A point mutation in MC06g1112 encoding FLOWERING LOCUS T decreases the first flower node in bitter gourd (Momordica charantia L.).

In Cucurbitaceae crops, the first flower node (FFN) is an important agronomic trait which can impact the onset of maturity, the production of female flowers, and yield. However, the gene responsible for regulating FFN in bitter gourd is unknown. Here, we used a gynoecious line (S156G) with low FFN as the female parent and a monoecious line (K8-201) with high FFN as the male parent to obtain F1 and F2 generations. Genetic analysis indicated that the low FFN trait was incompletely dominant over the high FFN trait. A major quantitative trait locus (QTL)-Mcffn and four minor effect QTLs-Mcffn1.1, Mcffn1.2, Mcffn1.3, and Mcffn1.4 were detected by whole-genome re-sequencing-based QTL mapping in the S156G×K8-201 F2 population (n=234) cultivated in autumn 2019. The Mcffn locus was further supported by molecular marker-based QTL mapping in three S156G×K8-201 F2 populations planted in autumn 2019 (n=234), autumn 2020 (n=192), and spring 2022 (n=205). Then, the Mcffn locus was fine-mapped into a 77.98-kb physical region on pseudochromosome MC06 using a large S156G×K8-201 F2 population (n=2,402). MC06g1112, which is a homolog of FLOWERING LOCUS T (FT), was considered as the most likely Mcffn candidate gene according to both expression and sequence variation analyses between parental lines. A point mutation (C277T) in MC06g1112, which results in a P93S amino acid mutation between parental lines, may be responsible for decreasing FFN in bitter gourd. Our findings provide a helpful resource for the molecular marker-assisted selective breeding of bitter gourd.

Map-based cloning of the APRR2 gene controlling green stigma in bitter gourd (Momordica charantia).

Bitter gourd is an economically important vegetable and medicinal crop distinguished by its bitter fruits. Its stigma color is widely used to assess the distinctiveness, uniformity, and stability of bitter gourd varieties. However, limited researches have been dedicated to genetic basis of its stigma color. In this study, we employed bulked segregant analysis (BSA) sequencing to identify a single dominant locus McSTC1 located on pseudochromosome 6 through genetic mapping of an F2 population (n =241) derived from the cross between green and yellow stigma parental lines. An F2-derived F3 segregation population (n = 847) was further adopted for fine mapping, which delimited the McSTC1 locus to a 13.87 kb region containing one predicted gene McAPRR2 (Mc06g1638), a homolog of the Arabidopsis two-component response regulator-like gene AtAPRR2. Sequence alignment analysis of McAPRR2 revealed that a 15 bp insertion at exon 9 results in a truncated GLK domain of its encoded protein, which existed in 19 bitter gourd varieties with yellow stigma. A genome-wide synteny search of the bitter gourd McAPRR2 genes in Cucurbitaceae family revealed its close relationship with other cucurbits APRR2 genes that are corresponding to white or light green fruit skin. Our findings provide insights into the molecular marker-assisted breeding of bitter gourd stigma color and the mechanism of gene regulation for stigma color.

Fine mapping and gene silencing pinpoint Capana10g002229 as a strong candidate gene regulating the deciduous character of ripe pepper fruit (Capsicum spp.).

KEY MESSAGE: The pepper S locus, which controls the deciduous character of ripe fruit, was first fine mapped into an interval with a physical length of ~ 38.03 kb on chromosome P10. Capana10g002229, encoding a polygalacturonase, was proposed as a strong candidate gene based on sequence comparison, expression pattern analysis and virus-induced gene silencing (VIGS). The deciduous character of ripe fruit, which is controlled by the dominant S locus, is a domesticated trait with potential value in the pepper processing industry (Capsicum spp.). However, the gene associated with the S locus has not been identified. Here, one major QTL designated S10.1 was detected by using the F2 population (n = 155) derived from BA3 (Capsicum annuum) × YNXML (Capsicum frutescens) and was further verified in an intraspecific backcross population (n = 254) derived from the cross between BB3 (C. annuum) and its wild relative Chiltepin (C. annuum var. glabriusculum) with BB3 as the recurrent parent. Then, a large BC1F2 population derived from the self-pollination of BB3 × (BB3 × Chiltepin) individuals and comprising 4217 individuals was used to screen the recombinants, and the S locus was ultimately delimited into a 38.03-kb region on chromosome P10 harbouring four annotated genes. Capana10g002229, encoding a polygalacturonase (PG), was proposed as the best candidate gene for S based on sequence comparison and expression pattern analyses. Downregulation of Capana10g002229 in fruits through VIGS significantly delayed fruit softening and abscission from the fruit-receptacle junction. Taken together, the results show that Capana10g002229 could be regarded as a strong candidate gene associated with the S locus in pepper. These findings not only lay a foundation for deciphering the molecular mechanisms underlying pepper domestication but also provide a strategy for genetic improvement of the deciduous character of ripe fruit using a marker-assisted selection approach.

