Fine Mapping of Five Grain Size QTLs Which Affect Grain Yield and Quality in Rice.

Grain size is a quantitative trait with a complex genetic mechanism, characterized by the combination of grain length (GL), grain width (GW), length to width ration (LWR), and grain thickness (GT). In this study, we conducted quantitative trait loci (QTL) analysis to investigate the genetic basis of grain size using BC1F2 and BC1F2:3 populations derived from two indica lines, Guangzhan 63-4S (GZ63-4S) and TGMS29 (core germplasm number W240). A total of twenty-four QTLs for grain size were identified, among which, three QTLs (qGW1, qGW7, and qGW12) controlling GL and two QTLs (qGW5 and qGL9) controlling GW were validated and subsequently fine mapped to regions ranging from 128 kb to 624 kb. Scanning electron microscopic (SEM) analysis and expression analysis revealed that qGW7 influences cell expansion, while qGL9 affects cell division. Conversely, qGW1, qGW5, and qGW12 promoted both cell division and expansion. Furthermore, negative correlations were observed between grain yield and quality for both qGW7 and qGW12. Nevertheless, qGW5 exhibited the potential to enhance quality without compromising yield. Importantly, we identified two promising QTLs, qGW1 and qGL9, which simultaneously improved both grain yield and quality. In summary, our results laid the foundation for cloning these five QTLs and provided valuable resources for breeding rice varieties with high yield and superior quality.

QTL detection for rice grain storage protein content and genetic effect verifications.

Rice grain quality is a multifarious attribute mainly governed by multiple nutritional factors. Grain protein is the central component of rice grain nutrition dominantly affecting eating-cooking qualities. Grain protein content is quantitatively influenced by its protein fractions. Genetic quantification of five protein fractions-albumins, globulins, prolamins, glutelin, and grain protein content-were evaluated by exploiting two BC3F2 mapping populations, derived from Kongyu131/TKM9 (population-I) and Kongyu131/Bg94-1 (population-II), which were grown in a single environment. Correlation studies among protein fractions and grain protein content were thoroughly investigated. A genetic linkage map was developed by using 146 single sequence repeat (SSR) markers in population-I and 167 markers in population-II. In total, 40 QTLs were delineated for five traits in both populations. Approximately 22 QTLs were dissected in population-I, derived from Kongyu131/TKM9, seven QTLs for albumin content, four QTLs for globulin content, three QTLs for prolamin content, four QTLs for glutelin content, and four QTLs for grain protein content. In total, 18 QTLs were detected in population-II, derived from Kongyu131/Bg94-1, five QTLs for albumin content, three QTLs for globulin content, four QTLs for prolamin content, two QTLs for glutelin content, and four QTLs for grain protein content. Three QTLs, qAlb7.1, Alb7.2, and qGPC7.2, derived from population-II (Kongyu131/Bg94-1) for albumin and grain protein content were successfully validated in the near isogenic line (NIL) populations. The localized chromosomal locus of the validated QTLs could be helpful for fine mapping via map-based cloning to discover underlying candidate genes. The functional insights of the underlying candidate gene would furnish novel perceptivity for the foundation of rice grain protein content and trigger the development of nutritionally important rice cultivars by combining marker-assisted selection (MAS) breeding. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-023-01436-7.

FLOURY ENDOSPERM19 encoding a class I glutamine amidotransferase affects grain quality in rice.

As a staple food for more than half of the world's population, the importance of rice is self-evident. Compared with ordinary rice, rice cultivars with superior eating quality and appearance quality are more popular with consumers due to their unique taste and ornamental value, even if their price is much higher. Appearance quality and CEQ (cooking and eating quality) are two very important aspects in the evaluation of rice quality. Here, we performed a genome-wide association study on floury endosperm in a diverse panel of 533 cultivated rice accessions. We identified a batch of potential floury genes and prioritize one (LOC_Os03g48060) for functional analyses. Two floury outer endosperm mutants (flo19-1 and flo19-2) were generated through editing LOC_Os03g48060 (named as FLO19 in this study), which encodes a class I glutamine amidotransferase. The different performances of the two mutants in various storage substances directly led to completely different changes in CEQ. The mutation of FLO19 gene caused the damage of carbon and nitrogen metabolism in rice, which affected the normal growth and development of rice, including decreased plant height and yield loss by decreased grain filling rate. Through haplotype analysis, we identified a haplotype of FLO19 that can improve both CEQ and appearance quality of rice, Hap2, which provides a selection target for rice quality improvement, especially for high-yield indica rice varieties. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-021-01226-z.

Total ankle replacement with INBONE-II prosthesis: A short-to- medium-term follow-up study in China.

