Diversity Of Rice Varieties Research Articles

Thousands of trait-specific KASP markers designed for diverse breeding applications in rice (Oryza sativa).

This study aimed to broaden applicability of KASP for Oryza sativa across diverse genotypes through incorporation of ambiguous (degenerate) bases into their primer designs and to validate 4000 of them for genotyping applications. A bioinformatics pipeline was used to compare 129 rice genomes from 89 countries with the indica reference genome R498 and generate ∼1.6 million KASP designs for the more common variants between R498 and the other genomes. Of the designs, 98,238 were for predicted functional markers. Up to five KASP each for 1024 breeder-selected loci were assayed in a panel of 178 diverse rice varieties, generating 3366 validated KASP. The 84% success rate was within the normal range for KASP demonstrating that the ambiguous bases do not compromise efficacy. The 3366-trait-specific marker panel was applied for population structure analysis in the diversity panel and resolved them into four expected groups. Target variations in thirteen of the genome sequences used for designs were compared with the corresponding KASP genotypes of other accessions of the same thirteen varieties in the diversity panel. There was agreement across 12 varieties for 79% of markers. Ten varieties had high agreement (>88%) but a variety selected from a landrace had only 46.5% agreement. Breeders can now search for the validated KASP and >1 million so-far untested designs across three alternative reference genomes (including Niponbare MSU7), search for designs proximal to previously published SSR markers and retrieve the target variations in 129 rice genomes plus their genomic locations with +/-25 bp flanking sequences.

NAVIGATING PERSISTENT CHALLENGES: ENVIRONMENTAL ATTITUDES AND EXPOSURE RISKS IN PADDY FIELDS

This study evaluates public exposure to and awareness of toxic metal and pesticide contamination in paddy fields, and examines attitudes toward paying a premium for safe rice. It also explores rice consumption patterns and sources to inform stakeholders such as farmers, policymakers, and marketers. Data were collected through a semi-structured questionnaire administered to 600 respondents across four rice-producing communities in Nigeria: Igbemo (Ekiti), Pategi (Kwara), Isoku (Ogun), and Akeke (Edo). The study used both close-ended and open-ended questions to capture detailed responses about public health risks related to pesticide and heavy metal contamination. Descriptive statistics and binary regression analysis were employed to analyze the data. The findings reveal that most Nigerians prefer locally grown rice, which they consume regularly or occasionally. About 13% of respondents reported chemical exposure from paddy fields via their diet, and 12-13.9% experienced health problems linked to contaminated rice. Approximately 36.6% were aware of pesticide and heavy metal contamination in their area. Those aware of mitigation efforts were 14.9 times more willing to pay a premium for safe rice (B = .879, X2 = 14.901; p < 0.05). Educational initiatives were identified as the most effective strategy to reduce contamination, with 44.1% of respondents supporting this approach. Improving agricultural practices (24.3%) and enforcing regulatory standards (23.4%) were also deemed important, while 8.3% favored promoting diverse rice varieties. These results underscore the need for enhanced public education, improved agricultural methods, and stricter regulations to ensure rice safety and sustainability.

Evaluation of Sheath Blight Resistance in Diverse Rice Varieties Under Artificial Inoculation and Field Conditions

Rice (Oryza sativa L.) a vital food crop for nearly half of the global population, facing significant threats from various biotic and abiotic stresses. Among biotic stresses, diseases pose the most common challenge. Sheath blight, caused by soil-borne fungal pathogen Rhizoctonia Solani Kühn (R. solani), is a major concern, leading to substantial damage to rice and cereal crops worldwide. This study evaluated sheath blight resistance across diverse rice varieties, including short grain, long grain, aromatic, hybrid, and wild types, under both artificial inoculation and field conditions. Ten host plant species were assessed for resistance to sheath blight caused by Rhizoctonia Solani, using physiological screening one-week post-inoculation. The highly virulent R. solani isolate (AG-1 IA anastomosis group) was cultured on PDA media, covering the entire plate 3 to 5 days. Screening of cultivated rice varieties, was conducted using field conditions and humidified chamber methods, with results confirmed through molecular characterization. Among the ten cultivated rice varieties, Arize 6444 and Dhanya 748 exhibited the lowest disease index, classifying them as moderately resistant. In contrast, Kalanamak and Pusa Basmati were highly susceptible, displaying high disease indices. Among wild rice accessions, Oryza rufipogon showed a disease index of five or less. Visual ratings indicated the highest susceptibility in Kalanamak, followed by Pusa Basmati and Swarna sub-1, while the lowest visual ratings were observed in wild rice accessions Oryza australiensis and Oryza rufipogon across all tested hosts. The findings underscore the importance of identifying resistant rice varieties to manage sheath blight effectively. The moderately resistant cultivars and wild rice accessions identified in this study offer valuable genetic resources for breeding programs aimed at enhancing sheath blight resistance in rice.

