Journal of Plant Molecular Breeding
Volume:10 Issue: 2, Summer and Autumn 2022

To evaluate the genetic basis of drought tolerance in rice, an experiment was conducted using 120 recombinant inbred lines (RILs) derived from Neda × Ahlamitarom cross. A factorial experiment based on completely randomized design with three replications was used under greenhouse conditions setting at Gonbad Kavous University. In this study, Polyethylene Glycol (PEG) 6000 was employed to induce osmotic stress (at levels of −4.5 and −9 bar) during both vegetative and reproductive stages. In addition to assessing root and shoot morphological characters, genetic linkage map was constructed using Simple Sequence Repeat (SSR), Inter Primer Binding Site (iPBS), Inter-Retrotransposon Amplified Polymorphism (IRAP), and Inter Simple Sequence Repeats (ISSR) markers. Sixteen Quantitative Trait Loci (QTLs) were identified during vegetative growth stage, while twenty QTLs were identified during the reproductive stage. Through a comparative analysis of the three evaluated treatments, the qRN-12, qRS-11, and qRV-12 lines were determined as stable QTLs  suitable for the selection of drought-tolerant lines at the vegetative stage under varying conditions. Several new alleles associated with drought-tolerant QTLs were identified in this study. Notably, in two distinct environmental conditions, crucial QTLs, such as qNTF-12 and qNL-3, related to the numbers of fertile tillers and leaves, were identified as stable QTLs at the reproductive stage. The QTLs identified at vegetative and reproductive stages in this study can serve as stable and major QTLs for  selecting drought-tolerant lines in marker-assisted selection (MAS).

The sexual reproduction of orchids is a notably slow process. This is due to their seeds lacking endosperm, which necessitates a fungal elicitor for germination in natural conditions. In the current study, we evaluated seed germination and the initial development of the protocorm of Orchis simia, an important medicinal orchid species, using a completely randomized design with three replications. The tetrazolium test revealed that 35% of the seeds were viable. Subsequently, we investigated the influence of casein, activated charcoal, indole acetic acid (IAA), photoperiod, and temperature on the germination of O. simia seeds. The analysis of variance demonstrated varying responses in terms of seed germination percentages, with photoperiod and temperature treatments having a more pronounced impact on germination. The optimal conditions for asymbiotic orchid seed germination in this experiment were achieved using Murashige and Skoog’s (MS) medium supplemented with one-fifth of nitrate concentration, casein (2.0 g/l), activated charcoal (2.0 g/l), and an IAA growth regulator (1.0 mg/l), resulting in a germination rate of 31%. After a three-month period, the nodes underwent transformation into protocorms. The findings presented in this report can serve as valuable insights for the production of orchid plants and the conservation of this medicinal species.

Drought is a severe abiotic stress factor that significantly impacts rice production globally. The investigation of drought stress response components, particularly in plant roots, holds great importance. Recent evidence highlights the critical role played by long non-coding RNAs (lncRNAs) in the response to abiotic stress. In this study, we identified drought stress-induced lncRNAs in the root tip region of rice using transcriptome sequencing analysis performed on seedlings of a sensitive rice genotype (IR64) under drought and control conditions. We identified a total of 358 differentially expressed lncRNAs (DElncRNA), more than 60% of which were in intergenic regions. Our results demonstrated that DElncRNAs can directly or indirectly regulate 710 and 7535 mRNAs in cis and trans, respectively. Additionally, the target genes of DElncRNAs were involved in drought resistance genes, lateral root growth, and genes affecting auxin transport. We also identified 24 conserved sequence motifs in the upstream regions of DElncRNAs and differentially expressed mRNAs (DEmRNAs) motifs through a search and functional analysis of these motifs indicated their involvement in regulation of transcription, translation, and the transmembrane receptor protein tyrosine kinase signaling pathway. Finally, we constructed a network of DElncRNAs and DEmRNAs. Our functional analysis of the top 10 hub lncRNAs in the network demonstrated their involvement in growth processes, cellular responses to stimuli, and signaling pathways. These results offer a comprehensive perspective on potentially functional lncRNAs and provide insight into the molecular mechanisms underlying drought resistance in the root tip region of rice.

