A massively parallel barcoded sequencing pipeline enables generation of the first ORFeome and interactome map for rice.

Systematic mappings of protein interactome networks have provided invaluable functional information for numerous model organisms. Here we develop PCR-mediated Linkage of barcoded Adapters To nucleic acid Elements for sequencing (PLATE-seq) that serves as a general tool to rapidly sequence thousands of DNA elements. We validate its utility by generating the ORFeome for Oryza sativa covering 2,300 genes and constructing a high-quality protein-protein interactome map consisting of 322 interactions between 289 proteins, expanding the known interactions in rice by roughly 50%. Our work paves the way for high-throughput profiling of protein-protein interactions in a wide range of organisms.

Genetic architecture of root and shoot ionomes in rice (Oryza sativa L.).

KEY MESSAGE: Association analysis for ionomic concentrations of 20 elements identified independent genetic factors underlying the root and shoot ionomes of rice, providing a platform for selecting and dissecting causal genetic variants. Understanding the genetic basis of mineral nutrient acquisition is key to fully describing how terrestrial organisms interact with the non-living environment. Rice (Oryza sativa L.) serves both as a model organism for genetic studies and as an important component of the global food system. Studies in rice ionomics have primarily focused on above ground tissues evaluated from field-grown plants. Here, we describe a comprehensive study of the genetic basis of the rice ionome in both roots and shoots of 6-week-old rice plants for 20 elements using a controlled hydroponics growth system. Building on the wealth of publicly available rice genomic resources, including a panel of 373 diverse rice lines, 4.8 M genome-wide single-nucleotide polymorphisms, single- and multi-marker analysis pipelines, an extensive tome of 321 candidate genes and legacy QTLs from across 15 years of rice genetics literature, we used genome-wide association analysis and biparental QTL analysis to identify 114 genomic regions associated with ionomic variation. The genetic basis for root and shoot ionomes was highly distinct; 78 loci were associated with roots and 36 loci with shoots, with no overlapping genomic regions for the same element across tissues. We further describe the distribution of phenotypic variation across haplotypes and identify candidate genes within highly significant regions associated with sulfur, manganese, cadmium, and molybdenum. Our analysis provides critical insight into the genetic basis of natural phenotypic variation for both root and shoot ionomes in rice and provides a comprehensive resource for dissecting and testing causal genetic variants.

Ecological Insights, and Fin Fish Diversity in Carps Spawning Grounds: Case Studies from the Surma River and Tanguar Haor, Bangladesh.

This study aims to provide a thorough ecological understanding of fin fish diversity within carp spawning grounds in the Surma River and Tanguar haor. Over two spawning seasons, this research investigates ecological factors impacting fin fish diversity and abundance in carp spawning grounds of the Surma River and Tanguar haor, emphasizing water quality, habitat features, spawn availability, and environmental influences. Fish spawn samples were collected with eight "Savar nets" at chosen sites and reared in a fiberglass tank at the mini hatchery for species identification. The representative spawn samples were examined under a microscope for preliminary species identification before rearing. The study found that both the Surma River and Tanguar haor offer ideal conditions for carp spawning due to factors such as water quality, natural food availability, habitat suitability, and favorable climatic conditions. The study identified 39 fish species under the 10 fish groups from both locations, with a higher percentage of carp species (31.42%) in the Surma River in 2021 compared to 2022 (22.50%). In Tanguar haor, the percentage of carp species was 7.55% and 6.50% in 2021 and 2022, respectively. The Surma River's ecological indices (2021-2022) indicated decreased diversity, likely due to environmental degradation, while Tanguar haor showed lower diversity possibly attributable to multiple environmental stressors. The dominant carp species, Labeo calbasu, Labeo bata, and Labeo gonius, were identified in both the Surma River and Tanguar haor. The spawning distribution varied among different locations, with some sites showing a presence of carp species, such as Hajipur (T1) in the Surma River and Alam Duar (T2) in Tanguar haor. The findings highlight the importance of hydrological and environmental parameters in shaping carp spawning habitat distribution and abundance, contributing to aquatic biodiversity conservation and resource management.

Corrigendum to "Tectonic setting, provenance, depositional, and paleo-climatic conditions of the late quaternary subcrop sediments of the southeastern coastal region of the Bengal basin".

[This corrects the article DOI: 10.1016/j.heliyon.2023.e12998.].

Tectonic setting, provenance, depositional, and paleo-climatic conditions of the late quaternary subcrop sediments of the southeastern coastal region of the Bengal basin.

