Grain shape is an important agronomic trait affecting rice yield and quality, and its development is regulated by the three-dimensional morphology of grain (grain length, grain width, grain thickness). Identification and cloning of grain shape regulatory genes can enrich the molecular mechanism of rice grain development regulation, and provide theoretical basis and genetic resources for high-yield molecular design breeding of rice.

A stable inherited grain type mutant sgd13 (small grain and dwarf 13) was screened from the mutant library of Nanjing 9108 induced by ethyl methane sulfonate (EMS). The grain morphology, 1000-grain weight, seed setting rate, yield per plant, plant height, panicle length and other phenotypes of the mutants were statistically analyzed. Paraffin sections and scanning electron microscopy were used to analyze the changes in the number and size of glume and stem cells. The genetic analysis of sgd13 and Nanjing 9108 was carried out. The F₂ population constructed by sgd13 and Nanjing 9108 was used to locate the gene by BSA-seq technology. The SWISS-MODEL website was used to predict the three-dimensional structure of wild-type and mutant proteins.

The grains of sgd13 were significantly smaller and narrower, the grain length decreased by 19.98%, and the grain width decreased by 7.81%. Compared with WT, the plant height, spike length and yield per plant of sgd13 were significantly reduced. There was no significant difference in the number of internodes between sgd13 and WT, but the lengths of the first, second, third and sixth internodes were shorter. Cytological analysis showed that the glume and stem cells of sgd13 became smaller and less, indicating that sgd13 may affect organ development by regulating cell division and expansion. Genetic analysis confirmed that the trait was controlled by a single recessive nuclear gene. The candidate gene was mapped to LOC_Os01g52550 by BSA-seq, which encodes an ATP-binding cassette (ABC) transporter. The ABC transporter contains two typical core domains: A highly conserved nucleotide binding domain (NBD) and a less conserved transmembrane domain (TMD). In the sgd13 mutant, a single base substitution (T→A) occurred in the exon region of the gene, which was located in the NBD domain. This single base substitution directly causes the encoded amino acid to change from glutamic acid (E) to aspartic acid (D). Due to the differences in side chain structure and chemical properties between glutamic acid and aspartic acid, this change is likely to affect the spatial structure of SGD13 protein, thereby interfering with its normal function, and ultimately leading to a unique phenotype of the mutant sgd13. Genetic complementation experiments showed that the introduction of wild-type LOC_Os01g52550 could restore the grain shape of sgd13 to the wild-type level.

The sgd13 mutant phenotype was controlled by a single recessive nuclear gene, which was caused by the LOC_Os01g52550 mutation. The T→A mutation in the exon region of the gene causes the glutamic acid in the NBD domain to become aspartic acid, which affects the three-dimensional structure of the protein.

Finding new loci and genes related to rice chlorophyll content, and providing new theoretical basis for the research on the genetic mechanism of rice chlorophyll content.

A recombinant inbred line (RIL) population containing 186 lines was constructed by crossing the japonica rice TD70 and the indica rice Kasalath with obvious difference in the chlorophyll content of the flag leaf. The two parents and RIL population were re-sequenced to construct a high-density genetic linkage map with 12 328 recombination Bin markers. The RILs and two parents were planted in fields at the Jiangsu Academy of Agricultural Sciences, in Nanjing in 2011 and 2020. The contents of chlorophyll of flag leaves were directly measured using the chlorophyll meter SPAD-502 on the 3^rd day after heading. QTLs that control the chlorophyll content of the flag leaf at the heading stage of rice were detected by IciMappingv3.4 software with inclusive compound interval mapping method. The photosynthesis parameters of 20 SPAD extreme strains in the RIL population were measured with a portable photosynthesis system.

19 QTLs controlling chlorophyll content of flag leaves were detected on 9 chromosomes except Chr.8, Chr.9 and Chr.10 in two years. The phenotype variation explained (PVE) of single QTL ranged from 3.09% to 13.13%, LOD value ranged from 2.74 to 14.08. After comparing the physical positions, 10 QTLs were found to locate in the same interval or adjacent to previously QTLs. qCHL2-1 and qCHL5-1 were detected every year showing their genetic stability. qCHL2-1 was mapped between the 7.63-7.71 Mb on chromosome 2, and the two-year LOD values are 14.08 and 7.93 with the PVE 13.13% and 7.94%, respectively. qCHL5-1 was mapped between the 23.44-23.49 Mb on chromosome 5, and the two-year LOD values are 4.31 and 3.76, respectively. After the annotation and sequences analysis of genes located in the region of qCHL2-1 and qCHL5-1, two genes, Os02g0236000 and Os05g0476700, were found to be associated with chlorophyll content of flag leaves in the rice. There are differences in sequences of the two genes between TD70 and Kasalath. Os02g0236000 is the AAT1 gene encoding the Aspartate Aminotransferase, which is an important enzyme in nitrogen metabolism and related to protein and amino acid content of rice. Os05g0476700 encodes protein relating to spotted leaf, which might associate with leaf color. Based on the mutation of AAT1 at CDS+273 bp, the haplotypes of ATT1 were classified in RIL population. Among the 20 extreme SPAD RIL lines, there were significant differences between different haplotype of ATT1 in SPAD value, chlorophyll content, water use efficiency, transpiration rate, stomatal conductance and net photosynthetic rate of flag leaf.

