Novel Salinity-Tolerant Third-Generation Hybrid Rice Developed via CRISPR/Cas9-Mediated Gene Editing.

Climate change has caused high salinity in many fields, particularly in the mud flats in coastal regions. The resulting salinity has become one of the most significant abiotic stresses affecting the world's rice crop productivity. Developing elite cultivars with novel salinity-tolerance traits is regarded as the most cost-effective and environmentally friendly approach for utilizing saline-alkali land. To develop a highly efficient green strategy and create novel rice germplasms for salt-tolerant rice breeding, this study aimed to improve rice salinity tolerance by combining targeted CRISPR/Cas9-mediated editing of the OsRR22 gene with heterosis utilization. The novel alleles of the genic male-sterility (GMS) and elite restorer line (733Srr22-T1447-1 and HZrr22-T1349-3) produced 110 and 1 bp deletions at the third exon of OsRR22 and conferred a high level of salinity tolerance. Homozygous transgene-free progeny were identified via segregation in the T2 generation, with osrr22 showing similar agronomic performance to wild-type (733S and HZ). Furthermore, these two osrr22 lines were used to develop a new promising third-generation hybrid rice line with novel salinity tolerance. Overall, the results demonstrate that combining CRISPR/Cas9 targeted gene editing with the "third-generation hybrid rice system" approach allows for the efficient development of novel hybrid rice varieties that exhibit a high level of salinity tolerance, thereby ensuring improved cultivar stability and enhanced rice productivity.

Dissecting the genetic basis of heterosis in elite super-hybrid rice.

Y900 is one of the top hybrid rice (Oryza sativa) varieties, with its yield exceeding 15 t·hm-2. To dissect the mechanism of heterosis, we sequenced the male parent line R900 and female parent line Y58S using long-read and Hi-C technology. High-quality reference genomes of 396.41 Mb and 398.24 Mb were obtained for R900 and Y58S, respectively. Genome-wide variations between the parents were systematically identified, including 1,367,758 single-nucleotide polymorphisms, 299,149 insertions/deletions, and 4,757 structural variations. The level of variation between Y58S and R900 was the lowest among the comparisons of Y58S with other rice genomes. More than 75% of genes exhibited variation between the two parents. Compared with other two-line hybrids sharing the same female parent, the portion of Geng/japonica (GJ)-type genetic components from different male parents increased with yield increasing in their corresponding hybrids. Transcriptome analysis revealed that the partial dominance effect was the main genetic effect that constituted the heterosis of Y900. In the hybrid, both alleles from the two parents were expressed, and their expression patterns were dynamically regulated in different tissues. The cis-regulation was dominant for young panicle tissues, while trans-regulation was more common in leaf tissues. Overdominance was surprisingly prevalent in stems and more likely regulated by the trans-regulation mechanism. Additionally, R900 contained many excellent GJ haplotypes, such as NARROW LEAF1, Oryza sativa SQUAMOSA PROMOTER BINDING PROTEIN-LIKE13, and Grain number, plant height, and heading date8, making it a good complement to Y58S. The fine-tuned mechanism of heterosis involves genome-wide variation, GJ introgression, key functional genes, and dynamic gene/allele expression and regulation pattern changes in different tissues and growth stages.

Mutation of Leaf Senescence 1 Encoding a C2H2 Zinc Finger Protein Induces ROS Accumulation and Accelerates Leaf Senescence in Rice.

Premature senescence of leaves causes a reduced yield and quality of rice by affecting plant growth and development. The regulatory mechanisms underlying early leaf senescence are still unclear. The Leaf senescence 1 (LS1) gene encodes a C2H2-type zinc finger protein that is localized to both the nucleus and cytoplasm. In this study, we constructed a rice mutant named leaf senescence 1 (ls1) with a premature leaf senescence phenotype using CRISPR/Cas9-mediated editing of the LS1 gene. The ls1 mutants exhibited premature leaf senescence and reduced chlorophyll content. The expression levels of LS1 were higher in mature or senescent leaves than that in young leaves. The contents of reactive oxygen species (ROS), malondialdehyde (MDA), and superoxide dismutase (SOD) were significantly increased and catalase (CAT) activity was remarkably reduced in the ls1 plants. Furthermore, a faster decrease in pigment content was detected in mutants than that in WT upon induction of complete darkness. TUNEL and staining experiments indicated severe DNA degradation and programmed cell death in the ls1 mutants, which suggested that excessive ROS may lead to leaf senescence and cell death in ls1 plants. Additionally, an RT-qPCR analysis revealed that most senescence-associated and ROS-scavenging genes were upregulated in the ls1 mutants compared with the WT. Collectively, our findings revealed that LS1 might regulate leaf development and function, and that disruption of LS1 function promotes ROS accumulation and accelerates leaf senescence and cell death in rice.

