Design and analysis of unequal aperture off-axis optical integrator for solar simulators.

The unequal aperture off-axis optical integrator design method is proposed to improve the irradiation uniformity of solar simulators and solve the problem of limited uniformity of optical integrator due to aberrations and uneven distribution of incident radiation. Firstly, the unequal aperture off-axis optical integrator structure is designed based on the scalar diffraction theory to analyze the factors affecting the optical homogenization ability of the optical integrator. Then, the relationship between sub-eye lens aperture and arrangement is explored in combination with Lagrange invariance principle and semi-definite programming theory. Finally, the optimum off-axis amount of sub-eye lens with different ring band is determined from the perspective of geometric optics by using the aberration theory and following the principle of edge light, so as to improve the evenness of optical integrator. The design results are verified by the simulation analysis. The simulation results show that: In the picture plane of optical integrator, the irradiation non-uniformity in the ф 26 mm irradiation plane is 14.87%, which is better than 26.02% in the traditional optical integrator. At the same time, at the effective irradiated surface, the irradiation non-uniformity of 0.53% within the ф 300 mm reaches the irradiation standard of the class A + solar simulator, and the irradiance only decreases by 16.5% compared with the traditional optical integrator, which still meets the index requirement of a solar constant. The goal of improving the evenness of optical integrator is realized without greatly affecting irradiance and without introducing aspherical design.

Research on ultraviolet-visible composite optical target simulation technology.

This study proposes an ultraviolet-visible composite optical target simulation technique based on a liquid crystal display (LCD) spatial light modulation device to solve the problem of not being able to satisfy the demand for optical target simulation for both ultraviolet and visible light operating spectral ranges in a single system when composite simulation of multi-source spatial targets is performed. We establish a composite light source model of an ultraviolet light emitting diode (LED) and a xenon lamp to enhance the energy simulation of the ultraviolet portion, and the light is mixed and homogenized by an integrating sphere. We analyze the light transmission principle of LCD display devices and derive the equation for the relationship between its working band and transmittance. We design a transmission-type projection system with a wide spectral range and simulate the transmittance of the whole system, and demonstrate the optical target simulator can realize the simulation requirements of a wide working spectral range, high interstellar angular distance accuracy, and high magnitude accuracy.

Research on optical simulation of dim target based on passive detection link analysis.

In order to meet the ground calibration requirements of optical detection equipment to identify optical characteristics of dim targets, an optical simulation method of dim targets based on passive detection link analysis and bidirectional scattering distribution function model is proposed. The off-axis collimation system for long focal length, the simulated energy transmission model of dim targets and the simplified model of bidirectional scattering distribution function are established. An internal stray light suppression baffle was designed to effectively suppress secondary scattering, and an optical simulation system for dim targets was built. The experimental results show that the system can simulate +7 Mv∼+20 Mv, and the simulation accuracy is better than 0.07 Mv. At the same time, the detection ability of the camera is tested by using the +15 Mv point simulated by the system. The signal-to-noise of the star point target reaches 6.7, which meets the requirements of detection rate and false alarm rate, and realizes the ground test of the camera's detection ability of the dim target.

Simulation method for multi-source information fusion space target.

Current space target simulation systems suffer from limitations, such as a single simulated spectral band, inability to allocate spectral ratios between bands, and poor imaging quality of multi-spectral simulated images. We propose a multi-source information fusion spatial target simulation method system that features a "series-parallel" hybrid connection. We optimize the design of a multi-spectral common aperture optical system and experimentally verify the proposed method. The experimental results show that the proposed system can simulate a wide range of spectral bands ranging from ultraviolet to long-wave infrared. Furthermore, it achieves precise control over the ratio of simulated radiant energy among spectral bands, with a spectral simulation error of less than 4.8%. Notably, it effectively images stars against the cosmic background and spacecraft across different spectral bands. This system serves as a theoretical cornerstone and provides crucial technological support for performance testing and rapid iterative development of multi-source information fusion space exploration systems.

Identification and characterization of candidate genes for primary root length in Asiatic cotton (Gossypium arboreum L.).

KEY MESSAGE: One major gene controlling primary root length (PRL) in Gossypium arboreum is identified and this research provides a theoretical basis for root development for cotton. Primary root elongation is an essential process in plant root system structure. Here, we investigated the primary root length (PRL) of 215 diploid cotton (G. arboreum) accessions at 5, 8, 10, 15 days after sowing. A Genome-wide association study was performed for the PRL, resulting in 49 significant SNPs associated with 32 putative candidate genes. The SNP with the strongest signal (Chr07_8047530) could clearly distinguish the PRLs between accessions with two haplotypes. GamurG is the only gene that showed higher relative expression in the long PRL genotypes than the short PRL genotypes, which indicated it was the most likely candidate gene for regulating PRL. Moreover, the GamurG-silenced cotton seedlings showed a shorter PRL, while the GamurG-overexpressed Arabidopsis exhibited a significantly longer PRL. Our findings provide insight into the regulation mechanism of cotton root growth and will facilitate future breeding programs to optimize the root system structure in cotton.

