Analysis of Non-pungency, Aroma, and Origin of a Capsicum chinense Cultivar from a Caribbean Island

Expression of alcohol acyltransferase is a potential determinant of fruit volatile ester variations in Capsicum

KEY MESSAGE

The transcript level of alcohol acyltransferase 1 (AAT1) may be the main factor influencing the variations in volatile esters that characterizing the fruity/exotic aroma of pepper fruit. Volatile esters are key components for characterizing the fruity/exotic aroma of pepper (Capsicum spp.) fruit. In general, the volatile ester content in the fruit is the consequence of a delicate balance between their synthesis by alcohol acyltransferases (AATs) and degradation by carboxylesterases (CXEs). However, the precise role of these families of enzymes with regard to volatile ester content remains unexplored in Capsicum. In this study, we found that the volatile ester content was relatively low in C. annuum and much higher in C. chinense, particularly in pungent varieties. Additionally, fruits collected from multiple non-pungent C. chinense varieties, which harbor loss-of-function mutations in capsaicinoid biosynthetic genes, acyltransferase (Pun1), putative aminotransferase (pAMT), or putative ketoacyl-ACP reductase (CaKR1) were analyzed. The volatile ester contents of non-pungent C. chinense varieties (pamt/pamt) were equivalent to those of pungent varieties, but their levels were significantly lower in non-pungent NMCA30036 (pun12/pun12) and C. chinense (Cakr1/Cakr1) varieties. Multiple AAT-like sequences were identified from the pepper genome sequences, whereas only one CXE-like sequence was identified. Among these, AAT1, AAT2, and CXE1 were isolated from fruits of C. chinense and C. annuum. Gene expression analysis revealed that the AAT1 transcript level is a potential determinant of fruit volatile ester variations in Capsicum. Furthermore, enzymatic assays demonstrated that AAT1 is responsible for the biosynthesis of volatile esters in pepper fruit. Identification of a key gene for aroma biosynthesis in pepper fruit will provide a theoretical basis for the development of molecular tools for flavor improvement.

Genetic mapping revealed that the Pun2 gene in Capsicum chacoense encodes a putative aminotransferase

Several genes regulating capsaicinoid biosynthesis including Pun1 (also known as CS), Pun3, pAMT, and CaKR1 have been studied. However, the gene encoded by Pun2 in the non-pungent Capsicum chacoense is unknown. This study aimed to identify the Pun2 gene by genetic mapping using interspecific (C. chacoense × Capsicum annuum) and intraspecific (C. chacoense × C. chacoense) populations. QTL mapping using the interspecific F₂ population revealed two major QTLs on chromosomes 3 and 9. Two bin markers within the QTL regions on two chromosomes were highly correlated with the capsaicinoid content in the interspecific population. The major QTL, Pun2_PJ_Gibbs_3.11 on chromosome 3, contained the pAMT gene, indicating that the non-pungency of C. chacoense may be attributed to a mutation in the pAMT gene. Sequence analysis revealed a 7 bp nucleotide insertion in the 8^th exon of pAMT of the non-pungent C. chacoense. This mutation resulted in the generation of an early stop codon, resulting in a truncated mutant lacking the PLP binding site, which is critical for pAMT enzymatic activity. This insertion co-segregated with the pungency phenotype in the intraspecific F₂ population. We named this novel pAMT allele pamt¹¹ . Taken together, these data indicate that the non-pungency of C. chacoense is due to the non-functional pAMT allele, and Pun2 encodes the pAMT gene.

Capsaicinoid biosynthesis in the pericarp of chili pepper fruits is associated with a placental septum-like transcriptome profile and tissue structure

