Pangenome analysis reveals transposon-driven genome evolution in cotton.

BACKGROUND: Transposable elements (TEs) have a profound influence on the trajectory of plant evolution, driving genome expansion and catalyzing phenotypic diversification. The pangenome, a comprehensive genetic pool encompassing all variations within a species, serves as an invaluable tool, unaffected by the confounding factors of intraspecific diversity. This allows for a more nuanced exploration of plant TE evolution. RESULTS: Here, we constructed a pangenome for diploid A-genome cotton using 344 accessions from representative geographical regions, including 223 from China as the main component. We found 511 Mb of non-reference sequences (NRSs) and revealed the presence of 5479 previously undiscovered protein-coding genes. Our comprehensive approach enabled us to decipher the genetic underpinnings of the distinct geographic distributions of cotton. Notably, we identified 3301 presence-absence variations (PAVs) that are closely tied to gene expression patterns within the pangenome, among which 2342 novel expression quantitative trait loci (eQTLs) were found residing in NRSs. Our investigation also unveiled contrasting patterns of transposon proliferation between diploid and tetraploid cotton, with long terminal repeat (LTR) retrotransposons exhibiting a synchronized surge in polyploids. Furthermore, the invasion of LTR retrotransposons from the A subgenome to the D subgenome triggered a substantial expansion of the latter following polyploidization. In addition, we found that TE insertions were responsible for the loss of 36.2% of species-specific genes, as well as the generation of entirely new species-specific genes. CONCLUSIONS: Our pangenome analyses provide new insights into cotton genomics and subgenome dynamics after polyploidization and demonstrate the power of pangenome approaches for elucidating transposon impacts and genome evolution.

Regulatory controls of duplicated gene expression during fiber development in allotetraploid cotton.

Polyploidy complicates transcriptional regulation and increases phenotypic diversity in organisms. The dynamics of genetic regulation of gene expression between coresident subgenomes in polyploids remains to be understood. Here we document the genetic regulation of fiber development in allotetraploid cotton Gossypium hirsutum by sequencing 376 genomes and 2,215 time-series transcriptomes. We characterize 1,258 genes comprising 36 genetic modules that control staged fiber development and uncover genetic components governing their partitioned expression relative to subgenomic duplicated genes (homoeologs). Only about 30% of fiber quality-related homoeologs show phenotypically favorable allele aggregation in cultivars, highlighting the potential for subgenome additivity in fiber improvement. We envision a genome-enabled breeding strategy, with particular attention to 48 favorable alleles related to fiber phenotypes that have been subjected to purifying selection during domestication. Our work delineates the dynamics of gene regulation during fiber development and highlights the potential of subgenomic coordination underpinning phenotypes in polyploid plants.

Genetic interrogation of phenotypic plasticity informs genome-enabled breeding in cotton.

Phenotypic plasticity, or the ability to adapt to and thrive in changing climates and variable environments, is essential for developmental programs in plants. Despite its importance, the genetic underpinnings of phenotypic plasticity for key agronomic traits remain poorly understood in many crops. In this study, we aim to fill this gap by using genome-wide association studies to identify genetic variations associated with phenotypic plasticity in upland cotton (Gossypium hirsutum L.). We identified 73 additive quantitative trait loci (QTLs), 32 dominant QTLs, and 6799 epistatic QTLs associated with 20 traits. We also identified 117 additive QTLs, 28 dominant QTLs, and 4691 epistatic QTLs associated with phenotypic plasticity in 19 traits. Our findings reveal new genetic factors, including additive, dominant, and epistatic QTLs, that are linked to phenotypic plasticity and agronomic traits. Meanwhile, we find that the genetic factors controlling the mean phenotype and phenotypic plasticity are largely independent in upland cotton, indicating the potential for simultaneous improvement. Additionally, we envision a genomic design strategy by utilizing the identified QTLs to facilitate cotton breeding. Taken together, our study provides new insights into the genetic basis of phenotypic plasticity in cotton, which should be valuable for future breeding.

Genomic innovation and regulatory rewiring during evolution of the cotton genus Gossypium.

