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 Analysis for Rice Quality-Related Traits and Fine Mapping of qWCR3.

The quality of rice, evaluated using multiple quality-related traits, is the main determinant of its market competitiveness. In this study, two japonica rice varieties with significant differences in quality-related traits were used as parents to construct two populations, BC3F2 and BC3F2:3, with Kongyu131 (KY131) as the recurrent parent. A genetic linkage map was constructed using the BC3F2 population based on 151 pairs of SSR/InDel polymorphic markers selected between the parents. Grain-shape-related traits (grain length GL, grain width GW, and length-to-width ratio LWR), chalkiness-related traits (white-core rate WCR, white-belly rate WBR, white-back rate BR, and chalkiness rate CR), and amylose content (AC) were investigated in the two populations in 2017 and 2018. Except for BR and CR, the traits showed similar characteristics with a normal distribution in both populations. Genetic linkage analysis was conducted for these quality-related traits, and a total of 37 QTLs were detected in the two populations. Further validation was performed on the newly identified QTLs with larger effects, and three grain shape QTLs and four chalkiness QTLs were successfully validated in different environments. One repeatedly validated QTL, qWCR3, was selected for fine mapping and was successfully narrowed down to a 100 kb region in which only two genes, LOC_0s03g45210 and LOC_0s03g45320, exhibited sequence variations between the parents. Furthermore, the variation of LOC_Os03g45210 leads to a frameshift mutation and premature protein termination. The results of this study provide a theoretical basis for positional cloning of the qWCR3 gene, thus offering new genetic resources for rice quality improvement.

Effects of Different Heating and Cooling Rates during Solution Treatment on Microstructure and Properties of AA7050 Alloy Wires.

In the present study, the effects of varying heating and cooling rates during the solution treatment process on the microstructure and properties of AA7050 alloy wires were investigated using tensile tests, metallographic microscopy, electron backscattered diffraction, and transmission electron microscopy. It was found that the recrystallized grain size of the alloy, subjected to method of rapid heating, exhibited a smaller and more uniform distribution in comparison to method of slow heating. The low density of η' strengthening phases after the artificial aging treatment was formed using air cooling method. Meanwhile, by using the water quenching method sufficient solute atoms and more nucleation sites were provided resulting in a large number of η' strengthening phases being formed. In addition, the alloy processed using the water quenching method displayed higher strength than that treated using the air cooling method for the T6 and T73 states. Furthermore, coarse precipitates formed and less clusters were observed in the matrix, while high density nanoscale clusters and no continuous precipitation are formed when using the water quenching method.

Improvement of Rice Blast Resistance in TGMS Line HD9802S through Optimized Anther Culture and Molecular Marker-Assisted Selection.

Rice blast caused by Magnaporthe oryzae is one of the most serious rice diseases worldwide. The early indica rice thermosensitive genic male sterile (TGMS) line HD9802S has the characteristics of stable fertility, reproducibility, a high outcrossing rate, excellent rice quality, and strong combining ability. However, this line exhibits poor blast resistance and is highly susceptible to leaf and neck blasts. In this study, backcross introduction, molecular marker-assisted selection, gene chipping, anther culture, and resistance identification in the field were used to introduce the broad-spectrum blast-resistance gene R6 into HD9802S to improve its rice blast resistance. Six induction media were prepared by varying the content of each component in the culture medium. Murashige and Skoog's medium with 3 mg/L 2,4-dichlorophenoxyacetic acid, 2 mg/L 1-naphthaleneacetic acid, and 1 mg/L kinetin and N6 medium with 800 mg/L casein hydrolysate, 600 mg/L proline, and 500 mg/L glutamine could improve the callus induction rate and have a higher green seedling rate and a lower white seedling rate. Compared to HD9802S, two doubled haploid lines containing R6 with stable fertility showed significantly enhanced resistance to rice blast and no significant difference in spikelet number per panicle, 1000-grain weight, or grain shape. Our findings highlight a rapid and effective method for improving rice blast resistance in TGMS lines.

Small-sample learning reveals propionylation in determining global protein homeostasis.

