Substitution mapping of QTLs controlling seed dormancy using single segment substitution lines derived from multiple cultivated rice donors in seven cropping seasons.

KEY MESSAGE: A permanent advanced population containing 388 SSSLs was used for genetic analysis of seed dormancy; 25 QTLs including eight stable, six major and five new were identified. Seed dormancy (SD) is not only a complex biological phenomenon, but also a key practical problem in agricultural production closely related with pre-harvest sprouting (PHS). However, the genetic mechanisms of SD remain elusive. Here, we report the genetic dissection of SD in rice using 388 single segment substitution lines (SSSLs) derived from 16 donor parents. Continuous variation and positive correlations in seed germination percentages were observed in seven seasons. Genetic analysis revealed the narrow sense heritability in different seasons varied from 31.4 to 82.2% with an average value of 56.8%. In addition, 49 SSSLs exhibited significant difference to recipient parent HJX74 on SD in at least two seasons, and 12 of them were stably identified with putative QTLs in all of their corresponding cropping seasons. Based on substitution mapping, a total of 25 dormancy QTLs were detected on 11 chromosomes except the chromosome 5 with an interval length of 1.1 to 31.3 cM. The additive effects of these QTLs changed from -0.31 to -0.13, and the additive effect contributions ranged from 16.7 to 41.4%. Six QTLs, qSD3-2, qSD4-1, qSD7-1, qSD7-2, qSD7-3 and qSD11-2, showed large additive effect contributions (≥30%). Five QTLs, qSD3-3, qSD7-1, qSD7-4, qSD9-1 and qSD10-1, may represent novel ones. Furthermore, linkage and recombinant analysis delimited qSD7-1 to a locus 1.5 cM away from marker Oi2 and a 355-kb fragment flanked by RM1134 and Ui159, respectively. Taken together, this work conducts a comprehensive genetic dissection of SD and will provide more selections for breeding elite PHS-resistant rice varieties.

Community dynamics of arbuscular mycorrhizal fungi in high-input and intensively irrigated rice cultivation systems.

Application of a mycorrhizal inoculum could be one way to increase the yield of rice plants and reduce the application of fertilizer. We therefore studied arbuscular mycorrhizal fungi (AMF) in the roots of wetland rice (Oryza sativa L.) collected at the seedling, tillering, heading, and ripening stages in four paddy wetlands that had been under a high-input and intensively irrigated rice cultivation system for more than 20 years. It was found that AMF colonization was mainly established in the heading and ripening stages. The AMF community structure was characterized in rhizosphere soils and roots from two of the studied paddy wetlands. A fragment covering the partial small subunit (SSU), the whole internal transcribed spacer (ITS), and the partial large subunit (LSU) rRNA operon regions of AMF was amplified, cloned, and sequenced from roots and soils. A total of 639 AMF sequences were obtained, and these were finally assigned to 16 phylotypes based on a phylogenetic analysis, including 12 phylotypes from Glomeraceae, one phylotype from Claroideoglomeraceae, two phylotypes from Paraglomeraceae, and one unidentified phylotype. The AMF phylotype compositions in the soils were similar between the two surveyed sites, but there was a clear discrepancy between the communities obtained from root and soil. The relatively high number of AMF phylotypes at the surveyed sites suggests that the conditions are suitable for some species of AMF and that they may have an important function in conventional rice cultivation systems. The species richness of root-colonizing AMF increased with the growth of rice, and future studies should consider the developmental stages of this crop in the exploration of AMF function in paddy wetlands.

Detection and characterization of epistasis between QTLs on plant height in rice using single segment substitution lines.