Phenotypic diversity and evolutionary innovation ultimately trace to variation in genomic sequence and rewiring of regulatory networks. Here, we constructed a pan-genome of the Gossypium genus using ten representative diploid genomes. We document the genomic evolutionary history and the impact of lineage-specific transposon amplification on differential genome composition. The pan-3D genome reveals evolutionary connections between transposon-driven genome size variation and both higher-order chromatin structure reorganization and the rewiring of chromatin interactome. We linked changes in chromatin structures to phenotypic differences in cotton fiber and identified regulatory variations that decode the genetic basis of fiber length, the latter enabled by sequencing 1,005 transcriptomes during fiber development. We showcase how pan-genomic, pan-3D genomic and genetic regulatory data serve as a resource for delineating the evolutionary basis of spinnable cotton fiber. Our work provides insights into the evolution of genome organization and regulation and will inform cotton improvement by enabling regulome-based approaches.

Genome-Wide Analysis of Auxin Response Factors in Lettuce (Lactuca sativa L.) Reveals the Positive Roles of LsARF8a in Thermally Induced Bolting.

Warm temperatures induce plant bolting accompanied by flower initiation, where endogenous auxin is dynamically associated with accelerated growth. Auxin signaling is primarily regulated by a family of plant-specific transcription factors, AUXIN RESPONSE FACTORS (ARFs), which either activate or repress the expression of downstream genes in response to developmental and environmental cues. However, the relationship between ARFs and bolting has not been completely understood in lettuce yet. Here, we identified 24 LsARFs (Lactuca sativa ARFs) in the lettuce genome. The phylogenetic tree indicated that LsARFs could be classified into three clusters, which was well supported by the analysis of exon-intron structure, consensus motifs, and domain compositions. RNA-Seq analysis revealed that more than half of the LsARFs were ubiquitously expressed in all tissues examined, whereas a small number of LsARFs responded to UV or cadmium stresses. qRT-PCR analysis indicated that the expression of most LsARFs could be activated by more than one phytohormone, underling their key roles as integrative hubs of different phytohormone signaling pathways. Importantly, the majority of LsARFs displayed altered expression profiles under warm temperatures, implying that their functions were tightly associated with thermally accelerated bolting in lettuce. Importantly, we demonstrated that silencing of LsARF8a, expression of which was significantly increased by elevated temperatures, resulted in delayed bolting under warm temperatures, suggesting that LsARF8a might conduce to the thermally induced bolting. Together, our results provide molecular insights into the LsARF gene family in lettuce, which will facilitate the genetic improvement of the lettuce in an era of global warming.

Electrophysiological measurements of holistic processing of Chinese characters.

Holistic processing (HP) is a marker of perceptual expertise in facial recognition. In the present study, we examined neural responses to the HP of Chinese characters, adopting the composite paradigm. The behavioral results showed that the discrimination of congruent trials was significantly higher than that of incongruent trials, and participants responded faster. Moreover, the congruent trials elicited significantly larger N170 amplitude than the incongruent trials. The HP effect of the N170 component was observed for upright characters, as the configural information of inverted characters and misaligned characters were destroyed. Right-lateralization of processing Chinese characters was observed in the N170 amplitudes and delta-theta band oscillations. The results suggested that Chinese character recognition employed a strategy of HP, and the finding that neural indicators provide a better signal of the strength of HP in Chinese characters than behavioral indicators was also crucial.

Genomic interrogation of a MAGIC population highlights genetic factors controlling fiber quality traits in cotton.

Cotton (Gossypium hirsutum L.) fiber is the most important resource of natural and renewable fiber for the textile industry. However, the understanding of genetic components and their genome-wide interactions controlling fiber quality remains fragmentary. Here, we sequenced a multiple-parent advanced-generation inter-cross (MAGIC) population, consisting of 550 individuals created by inter-crossing 11 founders, and established a mosaic genome map through tracing the origin of haplotypes that share identity-by-descent (IBD). We performed two complementary GWAS methods-SNP-based GWAS (sGWAS) and IBD-based haplotype GWAS (hGWAS). A total of 25 sQTLs and 14 hQTLs related to cotton fiber quality were identified, of which 26 were novel QTLs. Two major QTLs detected by both GWAS methods were responsible for fiber strength and length. The gene Ghir_D11G020400 (GhZF14) encoding the MATE efflux family protein was identified as a novel candidate gene for fiber length. Beyond the additive QTLs, we detected prevalent epistatic interactions that contributed to the genetics of fiber quality, pinpointing another layer for trait variance. This study provides new targets for future molecular design breeding of superior fiber quality.

