Identification of a Sidwf1 gene controlling short internode length trait in the sesame dwarf mutant dw607

Molecular and physiological characterization of early semi-dwarf mutants of rice and localization of SNP variants in Sd1 locus generated through gamma radiation

PURPOSE

The 'Improved White Ponni' (IWP) rice variety, which is susceptible to lodging, leading to yield losses. Our primary goal is to develop new rice lines with non-lodging traits, enhancing stem strength and resistance to adverse conditions. Additionally, we aim to improve yield-contributing agronomic traits, benefiting farmers, food security, and the environment. Our work contributes to scientific knowledge and addresses a significant issue in Southern Indian rice cultivation.

MATERIALS AND METHODS

In the present study, early and semi-dwarf early mutants of IWP were developed without altering the native grain quality traits using gamma ray-mediated mutagenesis. The seeds (500) were irradiated with γ-rays after fixing the Lethal Dose 50 (LD50), and selection for semi-dwarfism and earliness was imposed on a large M2 population. The selected traits were confirmed by evaluating the M3 lines at morpho-physiological, biochemical, and molecular levels.

RESULTS

The response of mutants to gibberellic acid has been studied, which identified responsive mutants as well as slow-responding mutant lines including IWP-11-2, IWP-48-2, IWP-50-11, and IWP-33-2. Agar plate assay indicated low α- amylase content in IWP-50-11, IWP-33-2, IWP-43-1, IWP-47-2, and IWP-18-1. The scanning electron microscopy demonstrated that the mutants displayed an increased cellular dimension in comparison to the wild type. In dwarf mutants, null alleles were observed for the SD1 gene-specific primers which depicts gene undergone mutation. Further sequencing revealed the presence of single nucleotide polymorphisms in the SD1 gene resulting in semi-dwarfism in the mutant IWP-D-1.

CONCLUSIONS

The impact of a defective gibberellic acid-mediated signaling pathway in mutants to produce a novel high-yielding and early maturing semi-dwarf rice variety.

Genomic evolution and insights into agronomic trait innovations of Sesamum species

Sesame is an ancient oilseed crop with high oil content and quality. However, the evolutionary history and genetic mechanisms of its valuable agronomic traits remain unclear. Here, we report chromosome-scale genomes of cultivated sesame (Sesamum indicum L.) and six wild Sesamum species, representing all three karyotypes within this genus. Karyotyping and genome-based phylogenic analysis revealed the evolutionary route of Sesamum species from n = 13 to n = 16 and revealed that allotetraploidization occurred in the wild species Sesamum radiatum. Early divergence of the Sesamum genus (48.5-19.7 million years ago) during the Tertiary period and its ancient phylogenic position within eudicots were observed. Pan-genome analysis revealed 9164 core gene families in the 7 Sesamum species. These families are significantly enriched in various metabolic pathways, including fatty acid (FA) metabolism and FA biosynthesis. Structural variations in SiPT1 and SiDT1 within the phosphatidyl ethanolamine-binding protein gene family lead to the genomic evolution of plant-architecture and inflorescence-development phenotypes in Sesamum. A genome-wide association study (GWAS) of an interspecific population and genome comparisons revealed a long terminal repeat insertion and a sequence deletion in DIR genes of wild Sesamum angustifolium and cultivated sesame, respectively; both variations independently cause high susceptibility to Fusarium wilt disease. A GWAS of 560 sesame accessions combined with an overexpression study confirmed that the NAC1 and PPO genes play an important role in upregulating oil content of sesame. Our study provides high-quality genomic resources for cultivated and wild Sesamum species and insights that can improve molecular breeding strategies for sesame and other oilseed crops.