Hua-jing-xian 74 and its 12 single segment substitution lines (SSSLs) in rice were used as crossing parents to construct a half diallel crossing population. A total number of 91 materials were grown under three planting densities. By analysis of average plant height (PH) over all environments 10 SSSLs were detected with significant additives and 6 SSSLs with significant dominances. These SSSLs were further tested under different densities respectively, indicating that some of single locus effects were sensitive to densities and the conditions under the density of 16.7 cm × 16.7 cm maybe inhibited the expressing of these PH QTLs. Qualitative and quantitative analyses of each four participating genotypes indicated that digenic interactions among these QTLs were prevalent. Of 66 tested interactions, about 42.4% were epistatic (P < 5%). Although some QTLs hadn't single locus effects, they were possible to form digenic interactions. A significant finding was that the detected epistases were mostly negative. Additionally, these epistases were also found being sensitive to planting densities, the conditions under the density of 10 cm × 16.7 cm perhaps promoted the expressing of epistatic interactions among PH QTLs.

Silicon Dioxide Nanoparticles-Based Amelioration of Cd Toxicity by Regulating Antioxidant Activity and Photosynthetic Parameters in a Line Developed from Wild Rice.

An extremely hazardous heavy metal called cadmium (Cd) is frequently released into the soil, causing a considerable reduction in plant productivity and safety. In an effort to reduce the toxicity of Cd, silicon dioxide nanoparticles were chosen because of their capability to react with metallic substances and decrease their adsorption. This study examines the processes that underlie the stress caused by Cd and how SiO2NPs may be able to lessen it through modifying antioxidant defense, oxidative stress, and photosynthesis. A 100 µM concentration of Cd stress was applied to the hydroponically grown wild rice line, and 50 µM of silicon dioxide nanoparticles (SiO2NPs) was given. The study depicted that when 50 µM SiO2NPs was applied, there was a significant decrease in Cd uptake in both roots and shoots by 30.2% and 15.8% under 100 µM Cd stress, respectively. The results illustrated that Cd had a detrimental effect on carotenoid and chlorophyll levels and other growth-related traits. Additionally, it increased the levels of ROS in plants, which reduced the antioxidant capability by 18.8% (SOD), 39.2% (POD), 32.6% (CAT), and 25.01% (GR) in wild rice. Nevertheless, the addition of silicon dioxide nanoparticles reduced oxidative damage and the overall amount of Cd uptake, which lessened the toxicity caused by Cd. Reduced formation of reactive oxygen species (ROS), including MDA and H2O2, and an increased defense system of antioxidants in the plants provided evidence for this. Moreover, SiO2NPs enhanced the Cd resistance, upregulated the genes related to antioxidants and silicon, and reduced metal transporters' expression levels.

Hybrid Rice Production: A Worldwide Review of Floral Traits and Breeding Technology, with Special Emphasis on China.

Rice is an important diet source for the majority of the world's population, and meeting the growing need for rice requires significant improvements at the production level. Hybrid rice production has been a significant breakthrough in this regard, and the floral traits play a major role in the development of hybrid rice. In grass species, rice has structural units called florets and spikelets and contains different floret organs such as lemma, palea, style length, anther, and stigma exsertion. These floral organs are crucial in enhancing rice production and uplifting rice cultivation at a broader level. Recent advances in breeding techniques also provide knowledge about different floral organs and how they can be improved by using biotechnological techniques for better production of rice. The rice flower holds immense significance and is the primary focal point for researchers working on rice molecular biology. Furthermore, the unique genetics of rice play a significant role in maintaining its floral structure. However, to improve rice varieties further, we need to identify the genomic regions through mapping of QTLs (quantitative trait loci) or by using GWAS (genome-wide association studies) and their validation should be performed by developing user-friendly molecular markers, such as Kompetitive allele-specific PCR (KASP). This review outlines the role of different floral traits and the benefits of using modern biotechnological approaches to improve hybrid rice production. It focuses on how floral traits are interrelated and their possible contribution to hybrid rice production to satisfy future rice demand. We discuss the significance of different floral traits, techniques, and breeding approaches in hybrid rice production. We provide a historical perspective of hybrid rice production and its current status and outline the challenges and opportunities in this field.