Fine-mapping and candidate gene analysis of the Mcgy1 locus responsible for gynoecy in bitter gourd (Momordica spp.).

KEY MESSAGE: The Mcgy1 locus responsible for gynoecy was fine-mapped into a 296.94-kb region, in which four single-nucleotide variations and six genes adjacent to them might be associate with sex differentiation in bitter gourd. Gynoecy plays an important role in high-efficiency hybrid seed production, and gynoecious plants are excellent materials for dissecting sex differentiation in Cucurbitaceae crop species, including bitter gourd. However, the gene responsible for gynoecy in bitter gourd is unknown. Here, we first identified a gynoecy locus designated Mcgy1 using the F2 population (n = 291) crossed from the gynoecious line S156G and the monoecious line K8-201 via bulked segregant analysis with whole-genome resequencing (BSA-seq) and molecular marker linkage analysis. Then, a large S156G × K8-201 F2 population (n = 5,656) was used for fine-mapping to delimit the Mcgy1 locus into a 296.94-kb physical region on pseudochromosome MC01, where included 33 annotated genes different from any homologous gynoecy genes previously reported in Cucurbitaceae species. Within this region, four underlying single-nucleotide variations (SNVs) that might cause gynoecy were identified by multiple genomic sequence variation analysis, and their six neighbouring genes were considered as potential candidate genes for Mcgy1. Of these, only MC01g1681 showed a significant differential expression at two-leaf developmental stage between S156G and its monoecious near-isogenic line S156 based on RNA sequencing (RNA-seq) and qRT-PCR analyses. In addition, transcriptome analysis revealed 21 key differentially expressed genes (DEGs) and possible regulatory pathways of the formation of gynoecy in bitter gourd. Our findings provide a new clue for researching on gynoecious plants in Cucurbitaceae species and a theoretical basis for breeding gynoecious bitter gourd lines by the use of molecular markers-assisted selection.

Quantification of dissipative effects in a complex Ginzburg-Landau equation governed laser system by tracing soliton dynamics.

The concept of dissipative solitons has provided new insight into the complex pulse dynamics in mode-locked lasers and stimulated novel laser cavity designs. However, most of these studies are restricted to qualitative regimes, because it is difficult to quantify dissipative effects in a mode-locked laser. Meanwhile, the quantification of dissipative effects is a general problem that can be also encountered in other dissipative systems. In this paper, we demonstrate a method for quantifying dissipative effects in a mode-locked laser based on analyzing the soliton dynamics traced by time-stretch dispersive Fourier transform. As a result, we are able to quantitatively reproduce the evolution of the pulse that seeds mode-locking through simulations and gain a deeper understanding of the whole process. The obtained physical picture of mode-locking allows us to propose a simple method to quantify the energy threshold for mode-locking buildup and the stability of mode-locked states. A parameter is introduced to evaluate mode-locking conditions, which can serve as a criterion for designing mode-locked lasers. This work opens up new possibilities in the diagnosis and improvement of mode-locked lasers and studies of soliton physics.

A 163-bp insertion in the Capana10g000198 encoding a MYB transcription factor causes male sterility in pepper (Capsicum annuum L.).

