Capsicum spp. is the most widely grown solanaceous crop. In worldwide view, the immature fruits, mature red, yellow to purplish, are consumed as vegetables, and dried red ripe fruits are used as a spice. The food industry is the primary user of chillies, where they are used as coloring and flavoring agents in processed products, snacks, candies, soft drinks, and alcoholic beverages (Pino et al., 2007). Oleoresin, a value-added product of Capsicum spp., is used as a food additive for its color and pungency. It is a resin-like viscous material that represents the complete flavor and non-volatile resinous fraction present in the spices. The resinous fraction comprises heat components (capsaicinoids), fixatives, natural antioxidants, and pigments (Sharma and Sharma, 2004). India is a major supplier of spice oil and oleoresin to global markets and earned ≈ 544.42 million (USD) from the export of 21,921 metric tons in 2021–2022 (Spice Board India., 2023). Spice oil and oleoresin account for 16% of the export share of spices in India. Capsaicinoids, a group of active compounds, are responsible for the pungency of the fruits. Among them, capsaicin is the most common capsaicinoid, has several nutraceutical and medicinal properties, and is used to relieve the pain of peripheral neuropathy (Backonja et al., 2008) in topical ointments, nasal sprays, and dermal patches, typically in concentrations between 0.025% and 0.25%. It also possesses antibacterial properties (Dorantes et al., 2000; Koffi-Nevry et al., 2012; Nascimento et al., 2014; El Ksibi et al., 2015) as well as anti-inflammatory and antioxidant activities and can inhibit various cancer cells (Mori et al., 2006; Baek et al., 2008). Furthermore, capsaicin inhibits obesity by decreasing energy intake (Reinbach et al., 2009), adipose tissue weight, and serum triglyceride through stimulation of lipid mobilization (Kawada et al., 1986).

Among the Capsicum spp., hot pepper is known to grow most widely under diverse climatic conditions in India. In North Eastern (NE) India, it is grown as a pure crop under irrigated conditions after the harvesting of rice in the valleys and as a rainfed crop under a mixed cropping system in the Jhum/Shifting cultivation. Moreover, the cropping period of the chillies varied in the region due to the diverse climate. Generally, the sowing period is during mid-February; however, it is January in Mizoram and Barak valleys due to mild winter and February to March in Jhum/shifting cultivation areas in the mid-hills. Out of the 30 species reported in the genus Capsicum, five species (C. annuum L., C. frutescens L., C. chinense Jacq., C. baccatum L., and C. pubescens R. and P.) are popular among them (Bosland and Votava, 2000). Previously, C. annuum (hot pepper and sweet pepper) was mainly grown for its fresh consumption, cooking, and processed products, like a dry powder for color and pungency in cooking (Selvakumar et al., 2022). Over a while, the other species of Capsicum have also gained importance, mainly due to their high oleoresin and capsaicin content, in the food and pharmaceutical industries in both domestic and international markets. The NE region of India comprises eight states with diverse agro-ecological conditions and is considered one of the richest reservoirs of flora and fauna as part of the Indo-Myanmar biodiversity hotspot, one of the 36 biodiversity hotspots recognized around the world (Myers et al., 2000). In the region, besides commercial cultivars of hot and sweet pepper (C. annuum), there are popular landraces, i.e., king-chilli/bhut jolokia (C. chinense), bird’s eye chilli (C. frutescens), dalle-khursani chilli/dalle-chilli, and cherry chilli (C. annuum) grown widely under different ecology and cropping systems. The capsaicin content of king-chilli and bird’s eye chilli has been reported to be the highest when grown in their niche areas compared to other country places (Tiwari et al., 2005; Verma et al., 2020). Furthermore, king-chilli has been found to be the most economical crop with higher (> 4.0) benefit-cost ratio over other high-value crops such as tomato, capsicum, and cucumber grown under protected conditions (Verma et al., 2018a). Botanically, king-chilli is considered C. chinense (Malakar et al., 2019). However, based on molecular analysis, king-chilli has been reported as a natural interspecific hybrid between C. chinense and C. frutescens (Bosland and Baral, 2007; Purkayastha et al., 2012; Kehie et al., 2016) in their niche areas, and seeds have erratic germination behavior as compared to other species (Verma et al., 2018b). Dalle-Khursani chilli, a winter-hardy, tall, and perennial Capsicum annuum, is grown widely in the mid-hills of Sikkim and Darjeeling (West Bengal), Nepal, and Bhutan. Based on agro-morphological traits, this species differs from other Capsicum spp (Jha et al., 2017). Furthermore, bird’s eye chilli (C. frutescens) is another prevalent species, grown in the entire eastern Himalayas of India. It is mainly grown in backyards and Jhum lands (shifting cultivation), and maximum diversity has been reported in Mizoram, Manipur, and Meghalaya (Dutta et al., 2017). Based on the landraces’ diversity, ecology, and quality traits, the geographical indications (GIs) tag has been granted to Nagaland for king-chilli (2008), Sikkim for dalle-chilli (2020), and Mizoram state for bird’s eye chilli (2023) by the government of India. Today, there are different value-added products processed and marketed commercially for these species under a particular brand, such as “Sikkim Supreme” pickles of dalle-chillies.