QTL mapping in sesame (Sesamum indicum L.): A review

Sesame (Sesamum indicum L.) is an important oilseed crop used for food, feed, medicinal, and industrial applications. Inherently low genetic yield potential and susceptibility to biotic and abiotic stresses contribute to low productivity in sesame. Development of stress resistant varieties coupled with high yield is a viable option to raise the genetic potential of sesame. Conventional phenotype-based breeding methods have made an important role in the last couple of decades by developing several sesame varieties with improved quality, yield, and tolerance to biotic and abiotic stresses. However, due to adverse environmental effects, time consuming to develop new variety, and low genetic gain, conventional phenotype-based approach is not adequate to satisfy the rising population growth. In this context, advanced method of genotype selection via modern techniques of biotechnology plays essential roles in reducing the constraints and boosting sesame production to satisfy the huge demand. In line to this, quantitative trait loci (QTL) mapping is considered as a promising method to address the problems of sesame breeding. Previously, huge data have been generated in the practical use of QTL for sesame improvement. Therefore, this paper aims to review recent advances in the area of QTL mapping for yield and yield related traits in sesame for enhancing and sustaining sesame production. In this section, we present an intensive review on the identification and mapping of the most desirable potential candidate genes/QTLs associated with desirable traits. Moreover, this review focuses on the major QTL regions and/or potential candidate genes and associated molecular markers that could provide potential genetic resources for molecular marker-assisted selection and further cloning of functional genes for yield and yield-related traits as well as various biotic and abiotic stress tolerances. Finally, the summarized QTL mapping data shed light on future directions for enhanced sesame breeding programs.

Important Factors Controlling Gibberellin Homeostasis in Plant Height Regulation

Plant height is an important agronomic trait that is closely associated with crop yield and quality. Gibberellins (GAs), a class of highly efficient plant growth regulators, play key roles in regulating plant height. Increasing reports indicate that transcriptional regulation is a major point of regulation of the GA pathways. Although substantial knowledge has been gained regarding GA biosynthetic and signaling pathways, important factors contributing to the regulatory mechanisms homeostatically controlling GA levels remain to be elucidated. Here, we provide an overview of current knowledge regarding the regulatory network involving transcription factors, noncoding RNAs, and histone modifications involved in GA pathways. We also discuss the mechanisms of interaction between GAs and other hormones in plant height development. Finally, future directions for applying knowledge of the GA hormone in crop breeding are described.

Improving desirable agronomic traits of M2 lines on fourteen Ethiopian Sesame (Sesamum indicum L.) genotypes using Ethyl Methane Sulphonate (EMS)

Sesame is an important oilseed crop cultivated in Ethiopia as a cash crop for small holder farmers. However, low yield is one of the main constraints of its cultivation. Boosting and sustaining production of sesame is thus timely to achieve the global oil demand. This study was, therefore, aimed at identifying mutant genotypes targeted to produce better agronomic traits of M2 lines on fourteen Ethiopian sesame genotypes through seed treatment with chemical mutagens. EMS was used as a chemical mutagen to treat the fourteen sesame genotypes. Quantitative and qualitative data were recorded and analyzed using analysis of variance with GenStat 16 software. Post-ANOVA mean comparisons were made using Duncan's Multiple Range Test (p≤ 0.01). Statistically significant phenotypic changes were observed in both quantitative and qualitative agronomic traits of the M2 lines. All mutant genotypes generated by EMS treatment showed a highly significant variation for the measured quantitative traits, except for the traits LBL and LTL. On the other hand, EMS-treated genotypes showed a significant change for the qualitative traits, except for PGT, BP, SSCS, LC, LH and LA traits. Mutated Baha Necho, Setit 3, and Zeri Tesfay showed the most promising changes in desirable agronomic traits. To the best of our knowledge, this study represents the first report on the treatment of sesame seeds with EMS to generate desirable agronomic traits in Ethiopian sesame genotypes. These findings would deliver an insight into the genetic characteristics and variability of important sesame agronomic traits. Besides, the findings set up a foundation for future genomic studies in sesame agronomic traits, which would serve as genetic resources for sesame improvement.

