Pepper Genome Research Articles

Small Heat Shock Protein (sHSP) Gene Family from Sweet Pepper (Capsicum annuum L.) Fruits: Involvement in Ripening and Modulation by Nitric Oxide (NO).

Small heat shock proteins (sHSPs) are usually upregulated in plants under diverse environmental stresses. These proteins have been suggested to function as molecular chaperones to safeguard other proteins from stress-induced damage. The ripening of pepper (Capsicum annuum L.) fruit involves important phenotypic, physiological, and biochemical changes, which have associated endogenous physiological nitro-oxidative stress, but they can also be significantly affected by environmental conditions, such as temperature. Based on the available pepper genome, a total of 41 sHSP genes were identified in this work, and their distributions in the 12 pepper chromosomes were determined. Among these genes, only 19 sHSP genes were found in the transcriptome (RNA-Seq) of sweet pepper fruits reported previously. This study aims to analyze how these 19 sHSP genes present in the transcriptome of sweet pepper fruits are modulated during ripening and after treatment of fruits with nitric oxide (NO) gas. The time-course expression analysis of these genes during fruit ripening showed that 6 genes were upregulated; another 7 genes were downregulated, whereas 6 genes were not significantly affected. Furthermore, NO treatment triggered the upregulation of 7 sHSP genes and the downregulation of 3 sHSP genes, whereas 9 genes were unchanged. These data indicate the diversification of sHSP genes in pepper plants and, considering that sHSPs are important in stress tolerance, the observed changes in sHSP expression support that pepper fruit ripening has an associated process of physiological nitro-oxidative stress, such as it was previously proposed.

The chloroplast genome of black pepper (Piper nigrum L.) and its comparative analysis with related Piper species.

Piper nigrum, also known as black pepper, is an economically and ecologically important crop of the genus Piper. It has been titled as the king of spices due to its wide consumption throughout the world. In the present investigation, the chloroplast genome of P. nigrum has been assembled from a whole genome sequence by integrating the short and long reads generated through Illumina and PacBio platforms, respectively. The chloroplast genome was observed to be 161,522 bp in size, having a quadripartite structure with a large single copy (LSC) region of 89,153 bp and a small single copy (SSC) region of 18,255 bp separated by a copy of inverted repeats (IRs), each 27,057 bp in length. Taking into consideration all the duplicated genes, a total of 131 genes were observed, which included 81 protein-coding genes, 37 tRNAs, 4 rRNAs, and 1 pseudogene. Individually, the LSC region consisted of 83 genes, the SSC region had 13 genes, and 18 genes were present in each IR region. Additionally, 216 SSRs were detected and 11 of these were validated through amplification in 12 species of Piper. The features of the chloroplast genome have been compared with those of the genus Piper. Our results provide useful insights into evolutionary and molecular studies of black pepper which will contribute to its further genetic improvement and breeding.

Phylogenomic analysis of cytochrome P450 multigene family and its differential expression analysis in pepper (Capsicum annuum L.).

Plant cytochrome P450 is a multifamily enzyme widely involved in biochemical reactions for the synthesis of antioxidants, pigments, structural polymers, and defense-related compounds. Pepper (Capsicum annuum L.) is an economically important plant. A comprehensive identification and characterization of P450 genes would provide valuable information on the evolutionary relationships of genes and their functional characteristics. In this study, we identified P450 genes in pepper with the aid of bioinformatics methods to investigate the phylogenetic relation, gene structure, chromosomal localization, duplicated events, and collinearity among Solanaceae species. We identified and classified 478 genes of P450 from the pepper genome into two major clades and nine subfamilies through phylogenetic analysis. Massive duplication events were found in the P450 gene family, which may explain the expansion of the P450 gene family. In addition, we also found that these duplication genes may have undergone strict purification selection during evolution. Gene expression analysis showed that some P450 genes that belong to clan 71 in pepper may play an important role in placenta and pericarp development. Through quantitative real-time polymerase chain reaction and transcriptome analysis, we also found that many P450 genes were related to defensive and phytohormone response in pepper. These findings provide insight for further studies to identify the biological functions of the P450 genes in pepper.

Genome-wide identification of RUB activating enzyme and conjugating enzyme gene families and their expression analysis under abiotic stresses in Capsicum annuum.

