BSA-Seq for the Identification of Major Genes for EPN in Rice.

Improving rice yield is one of the most important food issues internationally. It is an undeniable goal of rice breeding, and the effective panicle number (EPN) is a key factor determining rice yield. Increasing the EPN in rice is a major way to increase rice yield. Currently, the main quantitative trait locus (QTL) for EPN in rice is limited, and there is also limited research on the gene for EPN in rice. Therefore, the excavation and analysis of major genes related to EPN in rice is of great significance for molecular breeding and yield improvement. This study used japonica rice varieties Dongfu 114 and Longyang 11 to construct an F5 population consisting of 309 individual plants. Two extreme phenotypic pools were constructed by identifying the EPN of the population, and QTL-seq analysis was performed to obtain three main effective QTL intervals for EPN. This analysis also helped to screen out 34 candidate genes. Then, EPN time expression pattern analysis was performed on these 34 genes to screen out six candidate genes with higher expression levels. Using a 3K database to perform haplotype analysis on these six genes, we selected haplotypes with significant differences in EPN. Finally, five candidate genes related to EPN were obtained.

Joint QTL Mapping and Transcriptome Sequencing Analysis Reveal Candidate Genes for Salinity Tolerance in Oryza sativa L. ssp. Japonica Seedlings.

Salinity stress is one of the major abiotic stresses affecting crop growth and production. Rice is an important food crop in the world, but also a salt-sensitive crop, and the rice seedling stage is the most sensitive to salt stress, which directly affects the final yield formation. In this study, two RIL populations derived from the crosses of CD (salt-sensitive)/WD (salt-tolerant) and KY131 (salt-sensitive)/XBJZ (salt-tolerant) were used as experimental materials, and the score of salinity toxicity (SST), the relative shoot length (RSL), the relative shoot fresh weight (RSFW), and the relative shoot dry weight (RSDW) were used for evaluating the degree of tolerance under salt stress in different lines. The genetic linkage map containing 978 and 527 bin markers were constructed in two RIL populations. A total of 14 QTLs were detected on chromosomes 1, 2, 3, 4, 7, 9, 10, 11, and 12. Among them, qSST12-1, qSST12-2, and qRSL12 were co-localized in a 140-kb overlap interval on chromosome 12, which containing 16 candidate genes. Furthermore, transcriptome sequencing and qRT-PCR were analyzed in CD and WD under normal and 120 mM NaCl stress. LOC_Os12g29330, LOC_Os12g29350, LOC_Os12g29390, and LOC_Os12g29400 were significantly induced by salt stress in both CD and WD. Sequence analysis showed that LOC_Os12g29400 in the salt-sensitive parents CD and KY131 was consistent with the reference sequence (Nipponbare), whereas the salt-tolerant parents WD and XBJZ differed significantly from the reference sequence both in the promoter and exon regions. The salt-tolerant phenotype was identified by using two T3 homozygous mutant plants of LOC_Os12g29400; the results showed that the score of salinity toxicity (SST) of the mutant plants (CR-3 and CR-5) was significantly lower than that of the wild type, and the seedling survival rate (SSR) was significantly higher than that of the wild type, which indicated that LOC_Os12g29400 could negatively regulate the salinity tolerance of rice at the seedling stage. The results lay a foundation for the analysis of the molecular mechanism of rice salinity tolerance and the cultivation of new rice varieties.

Plastidic pyruvate dehydrogenase complex E1 component subunit Alpha1 is involved in galactolipid biosynthesis required for amyloplast development in rice.

