Genetic interaction involving photoperiod-responsive Hd1 promotes early flowering under long-day conditions in rice

Harnessing weedy rice as functional food and source of novel traits for crop improvement

A relative of cultivated rice (Oryza sativa L.), weedy or red rice (Oryza spp.) is currently recognized as the dominant weed, leading to a drastic loss of yield of cultivated rice due to its highly competitive abilities like producing more tillers, panicles, and biomass with better nutrient uptake. Due to its high nutritional value, antioxidant properties (anthocyanin and proanthocyanin), and nutrient absorption ability, weedy rice is gaining immense research attentions to understand its genetic constitution to augment future breeding strategies and to develop nutrition-rich functional foods. Consequently, this review focuses on the unique gene source of weedy rice to enhance the cultivated rice for its crucial features like water use efficiency, abiotic and biotic stress tolerance, early flowering, and the red pericarp of the seed. It explores the debating issues on the origin and evolution of weedy rice, including its high diversity, signalling aspects, quantitative trait loci (QTL) mapping under stress conditions, the intricacy of the mechanism in the expression of the gene flow, and ecological challenges of nutrient removal by weedy rice. This review may create a foundation for future researchers to understand the gene flow between cultivated crops and weedy traits and support an improved approach for the applicability of several models in predicting multiomics variables.

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.

Genetic Diversity of Weedy Rice and Its Potential Application as a Novel Source of Disease Resistance

Weeds that infest crops are a primary factor limiting agricultural productivity worldwide. Weedy rice, also called red rice, has experienced independent evolutionary events through gene flow from wild rice relatives and de-domestication from cultivated rice. Each evolutionary event supplied/equipped weedy rice with competitive abilities that allowed it to thrive with cultivated rice and severely reduce yields in rice fields. Understanding how competitiveness evolves is important not only for noxious agricultural weed management but also for the transfer of weedy rice traits to cultivated rice. Molecular studies of weedy rice using simple sequence repeat (SSR), restriction fragment length polymorphism (RFLP), and whole-genome sequence have shown great genetic variations in weedy rice populations globally. These variations are evident both at the whole-genome and at the single-allele level, including Sh4 (shattering), Hd1 (heading and flowering), and Rc (pericarp pigmentation). The goal of this review is to describe the genetic diversity of current weedy rice germplasm and the significance of weedy rice germplasm as a novel source of disease resistance. Understanding these variations, especially at an allelic level, is also crucial as individual loci that control important traits can be of great target to rice breeders.

Molecular Research in Rice

Rice is the most important source of nutrition for approximately half of the human population [...].

Copper oxide (CuO) nanoparticles affect yield, nutritional quality, and auxin associated gene expression in weedy and cultivated rice (Oryza sativa L.) grains

Weedy rice grows competitively with cultivated rice and significantly diminishes rice grain production worldwide. The different effects of Cu-based nanomaterials on the production of weedy and cultivated rice, especially the grain qualities are not known. Grains were collected from weedy and cultivated rice grown for four months in field soil amended with nanoscale CuO (nCuO), bulk CuO (bCuO), and copper sulfate (CuSO₄) at 0, 75, 150, 300, and 600 mg Cu/kg soil. Cu translocation, essential element accumulation, yield, sugar, starch, protein content, and the expression of auxin associated genes in grains were determined. The grains of weedy and cultivated rice were differentially impacted by CuO-based compounds. At ≥300 mg/kg, nCuO and bCuO treated rice had no grain production. Treatment at 75 mg/kg significantly decreased grain yield as compared to control with the order: bCuO (by 88.7%) > CuSO₄ (by 47.2%) ~ nCuO (by 38.3% only in cultivated rice); at the same dose, the Cu grain content was: nCuO ~ CuSO₄ > bCuO > control. In weedy grains, K, Mg, Zn, and Ca contents were decreased by 75 and 150 mg/kg nCuO by up to 47.4%, 34.3%, 37.6%, and 60.0%, but no such decreases were noted in cultivated rice, and Fe content was increased by up to 88.6%, and 53.2%. In rice spikes, nCuO increased Mg, Ca, Fe, and Zn levels by up to 118.1%, 202.6%, 133.8%, and 103.9%, respectively. Nanoscale CuO at 75 and 150 mg/kg upregulated the transcription of an auxin associated gene by 5.22- and 1.38-fold, respectively, in grains of weedy and cultivated rice. The biodistribution of Cu-based compounds in harvested grain was determined by two-photon microscopy. These findings demonstrate a cultivar-specific and concentration-dependent response of rice to nCuO. A potential use of nCuO at 75 and 150 mg/kg in cultivar-dependent delivery system was suggested based on enhanced grain nutritional quality, although the yield was compromised. This knowledge, at the physiological and molecular level, provides valuable information for the future use of Cu-based nanomaterials in sustainable agriculture.

