha&lt;sup&gt;−1&lt;/sup&gt;), BC-100614(8)-1 (1594 kg ha&lt;sup&gt;−1&lt;/sup&gt;) and BC-100614(7)-3 (1565 kg ha&lt;sup&gt;−1&lt;/sup&gt;) were noted as promising lines among the evaluated genotypes and suggested for future breeding program.

Diversity analysis of southern African Artemisia afra using a single nucleotide polymorphism derived from diversity arrays

Artemisia afra is an aromatic shrub used as a herbal remedy in southern Africa for various disorders, including coughs, colds, influenza, and, most notably, for the prophylaxis and treatment of Plasmodium falciparum infections. Modern high-throughput genotyping by sequencing, which combines next generation sequencing and diversity array technology (DArTseq) complexity reduction methods, allows for the generation of high-quality whole-genome profiles without any previous organismal genetic information that may hamper the diversity analyses. This study investigated the feasibility of incorporating DArTseq-derived single-nucleotide polymorphisms (SNPs) and bioactive compounds into a geographic information system to predict the spatial distribution of A. afra gene diversity in selected southern African environs. DNA extraction, sequencing, and SNP calling mineral analyses (using R Studio) were performed on a total of 80 genotypes collected around Roma and Mohale’s Hoek, Lesotho, and Wepener and Hobhouse, South Africa. The unweighted pair group method with arithmetic mean (UPGMA) and neighbour-joining dendrograms revealed three clusters of variation among genotypes; however, geographic distribution did not influence A. afra genetic diversity. The mean heterozygosity among genotypes was 7.7%. Genotypes collected in Roma and Mohale’s Hoek exhibited high levels of genetic diversity. Local A. afra genetic diversity was relatively low, indicating uniformity of subspecies per locality. The diversity among genotypes indicated that A. afra SNPs may occur despite the location. Given that genetic diversity enhances crop performance, our findings can be useful in germplasm management, industries producing by-products of A. afra, and plant breeding programs. For the long-term conservation of medicinal plants in South Africa, significant sampling and regional data are required. In addition to evaluating qualitative and quantitative assessments of phytochemicals, it is necessary to evaluate foliar mineral composition, as well as the agronomic and morphological characteristics of collected specimens from studied locations.

Development and Validation of Gene-Based SSR Markers in the Genus Mesembryanthemum.

Bioinformatics tools have been employed for the direct development of gene-based simple sequence repeat (SSR) markers. Through the analysis of 28,056 Mesembryanthemum expressed sequence tag (EST) sequences, a total of 5,851 ESTs containing SSRs were identified, amounting to approximately 17.07 Mb. Among these, 938 EST sequences harbored more than one SSR marker, and 788 EST-SSR sequences were found in compound form. The most prevalent types of SSR motifs were mononucleotide repeats (MNRs), accounting for 44%, followed by di-nucleotide repeats (DNRs) at 37%, and trinucleotide repeats (TNRs) at 16%. Notably, TNR or longer SSR motifs primarily consisted of shorter repeat lengths, with only 51 motifs containing 10 or more repeats. The BLASTX analysis successfully assigned functions to 4,623 (79%) of the EST sequences. Among the developed primer sets, 21 primers amplified a total of 65 alleles, with primer PMA79 EST-SSR exhibiting the maximum of six alleles. The polymorphic information content (PIC) values ranged from 0 to 0.76, with a mean of 0.47. The marker index (MI) and discriminating power (D) values reached 0.66 (primer PMA63) and 0.95 (primer PMA20), respectively. Utilizing the unweighted pair group method with arithmetic mean (UPGMA), a dendrogram was constructed, successfully segregating the 24 Mesembryanthemum genotypes into three distinct clusters, with a similarity coefficient ranging from 0.96 to 0.38. In this study, we have developed a total of 83 EST-SSR primer pairs specific to the Mesembryanthemum genus. These newly developed EST-SSRs will serve as valuable tools for researchers, particularly molecular breeders, enabling gene-based identification and trait selection through marker-assisted breeding approaches.

