Rice Accessions Research Articles

Morphological performance of local upland rice accessions from West Bangka for germplasm conservation

The genetic diversity of upland rice in West Bangka plays a crucial role in food security and germplasm conservation. This study aimed to identify the morphological characteristics of upland rice accessions from West Bangka. The research involved identifying seven local rice accessions from West Bangka and was conducted from March to July 2024. This study employed survey methods and field observations using Purposive Random Sampling based on type or accession, and data analysis was carried out through experimental methods. Data collection involved observing the morphology of the upland rice plants qualitatively and quantitatively. Data analyses were performed using variability tests. Local upland rice accessions in West Bangka Regency showed morphological diversity as indicated by the value of the broad variability in leaf width, leaf blade length, seed width, and seed thickness, while other traits showed narrow variability. The wide morphological diversity in certain characters showed that local accessions of upland rice in the West Bangka Regency had good genetic potential for utilization in plant breeding programs. Keywords: genetic resources; morphology; biodiversity conservation; agronomy; genetic variation

Evaluation of glycemic index, glycemic load and biochemical traits of rice associated with anti-diabetic properties

Diabetes mellitus, a modern lifestyle disease and metabolic disorder, is closely associated with an increased risk of cardiovascular disease. Research on carbohydrates, particularly white rice with a high glycemic index, has been linked to an increased risk of type II diabetes, heart disease, and cancer. In this study, we aimed to understand the nutritional composition, estimated glycemic index, and glycemic load of twenty-eight rice accessions, particularly focusing on those with low starch digestibility associated with low GI levels. The proximate composition analysis revealed that tested rice accessions exhibited higher levels of genetic variation for amylose (18.45 - 25.97%), phenolic content (5.00-34.08%), protein (5.52-14.54%), and crude fibre (1.64-3.91%) content in brown rice. Huge variability for estimat?ed glycemic index, ranging from low to high GI was observed among all the varieties (49.37 - 78.58%). Traditional varieties viz., Thavalakannan and Kavuni depicted low estimated glycemic index (49.37 % and 54.55 %) and moderate glycemic load (14.60 and 15.80), respectively. The estimated glycemic index exhibited significant and negative association with amylose (r = -0.57**), phenolic (r = -0.67**), and crude fibre (r = -0.52**) content. In contrast, glycemic load showed a significant positive correlation with the amount of carbohydrate content. Principal component analysis revealed considerable variability among rice accessions' biochemical traits with the first two principal components accounting for 68.57% of the total variance. The hierarchical clustering based on Darwin software identified two major clusters. Cluster I comprise popular varieties and Cluster II contains traditional varieties with low to moderate glycemic index. Moreover, identifying rice varieties with lower glycemic index can facilitate the development and enhancement of breeding lines for the diabetic population.

Estimates of genetic variability and interplay of germination and seedling traits conferring salinity tolerance in rice (Oryza sativa L.)

This study estimates genetic variability and correlations among germination and seedling traits conferring salinity tolerance in rice accessions. Five rice accessions were screened under salinity levels of 0, 50, 100, and 200 mM NaCl in a controlled laboratory setting. Traits such as germination energy, capacity, shoot and root length, and biomass were measured. Data were analyzed for variance and correlations to assess variability and trait relationships. Significant genetic variability was found among accessions for all traits. Germination energy showed the highest coefficient of variation (CV) at 22.29% under control conditions, while fresh shoot weight had the highest CV (34.35%) under 200 mM salinity. Accessions ACC2 and ACC5 consistently demonstrated higher performance in germination energy (23.33 to 53.33% and 10.00 to 41.67%), germination capacity (40.00 to 60.00% and 28.33 to 46.67%), and shoot length (0.67 to 2.97 cm and 0.40 to 3.93 cm) under various salinity stress levels. ACC1, ACC3, and ACC4 showed more variability but maintained some consistency in specific traits, with ACC4 generally showing lower performance across most traits. Genetic parameter estimates indicated high heritability (˃60%) for all traits, with the highest in germination capacity (96.88%). High genetic advance (GAM) was observed for all traits (˃20%), with germination energy showing the highest (107.00%). Traits with high heritability and genetic advance, such as germination energy, germination capacity, and root length, suggest strong genetic control and potential for improvement through selective breeding. Significant correlations were found between germination energy and capacity (r= 0.89 to 0.96) and between shoot length and leaf length (r= 0.92) under stress conditions. Stress tolerance indices identified accessions ACC2 and ACC5 as the most tolerant, with ACC1 showing consistent performance across traits. This study underscores the importance of identifying resilient traits and accessions to enhance salinity tolerance in rice, contributing to improved productivity in saline-affected regions.