NEDD8/RUB, as a ubiquitin-like protein, participates in the post-translational modification of protein and requires unique E1, E2, and E3 enzymes to bind to its substrate. The RUB E1 activating enzyme and E2 conjugating enzyme play a significant role in the neddylation. However, it is unknown whether RUB E1 and E2 exist in pepper and what its function is. In this study, a total of three putative RUB E1 and five RUB E2 genes have been identified in the pepper genome. Subsequently, their physical and chemical properties, gene structure, conserved domains and motifs, phylogenetic relationship, and cis-acting elements were analyzed. The structure and conserved domain of RUB E1 and E2 are similar to that of Arabidopsis and tomato. The RUB E1 and E2 genes were randomly distributed on seven chromosomes, and there were two pairs of collinearity between pepper and Arabidopsis and eight pairs of collinearity between pepper and tomato. Phylogenetic analysis reveals that RUB E1 and E2 genes of pepper have a closer relationship with that of tomato, potato, and Nicotiana attenuate. The cis-elements of RUB E1 and E2 genes contained hormone response and stress response. RUB E1 and E2 genes were expressed in at least one tissue and CaRCE1.3 and CaRCE2.1 were exclusively expressed in flowers and anthers. Moreover, the expression of RUB E1 genes (CaECR1, CaAXR1.1, and CaAXR1.2) and RUB E2 genes (CaRCE1.1, CaRCE1.2, and CaRCE2.1) was increased to varying degrees under low-temperature, drought, salt, ABA, and IAA treatments, while CaRCE1.3 and CaRCE2.2 were down-regulated under low-temperature treatment. In addition, these genes were hardly expressed under MeJA treatment. In summary, this study provides a theoretical foundation to explore the role of RUB E1 and E2 in the response of plants to stress.

Inheritance of androgenesis response in pepper.

Anther culture has become an important part of pepper breeding. Response to haploidy via androgenesis is highly genotype-specific. However, studies on the inheritance of response to anther culture are lacking. Therefore, the study aimed to determine the inheritance of androgenesis. The plant material included crosses involving Capsicum annuum L. (253A, and Inan3363) X C. chinense PI 159,236 populations. To estimate the heritability of the trait, two pepper lines with very high androgenesis responses were crossed with PI 159,236, a non-responsive accession. The androgenesis response was phenotyped using the parents, F1, F2, BC1P1, and BC1P2/P3 created through reciprocal crosses. Using variance components, the number of genes controlling the trait, broad (H2 = 0.97), and narrow sense heritabilities (h2 = 0.20), genetic variance (VG=113.8), the additive (VA=23.9), and the dominance gene variances (VD = 89.9), as well as the environmental variance (VE = 3.6) were calculated. Additive and dominant gene effects were 21% and 79%, respectively. Results derived from two different populations showed that the number of genes controlling the trait was between 1.96 and 2.46, and H2 = 0.96-0.97, h2 = 0.20-0.65, VG=91.8-113.8, VA, = 23.9-62.7, VD = 29.1-89.9, and VE=3.5-3.6 were calculated. The X2 analysis indicated that the most suitable one is the 9: 3: 4 epistatic genetic model (X2 = 2.13, P = 0.343, N = 155). Results obtained from two different populations indicate the existence of a few major genes for response to androgenesis in pepper. Elucidating the inheritance of androgenesis is expected to pave the way for tagging the gene(s) in the pepper genome.

Genome-wide analysis of histone acetyltransferase and histone deacetylase families and their expression in fruit development and ripening stage of pepper (Capsicum annuum).