Drought-tolerant sesame mutant lines assessed by physiological traits and stress indices under water deficit conditions

Climate change and water scarcity are the most important factors that affect crop production in dry areas. Sesame (Sesamum indicum L.) is a very ancient oilseed crop cultivated in arid and semi-arid regions and therefore its productivity is limited under drought conditions, which makes the selection and development of drought-tolerant cultivars imperative. This study aims to evaluate the responses to drought stress of eleven M4 sesame mutants, in addition to their two wild-type parents, cultivated in two contrasting environments. Drought stress was applied, under field conditions, by reducing the amount of irrigation water supplied by half, compared to the control. Physiological traits and various drought indices were measured/calculated. All data were subjected to analysis of variance and unweighted pair group method with arithmetic mean (UPGMA) to classify genotypes as drought sensitive or drought tolerant. Significant variations among genotypes were observed in their reactions to water regimes and environments. Overall, under water stress, proline content and stomatal resistance significantly increased, while chlorophyll content, seed yield, and relative water content significantly decreased in stressed plants. Drought indices revealed substantial differences among genotypes, with tolerant ones showing the best scores. Furthermore, correlation analysis demonstrated significant associations between physiological traits and drought indices. In light of all the traits/indices investigated, the mutant ‘US1-2’ was found to be very drought-sensitive, although it performed best under full-irrigation conditions. In contrast, the mutant lines ‘ML2-37’ and ‘ML2-37’ proved to be highly drought-tolerant and, therefore, they can be handled as an elite germplasm for the development of resilient cultivars adapted to arid and semi-arid regions where irrigation water is a limiting factor. This work constitutes a significant contribution to research on sesame drought tolerance and offers promising prospects for this crop in the context of global climate change.

Unlocking the genetic potential of Ethiopian durum wheat landraces with high protein quality: Sources to be used in future breeding for pasta production

AbstractThe content and composition of the grain storage proteins in wheat determine to a high extent its end‐use quality for pasta and bread production. This study aimed to evaluate the content and composition of the grain storage proteins in Ethiopian landraces and cultivars to contribute to future breeding toward improved pasta quality. Thus, 116 landraces and 34 cultivars originating from Ethiopia were grown in three locations, and the protein parameters were analyzed using size exclusion‐high performance liquid chromatography (SE‐HPLC). A considerable variation in the amount of the analyzed protein parameters was found. The genotypes, environments, and interactions contributed significantly (p &lt; 0.001) to the differences obtained. The broad‐sense heritability was high (0.75–0.98) for all protein parameters except for unextractable small monomeric protein (uSMP). Using the principal component analysis (PCA) to evaluate the impact of protein parameters and using either PCA or unweighted pair group method with arithmetic mean (UPGMA) to assess the impact of the genetic composition, the cultivar group was found to form a separate cluster. This indicates that durum wheat improvement in Ethiopia has relied on exotic materials, which might result from a narrow genetic base. Unlike most landraces, most released cultivars showed a high and stable gluten strength across environments. Two landraces, G057 and G107, were found genetically distinct from the released cultivars but with high and stable gluten. The two selected landraces might be of extremely high value for future use in durum wheat breeding programs, as they might be adapted to wide‐ranging Ethiopian growing conditions, they might carry genes of relevance to withstand abiotic and biotic stresses, and they seem to hold essential protein properties, which might result in high‐quality grains for industrial processes.

Serotypes, virulence factors and multilocus sequence typing of Glaesserella parasuis from diseased pigs in Taiwan.