Candidate genes for alkali tolerance identified by genome-wide association study at the seedling stage in rice (Oryza sativa L.)

Alkali stress is one of the most serious abiotic stresses limiting crop yield and it has become an increasingly serious global problem in recent years. Alkalinity tolerance (AT) at the seedling stage is one of the determinant factors for establishment of rice population under alkaline stress condition. Here, we evaluated and measured seven traits related to AT of 528 diverse rice accessions at the seedling stage. Xian accessions were generally more alkali-tolerant than Geng accessions. GJ-tmp accessions showed the most alkali tolerance in the Geng subgroups and XI-1B accessions had the weakest alkali tolerance in the Xian subgroups. A total of 121 QTLs were identified for AT by genome-wide association study (GWAS), and five important candidate genes, LOC_Os01g19800, LOC_Os01g20160, LOC_Os01g52500, LOC_Os01g67370 and LOC_Os03g03900, were selected by gene function annotation, haplotype analysis, and qRT-PCR. Pyramiding of multiple AT advanced candidate genes is a favorable strategy for improving AT of rice varieties. Our study has screened alkali-tolerant germplasm resources and provided valuable genetic information for alkali-tolerant rice breeding.

Improving grain yield and salt tolerance by optimizing plant height with beneficial haplotypes in rice (Oryza sativa).

Rice (Oryza sativa L.), a staple food for billions worldwide, is challenged by salt stress. Owing to the limited understanding of the physiological and genetic basis of rice salt tolerance, few genes have been identified as valuable in rice breeding, causing a major bottleneck in the development of high-yield, salt-tolerant rice varieties. This study aims to identify salt tolerance genes/quantitative trait loci (QTLs) with breeding potential in rice. Field trials were conducted with 166 Chinese rice cultivars from saline-affected regions and 412 global rice accessions to assess salt tolerance. Genome-wide association study (GWAS) was performed to identify key loci related to high yield and salt tolerance. Additionally, the impact of introducing beneficial haplotypes on grain yield and salt tolerance was assessed. The optimal rice plant height of 100-120 cm was crucial for sustaining high yield under both normal and salt stress conditions. GWAS revealed 6 novel QTLs/genes associated with rice plant growth and grain yield across various environments, distinct from previously recognized salt stress-related genes. Notably, the gene PHS10.1, encoding a serine/threonine protein kinase, may regulate carbon metabolism, starch and sucrose metabolism, influencing plant growth and grain yield. Certain haplotypes of the genes regulating plant height and grain yield, including SD1, Ghd7.1, GH3.5, and PHS10.1, were selected in traditional breeding. Moreover, optimizing plant height through the introgression of beneficial alleles of these genes increased grain yield in recipient lines under both normal and saline conditions. We propose that utilizing beneficial haplotypes to optimize plant height can effectively balance the growth-stress trade-offs in rice plants. This represents a promising breeding strategy for the development of crop varieties that are both high-yielding and salt-tolerant.