Starch accounts for over 80% of the total dry weight in cereal endosperm and determines the kernel texture and nutritional quality. Amyloplasts, terminally differentiated plastids, are responsible for starch biosynthesis and storage. We screened a series of rice mutants with floury endosperm to clarify the mechanism underlying amyloplast development and starch synthesis. We identified the floury endosperm19 (flo19) mutant which shows opaque of the interior endosperm. Abnormal compound starch grains (SGs) were present in the endosperm cells of the mutant. Molecular cloning revealed that the FLO19 allele encodes a plastid-localized pyruvate dehydrogenase complex E1 component subunit α1 (ptPDC-E1-α1) that is expressed in all rice tissues. In vivo enzyme assays demonstrated that the flo19 mutant showed decreased activity of the plastidic pyruvate dehydrogenase complex. In addition, the amounts of monogalactosyldiacylglycerol (MGDG) and digalactosyldiacylglycerol (DGDG) were much lower in the developing flo19 mutant endosperm, suggesting that FLO19 participates in fatty acid supply for galactolipid biosynthesis in amyloplasts. FLO19 overexpression significantly increased seed size and weight, but did not affect other important agronomic traits, such as panicle length, tiller number and seed setting rate. An analysis of single nucleotide polymorphism data from a panel of rice accessions identified that the pFLO19L haplotype was positively associated with grain length, implying a potential application in rice breeding. In summary, our study demonstrates that FLO19 is involved in galactolipid biosynthesis which is essential for amyloplast development and starch biosynthesis in rice.

OsWRKY115 on qCT7 links to cold tolerance in rice.

KEY MESSAGE: qCT7, a novel QTL for increasing seedling cold tolerance in rice, was fine-mapped to a 70.9-kb region on chromosome 7, and key OsWRKY115 was identified in transgenic plants. Cold stress caused by underground cold-water irrigation seriously limits rice productivity. We systemically measured the cold-responsive traits of 2,570 F2 individuals derived from two widely cultivated rice cultivars, Kong-Yu-131 and Dong-Nong-422, to identify the major genomic regions associated with cold tolerance. A novel major QTL, qCT7, was mapped on chromosome 7 associated with the cold tolerance and survival, using whole-genome re-sequencing with bulked segregant analysis. Local QTL linkage analysis with F2 and fine mapping with recombinant plant revealed a 70.9-kb core region on qCT7 encoding 13 protein-coding genes. Only the LOC_Os07g27670 expression level encoding the OsWRKY115 transcription factor on the locus was specifically induced by cold stress in the cold-tolerant cultivar. Moreover, haplotype analysis and the KASP8 marker indicated that OsWRKY115 was significantly associated with cold tolerance. Overexpression and knockout of OsWRKY115 significantly affected cold tolerance in seedlings. Our experiments identified OsWRKY115 as a novel regulatory gene associated with cold response in rice, and the Kong-Yu-131 allele with specific cold-induced expression may be an important molecular variant.

Identification and Functional Analysis of the Caffeic Acid O-Methyltransferase (COMT) Gene Family in Rice (Oryza sativa L.).

Caffeic acid O-methyltransferase (COMT) is one of the core enzymes involved in lignin synthesis. However, there is no systematic study on the rice COMT gene family. We identified 33 COMT genes containing the methyltransferase-2 domain in the rice genome using bioinformatic methods and divided them into Group I (a and b) and Group II. Motifs, conserved domains, gene structure and SNPs density are related to the classification of OsCOMTs. The tandem phenomenon plays a key role in the expansion of OsCOMTs. The expression levels of fourteen and thirteen OsCOMTs increased or decreased under salt stress and drought stress, respectively. OsCOMTs showed higher expression levels in the stem. The lignin content of rice was measured in five stages; combined with the expression analysis of OsCOMTs and multiple sequence alignment, we found that OsCOMT8, OsCOMT9 and OsCOMT15 play a key role in the synthesis of lignin. Targeted miRNAs and gene ontology annotation revealed that OsCOMTs were involved in abiotic stress responses. Our study contributes to the analysis of the biological function of OsCOMTs, which may provide information for future rice breeding and editing of the rice genome.

The trihelix transcription factor OsGTγ-2 is involved adaption to salt stress in rice.

