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SUMMARY: Despite extensive studies on cultivated rice, the population structure and genetic diversity of the indica photoperiod- and thermo-sensitive genic male sterility (P/TGMS) lines in China remains unclear. Using 48 simple sequence repeat (SSR) markers, we genotyped a panel of 208 indica P/TGMS lines and confirmed three subgroups, named indica-I, indica-II and indica-III, in indica P/TGMS lines. Further diversity analysis indicated indica-II had the highest genetic diversity. The genetic differentiation between indica-II and indica-III was demonstrated as the largest among the three subgroups. Moreover, indica/japonica component identification was detected that five P/TGMS lines possess indica components less than 0.900. These results improve our knowledge on the genetic background for P/TGMS lines in China and will be beneficial for hybrid rice breeding programs.

Abstract:: The critical node (CN) is an important stage during seed aging, which is related to effective genebank conservation. Previous studies have demonstrated that proteins undergo carbonylated modification at the CN in rice, indicating oxidative damage. However, the levels of reactive carbonyl species (RCS) and the associated scavenging system at the CN are largely unknown. In this study, we optimized methods for the extraction and analysis of RCS from dry rice embryos. In order to acquire seeds at the CN, rice seeds were subjected to natural conditions for 7, 9, 11 and 13 months, and the seed germination rates were reduced to 90%, 82%, 71% and 57%, respectively. We chose the stage with seed germination rate of 82% as the CN according to the rice seed vigor loss curve. The levels of crotonaldehyde and 4-hydroxy-(E)-2-nonenal (HNE) were significantly increased at the CN. In addition, genes encoding carbonyl-scavenging enzyme, including OsALDHs and OsAKRs, were significantly down-regulated at the CN, and reductions in the expression of OsALDH2-2, OsALDH2-5, OsALDH3-4, OsALDH7, OsAKR1 and OsAKR2 in particular could be responsible for RCS accumulation. Thus, the accumulations of crotonaldehyde and HNE and down-regulation of genes encoding carbonyl-scavenging enzyme might be related to an accelerating loss of seed viability at the CN. Key words: carbonyl-scavenging system, reactive carbonyl species, seed aging, crotonaldehyde, critical node, rice storage

Abstract Background Copy number variations (CNVs) can create new genes, change gene dosage, reshape gene structures, and modify elements regulating gene expression. As with all types of genetic variation, CNVs may influence phenotypic variation and gene expression. CNVs are thus considered major sources of genetic variation. Little is known, however, about their contribution to genetic variation in rice. Results To detect CNVs, we used a set of NimbleGen whole-genome comparative genomic hybridization arrays containing 718,256 oligonucleotide probes with a median probe spacing of 500 bp. We compiled a high-resolution map of CNVs in the rice genome, showing 641 CNVs between the genomes of the rice cultivars 'Nipponbare' (from O. sativa ssp. japonica) and 'Guang-lu-ai 4' (from O. sativa ssp. indica). The CNVs identified vary in size from 1.1 kb to 180.7 kb, and encompass approximately 7.6 Mb of the rice genome. The largest regions showing copy gain and loss are of 37.4 kb on chromosome 4, and 180.7 kb on chromosome 8. In addition, 85 DNA segments were identified, including some genic sequences. Contracted genes greatly outnumbered duplicated ones. Many of the contracted genes corresponded to either the same genes or genes involved in the same biological processes; this was also the case for genes involved in disease and defense. Conclusion We detected CNVs in rice by array-based comparative genomic hybridization. These CNVs contain known genes. Further discussion of CNVs is important, as they are linked to variation among rice varieties, and are likely to contribute to subspecific characteristics.

Genomic prediction (GP) uses single nucleotide polymorphisms (SNPs) to establish associations between markers and phenotypes. Selection of early individuals by genomic estimated breeding value shortens the generation interval and speeds up the breeding process. Recently, methods based on deep learning (DL) have gained great attention in the field of GP. In this study, we explore the application of Transformer-based structures to GP and develop a novel deep-learning model named GPformer. GPformer obtains a global view by gleaning beneficial information from all relevant SNPs regardless of the physical distance between SNPs. Comprehensive experimental results on five different crop datasets show that GPformer outperforms ridge regression-based linear unbiased prediction (RR-BLUP), support vector regression (SVR), light gradient boosting machine (LightGBM) and deep neural network genomic prediction (DNNGP) in terms of mean absolute error, Pearson's correlation coefficient and the proposed metric consistent index. Furthermore, we introduce a knowledge-guided module (KGM) to extract genome-wide association studies-based information, which is fused into GPformer as prior knowledge. KGM is very flexible and can be plugged into any DL network. Ablation studies of KGM on three datasets illustrate the efficiency of KGM adequately. Moreover, GPformer is robust and stable to hyperparameters and can generalize to each phenotype of every dataset, which is suitable for practical application scenarios. [ABSTRACT FROM AUTHOR]