The miR172a-SNB module orchestrates induced and adult resistance to multiple diseases via MYB30-mediated lignin accumulation in rice

Plants mount induced resistance and adult plant resistance against different pathogens during the whole growth period. Rice production faces threats from multiple major diseases, including rice blast, sheath blight, and bacterial leaf blight. Here we report that a microRNA module, miR172a-SNB-MYB30, regulates induced resistance and adult plant resistance to these three major diseases via lignification in rice. Mechanistically, pathogens induce expression of miR172a, which down-regulates transcription factor SNB to release its suppression on MYB30, leading to an increase in lignin biosynthesis and disease resistance during the whole growth period. Moreover, expression levels of miR172a and MYB30 are gradually increased and consistently correlated with lignin contents and disease resistance during rice development reaching a peak at full maturity stage, whereas SNB RNA levels are reversely correlated with lignin contents and disease resistance, indicating the involvement of the miR172a-SNB-MYB30 module in plant adult resistance. A high conservation exists in the functional domain of SNB protein and its binding sites in the MYB30 promoter among over 4000 rice accessions; moreover, abnormal expression of miR172a, SNB, or MYB30 compromises yield traits, suggesting an artificial selection of the miR172a-SNB-MYB30 module during rice domestication. Our results reveal a novel role for a conserved miRNA-regulated module that significantly contributes to induced and adult resistance against multiple pathogens via lignin accumulation, advancing our understanding in broad-spectrum resistance and adult resistance.

Identification of qTGW2, a Minor-Effect QTL Controlling Grain Weight in Rice

Grain weight and grain shape are key traits affecting grain yield and quality in rice. In this research, a quantitative trait locus (QTL), qTGW2, that controls 1000-grain weight (TGW), grain length (GL), and grain width (GW) in rice, was fine-mapped within an 84.7 kb region on chromosome 2 using three sets of near isogenic lines (NILs) originated from the indica rice cross, Teqing (TQ)/IRBB52. In the NIL populations, the TGW, GL, and GW of the IRBB52 homozygous lines increased by 0.22 g, 0.020 mm, and 0.009 mm compared with the TQ homozygous lines. Four annotated genes showed nucleotide polymorphisms between the two parental lines in the qTGW2 region. Only one annotated gene, LOC_Os02g57660, exhibited significant expression differences between NILTQ and NILIRBB52 in the young panicles performed by RNA sequencing and the quantitative real-time polymerase chain reaction. These results indicated that LOC_Os02g57660, which encodes phosphatidylinositol-4-phosphate 5-kinase (PIP5K), was the candidate gene of qTGW2. Then, one insertion-deletion (InDel) was found in the LOC_Os02g57660 coding region. The haplotype analysis was performed based on the phenotypic data of 4720 rice accessions from RiceVarMap V2.0. Two haplotypes, Hap1 (TQ-type) and Hap2 (IRBB52-type), were classified according to one InDel. Significant differences in grain weight traits were identified between Hap1 and Hap2. Hap2 has greater GL and RLW but lower GW, thus exhibiting potential to simultaneously improve grain yield and quality.

The rice genome annotation project: an updated database for mining the rice genome.

Rice (Oryza sativa L.) is a major cereal crop that provides calories across the world. With a small genome, rice has been used extensively as a model for genetic and genomic studies in the Poaceae. Since the release of the first rice genome sequence in 2002, an improved reference genome assembly, multiple whole genome assemblies, extensive gene expression profiles, and resequencing data from over 3000 rice accessions have been generated. To facilitate access to the rice genome for plant biologists, we updated the Rice Genome Annotation Project database (RGAP; https://rice.uga.edu) with new datasets including 16 whole genome rice assemblies and sequence variants generated from multiple rice pan-genome projects including the 3000 Rice Genomes Project. We updated gene expression abundance data with 80 RNA-sequencing datasets and to facilitate gene function discovery, performed gene coexpression resulting in 39 coexpression modules that capture highly connected sets of co-regulated genes. To facilitate comparative genome analyses, 32335 syntelogs were identified between the Nipponbare reference genome and other rice genomes and 19371 syntelogs were identified between Nipponbare and four other Poaceae genomes. Infrastructure improvements to the RGAP database include an upgraded genome browser and data access portals, enhanced website securityand increased performance of the website.

