Plant Molecular Biology Reporter

, Volume 30, Issue 6, pp 1470–1479

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

  • Julia S. Yumnam
  • Wricha Tyagi
  • Avinash Pandey
  • N. Tombisana Meetei
  • Mayank Rai
Original Paper

DOI: 10.1007/s11105-012-0466-y

Cite this article as:
Yumnam, J.S., Tyagi, W., Pandey, A. et al. Plant Mol Biol Rep (2012) 30: 1470. doi:10.1007/s11105-012-0466-y

Abstract

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.

Keywords

ChilliNorth eastern IndiaGenetic diversityAT3Single nucleotide polymorphism

Supplementary material

11105_2012_466_MOESM1_ESM.xls (22 kb)
Supplementary Table 1List of chilli genotypes with geographical distribution used in the current study (XLS 22 kb)
11105_2012_466_MOESM2_ESM.xls (26 kb)
Supplementary Table 2List of edited morphological descriptors used in the current study (XLS 25 kb)

Copyright information

© Springer-Verlag 2012

Authors and Affiliations

  • Julia S. Yumnam
    • 1
  • Wricha Tyagi
    • 1
  • Avinash Pandey
    • 2
  • N. Tombisana Meetei
    • 1
  • Mayank Rai
    • 1
  1. 1.School of Crop Improvement, College of Post Graduate StudiesCentral Agricultural UniversityUmiamIndia
  2. 2.Division of Crop ImprovementIndian Council of Agricultural Research Complex for North Eastern Hill RegionUmiamIndia