Proteostasis is fundamental for maintaining organismal health. However, the mechanisms underlying its dynamic regulation and how its disruptions lead to diseases are largely unclear. Here, we conduct in-depth propionylomic profiling in Drosophila, and develop a small-sample learning framework to prioritize the propionylation at lysine 17 of H2B (H2BK17pr) to be functionally important. Mutating H2BK17 which eliminates propionylation leads to elevated total protein level in vivo. Further analyses reveal that H2BK17pr modulates the expression of 14.7-16.3% of genes in the proteostasis network, and determines global protein level by regulating the expression of genes involved in the ubiquitin-proteasome system. In addition, H2BK17pr exhibits daily oscillation, mediating the influences of feeding/fasting cycles to drive rhythmic expression of proteasomal genes. Our study not only reveals a role of lysine propionylation in regulating proteostasis, but also implements a generally applicable method which can be extended to other issues with little prior knowledge.

Broad phosphorylation mediated by testis-specific serine/threonine kinases contributes to spermiogenesis and male fertility.

Genetic studies elucidate a link between testis-specific serine/threonine kinases (TSSKs) and male infertility in mammals, but the underlying mechanisms are unclear. Here, we identify a TSSK homolog in Drosophila, CG14305 (termed dTSSK), whose mutation impairs the histone-to-protamine transition during spermiogenesis and causes multiple phenotypic defects in nuclear shaping, DNA condensation, and flagellar organization in spermatids. Genetic analysis demonstrates that kinase catalytic activity of dTSSK, which is functionally conserved with human TSSKs, is essential for male fertility. Phosphoproteomics identify 828 phosphopeptides/449 proteins as potential substrates of dTSSK enriched primarily in microtubule-based processes, flagellar organization and mobility, and spermatid differentiation and development, suggesting that dTSSK phosphorylates various proteins to orchestrate postmeiotic spermiogenesis. Among them, the two substrates, protamine-like protein Mst77F/Ser9 and transition protein Mst33A/Ser237, are biochemically validated to be phosphorylated by dTSSK in vitro, and are genetically demonstrated to be involved in spermiogenesis in vivo. Collectively, our findings demonstrate that broad phosphorylation mediated by TSSKs plays an indispensable role in spermiogenesis.

Effects of Cu Addition on Age Hardening Behavior and Mechanical Properties of High-Strength Al-1.2Mg-1.2Si Alloy.

In this study, the effects of Cu addition on artificial age hardening behavior and mechanical properties of Al-1.2Mg-1.2Si-(xCu) alloy was investigated quantitatively and qualitatively by Vickers hardness, tensile test, and transmission electron microscope. The results indicated that Cu addition enhanced the aging response of the alloy at 175 °C. With the increase in Cu content, the time for the alloys to reach peak aging decreased from 12 h to 10 h and 8 h. The tensile strength of the alloy was obviously improved with Cu added in which was 421 MPa of 0Cu alloy, 448 MPa of 0.18Cu alloy, and 459 MPa of 0.37Cu alloy. The results of TEM observation revealed that the addition of 0.37Cu changed the aging precipitation sequence of the alloy, in which the precipitation sequence of 0Cu and 0.18Cu alloy was SSSS→GP zones/pre-ß″→ß″→ß″ + ß', 0.37Cu alloy was SSSS→GP zones/pre-ß″→ß″ + L→ß″ + L + Q'. Moreover, with the addition of Cu, the number density and volume fraction of precipitates of the Al-1.2Mg-1.2Si-(xCu) alloy was evidently increased. The number density was increased from 0.23 × 1023/m3 to 0.73 × 1023/m3 in the initial aging stage and from 1.9 × 1023/m3 to 5.5 × 1023/m3 in the peak aging stage. The volume fraction was increased from 0.27% to 0.59% in the early aging stage and from 4.05% to 5.36% in the peak aging stage. It indicated that Cu addition promoted the precipitation of strengthening precipitates and boosted the mechanical properties of the alloy accordingly.

Creation of Two-Line Fragrant Glutinous Hybrid Rice by Editing the Wx and OsBADH2 Genes via the CRISPR/Cas9 System.