Genetic variation and population structure of the rice accessions maintained in the AfricaRice genebank using DArTseq

AbstractUtilizing the full potential of rice collections mainly depends on an in‐depth exploration and understanding of the vast diversity in its germplasm. The AfricaRice genebank holds the largest collection of rice germplasm originating from the African continent. In the present study, we comprehensively characterized a collection of 9013 accessions, including Oryza barthii A. Chev., Oryza glaberrima Steud., Oryza longistaminata A. Chev. & Roehr., Oryza sativa L. ssp. indica, and Oryza sativa L. ssp. japonica, for genetic diversity and population structure using genotyping‐by‐sequencing through DArTseq analysis. We identified 27,718 high‐quality single nucleotide polymorphism markers after the genotypic data were filtered. Based on the analyses, the collection has extensive genetic diversity, and the average genetic distance of the entire set was 0.267 (range 0.001–0.469), with 45.1% of pairs of accessions being highly distant and 40.1% moderately distant from each other. Neighbor‐joining tree, principal component, and Bayesian population structure analyses clustered the 9013 accessions into six groups, based roughly on their taxonomic and biological status. The first, second, and third groups consisted of accessions belonging to O. glaberrima, O. barthii, and O. longistaminata, respectively. The fourth, fifth, and sixth groups were improved‐indica, japonica, and traditional‐indica accessions, respectively. The highest value of genetic variance proportion (PhiPT) was found in the species group followed by groups based on cluster analysis and on Bayesian population structure at K = 6. These results allow us to better understand the genetic diversity present in 9013 rice accessions maintained in the AfricaRice genebank and offer a valuable tool for pre breeding, breeding, and further genetic applications.

Inhibitory effects of N-trans-cinnamoyltyramine on growth of invasive weeds and weedy rice.

N-trans-cinnamoyltyramine (NTCT) has been identified from an allelopathic Vietnamese rice accession OM 5930. This study employed bioassays to analyze NTCT's effects on shoot and root growth of multiple test and weed species. NTCT demonstrated potent inhibitory effects on cress, lettuce, canola, palmer amaranth, timothy, barnyardgrass, red sprangletop, and weedy rice, with increasing concentrations leading to substantial reductions in growth in all species. Linear regression analysis of dose response curves revealed ED50 values for NTCT, providing critical insights into the concentration required for 50% growth inhibition in each species. They revealed high sensitivity of the test species cress and lettuce, intermediate sensitivities of barnyardgrass, red sprangletop, timothy, and amaranth, and comparatively lower sensitivity of two weedy rice accessions. The findings underscore NTCT's efficacy in suppressing the growth of a wide range of weeds, including both grasses and broadleaf species. As such, NTCT may hold promise as a tool for sustainable weed management, particularly in addressing herbicide-resistant weeds in diverse ecological settings.

Genome-Wide Association-Based Identification of Alleles, Genes and Haplotypes Influencing Yield in Rice (Oryza sativa L.) Under Low-Phosphorus Acidic Lowland Soils.

Rice provides poor yields in acidic soils due to several nutrient deficiencies and metal toxicities. The low availability of phosphorus (P) in acidic soils offers a natural condition for screening genotypes for grain yield and phosphorus utilization efficiency (PUE). The objective of this study was to phenotype a subset of indica rice accessions from 3000 Rice Genome Project (3K-RGP) under acidic soils and find associated genes and alleles. A panel of 234 genotypes, along with checks, were grown under low-input acidic soils for two consecutive seasons, followed by a low-P-based hydroponic screening experiment. The heritability of the agro-morphological traits was high across seasons, and Ward's clustering method identified 46 genotypes that can be used as low-P-tolerant donors in acidic soil conditions. Genotypes ARC10145, RPA5929, and K1559-4, with a higher grain yield than checks, were identified. Over 29 million SNPs were retrieved from the Rice SNP-Seek database, and after quality control, they were utilized for a genome-wide association study (GWAS) with seventeen traits. Ten quantitative trait nucleotides (QTNs) for three yield traits and five QTNs for PUE were identified. A set of 34 candidate genes for yield-related traits was also identified. An association study using this indica panel for an already reported 1.84 Mbp region on chromosome 2 identified genes Os02g09840 and Os02g08420 for yield and PUE, respectively. A haplotype analysis for the candidate genes identified favorable allelic combinations. Donors carrying the superior haplotypic combinations for the identified genes could be exploited in future breeding programs.