Estimation of Proximate Composition in Rice Using ATR-FTIR Spectroscopy and Chemometrics.

This study presents an innovative approach for estimating the proximate composition of diverse rice varieties using attenuated total reflectance fourier transform infrared (ATR-FTIR) spectroscopy and chemometric techniques. Principal component analysis (PCA) reveals distinct separations among the seven rice varieties based on their FTIR spectra. Robust partial least squares (PLS) regression models, developed with high calibration (R 2) values from 0.778 for protein up to 0.941 for moisture, demonstrate high accuracy in predicting proximate composition. The root mean squared error (RMSE) in percentage values, indicative of prediction accuracy, were low across all proximate components. To ensure the response variable of regression, proximate composition measurements were taken five times, while FTIR spectra were scanned tens of times, employing random numbers around the average with the same standard deviation as the measurement. Notably, the study emphasizes the pivotal role of the amide-III band in protein determination, alongside specific wavenumber regions associated with molecular changes in proximate components. This research underscores the potential of ATR-FTIR spectroscopy and chemometrics for rapid and accurate proximate assessment in food science and agriculture.

Genetic variation for grain yield and straw quality traits in 55 diverse rice varieties in Assam

Genetic variation for grain yield and straw quality traits in 55 diverse rice varieties in Assam

Sensitivity of genotypically diverse rice varieties to radiation and the related changes to antioxidant enzyme activities

PurposeRadiation mutagenesis, which typically involves gamma rays, is important for generating new rice germplasm resources. Determining the appropriate radiation dose range is critical for the success of radiation mutagenesis. Clarifying the sensitivity and tolerance of genotypically diverse rice varieties to gamma irradiation as well as the radiation-induced changes to reactive oxygen species (ROS) generation and antioxidant enzyme activities is crucial for increasing the utility of radiation mutagenesis in rice breeding programs.Materials and methodsThe seeds of the following four rice varieties with different genotypes were used as test materials: indica Zhe 1613, glutinous indica Zhe 1708, japonica Zhejing 100, and glutinous japonica Zhenuo 65. Additionally,60Co was used as the source of gamma rays. The rice seeds were irradiated with 14 doses (0, 150, 200, 250, 300, 350, 400, 450, 500, 550, 600, 650, 700, and 750 Gy). Non-irradiated seeds were used as the control. The seedling survival rate for each variety was recorded at 3, 7, 14, and 28 days after sowing. Moreover, the median lethal dose (LD50) and critical dose (LD40) were calculated according to the seedling survival rates at 28 days after sowing. The seedling superoxide anion (O2•−), hydrogen peroxide (H2O2), and malondialdehyde (MDA) contents and the superoxide dismutase (SOD), catalase (CAT), peroxidase (POD), and ascorbate peroxidase (APX) activities were analyzed at 7 days after sowing.ResultsAs the radiation dose increased, the seedling survival rate decreased. The seedling survival rate also decreased significantly as the number of days after sowing increased. Among the rice genotypes, the rank-order of the radiation tolerance was as follows: indica Zhe 1613 > glutinous indica Zhe 1708 > japonica Zhejing 100 > glutinous japonica Zhenuo 65. The LD50 values were 426.7 Gy for Zhe 1613, 329.2 Gy for Zhe 1708, 318.3 Gy for Zhejing 100, and 316.6 Gy for Zhenuo 65. Increases in the radiation dose resulted in significant increases in the seedling O2•− and H2O2 contents, but only up to a certain point. Further increases in the radiation dose caused the seedling O2•− and H2O2 contents to decrease. The H2O2 content for each variety peaked when the radiation dose was very close to the LD50. We propose that the radiation dose associated with the highest H2O2 content (±50 Gy) should be used as the recommended dose for the gamma irradiation of rice. The radiation dose that resulted in peak seedling O2•− contents in the analyzed rice varieties was very close to the LD40. In all rice varieties, the MDA content increased as the radiation dose increased. The SOD, CAT, POD, and APX activities increased as the radiation dose increased within a certain range (less than 600 Gy for Zhe 1613 and 400 Gy for the other varieties), but there were slight differences among the rice varieties.ConclusionsGenotypically diverse rice varieties vary regarding their sensitivity to gamma irradiation. Our findings suggest that ROS generation and antioxidant enzyme activities are important factors associated with the radiation mutagenesis of rice. The close relationship between the activities of key antioxidant enzymes, such as SOD, POD, APX, and CAT, and the LD50 and LD40 may be exploited to enhance radiation mutagenesis through the use of plant growth regulators.