CAP biosynthesis in the pericarp of chili pepper fruits occurs with an ambiguous boundary in the placental septum and pericarp. Capsaicinoid (CAP) is a pungent ingredient of chili pepper fruits. Generally, CAP biosynthesis is limited to the placental septum of fruits, but it has been reported that its biosynthesis occurs even in the pericarp of some extremely pungent varieties, resulting in a substantial increase in total content. To examine the mechanism of CAP biosynthesis in the pericarp, comparative transcriptome analysis of a variety that produces CAP in the pericarp (MY) and a variety that does not (HB) was carried out. RNA-seq revealed that 2264 genes were differentially expressed in the MY pericarp compared with the HB pericarp. PCA analysis and GO enrichment analysis indicated that the MY pericarp has a gene expression profile more like placental septum than the HB pericarp. The gene expression of CAP biosynthesis-related genes in the MY pericarp changed coordinately with the placental septum during fruit development. In most Capsicum accessions including HB, the distribution of slender epidermal cells producing CAP was limited to the placental septum, and the morphological boundary between the placental septum and pericarp was clear. In some extremely pungent varieties such as MY, slender epidermal cells ranged from the placental septum to the pericarp region, and the pericarp was morphologically similar to the placental septum, such as the absence of large sub-epidermal cells and abundant spaces in the parenchymal tissue. Our data suggest that CAP biosynthesis in the pericarp occurred with an ambiguous boundary in the placental septum and pericarp. These findings contribute to further enhancement of CAP production in chili pepper fruits.

Characterization of newly developed pepper cultivars (Capsicum chinense) 'Dieta0011-0301', 'Dieta0011-0602', 'Dieta0041-0401', and 'Dieta0041-0601' containing high capsinoid concentrations and a strong fruity aroma

Capsaicinoids are responsible for the pungent flavor of peppers (Capsicum sp.). The cultivar CH-19 Sweet is a non-pungent pepper mutant that biosynthesizes the low-pungent capsaicinoid analogs, capsinoids. Capsinoids possess important pharmaceutical properties. However, capsinoid concentrations are very low in CH-19 Sweet, and Capsicum cultivars with high content capsinoids are desirable for industrial applications of capsinoids. Habanero, Bhut Jolokia, and Infinity are species of Capsicum chinense, and have strong pungency and intense fruity flavors. In the present study, we report new cultivars with high concentrations of capsinoids (more than ten-fold higher than in CH-19 Sweet), and showed that these cultivars (Dieta0011-0301 and Dieta0011-0602 from Bhut Jolokia, Dieta0041-0401 and Dieta0041-0601 from Infinity) are of nutritional and medicinal value and have fruity aromas. We also obtained a vanilla bean flavor, vanillyl alcohol, and vanillyl ethyl ether from capsinoids in the fruit of these cultivars following the addition of ethanol at room temperature.

ABBREVIATIONS

p-AMT: putative aminotransferase; C. annuum: Capsicum annuum; C. chinense: Capsicum chinense; dCAPS: derived Cleaved Amplified Polymorphic Sequences.

Assessment of Capsaicinoid and Capsinoid Accumulation Patterns during Fruit Development in Three Chili Pepper Genotypes (Capsicum spp.) Carrying Pun1 and pAMT Alleles Related to Pungency

Quantification, using an accurate analytical approach, of capsinoids and capsaicinoids was performed on three chili pepper (Capsicum spp.) genotypes: "Chiltepı́n", "Tampiqueño 74", and "Bhut Jolokia" at various stages of fruit development. The accumulation of capsinoids, in all these peppers started between 10 to 20 days post-anthesis (dpa), increased and reached the highest capsinoid amount at 40 dpa, and then decreased until 60 dpa. Conversely, capsaicinoids could already be determined at 10 dpa in "Bhut Jolokia" and their accumulation pattern was different from that of the capsinoids in this genotype. The capsiate/dihydrocapsiate ratio presented a higher variation between genotypes and developmental stages than the capsaicin/dihydrocapsaicin ratio. Capsinoid ratios (4-24%) and Pun1/pAMT genotyping were determined. These results provide information on the progress of the accumulation of capsinoids in the aforementioned pungent and superhot cultivars and could support future breeding studies toward the understanding of the factors affecting their accumulation.