Glaesserella parasuis (G. parasuis) belongs to the normal microbiota of the upper respiratory tract in the swine, but virulent strains can cause systemic infections commonly known as Glässer's disease that leads to significant economic loss in the swine industry. Fifteen serotypes of G. parasuis have been classified by gel immunodiffusion test while the molecular serotyping based on variation within the capsule loci have further improved the serotype determination of unidentified field strains. Serovar has been commonly used as an indicator of virulence; however, virulence can be significantly differ in the field isolates with the same serotype. To date, investigations of G. parasuis isolated in Taiwan regarding antimicrobial resistance, serotypes, genotypes and virulence factors remain unclear. A total of 276 G.parasuis field isolates were collected from 263 diseased pigs at the Animal Disease Diagnostic Center of National Chiayi University in Taiwan from January 2013 to July 2021. Putative virulence factors and serotypes of the isolates were identified by polymerase chain reaction (PCR) and antimicrobial susceptibility testing was performed by microbroth dilution assay. Additionally, the epidemiology of G. parasuis was characterized by multilocus sequence typing (MLST). Serotype 4 (33.3%) and 5 (21.4%) were the most prevalent, followed by nontypable isolates (15.9%), serotype 13 (9.4%), 12 (6.5%), 14 (6.2%), 7 (3.3%), 1 (1.8%), 9 (1.1%), 11 (0.7%) and 6 (0.4%). Nine out of 10 putative virulence factors showed high positive rates, including group 1 vtaA (100%), fhuA (80.4%), hhdA (98.6%), hhdB (96.0%), sclB7 (99.6%), sclB11 (94.9%), nhaC (98.2%), HAPS_0254 (85.9%), and cirA (99.3%). According to the results of antimicrobial susceptibility testing, ceftiofur and florfenicol were highly susceptible (>90%). Notably, 68.8% isolates showed multidrug resistance. MLST revealed 16 new alleles and 67 new sequence types (STs). STs of these isolated G. parasuis strains were classified into three clonal complexes and 45 singletons by Based Upon Related Sequence Types (BURST) analysis. All the G. parasuis strains in PubMLST database, including strains from the diseased pigs in the study, were defined into two main clusters by Unweighted Pair Group Method with Arithmetic Mean (UPGMA). Most isolates in this study and virulent isolates from the database were mainly located in cluster 2, while cluster 1 included a high percentage of nasal isolates from asymptomatic carriers. In conclusion, this study provides current prevalence and antimicrobial susceptibility of G. parasuis in Taiwan, which can be used in clinical diagnosis and treatment of Glässer's disease.

Population structure and genetic diversity of Tamarix chinensis as revealed with microsatellite markers in two estuarine flats.

Tamarix chinensis Lour. is a 3-6-meter-tall small tree with high salt- and alkali- tolerance and aggressive invasiveness, mainly distributed in the eastern part of China in warm-temperate and subtropical climate zones, yet there is little information available regarding genetic diversity and population structure. A total of 204 individuals of nine T. chinensis populations were investigated for genetic diversity and population structure using a set of 12 highly polymorphic microsatellite markers. The total number of alleles detected was 162, the average number of effective allele was 4.607, the average polymorphism information content (PIC) value of the 12 loci was 0.685, and the mean observed heterozygosity (Ho) and the mean expected heterozygosity (He) was 0.653 and 0.711, respectively. Analysis of molecular variance (AMOVA) showed a 5.32% genetic variation among T. chinensis populations. Despite a low population differentiation, Bayesian clustering analysis, discriminant analysis of principal components (DAPC) and the unweighted pair group method with arithmetic mean (UPGMA) clearly identified three genetic clusters correlated to the populations' geographic origin: the northern populations including those from Yellow River Delta, the Fangshan (FS) population from Beijing, the Changyi (CY) population from Bohai Bay, the Huanjiabu (HHJ) population from Hangzhou Bay, and the remaining two populations from Hangzhou Bay. There was a significant relationship between the genetic distance and geographical distance of the paired populations. Gene flow (Nm) was 4.254 estimated from FST. T. chinensis possessed high genetic diversity comparable to tree species, and although the population differentiation is shallow, our results classified the sampled populations according to sampling localities, suggesting the different origins of the study populations.