Male sterility provides an efficient approach for commercial exploitation of heterosis. Despite more than 20 genic male sterile (GMS) mutants documented in pepper (Capsicum annuum L.), only two causal genes have been successfully identified. Here, a novel spontaneous recessive GMS mutant, designated msc-3, is identified and characterized at both phenotypic and histological levels. Pollen abortion of msc-3 mutant may be due to the delayed tapetum degradation, leading to the non-degeneration of tetrads callosic wall. Then, a modified MutMap method and molecular marker linkage analysis were employed to fine mapping the msc-3 locus, which was delimited to the ~139.91-kb region harboring 10 annotated genes. Gene expression and structure variation analyses indicate the Capana10g000198, encoding a R2R3-MYB transcription factor, is the best candidate gene for the msc-3 locus. Expression profiling analysis shows the Capana10g000198 is an anther-specific gene, and a 163-bp insertion in the Capana10g000198 is highly correlated with the male sterile (MS) phenotype. Additionally, downregulation of Capana10g000198 in male fertile plants through virus-induced gene silencing resulted in male sterility. Finally, possible regulatory relationships of the msc-3 gene with the other two reported pepper GMS genes, msc-1 and msc-2, have been studied, and comparative transcriptome analysis reveals the expression of 16 GMS homologs are significantly downregulated in the MS anthers. Overall, our results reveal that Capana10g000198 is the causal gene underlying the msc-3 locus, providing important theoretical clues and basis for further in-depth study on the regulatory mechanisms of pollen development in pepper.

Large steering range and low-loss integrated optical phased array with SiN-Si dual-layer non-uniform antenna.

We propose and demonstrate a 64-channel SiN-Si dual-layer optical phased array (OPA). By taking advantages of both SiN and Si materials, high-power handling and efficient modulation could be achieved simultaneously. In addition, steering range and emission loss are improved by introducing the non-uniform dual-layer antenna. Thinned array efficiently utilized in microwave phased array is first introduced to the OPA. Design details and the corresponding simulation results are presented, and the proposed OPA is successfully fabricated and experimentally characterized. 2D scanning with a steering range of 120°×13.9° and with a resolution of 0.052°×2.72° is demonstrated and a total loss of 12.66 dB is also measured, making it promising for high-resolution long-distance light detection and ranging (Lidar) applications.

Simple and cost-effective broad bandwidth fiber chirped pulse amplification laser system seeded by a nonlinear amplifier.

In this paper, we demonstrate a simple and cost-effective fiber chirped pulse amplification (CPA) laser system, where a nonlinear amplifier is employed to generate broadband seeding pulses. The nonlinear amplifier can generate stable pulses with 50 nm spectral bandwidth and linear chirp. With such a seeding configuration being adapted into a fiber CPA laser system, the output bandwidth can be expanded from 7 nm to 20 nm, with only minor changes to a standard industrial fiber CPA system. The increased bandwidth allows for pulse durations of less than 100 fs, which is significantly shorter than the original configuration's 250 fs. When combined with a Fourier pulse shaper, such a fiber laser system is expected to produce pulses with energy exceeding 100 µJ and duration shorter than 100 fs.

MC03g0810, an Important Candidate Gene Controlling Black Seed Coat Color in Bitter Gourd (Momordica spp.).

Seed coat color is one of the most intuitive phenotypes in bitter gourd (Momordica spp.). Although the inheritance of the seed coat color has been reported, the gene responsible for it is still unknown. This study used two sets of parents, representing, respectively, the intersubspecific and intraspecific materials of bitter gourd, and their respective F1 and F2 progenies for genetic analysis and primary mapping of the seed coat color. A large F2:3 population comprising 2,975 seedlings from intraspecific hybridization was used to fine-map the seed coat color gene. The results inferred that a single gene, named McSC1, controlled the seed coat color and that the black color was dominant over the yellow color. The McSC1 locus was mapped to a region with a physical length of ∼7.8 Mb and 42.7 kb on pseudochromosome 3 via bulked segregant analysis with whole-genome resequencing (BSA-seq) and linkage analysis, respectively. Subsequently, the McSC1 locus was further fine-mapped to a 13.2-kb region containing only one candidate gene, MC03g0810, encoding a polyphenol oxidase (PPO). Additionally, the variations of MC03g0810 in the 89 bitter gourd germplasms showed a complete correlation with the seed coat color. Expression and PPO activity analyses showed a positive correlation between the expression level of MC03g0810 and its product PPO and the seed coat color. Therefore, MC03g0810 was proposed as the causal gene of McSC1. Our results provide an important reference for molecular marker-assisted breeding based on the seed coat color and uncover molecular mechanisms of the seed coat color formation in bitter gourd.

