The genetic improvement program of the Seed Technology Training and Development Center works on the agronomic characterization and the content of bioactive compounds in eight genotypes of habanero pepper. The objective is to select genotypes with good agronomic performance that allow the generation of inbred lines to obtain hybrids. In this study, the agronomic performance and the content of bioactive compounds (capsaicinoids, polyphenols, and antioxidant capacity) were evaluated in eight genotypes of habanero pepper grown in the southeast of Coahuila, Mexico, identified as HNC-1, HNC-2, HNC-3, HNC-4, HNC-5, HNC-6, HNC-7, and HCC-8. The plants were grown in a greenhouse for 127 days, under a completely randomized design with four replications each. The results revealed that the yield (g·plant−1) and number of fruits per plant did not show significant differences between genotypes. However, for the fruit length, the genotypes HCC-8, HNC-7, HNC-6, and HNC-5 stood out with over 40 mm, while in equatorial diameter of the fruit, HCC-8, HNC-4, and HNC-2 stood out with 26.45, 26.46, and 25.12 mm, respectively. The results of the chemical analyses allowed us to identify that HNC-5 and HNC-6 had the highest capsaicin concentration (931.38 and 959.77 mg·kg−1), dihydrocapsaicin (434.95 and 445.89 mg·kg−1), Scoville Heat Units greater than 210,000, total phenols (67.54 and 71.15 mg/100 g) and total flavonoids (34.21 and 38.29 mg/100 g), respectively. The HNC-1 and HNC-6 genotypes had the highest carotenoids concentration with 103.96 and 105.07 mg/100 g, and HCC-8 registered the highest anthocyanin content with 22.08 mg C3GE/100 g. The antioxidant capacities showed significant differences (p ≤ 0.05) between genotypes, with a range of 43.22 to 110.39 µmol TE/100 g, 72.37 to 186.56 µmol TE/100 g, and 191.41 to 244.98 µmol TE/100 g for the tests of DPPH (2,2-diphenyl-1-picrylhydrazyl), ABTS (2,2′azino-bis(3-ethylbenzothiazoline-6-sulfonic acid)), and FRAP (ferric reducing antioxidant power). The results of this research will be used to select habanero pepper genotypes that can be used in genetic improvement programs to increase the productive potential and the content of bioactive compounds in the fruits to expand their applications in the food industry.
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