Whole-Genome Sequencing and RNA-Seq Reveal Differences in Genetic Mechanism for Flowering Response between Weedy Rice and Cultivated Rice

Flowering is a key agronomic trait that influences adaptation and productivity. Previous studies have indicated the genetic complexity associated with the flowering response in a photoinsensitive weedy rice accession PSRR-1 despite the presence of a photosensitive allele of a key flowering gene Hd1. In this study, we used whole-genome and RNA sequencing data from both cultivated and weedy rice to add further insights. The de novo assembly of unaligned sequences predicted 225 genes, in which 45 were specific to PSRR-1, including two genes associated with flowering. Comparison of the variants in PSRR-1 with the 3K rice genome (RG) dataset identified unique variants within the heading date QTLs. Analyses of the RNA-Seq result under both short-day (SD) and long-day (LD) conditions revealed that many differentially expressed genes (DEGs) colocalized with the flowering QTLs, and some DEGs such as Hd1, OsMADS56, Hd3a, and RFT1 had unique variants in PSRR-1. Ehd1, Hd1, OsMADS15, and OsMADS56 showed different alternate splicing (AS) events between genotypes and day length conditions. OsMADS56 was expressed in PSRR-1 but not in Cypress under both LD and SD conditions. Based on variations in both sequence and expression, the unique flowering response in PSRR-1 may be due to the high-impact variants of flowering genes, and OsMADS56 is proposed as a key regulator for its day-neutral flowering response.

OsPRR37 Alternatively Promotes Heading Date Through Suppressing the Expression of Ghd7 in the Japonica Variety Zhonghua 11 under Natural Long-Day Conditions

Heading date is an important agronomic trait of rice (Oryza sativa L.) and is regulated by numerous genes, some of which exhibit functional divergence in a genetic background-dependent manner. Here, we identified a late heading date 7 (lhd7) mutant that flowered later than wild-type Zhonghua 11 (ZH11) under natural long-day (NLD) conditions. Map-based cloning facilitated by the MutMap strategy revealed that LHD7 was on the same locus as OsPRR37 but exhibited a novel function as a promoter of heading date. A single-nucleotide mutation of G-to-A in the coding region caused a substitution of aspartic acid for glycine at site 159 within the pseudo-receiver (PR) domain of OsPRR37. Transcriptional analysis revealed that OsPRR37 suppressed Ghd7 expression in both ZH11 background under NLD conditions and the Zhenshan 97 background under natural short-day conditions. Consistently, the expression of Ehd1, Hd3a and RFT1 was enhanced by OsPRR37 in the ZH11 background. Genetic analysis indicated that the promotion of heading date and reduction in grain yield by OsPRR37 were partially dependent on Ghd7. Further investigation showed that the alternative function of OsPRR37 required an intact Ghd7-related regulatory pathway involving not only its upstream regulators OsGI and PhyB but also its interacting partner Hd1. Our study revealed the distinct role of OsPRR37 in the ZH11 background, which provides a more comprehensive understanding of OsPRR37 function and enriches the theoretical bases for improvement of rice heading date in the future.

K. K, Muthamilarasan M, Pillai MA. Assessment of efficacy of mutagenesis of gamma-irradiation in plant height and days to maturity through expression analysis in rice

Introduction of semi-dwarfism and early maturity in rice cultivars is important to achieve improved plant architecture, lodging resistance and high yield. Gamma rays induced mutations are routinely used to achieve these traits. We report the development of a semi-dwarf, early maturing and high-yielding mutant of rice cultivar ‘Improved White Ponni’, a popular cosmopolitan variety in south India preferred for its superior grain quality traits. Through gamma rays induced mutagenesis, several mutants were developed and subjected to selection up to six generations (M₆) until the superior mutants were stabilized. In the M₆ generation, significant reduction in days to flowering (up to 11.81% reduction) and plant height (up to 40% reduction) combined with an increase in single plant yield (up to 45.73% increase) was observed in the mutant population. The cooking quality traits viz., linear elongation ratio, breadthwise expansion ratio, gel consistency and gelatinization temperature of the mutants were similar to the parent variety Improved White Ponni. The genetic characterization with SSR markers showed variability between the semi-dwarf-early mutants and the Improved White Ponni. Gibberellin responsiveness study and quantitative real-time PCR showed a faulty gibberellin pathway and epistatic control between the genes such as OsKOL4 and OsBRD2 causing semi-dwarfism in a mutant. These mutants have potential as new rice varieties and can be used as new sources of semi-dwarfism and earliness for improving high grain quality rice varieties.