Positional differences of intronic transposons in pAMT affect the pungency level in chili pepper through altered splicing efficiency

Capsaicinoids are unique compounds that give chili pepper fruits their pungent taste. Capsaicinoid levels vary widely among pungent cultivars, which range from low pungency to extremely pungent. However, the molecular mechanisms underlying this quantitative variation have not been elucidated. Our previous study identified various loss-of-function alleles of the pAMT gene which led to low pungency. The mutations in these alleles are commonly defined by Tcc transposon insertion and its footprint. In this study, we identified two leaky pamt alleles (pamt^L1 and pamt^L2 ) with different levels of putative aminotransferase (pAMT) activity. Notably, both alleles had a Tcc transposon insertion in intron 3, but the locations of the insertions within the intron were different. Genetic analysis revealed that pamt^L1 , pamt^L2 and a loss-of-function pamt allele reduced capsaicinoid levels to about 50%, 10% and less than 1%, respectively. pamt^L1 and pamt^L2 encoded functional pAMT proteins, but they exhibited lower transcript levels than the functional type. RNA sequencing analysis showed that intronic transposons disrupted splicing in intron 3, which resulted in simultaneous expression of functional pAMT mRNA and non-functional splice variants containing partial sequences of Tcc. The non-functional splice variants were more dominant in pamt^L2 than in pamt^L1 . This suggested that the difference in position of the intronic transposons could alter splicing efficiency, leading to different pAMT activities and reducing capsaicinoid content to different levels. Our results provide a striking example of allelic variations caused by intronic transposons; these variations contribute to quantitative differences in secondary metabolite contents.

Carotenoids of Capsicum Fruits: Pigment Profile and Health-Promoting Functional Attributes

Pepper of the Capsicum species is a common ingredient in various food preparations by different cultures worldwide. The Capsicum is recognised by its five main domesticated species, namely Capsicum annuum, C. baccatum, C. chinense, C. frutescens and C. pubescens. The genetic diversity in Capsicum offers fruits in wide ranges of morphology and carotenoid profile. Carotenoids enhance the value of pepper from a nutritional standpoint, despite being commonly prized for the pharmacologically active pungent capsaicinoids. Carotenoids of pepper comprise mainly of the unique, powerful and highly stable capsanthin and capsoroubin, together with β-carotene, β-cryptoxanthin, lutein, zeaxanthin, antheraxanthin and violaxanthin. These carotenoids are present at diverse profile and varying levels, biosynthetically connected to the fruit maturity stages. This review describes the health-promoting functional attributes of the carotenoids that are mainly associated with their excellent role as lipophilic antioxidants. Capsicum as a great source of carotenoids is discussed in the aspects of main domesticated species, biosynthesis, pigment profile, antioxidant activity and safety. Findings from a number of in vitro, in vivo and clinical studies provided appreciable evidence on the protective effects of pepper’s carotenoids against degenerative diseases. Hence, pepper with its functional carotenoids might be recommended in health-promoting and disease preventing strategies.

Biochemistry and molecular biology of capsaicinoid biosynthesis: recent advances and perspectives

The most widely known characteristic of chili pepper fruits is their capacity to produce capsaicinoids, which are responsible for the pungent sensation. The capsaicinoids have several uses in different areas, such as the pharmaceutical, cosmetic and agronomic industries, among others. They are synthesized by the condensation of vanillylamine (derived from phenylalanine) with a branched-chain fatty acid (from valine or leucine precursors), and they generally accumulate in the placental tissue of the chili pepper fruits. The pungency grade depends on the genotype of the plant but is also affected by external stimuli. In recent years, new structural and regulatory genes have been hypothesized to participate in the capsaicinoid biosynthetic pathway. Moreover, the role of some of these genes has been investigated. Substantial progress has been made in discerning the molecular biology of this pathway; however, many questions remain unsolved. We previously reviewed some aspects of the biochemistry and molecular biology of capsaicinoid biosynthesis (Aza-González et al. Plant Cell Rep 30:695-706. Aza-González et al., Plant Cell Rep 30:695-706, 2011), and in this review, we describe advances made by different researchers since our previous review, including the contribution of omics to the knowledge of this pathway.

