Search Results (71)

Anaerobic germination (AG) is a pivotal trait for successful direct-seeded rice cultivation, encompassing rainfed and irrigated conditions. Elite rice cultivars are often vulnerable to flooding during germination, resulting in poor crop establishment. This drawback has led to the exploration of AG-tolerant rice landraces, which offer valuable insights into the genetic underpinnings of AG tolerance. Over the years, substantial progress has been made in identifying significant quantitative trait loci (QTLs) associated with AG tolerance, forming the basis for targeted breeding efforts. However, the intricate gene regulatory network governing AG tolerance remains enigmatic. This comprehensive review presents recent advances in understanding the physiological and genetic mechanisms underlying AG tolerance. It focuses on their practical implications in breeding elite rice cultivars tailored for direct-seeding systems. Full article

The architecture of rice tillers plays a pivotal role in yield potential, yet conventional phenotyping methods have struggled to capture these intricate three-dimensional (3D) structures with high fidelity. In this study, a 3D model reconstruction method was developed specifically for rice tillers to overcome the challenges posed by their slender, feature-poor morphology in multi-view stereo-based 3D reconstruction. By applying strategically designed colorful reference markers, high-resolution 3D tiller models of 231 rice landraces were reconstructed. Accurate phenotyping was achieved by introducing ScaleCalculator, a software tool that integrated depth images from a depth camera to calibrate the physical sizes of the 3D models. The high efficiency of the 3D model-based phenotyping pipeline was demonstrated by extracting the following seven key agronomic traits: flag leaf length, panicle length, first internode length below the panicle, stem length, flag leaf angle, second leaf angle from the panicle, and third leaf angle. Genome-wide association studies (GWAS) performed with these 3D traits identified numerous candidate genes, nine of which had been previously confirmed in the literature. This work provides a 3D phenomics solution tailored for slender organs and offers novel insights into the genetic regulation of complex morphological traits in rice. Full article

Mycorrhizal symbiosis in rice enhances drought adaptation but there are limited studies regarding the frequency and amplitude of mycorrhizae colonization in traditional landraces. This study investigates mycorrhizal colonization frequency (FMS) and intensity (IRS) in 12 rice landraces across three agroecological zones (Tarai, Inner-Tarai, Mid-hill) of Far-West Nepal under drought stress. Field experiments exposed landraces to control, intermittent, and complete drought treatments, with soil properties and root colonization analyzed. Results revealed FMS and IRS variations driven by soil composition and genotype. Mid-hill soils (acidic, high organic matter) showed lower FMS but elevated IRS under drought, while neutral pH in Tarai and silt/clay-rich soils supported higher FMS. Sandy soil in Inner-Tarai also promoted FMS. Drought significantly increased IRS, particularly in Anjana and Sauthiyari (Tarai), Chiudi and Shanti (Inner-Tarai), and Chamade and Jhumke (Mid-hill), which exhibited IRS surges of 171–388%. These landraces demonstrated symbiotic resilience, linking mycorrhizal networks to enhanced nutrient/water uptake. Soil organic matter and nutrient levels amplified IRS responses, underscoring fertility’s role in adaptation. FMS ranged from 50 to 100%, and IRS 1.20–19.74%, with intensity being a stronger drought-tolerance indicator than frequency. The study highlights the conservation urgency for these landraces, as traditional varieties decline due to hybrid adoption. Their drought-inducible mycorrhizal symbiosis offers a sustainable strategy for climate-resilient rice production, emphasizing soil–genotype interactions in agroecological adaptation. Full article

The continued emergence of weedy rice (Oryza sativa L.) in Taiwan poses serious challenges to seed purity and commercial rice cultivation, particularly under transplanting systems. These off-type individuals, often marked by a red pericarp, reduce varietal integrity and complicate seed propagation. This study evaluated the morphological variation among 117 Taiwan weedy rice (TWR) accessions and 55 control cultivars, which include 24 temperate japonica cultivars (TEJ), 24 indica cultivars, and seven U.S. weedy rice (UWR) types. Principal component analysis (PCA) showed that TWR shares vegetative traits with modern cultivars but exhibits grain morphology resembling indica landraces—indicating weak artificial selection pressure on grain traits during nursery propagation. TWR was also found to possess a suite of adaptive weedy traits, including semi-dwarfism, delayed heading, high shattering, and superior seed storability, facilitating its persistence in field conditions. These findings provide critical insights for integrated weed management and cultivar purity strategies, emphasizing the importance of certified seed use, stringent field hygiene, and disruption of weedy rice reproductive cycles. Full article