Genetic architecture of head rice and rice chalky grain percentages using genome-wide association studies.

High head rice and low chalky grain percentages are key grain quality traits selected in developing rice cultivars. The objectives of this research were to characterize the phenotypic variation of head rice and chalky grain percentages in a diverse collection of rice accessions, identify single nucleotide polymorphism (SNP) markers associated with each of these traits using genome-wide association studies (GWAS), and identify putative candidate genes linked to the SNPs identified by GWAS. Diverse rice varieties, landraces, and breeding lines were grown at the Texas A&M AgriLife Research Center in Beaumont. Head rice percentages (HRP) and chalky grain percentages (CGP) of 195 and 199 non-waxy accessions were estimated in 2018 and 2019, respectively. Phenotypic data were analyzed along with 854,832 SNPs using three statistical models: mixed linear model (MLM), multi-locus mixed model (MLMM), and fixed and random model circulating probability unification (FarmCPU). Significant variations in HRP and CGP were observed between rice accessions. Two significant marker-trait associations (MTAs) were detected on chromosomes 1 and 2, respectively, based on best linear unbiased prediction (BLUP) values in 2018, while in 2019, one SNP was significantly associated with HRP in each of chromosomes 6, 8, 9, and 11, and two in chromosome 7. CGP was significantly associated with five SNPs located in chromosomes 2, 4, 6, and 8 in the 2018 study and ten SNPs in chromosomes 1, 2, 3, 4, 7, 8, 11, and 12 in the 2019 study. The SNPs are located within or linked to putative candidate genes involved in HRP and CGP. This study reports five and ten novel MTAs for HRP and CGP, respectively, while three and five MTAs co-located with previously reported quantitative trait loci for HRP and CGP, respectively. The validation of candidate genes for their roles in determining HRP and CGP is necessary to design functional molecular markers that can be used to effectively develop rice cultivars with desirable grain quality.

Integrating genome-wide association study into genomic selection for the prediction of agronomic traits in rice (Oryza sativa L.)

Accurately identifying varieties with targeted agronomic traits was thought to contribute to genetic selection and accelerate rice breeding progress. Genomic selection (GS) is a promising technique that uses markers covering the whole genome to predict the genomic-estimated breeding values (GEBV), with the ability to select before phenotypes are measured. To choose the appropriate GS models for breeding work, we analyzed the predictability of nine agronomic traits measured from a population of 459 diverse rice varieties. By the comparison of eight representative GS models, we found that the prediction accuracies ranged from 0.407 to 0.896, with reproducing kernel Hilbert space (RKHS) having the highest predictive ability in most traits. Further results demonstrated the predictivity of GS is altered by several factors. Moreover, we assessed the method of integrating genome-wide association study (GWAS) into various GS models. The predictabilities of GS combined peak-associated markers generated from six different GWAS models were significantly different; a recommendation of Mixed Linear Model (MLM)-RKHS was given for the GWAS-GS-integrated prediction. Finally, based on the above result, we experimented with applying the P-values obtained from optimal GWAS models into ridge regression best linear unbiased prediction (rrBLUP), which benefited the low predictive traits in rice.