The fruit development and ripening process involve a series of changes regulated by fine-tune gene expression at the transcriptional level. Acetylation levels of histones on lysine residues are dynamically regulated by histone acetyltransferases (HATs) and histone deacetylases (HDACs), which play an essential role in the control of gene expression. However, their role in regulating fruit development and ripening process, especially in pepper (Capsicum annuum), a typical non-climacteric fruit, remains to understand. Herein, we performed genome-wide analyses of the HDAC and HAT family in the pepper, including phylogenetic analysis, gene structure, encoding protein conserved domain, and expression assays. A total of 30 HAT and 15 HDAC were identified from the pepper genome and the number of gene differentiation among species. The sequence and phylogenetic analysis of CaHDACs and CaHATs compared with other plant HDAC and HAT proteins revealed gene conserved and potential genus-specialized genes. Furthermore, fruit developmental trajectory expression profiles showed that CaHDAC and CaHAT genes were differentially expressed, suggesting that some are functionally divergent. The integrative analysis allowed us to propose CaHDAC and CaHAT candidates to be regulating fruit development and ripening-related phytohormone metabolism and signaling, which also accompanied capsaicinoid and carotenoid biosynthesis. This study provides new insights into the role of histone modification mediate development and ripening in non-climacteric fruits.

Genome-Wide Identification of Polyamine Oxidase (PAO) Family Genes: Roles of CaPAO2 and CaPAO4 in the Cold Tolerance of Pepper (Capsicum annuum L.).

Polyamine oxidases (PAOs), which are flavin adenine dinucleotide-dependent enzymes, catalyze polyamine (PA) catabolism, producing hydrogen peroxide (H2O2). Several PAO family members have been identified in plants, but their expression in pepper plants remains unclear. Here, six PAO genes were identified in the ‘Zunla-1’ pepper genome (named CaPAO1–CaPAO6 according to their chromosomal positions). The PAO proteins were divided into four subfamilies according to phylogenetics: CaPAO1 belongs to subfamily I; CaPAO3 and CaPAO5 belong to subfamily III; and CaPAO2, CaPAO4, and CaPAO6 belong to subfamily IV (none belong to subfamily II). CaPAO2, CaPAO4, and CaPAO6 were ubiquitously and highly expressed in all tissues, CaPAO1 was mainly expressed in flowers, whereas CaPAO3 and CaPAO5 were expressed at very low levels in all tissues. RNA-seq analysis revealed that CaPAO2 and CaPAO4 were notably upregulated by cold stress. CaPAO2 and CaPAO4 were localized in the peroxisome, and spermine was the preferred substrate for PA catabolism. CaPAO2 and CaPAO4 overexpression in Arabidopsis thaliana significantly enhanced freezing-stress tolerance by increasing antioxidant enzyme activity and decreasing malondialdehyde, H2O2, and superoxide accumulation, accompanied by the upregulation of cold-responsive genes (AtCOR15A, AtRD29A, AtCOR47, and AtKIN1). Thus, we identified candidate PAO genes for breeding cold-stress-tolerant transgenic pepper cultivars.

Identification and Mapping of bs8, a Novel Locus Conferring Resistance to Bacterial Spot Caused by Xanthomonas gardneri.

Although cultivars possessing recessive resistance alleles provide effective control of bacterial spot of pepper (Capsicum annuum), the deployed resistance gene, bs5, is ineffective against Xanthomonas gardneri, one of the pathogenic species. Resistance against X. gardneri was identified in C. annuum accession PI 163192, and this study sought to characterize this novel resistance and to map the resistance gene(s) to the pepper genome. We crossed PI 163192 with the susceptible cultivar Early Calwonder (ECW) to develop resistant near-isogenic lines (NILs) of ECW, designated ECW80R. The novel resistance in ECW80R was determined to be quantitative, recessively inherited, and non-hypersensitive-response causing, and inhibits lesion expansion and chlorosis. Presence of the resistance in NILs decreased the in planta bacterial population by ninefold compared with ECW. Bulked segregant analysis of resistant and susceptible individuals from an F2 population using whole genome single nucleotide polymorphisms identified a major resistance locus within an approximate 6-Mbp interval on the subtelomeric region of chromosome 11. We developed markers spanning this region and used these to genotype backcross F2 populations, which further delimited the resistance locus within a 2.3-Mbp interval. The novel resistance locus has been designated bs8. ECW80R and the linked markers developed in this study should prove useful for breeders seeking to advance this resistance into commercially relevant germplasm and for pyramiding bs8 with other resistance alleles such as bs5 and bs6. The allele bs8 will help prolong the durability of bacterial spot resistance in pepper and improve resistance to multiple species of Xanthomonas.