A Compensation Method for Full-Field-of-View Energy Nonuniformity in Dark-and-Weak-Target Simulators.

Dark-and-weak-target simulators are used as ground-based calibration devices to test and calibrate the performance metrics of star sensors. However, these simulators are affected by full-field-of-view energy nonuniformity. This problem impacts the quality of output images and the calibration accuracy of sensors and inhibits further improvements in navigational accuracy. In the study reported in this paper, we sought to analyze the factors which affect full-field-of-view energy uniformity in dark-and-weak-target simulators. These include uneven irradiation in backlight sources, the leakage of light from LCD display panels, and the vignetting of collimating optical systems. We then established an energy transfer model of a dark-and-weak-target simulator based on the propagation of a point light source and proposed a self-adaptive compensation algorithm based on pixel-by-pixel fitting. This algorithm used a sensor to capture the output image of a dark-and-weak-target simulator and iteratively calculated the response error matrix of the simulator. Finally, we validated the feasibility and effectiveness of the compensation algorithm by acquiring images using a self-built test system. The results showed that, after compensating an output image of the dark-and-weak-target simulator, the grayscale standard display function (SDF) of the acquired sensor image was reduced by about 50% overall, so the acquisition image was more accurately compensated, and the desired level of grayscale distribution was obtained. This study provides a reference for improving the quality of output images from dark-and-weak-target simulators, so that the working environments of star sensors may be more realistically simulated, and their detection performance improved.

Analysis on the instability of the surface profiles of precision molding chalcogenide glass aspherical lenses in mass production.

Chalcogenide glass lenses have been widely applied in infrared optical systems for their outstanding optical performance. It is a tendency for complex optical glass elements to be mass-produced with precision glass molding (PGM) technology, of course including chalcogenide glass aspheric lenses. But there is a problem that sometimes the surface profiles of the molded lenses are unstable which leads to a low pass-yield. Precision glass molding experiments and finite elements simulations are carried out to study the reasons for the mentioned problem in this paper. The results reveal that the laying error of the ball chalcogenide glass preform does not have a significant effect on the surface profile of the molded lens. However, in mass production the control of the temperature after forming stage in the PGM process is very important for obtaining the molded lenses with very similar surface profiles. The research results could help relevant researchers design the PGM processing parameters to overcome some errors in the mass production and manufacture precision glass molding machines. The increase in the yield of complex optical glass elements fabricated by PGM technology will further promote the application of such elements in various fields.

Design of an optical illumination system for a long wave infrared scene projector based on diffraction characteristics.

This study proposes an optical illumination system design based on vector diffraction characteristics and the Scheimpflug principle to determine an optimal relationship between illumination uniformity, energy utilization, and system size in an infrared scene projector. We investigate the influence of digital micromirror device (DMD) diffraction efficiency at different incidence angles on energy utilization rate and establish a two-dimensional diffraction grating model to determine the optimal incidence angle of the DMD beam. We demonstrate that the optical illumination system of a long-wave infrared (LWIR) scene projector based on diffraction characteristics can simulate an infrared scene with a compact structure, high energy efficiency, and high uniformity.

Integrating Genome-wide association and whole transcriptome analysis to reveal genetic control of leaf traits in Gossypium arboreum L.

Leaves are important organs for crop photosynthesis and transpiration, and their morphological characteristics can directly reflect the growth state of plants. Accurate measurement of leaf traits and mining molecular markers are of great significance to the study of cotton growth. Here, we performed a Genome-wide association study on 7 leaf traits in 213 Asian cotton accessions. 32 significant SNPs and 44 genes were identified. A field experiment showed significant difference in leaf hair and leaf area between DPL971 and its natural mutant DPL972. We also compared the leaf transcriptome difference between DPL971 and DPL972, and found a batch of differentially expressed genes and non-coding RNAs (including lncRNAs, microRNAs, and circRNAs). After integrating the GWAS and transcriptome results, we finally selected two coding genes (Ga03G2383 and Ga05G3412) and two microRNAs (hbr-miR156, unconservative_Chr03_contig343_2364) as the candidate for leaf traits. Those findings will provide important genomic resources for cotton leaf improvement breeding.