The coastal regions of Bangladesh host a rich diversity of Aman rice landraces, which are crucial for local agriculture but are highly vulnerable to natural disasters like cyclones and floods. Specifically, local landraces often experience flooding during grain filling and maturation stages, and sprouts in the field lead to a severe loss of yield. Seed dormancy, which delays germination, is a key trait for escaping sprouting in the field during harvesting. However, there is lack of information on genetic variability in the existing rice landraces grown in the coastal area of Bangladesh. This study evaluated the seed dormancy of 28 local Aman rice landraces, plus four varieties from the Bangladesh Institute of Nuclear Agriculture and Bangladesh Rice Research Institute. Germination tests were conducted under controlled conditions, and an electrical conductivity (EC) test was used to assess seed vigor. The results showed that Bari Mota, Tulsimala, Chinigura, Dishari, and Birindi exhibited the highest dormancy rates, i.e., 100%, 100%, 99%, 99%, and 99%, respectively, while BINA Dhan 10, Nona Bokra, and BINA Dhan 8 had the lowest dormancy rates, with values of 11%, 16%, and 24%, respectively. Priming treatments enhanced germination rates in some varieties; however, others, such as Bari Mota and Tulsimala, remained dormant, underscoring the variability in seed dormancy levels. Compared to non-priming, a significant improvement of germination was recorded in BRRI dhan 41 (85.3% vs. 9%), Motha mota (84% vs. 8%), Lal chikon (74.6% vs. 1%), Sadamota (74.6% vs. 5%), and Bashful (53.3% vs. 3%). Altogether, our results suggest that local landraces are diverse in seed dormancy, and genotypes with high dormancy, such as Bari Mota and Tulsimala, can potentially be grown in the disaster-prone coastal areas. In contrast, these genotypes can be used for future breeding programs. Therefore, this study carries significant implications for rice cultivation in the coastal areas of Bangladesh. Full article

Uptake of excess iron by lowland rice plants causes iron toxicity, which is a major problem in the affected areas. This study investigated molecular diversity, genetic structure, and marker–trait associations for tolerance to iron toxicity in a panel of germplasm lines using microsatellite markers. The studied population showed a moderate to high degree of genetic diversity, as revealed by the estimated molecular diversity parameters and principal component, cluster and box plot analyses. The landraces Mahipal, Dhusura, Dhabalabhuta, Champa, Sunapani and Kusuma were identified as suitable for cultivation in the areas affected by high iron levels. The landraces Dhusura, Kusuma, Kendrajhali, Ranisaheba, Panjabaniswarna, Mahipal, Dhinkisiali, Champa, Kalamara and Ratanmali, which showed low scores for tolerance, were considered good donors for iron toxicity tolerance improvement programs. Utilizing STRUCTURE software, a total of four genetic structure groups were detected in the panel germplasm of lines. These structural subgroups exhibited good correlations among their members for iron toxicity tolerance and other yield-related traits. Marker–trait association analysis validated the reported iron toxicity tolerance QTLs qFeTox 4.2 and qFeTox 4.3, which are useful for marker-assisted improvement. A new QTL, qFeTox 7.1, located on chromosome 7, was detected as controlling iron toxicity tolerance in rice. Full article

