A multi-omics approach identifies bHLH71-like as a positive regulator of yellowing leaf pepper mutants exposed to high-intensity light

Light quality and intensity can have a significant impact on plant health and crop productivity.Chlorophylls and carotenoids are classes of plant pigments that are responsible for harvesting light energy and protecting plants from the damaging effects of intense light.Our understanding of the role played by plant pigments in light sensitivity has been aided by light-sensitive mutants that change colors upon exposure to light of variable intensity.In this study,we conducted transcriptomic,metabolomic,and hormone analyses on a novel yellowing mutant of pepper(yl1)to shed light on the molecular mechanism that regulates the transition from green to yellow leaves in this mutant upon exposure to high-intensity light.Our results revealed greater accumulation of the carotenoid precursor phytoene and the carotenoids phytofluene,antheraxanthin,and zeaxanthin in yl1 compared with wild-type plants under high light intensity.A transcriptomic analysis confirmed that enzymes involved in zeaxanthin and antheraxanthin biosynthesis were upregulated in yl1 upon exposure to high-intensity light.We also identified a single basic helix–loop–helix(bHLH)transcription factor,bHLH71-like,that was differentially expressed and positively correlated with light intensity in yl1.Silencing of bHLH71-like in pepper plants suppressed the yellowing phenotype and led to reduced accumulation of zeaxanthin and antheraxanthin.We propose that the yellow phenotype of yl1 induced by high light intensity could be caused by an increase in yellow carotenoid pigments,concurrent with a decrease in chlorophyll accumulation.Our results also suggest that bHLH71-like functions as a positive regulator of carotenoid biosynthesis in pepper.

A global view of transcriptome dynamics during flower development in Capsicum annuum L.

An analysis of genome-wide gene expression profiles during floral organ development can provide important clues about the molecular basis of gene functions and developmental processes.In this study,we analyzed the transcriptome data of 36 samples obtained during floral organ development from pepper‘6421’and detected 30016 genes that were expressed in at least one sample.K-means clustering analysis was used to classify the data into 16 clusters based on the similarities between the dynamic expression profiles of genes.Of these,15 clusters exhibited notable up-regulation or down-regulation trends in different developmental stages or tissues of floral organs.We identified transcription factors expressed at the early,medium,and late stages of bud development(F1,F5,F9).Transcription factor families such as AP2-ERF,MADS-box,MYB,bHLH,and NAC showed significant levels of enrichment.In comparison with genes expressed in vegetative tissues at different stages,certain genes were specifically up-regulated during flower development;among these,the number of genes specifically up-regulated during the stamen(Sta10)and bud tetrad development(F4)stages was the highest.Through extensive studies of the ABCDE model of flower development in Arabidopsis,we identified 17 ABCDE model candidate genes in pepper,most of which were up-regulated at specific stages of flower bud development.The expression data provided in this study is the most comprehensive dataset available for pepper to date and will serve as a resource for identifying the functions of many specific genes involved in flower development in pepper and other Solanaceae plants.

Comparative Transcriptome Analysis between Cytoplasmic Male-sterile Line and Its Maintainer During the Floral Bud Development of Pepper

The male-sterile line has been largely used in the hybrid seed production of pepper, which can effectively improve the efficiency of hybrid seed production. However, the formation mechanism of male sterility in pepper remains unclear. In the present study, we compared the gene expression patterns between pepper cytoplasmic male sterile line 9704 A and its maintainer 9704 B during floral bud development using RNA sequencing technology. A total of 547 976 and 2 416 Differentially Expressed Genes(DEGs) were identified in the stage S1, S2 and S3, respectively,and more than 70% of the DEGs were down-regulated in the sterile line. Gene Ontology(GO), and Kyoto Encyclopedia of Genes and Genomes(KEGG) enrichment analyses were performed to further understand the functions of these identified DEGs. The results showed that the DEGs were mainly enriched in pathways of starch and sucrose metabolism, pentose and glucuronate interconversions. A number of genes, such as MS1, PME5, ATPB, and lots of transcription factors were found down-regulated in the sterile line, and we also identified a series of genes with large differences in expression patterns between sterile line and maintainer line. Collectively, our findings laid a foundation for further molecular breeding in pepper and provided new insights into its mechanism underlying the male sterility.

Novel structural annotation and functional expression analysis of GTP_EFTU conserved genes in pepper based on the PacBio sequencing data

Genes containing GTP_EFTU domain mainly express elongation factors(EF),Small GTPases,and GTP-binding proteins,which are closely related to protein synthesis,extension and ATP synthesis.In this study,we identified 39 genes containing GTP_EFTU domains from peppers.The evolutionary trees constructed from capsicum,Arabidopsis,rice,and tomato are mainly divided into 7 subfamilies.Using PacBio(Pacific Biosciences)sequencing and assembly data,we extracted these 39 gene sequences,fromwhich 25 genes had alternative splicing.Particularly,the Capana08g000545 had 16 alternative splicing processes.Accordingly,we performed promoter sequence analysis,subcellular location prediction,the expression analysis of different tissues and periods,and also the GO(Gene ontology)analysis of co-expressed genes.Lastly we did the qRTPCR analysis in 5 stages of pepper fruit development.These analyses revealed important structural and functional information for the identified 39 genes that contain GTP_EFTU domains,providing important references for further follow-up experiments to verify the genes function on plants or their unique roles in peppers.

PepperHub, an Informatics Hub for the Chili Pepper Research Community

Dear Editor Pepper belongs to the Solanaceae family, which includes many important vegetable crops such as tomato, potato, and eggplant. Not only widely used as vegetables and spicy ingredients, pepper also has diverse applications in pharmaceutics, natural coloring agents, cosmetics, defense repellents, and as ornamental plants （Kim et al., 2014; Qin et al., 2014）. Pepper is among the most widely cultivated and consumed vegetables in the world, with annual production reachincl to 38 million tons in 2011 （www.fao.