Diverse genetic resources are essential for crop improvement (Maxted et al., 2008; Maxted and Kell, 2009; Perrino and Wagensommer, 2021; Perrino and Wagensommer, 2022; Accogli et al., 2023). The region, in spite of having potential genetic diversity in the landraces of Capsicum spp., is yet to be efficiently utilized. Moreover, there is a need for systematic study on diversity, ecology of the landraces, evolution, and phylogenetic relationships, especially in popular landraces such as king-chilli and dalle-chilli. The genetic characterization of some Capsicum spp. has been previously carried out using agro-morphological and quality attributes (Dutta et al., 2017; Vaishnavi et al., 2018), cytogenetics (Jha et al., 2017), and different generations of markers such as sodium dodecyl-sulfate polyacrylamide gel electrophoresis (Mena et al., 2019); randomly amplified polymorphic DNA (RAPD) markers (Bosland and Baral, 2007), simple sequence repeats (SSR) markers (Adluri et al., 2017; Colney et al., 2018; Baruah et al., 2019), and internal transcribed spacer sequence of nuclear ribosomal DNA (Purkayastha et al., 2012); and sequencing of the ribosomal RNA (rRNA) gene-internal transcribed (ITS) region (Kehie et al., 2016). Due to genome-wide coverage, robust and high reproducibility, co-dominant inheritance, high polymorphism with multiple alleles per locus, and transferability between species, SSR markers have been widely used in fingerprinting, analysis of genetic diversity and population structure, association mapping, and linkage mapping (Lee et al., 2004; Minamiyama et al., 2006; Mimura et al., 2012; Yumnam et al., 2012; Sugita et al., 2013; Dhaliwal et al., 2014; Lee et al., 2016; Adluri et al., 2017; Colney et al., 2018; Baruah et al., 2019; Pereira-Dias et al., 2019; Solomon et al., 2019). Keeping the above facts in view, the present investigation was conducted to study the ecology of the GIs tags and other local landraces of Capsicum spp.; to study the genetic diversity and phylogenetic relationships in landraces of Capsicum spp. grown in the region based on SSR markers; to identify high-yielding genotypes; and to analyze economically important traits such as capsaicin and oleoresin content in superior genotypes.