Global food security has benefited from the development and promotion of the two-line hybrid rice system. Excellent eating quality determines the market competitiveness of hybrid rice varieties based on achieving the fundamental requirements of high yield and good adaptability. Developing sterile and restorer lines with improved quality for two-line hybrid breeding by editing quality genes with clustered regularly interspaced short palindromic repeat (CRISPR)/Cas9 is an efficient and practical alternative to the lengthy and laborious process of conventional breeding to improve rice quality. We edited Wx and OsBADH2 using CRISPR/Cas9 technology to produce both homozygous male sterile mutant lines and homozygous restorer mutant lines with Cas9-free. These mutants have a much lower amylose content while having a significantly higher 2-acetyl-1-pyrroline aroma content. Based on this, a fragrant glutinous hybrid rice was developed without too much effect on most agronomic traits. This study demonstrates the use of CRISPR/Cas9 in creating two-line fragrant glutinous hybrid rice by editing the components of the male sterile and the restorative lines.

Exploration of Alloying Elements of High Specific Modulus Al-Li Alloy Based on Machine Learning.

In the aerospace sector, the development of lightweight aircraft heavily relies on the utilization of advanced aluminum-lithium alloys as primary structural materials. This study introduces an investigation aimed at optimizing the composition of an Al-2.32Li-1.44Cu-2.78Mg-0.3Ag-0.3Mn-0.1Zr alloy. The optimization process involves the selection of alloying elements through the application of machine learning techniques, with a focus on expected improvements in the specific modulus of these alloys. Expanding upon the optimization of the benchmark alloy's components, a more generalized modulus prediction model for Al-Li alloys was formulated. This model was then employed to evaluate the anticipated specific modulus of alloys within a virtual search space, encompassing substitutional elements. The study proceeded to validate six Al-Li alloys with a notably high potential for achieving an improved specific modulus. The results revealed that an alloy incorporating 0.96 wt.% of Ga as a substitutional element exhibited the most favorable microstructure. This alloy demonstrated optimal tensile strength (523 MPa) and specific modulus (31.531 GPa/(g·cm-3)), closely resembling that of the benchmark alloy. This research offers valuable insights into the application of compositional optimization to enhance the mechanical properties of Al-Li alloys. It emphasizes the significance of selecting alloying elements based on considerations such as their solid solubility thresholds and the expected enhancement of the specific modulus in Al-Li alloys.

Cis- and trans-regulation by histone H4 basic patch R17/R19 in metazoan development.

The histone H4 basic patch is critical for chromatin structure and regulation of the chromatin machinery. However, the biological roles of these positively charged residues and the mechanisms by which they regulate gene expression remain unclear. In this study, we used histone mutagenesis to investigate the physiological function and downstream regulatory genes of H4 residues R17 and R19 in Drosophila. We found all histone mutations including R17A/E/H and R19A/E/H (R17 and R19 of H4 are substituted by A, E and H respectively) result in a range of growth defects and abnormalities in chromosomal high-order structures, whereas R17E mutation is embryonic lethal. RNA-seq demonstrates that downregulated genes in both R17A and R19A show significant overlap and are enriched in development-related pathways. In addition, Western and cytological analyses showed that the R17A mutation resulted in a significant reduction in H4K16 acetylation and male offspring, implying that the R17 may be involved in male dosage compensation mechanisms. R19 mutation on the other hand strongly affect Gpp (Dot1 homologue in flies)-mediated H3K79 methylation, possibly through histone crosstalk. Together these results provide insights into the differential impacts of positive charges of H4 basic patch R17/R19 on regulation of gene transcription during developmental processes.

Secure and noise-resistant underwater wireless optical communication based on spectrum spread and encrypted OFDM modulation.

In addition to requirements on increasing transmission distance and bitrate, the study of underwater wireless optical communication (UWOC) is also facing limitations and challenges, such as interference induced by background noise, demand of higher receiver sensitivity, and communication security issues. In this paper, we experimentally demonstrate a physical layer secure and noise-resistant UWOC system based on spectrum spread and encrypted orthogonal frequency division multiplexing (SSE-OFDM) modulation, transmission through a 14.2 m sediment circulating water tank. Firstly, experimental results show that the required optical power ratio of signal and noise light (OPR) for QPSK signal under BER threshold of 3.8×10-3 is around -5.77 dB for a spectrum spread factor (N) of 100, with a signal-to-noise ratio (SNR) improvement of 19.06 dB. Secondly, without the background noise interference, the receiver sensitivity is also improved from -50 dBm to -62.4 dBm by using the SSE-OFDM modulation, achieving a maximum attenuation length (AL) of 19.67. Thirdly, physical layer security of UWOC can also be realized, which suppresses the SNR of eavesdropper to -3.72 dB while improving SNR of the authorized receiver to 17.56 dB under the condition of no leakage of keys. Additionally, analytical expressions for SSE-OFDM based UWOC performance are also derived, which agree well with the experimental results. Based on the analytical expressions, the maximum secrecy capacity Cs for SSE-OFDM based UWOC system under eavesdropping can be obtained by optimizing the intentionally inserted artificial noise power ratio and the spectrum spread factor N.

