Identification of allele specific primers in chir pine (<em>Pinus roxburghii</em> Sarg.) through data mining

Abstract

<em>Pinus roxburghii Sarg</em>. commonly known as Chir pine, is a commercially exploited species for resin in India. Resin is a phenotypic trait which is expressed only in mature trees. Due to this a large number of trees are cut every year which pose a serious ecological threat. Recent advancements in bioinformatics and molecular biology have enabled scientists to identify high resin yielding pine genotypes at nursery stage using molecular markers. In the present study, investigation, 337 terpene coding sequences from the database were analyzed using data mining and 45 microsatellites allele specific primers were designed for marker assisted selection. Out of these 45 primers, only 22.2% primer pairs showed polymorphism within the 53 genotypes of Chir pine examined. A wide range of fragment size was observed from 100 - 600 bp. PCR amplification using allele specific markers produced a total of 22 bands, out of which 14 were found to be polymorphic. The total number of bands amplified per marker varied from of 1 to 3 with an average of 1.4. Genetic divergence in terms of percent polymorphism ranged from 50 to 100% with a mean of 63.3% per marker.