Analysis of genetic diversity and its stratification in pigeonpea germplasm using BES-derived microsatellite markers

Abstract

<span style="mso-ansi-language:EN-IN">Microsatellites have become the today’s markers of choice for molecular breeding and genome studies for their high polymorphism and transferability across related genera. The present study was conducted to analyze the genetic diversity in 58 pigeonpea accessions including 7 wild relatives using BAC (bacterial artificial chromosome)-end sequences derived simple sequence repeat markers. A total of 40 BES (BAC-end sequences)-SSR markers were characterized for diversity related parameters to identify most polymorphic markers. The cluster analysis based on Nei’s genetic distance coefficients grouped all genotypes into 3 clusters. The wild species were placed in a separate cluster, while the clustering pattern revealed no relationship between geographic origin and genetic diversity. Test for Hardy Weinberg equilibrium resulted in identification of 4 SSRs, which were not under population equilibrium and hence were not used in further diversity analyses. In order to test the degree of differentiation of the accessions from different regions of India, analysis of molecular variance (AMOVA) was conducted. <span style="mso-ansi-language:EN-IN">The value of Fst across groups was observed to be 0.17, indicating moderately high differentiation among groups. The population diversity measures were calculated using POPGEN32 software. The results clearly indicated the presence of higher genetic diversity in peninsular and northern regions compared to in north-western and northern plains. Analysis across the four eco-geographic regions indicated presence of highest number of alleles per locus (2.550<u>+</u>0.904) for peninsular India (Andhra Pradesh & Maharashtra), followed by northern region (2.350<u>+</u>0.893). The statistics developed for the BES-SSR markers will be useful for selection of most informative marker sets for genetic diversity analysis, <span style="mso-ansi-language:EN-IN">for tagging genes for biotic or abiotic stress resistance and mapping of important agronomical traits in pigeonpea.<span style="font-size:10.0pt;mso-bidi-font-size:9.0pt" lang="EN-US">

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