Chilli pepper Genome provides insight into organoleptic sensation
Prasanta K Dash and Rhitu Rai
National Research Centre on Plant Biotechnology (NRCPB), LBS building, PUSA, New Delhi-110012.


Spices and condiments are part of human food as they add taste/aroma to culinary items. It is hard to imagine a dish without these essential ingredients in Indian culinary. Not only in India but worldwide, chilli-referred as 'chilli pepper' is a popular spice for its colour, pungency, flavor and sensory attributes. The whole plant is also grown for aesthetic purposes as an ornamental plant in kitchen garden. Due to its refreshing aroma, palatability and medicinal properties, it is used for pickle preparation, flavouring curries besides being used in home remedies for ailments like gastritis, arthritis and chronic indigestion problems. It is also used as a remedy to summer heat, presumably by inducing perspiration. For instance, capsaicin is known to have anti-inflammatory and antioxidant activities, inhibits obesity by decreasing energy intake, adipose tissue weight and serum triglyceride by stimulation of lipid mobilization. Also, it provides many essential vitamins, minerals and nutrients that have great importance in human health.

Besides individual consumption, food industries heavily rely on this spice to top up colour and flavor of food items such as sauce, ketchup, soups, candies, snacks and bottled carbonated drinks.Pungency is the unique character of this crop and is dependent both on genetic constituency and environmental conditions such as ambient temperature and soil conditions in which the crop is grown. High dose of nitrogen, bright and hot weather coupled with good drainage in soil helps accumulation of higher pungency. Many a times, environmental stresses such as high temperature, water stress (both deficiency and water logging) increase or decrease pungency of this fruit.

As per Guinness book of world records; India holds the record for world's hottest chili variety, "Bhut Jolokia" (Fig 1) that originated and currently being cultivated in northeast region of India which has unique ecological environment with high humidity conditions and regarded as the 'hot spots' of speciation of this variety. It is being grown and consumed in different states of northeast India including Assam, Nagaland, Manipur and Mizoram since ancient times. The organoleptic sensation of this variety is such that one seed of it imparts intense thermal (pain) sensation for 30 min in the mouth. This sensation of chili pepper is due to presence of an alkaloid "Capsaicin" in its seeds. Capsaicin, dihydrocapsaicin and nordihydro-capsaicin constitute the primary capsaicinoids, which are produced exclusively in glands on the placenta of the fruit of chilli and is measured as Scoville heat units (SHU). Thus unit is a measure of the 'hotness' of chilli pepper and the scale is named after Wilbur Scoville who developed the test in 1912. "Bhut Jolokia" is reported to have a rating of 1,001,304 SHU. "Red Savina", previously considered to be the hottest chili and now the second hottest chili of the world has a rating of 577,000 SHUs.

Genomics in chilli

Chilli (Capsicum spp) belongs to the botanical family of solanaceae that includes other important crops such as potato, tomato, brinjal and tobacco. It is a diploid plant with 12 chromosomes having self-pollinating method of seed setting/ propagation. Indian variety Bhut Jolokia is considered to be a natural hybrid of the two species C. frutescens and C. chinense. Genome sequencing of many crop plants [2, 3, 4] recently has been yielding insight into mechanism of many agronomic traits unique to that particular crop [5,6]. Recently, a high-quality genome sequence of a land race of hot pepper C. annuum collected from Mexico provides an evolutionary view into the origin of pungency, distinct ripening process and disease resistance of hot pepper [7]. Previously, this landrace has been extensively used in hot pepper research as it exhibits high levels of resistance to pathogen and nematode attack.

Within Solanaceae family, genome of chilli shares maximum similarity (synteny) with the genome of tomato. The whole-genome sequencing of chilli was accomplished by shotgun sequencing method using Illumina sequencing approach. The size of its genome is now estimated to be 3.48 Gb and found to contain 34,903 protein-coding genes in its genome. Sequence information also revealed presence of multiple "Transposable elements (TEs)" with long terminal repeat (LTR) Gypsy elements and large number of Caulimoviridae elements in the genome7. Despite belonging to the same family, the size of pepper genome is four times bigger than tomato because of accumulation of repetitive elements such as Gypsy LTR transposons.

Biology of pungency in chilli
The pungency in chilli is attributed to presence of secondary metabolites "Capsaicinoids" that are synthesized by capsaicin synthase (CS) and branched-chain amino acid aminotransferase(BCAT). Although, both the genes are found in related tomato and potato genome, differential expression pattern of both genes imparts pungency to chilli while tomato is devoid of it. CS gene primarily expresses in chilli during placenta development at 16d, 25d after-anthesis and in mature green (MG) fruits during which capsaicinoids are synthesized in the placenta. However, the orthologous genes present in tomato and potato are rarely expressed at this stage. These changes in chilli vis a vis potato and tomato imparts organoleptic attributes exclusively to pepper fruits. Genomic comparison for pungent and non-pungent varieties among chilli varieties reveal that non-pungent peppers have a large deletion in CS genes, while pungent varieties have functional full length of CS gene. During placenta development, CS gene is highly expressed only in pungent pepper and was barely expressed in non-pungent pepper. Thus, non-pungent chilli is believed to have evolved from pungent chilli by loss of CS gene [7].

Discovery of genome sequence of hot pepper additionally provides basis for comparative genomics in solanaceae family and opportunity for metabolic engineering of capsaicinoid biosynthesis in chilli. With availability of genome sequence of two related crops tomato and potato, the hot pepper genome will enable advancement of new breeding technologies through the exploration of genome-wide associations and genomic selection studies on horticulturally important traits such as fruit size, yield, pungency, tolerance to abiotic stresses, nutritional content and resistance to multiple diseases in chilli through breeding efforts [8].

Fig 1. "Bhut Jolokia" hottest chilli pepper of the world.


1. Image source - Asit K. ghosh Thaumaturgist

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