Energy deposition and incubation effects of nonlinear absorption of ultrashort laser pulses in dielectrics.

Although ultrashort laser has been widely employed in micromachining thanks to its excellent processing precision, one of the main challenges it faces when applied to 3D modification inside dielectrics is its processing efficiency. Many applications require multiple pulses to achieve significant modification to create structure such as microlenses. We report incubation experiments on energy deposition and the control of material modification in fused silica. This allows us to develop a practical incubation model by taking account different ionization mechanisms, in which coefficients relating to multiphoton and avalanche ionization change with laser shots due to accumulating defects. We then extend our study to the scheme where a pre-pulse is used to limit the absorption volume through pre-seeding. Both experiments and simulations show that the efficiency of laser processing can be significantly improved without sacrificing the spatial resolution with this method, especially for longer pulses.

Study on the polarization dependence of nonlinear absorption of ultrafast laser pulses in bulk fused silica.

By studying the nonlinear absorption of ultrafast laser pulses in fused silica, we examine, both with experiments and numerical simulations, the different polarization dependence of multiphoton ionization and avalanche ionization. Results show multiphoton ionization and avalanche ionization play different roles in femtosecond and picosecond laser micromachining, and the contribution via avalanche ionization increases with pulse duration. Meanwhile, the spatial distribution of the free carriers generated by circularly polarized pulses is more concentrated than those generated by linear polarization for picosecond laser pulses. These properties make the circular polarized ultrafast laser a possible way to improve the ultrafast laser micromachining efficiency and spatial quality, and can help to reduce some problematic nonlinear effects in ultrafast laser micromachining of low energy band materials.

Single-shot method to study high order solitons in all-polarization-maintaining soliton mode-locked fiber lasers.

A single-shot experimental method is proposed to study non-repetitive evolutions of high order solitons. In our experiments, high order solitons are prepared in the building up process of a soliton fiber laser, and the order of high order soliton is controlled via changing the parameters of the laser. The evolution of high order soliton is recorded by the single-shot spectral measurements-time stretch dispersive Fourier transform. A 4th order soliton evolution under perturbations of gain saturation and saturable loss is studied, showing how a leading pulse wins the competition against the tailing one. Our work provides a controllable technique to study the high order solitons evolutions, which can be applied in the research of ultrafast laser amplifications and supercontinuum generations.

Fine mapping and candidate gene analysis of the up locus determining fruit orientation in pepper (Capsicum spp.).

KEY MESSAGE: The up locus determining fruit orientation was fine-mapped into a region with a physical length of ~169.51 kb on chromosome P12 in pepper. Capana12g000958, encoding a developmentally regulated G protein 2, was proposed as the strongest candidate via sequence comparison and expression analysis. Fruit orientation is an important horticultural and domesticated trait, which is controlled by a single semi-dominant gene (up) in pepper. However, the gene underlying up locus has not yet been identified. In this study, the previously detected major QTL UP12.1 was firstly verified using a backcross population (n = 225) stem from the cross of BB3 (C. annuum) and its wild relative Chiltepin (C. annuum var. glabriusculum) using BB3 as the recurrent parent. Then, a large BC1F2 population (n = 1827) was used for recombinant screening to delimit the up locus into an interval with ~ 169.51 kb in length. Sequence comparison and expression analysis suggested that Capana12g000958, encoding a developmentally regulated G protein 2, was the most likely candidate gene for the up locus. There is no difference within the coding sequences of Capana12g000958 between BB3 and Chiltepin, while a SNP in the upstream of Capana12g000958 showed a complete correlation with the fruit orientation among a panel of 40 diverse pepper inbred lines. These findings will form a basis for gene isolation and reveal of genetic mechanism underlying the fruit orientation domestication in pepper.