Detecting CSSLs and yield QTLs with additive, epistatic and QTL×environment interaction effects from Oryza sativa × O. nivara IRGC81832 cross

Chromosome segment substitution lines (CSSLs) are useful tools for precise mapping of quantitative trait loci (QTLs) and the evaluation of gene action and interaction in inter-specific crosses. In this study, a set of 90 back cross lines at BC2F8 generation derived from Swarna x Oryza nivara IRGC81832 was evaluated for yield traits under irrigated conditions in wet seasons of 3 consecutive years. We identified a set of 70 chromosome segment substitution lines, using genotyping data from 140 SSR markers covering 94.4% of O. nivara genome. Among these, 23 CSSLs were significantly different for 7 traits. 22 QTLs were detected for 11 traits with 6.51 to 46.77% phenotypic variation in 90 BILs. Three pleiotropic genomic regions associated with yield traits were mapped on chromosomes 1, 8 and 11. The marker interval RM206-RM144 at chromosome 11 was recurrently detected for various yield traits. Ten QTLs were identified consistently in the three consecutive years of testing. Seventeen pairs of significant epistatic QTLs (E-QTLs) were detected for days to flowering, days to maturity and plant height. Chromosome segments from O. nivara contributed trait enhancing alleles. The significantly improved lines and the stable QTLs identified in this study are valuable resource for gene discovery and yield improvement.

Genome wide screening and comparative genome analysis for Meta-QTLs, ortho-MQTLs and candidate genes controlling yield and yield-related traits in rice

Background

Improving yield and yield-related traits is the crucial goal in breeding programmes of cereals. Meta-QTL (MQTL) analysis discovers the most stable QTLs regardless of populations genetic background and field trial conditions and effectively narrows down the confidence interval (CI) for identification of candidate genes (CG) and markers development.

Results

A comprehensive MQTL analysis was implemented on 1052 QTLs reported for yield (YLD), grain weight (GW), heading date (HD), plant height (PH) and tiller number (TN) in 122 rice populations evaluated under normal condition from 1996 to 2019. Consequently, these QTLs were confined into 114 MQTLs and the average CI was reduced up to 3.5 folds in compare to the mean CI of the original QTLs with an average of 4.85 cM CI in the resulted MQTLs. Among them, 27 MQTLs with at least five initial QTLs from independent studies were considered as the most stable QTLs over different field trials and genetic backgrounds. Furthermore, several known and novel CGs were detected in the high confident MQTLs intervals. The genomic distribution of MQTLs indicated the highest density at subtelomeric chromosomal regions. Using the advantage of synteny and comparative genomics analysis, 11 and 15 ortho-MQTLs were identified at co-linear regions between rice with barley and maize, respectively. In addition, comparing resulted MQTLs with GWAS studies led to identification of eighteen common significant chromosomal regions controlling the evaluated traits.

Conclusion

This comprehensive analysis defines a genome wide landscape on the most stable loci associated with reliable genetic markers and CGs for yield and yield-related traits in rice. Our findings showed that some of these information are transferable to other cereals that lead to improvement of their breeding programs.

Genetic diversity of Indo-China rice varieties using ISSR, SRAP and InDel markers

Rice is believed to have originated from Indo-China, area between China and India, and then spread throughout the world. The Indochina region mainly includes countries like Thailand, Laos and Vietnam, which are the world's major rice exporters. Rice varieties grown in this area are highly diverse due to their different environment, ecosystem and climatic conditions. The objective of this study was to evaluate the genetic relationship of Indochina rice varieties using intersimple sequence repeat (ISSR), sequence-related amplified polymorphism (SRAP) and insertion-deletion (InDel) markers. Forty-six rice varieties, including 16, 4,11 and 15 from Thailand, China, Laos and Vietnam, respectively were used in this study. Seventeen of the 20 ISSR primers showed 82.96% polymorphism. At the same time, 17 of the 30 primer pairs of SRAP marker showed clear DNA amplification, which resulted in 84.79% polymorphism. Ninety-seven of 133 InDel markers have about 99.47% polymorphism. Three markers showed average PIC score ranging from 0.20 to 0.26. When the analysis was conducted using UPGMA clustering method, it was found that the combined data from three markers gave a better result than each marker separately. The results from clustering analysis showed that all accessions can be grouped based on their location and can be categorized into two major groups. Useful results from this study could bring substantial benefits and ultimately help the rice breeders to develop elite rice varieties in future.

The CRISPR/Cas9 system and its applications in crop genome editing

The CRISPR/Cas9 (clustered regularly interspaced short palindromic repeats/CRISPR associated protein9) system is an RNA-guided genome editing tool that consists of a Cas9 nuclease and a single-guide RNA (sgRNA). By base-pairing with a DNA target sequence, the sgRNA enables Cas9 to recognize and cut a specific target DNA sequence, generating double strand breaks (DSBs) that trigger cell repair mechanisms and mutations at or near the DSBs sites. Since its discovery, the CRISPR/Cas9 system has revolutionized genome editing and is now becoming widely utilized to edit the genomes of a diverse range of crop plants. In this review, we present an overview of the CRISPR/Cas9 system itself, including its mechanism of action, system construction strategies, and the screening methods used to identify mutants containing edited genes. We evaluate recent examples of the use of CRISPR/Cas9 for crop plant improvement, and research into the function(s) of genes involved in determining crop yields, quality, environmental stress tolerance/resistance, regulation of gene transcription and translation, and the construction of mutant libraries and production of transgene-free genome-edited crops. In addition, challenges and future opportunities for the use of the CRISPR/Cas9 system in crop breeding are discussed.