Differential role of Capsicum annuum FANTASTIC FOUR-like gene CaFAF1 on drought and salt stress responses

As sessile organisms, plants are potentially susceptible to diverse environmental stresses, including drought, salt, and extreme temperatures. To adapt and survive under these adverse conditions, plants have evolved sophisticated defense mechanisms. Here, we isolated the FANTASTIC FOUR-like gene CaFAF1 ( Capsicum annuum Fantastic Four 1 ) from pepper and functionally characterized this gene with respect to its responses to drought and salt stresses. We found that CaFAF1 expression was relatively abundant in all examined pepper tissues and was significantly induced by drought and salt stress. Compared with control plants, CaFAF1 -silenced pepper plants exhibited enhanced drought tolerance, accompanied by a high expression of stress-related genes and enhanced abscisic acid-mediated stomatal closure. In contrast, CaFAF1 -silenced pepper plants were sensitive to salt stress, with high electrolyte leakage and lipid peroxidation. CaFAF1 overexpression in Arabidopsis resulted in a phenotype that is the opposite of that after CaFAF1 silencing in pepper. A cell-free degradation assay using leaf crude extracts from drought- or salt-stressed pepper plants revealed that CaFAF1 degradation was promoted by drought and delayed by salt stress. Thus, we suggest that CaFAF1 plays negative and positive roles in response to drought and salt stresses, respectively, possibly via modulation of its protein stability. • We found four FANTASTIC FOUR (FAF) domain-containing genes CaFAFs in pepper genome. • CaFAF1 shows the highest induction in response to high salinity. • CaFAF1 negatively regulates drought tolerance via ABA-mediated stomatal movement. • CaFAF1 positively regulates high slat tolerance via modulation of its protein stability.

The 3D architecture of the pepper genome and its relationship to function and evolution

The organization of chromatin into self-interacting domains is universal among eukaryotic genomes, though how and why they form varies considerably. Here we report a chromosome-scale reference genome assembly of pepper (Capsicum annuum) and explore its 3D organization through integrating high-resolution Hi-C maps with epigenomic, transcriptomic, and genetic variation data. Chromatin folding domains in pepper are as prominent as TADs in mammals but exhibit unique characteristics. They tend to coincide with heterochromatic regions enriched with retrotransposons and are frequently embedded in loops, which may correlate with transcription factories. Their boundaries are hotspots for chromosome rearrangements but are otherwise depleted for genetic variation. While chromatin conformation broadly affects transcription variance, it does not predict differential gene expression between tissues. Our results suggest that pepper genome organization is explained by a model of heterochromatin-driven folding promoted by transcription factories and that such spatial architecture is under structural and functional constraints.

Identification and expression analysis of capsaicin biosynthesis pathway genes at genome level in Capsicum chinense

Capsicum chinense is one of the best ingredients for making chili sauces and extracting capsaicin. In this study, we identified 59 genes associated with shikimic acid, phenylpropane, unsaturated fatty acids, phenylalanine, valine, leucine, isoleucine and other metabolic pathways based on pepper genome. In the present study, 58 of the 59 genes involved in capsaicin synthesis were found to be unevenly distributed on 11 chromosomes, and several genes with the same number of exons and high homology were found to be clustered in a duplication region of the chromosome. The promoter regions of these genes were predicted and analyzed, and multiple gene promoters were found to contain MYB binding sites, which provided a reference for the subsequent exploration of MYB target genes. At the same time, the expression levels of genes related to capsaicin synthesis were analyzed based on different transcriptomes, and it was found that these genes showed significant differences in different plant development stages and different tissues. The results of this study will be helpful to further study the synthesis mechanism of capsaicin in Capsicum chinense and the functional relationship between genes.

Rapid Genome-Wide Location-Specific Polymorphic SSR Marker Discovery in Black Pepper by GBS Approach.