KEY MESSAGE: OsGTγ-2, a trihelix transcription factor, is a positive regulator of rice responses to salt stress by regulating the expression of ion transporters. Salinity stress seriously restricts rice growth and yield. Trihelix transcription factors (GT factors) specifically bind to GT elements and play a diverse role in plant morphological development and responses to abiotic stresses. In our previous study, we found that the GT-1 element (GAAAAA) is a key element in the salinity-induced OsRAV2 promoter. Here, we identified a rice OsGTγ family member, OsGTγ-2, which directly interacted with the GT-1 element in the OsRAV2 promoter. OsGTγ-2 specifically targeted the nucleus, was mainly expressed in roots, sheathes, stems and seeds, and was induced by salinity, osmotic and oxidative stresses and abscisic acid (ABA). The seed germination rate, seedling growth and survival rate under salinity stress was improved in OsGTγ-2 overexpressing lines (PZmUbi::OsGTγ-2). In contrast, CRISPR/Cas9-mediated OsGTγ-2 knockout lines (osgtγ-2) showed salt-hypersensitive phenotypes. In response to salt stress, different Na+ and K+ acclamation patterns were observed in PZmUbi::OsGTγ-2 lines and osgtγ-2 plants were observed. The molecular mechanism of OsGTγ-2 in rice salt adaptation was also investigated. Several major genes responsible for ion transporting, such as the OsHKT2; 1, OsHKT1; 3 and OsNHX1 were transcriptionally regulated by OsGTγ-2. A subsequent yeast one-hybrid assay and EMSA indicated that OsGTγ-2 directly interacted with the promoters of OsHKT2; 1, OsNHX1 and OsHKT1; 3. Taken together, these results suggest that OsGTγ-2 is an important positive regulator involved in rice responses to salt stress and suggest a potential role for OsGTγ-2 in regulating salinity adaptation in rice.

Genome-Wide Association Analysis Unravels New Quantitative Trait Loci (QTLs) for Eight Lodging Resistance Constituent Traits in Rice (Oryza sativa L.).

Lodging poses a significant challenge to rice yield, prompting the need to identify elite alleles for lodging resistance traits to improve cultivated rice varieties. In this study, a natural population of 518 rice accessions was examined to identify elite alleles associated with plant height (PH), stem diameter (SD), stem anti-thrust (AT/S), and various internode lengths (first (FirINL), second (SecINL), third (ThirINL), fourth (ForINL), and fifth (FifINL) internode lengths). A total of 262 SSR markers linked to these traits were uncovered through association mapping in two environmental conditions. Phenotypic evaluations revealed striking differences among cultivars, and genetic diversity assessments showed polymorphisms across the accessions. Favorable alleles were identified for PH, SD, AT/S, and one to five internode lengths, with specific alleles displaying considerable effects. Noteworthy alleles include RM6811-160 bp on chromosome 6 (which reduces PH) and RM161-145 bp on chromosome 5 (which increases SD). The study identified a total of 42 novel QTLs. Specifically, seven QTLs were identified for PH, four for SD, five for AT/S, five for FirINL, six for SecINL, five for ThirINL, six for ForINL, and four for FifINL. QTLs qAT/S-2, qPH2.1, qForINL2.1, and qFifINL exhibited the most significant phenotypic variance (PVE) of 3.99% for the stem lodging trait. AT/S, PH, ForINL, and FifINL had additive effects of 5.31 kPa, 5.42 cm, 4.27 cm, and 4.27 cm, respectively, offering insights into eight distinct cross-combinations for enhancing each trait. This research suggests the potential for crossbreeding superior parents based on stacked alleles, promising improved rice cultivars with enhanced lodging resistance to meet market demands.

Self-assembled nanomaterials for ferroptosis-based cancer theranostics.

Most ferroptosis nanomedicines based on organic or inorganic carriers have difficulties in further clinical translation due to their serious side effects and complicated preparation. Self-assembled nanomedicines can reduce the biological toxicity caused by additional chemical modifications and excipients, offering better biocompatibility and safety. Ferroptosis therapy is an iron-associated programmed cell death dependent on lipid peroxidation with efficient tumor selectivity and biosafety. Therefore, the application of self-assembled nanomedicines with good biosafety in the ferroptosis treatment of tumors has attracted extensive attention. In this review, recent advances in the field of ferroptosis-based self-assembled nanomaterials for cancer therapy are presented, with emphasis on how these nanomaterial components interact and their distinct mechanisms for inducing ferroptosis in tumor cells, including iron metabolism, amino acid metabolism and CoQ/FSP1, as well as their respective advantages and challenges. This review would therefore help the spectrum of advanced and novice researchers interested in this area to quickly zoom in on the essential information and glean some thought-provoking ideas to advance this subfield in cancer nanomedicine.