19 QTLs associated with chlorophyll content in flag leaf at heading stage of rice were detected and two stable QTL loci, qCHL2-1 and qCHL5-1 were identified. Two candidate genes were obtained after annotation and sequence comparison. One of them, ATT1, was considered as the most possible candidate gene after effort analysis of different haplotypes in photosynthetic efficiency. The QTLs and gene we obtained could be used for subsequent functional studies of flag leaf chlorophyll regulation and molecular marker breeding.

A set of variety DNA fingerprint identification system based on the core markers of genes regulating rice important traits was constructed, which will establish a foundation for strengthening the germplasm management and protection of the mainly promoted semi-waxy japonica rice varieties with high eating quality.

34 semi-waxy japonica rice varieties mainly cultivated in Jiangsu, Zhejiang and Shanghai were used as the test materials. The key differential sequence sites in genes regulating rice important traits were screened and core SNP or InDel markers were developed through multiple methods such as polymorphism testing of existing markers, gene sequence alignment from public databases and genome resequencing. SNP markers were developed into simple PCR markers based on electrophoretic bands by As-PCR technology. Genotype information was obtained by electrophoretic band characterization and type analysis, and the DNA fingerprint database of the semi-waxy japonica rice varieties was constructed.

54 core markers derived from 40 key genes regulating rice important traits were obtained, including 18 SNP and 36 InDel markers; 155 characteristic and effective bands were identified by 54 markers in the tested rice varieties, which were transformed into 155 0/1 data sites. The DNA fingerprint database of each variety was established and could distinguish it from all tested varieties. Genetic diversity analysis showed that the variation range of genetic similarity among varieties was 0.47-0.90, among which the lowest similarity coefficient was detected between Nanjing 7718 and Suxiangjing 100, while the highest similarity coefficient was detected between Nanjing 9308 and Nanjing 9036, among which there were 8 differential data sites. Genetic relationship analysis indicated that 34 varieties were divided into 6 branches, of which Nanjing 7718 was an independent branch, suggesting it has a distant relationship from other varieties. Further verification of the identification effect of core markers showed that the set of markers could effectively distinguish 14 new semi-waxy japonica rice varieties. The cluster diagram showed that they were distributed in three groups of Ⅱ, Ⅲ and Ⅳ, confirming the differences of genotype information among varieties; using this set of markers, the authenticity of an unknown semi-waxy rice variety was also identified. According to genotype and cluster analysis, it was determined as Nanjing 9108.

After optimization and screening, 54 core markers that could accurately distinguish all the tested semi-waxy japonica varieties were obtained, and developed into simple PCR markers detected by electrophoresis. Using this set of marker combinations, the DNA fingerprints of 34 semi-waxy japonica varieties in Jiangsu, Zhejiang and Shanghai were constructed.

Rice panicle apical abortion affects yield. Identification and cloning of genes related to rice panicle apical abortion can enrich the molecular mechanism of rice panicle development regulation, and provide theoretical basis and genetic resources for rice high-yield molecular design breeding.

Here, a stably inherited panicle apical abortion 21 (paa21) mutant was screened from EMS mutant library of the japonica rice variety "Wuyunjing 30". Agronomic traits, such as ratio of degraded primary branches, degraded apical spikelets, grains per panicle, plant height, panicle length, and grain yield per plant, were statistically analyzed. Trypan blue and Evans blue staining were used to detect whether programmed cell death occurred in the apical spikelets. H₂O₂ content in young panicles at different development stages and different panicle parts of WT and paa21 was determined. Genetic analysis was carried out by reciprocal cross of paa21 with indica rice II-32B and 9311 respectively. The F₂ population constructed by crossing paa21 with indica rice II-32B was used for gene mapping and cloning. The three-dimensional structure of wild-type and paa21 proteins were predicted using SWISS-MODEL website. The expression levels of ROS response marker genes, programmed cell death related genes and catalase related genes were analyzed by RT-qPCR.

