Alfalfa (Medicago sativa L.) is a major forage crop of family Fabaceae and is frequently cultivated in Egypt. The present study is concerned with the genetic discrimination of fifteen alfalfa cultivars from three different countries (Egypt, Australia, and USA) using two molecular approaches: inter-retrotransposon-amplified polymorphism (IRAP) markers and two chloroplast DNA barcodes matK and the trnH in addition to the analysis of fifteen morpho-agronomic traits. The genetic relatedness, based on analysis of IRAP marker polymorphism and produced using eleven primers by clustering via principal component analysis (PCA) and multivariate heatmap biostatistical methods differentiated the two Egyptian cultivars EGY1-Ismailia1 and EGY2-Nubaria1 from the three Australian and seven American cultivars, with some distinction of the cv. USA6-SW9720 and cv. AUS4-SuperFast. The results were also supported by the sequence analysis of the matK and the trnH genes on the genetic relatedness between eight cultivars. Moreover, it might be suggested that breeding lines from M. sativa cultivars may provide novel insights and a better understanding of the domestication of M. sativa genetic diversity. The classification of the eight cultivars, as revealed by morpho-agronomic traits, confirmed the close genetic relationship between the two Egyptian cultivars and indicated some resemblance between them and the AUS2-Siri Nafa, whereas the two American cultivars, USA1-Super supreme and USA4-Cuf101, were clearly isolated from a cluster of other three cultivars USA7-SW9628, USA8-Magna901, and USA9-Perfect. The results are useful sources of genetic information for future breeding programs in crop development and open new possibilities of producing M. sativa lines harboring high forage quality, productivity, and resistance to biotic and abiotic stresses.

Fine mapping becomes a routine trial following quantitative trait loci (QTL) mapping studies to shrink the size of genomic segments underlying causal variants. The availability of whole genome sequences can facilitate the development of high marker density and predict gene content in genomic segments of interest. Correlations between genetic and physical positions of these loci require handling of different experimental genetic data types, and ultimately converting them into positioning markers using a routine and efficient tool. To convert classical QTL markers into KASP assay primers, KASPspoon simulates a PCR by running an approximate-match searching analysis on user-entered primer pairs against the provided sequences, and then comparing in vitro and in silico PCR results. KASPspoon reports amplimers close to or adjoining genes/SNPs/simple sequence repeats and those that are shared between in vitro and in silico PCR results to select the most appropriate amplimers for gene discovery. KASPspoon compares physical and genetic maps, and reports the primer set genome coverage for PCR-walking. KASPspoon could be used to design KASP assay primers to convert QTL acquired by classical molecular markers into high-throughput genotyping assays and to provide major SNP resource for the dissection of genotypic and phenotypic variation. In addition to human-readable output files, KASPspoon creates Circos configurations that illustrate different in silico and in vitro results. Code available under GNU GPL at (http://www.ageri.sci.eg/index.php/facilities-services/ageri-softwares/kaspspoon). Supplementary data are available at Bioinformatics online.

Phytoremediation is determined as an emerging green technology suitable for the safe remediation and restoration of polluted terrestrial and aquatic environments. In this study, the assessment of an ornamental plant, Vinca rosea L., as a phytoremediator of crude oil in polluted soils was conducted. In an open greenhouse experiment, plants were raised in sandy-clayey soils treated with 1, 3, 5, and 7% oil by weight. The experiment was conducted over 5 months. Total petroleum hydrocarbon (TPH) degradation percentage by V. rosea after a 5-month growth period ranged from 86.83 ± 0.44% to 59.05% ± 0.45% in soil treated with 1 and 7%, respectively. Plants raised in polluted soils demonstrated a dramatic reduction in germination rates, in addition to growth inhibition outcomes shown from decreased plant height. An increase in branching was observed with an increase in oil pollution percentages. Moreover, the phytomass allocated to the leaves was higher, while the phytomass witnessed lower values for fine roots, flowering and fruiting when compared to the controls. Apart from the apparent morphological changes, there was a decrease in chlorophyll a/b ratio, which was inversely proportional to the oil pollution level. The contents of carotenoids, tannins, phenolics, flavonoids, and antioxidant capacity were elevated directly with an increase in oil pollution level. The start codon-targeted (SCoT) polymorphisms and inter-simple sequence repeat (ISSR) primers showed the molecular variations between the control and plants raised in polluted soils. The genetic similarity and genomic DNA stability were negatively affected by increased levels of crude oil pollution. The ability of V. rosea to degrade TPH and balance the increased or decreased plant functional traits at the macro and micro levels of plant structure in response to crude oil pollution supports the use of the species for phytoremediation of crude oil-polluted sites. The genotoxic effects of crude oil on V. rosea still require further investigation. Further studies are required to demonstrate the mechanism of phenolic, flavonoid, and antioxidant compounds in the protection of plants against crude oil pollution stress. Testing different molecular markers and studying the differentially expressed genes will help understand the behavior of genetic polymorphism and stress-resistant genes in response to crude oil pollution.

Abiotic stresses such as heat and cold temperatures, salinity, and drought are threatening global food security by affecting crop quality and reproductivity. Wheat is the most essential staple crop in the world, its complex genome is the main barrier to finding valuable genes responsive to different stresses. Thus, in our study we conducted differential RNA-seq analysis to identify Differentially Expressed Genes (DEGs) involved in 4 different stresses such as drought, heat, freeze resistance, and water-deficit stress, then applied two machine learning models; the "Extra-tree regressor" and LIME algorithms to accurately predict and select the highly significant genes. Our findings identified a set of 36 significant genes, many of which play important roles in various molecular functions, cellular components, and biological processes related to the response or resistance to abiotic stress in wheat. For example, Hsp101b is a member of the heat shock protein family, which protects cells against stress by stabilizing proteins. BADH, an enzyme involved in the synthesis of stress hormones, is important for the plant’s response to different stresses. AGL14 is a member of the AGL protein family, which regulates gene expression and is involved in the plant’s response to drought, cold, and salinity stresses. This study demonstrates the prospects of the integration of bioinformatics tools as well as machine learning models to assess the genes responsible for wheat stress resistance, genes’ regulatory networks, and their functions in order to save time and cost to improve wheat productivity.

Coriandrum sativum L. faced a new and previously undocumented leaf blight disease for the first time. This disease manifests initially as small, circular, or irregular brown spots on older leaves, which gradually expand and merge into dark brownish blotches over time. This disease's impact is detrimental to plant health and seed quality. Through comprehensive morphological characteristics, and molecular identification (GenBank OL823169), the pathogen was conclusively identified as Alternaria radicina. Further confirmation was obtained by analyzing target sequences for the Alt-a-1 gene (GenBank OR492259). Koch's postulates were strictly adhered to, leading to the successful re-isolation of A. radicina from artificially infected 8-week-old coriander plants (local variety; Balady), providing unequivocal evidence that the fungus is responsible for leaf blight disease, marking the first such confirmation worldwide. The significant activity of fungal enzymes may be associated with pathogenicity. The seed-health test supported the hypothesis that seeds play a central role in the transmission of A. radicina, as it was detected in 40 % of seed lots, alongside other common pathogenic and saprophytic genera. This study underscores the urgency of implementing seed treatments to curtail the pathogen's spread. The emergence of coriander leaf blight disease documented here (Egypt; 30° 57′ 25″ N and 31° 35 ′ 54″E) for the first time, necessitates heightened awareness and proactive measures to protect coriander plants all over the world.