Optimal conditions for self-starting of soliton mode-locked fiber lasers with a saturable absorber.

With the recently developed single-shot time-stretch dispersive Fourier transform technique, we investigate the buildup process of an all-polarization-maintaining soliton mode-locked fiber laser. Considering the multi-pulse competitions and the evolution of the survived pulse, we find an optimal range of intra-cavity energy for self-starting related to the saturation energy of the employed saturable absorber. Under the conditions, one dominant pulse can build up quickly against the others, and it finally drives to single-pulse operation. The conclusions drawn here hold for other soliton mode-locked lasers.

Development and validation of genome-wide InDel markers with high levels of polymorphism in bitter gourd (Momordica charantia).

BACKGROUND: The preferred choice for molecular marker development is identifying existing variation in populations through DNA sequencing. With the genome resources currently available for bitter gourd (Momordica charantia), it is now possible to detect genome-wide insertion-deletion (InDel) polymorphisms among bitter gourd populations, which guides the efficient development of InDel markers. RESULTS: Here, using bioinformatics technology, we detected 389,487 InDels from 61 Chinese bitter gourd accessions with an average density of approximately 1298 InDels/Mb. Then we developed a total of 2502 unique InDel primer pairs with a polymorphism information content (PIC) ≥0.6 distributed across the whole genome. Amplification of InDels in two bitter gourd lines '47-2-1-1-3' and '04-17,' indicated that the InDel markers were reliable and accurate. To highlight their utilization, the InDel markers were employed to construct a genetic map using 113 '47-2-1-1-3' × '04-17' F2 individuals. This InDel genetic map of bitter gourd consisted of 164 new InDel markers distributed on 15 linkage groups with a coverage of approximately half of the genome. CONCLUSIONS: This is the first report on the development of genome-wide InDel markers for bitter gourd. The validation of the amplification and genetic map construction suggests that these unique InDel markers may enhance the efficiency of genetic studies and marker-assisted selection for bitter gourd.

Simultaneous In Situ Characterizations of Ultrashort Laser Pulses and the Nonlinear Susceptibility of the Irradiated Medium via Time-Resolved Hybrid Coherent Anti-Stokes Raman Scattering Spectroscopy.

We propose and test a method of simultaneously characterizing ultrashort laser pulses and the nonlinear susceptibility of the irradiated medium at the site where nonlinear interactions occur. In this method, a coherent anti-Stoke Raman scattering (CARS) spectrogram is generated with the hybrid CARS technique. We confirm that abundant information is contained in, and can be extracted from, this spectrogram and develop an extraction algorithm. With this method, quantitative and comparable broadband CARS imaging based on phase retrieval is achievable without a second material for nonresonant background generation. Furthermore, this method also paves the way for studying highly localized nonlinear light-matter interactions.

Integrative Analysis of the Metabolome and Transcriptome of a Cultivated Pepper and Its Wild Progenitor Chiltepin (Capsicum annuum L. var. glabriusculum) Revealed the Loss of Pungency During Capsicum Domestication.

Pungency is a unique characteristic of chili peppers (Capsicum spp.) caused by capsaicinoids. The evolutionary emergence of pungency is thought to be a derived trait within the genus Capsicum. However, it is not well-known how pungency has varied during Capsicum domestication and specialization. In this study, we applied a comparative metabolomics along with transcriptomics analysis to assess various changes between two peppers (a mildly pungent cultivated pepper BB3 and its hot progenitor chiltepin) at four stages of fruit development, focusing on pungency variation. A total of 558 metabolites were detected in two peppers. In comparison with chiltepin, capsaicinoid accumulation in BB3 was almost negligible at the early stage. Next, 412 DEGs associated with the capsaicinoid accumulation pathway were identified through coexpression analysis, of which 18 genes (14 TFs, 3 CBGs, and 1 UGT) were deemed key regulators due to their high coefficients. Based on these data, we speculated that downregulation of these hub genes during the early fruit developmental stage leads to a loss in pungency during Capsicum domestication (from chiltepin to BB3). Of note, a putative UDP-glycosyltransferase, GT86A1, is thought to affect the stabilization of capsaicinoids. Our results lay the foundation for further research on the genetic diversity of pungency traits during Capsicum domestication and specialization.

