Trait profiling and genotype selection in oilseed rape using genotype by trait and genotype by yield*trait approaches.

Selection and breeding for high-yielding in oilseed rape have always been one of the leading objectives for oilseed rape breeders. This process becomes more complicated when all quantitative traits are considered in selection in addition to grain yield. In the present study, 18 oilseed rape genotypes along with 2 check cultivars (RGS003 and Dalgan) were evaluated across 16 environments (a combination of 2 years and eight locations) in the tropical climate regions of Iran during 2018-2019 and 2019-2020 cropping seasons. The experiments were conducted in a format of randomized complete block design (RCBD) with three replications. The obtained multienvironmental trial data were utilized to conduct multivariate analysis, genotype by trait (GT) biplot, and genotype by yield*trait (GYT) biplot (Breeding, Genetics and Genomics, 1:2019). The GT and GYT biplot accounted for 55.5% and 93.6% of the total variation in the first two main components. Based on multivariate analysis and GT biplot, pod numbers in plant (PNP) and plant height (PH) were chosen as two key traits in spring oilseed rape genotypes for indirect selection due to high variation, strong positive correlation with grain yield (GY), and their high representatively and discriminability in genotype selection. The mean × stability GT biplot represented G10 (SRL-96-17) as the superior genotype. Based on the mean × stability GYT biplot, eight above-average genotypes were identified that took high scores in stability, high-yielding, and all evaluated quantitative traits at the same time. Based on the superiority index of GYT data, G10 (SRL-96-17) and G5 (SRL-96-11) indicated the best yield-trait combinations profile and ranked above check cultivars and then selected as superior genotypes. Similarly, cluster analysis using the WARD method also separated eight superior genotypes. Based on the result of the present study, GT ad GYT methodologies are recommended for trait profiling and genotype selection in oilseed rape breeding projects, respectively.

Phenotyping new rapeseed lines based on multiple traits: Application of GT and GYT biplot analyses.

The selection based on multiple traits enhances the crop cultivars merit to farmers. In this regard, 19 breeding lines as well as two commercial cultivars were studied using a randomized complete block design (RCBD) with three replications in three locations during the 2020-2021 growing season. In this study, to identify the association among different traits and to select the best rapeseed lines based on multiple traits, genotype × trait (GT) and genotype × yield × trait (GYT) biplot analyses were used. The results showed that using GYT biplot is more efficient than GT biplot. Based on the GYT biplot and superiority index (SI), the breeding lines G16 and G18 were considered as superior genotypes in combination with the agronomical traits, that is, 1000-seed weight, number of seeds per pod, number of pods per plant, number of lateral branches, plant height, and pod length with seed yield, which represents a genetic gain in rapeseed breeding program. Based on seed yield combination with phenological traits (early maturity), the breeding line G15 was selected as the best one. Moreover, the line G2 was defined as the superior one in combination of seed yield with pod length. The results indicated that there is a potential for simultaneous genetic improvement of the characteristics (i.e., plant height, number of seeds per pod, early maturity) in rapeseed. Generally, the graphical method of the GYT biplot represented an efficient and practical new way to recognize superior genotypes based on multiple traits in rapeseed breeding programs.

Plant isomiRs: origins, biogenesis, and biological functions.

MicroRNAs (miRNAs) are small endogenous non-coding RNAs in eukaryotes which regulate the expression of numerous genes post-transcriptionally, thereby playing critical roles in cells and organismal development. The high-throughput sequencing technologies enable the effective detection and annotation of miRNAs. Several miRNA variants with heterogeneous ends, lengths, and sequences can be generated from a single miRNA locus. Discovery of these miRNA variants, also known as miRNA isoforms or isomiRs, has made our understanding of the cells' miRNome deeper than previously pictured. Despite their wide presence in multiple datasets, the different possible origins and true biological significance of isomiRs are yet to be uncovered. Several recent emerging studies suggest that isomiRs are biologically active and non-randomly formed. This review aims to provide a comprehensive insight into the origins and biological importance of isomiRs, highlighting the enormous complexity of miRNA regulatory networks which broadens our knowledge about the post-transcriptional gene regulation in plants.