Machine learning-based nomogram to predict poor response to overnight orthokeratology in Chinese myopic children: A multicentre, retrospective study.

PURPOSE: To develop and validate an effective nomogram for predicting poor response to orthokeratology. METHODS: Myopic children (aged 8-15 years) treated with orthokeratology between February 2018 and January 2022 were screened in four hospitals of different tiers (i.e. municipal and provincial) in China. Potential predictors included 32 baseline clinical variables. Nomogram for the outcome (1-year axial elongation ≥0.20 mm: poor response; <0.20 mm: good response) was computed from a logistic regression model with the least absolute shrinkage and selection operator. The data from the First Affiliated Hospital of Chengdu Medical College were randomly assigned (7:3) to the training and validation cohorts. An external cohort from three independent multicentre was used for the model test. Model performance was assessed by discrimination (the area under curve, AUC), calibration (calibration plots) and utility (decision curve analysis). RESULTS: Between January 2022 and March 2023, 1183 eligible subjects were screened from the First Affiliated Hospital of Chengdu Medical College, then randomly divided into training (n = 831) and validation (n = 352) cohorts. A total of 405 eligible subjects were screened in the external cohort. Predictors included in the nomogram were baseline age, spherical equivalent, axial length, pupil diameter, surface asymmetry index and parental myopia (p < 0.05). This nomogram demonstrated excellent calibration, clinical net benefit and discrimination, with the AUC of 0.871 (95% CI 0.847-0.894), 0.863 (0.826-0.901) and 0.817 (0.777-0.857) in the training, validation and external cohorts, respectively. An online calculator was generated for free access (http://39.96.75.172:8182/#/nomogram). CONCLUSION: The nomogram provides accurate individual prediction of poor response to overnight orthokeratology in Chinese myopic children.

Substitution Mapping and Allelic Variations of the Domestication Genes from O. rufipogon and O. nivara.

BACKGROUND: Domestication from wild rice species to cultivated rice is a key milestone, which involved changes of many specific traits and the variations of the genetic systems. Among the AA-genome wild rice species, O. rufipogon and O. nivara, have many favorable genes and thought to be progenitors of O. sativa. RESULTS: In the present study, by using O. rufipogon and O. nivara as donors, the single segment substitution lines (SSSLs) have been developed in the background of the elite indica cultivar, HJX74. In the SSSLs population, 11 genes for 5 domestication traits, including tiller angle, spreading panicle, awn, seed shattering, and red pericarp, were identified and mapped on 5 chromosomes through substitution mapping. Herein, allelic variations of 7 genes were found through sequence alignment with the known genes, that is, TA7-RUF was allelic to PROG1, TA8-RUF was allelic to TIG1, SPR4-NIV was allelic to OsLG1, AN4-RUF was allelic to An-1, SH4-NIV was allelic to SH4, and both RC7-RUF and RC7-NIV were allelic to Rc. Meanwhile, 4 genes, TA11-NIV, SPR3-NIV, AN3-NIV, and AN4-NIV, were considered as the novel genes identified in these SSSLs, because of none known genes for the related domestication traits found in the chromosomal locations of them. CONCLUSION: The results indicated that the SSSLs would be precious germplasm resources for gene mining and utilization from wild rice species, and it laid the foundation for further analyses of the novel domestication genes to better understand the genetic basis in regulating the traits variation during domestication.

Substitution Mapping of the Major Quantitative Trait Loci Controlling Stigma Exsertion Rate from Oryza glumaepatula.