OsPDCD5 negatively regulates plant architecture and grain yield in rice.

Plant architecture is an important agronomic trait that affects crop yield. Here, we report that a gene involved in programmed cell death, OsPDCD5, negatively regulates plant architecture and grain yield in rice. We used the CRISPR/Cas9 system to introduce loss-of-function mutations into OsPDCD5 in 11 rice cultivars. Targeted mutagenesis of OsPDCD5 enhanced grain yield and improved plant architecture by increasing plant height and optimizing panicle type and grain shape. Transcriptome analysis showed that OsPDCD5 knockout affected auxin biosynthesis, as well as the gibberellin and cytokinin biosynthesis and signaling pathways. OsPDCD5 interacted directly with OsAGAP, and OsAGAP positively regulated plant architecture and grain yield in rice. Collectively, these findings demonstrate that OsPDCD5 is a promising candidate gene for breeding super rice cultivars with increased yield potential and superior quality.

Senescence-Specific Expression of RAmy1A Accelerates Non-structural Carbohydrate Remobilization and Grain Filling in Rice (Oryza sativa L.).

Remobilization of pre-anthesis NSCs (non-structural carbohydrates) is significant for effective grain filling in rice (Oryza sativa L.). However, abundant starch particles as an important component of NSCs are still present in the leaf sheath and stem at the late stage of grain filling. There are no studies on how bioengineering techniques can be used to improve the efficiency of NSC remobilization. In this study, RAmy1A was expressed under the senescence-specific promoter of SAG12, which was designed to degrade starch in the leaf sheath and stem during grain filling. RAmy1A mRNA successfully accumulated in the leaf, stem, and sheath of transgenic plants after anthesis. At the same time, the starch and total soluble sugar content in the leaf, stem, and leaf sheath were obviously decreased during the grain-filling period. The photosynthetic rate of transgenic lines was higher than that of the wild types by an average of 4.0 and 9.9%, at 5 and 10 days after flowering, respectively. In addition, the grain-filling rate of transgenic lines was faster than that of the wild types by an average of 26.09%. These results indicate an enhanced transport efficiency of NSCs from source tissues in transgenic rice. Transgenic rice also displayed accelerated leaf senescence, which was hypothesized to contribute to decreased grain weight.

CBCT study of the root and root canal morphology of mandibular second molars in a population in western Guangxi / 口腔疾病防治

Objective@#To observe the root and root canal morphology of mandibular second molars in Western Guangxi by CBCT, to provide a reference for clinical diagnosis and treatment.@*Methods@#In total, 564 patients′ 1 128 mandibular second molars that satisfy the inclusion criteria were analyzed with a planmecaromexis CBCT machine and its own image analysis software. The patients′ gender, age and ethnic differences in the root and canal morphology and the symmetry of the bilateral root and canal were statistically analyzed. @*Results@# Among the 1 128 mandibular second molars, 662 were the Zhuang ethnic group and 384 were the Han ethnic group, and 82 were other ethnic groups; the double root type and C-shaped root type accounted for a relatively high proportion: 73.94% and 24.47%, respectively. The detection rates of the double root type were higher in males than in females (P < 0.05); the detection rates of the C-shaped root type were higher in females than in males (P <0.05); the root type of the teeth was mainly double-rooted in the Zhuang ethnic group (P<0.01). The incidence of type IV in the mesial root of the double root type mandibular second molar was the highest (P < 0.01), and the incidence of type I in the distal root was the highest (P < 0.01). The C-shaped root canal is more continuous at the mouth of the root canal, more downward corresponds to a worse continuity: in three different levels of root canal orifice, root middle and root apex, the root canal orifice is dominated by the C1 type, and both root middle and root apex are mainly C3-type (P < 0.01). The difference in symmetry of bilateral roots and root canals was statistically significant among different gender groups, age groups, and ethnic groups (P < 0.05): there were more males than females, the results in the 18-35-year-old group and the Zhuang ethnic group were higher.@*Conclusion@# The root and root canal morphology of mandibular second molars in western Guangxi people are complex and changeable. The roots are mainly double root type in the Han ethnic group and the Zhuang ethnic group. C-shaped roots are also common. The detection rate of C-shaped roots in the Zhuang ethnic group was higher, and the symmetry rate of bilateral roots and that of bilateral root canals was higher in the Zhuang ethnic group than in the Han ethnic group.

