Fusarium disease presents a formidable challenge to shallot (Allium cepa L.) production globally, necessitating a profound understanding of the plant’s defense mechanisms. Secondary metabolites play a pivotal part in plant-pathogen dynamics, yet their roles against Fusarium oxysporum f. sp. cepae (FOC) in shallots remain underexplored. In the presented study, the use of Gas Chromatography-Mass Spectrometry (GC-MS) helped profile the secondary metabolites in six shallot genotypes, i.e., Bima Brebes, Sumenep, Tajuk, Katumi, Biru Lancor, and Maja Cipanas. The analysis revealed substantial variations in the quantity and diversity of compounds between the Fusarium disease infected and non-infected shallot treatments. However, the infected shallots exhibited a more pronounced metabolite profile (168 vs. 95). Notably, the susceptible shallot cultivar Katumi enunciated the highest metabolite production across both conditions. Clustering analysis identified four distinct metabolite clusters for infected and non-infected shallots. Heatmap analysis highlighted elevated levels of cholesterol derivatives, sterol, and linoleic acid in the shallot resistant cultivar Sumenep, positioning these compounds as promising biomarkers and crucial elements in the defense strategy of shallots against Fusarium disease.

Keywords: Shallot (A. cepa L.), biomarkers, clustering analysis, Fusarium disease, GC-MS, resistance mechanism, secondary metabolites

Key findings: The study unveiled significant variations in secondary metabolites between the Fusarium disease infected and non-infected shallot (Allium cepa L.). However, the infected treatments showed greater diversity and expression (168 compared with 95). Notably, in the shallot resistant cultivar Sumenep, the cholesterol derivatives, sterol, and linoleic acid were considerably higher, indicating their potential as biomarkers for resistance against Fusarium disease.

The innovative research employed rbcL (ribulose bisphosphate carboxylase) primers in detecting the internal transcribed spacer (ITS) region on the chloroplast cpDNA of five species of the genus Rosa L., using the polymerase chain reaction (PCR) and phylogenetic relationship. The species are R. gallica, R. hemisphaerica, R. foetida, Rosa x damascene, and R. centifolia. The results revealed the presence of a major band (1700 bp) in all studied species. Based on a phylogenetic analysis of the rbcL gene sequence data, two major clusters were evident in the dendrogram. The species R. gallica and R. hemisphaerica have a good bootstrap value of 99%. The rest of the three species (R. centifolia, R. foetida, and Rosa x damascene) has a bootstrap value ranging between 55%–57%. The study also authenticated the species R. hemisphaerica and R. foetida were newly recorded species in the international GenBank NCBI (National Center for Biotechnology Information).

Keywords: Rosa L. species, chloroplast DNA, identification, ITS, phylogenetic analysis, rbcL gene

Key findings: Using the rbcL gene of chloroplast (DNA), the study identified five different species belonging to the genus Rosa L. (Rosaceae) grown in the Kurdistan Region, Iraq.

Molecular information has been available about the genome of proso millet (Panicum miliaceum L.), which include about 18 nucleus’ chromosomes, one chloroplast chromosome, and more than 100 main genes with a total sequence length of proso millet 854,793,052 nucleotides. All chromosomes also differed in total length, ungapped length, Scaffold N50, and spanned gaps, however, did not differ in scaffold count and unspanned gaps. All genes in the genomic classification resulted into 17 groups according functions. Therefore, some genes encode functional enzymes with links to organelles in the cytoplasm and inside the nucleus to perform a specific function or structural proteins involved in plant biosynthesis. The 17 groups observed had main functions of the protein (ribosomal RNA protein, ATP synthase enzyme, NADH-plastoquinone oxidoreductase enzyme, cytochrome protein, photosystem, ribosomal Protein L, ribosomal Protein S, RNA polymerase, tRNA protein, Hypothetical chloroplast RF, and single proteins). The genes also differed in size, and the smaller gene included 65 nucleotides, while the bigger gene included 2883 nucleotides. The local variety of millet grown in Iraq possesses most genes registered among the international millet varieties of the Gene Bank, according to the National Center for Biotechnology. This study validated such results of gene detection.