Leaf length and width are two of the most important components of rice (Oryza sativa L.) plant architecture and directly contribute to yield. The genetic effects of leaf length and width are controlled by quantitative trait loci (QTLs). In this study, a double haploid (DH) population derived from a cross of O. sativa subsp. japonica cultivar 'Maybelle' and subsp. indica cultivar 'Baiyeqiu' ('BYQ') was used to determine genetic effects on leaf length and width. Analysis of phenotypic effects indicated that all of the detected traits exhibited continuous, transgressive distributions in the DH population. Correlation analysis revealed a strong association between the two adjacent leaves for the same trait. A total of 25 QTLs within 17 genetic intervals distributed on chromosomes 1, 2, 3, 4, 5, 6, 8, and 12 were detected for rice leaf length and width, with likelihood of odds values that ranged from 2.75 to 10.62. Among these loci, two major QTLs, which were located in the intervals RM3262-RM3452 and RM16432-RM7472, played very important roles in regulating leaf length and width, respectively. Diversity analysis of the two major QTLs revealed that the genetic interval RM16432-RM7472 should be an optimal target for rice breeding programs, and may inspire new research efforts. Key words: rice, QTL, leaf length and width, genetic diversity. La longueur et la largeur de la feuille sont deux des composantes les plus importantes de l'architecture du plant de riz (Oryza sativa L.) qui contribuent directement au rendement de la recolte. Les effets de la genetique sur la longueur et la largeur de la feuille sont controles par des locus quantitatifs (QTL). Dans cette etude, une population d'individus doubles haploides (DH) issus d'un croisement entre le cultivar O. sativa subsp. japonica 'Maybelle' et le cultivar O. sativa subsp. indica 'Baiyeqiu' ('BYQ') a ete utilisee pour dissequer les effets de la genetique sur la longueur et la largeur de la feuille. L'analyse des phenotypes indiquait que tous les caracteres detectes presentaient des distributions continues transgressives dans la population DH. L'analyse de correlation revelait une forte association entre deux feuilles adjacentes pour le meme caractere. Un total de 25 QTL a l'interieur de 17 intervalles genetiques distribues sur les chromosomes 1, 2, 3, 4, 5, 6, 8 et 12 a ete detecte pour la longueur et la largeur de la feuille de riz, avec des lod scores allant de 2,75 a 10,62. Parmi ces locus, deux QTL majeurs localises dans les intervalles RM3262-RM3452 et RM16432-RM7472 jouaient un role tres important dans la regulation de la longueur et la largeur de la feuille, respectivement. L'analyse de diversite des deux QTL majeurs a revele que l'intervalle genetique RM16432-RM7472 devrait etre cible dans les programmes de croisement de riz, et faire l'objet de nouvelles initiatives de recherche. [Traduit par la Redaction] Mots-cles: riz, QTL, longueur et largeur de la feuille, diversite genetique., Introduction As a staple food, rice (Oryza sativa L.) is the main food source for more than half of the world's population (Delseny et al. 2001). Improving grain yield, which [...]

Aim: To evaluate the efficacy and safety of intravesical electrical stimulation (IVES) performed with a novel device in patients with underactive bladder (UAB). Patients and Methods: This was a multicentre, prospective, single‐blind, randomized controlled clinical trial of patients with UAB in China. Eligible patients were randomly assigned in a 1:1 ratio to receive conventional IVES (n = 38) or IVES with an open circuit (n = 38). The primary efficacy measure was change from baseline in post‐void residual urine volume (PVR) after 4 weeks of treatment. Secondary efficacy measures included changes in maximum urinary flow rate (Qmax), bladder voiding efficiency (BVE), number of 24‐h clean intermittent catheterization (CIC) procedures, and Patient Perception of Bladder Condition‐Scale (PPBC‐S) and American Urological Association Symptom Index Quality of Life (AUA‐SI‐QoL) scores from baseline after 4 weeks of treatment. Adverse events (AEs) were monitored throughout the trial. Results: In the full analysis set (FAS), the mean (sd) PVR changes in the trial and control groups at 4 weeks were −97.1 (107.5) mL and −10.5 (86.7) mL, respectively (P < 0.01). Similar results were obtained in the per‐protocol set (PPS): −102.9 (100.0) mL vs 0.7 (82.5) mL (P < 0.01). In the FAS and PPS, Qmax improved significantly at 4 weeks (P = 0.04 and P = 0.03). In the FAS and PPS, BVE was significantly improved at 4 weeks in the two groups (P < 0.01 and P < 0.01), whereas no significant differences in the number of 24‐h CIC procedures, PPBC‐S score or AUA‐SI‐QoL score were observed between the groups. Six possible therapy‐related AEs occurred in six patients (four in the trial group and two in the control group; P = 0.67), all of which were urinary tract infections. No severe AEs were reported. Conclusions: The results of this clinical study strongly demonstrate that UAB patients benefit from this novel IVES device. More research is needed to validate the clinical utility of this device. [ABSTRACT FROM AUTHOR]