Effects of Wx Genotype, Nitrogen Fertilization, and Temperature on Rice Grain Quality.

Quality is a complex trait that is not only the key determinant of the market value of the rice grain, but is also a major constraint in rice breeding. It is influenced by both genetic and environmental factors. However, the combined effects of genotypes and environmental factors on rice grain quality remain unclear. In this study, we used a three-factor experimental design to examine the grain quality of different Wx genotypes grown under different nitrogen fertilization and temperature conditions during grain development. We found that the three factors contributed differently to taste, appearance, and nutritional quality. Increased Wx function and nitrogen fertilization significantly reduced eating quality, whereas high temperature (HT) had almost no effect. The main effects of temperature on appearance quality and moderate Wx function at low temperatures (LTs) contributed to better appearance, and higher nitrogen fertilization promoted appearance at HTs. With regard to nutritional quality, Wx alleles promoted amylose content (AC) as well as starch-lipids content (SLC); nitrogen fertilization increased storage protein content (PC); and higher temperature increased lipid content but decreased the PC. This study helps to broaden the understanding of the major factors that affect the quality of rice and provides constructive messages for rice quality improvement and the cultivation of high-quality rice varieties.

Microstructure, Precipitates Behavior, and Mechanical Properties of Age-Hardened Al-Mg-Si Alloy Sheet Fabricated by Twin-Roll Casting.

Twin-roll casting (TRC), as a near-net-shape technology, is employed to fabricate age-hardened Al-Mg-Si alloy. Compared with conventional direct chill (DC) casting, the TRC method is much more economical and efficient. In this work, the microstructure, precipitates behavior, and mechanical properties of age-hardened Al-Mg-Si alloy sheet fabricated by TRC were investigated by hardness measurements and tensile tests, metallographic microscopy, field emission gun scanning electron microscope, electron backscatter diffraction, transmission electron microscopy, and differential scanning calorimetry analyses. It was found that the size of recrystallized grains for DC casting alloy with finely dispersed particles was larger than that of TRC alloy with coarse particles. Typical CubeND texture accompanied by P texture formed after solution treatment made the value of r reach ~0.7 in the TRC alloy due to the PSN effect caused by the segregation of particles. More GP zones resulted in the strength of TRC alloy being higher than that of DC casting alloy after T8X treatment. With the time of paint-bake hardening extended to 8 h, few segregation particles remained in the TRC alloy. This decreased the concentration of supersaturated atoms. The hardness of the TRC alloy with the lower density of the ß″ strengthening phase was lower compared to the DC casting alloy.

Transcription-coupled donor DNA expression increases homologous recombination for efficient genome editing.

Genomes can be edited by homologous recombination stimulated by CRISPR/Cas9 [clustered regularly interspaced short palindromic repeats (CRISPR)/CRISPR-associated peptide 9]-induced DNA double-strand breaks. However, this approach is inefficient for inserting or deleting long fragments in mammalian cells. Here, we describe a simple genome-editing method, termed transcription-coupled Cas9-mediated editing (TEd), that can achieve higher efficiencies than canonical Cas9-mediated editing (CEd) in deleting genomic fragments, inserting/replacing large DNA fragments and introducing point mutations into mammalian cell lines. We also found that the transcription on DNA templates is crucial for the promotion of homology-directed repair, and that tethering transcripts from TEd donors to targeted sites further improves editing efficiency. The superior efficiency of TEd for the insertion and deletion of long DNA fragments expands the applications of CRISPR for editing mammalian genomes.

OsHXK3 encodes a hexokinase-like protein that positively regulates grain size in rice.