Background: Rice blast, caused by Magnaporthe oryzae, seriously damages the yield and quality of rice worldwide. Pi-ta is a durable resistance gene that combats M. oryzae carrying AVR-Pita1. However, the distribution of the Pi-ta gene in rice germplasms in Yunnan Province has been inadequately studied. Methods: We analyzed the potential molecular evolution pattern of Pi-ta alleles by examining the diversity in the coding sequence (CDS) among rice varieties. Results: The results revealed that 95% of 405 rice landraces collected from different ecological regions in Yunnan Province carry Pi-ta alleles. We identified 17 nucleotide variation sites in the CDS regions of the Pi-ta gene across 385 rice landraces. These variations led to the identification of 28 Pi-ta haplotypes, encoding 12 novel variants. Among these, 5 Pi-ta haplotypes (62 rice landraces) carried R alleles. The evolutionary cluster and network of the Pi-ta haplotypes suggested that the Pi-ta S alleles were the ancestral alleles, which could potentially evolve into R variants through base substitution. Conclusions: This study suggests that Pi-ta alleles are diverse in the rice landraces in Yunnan, and the Pi-ta sites resistant to blast evolved from the susceptible plants of the rice landraces. These results provide the basis for breeding resistant varieties. Full article

Rice blast is one of the most devastating biotic stresses that limits rice productivity. The North Eastern Hill (NEH) region of India is considered to be one of the primary centres of diversity for both rice and pathotypes of Magnaporthe grisea. Therefore, the present study was carried out to elucidate the genetic basis of leaf and neck blast resistance under Meghalaya conditions. A set of 80 diverse genotypes (natural population) and 2 F₂ populations involving resistant parent, a wildtype landrace, LR 5 (Lal Jangali) and susceptible genotypes Sambha Mahsuri SUB 1 (SMS) and LR 26 (Chakhao Poireiton) were used for association analysis of reported major gene-linked markers with leaf and neck blast resistance to identify major effective genes under local conditions. Genotyping using twenty-five gene-specific markers across diverse genotypes and F₂ progenies revealed genes Pi5 and Pi54 to be associated with leaf blast resistance in all three populations. Genes Pib and qPbm showed an association with neck blast resistance in both natural and LR 5 × SMS populations. Additionally, a set of 184 genome-wide polymorphic markers (SSRs and SNPs), when applied to F₂-resistant and F₂-susceptible DNA bulks derived from LR 5 × LR 26, suggested that Pi20(t) on chromosome 12 is one of the major genes imparting disease resistance. Markers snpOS318, RM1337 and RM7102 and RM247 and snpOS316 were associated with leaf blast and neck blast resistance, respectively. The genotypes, markers and genes will help in marker-assisted selection and development of varieties with durable resistance. Full article

The Jinwu pig (JW) is a hybrid breed originating from the Chinese indigenous Jinhua pig and Duroc pig, boasting excellent meat quality and fast growth rates. This study aimed to verify the tolerance of JW to roughage, similar to most Chinese indigenous pigs. In this research, two types of feed were provided to JW and Duroc × Landrace × Yorkshire pigs (DLY): a basal diet and a roughage diet (increasing the rice bran and wheat bran content in the basal diet from 23% to 40%) for a 65-day experimental period. The roughage diet showed an increasing trend in the feed conversion ratio (F/G), with a 17.61% increase in feed consumption per unit weight gain for DLY, while the increase for JW was only 4.26%. A 16S rRNA sequencing analysis revealed that the roughage diet increased the relative abundance of beneficial bacteria, such as Lactobacillus and Clostridium, while reducing the relative abundance of some potential pathogens, thus improving the gut microbiota environment. After being fed with the roughage diet, the abundance of bacterial genera, such as Treponema, Terrisporobacter, Coprococcus, and Ruminococcaceae, which aid in the digestion and utilization of dietary fiber, were significantly higher in Jinwu compared to DLY, indicating that these bacterial genera confer Jinwu with a higher tolerance to roughage than DLY. Full article

