Causal role of the frontal eye field in attention-induced ocular dominance plasticity.

Previous research has found that prolonged eye-based attention can bias ocular dominance. If one eye long-termly views a regular movie meanwhile the opposite eye views a backward movie of the same episode, perceptual ocular dominance will shift towards the eye previously viewing the backward movie. Yet it remains unclear whether the role of eye-based attention in this phenomenon is causal or not. To address this issue, the present study relied on both the functional magnetic resonance imaging (fMRI) and transcranial magnetic stimulation (TMS) techniques. We found robust activation of the frontal eye field (FEF) and intraparietal sulcus (IPS) when participants were watching the dichoptic movie while focusing their attention on the regular movie. Interestingly, we found a robust effect of attention-induced ocular dominance shift when the cortical function of vertex or IPS was transiently inhibited by continuous theta burst stimulation (cTBS), yet the effect was significantly attenuated to a negligible extent when cTBS was delivered to FEF. A control experiment verified that the attenuation of ocular dominance shift after inhibitory stimulation of FEF was not due to any impact of the cTBS on the binocular rivalry measurement of ocular dominance. These findings suggest that the fronto-parietal attentional network is involved in controlling eye-based attention in the 'dichoptic-backward-movie' adaptation paradigm, and in this network, FEF plays a crucial causal role in generating the attention-induced ocular dominance shift.

Genome-Wide Identification of the Thaumatin-like Protein Family Genes in Gossypium barbadense and Analysis of Their Responses to Verticillium dahliae Infection.

(1) Background: Plants respond to pathogen challenge by activating a defense system involving pathogenesis-related (PR) proteins. The PR-5 family includes thaumatin, thaumatin-like proteins (TLPs), and other related proteins. TLPs play an important role in response to biotic and abiotic stresses. Many TLP-encoding genes have been identified and functionally characterized in the model plant species. (2) Results: We identified a total of 90 TLP genes in the G. barbadense genome. They were phylogenetically classified into 10 subfamilies and distributed across 19 chromosomes and nine scaffolds. The genes were characterized by examining their exon-intron structures, promoter cis-elements, conserved domains, synteny and collinearity, gene family evolution, and gene duplications. Several TLP genes were predicted to be targets of miRNAs. Investigation of expression changes of 21 GbTLPs in a G. barbadense cultivar (Hai7124) resistance to Verticillium dahliae revealed 13 GbTLPs being upregulated in response to V. dahliae infection, suggesting a potential role of these GbTLP genes in disease response. (3) Conclusions: The results of this study allow insight into the GbTLP gene family, identify GbTLP genes responsive to V. dahliae infection, and provide candidate genes for future studies of their roles in disease resistance.

Rapid Mining of Candidate Genes for Verticillium Wilt Resistance in Cotton Based on BSA-Seq Analysis.

Cotton is a globally important cash crop. Verticillium wilt (VW) is commonly known as "cancer" of cotton and causes serious loss of yield and fiber quality in cotton production around the world. Here, we performed a BSA-seq analysis using an F2:3 segregation population to identify the candidate loci involved in VW resistance. Two QTLs (qvw-D05-1 and qvw-D05-2) related to VW resistance in cotton were identified using two resistant/susceptible bulks from the F2 segregation population constructed by crossing the resistant cultivar ZZM2 with the susceptible cultivar J11. A total of 30stop-lost SNPs and 42 stop-gained SNPs, which included 17 genes, were screened in the qvw-D05-2 region by SnpEff analysis. Further analysis of the transcriptome data and qRT-PCR revealed that the expression level of Ghir_D05G037630 (designated as GhDRP) varied significantly at certain time points after infection with V. dahliae. The virus-induced gene silencing of GhDRP resulted in higher susceptibility of the plants to V. dahliae than the control, suggesting that GhDRP is involved in the resistance to V. dahlia infection. This study provides a method for rapid mining of quantitative trait loci and screening of candidate genes, as well as enriches the genomic information and gene resources for the molecular breeding of disease resistance in cotton.

GhTBL34 Is Associated with Verticillium Wilt Resistance in Cotton.

Verticillium wilt (VW) is a typical fungal disease affecting the yield and quality of cotton. The Trichome Birefringence-Like protein (TBL) is an acetyltransferase involved in the acetylation process of cell wall polysaccharides. Up to now, there are no reports on whether the TBL gene is related to disease resistance in cotton. In this study, we cloned a cotton TBL34 gene located in the confidence interval of a major VW resistance quantitative trait loci and demonstrated its relationship with VW resistance in cotton. Analyzing the sequence variations in resistant and susceptible accessions detected two elite alleles GhTBL34-2 and GhTBL34-3, mainly presented in resistant cotton lines whose disease index was significantly lower than that of susceptible lines carrying the allele GhTBL34-1. Comparing the TBL34 protein sequences showed that two amino acid differences in the TBL (PMR5N) domain changed the susceptible allele GhTBL34-1 into the resistant allele GhTBL34-2 (GhTBL34-3). Expression analysis showed that the TBL34 was obviously up-regulated by infection of Verticillium dahliae and exogenous treatment of ethylene (ET), and salicylic acid (SA) and jasmonate (JA) in cotton. VIGS experiments demonstrated that silencing of TBL34 reduced VW resistance in cotton. We deduced that the TBL34 gene mediating acetylation of cell wall polysaccharides might be involved in the regulation of resistance to VW in cotton.

