Abstract:

Chilli is a dicotyledonous flowering plant under the genus Capsicum belonging to the family Solanaceace. A wide variability in chilli with respect to fruit morphology, pungency, bearing habit, and crop duration is found throughout north-eastern India. But the genetic resources of its landraces in the NE region are not well documented which suggests the possibility of finding new alleles and gene combinations. Diverse chilli germ plasm (thirty-eight in number) was collected from different areas of the North-East and grown till maturity. Morphological parameters were taken according to International Board of Plant Genetic Resource, 1983. Apart from morphological markers, 52 SSR primers were also used, out of which 27 were found to be polymorphic. Type specimen viz. Capsicum annuum (variety- Pusa Jwala), Capsicum chinense (variety- COO304), Capsicum frutescens (variety- COO904) obtained from IVRI, Varanasi were used as standard. The number of alleles per locus, major alleles per locus, genetic diversity and polymorphism information content (PIC) were determined using the genetic analysis software, POWER MARKER version 3.25. The number of alleles per locus ranged from 2 to 7 with an average of 3.74. The size of amplicons ranged between 100 and 270 base pairs. The highest number of alleles was detected in microsatellites Hpms116 (7 alleles). The polymorphic information content values (PIC) value ranged from 0.73 to 0.06 per locus with a mean of 0.43. Cluster analysis was done based on the morphological and molecular data according to C.S. Chord 1967. Four clusters were observed in both cases. It was observed that plants having erect fruits clustered together and so was the case with campanulate fruits. Molecular data showed the clustering of Capsicum annuum, Capsicum chinense and Capsicum frutescens together. Mantel test performed to find the correlation between morphological and molecular data revealed a correlation value of 0.26 at p=0.001 which was low but significant at 5% level of probability. The maximum genetic distance calculated according to C.S. Chord 1967 was found to be 0.8 (J-4 and J-40) and minimum to be 0.20 (J-50 and Capsicum frutescens). Percentage variation among populations, within individuals of population and within individuals was found to be were 29.43%, 14.62% and 55.95% respectively indicating diversity in the landraces sampled. The markers used were not able to distinguish the species identity of Capsicum annuum and Capsicum chinense suggesting need for species-specific makers which might not be an easy task as chilli genome is well conserved.