BACKGROUND: Stigma exsertion rate (SER) is a key determinant for the outcrossing ability of male sterility lines (MSLs) in hybrid rice seed production. In the process of domestication, the outcrossing ability of cultivated rice varieties decreased, while that of wild Oryza species kept strong. Here, we detected the quantitative trait loci (QTLs) controlling SER using a set of single-segment substitution lines (SSSLs) derived from O. glumaepatula, a wild Oryza species. RESULTS: Seven QTLs for SER were located on 5 chromosomes. qSER-1a and qSER-1b were located on chromosome 1. qSER-3a and qSER-3b were mapped on chromosome 3, and qSER-3b was further located at an estimated interval of 898.8 kb by secondary substitution mapping. qSER-5, qSER-9 and qSER-10 were identified on chromosomes 5, 9 and 10, respectively, and qSER-9 was delimited to an estimated region of 551.9 kb by secondary substitution mapping. The additive effects of the 7 QTLs ranged from 10.6% to 14.8%, which were higher than those of most loci for SER reported previously. CONCLUSIONS: qSER-1a and qSER-1b are novel loci for SER on chromosome 1. All of the 7 QTLs have major effects on SER. The major QTLs of SER will help to develop MSLs with strong outcrossing ability.

Crossability barriers in the interspecific hybridization between Oryza sativa and O. meyeriana.

Oryza meyeriana Baill (GG genome) is a precious germplasm in the tertiary gene pool of cultivated rice (AA genome), and possesses important traits such as resistance and tolerance to biotic and abiotic stress. However, interspecific crossability barrier, a critical bottleneck restricting genes transfer from O. meyeriana to cultivars has led to no hybrids through conventional reproduction. Therefore, the reasons underlying incrossability were investigated in the present report. The results showed that: (i) at 3-7 d after pollination (DAP), many hybrid embryos degenerated at the earlier globular-shaped stage, and could not develop into the later pear-shaped stage. Meanwhile, free endosperm nuclei started to degenerate at 1 DAP, and cellular endosperm could not form at 3 DAP, leading to nutrition starvation for young embryo development; (ii) at 11-13 DAP, almost all hybrid ovaries aborted. Even though 72.22% of hybrid young embryos were produced in the interspecific hybridization between O. sativa and O. meyeriana, young embryos were not able to further develop into hybrid plantlets via culturing in vitro. The main reason for the incrossability was hybrid embryo inviability, presenting as embryo development stagnation and degeneration since 3 DAP. Some possible approaches to overcome the crossability barriers in the interspecific hybridization between O. sativa and O. meyeriana are discussed.

[Study of association of platelet endothelial cell adhesion molecule-1 gene polymorphism with acute myocardial infarction].

OBJECTIVE: To investigate the association of single nucleotide polymorphism (SNP) and its haplotypes of platelet endothelial cell adhesion molecule-1 (PECAM-1) gene with susceptibility to acute myocardial infarction (AMI), and to analyze association the serum levels and genotypes of PECAM-1 with AMI. METHODS: Three SNPs of PECAM-1 gene Leu125Val, Asn563Ser and Gly670Arg were analyzed in 180 patients with AMI and 200 age and sex matched controls, using a polymerase chain reaction-restriction fragment length polymorphism (PCR-RFLP) strategy, and the serum level of PECAM-1 was determined by enzyme linked immunosorbent assay (ELISA). Frequency of haplotypes and linkage disequilibrium of PECAM-1 gene in different groups were analyzed by SHEsis programs. RESULTS: The distributions of PECAM-1 gene Asn563Ser and Gly670Arg polymorphisms were not different between AMI and control group (P>0.05), but the PECAM-1 gene Leu125Val polymorphism was significantly different (P<0.05). The relative risk suffered from AMI of Val allele was 1.480 folds of the Leu allele carriers [odds ratio (OR)=1.480, 95% confidence interval (CI): 1.111-1.972, P=0.007]; the serum level of PECAM-1 Val allele carriers was significantly higher than that of noncarriers (P<0.01). With the results of the genotyping analyses, PECAM-1 gene Leu125Val, Asn563Ser and Gly670Arg polymorphisms showed strong linkage disequilibrium, and the Val-Ser-Arg haplotype was associated with a significantly increased risk of AMI as compared with the controls (OR=1.489, 95%CI: 1.118-1.984, P=0.006). CONCLUSION: PECAM-1 gene Leu125Val polymorphism and its Val-Ser-Arg haplotype are associated with AMI, Val allele is an important genetic susceptibility gene for AMI. The PECAM-1 Val allele carriers may have a higher risk by enhancing the PECAM-1 expression in the pathogenesis of AMI.