Mapping of dwarfing QTL of Ari1327, a semi-dwarf mutant of upland cotton.

BACKGROUND: Upland Cotton (Gossypium hirsutum L.) has few cotton varieties suitable for mechanical harvesting. The plant height of the cultivar is one of the key features that need to modify. Hence, this study was planned to locate the QTL for plant height in a 60Co γ treated upland cotton semi-dwarf mutant Ari1327. RESULTS: Interestingly, bulk segregant analysis (BSA) and genotyping by sequencing (GBS) methods exhibited that candidate QTL was co-located in the region of 5.80-9.66 Mb at D01 chromosome in two F2 populations. Using three InDel markers to genotype a population of 1241 individuals confirmed that the offspring's phenotype is consistent with the genotype. Comparative analysis of RNA-seq between the mutant and wild variety exhibited that Gh_D01G0592 was identified as the source of dwarfness from 200 genes. In addition, it was also revealed that the appropriate use of partial separation markers in QTL mapping can escalate linkage information. CONCLUSIONS: Overwhelmingly, the results will provide the basis to reveal the function of candidate genes and the utilization of excellent dwarf genetic resources in the future.

Genome-wide association study for seedling biomass-related traits in Gossypium arboreum L.

BACKGROUND: Seedling stage plant biomass is usually used as an auxiliary trait to study plant growth and development or stress adversities. However, few molecular markers and candidate genes of seedling biomass-related traits were found in cotton. RESULT: Here, we collected 215 Gossypium arboreum accessions, and investigated 11 seedling biomass-related traits including the fresh weight, dry weight, water content, and root shoot ratio. A genome-wide association study (GWAS) utilizing 142,5003 high-quality SNPs identified 83 significant associations and 69 putative candidate genes. Furthermore, the transcriptome profile of the candidate genes emphasized higher expression of Ga03G1298, Ga09G2054, Ga10G1342, Ga11G0096, and Ga11G2490 in four representative cotton accessions. The relative expression levels of those five genes were further verified by qRT-PCR. CONCLUSIONS: The significant SNPs, candidate genes identified in this study are expected to lay a foundation for studying the molecular mechanism for early biomass development and related traits in Asian cotton.

Deltapine 15 contributes to the genomic architecture of modern upland cotton cultivars.

Foundation parents play a critical role in the genetic constituents of the derived genotypes. Deltapine-15 (DLP-15), introduced to China in 1950, is one of the most commonly used parents for early breeding programs in China. However, the formation and inheritance patterns of genomic constituents have not been studied. Therefore, this study aimed at understanding and exploring the genomic architecture of 146 DLP-15 derived cultivars with a common foundation parent DLP-15. Population structure based on sequencing data clustered genotypes into two groups (G1 and G2) supported by principal component analysis. Further exploration led to the identification of Chr-A08 with significantly differentiated regions between two groups. Moreover, we identified genome-wide identity by descent (IBD) segments (840 segments) to understand the genomic inheritance pattern in DLP-15 derived cultivars, spanning the 20-95 Mb region on Chr-A08. Interestingly, Chr-A08 depicted a unique inheritance pattern from DLP-15 to its derived cultivars. IBD-segment-based haplotype analysis suggested significant differences among the two groups. Phenotypic trait association with DLP-derived haplotypes concerning Chr-A08 suggested a significant increase in yield and fiber quality. Furthermore, distinguished IBD segments overlapped with previously reported QTLs concerning fiber yield and quality. Our results systematically identified genomic signatures transmitted from the foundation parent DLP-15 to its derived cultivars and provided a basis for further exploiting excellent haplotypes associated with DLP-15.

Genome-wide dissection of hybridization for fiber quality- and yield-related traits in upland cotton.

An evaluation of combining ability can facilitate the selection of suitable parents and superior F1 hybrids for hybrid cotton breeding, although the molecular genetic basis of combining ability has not been fully characterized. In the present study, 282 female parents were crossed with four male parents in accordance with the North Carolina II mating scheme to generate 1128 hybrids. The parental lines were genotyped based on restriction site-associated DNA sequencing and 306 814 filtered single nucleotide polymorphisms were used for genome-wide association analysis involving the phenotypes, general combining ability (GCA) values, and specific combining ability values of eight fiber quality- and yield-related traits. The main results were: (i) all parents could be clustered into five subgroups based on population structure analyses and the GCA performance of the female parents had significant differences between subgroups; (ii) 20 accessions with a top 5% GCA value for more than one trait were identified as elite parents for hybrid cotton breeding; (iii) 120 significant single nucleotide polymorphisms, clustered into 66 quantitative trait loci, such as the previously reported Gh_A07G1769 and GhHOX3 genes, were found to be significantly associated with GCA; and (iv) identified quantitative trait loci for GCA had a cumulative effect on GCA of the accessions. Overall, our results suggest that pyramiding the favorable loci for GCA may improve the efficiency of hybrid cotton breeding.