Keywords: Proso millet (P. miliaceum L.), molecular studies, gene map, chromosomes, gene functions, nucleotides, proteins

Key findings: The presented molecular study detected 17 functional gene groups in the local cultivar of Proso millet (P. miliaceum L.).

The heat shock protein (HSP) plays an essential role in adaptation mechanisms under heat stress conditions. This work aimed to explore the response of HSP across seven diverse bread wheat (Triticum aestivum L.) cultivars. The utilized dual approach combined biochemical assessment via sodium dodecyl sulfate-polyacrylamide gel electrophoresis (SDS-PAGE) with molecular analysis through a quantitative RT-PCR. Seedlings of seven wheat commercial cultivars sustained exposure to thermal shock conditions of 45 °C for 4 h compared with a control temperature of 25 °C to elicit HSP production in significant quantities. Among the tested cultivars, Sids.1, Misr.2, and Giza.168 exhibited the highest levels of heat shock proteins, with distinct bands observed at 83, 71, 37, 36, and 31 kDa. Conversely, Gemmeiza.11 displayed the least heat shock proteins, characterized by a single band at 32 kDa. Furthermore, the thermal shock treatment affected the quantity and diversity of proteins produced by Gemmeiza.10 and Gemmeiza.7 by reducing observed bands under treated conditions. Real-time qPCR analysis proceeded to evaluate the expression of HSP genes utilizing RNA extracts from Sids.1 and Gemmeiza.10. The Sids.1 exhibited robust gene expression while Gemmeiza.10 displayed a low gene expression. The detected expression of HSP22 suggests a plausible involvement in conferring heat tolerance in bread wheat.

Keywords: read wheat (T. aestivum L.), differential heat shock response, heat shock proteins, gene expression analysis, environmental stress adaptation

Key findings: Bread wheat (T. aestivum L.) cultivar Sids.1 exhibited resilience to heat stress, contrasting with the other genotype Gemmeiza.10, which showed higher susceptibility. Tolerant genotypes to heat stress displayed increased HSP gene expression compared with sensitive varieties.

Dendrobium contains alkaloids, flavonoids, saponins, tannins, and triterpenoids, which served as medicines, including antioxidants and skin brighteners. The presented research sought to determine the conservation through morphological and phytochemical characterization and the potential of native orchids of Dendrobium in Lampung, Indonesia. This research transpired on the entire native collection of Dendrobium at the Liwa Botanical Garden, West Lampung, Indonesia, particularly, 13 samples with four Dendrobium species (D. nobile, D. purpureum, D. minutigibbum, and D. montanum) as comparative controls. Morphological characterization relied on 13 leaf and nine phytochemical characters using the spot test method. The results showed six of the 13 traits, i.e., leaf shape, width, length, shape, tip shape, and cross-section, could be beneficial in identifying orchid species. Cluster analysis on morphological traits based on the phenetic and PCA analyses enunciated positive correlation in the native Dendrobium species identification. The phytochemical characterization revealed Dendrobium contained alkaloids, flavonoids, saponins, tannins, and triterpenoids with potential as herbal medicines. The results indicated leaf morphology and phytochemical characterization can be applicable for identifying plant types and their potential.

Keywords: herbal medicines, leaf traits, phytochemicals, morphological characterization, native Dendrobium

Key findings: In morphological characterization, 13 leaf traits emerged as key characters in identifying the Dendrobium species. Phytochemical characterization of Dendrobium exhibited contents of the alkaloids, flavonoids, saponins, tannins, and triterpenoids, with the potential as herbal medicines.