Black pepper (Piper nigrum), the “King of Spices,” is an economically important spice in India and is known for its medicinal and cultural values. SSRs, the tandem repeats of small DNA sequences, are often polymorphic in nature with diverse applications. For population structure, QTL/gene discovery, MAS, and diversity analysis, it is imperative to have their location specificity. The existing PinigSSRdb catalogs ~70K putative SSR markers but these are anonymous (unknown chromosomal location), based on 916 scaffolds rather than 26 chromosomes. Under this study, we generated ddRAD sequence data of 29 black pepper genotypes from all over India, being low-cost and most efficient technique for the identification of polymorphic markers. The major limitation of ddRAD with compromised/non-uniform coverage has been successfully overcome by taking advantage of chromosome-wise data availability. The latest black pepper genome assembly was used to extract genome-wide SSRs. A total of 276,230 genomic SSRs were mined distributed over 26 chromosomes, with relative density of 362.88 SSRs/Mb and average distance of 2.76 Kb between two SSRs. This assembly was also used to find the polymorphic SSRs in the generated GBS data of 29 black pepper genotypes utilizing rapid and cost-effective method giving 3,176 polymorphic SSRs, out of which 2015 were found to be hypervariable. The developed web-genomic resource, BlackP2MSATdb (http://webtom.cabgrid.res.in/blackp2msatdb/), is the largest and first reported web resource for genomic and polymorphic SSRs of black pepper, which is useful to develop varietal signature, coreset, physical map, QTL/gene identification, and MAS in endeavor of black pepper production.

Genome-wide identification and expression analysis of Raf-like kinase gene family in pepper (Capsicum annuum L.)

ABSTRACT As highly conserved signaling pathway modules, mitogen-activated protein kinase (MAPK) cascades play vital roles in a diverse range of stress and hormonal responses in plants. Among the established components of MAPK cascades, Raf-like MAPK kinase kinases (MAPKKKs) are associated with abscisic acid (ABA) signaling and osmotic stress responses. However, despite the availability of a pepper reference genome, few of the Raf-like kinases in pepper plants have been functionally characterized. In this study, we isolated 47 putative Raf-like kinase genes from the pepper genome based on in silico analysis, which were classified into two major categories, namely, groups B and C (further sub-grouped into B1–B4 and C1–C7, respectively) and named sequentially as CaRaf1 to CaRaf47. Subcellular localization prediction analysis revealed that most of the group B CaRaf-like kinases are probably nuclear-localized, whereas a majority of group C members targeted into the cytoplasm. Transcriptional regulation of the 47 CaRaf genes in response to treatment with ABA, drought, NaCl, and mannitol was quantitatively analyzed by reverse-transcription PCR analysis. This revealed a significant induction of subgroup B3, C2, C3, and C5 members, indicating that these genes may be functionally associated with the response to osmotic stress, mediated via both ABA-dependent and -independent pathways. The findings of this study can accordingly serve as a basis for the identification of CaRaf genes associated with the regulation of ABA signaling and osmotic stress response and thus contribute to enhancing our understanding of the biological functions of CaRaf kinases in the responses of plants to different abiotic stresses.

Genome-wide identification and expression analysis of HAK/KUP/KT potassium transporter provides insights into genes involved in responding to potassium deficiency and salt stress in pepper (Capsicum annuum L.).

The online version contains supplementary material available at 10.1007/s13205-022-03136-z.

Tomato zonate spot virus induced hypersensitive resistance via an auxin-related pathway in pepper

Tomato zonate spotvirus (TZSV) often incurs significant losses in many food and ornamental crops in Yunnan province, China, and the surrounding areas. The pepper (Capsicum chinensePI152225)can develop hypersensitive resistance following infection with TZSV, through an as yet unknown mechanism. The transcriptome dataset showed a total of 45.81 GB of clean data were obtained from six libraries, and the average percentage of the reads mapped to the pepper genome was over 90.00 %. A total of 1403 differentially expressed genes (DEGs) were obtained after TZSV infection, including 825significantly up-regulated genes and 578 down-regulated genes. The Gene Ontology (GO) and Kyoto Encyclopedia of Genes and Genomes (KEGG) pathway analyses indicated that most up-regulated DEGs were involved in basal defenses. RT-qPCR, and virus induced gene silencing (VIGS) were used preliminarily to identifyBBC_22506 and BBC_18917, among total of 71 differentially expressed genes (DEGs), that play a key role in mediating the auxin-induced signaling pathway that might take part in hypersensitive response (HR) conferred resistance to viral infection in pepper (PI152225) byTZSV. This is the first study on the mechanism of auxin resistance, involved in defense responses of pepper against viral diseases, which lay the foundation for further study on the pathogenic mechanism of TZSV, as well as the mechanism of resistance to TZSV, in peppers.

