Identification and Regulation of Hypoxia-Tolerant and Germination-Related Genes in Rice.

In direct seeding, hypoxia is a major stress faced by rice plants. Therefore, dissecting the response mechanism of rice to hypoxia stress and the molecular regulatory network is critical to the development of hypoxia-tolerant rice varieties and direct seeding of rice. This review summarizes the morphological, physiological, and ecological changes in rice under hypoxia stress, the discovery of hypoxia-tolerant and germination-related genes/QTLs, and the latest research on candidate genes, and explores the linkage of hypoxia tolerance genes and their distribution in indica and japonica rice through population variance analysis and haplotype network analysis. Among the candidate genes, OsMAP1 is a typical gene located on the MAPK cascade reaction for indica-japonica divergence; MHZ6 is involved in both the MAPK signaling and phytohormone transduction pathway. MHZ6 has three major haplotypes and one rare haplotype, with Hap3 being dominated by indica rice varieties, and promotes internode elongation in deep-water rice by activating the SD1 gene. OsAmy3D and Adh1 have similar indica-japonica varietal differentiation, and are mainly present in indica varieties. There are three high-frequency haplotypes of OsTPP7, namely Hap1 (n = 1109), Hap2 (n = 1349), and Hap3 (n = 217); Hap2 is more frequent in japonica, and the genetic background of OsTPP7 was derived from the japonica rice subpopulation. Further artificial selection, natural domestication, and other means to identify more resistance mechanisms of this gene may facilitate future research to breed superior rice cultivars. Finally, this study discusses the application of rice hypoxia-tolerant germplasm in future breeding research.

Analysis of the Rice Raffinose Synthase (OsRS) Gene Family and Haplotype Diversity.

Based on the genome information of rice (Nipponbare), this study screened and identified six raffinose synthase (RS) genes and analyzed their physical and chemical properties, phylogenetic relationship, conserved domains, promoter cis-acting elements, and the function and genetic diversity of the gene-CDS-haplotype (gcHap). The results showed that these genes play key roles in abiotic stress response, such as OsRS5, whose expression in leaves changed significantly under high salt, drought, ABA, and MeJA treatments. In addition, the OsRS genes showed significant genetic variations in different rice populations. The main gcHaps of most OsRS loci had significant effects on key agronomic traits, and the frequency of these alleles varied significantly among different rice populations and subspecies. These findings provide direction for studying the RS gene family in other crops.

Genome-wide identification of rice CXE gene family and mining of alleles for potential application in rice improvement.

Carboxylesterases (CXE, EC 3.1.1.1), a class of hydrolases with an α/ß folding domain, play important roles in plant growth and development and stress response. Here, we identified 32, 63, 41, and 45 CXE genes in Oryza sativa Japonica (Nipponbare), Oryza sativa Indica (93-11), Oryza sativa Indica (Xian-1B1 var.IR64), and Oryza sativa Japonica (Geng-sbtrp var.ChaoMeo), respectively. Then, we analyzed the chromosomal location, physical and chemical properties, subcellular localization, collinearity, and selection pressure of CXE genes in four rice varieties. We also analyzed the functional interaction network, cis-regulatory elements, evolutionary relationship, and protein tertiary structure, and performed gene expression profiling and qPCR verification under abiotic stress, as well as diversity analysis of 3010 gene-CDS-haplotype (gcHap) rice samples, aiming to understand the potential function of the 32 OsCXE genes. Our results indicated that fragment replication is the main reason for amplification of the CXE gene family in rice, and the gene family has undergone strong purification selection. OsCXE3.1, OsCXE3.2, OsCXE3.3, OsCXE5.1, and OsCXE7.3 may be used to improve the tolerance of rice to abiotic stress. OsCXE play important roles in rice population differentiation and improvement, and the major gcHaps at most OsCXE locus are significantly associated with yield traits. Therefore, natural variations of most OsCXE locus have great potential value for improvement of rice productivity.

Identification of the CNGC Gene Family in Rice and Mining of Alleles for Application in Rice Improvement.

Cyclic nucleotide-gated ion channel (CNGC) gene regulation plays important roles in plant immune and abiotic stress response. Here, we identified 16 CNGC genes in rice (Oryza sativa). Then, we analyzed their chromosomal location, physicochemical properties, subcellular localization, gene functional interaction network, cis-acting elements, phylogenetic relationships, collinearity, expression in tissues under normal conditions and abiotic stresses, and geng-cds-haplotype (gcHap) diversity in 3010 gcHaps. As a result, OsCNGC3 (Os06g0527300) was identified as a gene different from previous report, and OsCNGC genes were found to play important roles in rice population differentiation and rice improvement. Our results revealed their very strong differentiation between subspecies and populations, important roles in response to abiotic stresses, as well as strong genetic bottleneck effects and artificial selection of gcHap diversity in the modern breeding process of Xian (indica) and Geng (japonica) populations. The results also suggested that natural variations in most rice CNGC loci are potentially valuable for improving rice productivity and tolerance to abiotic stresses. The favorable alleles at the CNGC loci should be explored to facilitate their application in future rice improvement.