Snake fruit (Salacca spp.), also called Salak, is a unique tropical fruit. The salak wild germplasm is distinct in Aceh, Indonesia, and with its larger variation, it has the potential for further development through breeding. Therefore, in Aceh, the identification and relationship of various salak accessions are necessary in producing superior genotypes; however, complete information is still unavailable. The presented study aimed to construct the relationship about the salak found in Aceh using the trnL-F intergenic spacer sequence. The salak different accessions collected from several areas in Aceh included the Seulawah Valley, Montasik, Sabang, Kutacane, and Leuser Ecosystem. In the phylogenetic tree construction, using the maximum parsimony (MP) and neighbor-joining (NJ) methods helped in the Phylogenetic Analysis Using Parsimony (PAUP). The results showed there are 206 parsimony informative characters to construct a phylogenetic tree. The MP cladogram separated the 18 salak wild and cultivated accessions into two groups. Based on the NJ analysis, evolutionarily wild type salak is assumedly the most primitive accession and could have genes for the various traits that may disappear in cultivated types due to domestication pressure. The same was also valid from the neighbor-joining cladogram with the shortest clade branch.

Keywords: Salak, cultivated types, wild type, maximum parsimony method, neighbor-joining method, PAUP, trnL-F intergenic spacer

Key findings: Relationship information of the salak (Salacca spp.) is crucial in developing future superior genotypes. Based on molecular data, the cladogram was able to separate the salak wild and cultivated types. Evolutionarily, the wild type could be the most primitive accession and seemed to have viable genes for the various traits.

The article presents data reflecting the uniqueness and adaptive traits of landrace wheat varieties of the Western Pamir, continuously cultivated in highland small farms at altitudes of more than 2000 masl. For the important traits, like lodging resistance and quality, the bread wheat (Triticum aestivum L.) varietal improvement is possible. Protein labeling showed the significant polymorphism and distinctiveness in varietal samples within all α, β, γ, and ω subfractions of storage seed proteins – gliadins, which is the specificity of wheat cultivars of Tajik Badakhshan on Gli-B1 locus. Most of the local bread wheat cultivars had the composition of high molecular weight glutenin subunits, i.e., null (Glu-1A), 7+8 (Glu-B1), and 2+12 (Glu-D1). Genetic diversity analysis of West Pamir landraces by the alleles of VRN-A1 and VRN-D1 vernalization genes showed their identity that all cultivars had recessive (vrn-A1) and dominant allele (Vrn-D1). For PPD-1 genes, the allelic composition of the wheat cultivars revealed a representation of an allele of insensitivity to day length (Ppd-A1a) and two alleles (Ppd-B1b and Ppd-D1b) providing sensitivity to the photoperiod.

Keywords: Local bread wheat (T. aestivum L.), West Pamir, molecular markers, diversity of VRN-1, PPD-1, Glu-1 genes, polymorphism, quality traits

Key findings: The combination of recessive allele (vrn-A1) and dominant allele (Vrn-D1) with the main genes of sensitivity to photoperiod (Ppd-1D, Ppd-1B) promotes the adaptation of Western Pamir bread wheat (T. aestivum L.) landraces to conditions of the highlands.

Spring durum wheat (Triticum durum Desf. L.) is an important staple crop throughout the world, and its productivity enhancement can use the advanced nanotechnologies. Nanoparticles have become an environmentally safe fertilizer for grain crops. The presented work aimed to determine the effects of pre-sowing seed treatment with iron nanoparticles (Fe NPs) on the growth of six durum wheat cultivars (Milyana, Orenburgskaya-21, Bourbon, Bezenchukskaya Zolotistaya, Tselinnitsa, and Luch-25), as well as, assessing the toxicity of Fe NPs. The toxicity detection of nanoparticles employed the bacterial luminescence test system of Escherichia coli strain K12 TG1. For bioluminescence on a bacterial test model and assessing the effect of Fe NPs on plants, the experiment had the concentration range below 8 × 10^-4 mg/ml. For each durum wheat cultivar, four experimental options included the control (seeds without treatment) and wheat seeds’ treatment with four concentrations of Fe NPs (10^-4%, 10^-5%, 10^-6%, and 10^-7%). Afterward, the assessment of germination energy after five days and morphometric parameters of seedlings after seven days ensued.