Resequencing of 1,143 indica rice accessions reveals important genetic variations and different heterosis patterns.

Obtaining genetic variation information from indica rice hybrid parents and identification of loci associated with heterosis are important for hybrid rice breeding. Here, we resequence 1,143 indica accessions mostly selected from the parents of superior hybrid rice cultivars of China, identify genetic variations, and perform kinship analysis. We find different hybrid rice crossing patterns between 3- and 2-line superior hybrid lines. By calculating frequencies of parental variation differences (FPVDs), a more direct approach for studying rice heterosis, we identify loci that are linked to heterosis, which include 98 in superior 3-line hybrids and 36 in superior 2-line hybrids. As a proof of concept, we find two accessions harboring a deletion in OsNramp5, a previously reported gene functioning in cadmium absorption, which can be used to mitigate rice grain cadmium levels through hybrid breeding. Resource of indica rice genetic variation reported in this study will be valuable to geneticists and breeders.

The Cds.71 on TMS5 May Act as a Mutation Hotspot to Originate a TGMS Trait in Indica Rice Cultivars.

The gene tms5, which controls thermo-sensitive genic male sterility (TGMS), has been widely used in two-line hybrid rice breeding in China. The tms5 lines have two sources, namely, AnnongS-1 (AnS) and Zhu1S (ZhS) and, interestingly, are commonly subject to an alteration at cds.71. However, whether cds.71 acts as a mutation hotspot is unknown. Herein, another tms5 mutant named T98S (induced from T98B by irradiation) was used to explore this. First, the gene of tms(t) responsible for T98S was fine-mapped on chromosome 2 based on an F2 group of T98S/R893. In T98S, the candidate gene TMS5 (LOC_Os02g12290.1) mutated at cds.71 with a transversion from cytosine (C) to adenine (A), as also observed in AnS and ZhS. Moreover, the entire coding sequence of TMS5 from T98B converted T98S from sterile to fertile by Agrobacterium tumefaciens-mediated transformation, confirming that T98S is controlled by tms5. Next, detection on nearly 40,000 single nucleotide polymorphisms (SNPs) on Rice 56K SNP Array revealed T98S was 99.99% similar to T98B but only 72.84% and 77.47% similar to AnS and ZhS, respectively, demonstrating that T98S originated from T98B rather than from existing tms5 lines. Furthermore, the cds.70 was found to exist as a T/G haplotype, and it was T rather than G that helped to induce a TGMS trait. The T frequency was 67.52% in indica rice but decreased to 1.75% in japonica rice in 2,644 cultivars tested, which partly explains why tms5 mutants were mostly found in indica lines. Our findings provide evidence that cds.71 may act as a mutation hotspot and clues for breeding TGMS lines in a more efficient way.

Improvement of the Rice "Easy-to-Shatter" Trait via CRISPR/Cas9-Mediated Mutagenesis of the qSH1 Gene.