Universal gene co-expression network reveals receptor-like protein genes involved in broad-spectrum resistance in pepper (Capsicum annuum L.).

Receptor-like proteins (RLPs) on plant cells have been implicated in immune responses and developmental processes. Although hundreds of RLP genes have been identified in plants, only a few RLPs have been functionally characterized in a limited number of plant species. Here, we identified RLPs in the pepper (Capsicum annuum) genome and performed comparative transcriptomics coupled with the analysis of conserved gene co-expression networks (GCNs) to reveal the role of core RLP regulators in pepper–pathogen interactions. A total of 102 RNA-seq datasets of pepper plants infected with four pathogens were used to construct CaRLP-targeted GCNs (CaRLP-GCNs). Resistance-responsive CaRLP-GCNs were merged to construct a universal GCN. Fourteen hub CaRLPs, tightly connected with defense-related gene clusters, were identified in eight modules. Based on the CaRLP-GCNs, we evaluated whether hub CaRLPs in the universal GCN are involved in the biotic stress response. Of the nine hub CaRLPs tested by virus-induced gene silencing, three genes (CaRLP264, CaRLP277, and CaRLP351) showed defense suppression with less hypersensitive response-like cell death in race-specific and non-host resistance response to viruses and bacteria, respectively, and consistently enhanced susceptibility to Ralstonia solanacearum and/or Phytophthora capsici. These data suggest that key CaRLPs are involved in the defense response to multiple biotic stresses and can be used to engineer a plant with broad-spectrum resistance. Together, our data show that generating a universal GCN using comprehensive transcriptome datasets can provide important clues to uncover genes involved in various biological processes.

High-quality chromosome-scale genomes facilitate effective identification of large structural variations in hot and sweet peppers.

Pepper (Capsicum annuum) is an important vegetable crop that has been subjected to intensive breeding, resulting in limited genetic diversity, especially for sweet peppers. Previous studies have reported pepper draft genome assemblies using short read sequencing, but their capture of the extent of large structural variants (SVs), such as presence-absence variants (PAVs), inversions, and copy-number variants (CNVs) in the complex pepper genome falls short. In this study, we sequenced the genomes of representative sweet and hot pepper accessions by long-read and/or linked-read methods and advanced scaffolding technologies. First, we developed a high-quality reference genome for the sweet pepper cultivar 'Dempsey' and then used the reference genome to identify SVs in 11 other pepper accessions and constructed a graph-based pan-genome for pepper. We annotated an average of 42 972 gene families in each pepper accession, defining a set of 19 662 core and 23 115 non-core gene families. The new pepper pan-genome includes informative variants, 222 159 PAVs, 12 322 CNVs, and 16 032 inversions. Pan-genome analysis revealed PAVs associated with important agricultural traits, including potyvirus resistance, fruit color, pungency, and pepper fruit orientation. Comparatively, a large number of genes are affected by PAVs, which is positively correlated with the high frequency of transposable elements (TEs), indicating TEs play a key role in shaping the genomic landscape of peppers. The datasets presented herein provide a powerful new genomic resource for genetic analysis and genome-assisted breeding for pepper improvement.

Differential Functions of Pepper Stress-Associated Proteins in Response to Abiotic Stresses.

Stress-associated proteins (SAPs), a group of zinc-finger-type proteins, have been identified as novel regulators of plant abiotic and biotic stresses. However, although they have been discovered in different plant species, their precise functional roles remain unclear. Here, we identified 14 SAP subfamily genes in the pepper genome. An investigation of the promoter regions of these genes for cis-regulatory elements associated with abiotic stress responses revealed the presence of multiple stress-related elements. Domain and phylogenetic analyses using the corresponding protein sequences revealed that the CaSAP genes can be classified into six groups (I–VI) and sorted into two broad types. Expression levels of the CaSAP genes were found to be differentially induced by low temperature, the dehydration stress, or exogenous abscisic acid. Group II and IV genes were highly induced by the low temperature and dehydration treatments, respectively. Moreover, subcellular localization analysis indicated that the proteins in these two groups are distributed in the nucleus, cytoplasm, and plasma membrane. Among the pepper plants silenced with the three identified group II CaSAP genes, the CA02g10410-silenced plants showed tolerance to low temperature, whereas the CA03g17080-silenced plants were found to have temperature-sensitive phenotypes. Interestingly, group IV CaSAP-silenced pepper plants showed drought-tolerant phenotypes. These findings contribute to a preliminary characterization of CaSAP genes and provide directions for future research on the biological role of CaSAPs in response to different abiotic stresses.