Comprehensive evaluation and screening of saline–alkali tolerant Japonica rice accessions during the whole growth stage

Comprehensive evaluation and screening of saline–alkali tolerant Japonica rice accessions during the whole growth stage

A Cyclin Gene OsCYCB1;5 Regulates Seed Callus Induction in Rice Revealed by Genome Wide Association Study

Plant tissue culture is extensively employed in plant functional genomics research and crop genetic improvement breeding. The callus induction ability is critical for utilizing Agrobacterium-mediated genetic transformation. In this study, we conducted a genome-wide association study (GWAS) utilizing 368 rice accessions to identify traits associated with callus induction rate (CIR), resulting in the identification of a total of 104 significant SNP loci. Integrated with gene function annotation and transcriptome analysis, 13 high-confidence candidate genes involved in auxin-related, CYC cyclins, and histone H3K9-specific methyltransferase were identified in significant loci. Furthermore, we also verified a candidate gene, Os05g0493500 (OsCycB1;5), and employed the CRISPR/Cas9 system to generate OsCycB1;5 knockout mutants in rice (Oryza sativa L.). The OscycB1;5 mutant displays significantly reduced callus induction and proliferation capacity, this result indicating OsCycB1;5 is required for the callus formation in rice. Overall, this study provides several reliable loci and high-confidence candidate genes that may significantly affect callus formation in rice. This information will offer valuable insights into the mechanisms underlying callus formation not only in rice but also in other plants.

Genome-wide association study and genotypic variation for the major tocopherol content in rice grain.

Rice tocopherols, vitamin E compounds with antioxidant activity, play essential roles in human health. Even though the key genes involved in vitamin E biosynthetic pathways have been identified in plants, the genetic architecture of vitamin E content in rice grain remains unclear. A genome-wide association study (GWAS) on 179 genotypically diverse rice accessions with 34,323 SNP markers was conducted to detect QTLs that define total and α- tocopherol contents in rice grains. Total and α-tocopherol contents had a strong positive correlation and varied greatly across the accessions, ranging from 0.230-31.76 and 0.011-30.83 (μg/g), respectively. A total of 13 QTLs were identified, which were spread across five of the rice chromosomes. Among the 13 QTLs, 11 were considered major with phenotypic variation explained (PVE) greater than 10%. Twelve transcription factor (TF) genes, one microprotein (miP), and a transposon were found to be associated with the QTLs with putative roles in controlling tocopherol contents. Moreover, intracellular transport proteins, ABC transporters, nonaspanins, and SNARE, were identified as associated genes on chromosomes 1 and 8. In the vicinity of seven QTLs, protein kinases were identified as key signaling factors. Haplotype analysis revealed the QTLs qAlph1.1, qTot1.1, qAlph2.1, qAlph6.1, qTot6.1, and qTot8.3 to have significant haplogroups. Quantitative RT-PCR validated the expression direction and magnitude of WRKY39 (Os02g0265200), PIP5Ks (Os08g0450800), and MADS59 (Os06g0347700) in defining the major tocopherol contents. This study provides insights for ongoing biofortification efforts to breed and/or engineer vitamin E and antioxidant levels in rice and other cereals.