The NE region of India is considered one of the biodiversity hotspots globally (Thamburaj and Singh, 2003; Adluri et al., 2017; Colney et al., 2018; Vaishnavi et al., 2018; Baruah et al., 2019; Mena et al., 2019) and has diverse climatic ranges, from tropical to alpine (Verma et al., 2023). Capsicum spp. has wider adoptability and is grown throughout the country. The GI tag landraces of the region are known for their distinct agro-morphological characteristics and unique quality traits, performing well in a particular niche area. This is due to the favorable agro-climatic conditions of the region, which comes under a humid subtropical climate with relative humidity (81.2%–91.5% in the morning and 52.6%–81.8% in the evening) during the crop period. The results of the CCA have also shown the significant relationship between the climatic variables (temperature) of the niche area with landraces and the quantitative traits. The landraces of cool to mild-warm climate were differentiated from the landraces adapted to warm climatic conditions. The ecology of the niche area of dalle-chillies (C. annuum) is characterized by a cool and humid climate during the crop period (March to October). Compared to other landraces, dalle-chilli is adapted to low temperatures and goes dormant during the winter, when the average minimum temperature is 2.9°C–6.3°C in their niche area. Likewise, the niche area (Nagaland, Assam, and Manipur) of landrace king-chilli has shown mildly warmer than the weather parameters of a niche area of dalle-chilli. We could also observe poor fruit setting (< 43.3% ± 4.2%) under weather conditions (mint < 8.0°C; maxT < 23.5°C; minRH = 48.8%; maxRH = 72.3%) at our experimental farm during the winter. Under these conditions, the fruits even after fruit sets failed to develop; remaining small, red-colored fruits without seeds and this could be due to a lack of pollination and fertilization. Similarly, the climate of the niche area of bird’s eye chilli (C. frutescens) is characterized by a cool to warm and humid climate (Mizoram, Manipur, and Meghalaya), during the cropping period. The range of weather parameters (temp) has shown comparatively, the wider adoptability of the bird’s eye chillies over the king-chillies (C. chinense) and dalle-chillies (C. annuum). Due to its wider adaptability, it is also grown in other parts of the country, such as Kerala, Karnataka, Maharashtra, and Andhra Pradesh under the warm and humid climatic conditions (Thamburaj and Singh, 2003). The yield and quality of Capsicum spp. are highly influenced by genotype and environment (Tiwari et al., 2005; Gurung et al., 2012); hence, these landrace can be grown year-round under protected conditions by maintaining the growing environments of their niche area during the cropping period, and there is also a possibility for area expansion to other parts of the world having similar agro-climatic conditions.

A wider variability was observed for fruit color, shape, and size of leaves and fruits, as well as other yield attributes, especially in the niche area of the landraces. This may be due to adaptability to the varied climate of the region, natural crossings, and selection. Similarly, the broader variability in niche area was also reported earlier in bird’s eye chilli (C. frutescens) (Dutta et al., 2017; Vaishnavi et al., 2018; Santhosha et al., 2019) and king-chilli (C. chinense) (Bhagowati and Changkija, 2009). The GCV is an accurate indicator of the extent of genetic variability in the population. Our study exhibited that all the quantitative traits had a slightly higher PCV than the GCV, indicating the influence of some degree of the environment on the phenotypic expression of these characters. It suggests that selection based on all these traits would be helpful for future crossing programs. Furthermore, all the traits showed high heritability coupled with high GA, except for leaf length, which indicates the strong influence of an additive gene on these traits is under action. Hence, simple selection based on the phenotypic performance of these traits would be more effective and efficient. The findings are in congruence with those reported earlier in Capsicum spp (Manju and Sreelathakumary, 2002; Pandiyaraj et al., 2017; Solomon et al., 2019). Fruit size is an important economic trait; for export, large fruit sizes usually fetch premium prices, especially in king-chilli (C. chinense), bird’s eye chilli (C. frutescens), and dalle-chilli (C. annuum). Hence, genotypes SKCC-5 and SKCC-4 of dalle-chilli, King-chilli-4 and King-chilli-1 of king-chilli, and MZBEC-13 and MLCC-2 of bird’s eye chilli having large fruit sizes could be promoted for the export market. Furthermore, fruit length, diameter, weight, number of fruits per plant, and yield in Capsicum spp. are governed by additive gene action and responsive to selection (Manju and Sreelathakumary, 2002; Rosmaina et al., 2016; Singh et al., 2017), and the superior genotypes for these traits can be used for future hybridization and selection. Moreover, identified high-yielding genotypes of the dalle-chilli (SKCC-7, SKCC-5, and SKCC-1), king-chilli (King-chilli-1 and King-chilli-4), cherry chilli (MLCC-34), bird’s eye chilli (MZBEC-13, MZBEC-1, and MLCC-1), hot pepper (MLCC-36, ASCC-2, NLCC-4, and NLCC-10), and sweet pepper (California Wonder) can be promoted for commercial production.