Study of QTLs linked to awn length and their relationships with chloroplasts under control and saline environments in bread wheat.

INTRODUCTION: Some studies in wheat showed that awns may have a useful effect on yield, especially under drought stress. Up to this time few researches has identified the awn length QTLs with different effect in salinity stress. OBJECTIVE: The primary objective of this study was to examine the additive (a) and the epistatic (aa) QTLs involve in wheat awns length in control and saline environments. METHODS: A F7 RIL population consisting of 319 sister lines, derived from a cross between wheat cultivars Roshan and Falat (seri82), and the two parents were grown in two environments (control and Saline) based on an alpha lattice design with two replications in each environment. At flowering, awn length was measured for each line. For QTL analysis, the linkage map of the ''Roshan × Falat'' population was used, which included 748 markers including 719 DArT, 29 simple sequenced repeats (SSRs). Additive and pleiotropic QTLs were identified. In order to reveal the relationship between the identified QTL for awns length and the role of the gene or genes that it expresses, the awns length locus location and characteristics of its related CDS, gene, UTRs, ORF, exons and Introns were studied using ensemble plant ( http://plants.ensembl.org/Triticum_aestivum ). Furthermore, the promoter analysis has been done using NSITE-PL. RESULTS: We identified 6 additive QTLs for awn length by QTL Cartographer program using single-environment phenotypical values. Also, we detected three additive and two epistatic QTLs for awn length by the QTLNetwork program using multi-environment phenotypical values. Our results showed that none of the additive and epistatic QTLs had interactions with environment. One of the additive QTLs located on chromosome 4A was co-located with QTLs for number of sterile spikelet per spike in both environment and number of seed per spike in control environment. COCLUSION: Studies of the locus linked to the awns length QTL revealed the role of awn and its chloroplasts in grain filing during abiotic stress could be enhanced by over expression of some genes like GTP-Binding proteins which are enriched in chloroplasts encoded by genes included wPt-5730 locus.

MicroRNAs regulate the main events in rice drought stress response by manipulating the water supply to shoots.

MicroRNAs (miRNAs) are small endogenous regulatory RNAs that are involved in a variety of biological processes related to proliferation, development, and response to biotic and abiotic stresses. miRNA profiles of rice (Oryza sativa L. cv. IR64.) leaves in a partial root zone drying (PRD) system were analysed using a high-throughput sequencing approach to identify miRNAs associated with drought signalling. The treatments performed in this study were as follows: well-watered ("wet" roots, WW), wherein both halves of the pot were watered daily; drought ("dry" roots, DD), wherein water was withheld from both halves of the pot; and well-watered/drought ("wet" and "dry" roots, WD), wherein one half of each pot was watered daily, the same as in WW, and water was withheld from the other part, the same as in DD. High-throughput sequencing enabled us to detect novel miRNAs and study the differential expression of known miRNAs. A total of 209 novel miRNAs were detected in this study. Differential miRNA profiling of the DD, WD and WW conditions showed differential expression of 159 miRNAs, among which 83, 44 and 32 miRNAs showed differential expression under both DD and WD conditions. The detection of putative targets of the differentially expressed miRNAs and investigation of their functions showed that most of these genes encode transcription factors involved in growth and development, leaf morphology, regulation of hormonal homeostasis, and stress response. The most important differences between the DD and WD conditions involved regulation of the levels of hormones such as auxin, cytokinin, abscisic acid, and jasmonic acid and also regulation of phosphor homeostasis. Overall, differentially expressed miRNAs under WD conditions were found to differ from those under DD conditions, with such differences playing a role in adaptation and inducing the normal condition. The mechanisms involved in regulating hormonal homeostasis and involved in energy production and consumption were found to be the most important regulatory pathways distinguishing the DD and WD conditions.

Drought responsive microRNAs in two barley cultivars differing in their level of sensitivity to drought stress.