Sequence-based analysis of the rice CAMTA family: haplotype and network analyses

The calmodulin-binding transcription activator (CAMTA) family contributes to stress responses in many plant species. The Oryza sativa ssp. japonica genome harbors seven CAMTA genes; however, intraspecific variation and functional roles of this gene family have not been determined. Here, we comprehensively evaluated the structure and characteristics of the CAMTA genes in japonica rice using bioinformatics approaches and RT-qPCR. Within the CAMTA gene and promoter sequences, 527 single nucleotide polymorphisms were retrieved from 3,024 rice accessions. The CAMTA genes could be subdivided into 5–14 haplotypes. Association analyses between haplotypes and phenotypic traits, such as grain weight and salt stress parameters, identified phenotypic differences between rice subpopulations harboring different CAMTA haplotypes. Co-expression analyses and the identification of CAMTA-specific binding motifs revealed candidate genes regulated by CAMTA. A Gene Ontology functional enrichment analysis of 690 co-expressed genes revealed that CAMTA genes have key roles in defense responses. An interaction analysis identified 30 putative CAMTA interactors. Three genes were identified in co-expression and interaction network analyses, suggesting that they are potentially regulated by CAMTAs. Based on all information obtained together with the phenotypes of the CRISPR-Cas9 knockout mutant lines of three OskCAMTA genes generated, CAMTA1 likely plays important roles in the response to salt stress in rice. Overall, our findings suggest that the CAMTA gene family is involved in development and the salt stress response and reveal candidate target genes, providing a basis for further functional characterization.

Studies on the tolerance mechanism in selected rice accession against yellow stem borer, Scirpophaga incertulas (Walker)

Studies on the tolerance mechanism in selected rice accession against yellow stem borer, Scirpophaga incertulas (Walker)

Transcriptome-based prediction for polygenic traits in rice using different gene subsets

BackgroundTranscriptome-based prediction of complex phenotypes is a relatively new statistical method that links genetic variation to phenotypic variation. The selection of large-effect genes based on a priori biological knowledge is beneficial for predicting oligogenic traits; however, such a simple gene selection method is not applicable to polygenic traits because causal genes or large-effect loci are often unknown. Here, we used several gene-level features and tested whether it was possible to select a gene subset that resulted in better predictive ability than using all genes for predicting a polygenic trait.ResultsUsing the phenotypic values of shoot and root traits and transcript abundances in leaves and roots of 57 rice accessions, we evaluated the predictive abilities of the transcriptome-based prediction models. Leaf transcripts predicted shoot phenotypes, such as plant height, more accurately than root transcripts, whereas root transcripts predicted root phenotypes, such as crown root length, more accurately than leaf transcripts. Furthermore, we used the following three features to train the prediction model: (1) tissue specificity of the transcripts, (2) ontology annotations, and (3) co-expression modules for selecting gene subsets. Although models trained by a gene subset often resulted in lower predictive abilities than the model trained by all genes, some gene subsets showed improved predictive ability. For example, using genes expressed in roots but not in leaves, the predictive ability for crown root diameter was improved by more than 10% (R2 = 0.59 when using all genes; R2 = 0.66, using 1,554 root-specifically expressed genes). Similarly, genes annotated as “gibberellic acid sensitivity” showed higher predictive ability than using all genes for root dry weight.ConclusionsOur results highlight both the possibility and difficulty of selecting an appropriate gene subset to predict polygenic traits from transcript abundance, given the current biological knowledge and information. Further integration of multiple sources of information, as well as improvements in gene characterization, may enable the selection of an optimal gene set for the prediction of polygenic phenotypes.

Identification of Candidate Genes for Cold Tolerance at Seedling Stage by GWAS in Rice (Oryza sativa L.).

Due to global climate change, cold temperatures have significantly impacted rice production, resulting in reduced yield and quality. In this study, we investigated two traits related to the cold tolerance (CT) of 1992 diverse rice accessions at the seedling stage. Geng accessions exhibited higher levels of CT compared to xian accessions, with the GJ-tmp subgroup displaying the strongest CT. However, extreme CT accessions were also identified within the xian subspecies. Through GWAS analysis based on the survival rate (SR) and leaf score of cold tolerance (SCT), a total of 29 QTLs associated with CT at the seedling stage were identified, among which four QTLs (qSR3.1a, qSR4.1a, qSR11.1x, and qSR12.1a) were found to be important. Furthermore, five candidate genes (LOC_Os03g44760, LOC_Os04g06900, LOC_Os04g07260, LOC_Os11g40610, and LOC_Os12g10710) along with their favorable haplotypes were identified through gene function annotation and haplotype analysis. Pyramiding multiple favorable haplotypes resulted in a significant improvement in CT performance. Subsequently, three selected accessions (CX534, B236, and IRIS_313-8565), carrying different superior alleles for CT, were selected and recommended for molecular breeding for CT using marker-assisted selection (MAS). The findings from this study provide valuable resources for enhancing rice's ability for CT while laying a foundation for the future cloning of novel genes involved in conferring CT.