Effect of milling degree on volatile profiles of cooked rice determined by electronic nose and HS‐SPME‐GC‐MS

AbstractBackground and ObjectivesVolatile components are mainly distributed in the rice bran layer; thus, rice with different milling levels exhibit different volatile profiles, which affects the aroma of rice and cooked rice. Seven diverse rice varieties were investigated to explore the effect of milling degree on volatile profiles of cooked rice, odor activity value (OAV) was applied to identify key aroma compounds, and partial least squares discriminant analysis (PLS‐DA) was applied to determine important marker compounds that may affect aroma.FindingsThe volatile profiles of cooked rice with different milling times were different according to the result of electronic nose. A total of 82 volatiles were identified by headspace solid‐phase microextraction‐gas chromatography‐mass spectrometry. The number and total content of volatile compounds in most samples decreased with increasing milling time. The number of key aroma compounds (OAV > 1) in most samples also showed a decreasing trend with increasing milling time. PLS‐DA model successfully discriminated the differential volatile compounds in cooked rice samples with different milling times. Tridecane, 6‐methyl‐5‐heptene‐2‐one, nonanal, decanal, 2‐butyl‐2‐octenal, pentadecanal, 2,4‐decadienal, anethole, geranylacetone, 1‐dodecanol, 2‐pentadecanone, 2‐methoxy‐4‐vinylphenol, and indole were identified as 13 marker aroma‐active compounds.ConclusionsThe effect of milling degree on the volatile profiles of cooked rice was closely related to the rice varieties. Longer milling time was not in favor of the aroma of cooked rice. Milling degree mainly affected the nutty, citrus, fruity, waxy, herbal, fatty, celery, smoky, and floral aromas of cooked rice.Significance and NoveltyThe study provided important information for understanding the impacts of milling degree on volatile compounds and aroma properties of cooked rice. This is of great significance for advocating moderate processing of rice and regulating the aroma quality of cooked rice.

The role of crop diversity in escape agriculture; rice cultivation among Maroon communities in Suriname

Societal Impact StatementAgricultural techniques are inherently connected to social organization. Under colonialism, broadly understood as foreign powers suppressing (parts of) a local population, escape agriculture offers a way to avoid despotism by producing food and other produce in independent and sustainable ways. Crop diversity plays an important role in escape agriculture, demonstrated here by the variation of rice varieties on Maroon farms in Suriname. Histories of Maroon agricultural practices, and similarly marginalized groups in (formerly) colonized regions, are informative for current interventions in agriculture. Agronomic support to marginalized groups will only be successful when addressing historically grown social disengagement.SummaryRationale: Food is essential for successfulmarronageand produced by means of escape agriculture. Today, communities in the interior of Suriname continue to farm by following practices of escape agriculture. Our study traces the historical development of these farming practices, in particular the extensive cultivation of rice. Our aim is to show that the diversity of rice varieties used in their fields reveals the sophisticated farming techniques and social significance of escape agriculture.Methods: We visited about 60 farm plots upstream the main rivers of Suriname where we interviewed the person in charge about the rice varieties grown in their fields. We asked about origin, names, and characteristics of each rice variety. We also screened historical sources, primary and secondary, as well as anthropological accounts of these communities for historical evidence of rice cultivation and varietal diversity.Results: Plots were farmed primarily by women and contained a broad range of different rice varieties. Naming and origin stories show a clear reference to the escape from plantations and the leading role of women in farming and food security. In some fields, a small patch was reserved for a rice type with very dark grains, used mostly for ritual purposes. Results also show adoption of more recently introduced rice varieties.Conclusion: Rice plays a key role in escape agriculture as practiced by Maroon communities in Suriname. Rice varieties are used as agricultural markers of difference.