"Easy-to-shatter" trait is a major cause of rice crop yield losses, emphasizing the economic value of developing elite rice cultivars with reduced seed shattering capable of achieving higher yields. In the present study, we describe the development of new indica rice lines that exhibit lower rates of seed shattering following the targeted CRISPR/Cas9-mediated editing of the qSH1 gene. We were able to identify qSH1 mutant T0 transgenic plants, with transgene-free homozygous mutants being obtained via segregation in the T1 generation. We then utilized two T2 transgene-free homozygous lines in order to assess the degree of seed shattering and major agronomic traits of these mutant lines and of wild-type rice plants (HR1128-WT). This approach revealed that qsh1 homozygous mutant lines exhibited significantly reduced seed shattering relative to HR1128-WT without any significant changes in other analyzed agronomic traits. We then used these mutant lines to develop new promising hybrid rice lines with intermediate seed shattering. Overall our results reveal that combining targeted gene editing via CRISPR/Cas9 with heterosis utilization approach can allow for the efficient development of novel promising hybrid rice cultivars that exhibit a intermediate of seed shattering, thereby ensuring better stability and improved rice yields.

Cyclic Digestion and Ligation-Mediated PCR Used for Flanking Sequence Walking.

Ligation-mediated PCR (LM-PCR) is a classical method for isolating flanking sequences; however, it has a common limitation of reduced success rate owing to the circularization or multimerization of target restriction fragments including the known sequence. To address this limitation, we developed a novel LM-PCR method, termed Cyclic Digestion and Ligation-Mediated PCR (CDL-PCR). The novelty of this approach involves the design of new adapters that cannot be digested after being ligated with the restriction fragment, and cyclic digestion and ligation may be manipulated to block the circularization or multimerization of the target restriction fragments. Moreover, to improve the generality and flexibility of CDL-PCR, an adapter precursor sequence was designed, which could be digested to prepare 12 different adapters at low cost. Using this method, the flanking sequences of T-DNA insertions were obtained from transgenic rice and Arabidopsis thaliana. The experimental results demonstrated that CDL-PCR is an efficient and flexible method for identifying the flanking sequences in transgenic rice and Arabidopsis thaliana.

Conversion of a rice CMS maintainer into a photo- or thermo-sensitive genetic male sterile line.

A maintainer line of 3-line hybrid rice commonly presents a certain genetic distance to a 2-line restorer line, but in many cases, 2-line restorer lines present defects upon recovery of the object cytoplasmic male sterile (CMS) line of the maintainer line, which impedes the utilization of their heterosis. Here, we report a strategy and an example of converting a maintainer into a photoperiod/temperature-sensitive genic male sterile (P/TGMS) line with an almost identical genetic background, thus maximizing the heterosis. Firstly, through treatment of maintainer line T98B with 60CO-γ irradiation, we identified the TGMS line T98S, which is sterile at higher temperatures and fertile at lower temperatures. Secondly, the T98S line was proven to be identical to T98B with regard to genetic background via an examination of 48 parental polymorphous SSR markers and exhibited excellent blossom traits similar to those of T98B, with an extensive forenoon flowering rate of 75.92% and a high exertion rate of 64.59%. Thirdly, in a combination test, three out of six hybrids from T98S crossed with 2-line restorer lines showed a yield increase of 6.70-15.69% for 2 consecutive years. These results demonstrated that the strategy can generate a new P/TGMS line with strong general combining ability (converted from a maintainer line), thus helping to increase the genetic diversity of male sterile heterotic groups.

In Vitro Seamless Stack Enzymatic Assembly of DNA Molecules Based on a Strategy Involving Splicing of Restriction Sites.

The standard binary enzymatic assembly, which operates by inserting one DNA fragment into a plasmid, has a higher assembly success rate than the polynary enzymatic assembly, which inserts two or more fragments into the plasmid. However, it often leaves a nucleotide scar at the junction site. When a large DNA molecule is assembled stepwise into a backbone plasmid in a random piecewise manner, the scars will damage the structure of the original DNA sequence in the final assembled plasmids. Here, we propose an in vitro Seamless Stack Enzymatic Assembly (SSEA) method, a novel binary enzymatic assembly method involving a seamless strategy of splicing restriction sites via a stepwise process of multiple enzymatic reactions that does not leave nucleotide scars at the junction sites. We have demonstrated the success and versatility of this method through the assembly of 1) a 4.98 kb DNA molecule in the 5' → 3' direction using BamHI to generate the sticky end of the assembly entrance, 2) a 7.09 kb DNA molecule in the 3' → 5' direction using SmaI to generate the blunt end of the assembly entrance, and 3) an 11.88 kb DNA molecule by changing the assembly entrance.