Genome-wide association and transcriptome analysis of root color-related genes in Gossypium arboreum L.

MAIN CONCLUSION: The significant number loci and candidate genes of root color in Gossypium arboreum are identified and provide a theoretical basis of root color for cotton. A stimulating phenomenon was observed on the 4th day of sowing in the root color of some G. arboreum accessions that turned red. To disclose the genetic mechanisms of root color formation via genome and transcript levels, we identified the significant number of SNPs and candidate genes that are related to root color through genome-wide association study (GWAS) and RNAseq analysis in G. arboreum. Initially, 215 no. of G. arboreum accessions was collected, and the colors of root on the 4th, 6th and 9th day of germination were recorded. The GWAS demonstrated that 225 significant SNPs and 47 candidate genes have been identified totally. The strongest signal SNP A04_91824 could greatly distinguish the root color with most "C" allele accessions have displayed white and "T" allele accessions displayed red. RNAseq was performed on accessions having the white and red root, and results revealed that 12 and 138 DEGs were detected on 2nd and 4th day, respectively. ACD6, UFGT, and LYM2 were the most related genes of root color, later, verified by qRT-PCR. The mature zone of red and the white roots was observed by the histological section method, and results shown that cells were more closely arranged in the white root, and both average cell length and cell width were longer in the red root. This study will be helpful to cotton breeders for utilization of several elite genes and related SNPs related to root color, in addition to find linkage with economically important traits of interests.

Large-fragment insertion activates gene GaFZ (Ga08G0121) and is associated with the fuzz and trichome reduction in cotton (Gossypium arboreum).

Cotton seeds are typically covered by lint and fuzz fibres. Natural 'fuzzless' mutants are an ideal model system for identifying genes that regulate cell initiation and elongation. Here, using a genome-wide association study (GWAS), we identified a ~ 6.2 kb insertion, larINDELFZ , located at the end of chromosome 8, composed of a ~ 5.0 kb repetitive sequence and a ~ 1.2 kb fragment translocated from chromosome 12 in fuzzless Gossypium arboreum. The presence of larINDELFZ was associated with a fuzzless seed and reduced trichome phenotypes in G. arboreum. This distant insertion was predicted to be an enhancer, located ~ 18 kb upstream of the dominant-repressor GaFZ (Ga08G0121). Ectopic overexpression of GaFZ in Arabidopsis thaliana and G. hirsutum suggested that GaFZ negatively modulates fuzz and trichome development. Co-expression and interaction analyses demonstrated that GaFZ might impact fuzz fibre/trichome development by repressing the expression of genes in the very-long-chain fatty acid elongation pathway. Thus, we identified a novel regulator of fibre/trichome development while providing insights into the importance of noncoding sequences in cotton.

Extensive haplotypes are associated with population differentiation and environmental adaptability in Upland cotton (Gossypium hirsutum).

KEY MESSAGE: Three extensive eco-haplotypes associated with population differentiation and environmental adaptability in Upland cotton were identified, with A06_85658585, A08_43734499 and A06_113104285 considered the eco-loci for environmental adaptability. Population divergence is suggested to be the primary force driving the evolution of environmental adaptability in various species. Chromosome inversion increases reproductive isolation between subspecies and accelerates population divergence to adapt to new environments. Although modern cultivated Upland cotton (Gossypium hirsutum L.) has spread worldwide, the noticeable phenotypic differences still existed among cultivars grown in different areas. In recent years, the long-distance migration of cotton cultivation areas throughout China has demanded that breeders better understand the genetic basis of environmental adaptability in Upland cotton. Here, we integrated the genotypes of 419 diverse accessions, long-term environment-associated variables (EAVs) and environment-associated traits (EATs) to evaluate subgroup differentiation and identify adaptive loci in Upland cotton. Two highly divergent genomic regions were found on chromosomes A06 and A08, which likely caused by extensive chromosome inversions. The subgroups could be geographically classified based on distinct haplotypes in the divergent regions. A genome-wide association study (GWAS) also confirmed that loci located in these regions were significantly associated with environmental adaptability in Upland cotton. Our study first revealed the cause of population divergence in Upland cotton, as well as the consequences of variation in its environmental adaptability. These findings provide new insights into the genetic basis of environmental adaptability in Upland cotton, which could accelerate the development of molecular markers for adaptation to climate change in future cotton breeding.