Structure and function of rice hybrid genomes reveal genetic basis and optimal performance of heterosis

Exploitation of crop heterosis is crucial for increasing global agriculture production. However, the quantitative genomic analysis of heterosis was lacking, and there is currently no effective prediction tool to optimize cross-combinations. Here 2,839 rice hybrid cultivars and 9,839 segregation individuals were resequenced and phenotyped. Our findings demonstrated that indica–indica hybrid-improving breeding was a process that broadened genetic resources, pyramided breeding-favorable alleles through combinatorial selection and collaboratively improved both parents by eliminating the inferior alleles at negative dominant loci. Furthermore, we revealed that widespread genetic complementarity contributed to indica–japonica intersubspecific heterosis in yield traits, with dominance effect loci making a greater contribution to phenotypic variance than overdominance effect loci. On the basis of the comprehensive dataset, a genomic model applicable to diverse rice varieties was developed and optimized to predict the performance of hybrid combinations. Our data offer a valuable resource for advancing the understanding and facilitating the utilization of heterosis in rice.

Seed-Borne Fungi Associated with Diverse Rice Varieties Cultivated in the Western North Region of Ghana.

Rice is a major staple in the Ghanaian diet. However, its production is constrained by fungal diseases. A survey was conducted in 2018 in three selected districts in the Western North Region of Ghana using a structured questionnaire and face-to-face interaction with 230 farmers to assess their knowledge, perceptions of seed-borne fungal diseases, and management practices. Additionally, fungi associated with farmer's seeds were isolated and identified through the Agar and Blotter tests. Findings indicate that 72.7% of the farmers in the selected districts relied on their saved seeds for planting. Thirteen fungal genera were associated with the rice seed samples collected from the three districts. The Juaboso district had the majority (13) of seed-borne fungi. The seed samples were categorized into various forms of discolouration, and significant differences (P < 0.05) existed among the seed samples for this parameter. The AGRA rice, a farmer-saved seed from Juaboso, had the highest level of seed discolouration (41.96%). Fungi identified to be associated with the dark brown/brown discolouration of rice seeds were Bipolaris spp., Fusarium spp., Macrophomina phaseolina and Aspergillus spp. The only fungus associated with the yellow/pale yellow colour was Bipolaris spp. The fungi Bipolaris spp., Curvularia spp., and Botryodiplodia spp. were associated with the dark spot discolouration. Alternaria spp., and Aspergillus spp. were observed on the greyish white seed discolouration sample. Fungi are associated with rice cultivation and vary according to district and rice variety. A complex of pathogenic and saprophytic fungi therefore infects rice grains both in field and storage conditions.

Mixed cropping with duck co-culture: an agroecological system to improve grain quality and farm profitability.

Previous studies found that mixed cropping combined with duck co-culture (MCDC) system could improve the efficiency of grain production and positively affect soil nutrient contents. However, the effects on grain quality, and profitable income have not been evaluated yet. In this study, a field experiment with four combinations of different rice varieties and ducks was conducted during both the early and late rice growing seasons. The field survey demonstrated that MCDC system significantly decreased the grain appearance of chalky rice rate and the chalkiness degree with an average of 56.82%, and 54.28%, respectively. Leaf SPAD value, photosynthetic rate, and aboveground dry weight were all improved in the MCDC and mixed-cropping systems, relative to the mono-cropping system. The net income obtained from the mono-cropping, mixed cropping (no ducks), and MCDC (with ducks) systems (from grain and ducks' meat) was 581.2 USD ha-1 yr-1 , 1001.8 USD ha-1 yr-1 , and 5242.1 USD ha-1 yr-1 in both growing seasons, respectively. Planting genetically diverse rice varieties and co-culture with ducks increased rice growth rates, productivity and grain quality. The MCDC system would provide more ecological and economic benefits compared with the conventional mono-cropping system. © 2022 Society of Chemical Industry.

Volatiles recovered in novel, diverse, and uncharacterized rice varieties

AbstractBackground and ObjectivesThere is interest in developing value added rice based products with enhanced nutritional value, however organoleptic properties are critical for product acceptance. Five diverse rice varieties, four of which were previously uncharacterized, were evaluated for volatile compounds in whole grain, milled rice, bran, and flour to determine compound differences that may affect flavor.FindingsThis is the first report of gas chromatography mass spectrometry volatiles recovered in Rondo (used for beverages and flour), Cahokia (a high protein brown rice), and two new pigmented bran varieties: Scarlett (red) and Tiara (purple) rice.ConclusionTiara delivered some of the highest levels for five key aroma‐impact volatiles known in rice (heptanal, 2‐AP, 2‐pentyl furan, benzaldehyde, guaiacol), especially regarding those varieties with pigmented bran. Cahokia also delivered a high volatile load of several compounds that indicate possible postharvest shipping/handling oxidation in the paddy rice. Several compounds were identified that are associated with pleasant fragrances in other commodities.Significance and NoveltyFive diverse rice varieties developed for specialty culinary and nutritional markets were characterized for 19 volatile compounds in whole grain and milled rice and their associated bran and flour. These volatiles may impact organoleptic properties influencing utilization of these varieties for future value added product development.