Identification of S23 causing both interspecific hybrid male sterility and environment-conditioned male sterility in rice.

BACKGROUND: Oryza glumaepatula represents an important resource of genetic diversity that can be used to improve rice production. However, hybrid sterility severely restricts gene flow between Oryza species, and hinders the utilization of distant heterosis in hybrid rice breeding. RESULTS: In order to fully exploit the beneficial genes of O. glumaepatula and facilitate the conservation of these gene resources, a set of chromosome single-segment substitution lines (SSSLs) was developed using an indica variety HJX74 as the recurrent parent and an accession of O. glumaepatula as the donor parent. During the process of SSSLs development, S23, a locus conferring hybrid male sterility between O. sativa and O. glumaepatula, was identified and fine mapped to 11.54 kb and 7.08 kb genomic region in O. sativa and O. glumaepatula, respectively, encoding three and two candidate ORFs, respectively. qRT-PCR and sequence analysis excluded one common ORF as the candidate gene. In addition, hybrid male sterility caused by S23 was environment-sensitive, and could be observed only in natural short-day (NSD). CONCLUSION: Identification and candidate genes analysis of S23 in this study provides a valuable example to study the crosstalk between interspecific F1 hybrid male sterility and environment-conditioned male sterility in rice, facilitates reserving and utilizing favorable genes or alleles of wild Oryza species, and allows for a more efficient exploitation of distant heterosis in hybrid rice breeding.

Overcoming inter-subspecific hybrid sterility in rice by developing indica-compatible japonica lines.

Rice (Oryza sativa L.) is an important staple crop. The exploitation of the great heterosis that exists in the inter-subspecific crosses between the indica and japonica rice has long been considered as a promising way to increase the yield potential. However, the male and female sterility frequently occurred in the inter-subspecific hybrids hampered the utilization of the heterosis. Here we report that the inter-subspecific hybrid sterility in rice is mainly affected by the genes at Sb, Sc, Sd and Se loci for F1 male sterility and the gene at S5 locus for F1 female sterility. The indica-compatible japonica lines (ICJLs) developed by pyramiding the indica allele (S-i) at Sb, Sc, Sd and Se loci and the neutral allele (S-n) at S5 locus in japonica genetic background through marker-assisted selection are compatible with indica rice in pollen fertility and in spikelet fertility. These results showed a great promise of overcoming the inter-subspecific hybrid sterility and exploiting the heterosis by developing ICJLs.

Characterization of epistatic interaction of QTLs LH8 and EH3 controlling heading date in rice.

Heading date is a critical trait for adaptation of rice to different cultivation areas and cropping seasons. We evaluated the heading dates of 1,123 chromosome segments substitution lines (CSSLs) in the genetic background of an elite rice variety Huajingxian74 (HJX74). A CSSL with the substituted segments from Zihui100 exhibited late heading under both natural long-day (NLD) and natural short-day (NSD) conditions, and the late heading phenotype was controlled by two novel epistatic loci on chromosome 8 and chromosome 3, respectively, termed LH8 and EH3. The function of EH3 was dependent on the LH8 genotype through epistatic interaction between EH3(Zihui100) and LH8(Zihui100) alleles. Genetic and molecular characterization revealed LH8 encodes a CCAAT-box-binding transcription factor with Heading date1 (Hd1)-binding activity and may delay flowering by repressing the expression of Early heading date1 (Ehd1). Our work provides a solid foundation for further study on gene interaction in heading date and has application in breeding rice with greater adaptability.