Genome-Wide Study of NOT2_3_5 Protein Subfamily in Cotton and Their Necessity in Resistance to Verticillium wilt.

The Negative on TATA-less (NOT) 2_3_5 domain proteins play key roles in mRNA metabolism and transcription regulation, but few comprehensive studies have focused on this protein family in plants. In our study, a total of 30 NOT2_3_5 genes were identified in four cotton genomes: Gossypium. arboretum, G. raimondii, G. hirsutum and G. barbadense. Phylogenetic analysis showed that all the NOT2_3_5 domain proteins were divided into two classes. The NOT2_3_5 genes were expanded frequently, and segmental duplication had significant effects in their expansion process. The cis-regulatory elements analysis of NOT2_3_5 promoter regions indicated that NOT2_3_5 domain proteins might participate in plant growth and development processes and responds to exogenous stimuli. Expression patterns demonstrated that all of the GhNOT2_3_5 genes were expressed in the majority of tissues and fiber development stages, and that these genes were induced by multiple stresses. Quantitative real-time PCR showed that GbNOT2_3_5 genes were up-regulated in response to verticillium wilt and the silencing of GbNOT2_3_5-3/8 and GbNOT2_3_5-4/9 led to more susceptibility to verticillium wilt than controls. Identification and analysis of the NOT2_3_5 protein family will be beneficial for further research on their biological functions.

Detection of candidate genes and development of KASP markers for Verticillium wilt resistance by combining genome-wide association study, QTL-seq and transcriptome sequencing in cotton.

KEY MESSAGE: Combining GWAS, QTL-seq and transcriptome sequencing detected basal defense-related genes showing gDNA sequence variation and expression difference in diverse cotton lines, which might be the molecular mechanisms of VW resistance in G. hirsutum. Verticillium wilt (VW), which is caused by the soil-borne fungus Verticillium dahliae, is a major disease in cotton (Gossypim hirsutum) worldwide. To facilitate the understanding of the genetic basis for VW resistance in cotton, a genome-wide association study (GWAS), QTL-seq and transcriptome sequencing were performed. The GWAS of VW resistance in a panel of 120 core elite cotton accessions using the Cotton 63K Illumina Infinium SNP array identified 5 QTL from 18 significant SNPs meeting the 5% false discovery rate threshold on 5 chromosomes. All QTL identified through GWAS were found to be overlapped with previously reported QTL. By combining GWAS, QTL-seq and transcriptome sequencing, we identified eight candidate genes showing both gDNA sequence variation and expression difference between resistant and susceptible lines, most related to transcription factors (TFs), flavonoid biosynthesis and those involving in the plant basal defense and broad-spectrum disease resistance. Ten KASP markers were successfully validated in diverse cotton lines and could be deployed in marker-assisted breeding to enhance VW resistance. These results supported our inference that the gDNA sequence variation or expression difference of those genes involving in the basal defense in diverse cotton lines might be the molecular mechanisms of VW resistance in G. hirsutum.

Regional association analysis-based fine mapping of three clustered QTL for verticillium wilt resistance in cotton (G. hirsutum. L).

BACKGROUND: Verticillium wilt is one of the most destructive diseases affecting global cotton production. The most effective way to control wilt disease has been the development of new cotton varieties that are resistant to VW. VW-resistant Upland cotton cultivars have been created in both the USA and China by Gossypium barbadense introgression. More than 100 VW resistance quantitative trait loci have been detected. RESULTS: Three clustered VW resistance-related QTL were detected in a 120-line association population and assigned to a genome region of 14,653,469-55,190,112 bp in Dt_chr9. A regional association analysis-based fine-mapping strategy was developed to narrow down the confidence intervals of the above QTL. The estimated LD decay of the genome region of interest was much faster than those of the Dt_chr9 chromosome and the whole genome, suggesting the existence of a recombination hotspot. Thirty-seven haplotype blocks were detected. The confidence intervals of the three clustered QTL were narrowed down to a region of 937,906 bp involving QTL-i23734Gh and a region of 1,389,417 bp involving QTL- i10740Gh, respectively. Each region contained the strongest association signal. Comparative analysis redefined the confidence intervals of the other three QTLs, qDL52T2-c19, QTL-BNL4069, and QTL-JESPR0001. The broad-spectrum VW resistance QTL qVW-D9-1 was demonstrated to be closely linked with the three redefined QTL, QTL-i23734Gh, QTL- i10740Gh and QTL-JESPR0001. Twelve functional genes were detected to be located within the redefined confidence intervals of VW resistance QTL. The mRNA CotAD_60243, encoding E3 ubiquitin-protein ligase UPL2-like, responsible for plant innate immunity and broad-spectrum disease resistance, was found to be overlapped with the strongest association signal i10740Gh. Six mRNAs encoding putative disease-resistance proteins were within the redefined confidence interval of QTL-JESPR0001, suggesting a tandem arrangement of R genes. CONCLUSIONS: Our results proved that the VW resistance effect related to three clustered VW resistance-related QTL was actually controled by two redefined major QTL and severlal minor loci. The broad-spectrum VW resistance QTL qVW-D9-1 may be closely linked with the two redefined major QTLs. The tandem arrangement of R genes were detected in the redefined confidence interval of QTL-JESPR0001. The candidate genes obtained should be helpful in identifying and characterizing defense genes related to VW resistance QTL.