A MYB transcription factor is a candidate to control pungency in Capsicum annuum

Identification of a novel pungency-controlling gene Pun3, which acts as a master regulator of capsaicinoid biosynthetic genes in Capsicum annuum. Capsaicinoid is a unique compound that gives hot peppers (Capsicum spp.) their spicy taste. The Pun1 and Pun2 loci are known to control pungency in Capsicum species. Whereas Pun1 encodes an acyltransferase, the identity of Pun2 is currently unknown. Here, we used recombinant inbred lines and F₂ plants derived from a cross between the non-pungent C. annuum accession 'YCM334' and the pungent C. annuum cultivar 'Tean' to identify a novel non-pungency locus. Inheritance studies showed that non-pungency in C. annuum 'YCM334' is controlled by a single recessive gene, which we named Pun3. Using a high-density SNP map derived from genotyping-by-sequencing, Pun3 was mapped to chromosome 7. By comparing physical information about the Pun3 region in the C. annuum 'Zunla-1' and C. chinense 'PI159236' reference genomes, we identified candidate genes in this target region. One cDNA sequence from 'PI159236' was homologous to an unannotated gene in 'Zunla-1.' This sequence was also homologous to CaMYB31, which is expressed only in 'Tean' and harbors one stop codon in the non-pungent accession 'YCM334.' RNA-Seq analysis showed that major structural genes in the capsaicinoid biosynthetic pathway were significantly downregulated in 'YCM334' compared to pungent pepper. Therefore, CaMYB31 is a candidate gene for Pun3, which may act as a master regulator of capsaicinoid biosynthetic genes in pepper.

Mutation in the putative ketoacyl-ACP reductase CaKR1 induces loss of pungency in Capsicum

A putative ketoacyl-ACP reductase (CaKR1) that was not previously known to be associated with pungency of Capsicum was identified from map-based cloning and functional characterization. The pungency of chili pepper fruits is due to the presence of capsaicinoids, which are synthesized through the convergence of the phenylpropanoid and branched-chain fatty acid pathways. The extensive, global use of pungent and non-pungent peppers underlines the importance of understanding the genetic mechanism underlying capsaicinoid biosynthesis for breeding pepper cultivars. Although Capsicum is one of the earliest domesticated plant genera, the only reported genetic causes of its loss of pungency are mutations in acyltransferase (Pun1) and putative aminotransferase (pAMT). In this study, a single recessive gene responsible for the non-pungency of pepper No.3341 (C. chinense) was identified on chromosome 10 using an F₂ population derived from a cross between Habanero and No.3341. Five candidate genes were identified in the target region, within a distance of 220 kb. A candidate gene, a putative ketoacyl-ACP reductase (CaKR1), of No.3341 had an insertion of a 4.5-kb transposable element (TE) sequence in the first intron, resulting in the production of a truncated transcript missing the region coding the catalytic domain. Virus-induced gene silencing of CaKR1 in pungent peppers resulted in the decreased accumulation of capsaicinoids, a phenotype consistent with No.3341. Moreover, GC-MS analysis of 8-methyl-6-nonenoic acid, which is predicted to be synthesized during the elongation cycle of branched-chain fatty acid biosynthesis, revealed that its deficiency in No.3341. Genetic, genomic, transcriptional, silencing, and biochemical precursor analyses performed in combination provide a solid ground for the conclusion that CaKR1 is involved in capsaicinoid biosynthesis and that its disruption results in a loss of pungency.

QTL mapping and GWAS reveal candidate genes controlling capsaicinoid content in Capsicum

Capsaicinoids are unique compounds produced only in peppers (Capsicum spp.). Several studies using classical quantitative trait loci (QTLs) mapping and genomewide association studies (GWAS) have identified QTLs controlling capsaicinoid content in peppers; however, neither the QTLs common to each population nor the candidate genes underlying them have been identified due to the limitations of each approach used. Here, we performed QTL mapping and GWAS for capsaicinoid content in peppers using two recombinant inbred line (RIL) populations and one GWAS population. Whole-genome resequencing and genotyping by sequencing (GBS) were used to construct high-density single nucleotide polymorphism (SNP) maps. Five QTL regions on chromosomes 1, 2, 3, 4 and 10 were commonly identified in both RIL populations over multiple locations and years. Furthermore, a total of 109 610 SNPs derived from two GBS libraries were used to analyse the GWAS population consisting of 208 C. annuum-clade accessions. A total of 69 QTL regions were identified from the GWAS, 10 of which were co-located with the QTLs identified from the two biparental populations. Within these regions, we were able to identify five candidate genes known to be involved in capsaicinoid biosynthesis. Our results demonstrate that QTL mapping and GBS-GWAS represent a powerful combined approach for the identification of loci controlling complex traits.