Virus-induced gene silencing (VIGS) analysis shows involvement of the LsSTPK gene in lettuce (Lactuca sativaL.) in high temperature-induced bolting.

To determine the effect of the serine/threonine protein kinase (STPK) gene on leaf lettuce bolting, we utilized virus-induced gene silencing (VIGS) using the TRV vector to silence the target gene. The 'GB30' leaf lettuce cultivar was the test material, and the methods included gene cloning, bioinformatics analysis, quantitative real-time PCR (qRT-PCR) and VIGS. LsSTPK, was cloned from the 'GB30' leaf lettuce cultivar via reverse transcription-polymerase chain reaction (RT-PCR). qRT-PCR analysis showed that the expression of LsSTPK in the stem of leaf lettuce was significantly greater than that in the roots and leaves, and after high-temperature treatment, the gene expression in the stems in the experimental group was markedly lower than that in the control groups. Following LsSTPK silencing via the VIGS method, the stem length in the treatment group was significantly greater than that in the blank and negative control groups, and the contents of auxin (IAA), GA3 and abscisic acid (ABA) in the treatment group were greater than those in the other two groups. Flower bud differentiation occurred in the treatment group but not in the control group. The above findings suggested that LsSTPK inhibits the bolting of leaf lettuce under high-temperature conditions.

Quantitative Proteomics Analysis of Lettuce (Lactuca sativa L.) Reveals Molecular Basis-Associated Auxin and Photosynthesis with Bolting Induced by High Temperature.

Bolting is a key process in the growth and development of lettuce (Lactuca sativa L.). A high temperature can induce early bolting, which decreases both the quality and production of lettuce. However, knowledge of underlying lettuce bolting is still lacking. To better understand the molecular basis of bolting, a comparative proteomics analysis was conducted on lettuce stems, during the bolting period induced by a high temperature (33 °C) and a control temperature (20 °C) using iTRAQ-based proteomics, phenotypic measures, and biological verifications using qRT-PCR and Western blot. The high temperature induced lettuce bolting, while the control temperature did not. Of the 5454 identified proteins, 619 proteins presented differential abundance induced by high-temperature relative to the control group, of which 345 had an increased abundance and 274 had a decreased abundance. Proteins with an abundance level change were mainly enriched in pathways associated with photosynthesis and tryptophan metabolism involved in auxin (IAA) biosynthesis. Moreover, among the proteins with differential abundance, proteins associated with photosynthesis and tryptophan metabolism were increased. These findings indicate that a high temperature enhances the function of photosynthesis and IAA biosynthesis to promote the process of bolting, which is in line with the physiology and transcription level of IAA metabolism. Our data provide a first comprehensive dataset for gaining novel understanding of the molecular basis underlying lettuce bolting induced by high temperature. It is potentially important for further functional analysis and genetic manipulation for molecular breeding to breed new cultivars of lettuce to restrain early bolting, which is vital for improving vegetable quality.

The Early Facilitative and Late Contextual Specific Effect of the Color Red on Attentional Processing.

Many studies have proved that color represents a variety of emotionally meaningful information. Researchers have proposed that context information endows colors with different associated meanings, and elicits corresponding behavior. Others have contended that the color red intensifies the stimulus' existing valence or motivation tendency in the early processing step. The present study attempts to incorporate these two effects of the color red to explore their differences in a dot probe task, using event-related potential (ERP). Our ERP results indicate that the color red intensifies the initial attention to emotion-congruent conditions, as indicated by the P1 component. However, the colors red and green lead to sustained attention to the expression of anger and happiness, respectively, but not fear, as shown by the late positive complex component (all results are available at: https://osf.io/k3b8c/). This study found the different processing stages of the effect of the color red during attentional processing in a discrete emotional context, using ERPs, and may refine the Color-in-Context theory.

Distraction and Expressive Suppression Strategies in Regulation of High- and Low-Intensity Negative Emotions.