Integrating transcriptome and phytohormones analysis provided insights into plant height development in sesame

Plant height is a key agronomic trait influencing crops yield. The height of sesame plants is important for yield performance, lodging resistance and plant architecture. Although plant height is significantly distinct among sesame varieties, the genetic basis of plant height remains largely unknown. In this study, in order to tackle genetic insights into the sesame plant height development, a comprehensive transcriptome analysis was conducted using the stem tips from two sesame varieties with distinct plant height, Zhongzhi13 and ZZM2748, at five time points by BGI MGIseq2000 sequencing platform. A total of 16,952 genes were differentially expressed between Zhongzhi13 and ZZM2748 at five time points. KEGG and MapMan enrichment analyses and quantitative analysis of phytohormones indicated that hormones biosynthesis and signaling pathways were associated with sesame plant height development. Plenty of candidate genes involved in biosynthesis and signaling of brassinosteroid (BR), cytokinin (CK) and gibberellin (GA) which were major differential hormones between two varieties were identified, suggesting their critical roles in plant height regulation. WGCNA revealed a module which was significantly positively associated with the plant height trait and founded SiSCL9 was the hub gene involved in plant height development in our network. Further overexpression in transgenic Arabidopsis validated the function of SiSCL9 in the increase of plant height by 26.86%. Collectively, these results increase our understanding of the regulatory network controlling the development of plant height and provide a valuable genetic resource for improvement of plant architecture in sesame.

The Overexpression of Oryza sativa L. CYP85A1 Promotes Growth and Biomass Production in Transgenic Trees

Brassinosteroids (BRs) are important hormones that play crucial roles in plant growth, reproduction, and responses to abiotic and biotic stresses. CYP85A1 is a castasterone (CS) synthase that catalyzes C-6 oxidation of 6-deoxocastasterone (6-deoxoCS) to CS, after which CS is converted into brassinolide (BL) in a reaction catalyzed by CYP85A2. Here, we report the functional characteristics of rice (Oryza sativa L.) OsCYP85A1. Constitutive expression of OsCYP85A1 driven by the cauliflower mosaic virus 35S promoter increased endogenous BR levels and significantly promoted growth and biomass production in three groups of transgenic Populus tomentosa lines. The plant height and stem diameter of the transgenic poplar plants were increased by 17.6% and 33.6%, respectively, in comparison with control plants. Simultaneously, we showed that expression of OsCYP85A1 enhanced xylem formation in transgenic poplar without affecting cell wall thickness or the composition of cellulose. Our findings suggest that OsCYP85A1 represents a potential target candidate gene for engineering fast-growing trees with improved wood production.

Biomolecular Strategies for Vascular Bundle Development to Improve Crop Yield

The need to produce crops with higher yields is critical due to a growing global population, depletion of agricultural land, and severe climate change. Compared with the "source" and "sink" transport systems that have been studied a lot, the development and utilization of vascular bundles (conducting vessels in plants) are increasingly important. Due to the complexity of the vascular system, its structure, and its delicate and deep position in the plant body, the current research on model plants remains basic knowledge and has not been repeated for crops and applied to field production. In this review, we aim to summarize the current knowledge regarding biomolecular strategies of vascular bundles in transport systems (source-flow-sink), allocation, helping crop architecture establishment, and influence of the external environment. It is expected to help understand how to use sophisticated and advancing genetic engineering technology to improve the vascular system of crops to increase yield.

Genome-wide association analysis uncovers the genetic architecture of tradeoff between flowering date and yield components in sesame

BACKGROUND

Unrevealing the genetic makeup of crop morpho-agronomic traits is essential for improving yield quality and sustainability. Sesame (Sesamum indicum L.) is one of the oldest oil-crops in the world. Despite its economic and agricultural importance, it is an 'orphan crop-plant' that has undergone limited modern selection, and, as a consequence preserved wide genetic diversity. Here we established a new sesame panel (SCHUJI) that contains 184 genotypes representing wide phenotypic variation and is geographically distributed. We harnessed the natural variation of this panel to perform genome-wide association studies for morpho-agronomic traits under the Mediterranean climate conditions.

RESULTS

Field-based phenotyping of the SCHUJI panel across two seasons exposed wide phenotypic variation for all traits. Using 20,294 single-nucleotide polymorphism markers, we detected 50 genomic signals associated with these traits. Major genomic region on LG2 was associated with flowering date and yield-related traits, exemplified the key role of the flowering date on productivity.

CONCLUSIONS

Our results shed light on the genetic architecture of flowering date and its interaction with yield components in sesame and may serve as a basis for future sesame breeding programs in the Mediterranean basin.