Grain-related traits are pivotal in rice cultivation, influencing yield and consumer preference. The complex inheritance of these traits, involving multiple alleles contributing to their expression, poses challenges in breeding. To address these challenges, a multi-locus genome-wide association study (ML-GWAS) utilizing 35,286 high-quality single-nucleotide polymorphisms (SNPs) was conducted. Our study utilized an association panel comprising 483 rice genotypes sourced from a northeast core set and a landraces set collected from various regions in India. Forty quantitative trait nucleotides (QTNs) were identified, associated with four grain-related traits: grain length (GL), grain width (GW), grain aroma (Aro), and length–width ratio (LWR). Notably, 16 QTNs were simultaneously identified using two ML-GWAS methods, distributed across multiple chromosomes. Nearly 258 genes were found near the 16 significant QTNs. Gene annotation study revealed that sixty of these genes exhibited elevated expression levels in specific tissues and were implicated in pathways influencing grain quality. Gene ontology (GO), trait ontology (TO), and enrichment analysis pinpointed 60 candidate genes (CGs) enriched in relevant GO terms. Among them, LOC_Os05g06470, LOC_Os06g06080, LOC_Os08g43470, and LOC_Os03g53110 were confirmed as key contributors to GL, GW, Aro, and LWR. Insights from QTNs and CGs illuminate rice trait regulation and genetic connections, offering potential targets for future studies. Full article

The current study aims to identify candidate insertion/deletion (INDEL) markers associated with photoperiod sensitivity (PS) in rice landraces from the Vietnamese Mekong Delta. The whole-genome sequencing of 20 accessions was conducted to analyze INDEL variations between two photoperiod-sensitivity groups. A total of 2240 INDELs were identified between the two photoperiod-sensitivity groups. The selection criteria included INDELs with insertions or deletions of at least 20 base pairs within the improved rice group. Six INDELs were discovered on chromosomes 01 (5 INDELs) and 6 (1 INDEL), and two genes were identified: LOC_Os01g23780 and LOC_Os01g36500. The gene LOC_Os01g23780, which may be involved in rice flowering, was identified in a 20 bp deletion on chromosome 01 from the improved rice accession group. A marker was devised for this gene, indicating a polymorphism rate of 20%. Remarkably, 20% of the materials comprised improved rice accessions. This INDEL marker could explain 100% of the observed distinctions. Further analysis of the mapping population demonstrated that an INDEL marker associated with the MADS-box gene on chromosome 01 was linked to photoperiod sensitivity. The F1 population displayed two bands across all hybrid individuals. The marker demonstrates efficacy in distinguishing improved rice accessions within the indica accessions. This study underscores the potential applicability of the INDEL marker in breeding strategies. Full article

Silicon (Si) is a beneficial nutrient that has been shown to increase rice productivity and grain quality. Fragrant rice occupies the high end of the rice market with prices at twice to more than three times those of non-fragrant rice. Thus, this study evaluated the effects of increasing Si on the yield and quality of fragrant rice. Also measured were the content of proline and the expression of the genes associated with 2AP synthesis and Si transport. The fragrant rice varieties were found to differ markedly in the effect of Si on their quality, as measured by the grain 2AP concentration, while there were only slight differences in their yield response to Si. The varieties with low 2AP when the Si supply is limited are represented by either PTT1 or BNM4 with only slight increases in 2AP when Si was increased. Si affects the gene expression levels of the genes associated with 2AP synthesis, and the accumulation of 2AP in fragrant rice mainly occurred through the upregulation of Badh2, DAO, OAT, ProDH, and P5CS genes. The findings suggest that Si is a potential micronutrient that can be utilized for improving 2AP and grain yield in further aromatic rice breeding programs. Full article

Soil salinity imposes osmotic, ionic, and oxidative stresses on plants, resulting in growth inhibition, developmental changes, metabolic adaptations, and ion sequestration or exclusion. Identifying salinity-tolerant resources and understanding physiological and molecular mechanisms of salinity tolerance could lay a foundation for the improvement of salinity tolerance in rice. In this study, a series of salinity-tolerance-related morphological and physiological traits were investigated in 46 rice genotypes, including Sea Rice 86, to reveal the main strategies of rice in responding to salinity stress at the seedling stage. No genotypes showed the same tolerance level as the two landraces Pokkali and Nona Bokra, which remain the donors for improving the salinity tolerance of rice. However, due to undesirable agronomic traits of these donors, alternative cultivars such as JC118S and R1 are recommended as novel source of salinity tolerance. Correlation and principal component analyses revealed that the salinity tolerance of rice seedlings is not only controlled by growth vigor but also regulated by ion transport pathways such as long-distance Na⁺ transport, root Na⁺ sequestration, and root K⁺ retention. Therefore, such key traits should be targeted in future breeding programs as the strategy of obtaining better Na⁺ exclusion is still the bottleneck for improving salinity tolerance in rice. Full article