The current study compared the effectiveness of distraction, an antecedent-focused strategy that involves diverting an individual's attention away from affective terms, and expressive suppression, a response-focused strategy that involves inhibiting conscious emotion-expressive behavior during an emotionally aroused state, in the regulation of high- and low-intensity unpleasant stimuli, using event-related potentials (ERPs). Sixteen participants completed an emotion regulation experiment in which they passively viewed high- or low-intensity unpleasant images (view), solved a mathematical equation presented on high- or low-intensity negative images (distraction), or suppressed their emotional expression in response to high- or low-intensity unpleasant images (suppression). Their negative experiences after implementation of these strategies were rated by participants on a 1-9 scale. We mainly found that compared with expressive suppression, distraction yielded greater attenuation of the early phase of centro-parietal LPP when the participants responded to high-intensity stimuli. In the low-intensity condition, distraction, but not expressive suppression, effectively decreased the early phase of LPP. The findings suggest that expressive suppression works as early as distraction in the high-intensity condition; more importantly, distraction is superior to expressive suppression in regulating negative emotion, which is influenced by emotional intensity.

Correlations of Electrophysiological Measurements with Identification Levels of Ancient Chinese Characters.

Studies of event-related potential (ERP) in the human brain have shown that the N170 component can reliably distinguish among different object categories. However, it is unclear whether this is true for different identifiable levels within a single category. In the present study, we used ERP recording to examine the neural response to different identification levels and orientations (upright vs. inverted) of Chinese characters. The results showed that P1, N170, and P250 were modulated by different identification levels of Chinese characters. Moreover, time frequency analysis showed similar results, indicating that identification levels were associated with object recognition, particularly during processing of a single categorical stimulus.

The time course of emotional picture processing: an event-related potential study using a rapid serial visual presentation paradigm.

The present study recorded event-related potentials using rapid serial visual presentation paradigm to explore the time course of emotionally charged pictures. Participants completed a dual-target task as quickly and accurately as possible, in which they were asked to judge the gender of the person depicted (task 1) and the valence (positive, neutral, or negative) of the given picture (task 2). The results showed that the amplitudes of the P2 component were larger for emotional pictures than they were for neutral pictures, and this finding represents brain processes that distinguish emotional stimuli from non-emotional stimuli. Furthermore, positive, neutral, and negative pictures elicited late positive potentials with different amplitudes, implying that the differences between emotions are recognized. Additionally, the time course for emotional picture processing was consistent with the latter two stages of a three-stage model derived from studies on emotional facial expression processing and emotional adjective processing. The results of the present study indicate that in the three-stage model of emotion processing, the middle and late stages are more universal and stable, and thus occur at similar time points when using different stimuli (faces, words, or scenes).

Emotional noun processing: an ERP study with rapid serial visual presentation.

Reading is an important part of our daily life, and rapid responses to emotional words have received a great deal of research interest. Our study employed rapid serial visual presentation to detect the time course of emotional noun processing using event-related potentials. We performed a dual-task experiment, where subjects were required to judge whether a given number was odd or even, and the category into which each emotional noun fit. In terms of P1, we found that there was no negativity bias for emotional nouns. However, emotional nouns elicited larger amplitudes in the N170 component in the left hemisphere than did neutral nouns. This finding indicated that in later processing stages, emotional words can be discriminated from neutral words. Furthermore, positive, negative, and neutral words were different from each other in the late positive complex, indicating that in the third stage, even different emotions can be discerned. Thus, our results indicate that in a three-stage model the latter two stages are more stable and universal.

N170 changes reflect competition between faces and identifiable characters during early visual processing.

According to the neuronal recycling hypothesis, brain circuits can gain new functions through cultural learning, which are distinct from their evolutionarily established functions, creating competition between processes such as facial and identifiable character processing. In the present study, event-related potential (ERP) recording was used to examine electrophysiological correlates of identification levels of Chinese characters as well as the competition between facial and Chinese character processing after the characters were learnt. Twenty volunteers performed a lateralized face detection task, and N170 responses were recorded when the participants viewed only Chinese characters (identifiable or unidentifiable in Xiaozhuan font), or Chinese characters and faces concurrently. Viewing identifiable Chinese characters bilaterally elicited larger N170 amplitudes than viewing unidentifiable ones. N170 amplitudes in response to faces bilaterally declined when identifiable Chinese characters and faces were viewed concurrently as compared to viewing unidentifiable Chinese characters and faces concurrently. These results indicate that the N170 component is modulated by the observer's identification level of Chinese characters, and that identifiable Chinese characters compete with faces during early visual processing.