QTL mapping of yield-related traits in sesame

Improving yield is one of the most important targets of sesame breeding. Identifying quantitative trait loci (QTLs) of yield-related traits is a prerequisite for marker-assisted selection (MAS) and QTL/gene cloning. In this study, a BC1 population was developed and genotyped with the specific-locus amplified fragment (SLAF) sequencing technology, and a high-density genetic map was constructed. The map consisted of 13 linkage groups, contained 3528 SLAF markers, and covered a total of 1312.52 cM genetic distance, with an average distance of 0.37 cM between adjacent markers. Based on the map, 46 significant QTLs were identified for seven yield-related traits across three environments. These QTLs distributed on 11 linkage groups, each explaining 2.34-71.41% of the phenotypic variation. Of the QTLs, 23 were stable QTLs that were detected in more than one environment, and 20 were major QTLs that explained more than 10% of the corresponding phenotypic variation in at least one environment. Favorable alleles of 38 QTLs originated from the locally adapted variety, Yuzhi 4; the exotic germplasm line, BS, contributed favorable alleles to only 8 QTLs. The results should provide useful information for future molecular breeding and functional gene cloning.

Supplementary Information

The online version contains supplementary material available at 10.1007/s11032-021-01236-x.

Phenotypic Characterization and Differential Gene Expression Analysis Reveal That Dwarf Mutant dwf Dwarfism Is Associated with Gibberellin in Eggplant

Dwarfism is a desirable trait in eggplant breeding, as it confers higher lodging resistance and allows simplified management and harvest. However, a few dwarf mutants have been reported, and the molecular mechanism underlying dwarfism in eggplant is completely unknown. Here, we report a dwarf mutant (dwf) isolated from an ethyl methyl sulfonate (EMS)-induced mutant library. The hypocotyl length, plant height, and length of internode cells of dwf were significantly decreased compared to those of the wild-type parent ‘14-345’ (WT). Differential gene expression analysis revealed that GA-related genes, including GA2ox and DELLA, were up-regulated whereas the gibberellin (GA3) content decreased in dwf. Moreover, exogenous GA3 treatment significantly increased the relative growth rate of dwf compared to WT, further indicating the important roles of GA in regulating the dwarf phenotype of dwf. Collectively, our findings shed light on GA-mediated dwarfism in dwf plants and offer a good germplasm that could be used for eggplant dwarfism breeding in the future.

Effect of Sodium Azide on Quantitative and Qualitative Stem Traits in the M2 Generation of Ethiopian Sesame (Sesamum indicum L.) Genotypes

The emerging oilseed crop Sesamum indicum, also known as the queen of oilseeds, is being grown globally for its oil content for medicinal and nutritional values. One of the key challenges of sesame cultivation is its low productivity. In the present study, sodium azide (NaN3) was used as a chemical mutagen. The aim of this study was to examine the effect of NaN3 on quantitative and qualitative stem traits in the M2 generation of Ethiopian sesame (Sesamum indicum L.) genotypes. Seeds of fourteen sesame genotypes were used in this study and germinated and grown under greenhouse conditions. Different qualitative and quantitative data were collected and analyzed. Traits such as plant height, ground distance to first distance, and internode length were significantly affected by NaN3 treatment. The highest plant height was recorded in the control on Humera 1 and Baha Necho genotypes, while the lowest was observed on Setit 2 and Hirhir treated with the chemical. The highest ground distance to the first branch was observed in Gumero, while the least ground distance was recorded in Setit 1 in the treated and control genotypes, respectively. The best internode length was recorded on Setit 2 and ADI in the control, while the lowest internode length was observed in Setit 1 genotype treated with sodium azide. Genotypes such as ACC44, ADI, Baha Necho, Borkena, Gonder 1, and Setit 1 treated with NaN3 have showed glabrous type of stem hairiness. All the fourteen genotypes (both treated and control) were clustered into four groups. In conclusion, we observed a highly significant variation among the genotypes due the effect of the chemical and genotypes themselves. Hence, this report would create more genetic diversity for further sesame genetic research improvements.