The Shanlan landrace rice in Hainan Province, China, is a unique upland rice germplasm that holds significant value as a genetic resource for rice breeding. However, its genetic diversity and its usefulness in rice breeding have not been fully explored. In this study, a total of eighty-four Shanlan rice, three typical japonica rice cultivars, and three typical indica rice cultivars were subjected to resequencing of their genomes. As a result, 11.2 million high-quality single nucleotide polymorphisms (SNPs) and 1.6 million insertion/deletions (InDels) were detected. Population structure analysis showed all the rice accessions could be divided into three main groups, i.e., Geng/japonica 1 (GJ1), GJ2, and Xian/indica (XI). However, the GJ1 group only had seven accessions including three typical japonica cultivars, indicating that most Shanlan landrace rice are different from the modern japonica rice. Principal component analysis (PCA) showed that the first three principal components explained 60.7% of the genetic variation. Wide genetic diversity in starch physicochemical parameters, such as apparent amylose content (AAC), pasting viscosity, texture properties, thermal properties, and retrogradation representing the cooking and eating quality was also revealed among all accessions. The genome-wide association study (GWAS) for these traits was conducted and identified 32 marker trait associations in the entire population. Notably, the well-known gene Waxy (Wx) was identified for AAC, breakdown viscosity, and gumminess of the gel texture, and SSIIa was identified for percentage of retrogradation and peak gelatinization temperature. Upon further analysis of nucleotide diversity in Wx, six different alleles, wx, Wx^a, Wx^b, Wxⁱⁿ, Wx^la/mw, and Wx^lv in Shanlan landrace rice were identified, indicating rich gene resources in Shanlan rice for quality rice breeding. These findings are expected to contribute to the development of new rice with premium quality. Full article

Parboiling influences chemical compositions in rice grains. The objectives of this study were to evaluate the change in chemical content, total phenolic content and antioxidant capacity of landrace rice genotypes under parboiling conditions and to identify the genotypes suitable for production of parboiled rice. Landrace rice varieties used in this study consisted of Glam Feang, Glam Tonkeaw, Kawgum, Glam Luem Phua, Medmakham, Deang Sakonnakhon, Sang Yod, Kawniewd-eang, Mali Deang, KDML105 and RD6. Parboiling reduced fiber content, total phenolic content and 2,2-diphenyl-1-picrylhydrazyl (DPPH) radical-scavenging activity in rice grains. Fiber contents were 1.46% in brown rice (unpolished rice) and 1.40% in parboiled rice (24 h of soaking and 48 h of incubation). Total phenolic contents were 205.67 mg/100 g seed in brown rice and 35.34 mg/100 g seed in parboiled rice. Antioxidant capacity (DPPH) reduced from 68.45% in brown rice to 26.23% in parboiled rice. Ash content and protein content were not significantly affected by the parboiling process. Medmakham cv. had the highest total phenolic content and antioxidant capacity in brown rice and parboiled rice. Gum Leamphea cv. and Medmakham cv. were the best genotypes for ash content, protein content, total phenolic content and antioxidant capacity (DPPH) in brown rice and parboiled rice. Glam Feang cv. had the highest protein contents in brown rice and parboiled rice although it had low total phenolic content and antioxidant capacity. Cluster analysis further showed variation among genotypes, revealing distinct groupings in brown rice and parboiled rice based on chemical properties, phenolic content and antioxidant capacity. This research significantly contributes to a better understanding on how parboiling affects rice compositions and nutritional values. It emphasizes the importance of nuanced comprehension of how different rice varieties respond to parboiling, aiding informed decisions in rice processing and selection to meet specific nutritional needs. Full article