MicroRNAs (miRNAs) are known to be involved in the regulation of gene expression, including that of genes involved in the response to stress. Here, a comparison has been drawn between the miRNA profiles of a drought susceptible, 'Morocco 9-75', and a drought tolerant, 'Yousef', barley cultivars. Leaf water content, shoot dry matter and chlorophyll content decreased in 'Morocco 9-75' more considerably compared with 'Yousef' under drought stress. Furthermore, lower stomatal conductance and higher leaf temperature were observed in 'Morocco 9-75' compared with 'Yousef'. Based on the criteria set for differential abundance, 118 of conserved and novel miRNAs were identified as being responsive to soil water status. Although drought stress resulted in an altered abundance of more miRNAs in 'Morocco 9-75' than in 'Yousef', drought stress was generally associated with an increased miRNA abundance in 'Yousef' and a decreased abundance in 'Morocco 9-75'. An in silico analysis identified 645 genes as putative targets for the drought-responsive miRNAs in 'Yousef' and 3735 in 'Morocco 9-75'. Gene ontology analysis showed that drought stress was associated with the altered abundance of miRNAs targeting growth, development, the juvenile to adult transition and hormone signaling. Some miRNAs which became more abundant in 'Yousef' are thought to target genes intimately involved in development and stress adaptation. In 'Morocco 9-75', drought stress induced changes in the abundance of miRNAs associated with genes affecting growth, development, the juvenile to adult transition and ABA signaling. The data imply that miRNAs may affect the tolerance/sensitivity of barley to drought stress by modulating the expression of a wide set of genes and induction of some physiological changes.

The contrasting microRNA content of a drought tolerant and a drought susceptible wheat cultivar.

Drought stress represents one of the most common stresses affecting the productivity of crop plants. A rather recently discovered component of the plant response to drought is the cellular population of microRNAs. Here, the microRNA content was revealed of two bread wheat cultivars contrasting strongly with respect to the ability to withstand drought stress. A total of 1813 miRNAs was identified, grouped into 106 families. Some 104 of these miRNAs were predicted to match 212 novel miRNA precursors. In the drought tolerant cultivar (SM), 105 (33 known and 72 novel) miRNAs were altered in abundance by the imposition of drought stress, while the equivalent number in the more sensitive cultivar (SW) was 51 (20 and 31). An in silico analysis predicted that these miRNAs target at least 1959 genes in SM and 1111 in SW, suggesting their broad contribution to the drought stress response. Among the target genes were several known stress-related genes, encoding, for example, superoxide dismutase, various MYB transcription factors, various ABA signaling proteins and various MADS-box transcription factors. In many cases, the more susceptible cultivar SW behaved in a contrasting manner. The suggestion is that miRNAs represent an important aspect of the drought stress response, post-transcriptionally regulating a range of stress-related genes.

MicroRNA Signatures of Drought Signaling in Rice Root.

BACKGROUND: Drought stress is one of the most important abiotic stresses and the main constraint to rice agriculture. MicroRNA-mediated post-transcriptional gene regulation is one of the ways to establish drought stress tolerance in plants. MiRNAs are 20-24-nt regulatory RNAs that play an important role in regulating plant gene expression upon exposure to biotic and abiotic stresses. METHODOLOGY/PRINCIPAL FINDINGS: In this study, we applied a partial root drying system as well as a complete root drying system to identify miRNAs involved in conditions of drought stress, drought signaling and wet signaling using high-throughput sequencing. To this end, we produced four small RNA libraries: (1) fully-watered (WW), (2) fully-droughted (WD), and split-root systems where (3) one-half was well watered (SpWW) and (4) the other half was water-deprived (SpWD). Our analysis revealed 10,671 and 783 unique known and novel miRNA reads in all libraries, respectively. We identified, 65 (52 known + 13 novel), 72 (61 known + 11 novel) and 51 (38 known + 13 novel) miRNAs that showed differential expression under conditions of drought stress, drought signaling and wet signaling, respectively. The results of quantitative real-time PCR showed expression patterns similar to the high-throughput sequencing results. Furthermore, our target prediction led to the identification of 244, 341 and 239 unique target genes for drought-stress-, drought-signaling- and wet-signaling-responsive miRNAs, respectively. CONCLUSIONS/SIGNIFICANCE: Our results suggest that miRNAs that are responsive under different conditions could play different roles in the regulation of abscisic acid signaling, calcium signaling, detoxification and lateral root formation.