QTL analysis and dissection of panicle components in rice using advanced backcross populations derived from Oryza Sativa cultivars HR1128 and 'Nipponbare'.

Panicle traits are among the most important agronomic characters which directly relate to yield in rice. Grain number (GN), panicle length (PL), primary branch number (PBN), and secondary branch number (SBN) are the major components of rice panicle structure, and are all controlled by quantitative trait loci (QTLs). In our research, four advanced backcross overlapping populations (BIL152, BIL196a, BIL196b, and BIL196b-156) carrying introgressed segments from chromosome 6 were derived from an indica/japonica cross that used the super-hybrid rice restorer line HR1128 and the international sequenced japonica cultivar 'Nipponbare' as the donor and recurrent parents, respectively. The four panicle traits, GN, PL, PBN, and SBN, were evaluated for QTL effects using the inclusive composite interval mapping (ICIM) method in populations over two years at two sites. Results showed that a total of twelve QTLs for GN, PL, PBN, and SBN were detected on chromosome 6. Based on marker loci physical positions, the QTLs were found to be tightly linked to three important chromosomal intervals described as RM7213 to RM19962, RM20000 to RM20210, and RM412 to RM20595. Three QTLs identified in this study, PL6-5, PBN6-1, and PBN6-2, were found to be novel compared with previous studies. A major QTL (PL6-5) for panicle length was detected in all four populations at two locations, and its position was narrowed down to a 1.3Mb region on chromosome 6. Near isogenic lines (NILs) carrying PL6-5 will be developed for fine mapping of the QTL, and our results will provide referable information for gene excavation of panicle components in rice.

Genetic analysis of an elite super-hybrid rice parent using high-density SNP markers.

BACKGROUND: With an increasing world population and a gradual decline in the amount of arable land, food security remains a global challenge. Continued increases in rice yield will be required to break through the barriers to grain output. In order to transition from hybrid rice to super-hybrid rice, breeding demands cannot be addressed through traditional heterosis. Therefore, it is necessary to incorporate high yield loci from other rice genetic groups and to scientifically utilize intersubspecific heterosis in breeding lines. In this study, 781 lines from a segregating F2 population constructed by crossing the indica variety, "Giant Spike Rice" R1128 as trait donor with the japonica cultivar 'Nipponbare', were re-sequenced using high-throughout multiplexed shotgun genotyping (MSG) technology. In combination with high-density single nucleotide polymorphisms, quantitative trait locus (QTL) mapping and genetic effect analysis were performed for five yield factors (spikelet number per panicle, primary branches per panicle, secondary branches per panicle, plant height, and panicle length) to explore the genetic mechanisms underlying the formation of the giant panicle of R1128. Also, they were preformed to locate new high-yielding rice genetic intervals, providing data for super-high-yielding rice breeding. RESULTS: QTL mapping and genetic effect analysis for five yield factors in the population gave the following results: 49 QTLs for the five yield factors were distributed on 11 of 12 chromosomes. The super-hybrid line R1128 carries multiple major genes for good traits, including Sd1 for plant height, Hd1 and Ehd1 for heading date, Gn1a for spikelet number and IPA1 for ideal plant shape. These genes accounted for 44.3%, 21.9%, 6.2%, 12.9% and 10.6% of the phenotypic variation in the individual traits. Six novel QTLs, qph1-2, qph9-1, qpl12-1, qgn3-1, qgn11-1and qsbn11-1 are reported here for the first time. CONCLUSIONS: High-throughout sequencing technology makes it convenient to study rice genomics and makes the QTL/gene mapping direct, efficient, and more reliable. The genetic regions discovered in this study will be valuable for breeding in rice varieties because of the diverse genetic backgrounds of the rice.

Indication of the expression of transgene in rice plant based on hyperspectral remote sensing technique II--growth monitoring of samples in the contrast experiment.