Dynamics of Pyricularia oryzae Population Race Structures from 2003 to 2017 in Jiangsu Province, China

Rice blast, caused by Pyricularia oryzae, is one of the most destructive rice diseases worldwide. It is essential to understand the population structure and race distribution of P. oryzae for the prevention and control of rice blast. This study collected 1584 isolates across Jiangsu province from 2003 to 2017 to determine race diversity, common and dominant race structures, and resistance profiles using eight parameters from the Chinese differential cultivars (CDC) entries. Race diversity analysis indicated that the race diversity of 1584 isolates in Jiangsu province increased from 2003 to 2006 and fluctuated steadily from 2007 to 2017. Common race structure analysis showed that the common race structure of the isolates fluctuated wildly on an annual basis. Moreover, the race ZG1 was the dominant race, suggesting that the most commonly grown rice varieties in Jiangsu are highly adaptive to race ZG1. In addition, due to a higher level (&gt;85%) of resistance to the population of isolates from 2003 to 2017, Tetep may be conformed as the most promising donor of blast resistance for resistance breeding in Jiangsu province. In summary, it is beneficial to control rice blast by continuous monitoring of the population structure and distribution of P. oryzae with the monogenic germplasm entries and by maintaining a diversity of rice varieties.

Molecular Characterization of Different Varieties of rice (Oryza sativa L.) using SSR Markers

The present study was performed to analyze molecular diversity among different varieties of rice using SSR markers, which are effective and reliable tools for this type of analysis. A total of 34 different alleles were generated using 17 SSR primers. Out of these 33 alleles were found to be polymorphic and only one was monomorphic. On average, 2 alleles per primer and 1.94 polymorphic alleles per primer was calculated. In the cluster analysis three varieties KATKIRICE, SONUMRICE and 1010 were found to be diverse from other varieties of rice. These varieties may be used as diverse parents for the future breeding programs for rice improvement. According to Jaccard’s similarity coefficient, the highest genetic diversity was observed between KATKIRICE and CHANDRAHASNI. Both varieties were grouped distantly. Out of 17 primers, the best 10 primers were selected based on polymorphic banding patterns for genetic diversity analysis. These selected 10 primers are sufficient to discriminate the group of rice varieties. These findings not only highlight the capacity of the SSR technique but also help in the selection of diverse rice varieties for conservation and crop improvement.

Molecular, physiological and agronomic assessment of genetic diversity in rice varieties in relation to drought treatment

The study presents the morpho-physiological performance under induced drought condition and molecular marker based genetic variability amongst 13 rice varieties released for cultivation in Uttar Pradesh, India. An attempt was made to identify suitable genotypes for drought affected areas, based on their morpho-physiological characteristics and genetic diversity. The physiological parameters of photosynthesis rate (A), transpiration rate (E), water use efficiency (WUE), along with the yield parameters and genetic diversity by simple sequence repeats marker (SSR) profile were analysed. The rice varieties PR-115 and PR-113 exhibited high water use efficiency, suggesting its possible advantageous response to drought due to low transpiration and high rate of net photosynthesis. The varieties, PR-115 and PR-113 were also found to be best performer in terms of yield under drought conditions. However, the more widely cultivated varieties namely Basmati, IR-36 and IR-20 were found to be intermediate in their response to drought for both yield and physiological parameters. The 19 simple sequence repeats marker (SSR) produces a total of 64 alleles across the 13 varieties, with alleles ranging from 2 to 7 per locus (average 3 alleles). The Polymorphic information content (PIC) value ranged from 0.13 to 0.78 with an average of 0.45 ± 0.19.