KEY MESSAGE: We report the map-based cloning and functional characterization of SNG1, which encodes OsHXK3, a hexokinase-like protein that plays a pivotal role in controlling grain size in rice. Grain size is an important agronomic trait determining grain yield and appearance quality in rice. Here, we report the discovery of rice mutant short and narrow grain1 (sng1) with reduced grain length, width and weight. Map-based cloning revealed that the mutant phenotype was caused by loss of function of gene OsHXK3 that encodes a hexokinase-like (HKL) protein. OsHXK3 was associated with the mitochondria and was ubiquitously distributed in various organs, predominately in younger organs. Analysis of glucose (Glc) phosphorylation activities in young panicles and protoplasts showed that OsHXK3 was a non-catalytic hexokinase (HXK). Overexpression of OsHXK3 could not complement the Arabidopsis glucose insensitive2-1 (gin2-1) mutant, indicating that OsHXK3 lacked Glc signaling activity. Scanning electron microscopy analysis revealed that OsHXK3 affects grain size by promoting spikelet husk cell expansion. Knockout of other nine OsHXK genes except OsHXK3 individually did not change grain size, indicating that functions of OsHXKs have differentiated in rice. OsHXK3 influences gibberellin (GA) biosynthesis and homeostasis. Compared with wild type, OsGA3ox2 was significantly up-regulated and OsGA2ox1 was significantly down-regulated in young panicle of sng1, and concentrations of biologically active GAs were significantly decreased in young panicles of the mutants. The yield per plant of OsHXK3 overexpression lines (OE-4 and OE-35) was increased by 10.91% and 7.62%, respectively, compared to that of wild type. Our results provide evidence that an HXK lacking catalytic and sensory functions plays an important role in grain size and has the potential to increase yield in rice.

GLW7.1, a Strong Functional Allele of Ghd7, Enhances Grain Size in Rice.

Grain size is a key determinant of both grain weight and grain quality. Here, we report the map-based cloning of a novel quantitative trait locus (QTL), GLW7.1 (Grain Length, Width and Weight 7.1), which encodes the CCT motif family protein, GHD7. The QTL is located in a 53 kb deletion fragment in the cultivar Jin23B, compared with the cultivar CR071. Scanning electron microscopy analysis and expression analysis revealed that GLW7.1 promotes the transcription of several cell division and expansion genes, further resulting in a larger cell size and increased cell number, and finally enhancing the grain size as well as grain weight. GLW7.1 could also increase endogenous GA content by up-regulating the expression of GA biosynthesis genes. Yeast two-hybrid assays and split firefly luciferase complementation assays revealed the interactions of GHD7 with seven grain-size-related proteins and the rice DELLA protein SLR1. Haplotype analysis and transcription activation assay revealed the effect of six amino acid substitutions on GHD7 activation activity. Additionally, the NIL with GLW7.1 showed reduced chalkiness and improved cooking and eating quality. These findings provide a new insight into the role of Ghd7 and confirm the great potential of the GLW7.1 allele in simultaneously improving grain yield and quality.

Natural variation in WHITE-CORE RATE 1 regulates redox homeostasis in rice endosperm to affect grain quality.

Grain chalkiness reduces the quality of rice (Oryza sativa) and is a highly undesirable trait for breeding and marketing. However, the underlying molecular cause of chalkiness remains largely unknown. Here, we cloned the F-box gene WHITE-CORE RATE 1 (WCR1), which negatively regulates grain chalkiness and improves grain quality in rice. A functional A/G variation in the promoter region of WCR1 generates the alleles WCR1A and WCR1G, which originated from tropical japonica and wild rice Oryza rufipogon, respectively. OsDOF17 is a transcriptional activator that binds to the AAAAG cis-element in the WCR1A promoter. WCR1 positively affects the transcription of the metallothionein gene MT2b and interacts with MT2b to inhibit its 26S proteasome-mediated degradation, leading to decreased reactive oxygen species production and delayed programmed cell death in rice endosperm. This, in turn, leads to reduced chalkiness. Our findings uncover a molecular mechanism underlying rice chalkiness and identify the promising natural variant WCR1A, with application potential for rice breeding.

Fine mapping of qTGW2b and qGL9, two minor QTL conferring grain size and weight in rice.