BACKGROUND: Total ankle replacement (TAR) is a viable option for the treatment of end-stage ankle arthritis. In China, the INBONE-II implant is the only total ankle prosthesis approved since 2016. The purpose of this study is to report a large sample of findings for the TAR with INBONE-II prosthesis. METHODS: A total of 64 patients with end-stage ankle arthritis, who underwent primary TAR using INBONE-II by the same surgeon from 2016 to 2019, at a single institution were included in this retrospective, single-center study. Clinical data, radiographic findings, survival rate, and complications were recorded and assessed pre-operatively and at the most recent follow-up. RESULTS: A total of 64 patients were available for follow-up at least 2 years after surgery; the mean follow-up duration for clinical outcomes was 37.9 months (24-59 months), and for radiographic findings was 22.8 months (12-59 months). There were significant improvements ( P  < 0.01) in the American Orthopedic Foot and Ankle Society hindfoot scale, the visual analog scale for pain, and the Short Form-36. There were statistically significant differences between pre-operative and post-operative comparisons of the talar tilt angle (TT) and the tibial lateral surface angle (TLS) in the radiographic findings (TT from 4.7 ±â€Š4.3° to 1.3 ±â€Š1.3°, TLS from 80.4 ±â€Š7.7° to 87.4 ±â€Š2.3°, P  < 0.01). There was no statistically significant difference in improvement of the tibial anterior surface angle ( P  = 0.14). Ten complications (all low grade) were recorded according to the Glazebrook classification system. The survivorship of the prosthesis was 100% (64/64). CONCLUSION: Patients who underwent TAR with INBONE-II prosthesis demonstrated significant improvements in all measures of pain and function as well as in radiographic findings. High survival and a low incidence of complications were observed in this study.

A Natural Language Processing Tool to Extract Quantitative Smoking Status from Clinical Narratives.

This study presents a natural language processing (NLP) tool to extract quantitative smoking information (e.g., Pack-Year, Quit Year, Smoking Year, and Pack per Day) from clinical notes and standardized them into Pack-Year unit. We annotated a corpus of 200 clinical notes from patients who had low-dose CT imaging procedures for lung cancer screening and developed an NLP system using a two-layer rule-engine structure. We divided the 200 notes into a training set and a test set and developed the NLP system only using the training set. The experimental results on the test set showed that our NLP system achieved the best F1 scores of 0.963 and 0.946 for lenient and strict evaluation, respectively.

A Natural Language Processing Tool to Extract Quantitative Smoking Status from Clinical Narratives.

This study presents a natural language processing (NLP) tool to extract quantitative smoking information (e.g., Pack-Year, Quit Year, Smoking Year, and Pack per Day) from clinical notes and standardized them into Pack-Year unit. We annotated a corpus of 200 clinical notes from patients who had low-dose CT imaging procedures for lung cancer screening and developed an NLP system using a two-layer rule-engine structure. We divided the 200 notes into a training set and a test set and developed the NLP system only using the training set. The experimental results on the test set showed that our NLP system achieved the best F1 scores of 0.963 and 0.946 for lenient and strict evaluation, respectively. NOTE: Accepted as a presentation at the 2020 IEEE International Conference on Healthcare Informatics (ICHI) Workshop on Health Natural Language Processing (HealthNLP 2020). https://ohnlp.github.io/HealthNLP2020/healthnlp2020# .

Genome-Wide Association Studies Reveal the Genetic Basis of Fertility Restoration of CMS-WA and CMS-HL in xian/indica and aus Accessions of Rice (Oryza sativa L.).

BACKGROUND: Wild-abortive cytoplasmic male sterility (CMS-WA) and Honglian CMS (CMS-HL) are the two main CMS types utilized in production of three-line hybrid rice in xian/indica (XI) rice. Dissection of the genetic basis of fertility restoration of CMS-WA and CMS-HL in the core germplasm population would provide valuable gene and material resources for development of three-line hybrid combinations. RESULTS: In this study, two F1 populations with CMS-WA and CMS-HL background respectively were developed using 337 XI and aus accessions being paternal parents. Genome-wide association studies on three fertility-related traits of the two populations for two consecutive years revealed that both fertility restoration of CMS-WA and CMS-HL were controlled by a major locus and several minor loci respectively. The major locus for fertility restoration of CMS-WA was co-located with Rf4, and that for fertility restoration of CMS-HL was co-located with Rf5, which are cloned major restorer of fertility (Rf) genes. Furthermore, haplotype analysis of Rf4, Rf5 and Rf6, the three cloned major Rf genes, were conducted using the 337 paternal accessions. Four main haplotypes were identified for Rf4, and displayed different subgroup preferences. Two main haplotypes were identified for Rf5, and the functional type was carried by the majority of paternal accessions. In addition, eight haplotypes were identified for Rf6. CONCLUSIONS: Haplotype analysis of three Rf genes, Rf4, Rf5 and Rf6, could provide valuable sequence variations that can be utilized in marker-aided selection of corresponding genes in rice breeding. Meanwhile, fertility evaluation of 337 accessions under the background of CMS could provide material resources for development of maintainer lines and restorers.

Microplastic pollution in the rivers of the Tibet Plateau.

The Tibet Plateau, the so-called Third Pole of the world, is home to the headstreams of many great rivers. The levels of microplastic pollution in those rivers, however, are unknown. In this study, surface water and sediment samples were collected from six sampling sites along five different rivers. The surface water and sediment samples were collected with a large flow sampler and a stainless steel shovel, respectively. The abundance of microplastics ranged from 483 to 967 items/m3 in the surface water and from 50 to 195 items/kg in the sediment. A large amount of small, fibrous, transparent microplastics were found in this study. Five types of microplastics with different chemical compositions were identified using micro-Raman spectroscopy: polyethylene terephthalate (PET), polyethylene (PE), polypropylene (PP), polystyrene (PS), and polyamide (PA). These results demonstrate that rivers in the Tibet Plateau have been contaminated by microplastics, not only in developed areas with intense human activity but also in remote areas, where microplastic pollution requires further attention.