Russian wheat aphid (RWA, Diuraphis noxia Kurdjumov), a common pest on barley around the world, can severely damage barley yield and grain quality. The present study aimed to identify simple sequence repeat markers associated with RWA resistance in wild barley (Hordeum vulgare subsp. spontaneum). A panel of 30 wild barely accessions was selected from the ICARDA gene bank and Iran to represent 10 Asia countries scattered along the natural geographic distribution of the species for RWA resistance. Five traits including leaf chlorosis, leaf rolling, chlorophyll a, b, and total chlorophyll concentration were evaluated. Fourteen SSR markers were used to study genetic diversity. The relationship of 52 polymorphic SSR markers with the associated RWA resistance traits was tested using general linear model (GLM) and mixed linear model (MLM) approaches. The population structure analysis revealed seven subpopulations in the entire collection (K=7). Eleven trait marker-trait associations (MTA) were identified on chromosomes 1H, 2H, 3H, 4H, and 7H. Markers Bmag007, Bmag6, Bmac0399, Bmag0125, and EBmac0701 which exhibited significant associations with RWA resistance traits. All five markers were associated with traits in both GLM and MLM analyzes. This study identified novel genomic regions putatively linked with RWA resistance traits, which could be further investigated for shedding light on the genetic architecture of RWA resistance in barley. The findings could be useful for using the RWA resistance accessions of H. spontaneum as parents for breeding barley cultivars.

Catharanthus roseus, produces a diverse array of specialized metabolites known as monoterpene indole alkaloids (MIAs) through an extensive and intricately branched metabolic pathway. It is imperative to unravel the intricate regulatory networks and relationships between the genes involved in the production of these metabolites. Long non-coding RNAs (lncRNAs) are emerging as significant regulatory factors in various biological processes. In this study, 4303 out of 86726 transcripts were identified as potential lncRNAs in C. roseus. Subsequently, we identified coding genes that exhibited a high correlation with CrlncRNA, designating them as potential target genes for collectively modulating the MIA pathway using Weighted Gene Co-Expression Network Analysis (WGCNA), leading to the identification of crucial gene clusters associated with the biosynthesis of MIAs. Based on the findings, three modules (dark turquoise, magenta, and orange) and hub genes were pinpointed as being linked to MIAs. Additionally, the most prominent known coding genes were 10-hydroxygeraniol oxidoreductase, GATA-like transcription factor (GATA1), 7-deoxyloganetic acid UDP-glucosyltransferase (7DLGT), desacetoxyvindoline 4-hydroxylase (DH4), MYC2, and MPK6. The unknown target genes were related to stress response and the intricate process of hormone transduction. ORCA, MYC2, and GATA1 are crucial in regulating the MIA pathway, likely requiring cooperation with CrlncRNAs.

Calcineurin B-like (CBL) proteins, as calcium sensors, serve roles in plant responses to varied abiotic stressors and in growth and development through interaction with CBL-interacting protein kinases (CIPKs). However, information on the roles and development of CBLs in sweet orange plants is limited. We surveyed the whole Citrus sinensis genome and found eight CBL genes. Domains features, position and distribution, and conserved motif revealed that the EF-hands domain was conserved across the eight CsCBLs. CsCBL proteins are classed as acidic CBL, and five myristoylation sites and six palmitoylation sites were predicted. Eight CsCBLs were distributed across chromosomes Chr01, Chr02, Chr04, and Chr05 and contig chrNW-006257104.1. In chromosome 05, tandem duplications likely gave rise to two CsCBL4 and CsCBL5 genes. The phylogeny tree of 37 CBL proteins from different plant species including Arabidopsis thaliana, Oryza sativa, Sesamum indicum, and C. sinensis showed that these CBLs are closely related. A meta-analysis of the CsCBL gene family's expression in different tissues/stresses revealed that CsCBL genes expressed differently in tissues, which could be evidence for CsCBL tissue/stress-specific expression. The results of this study highlight the functional properties of the CsCBL gene family and provide crucial data for future research on their functional activities.