Rice grain size is a key determinant of both grain yield and quality. In this study, we conducted QTL mapping on grain size using a recombinant inbred line (RIL) population derived from a cross between japonica variety Beilu130 (BL130) and indica variety Jin23B (J23B). A total of twenty-two QTL related to grain length (GL), grain width (GW), grain length-to-width ratio (LWR), grain thickness (GT), and thousand grain weight (TGW) were detected under two environments, and 14 of them were repeatedly detected. Two minor QTL, qTGW2b and qGL9, were validated and further delimited to regions of 631 kb and 272 kb, respectively. Parental sequence comparison of genes expressed in inflorescence in corresponding candidate regions identified frameshifts in the exons of LOC_Os02g38690 and LOC_Os02g38780, both of which encode protein phosphatase 2C-containing protein, and LOC_Os09g29930, which encodes a BIM2 protein. Scanning electron microscopy (SEM) analysis revealed that the increase of cell size rather than cell number caused the differences in grain size between NILs of qTGW2b and qGL9. Quantitative RT-PCR analysis showed that the expression levels of EXPA4, EXPA5, EXPA6, EXPB3, EXPB4, and EXPB7 were significantly different in both qTGW2b NILs and qGL9 NILs. Our results lay the foundation for the cloning of qTGW2b and qGL9, and provide genetic materials for the improvement of rice yield and quality. Supplementary Information: The online version contains supplementary material available at 10.1007/s11032-022-01328-2.

Data-aided channel equalization scheme for FAST radio over fiber transmission system.

The Five-hundred-meter Aperture Spherical radio Telescope (FAST) located in Guizhou, China, is a very sensitive single dish telescope. Due to the large size of the telescope, optical fiber is used for the transmission of the 3-km astronomical signal from the telescope to the signal processing center. The optical fibers are suspended in the air above the telescope reflector, very easy to slide when the telescope feed cabin moves, resulting in phase drifts for the transmission signal. This phase drift has a negative impact on the observation mode of very long baseline interferometry, and can be compensated by the frequency transfer system in the FAST. In this manuscript, we propose a new phase drift compensation scheme, which is denoted as data-aided channel equalization scheme. The proposed scheme is based on a hypothesis of linear phase relationship between different wavelengths in the same optical fiber, and uses the channel response information of the data-aided channel to conduct signal recovery for the astronomical signal channel. Not only the phase drift, but also the frequency-dependent distortion of the broadband transmission link can be compensated. The proposed scheme has simple transmission structure, and the function part is well modularized, so that the Astronomer users can easily turn it on or off. In the proof-of-concept experiments, the estimation deviation can be significantly reduced by estimated channel responses averaging over training sequence repetitions, showing very high accuracy of the astronomical signal channel estimation.

Combinations of Ghd7, Ghd8, and Hd1 determine strong heterosis of commercial rice hybrids in diverse ecological regions.

Heterosis of grain yield is closely associated with heading date in crops. Gene combinations of the major heading date genes Ghd7, Ghd8, and Hd1 play important roles in enhancing grain yield and adaptation to ecological regions in rice. However, the predominant three-gene combinations for a specific ecological region remain unclear in both three-line and two-line hybrids. In this study, we sequenced these three genes of 50 cytoplasmic male sterile/maintainer lines, 31 photo-thermo-sensitive genic male sterile lines, and 109 restorer lines. Sequence analysis showed that hybrids carrying strong functional alleles of Ghd7 and Hd1 and non-functional Ghd8 are predominant in three-line hybrids and are recommended for rice production in the subtropics around 30°N/S. Hybrids carrying strong functional Ghd7 and Ghd8 and non-functional Hd1 are predominant in two-line hybrids and are recommended for low latitude areas around 23.5°N/S rich in photothermal resources. Hybrids carrying strong functional Ghd7 and Ghd8 and functional Hd1 were not identified in commercial hybrids in the middle and lower reaches of the Yangtze River, but they have high yield potential in tropical regions because they have the strongest photoperiod sensitivity. Based on these findings, two genic sterile lines, Xiangling 628S and C815S, whose hybrids often head very late, were diagnosed with these three genes, and Hd1 was targeted to be knocked out in Xiangling 628S and replaced with hd1 in C815S. The hybrids developed from both modified sterile lines in turn had appropriate heading dates and significantly improved grain yield. This study provides new insights for breeding design to develop hybrids for various regions.