Genes responsible for pepper heat
Authors: Arpita Srivastava and Manisha Mangal
Indian Agricultural Research Institute, Pusa Campus, New Delhi

Pungency is specific to pepper group which is caused by a group of alkaloids popularly called capsaicinoids. Human being has since time immemorial being enjoying the heat from pepper and spices derived from pepper. Capsaicin also has wide application as a pain reliever in medicine. All the aforementioned features make peppers one of the most important vegetables produced globally.

Capsaicinoid biosynthesis and accumulation in pepper fruits besides being genetically determined are also developmentally and environmentally regulated. The Capsicum genus includes over 33 species of peppers, from which C. annuum, C. frutescens, C. chinense, C. baccatum, and C. pubescens are the most widely cultivated ones. Wide genetic variation in pungency level has been observed across Capsicum species. For example, the non-pungent sweet bell pepper from C. annuum scored 0 SHU (Scoville Heat Unit; a scale that indicates the amount of capsaicin), while 'Bhut Jolokia', a putative interspecific hybrid between C. chinense and C. frutescens from Northeastern India, scores up to 1,001,304 SHUs. The latter has made its place as the hottest pepper in the world. High genetic variability for pungency provides us with opportunities to breed for pepper varieties with different levels of pungency.

Capsaicinoids are a result of the convergence of the phenylpropanoid and the branched-chain fatty acid synthesis pathways derived from vanillylamine and an acyl group. Starting from the phenylpropanoid pathway, vanillylamine is produced after a series of steps. At last, vanillyamine is transformed into an amide (capsaicinoid) after the vanillyamine reacts with an acyl group contained in a fatty acid. Therefore, enzymes involved in vanillylamine synthesis and fatty acid synthesis are important for capsaicinoid synthesis. Variation in the structure of the acyl groups in particular, determines the intensity of pungency. Although more than ten different capsaicinoid structures exist in chili pepper, capsaicin is the most abundantly present resulting in pepper hottness.

Genetics of capsaicinoid levels still remains poorly understood though with the recent sequencing of pepper genome shows promise in better understanding of the capsaicinoid synthesis pathway. Till date fifty five candidate genes have been proposed to be involved in capsaicinoid synthesis among which the Pun1 gene is the only gene identified to date and reported to have significant effect on capsaicin levels. Pun1 has been mapped on chromosome 2 and said to have dominant nature as reported from the works Blum et al., 2002 and Stewart et al., 2005. This gene is reported to have two allelic forms which are recessive in nature and confers non-pungency. Pun1 is involved in synthesis of an enzyme acyltransferase 3 (AT3) the expression of which is up-regulated in the early fruit development stages and downregulated nearly 40 days after anthesis. Molecular characterization of the pun1 gene has shown that a 2.5-kb deletion comprising the promoter and the first exon significantly reduces AT3 protein synthesis. Moreover, a 4-bp deletion located in the first exon of allele pun12 leads to a frame shift mutation resulting in an aberrant AT3 protein and therefore reduced levels of capsaicin. These genetic disruptions can reduce capsaicin levels up to 70%.

Accumulation of capsaicinoids occur in specialized structures named as blisters, formed along the interlocular septum of pepper fruits. A recessive gene 'lov' controls the formation of blisters which co-segregated with the pun12 allele, and later on further studies, they turned out to be the same allele of the Pun1 gene. A SNP located at the 3' end of the Pun1 gene was also identified between pungent and non-pungent peppers which promises to be used as a marker for selection of pungency and non-pungency traits.

In addition to Pun1 locus on chromosome 2, two major QTLs identified on chromosome 7 play an important role in capsaicin production. Strong interaction of these QTLs with another QTL fw2 located on chromosome 2 and determining fruit weight has been discovered. The interaction between QTLs on chromosome 7 and 2 explained 37-42% of the variation in capsaicin contents, while the QTLs on chromosome 7 alone explained only 16-17% of the variation in capsaicin. Two to three minor QTLs responsible for capsaicin and dihydrocapsaicin have also been identified on chromosomes 3 and 4. Candidate genes important in capsaicin synthesis have also been mapped to chromosomes 1, 2, 3, 4, 6, 7, 8, 11, and 12. The chromosomes where these genes localize correspond to previous QTL mapping results.

Table1. Chromosomal co-localization between QTLs associated with capsaicin and dihydrocapsaicin synthesis (Ben-Chaim et al., 2006) and candidate genes proposed by Mazourek et al. (2009). cap: capsaicin synthesis QTLs; dhc: dihydrocapsaicin synthesis QTLs.

Gene and QTLs

Chromosomal Location

Candidate genes

Pun1 , fw2.1


Kas1 (3-xooacyl-[acyl-carrier-protein] synthase), Acl (acyl carrier protein)



fw3 .1, cap3.1


Kas1 , pAMT(aminotransferase)

cap4 (1, 2), dhc4 (1, 2)


BCAT (branched-chain amino-acid aminotransferase)


FatA (acyl-ACP thioesterase), Ca4H(cinnamic caffeic acid-3-O-methyltransferase)

ndhc7 , cap7 (1, 2),dhc7 (1, 2)


pAMT , 4A1 (acylCoA transferase)


Kas1 , Acl





Although the capsaicin biosynthesis pathway has been established, its genes and enzymes have been poorly characterized. The recent release of genome sequences of pepper and the use of genome-wide transcript profiling such as RNAseq will surely facilitate the elucidation of the genes forming the capsaicinoid pathway.

1. Blum, E., K. Liu, M. Mazourek, E. Y. Yoo, M. Jahn, and I. Paran. 2002. Molecular mapping of the Clocus for presence of pungency in Capsicum. Genome 45: 702-705.
2. Stewart, C., B. C. Kang, K. Liu, M. Mazourek, S. L. Moore, E. Y. Yoo, B. D. Kim, I. Paran, and M. M. Jahn. 2005. The Pun1 gene for pungency in pepper encodes a putative acyltransferase. Plant Journal 42: 675-688

About Author / Additional Info:
I am working as a scientist at Indian Agricultural Research Institute, New Delhi with specialisation in Genetics and Plant Breeding. Basically involved in hot pepper improvement programs.