Assessment of antioxidant properties in selected pigmented and non-pigmented rice (Oryza sativa L.) germplasm and determination of its association with Rc gene haplotypes

BackgroundAntioxidant properties of rice provide various health benefits due to its ability to inhibit cellular oxidation. Antioxidant content of rice is known to be linked with the pericarp pigmentation. The Rc gene of rice (Os07g0211500) codes for a basic helix-loop-helix (bHLH) protein, acting as a transcriptional factor in regulating proanthocyanidin biosynthesis. The current study was carried out to evaluate the variation of antioxidant properties in a selected panel of rice accessions and assess the possibility of using haplotypes defined based on the Rc gene to predict pericarp pigmentation and antioxidant content in rice.ResultsThirty-two rice accessions were evaluated for grain pericarp colour and antioxidant properties; total phenolic content (TPC), total flavonoids (TFC), proanthocyanidins (PAC) and radical scavenging activity (RSA). The parameters TPC, TFC and PAC showed significant positive correlation with RSA (r > 0.69; P < 0.01). The study panel showed a wide variation for antioxidant properties and rice accessions such as Sudu Heenati, Deweraddiri, Madathawalu, Masuran, Ld 368, At 311, Kalu Heenati, Bw 272-6B, Pokkali, At 362 and Wanni Dahanala exhibited profound potential with respect to antioxidant properties. Based on three-target sites previously reported as critical for the function of the coded bHLH protein (an A/C SNP at 1,353-bp, a 1-bp insertion/deletion at 1,388-bp, and a 14-bp insertion/deletion at 1,408-1,421-bp positioned in the mRNA corresponding to the exon 6 of rice Rc gene), three haplotypes were defined (H1-H3). Pigmentation of the rice pericarp could be successfully explained based on the defined haplotypes (H1 (C/G/+): red, and H2 (A/G/+) and H3 (C/G/-): white), and the H1 haplotype corresponded to a significantly (P < 0.05) higher TPC, TFC, PAC and RSA compared to the other haplotypes.ConclusionsThe studied rice accessions showed a significant variation with respect to antioxidant properties. Haplotype H1 defined based on the three-target sites in the exon 6 of Rc gene can detect rice accessions with red pigmented pericarp and high antioxidant properties effectively. Hence, its use can be recommended as an alternative to biochemical assays for screening during rice breeding programs.

Identification of African rice genotypes with early morning flowering trait to avoid heat stress

AbstractEarly morning flowering (EMF) is a desirable trait in rice to avoid heat stress as temperatures in early morning hours are low compared to afternoon and flowering is the most sensitive stage to heat exposure. Cultivated rice accessions including both Oryza glaberrima and O. sativa were phenotyped for an EMF trait in 2016–2018 in two locations viz. Cotonou in Benin Republic and Ibadan in Nigeria. The initial screening was done in Cotonou in three phases in 2016 dry season, 2017 wet season and 2017 dry season, respectively. The 2093 accessions used in initial screening were subdivided into three groups based on flowering duration ensuring that each accession was grown under conditions which were best suited to their flowering duration. Further screening was done in Ibadan in 2018 dry season and 2018 wet season. Out of 2093 accessions taken in the initial screening only 1754 accessions germinated out of which only 64 accessions exhibited EMF phenotype consistently across the cultivated years, seasons and locations. Among the 64 accessions exhibiting EMF phenotype, 15 accessions also showed an early peak in spikelet opening time (EPSOT) trait, more than 80% flowering before 09:00 h. We conclude that 15 O. glaberrima accessions identified possessing both the EMF and EPSOT traits are suitable donors for use in breeding for heat escape in rice.