Disturbing cytoskeleton by engineered nanomaterials for enhanced cancer therapeutics.

Cytoskeleton plays a significant role in the shape change, migration, movement, adhesion, cytokinesis, and phagocytosis of tumor cells. In clinical practice, some anti-cancer drugs achieve cytoskeletal therapeutic effects by acting on different cytoskeletal protein components. However, in the absence of cell-specific targeting, unnecessary cytoskeletal recombination in organisms would be disastrous, which would also bring about severe side effects during anticancer process. Nanomedicine have been proven to be superior to some small molecule drugs in cancer treatment due to better stability and targeting, and lower side effects. Therefore, this review summarized the recent developments of various nanomaterials disturbing cytoskeleton for enhanced cancer therapeutics, including carbon, noble metals, metal oxides, black phosphorus, calcium, silicon, polymers, peptides, and metal-organic frameworks, etc. A comprehensive analysis of the characteristics of cytoskeleton therapy as well as the future prospects and challenges towards clinical application were also discussed. We aim to drive on this emerging topic through refreshing perspectives based on our own work and what we have also learnt from others. This review will help researchers quickly understand relevant cytoskeletal therapeutic information to further advance the development of cancer nanomedicine.

Identification of candidate genes for salinity tolerance in Japonica rice at the seedling stage based on genome-wide association study and linkage mapping.

Background: Salinity tolerance plays a vital role in rice cultivation because the strength of salinity tolerance at the seedling stage directly affects seedling survival and final crop yield in saline soils. Here, we combined a genome-wide association study (GWAS) and linkage mapping to analyze the candidate intervals for salinity tolerance in Japonica rice at the seedling stage. Results: We used the Na+ concentration in shoots (SNC), K+ concentration in shoots (SKC), Na+/K+ ratio in shoots (SNK), and seedling survival rate (SSR) as indices to assess the salinity tolerance at the seedling stage in rice. The GWAS identified the lead SNP (Chr12_20864157), associated with an SNK, which the linkage mapping detected as being in qSK12. A 195-kb region on chromosome 12 was selected based on the overlapping regions in the GWAS and the linkage mapping. Based on haplotype analysis, qRT-PCR, and sequence analysis, we obtained LOC_Os12g34450 as a candidate gene. Conclusion: Based on these results, LOC_Os12g34450 was identified as a candidate gene contributing to salinity tolerance in Japonica rice. This study provides valuable guidance for plant breeders to improve the response of Japonica rice to salt stress.

Physiological and transcriptional response to heat stress in heat-resistant and heat-sensitive maize (Zea mays L.) inbred lines at seedling stage.

To understand the molecular and physiological mechanism underlying the heat stress in maize, transcriptional and physiological response to heat stress in the heat-resistant Huangzaosi (HZS) and heat-sensitive Lv-9-Kuan (L9K) inbred lines at seedling stage were analyzed and compared at seedling stage. Our results indicated that MDA content of the two inbred lines increased significantly under heat stress; the values of MDA in L9K was significantly higher than that in HZS. The level of SOD, CAT, and POD enzyme activities in HZS was higher than those in L9K for both the heat-treated group and controls. The values of Fv/Fm, qP, and ФPSII reduced by heat stress in L9K were higher than the respective values in HZS. RNA-seq data showed that heat stress induced more heat stress-related genes in HZS (257 heat stress-related genes) than in L9K (224 heat stress-related genes). GO and KEGG enrichment analyses indicated that HZS and L9K changed their physiological and biochemical mechanisms in response to heat stress through different molecular mechanisms. Weighted Gene Co-expression Network Analysis showed that HZS might obtain stronger heat resistance than L9K through a unique transcriptional regulatory network. Our findings provide insights into the molecular networks that mediate the tolerance of maize heat stress and also help us to mine key heat stress-related genes.