Keywords: Spring durum wheat (T. durum Desf. L.), nanoparticles, Fe, pre-sowing treatment, toxicity, cultivar specificity, growth traits

Key findings: Spring durum wheat (T. durum Desf. L.) seed treatment with Fe NPs enhanced plants’ shoot and root length and stimulated the seedling biomass accumulation. However, these effects depended on the metal concentration in the polymer composition and the wheat genotype.

Shallot (Allium cepa L.) is one of the favorite commodities cultivated by the farming community in West Nusa Tenggara (NTB), Indonesia. However, its potential yield may decline both in quantity and quality due to the fusarium wilt disease and because of the limited information about the wilt disease in shallots. Therefore, the presented research aimed to a) determine the percentage of fusarium wilt disease incidence, b) investigate the new species of pathogen that causes fusarium wilt disease in shallots, and c) identify the distribution of fusarium pathogen species in shallots. The collected shallot samples came from 69 cultivation centers in Lombok Island, identifying the fungus based on morphological characteristics (colony shape, color, hyphae, conidia, and chlamydospores), while applying the ITS (Internal Transcript Spacer) rDNA sequences for molecular examination. The results showed fusarium wilt disease incidence in shallots (A. cepa L.) was 45.67%. Various Fusarium species as a causative disease on shallot plants were Fusarium oxysporum, F. solani, and F. proliferatum, distributed in 60 (86.96%), 54 (78.36%), and 43 (60.87%) locations, respectively. Furthermore, a new species (Fusarium proliferatum) of causative disease as fusarium wilt on shallots was evident in Lombok Island, West Nusa Tenggara, Indonesia.

Keywords: Shallots (A. cepa L.), fusarium wilt disease, pathogen, Fusarium oxysporum, Fusarium solani, Fusarium proliferatum

Key findings: The filamentous fungus from Fusarium proliferatum was the firstly recognized species causing fusarium wilt disease in shallots (A. cepa L.) on Lombok Island, NTB, Indonesia. The fusarium species Fusarium proliferatum infestation was prevalent in more than 50% of locations, which confirmed the said species had a remarkable role in shallot yield losses.

The androgenic callus induction and plant regeneration with the least response through anther culture are the key problems in biotechnology-based papaya (Carica papaya L.) breeding. Improvement of papaya response by anther culture through flower size and PGRs’ combinations earnestly need investigation. The presented research aimed to determine the microspore stage and viability based on the flower size and a combination of plant growth regulators (PGRs) in MS (Murashige and Skoog) medium to induce embryogenic callus and somatic embryos in papaya. Explants used in the study were the anthers of hermaphrodite flowers. This study comprised three different experiments, i.e., microspore development and viability test, 2,4-D (2,4-Dichlorophenoxyacetic acid) and TDZ (Thidiazuron) optimization for embryogenic callus induction, and NAA (naphthalene acetic acid) and CPPU (N-[2-Chloro-4-pyridyl]-N’-phenylurea) optimization for somatic embryos’ formation. Results revealed hermaphrodite flower buds were 10–25 mm in length, which can be effective for embryogenic callus induction as they contained the high percentage of uninucleate stage microspores and demonstrated high viability (>95%). The combination treatment of 2,4-D (0.1 mg L^-1) and TDZ (0.5 mg L^-1) induced the most percentage of anther forming callus (20.4%), with 58.7% of that as embryogenic callus. The combination of NAA (0.1 mg L^-1) and CPPU (0.5 mg L^-1) resulted in 70% embryogenic callus plated developed into the maximum average globular embryos (38.8).

Keywords: Papaya (C. papaya L.), callus induction, flower size, hermaphrodite flowers, microspores stage, 2,4-D, TDZ, NAA, CPPU

Key findings: The induction of somatic embryos in papaya (C. papaya L.) anther culture can be successful through an appropriate size of hermaphrodite flowers and the use of PGRs’ combination in the culture medium. This information is crucial to support papaya breeding programs to obtain double haploid lines through anther culture.