Evaluation of Genetic Diversity of Chilli Landraces from North Eastern India Based on Morphology, SSR Markers and the Pun1 Locus

The chilli (Capsicum sp.) germplasm found throughout North Eastern (NE) India exhibits wide variability in fruit morphology, pungency, bearing habit and crop duration. As the genetic resources of chilli landraces from this region are not well documented, it is likely that they have hitherto unknown alleles and/or genes for economically important traits. In this study, 53 chilli accessions from different areas of this NE region were evaluated for genetic diversity using various morphological characters and 50 simple sequence repeat markers. It was found that erect and campanulate fruit types are grouped in separate clusters. The number of alleles per locus ranged from 3 to 9 with an average of 5.36. The average polymorphic information content value was 0.52. Percentage variation among populations, within individuals of population and within individuals was found to be 34, 57.9 and 8.05 %, respectively, indicating diversity in the landraces sampled. Allele mining across acyltransferase 3 (AT3) gene in a set of landraces led to identification of new single nucleotide polymorphisms (SNPs). Sequence analysis of the 2,349 bp AT3 region revealed the presence of a total of 79 SNPs and 3 indels. This overview of diversity of chilli landraces from NE India paves the way for conservation and utilisation of germplasm and contributes to the development of systematic breeding strategies.