This is a systematic attempt to depict the genetic evolution of the Late Quaternary sediments of the southeastern (SE) coastal region of the Bengal basin regarding paleotectonic settings, sedimentation, provenance, paleo-climatic conditions, weathering condition and age. The study has considered multiple attributes such as, lithology/lithofacies, sedimentary features/records, major oxides, clay minerals, foraminifera, and radiocarbon dating. The lithological characters along with associated clay minerals confirmed that a Pleistocene paleosol horizon (over-bank deposits) of warm-humid nature is commonly encountered immediately on top of the sub-crop bed-rock in the area overlain by Holocene fluvio-marine sediments of the same nature. The lithofacies, foraminiferal assemblages, and sedimentary structures of the analyzed samples suggest that the Holocene sediments have been presumably deposited in a fluvio-marine condition after the Last Glacial Maximum (LGM) due to the transgression of the sea. Geochemically, the sediments are classified as Fe-rich shale, shale, and wake and primarily intermediate to felsic orogen provenance. These are possibly derived from intense weathered sources from the upheaval of Himalayan ranges of both active continental margin and Island Arc paleotectonic setting. The plot of the Index of Compositional Variability versus the Chemical Index of Alteration indicates that the sediments seemingly experienced intense weathering associated with warm and humid climatic conditions. The sedimentation rates of the area vary from place to place and layer to layer due to the complex delta-building process. The reconstructed Relative Sea Level Curve reveals that presumably, the sea level has reached its current position after the LGM. The deduction possibly will facilitate the (1) reconstruction of Late Quaternary coastal evolution after LGM, (2) support for future urbanization, land use plans, etc., and (3) also be helpful for international researchers to understand the possible sources of sediment input in the area from the complex interplay of the Indian-, Eurasian- and Myanmar-plates.

Identifying genes associated with abiotic stress tolerance suitable for CRISPR/Cas9 editing in upland rice cultivars adapted to acid soils.

Five genes of large phenotypic effect known to confer abiotic stress tolerance in rice were selected to characterize allelic variation in commercial Colombian tropical japonica upland rice cultivars adapted to drought-prone acid soil environments (cv. Llanura11 and Porvenir12). Allelic variants of the genes ART1, DRO1, SUB1A, PSTOL1, and SPDT were characterized by PCR and/or Sanger sequencing in the two upland cultivars and compared with the Nipponbare and other reference genomes. Two genes were identified as possible targets for gene editing: SUB1A (Submergence 1A), to improve tolerance to flooding, and SPDT (SULTR3;4) (SULTR-like Phosphorus Distribution Transporter), to improve phosphorus utilization efficiency and grain quality. Based on technical and regulatory considerations, SPDT was targeted for editing. The two upland cultivars were shown to carry the SPDT wild-type (nondesirable) allele based on sequencing, RNA expression, and phenotypic evaluations under hydroponic and greenhouse conditions. A gene deletion was designed using the CRISPR/Cas9 system, and specialized reagents were developed for SPDT editing, including vectors targeting the gene and a protoplast transfection transient assay. The desired edits were confirmed in protoplasts and serve as the basis for ongoing plant transformation experiments aiming to improve the P-use efficiency of upland rice grown in acidic soils.

A Coordinated Suite of Wild-Introgression Lines in Indica and Japonica Elite Backgrounds.

Rice, Oryza sativa L., is a cultivated, inbreeding species that serves as the staple food for the largest number of people on earth. It has two strongly diverged varietal groups, Indica and Japonica, which result from a combination of natural and human selection. The genetic divergence of these groups reflects the underlying population structure of their wild ancestors, and suggests that a pre-breeding strategy designed to take advantage of existing genetic, geographic and ecological substructure may provide a rational approach to the utilization of crop wild ancestors in plant improvement. Here we describe the coordinated development of six introgression libraries (n = 63 to 81 lines per library) in both Indica (cv. IR64) and Japonica (cv. Cybonnet) backgrounds using three bio-geographically diverse wild donors representing the Oryza rufipogon Species Complex from China, Laos and Indonesia. The final libraries were genotyped using an Infinium 7K rice SNP array (C7AIR) and analyzed under greenhouse conditions for several simply inherited (Mendelian) traits. These six interspecific populations can be used as individual Chromosome Segment Substitution Line libraries and, when considered together, serve as a powerful genetic resource for systematic genetic dissection of agronomic, physiological and developmental traits in rice.

Corrigendum: A Coordinated Suite of Wild-Introgression Lines in Indica and Japonica Elite Backgrounds.

[This corrects the article DOI: 10.3389/fpls.2020.564824.].