Genome-wide identification and analysis of highly specific CRISPR/Cas9 editing sites in pepper (Capsicum annuum L.).

The CRISPR/Cas9 system is an efficient genome editing tool that possesses the outstanding advantages of simplicity and high efficiency. Genome-wide identification and specificity analysis of editing sites is an effective approach for mitigating the risk of off-target effects of CRISPR/Cas9 and has been applied in several plant species but has not yet been reported in pepper. In present study, we first identified genome-wide CRISPR/Cas9 editing sites based on the 'Zunla-1' reference genome and then evaluated the specificity of CRISPR/Cas9 editing sites through whole-genome alignment. Results showed that a total of 603,202,314 CRISPR/Cas9 editing sites, including 229,909,837 (~38.11%) NGG-PAM sites and 373,292,477 (~61.89%) NAG-PAM sites, were detectable in the pepper genome, and the systematic characterization of their composition and distribution was performed. Furthermore, 29,623,855 highly specific NGG-PAM sites were identified through whole-genome alignment analysis. There were 26,699,38 (~90.13%) highly specific NGG-PAM sites located in intergenic regions, which was 9.13 times of the number in genic regions, but the average density in genic regions was higher than that in intergenic regions. More importantly, 34,251 (~96.93%) out of 35,336 annotated genes exhibited at least one highly specific NGG-PAM site in their exons, and 90.50% of the annotated genes exhibited at least 4 highly specific NGG- PAM sites, indicating that the set of highly specific CRISPR/Cas9 editing sites identified in this study was widely applicable and conducive to the minimization of the off-target effects of CRISPR/Cas9 in pepper.

The SnRK2 family in pepper (Capsicum annuum L.): genome-wide identification and expression analyses during fruit development and under abiotic stress.

Plant-specific SnRK2 (sucrose nonfermenting-1-related protein kinase 2) genes play crucial roles in the coordination of plant growth and development and responses to stress. However, comprehensive studies have not been performed for this gene family in pepper (Capsicum annuum), a very important Solanaceous vegetable worldwide. To fully understand the status of SnRK2s in chili pepper, a total of 9 putative SnRK2 genes (named CaSnRK2.1-2.9) were identified in pepper in the present study. These genes were located on 7 different chromosomes and classified into three subfamilies based on the phylogenetic tree. Their conserved motif compositions and exon-intron structures were systematically analyzed, and the results strongly supported the classification. Furthermore, a total of 81 putative cis-elements were found in the promoter regions, and the cis-elements related to hormone and stress signaling were abundant. Finally, the CaSnRK2 gene expression profiles among different tissues, especially developing fruit tissue, and under various abiotic stresses were investigated to identify tissue-specific or stress-responsive candidates. This study was the first to comprehensively investigate the SnRK2 family in pepper, and the results provide important clues for further functional analyses of fruit development and abiotic stress responses.

Whole-genome sequencing provides insights into the genetic diversity and domestication of bitter gourd (Momordica spp.).

Bitter gourd (Momordica charantia) is a popular cultivated vegetable in Asian and African countries. To reveal the characteristics of the genomic structure, evolutionary trajectory, and genetic basis underlying the domestication of bitter gourd, we performed whole-genome sequencing of the cultivar Dali-11 and the wild small-fruited line TR and resequencing of 187 bitter gourd germplasms from 16 countries. The major gene clusters (Bi clusters) for the biosynthesis of cucurbitane triterpenoids, which confer a bitter taste, are highly conserved in cucumber, melon, and watermelon. Comparative analysis among cucurbit genomes revealed that the Bi cluster involved in cucurbitane triterpenoid biosynthesis is absent in bitter gourd. Phylogenetic analysis revealed that the TR group, including 21 bitter gourd germplasms, may belong to a new species or subspecies independent from M. charantia. Furthermore, we found that the remaining 166 M. charantia germplasms are geographically differentiated, and we identified 710, 412, and 290 candidate domestication genes in the South Asia, Southeast Asia, and China populations, respectively. This study provides new insights into bitter gourd genetic diversity and domestication and will facilitate the future genomics-enabled improvement of bitter gourd.