paa21 produced panicle apical abortion phenotype and the degenerated spikelets were mainly located on the primary branches at the apical panicle. The plant height, grain number per panicle, panicle length and grain yield per plant of paa21 were lower than those of WT. After observing the young panicles at different development stages, we found that the paa21 mutant had a panicle apical abortion phenotype when panicle developed to 12 cm. Trypan blue and Evans blue staining results showed that the apical spikelets of the paa21 mutant had programmed cell death. Stronger DAB staining was observed in the degenerated apical spikelets of paa21 than WT. The results of H₂O₂ content determination showed that higher level of ROS was accumulated in panicle of paa21 compared with WT. Genetic analysis suggested that paa21 mutant phenotype is controlled by a pair of recessive nuclear genes. The results of map-based cloning showed that a C to T mutation occurred in the second exon of Os02g0673100 in paa21, resulting in the mutation of alanine to valine. This gene encodes an aluminum activated malate transporter, ALMT7. The mutation site was located at the fourth transmembrane helix. SWISS-MODEL prediction results showed that the mutation site did not significantly affect the three-dimensional structure of the mutant protein. The expression level of ROS response marker genes Os01g0826400, Os05g0474800 and Os02g0181300 in paa21 was significantly higher than that in WT when the young spike developed to 10 cm. Compared with WT, the expression level of programmed cell death related genes VPE2 and VPE3 increased significantly in paa21. The expression level of CATA, CATB and CATC which encode catalase in 10 cm young panicle of paa21 was significantly higher than that of WT. The activity of CAT in paa21 10 cm young spikelet was significantly lower than that of WT.

paa21 accumulate excess ROS in the apical spikelet at late stage of panicle development, resulting in programmed cell death, which eventually leads to the degeneration of the apical spikelet. These results lay a good foundation for further enriching the genetic regulatory network of panicle development.

The aim of this study was to investigate the characteristics of the transport and distribution of photosynthetic products and related gene expression levels during the grain filling period of the Nanjing series of super rice, as well as the differences with the control varieties, to summarize the physiological advantages of high-yield in the Nanjing series super rice, so as to provide the theoretical basis for the development of high-quality and high-yield japonica rice.

Nanjing 5718, Nanjingjinggu, Nanjing 3908, and Nanjing 5055 were used as the research materials, with Huaidao 5 as the control. The photosynthetic rate of flag leaves, distribution and transportation of aboveground dry matter, and expression levels of photosynthetic product transport related genes at different stages of flag leaf and seed development were measured every 7 days during the booting stage, flowering stage, and flowering to maturity stage, and yield differences were statistically analyzed too.

The yield and 1000-grain weight of the Nanjing series of super rice were higher than those of Huaidao 5, and its net photosynthetic rate of flag leaves was significantly higher than that in Huaidao 5 during the booting stage and 28 days after flowering. In terms of photosynthetic product transport, the stem and leaf dry weight, leaf output, output rate, and transport rate of the Nanjing series super rice were significantly higher than those of Huaidao 5 after flowering, with Nanjing 5718 having the highest leaf output and output rate. The expression of genes related to starch degradation and carbohydrate metabolism (OsSPS1, OsSUT2, and OsGWD1) in the flag leaves of Nanjing 5718 was initiated earlier than other varieties, and the highest expression level was also higher than other varieties. The SWEET gene in grains played an important role in early sucrose transport during grain filling, while the OsPK3, OsSUT1, and OsSUT2 genes played an important role in sugar transport and unloading during the middle and late filling stages. The OsAGPL2 and OsDPE1 genes played the important roles in starch synthesis during the middle and late filling stages. The expression levels of genes related to starch synthesis and sugar transport in grains of Nanjing 5718, Nanjingjinggu, and Nanjing 3908 were significantly higher than those of Huaidao 5 at different stages.

The higher yield of the Nanjing series of super rice was mainly characterized by the following characteristics in terms of material transport: a large accumulation of dry matter in stem, leaf and panicles, and a high transport rate of leaf and stem dry matter; the high expression levels of genes related to sucrose metabolism and transport in leaves were beneficial for the synthesis, loading, and transport of sucrose at the source end; the high expression levels of genes related to sucrose transport and starch synthesis in grains were conducive to the unloading of sucrose at the storage end and the synthesis of starch in grains.