Since the complication of monitoring and evaluating the problems about the transgenic expression and its impacts on the receptor in the transgenic crop breeding and other relevant evaluated works, the authors in the present work tried to assess the differences of spectral parameters of the transgenic rice in contrast with its parent group quantitatively and qualitatively, fulfilling the growth monitoring of the transgenic samples. The spectral parameters (spectral morphological characteristics and indices) chosen are highly related to internal or external stresses to the receipts, and thus could be applied as indicators of biophysical or biochemical processes changes of plant. By ASD portable field spectroradiometer with high-density probe, fine foliar spectra of 8 groups were obtained. By analyzing spectral angle and continuum removal, the spectral morphological differences and their locations of sample spectra were found which could be as auxiliary priori knowledge for quantitative analysis. By investigating spectral indices of the samples, the quantitative differences of spectra were revealed about foliar chlorophyll a+b and carotenoid content. In this study both the spectral differences between transgenic and parent groups and among transgenic groups were investigated. The results show that hyperspectral technique is promising and a helpful auxiliary tool in the study of monitoring the transgenic crop and other relevant researches. By this technique, quantitative and qualitative results of sample spectra could be provided as prior knowledge, as certain orientation, for laboratory professional advanced transgenic breeding study.

[Detection of the expression of transgene in rice plant based on hyperspectral remote sensing technique].

The present study aims to identify the expression of transgene in given rice plant samples in certain conditions. To avoid external noise caused by temperature change and water-loss, field spectrum was collected with ASD field spectrometer in natural state. The study calculated the mean spectrum of samples as main data set analyzed which were controlled by inner clustering coefficient to ensure data quality. By mean spectrum, the noise from random distinctions in few individual cultivators, which could not be expressed in the class stably, could be weakened even with filtering. With the help of parameters, such as red edge and green peak, this study gave qualitative spectral differences between transgenic samples and their parents. The results show that the transgenes in rice plant were expressed and influenced the samples. Moreover, it was found that the parameters of area are more suitable for describing the differences/changes of the samples, while PRI and SR-PRI are more sensitive to indicate them. Most of the above results could be found on the continuum-removal spectrum curve of samples. These conclusive results demonstrate that hyperspectral remote sensing technique has good prospects and application potential in transgene expression detection and monitoring, especially in plant breeding process.

[Quick testing-technology of transgenic rice with npt- screen marker gene].

By using npt-gene as assistant selection-marker, treating Japonica rice Zhonghua 9 [ZH9 (CK)] and transferred lysozyme gene rice (the donor rice is Japonica rice Zhonghua 9) [ZH9(R)] with antibiotics, we built a system of quickly testing transgenic rice offspring. Detached leaves of ZH9(R) and ZH9(CK) were treated by Kanamycin (0, 400, 450, 500, 550, 600 and 700 mg/L) and G418 (0, 40, 60, 80, 100, 150 and 200 mg/L) with different concentrations. The result show effect of Kanamycin is not evident and G418 is the best antibiotics to test transgenic rice with npt- gene. The data showed that 80 mg/L G418 (treating 4 d) was optimal to test transgenic rice. Further study was done with seeds, young embryos and seedlings by G418 testing: the alive seeds were cultured in the culture dishes which filled with a series of G418 solution with different concentration of 0, 100, 150, 200, 250, 300 and 350 mg/L; in the tissue culture room, the germinating embryos were inoculated in the culture medium (1/2 MS+0.5 mg/L 6-BA+1.5% sucrose) which contains G418 with 0, 150, 200, 250 and 300 mg/L concentration; the aseptic seedlings were inoculated in the the same culture medium (1/2 MS+0.5 mg/L 6-BA+1.5% sucrose) which contains G418 with 0, 100, 150, 200 and 250 mg/L concentration. The conclusions indicated that 300 mg/L (treating 7 d) was the critical concentration to test seeds of transgenic rice; 200 mg/L (treating 10 d) was the critical concentration to test young embryo of transgenic rice; 150 mg/L (treating 12 d) was the critical concentration to test seedlings of transgenic rice. Two primers were designed based on npt- and lysozyme gene sequences. PCR technology confirmed the above detection system. The preliminary results showed npt-was tightly linked with lysozyme gene. Above confirmed critical concentrations were applied to test detached leaves, seeds, young embryos and seedlings of transferred generations. The effect was very obvious. It is convenient, intuitionistic, and exact way that aparting the positive plants from the mixture of transgenic positive and negative plants with G418.