Comparative effect of allopolyploidy on transposable element composition and gene expression between Gossypium hirsutum and its two diploid progenitors.

An allopolyploidization event formed allotetraploid Gossypium species from an A-genome diploid species and a D-genome diploid species. To explore the responses of transposable elements (TEs) to allopolyploidy, we assembled parallel TE datasets from G. hirsutum, G. arboreum and G. raimondii and analyzed the TE types and the effects of TEs on orthologous gene expression in the three Gossypium genomes. Gypsy was the most abundant TE type and most TEs were located ∼500 bp from genes in all three genomes. In G. hirsutum, 35.6% of genes harbored TE insertions, whereas insertions were more frequent in G. arboreum and G. raimondii. G. hirsutum had the highest proportion of uniquely matching 24-nt small interfering RNAs (siRNAs) that targeted TEs. TEs, particularly those targeted by 24-nt siRNAs, were associated with reduced gene expression, but the effect of TEs on orthologous gene expression varied substantially among species. Orthologous gene expression levels in G. hirsutum were intermediate between those of G. arboreum and G. raimondii, which did not experience TE expansion or reduction resulting from allopolyploidization. This study underscores the diversity of TEs co-opted by host genes and provides insights into the roles of TEs in regulating gene expression in Gossypium.

Genomic divergence in cotton germplasm related to maturity and heterosis.

Commercial varieties of upland cotton (Gossypium hirsutum) have undergone extensive breeding for agronomic traits, such as fiber quality, disease resistance, and yield. Cotton breeding programs have widely used Chinese upland cotton source germplasm (CUCSG) with excellent agronomic traits. A better understanding of the genetic diversity and genomic characteristics of these accessions could accelerate the identification of desirable alleles. Here, we analyzed 10,522 high-quality single-nucleotide polymorphisms (SNP) with the CottonSNP63K microarray in 137 cotton accessions (including 12 hybrids of upland cotton). These data were used to investigate the genetic diversity, population structure, and genomic characteristics of each population and the contribution of these loci to heterosis. Three subgroups were identified, in agreement with their known pedigrees, geographical distributions, and times since introduction. For each group, we identified lineage-specific genomic divergence regions, which potentially harbor key alleles that determine the characteristics of each group, such as early maturity-related loci. Investigation of the distribution of heterozygous loci, among 12 commercial cotton hybrids, revealed a potential role for these regions in heterosis. Our study provides insight into the population structure of upland cotton germplasm. Furthermore, the overlap between lineage-specific regions and heterozygous loci, in the high-yield hybrids, suggests a role for these regions in cotton heterosis.

Dissection of complicate genetic architecture and breeding perspective of cottonseed traits by genome-wide association study.

BACKGROUND: Cottonseed is one of the most important raw materials for plant protein, oil and alternative biofuel for diesel engines. Understanding the complex genetic basis of cottonseed traits is requisite for achieving efficient genetic improvement of the traits. However, it is not yet clear about their genetic architecture in genomic level. GWAS has been an effective way to explore genetic basis of quantitative traits in human and many crops. This study aims to dissect genetic mechanism seven cottonseed traits by a GWAS for genetic improvement. RESULTS: A genome-wide association study (GWAS) based on a full gene model with gene effects as fixed and gene-environment interaction as random, was conducted for protein, oil and 5 fatty acids using 316 accessions and ~ 390 K SNPs. Totally, 124 significant quantitative trait SNPs (QTSs), consisting of 16, 21, 87 for protein, oil and fatty acids (palmitic, linoleic, oleic, myristic, stearic), respectively, were identified and the broad-sense heritability was estimated from 71.62 to 93.43%; no QTS-environment interaction was detected for the protein, the palmitic and the oleic contents; the protein content was predominantly controlled by epistatic effects accounting for 65.18% of the total variation, but the oil content and the fatty acids except the palmitic were mainly determined by gene main effects and no epistasis was detected for the myristic and the stearic. Prediction of superior pure line and hybrid revealed the potential of the QTSs in the improvement of cottonseed traits, and the hybrid could achieve higher or lower genetic values compared with pure lines. CONCLUSIONS: This study revealed complex genetic architecture of seven cottonseed traits at whole genome-wide by mixed linear model approach; the identified genetic variants and estimated genetic component effects of gene, gene-gene and gene-environment interaction provide cotton geneticist or breeders new knowledge on the genetic mechanism of the traits and the potential molecular breeding design strategy.