Development and Utilization of SSRs to Estimate the Degree of Genetic Relationships in a Collection of Pearl Millet Germplasm

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Abstract
Pearl millet [Pennisetum glaucum (L.) R. Br.] cultivars derive from a narrow gene pool, and studies of genetic diversity in Pennisetum germplasm suggest promising opportunities for the use of undomesticated materials for improving pearl millet varieties. However, efficient utilization of wild germplasm will require effective DNA marker‐based fingerprinting strategies for rapid assessment of genetic relationships. The present study aims at development and utilization of a collection of microsatellite (SSR, simple sequence repeat) markers for assessing the genetic diversity of 53 lines of millet. A small insert genomic library was screened with a (CT)15 oligonucleotide probe. A total of 34 (CT)n–containing clones were identified, and specific primers were designed for 18 of these. Of 18 new microsatellites developed as a part of this work, 11 were used to estimate the genetic diversity, along with 19 from other sources. Cluster analysis by the unweighted pair‐group method with arithmetic averages (UPGMA) showed two major and eight minor clusters, suggesting that the millet germplasm could readily be distinguished by UPGMA. The coefficients of genetic distance among germplasm lines were high and averaged D = 0.60 (range 0.28–0.92). Genetic diversity averaged 0.38. These results demonstrated that genotypes with potential traits are maximally different from the cultivated gene pool and could readily be distinguished. Development and utilization of polymerase‐chain‐reaction‐(PCR)‐based markers such as SSRs is a valuable asset for estimating genetic diversity, the identification of unique genotypes as potentially important new sources of alleles for enhancing important characteristics, and analyzing the evolutionary and historical development of cultivars at the genomic level in pearl millet breeding programs.