Genome-Wide Association Study of Rice Grain Shape and Chalkiness in a Worldwide Collection of Xian Accessions.

Rice (Oryza sativa L.) appearance quality, which is mainly defined by grain shape and chalkiness, is an important target in rice breeding. In this study, we first re-sequenced 137 indica accessions and then conducted a genome-wide association study (GWAS) for six agronomic traits with the 2,998,034 derived single nucleotide polymorphisms (SNPs) by using the best linear unbiased prediction (BLUP) values for each trait. The results revealed that 195 SNPs had significant associations with the six agronomic traits. Based on the genome-wide linkage disequilibrium (LD) blocks, candidate genes for the target traits were detected within 100 kb upstream and downstream of the relevant SNP loci. Results indicate that six quantitative trait loci (QTLs) significantly associated with six traits (qTGW4.1, qTGW4.2, qGL4.1, qGL12.1, qGL12.2, qGW2.1, qGW4.1, qGW6.1, qGW8.1, qGW8.2, qGW9.1, qGW11.1, qGLWR2.1, qGLWR2.2, qGLWR4.2, qPGWC5.1 and qDEC6.1) were identified for haplotype analysis. Among these QTLs, two (qTGW4.2 and qGW6.1), were overlapped with FLO19 and OsbZIP47, respectively, and the remaining four were novel QTLs. These candidate genes were further validated by haplotype block construction.

[Change of NK Cell Number in Peripheral Blood of Patients with Mantle Cell Lymphoma and Its Clinical Significance].

OBJECTIVE: To investigate the clinical significance of peripheral blood NK cell number change in patients with mantle cell lymphoma. METHODS: Eight-four patients with mantle cell lymphoma treated in our hospital from November 2003 to November 2011 were studied, the venous blood was collected from all patients and detected with flow cytometry. The age, sex, pathologic type, B-symptoms, clinical stage, absolute NK count(ANKC), hemoglobin(Hb), lactate dehydrogenase(LDH) and ß2-microglobulin(ß2-MG) levels, bone marrow involuement(BMI) and the international prognostic index of mantle cell lymphoma(MIPI) were recorded. All patients were followed up. RESULTS: There were no significant differences in ANKC among different age, sex, B symptom, Ann Arbor stages, Hb, LDH and ß2-MG levels, BMI and MIPI of patients with MCL(P>0.05). The sensitivity and specificity of ANKC were 76.6% and 73.8%, respectively. The optimal throshold of ANKC was 0.10×109/L and AUC was 0.798(95% CI: 0.689-0.902)(P<0.01). The 3 year-PFS rate in patients with ANKC≥0.10×109/L was higher than that in patients with ANKC<0.10×109/L(68.2% vs 32.10%)(P<0.01). The 3 year-OS rate in patients with ANKC≥0.10×109/L was significantly higher than that in patients with ANKC<0.10×109/L (85.1% vs 43.8%)(P<0.01). Multivariate analysis showed that the independent predictors of PFS and OS in patients with MCL were ANKC and MIPI(P<0.05). CONCLUSION: The ANKC in peripheral blood has an important value for judging the prognosis of patients with MCL and can be used as an important index to judge the disease status of patients with MCL.

A bioconjugated design for amino acid-modified mesoporous silicas as effective adsorbents for toxic chemicals.

A general synthetic method for functionalization of mesoporous silica with amino acid has been developed. The carboxylic acid functionalized SBA-15 was conjugated with l-phenylalanine (Phe) and l-tryptophan (Trp) to obtain nontoxic amino acid-conjugated functionalized mesoporous silica materials. The materials were used as adsorbents for the removal of the herbicide Paraquat (PQ) and its analog, ethyl viologen dibromide (EVB) from aqueous solutions. In comparison to the commercially available activated carbon adsorbents, the silica-based adsorbents prepared in this study exhibited relatively higher PQ removal efficiency in aqueous solutions at room temperature and pH 7.0. The silica-based adsorbents, pendant with amino acid moieties exhibited greater adsorption capacities toward PQ and EVB than the analogs but without the amino acid moiety, suggesting that there is a benefit for the enhanced π-π interaction between the aromatic groups of the conjugated amino acid moieties and the adsorbate. This bioconjugated method developed here provides a promising new tool to synthesize new materials for detoxification of herbicides in clinical trials.