Population Structure of Nation-Wide Rice in Thailand

BackgroundThailand is a country with large diversity in rice varieties due to its rich and diverse ecology. In this paper, 300 rice accessions from all across Thailand were sequenced to identify SNP variants allowing for the population structure to be explored.ResultsThe result of inferred population structure from admixture and clustering analysis illustrated strong evidence of substructure in each geographical region. The results of phylogenetic tree, PCA analysis, and machine learning on population identifying SNPs also supported the inferred population structure.ConclusionThe population structure inferred in this study contains five subpopulations that tend to group individuals based on location. So, each subpopulation has unique genetic patterns, agronomic traits, as well as different environmental conditions. This study can serve as a reference point of the nation-wide population structure for supporting breeders and researchers who are interested in Thai rice.

Identification of rice (Oryza sativa L.) genes involved in sheath blight resistance via a genome-wide association study.

SummaryRice sheath blight (RSB) is an economically significant disease affecting rice yield worldwide. Genetic resistance to RSB is associated with multiple minor genes, with each providing a minor phenotypic effect, but the underlying dominant resistance genes remain unknown. A genome‐wide association study (GWAS) of 259 diverse rice varieties, with genotypes based on a single nucleotide polymorphism (SNP) and haplotype, was conducted to assess their sheath blight reactions at three developmental stages (seedlings, tillering and booting). A total of 653 genes were correlated with sheath blight resistance, of which the disease resistance protein RPM1 (OsRSR1) and protein kinase domain‐containing protein (OsRLCK5) were validated by overexpression and knockdown assays. We further found that the coiled‐coil (CC) domain of OsRSR1 (OsRSR1‐CC) and full‐length OsRLCK5 interacted with serine hydroxymethyltransferase 1 (OsSHM1) and glutaredoxin (OsGRX20), respectively. It was found that OsSHM1, which has a role in the reactive oxygen species (ROS) burst, and OsGRX20 enhanced the antioxidation ability of plants. A regulation model of the new RSB resistance though the glutathione (GSH)‐ascorbic acid (AsA) antioxidant system was therefore revealed. These results enhance our understanding of RSB resistance mechanisms and provide better gene resources for the breeding of disease resistance in rice.

Genetic analysis of rice seedling traits related to machine transplanting under different seeding densities

BackgroundDue to the diversity of rice varieties and cropping systems in China, the limitation of seeding density and seedling quality makes it hard to improve machine-transplanted efficiency. Previous studies have shown that indica and japonica varieties varied in machine transplanting efficiency and optimal seeding density. In this study, a RIL population derived from ‘9311’ and ‘Nipponbare’ were performed to explore the seedling traits variations and the genetic mechanism under three seeding densities.ResultsThe parents and RIL population exhibited similar trends as the seeding density increased, including seedling height and first leaf sheath length increases, shoot dry weight and root dry weight decreases. Among the 37 QTLs for six traits detected under the three seeding densities, 12 QTLs were detected in both three seeding densities. Five QTL hotspots identified clustered within genomic regions on chromosomes 1, 2, 4, 6 and 11. Specific QTLs such as qRDW1.1 and qFLSL5.1 were detected under low and high seeding densities, respectively. Detailed analysis the QTL regions identified under specific seeding densities revealed several candidate genes involved in phytohormones signals and abiotic stress responses. Whole-genome additive effects showed that ‘9311’ contributed more loci enhancing trait performances than ‘Nipponbare’, indicating ‘9311’ was more sensitive to the seeding density than ‘Nipponbare’. The prevalence of negative epistasis effects indicated that the complementary two-locus homozygotes may not have marginal advantages over the means of the two parental genotypes.ConclusionsOur results revealed the differences between indica rice and japonica rice seedling traits in response to seeding density. Several QTL hotspots involved in different traits and specific QTLs (such as qRDW1.1 and qFLSL5.1) in diverse seeding densities had been detected. Genome-wide additive and two-locus epistasis suggested a dynamic of the genetic control underlying different seeding densities. It was concluded that novel QTLs, additive and epistasis effects under specific seeding density would provide adequate information for rice seedling improvement during machine transplanting.