Genome-wide identification and genetic characterization of the CaMYB family and its response to five types of heavy metal stress in hot pepper (Capsicum annuum cv. CM334)

MYB proteins play a crucial role in plant growth and development and stress responses. In this study, 160 members of the MYB gene family from the pepper genome database were used to analyze gene structures, chromosome localization, collinearity, genetic affinity and expression in response to heavy metals. The results identified R2R3-MYB members and further phylogenetically classified them into 35 subgroups based on highly conserved gene structures and motifs. Collinearity analysis showed that segmental duplication events played a crucial role in the functional expansion of the CaMYB gene family by intraspecific collinearity, and at least 12 pairs of CaMYB genes existed between species prior to the differentiation between monocots and dicots. Moreover, the upstream CaMYB genes were mainly localized to the phytohormone elements ABRE and transcription factor elements MYB and MYC. Further analysis revealed that MYB transcription factors were closely associated with a variety of abiotic stress-related proteins (e.g., MAC-complex and SKIP). Under the stress of five metal ions, Cd2+, Cu2+, Pb2+, Zn2+, and Fe3+, the expression levels of some CaMYB family genes were upregulated. Of these genes, pairing homologous 1 (PH-1), PH-13, and PH-15 in the roots of Capsicum annuum were upregulated to the greatest extent, indicating that these three MYB family members are particularly sensitive to these five metals. This study provides a theoretical reference for the analysis of the molecular regulatory mechanism of MYB family genes in mediating the response to heavy metals in plants. This study reveals the mode of interaction between MYB and a variety of abiotic stress proteins and clarifies the biological functions of CaMYB family members in the regulation of heavy metal stress.

A consensus and saturated genetic map provides insight into genome anchoring, synteny of Solanaceae and leaf- and fruit-related QTLs in wolfberry (Lycium Linn.)

BackgroundLycium Linn. (Solanaceae) is a genus of economically important plants producing fruits and leaves with high nutritional value and medicinal benefits. However, genetic analysis of this plant and molecular breeding for quality improvement are limited by the lack of sufficient molecular markers.ResultsIn this study, two parental strains, ‘Ningqi No. 1’ (Lycium barbarum L.) and ‘Yunnan Gouqi’ (Lycium yunnanense Kuang et A.M. Lu), and 200 F1 hybrid individuals were resequenced for genetic analysis. In total, 8,507 well-selected SNPs were developed, and a high-density genetic map (NY map) was constructed with a total genetic distance of 2,122.24 cM. A consensus genetic map was established by integrating the NY map and a previously published genetic map (NC map) containing 15,240 SNPs, with a total genetic distance of 3,058.19 cM and an average map distance of 0.21 cM. The 12 pseudochromosomes of the Lycium reference genome were anchored using this consensus genetic map, with an anchoring rate of 64.3%. Moreover, weak collinearities between the consensus map and the pepper, potato, and tomato genomes were observed. Twenty-five stable QTLs were identified for leaf- and fruit-related phenotypes, including fruit weight, fruit longitude, leaf length, the fruit index, and the leaf index; these stable QTLs were mapped to four different linkage groups, with LOD scores ranging from 2.51 to 19.37 and amounts of phenotypic variance explained from 6.2% to 51.9%. Finally, 82 out of 188 predicted genes underlying stable QTLs for fruit-related traits were differentially expressed according to RNA-seq analysis.ConclusionsA chromosome-level assembly can provide a foundation for further functional genomics research for wolfberry. The genomic regions of these stably expressed QTLs could be used as targets for further fine mapping and development of molecular markers for marker-assisted selection (MAS). The present study provided valuable information on saturated SNP markers and reliable QTLs for map-based cloning of functional genes related to yield and morphological traits in Lycium spp.