Our results of molecular analyses have shown the presence of wider genetic diversity among the accessions of Capsicum spp. This high diversity has also been proven by the higher (4.89) average number of alleles per locus as compared to 2.78 and 3.5 alleles per locus reported by Dhaliwal et al. (2014) and Hanácek et al. (2009), respectively. PIC estimates the discriminating power of a marker by taking into account the number of alleles at a locus and the relative frequencies of these alleles. The PIC value depends on the genetic diversity among the populations. The present study showed the PIC value varied (0.20–0.85) with an average of 0.61, which was greater than the value reported by many researchers (Minamiyama et al., 2006; Yumnam et al., 2012; Sharmin et al., 2018) but lower than the value of 0.76 described by Lee et al. (2016) from diverse Caspsicum spp. According to Xie et al. (2010), high, medium, and low locus polymorphisms are defined as PIC > 0.5, PIC 0.25–0.5, and PIC < 0.25, respectively. Accordingly, PIC in our investigation indicated a wider genetic base due to high locus polymorphism. The results of a higher PIC value coupled with a higher Shannon information index also prove the locus diversity in the population.

Capsicum spp. is considered an often cross-pollinated crop; 25 SSR loci have shown heterozygosity among the genotypes. The extent of genetic variations is also measured as the amount of actual or potential heterozygosity existing in the population. The observed heterozygosity was lower than the expected value, showing a departure from HWE and the possibility of inbreeding for a long time under different geographical conditions due to natural barriers and isolation, which could be attributed to the interplay of different factors such as artificial selection, selective collection, non-random mating between individuals, population structure and size, and the Wahlund effect, i.e., mixing of individuals from different genetic sources (Johnson and Black, 1984; Hernández-Verdugo et al., 2001). Similarly, Lee et al. (2016) also observed lower values for observed heterozygosity in four domesticated species (C. annuum, C. baccatum, C. chinense, and C. frutescens) and two wild species (C. chacoense and C. eximium), whereas C. cardenasii, C. galapagoense, C. pratermissum, C. pubescens, and C. tovarii had relatively higher values.

From cluster analysis, the landraces bird’s eye chilli (C. frutescens) and king-chilli were found to be closer to each other in our study. Pereira-Dias et al. (2019) also reported kinship between C. chinense and C. frutescens. However, landraces of dalle-chilli (C. annuum) were found closer to hot pepper and sweet pepper (C. annuum). Colney et al. (2018) also reported a close association between C. annuum and dalle-chilli, whereas Cheng et al. (2016) found Capsicum annuum closer to C. frutescens than C. chinense. Furthermore, cherry-chilli (C. annuum) genotypes (MLCC-34 and MLCC-35) clustered together with landraces of dalle-chilli (SKCC-1 to SKCC-8) and were found closer to C. annuum. This indicates that the landrace dalle-chilli, an allotetraploid (Jha et al., 2017), evolved as a naturally fertile C. annuum. In contrast, Indira and Abraham (1977) reported sterility in tetraploid C. annuum developed through induced mutation. Among the genotypes of commercial cultivars of both C. annuum (hot and sweet pepper), they were found to be closer to each other in their respective groups. Among the populations based on pair-wise Nei genetic distance, the maximum genetic distance (1.30) was observed between king-chilli (C. chinense) and bird’s eye chilli (C. frutescens), followed by king-chilli and sweet pepper (1.27) and dalle-chilli and sweet pepper. The maximum genetic distance between the landraces may be due to associated with different geographical origins, poor cross-compatibility (Martins et al., 2015), and selection and polyploidy in dalle-chilli. While the least genetic distance was between hot pepper and sweet pepper, this could be due to free gene flow among the C. annuum (hot pepper and sweet pepper) genotypes.

The results of both AMOVA and Gst analyses have confirmed the presence of wider diversity within and between the populations of Capsicum spp. The results of model-based clustering using STRUCTURE 2.3.4 agreed with Nei’s genetic distance-based clustering, PCoA, and multiple correspondence analyses. Among the genotypes, the proportions of genotypes with admixture were few, possibly due to the different geographical origins. The admixture in landraces of hot pepper (C. annuum) and king-chilli (C. chinense) may be due to free natural gene flow between them, hybridization, and selection. Due to open pollination and selection in different ecogeographic regions, variability is maintained. Gu et al. (2019) also observed the genetic differentiation in the Capsicum genotypes for fruit type and geographical distribution. Landrace king-chilli is considered as an interspecific hybrid between C. chinense and C. frutescens based on molecular analysis (Bosland and Baral, 2007; Verma et al., 2018a; Malakar et al., 2019). In our study, the structure analysis has shown admixture between king-chilli (C. chinense) and bird’s eye chilli (C. frutescens). This could be due to the closeness and cross-compatibility between C. chinense and C. frutescens (Nicolaï et al., 2013). Moreover, the presence of calyx teeth in king-chilli morphologically differentiates it from C. chinense. Furthermore, landrace dalle-chilli (C. annuum) constituted a separate group with the least admixture and was found to be closer to C. annuum. However, based on flower characters, i.e., light yellow-green corolla and teeth on the calyx, indicate closeness to C. frutescens and differentiation from C. chinense. Jha et al. (2017) reported dalle-chilli as an allopolyploid with an absolute difference from the diploid members of C. annuum. The genetic similarity with C. annuum and morphological similarity with C. frutescens indicate that dalle-chilli probably evolved naturally as an interspecific hybrid between C. annuum and C. frutescens.

Comparatively, among the selected landraces, king-chilli (C. chinense) and dalle-chilli (C. annuum) were found to be superior for economically important traits, capsaicin, and oleoresin content, over the bird’s eye chilli (C. frutescens) and hot pepper (C. annuum). Similar findings were also observed by Mini (Pandey et al., 2008) and Jyoti et al (Mini, 1997). in different Capsicum species. These superior landraces can be promoted for commercial production in their niche areas for value-added products like oleoresin and capsaicin extraction and further export to international markets.

Our study showed that certain pockets of the NE region are a center of the evolution and hot spot of unique GI tag landraces (king-chilli, C.chinense; bird’s eye chilli, C. frutescens; and dalle-chilli, C. annuum) of the Capsicum species. The evolution of these landraces occurs through natural interspecific hybridization and selection and is adapted to the different ecology of the region, characterized as cool-humid and moderately warm-humid climates for dalle-chilli (C. annuum) and king-chilli (C. chinense), respectively. The climatic variables (temperature) have shown significant impact on agro-morphological traits and adoptability of the landraces to their niche areas of the region. Both quantitative traits and molecular analysis have shown wider variability for traits and diversity within and between the groups. High heritability and GA for all the fruit traits have also indicated that these traits are highly responsive to selection. The molecular analyses and flowering features of landrace king-chilli (C.chinense) also suggested that it was more closely related to bird’s eye chilli (C. frutescens), confirming their evolution in the niche area (Nagaland, Manipur, and parts of Upper Assam) as an interspecific hybrid between C. chinense and C. frutescens. Dalle-chilli (C. annuum) was reported as an allotetraploid species and was found to be genetically closely related to C. annuum. Considering the flower traits, dalle-chilli probably originated from the natural cross between C. annuum and C. frutescens in the niche area of Sikkim and West Bengal. Dalle-chilli, a winter-hardy landrace that is also grown as a perennial crop in backyards, can be utilized in varietal development programs against abiotic stresses like low temperatures and frost. Furthermore, the identified superior genotypes among the landraces can be promoted for in situ conservation, production, value addition, and sources of desirable genes in niche areas as well as in suitable climatic conditions in other parts of the country and world.

The original contributions presented in the study are included in the article/ Supplementary Material . Further inquiries can be directed to the corresponding author.

VV: Writing – original draft, Supervision, Software, Resources, Methodology, Investigation, Formal analysis, Data curation, Conceptualization. AP: Writing – review & editing, Visualization, Software, Investigation, Formal analysis, Data curation. AT: Writing – review & editing, Resources. HR: Writing – review & editing. ND: Writing – review & editing, Data curation. AK: Writing – review & editing, Formal analysis. TB: Writing – review & editing, Resources. AJ: Writing – review & editing, Supervision, Investigation. VM: Writing – review & editing, Resources.