A genome-wide resource of intron spanning primers compatible for quantitative PCR and intron length polymorphism in rice Ram Hasthi, Singh Bikram Pratap1, Katara Jawaharlal2, Chopra Radha, Kumar Pankaj, Jaiswal Rajdeep, Geetika, Deshmukh Rupesh**, Sonah Humira* National Agri-Food Biotechnology Institute (NABI), Mohali, India 1National Research Centre on Plant Biotechnology, New Delhi 2National Rice Research Institute, Cuttack, Odisha *Corresponding author's e-mail: biohuma@gmail.com
**rupesh0deshmukh@gmail.com
Online published on 12 September, 2019. Abstract Whole genome sequence availability in rice has provided several advantages for genomics as well as other omics assisted applications. Genome-wide molecular markers are one of such availability that has exceptional importance in modern plant breeding. In the present study, a resource of intron-spanning primers (ISPs) was developed using whole genome sequence information of two rice subspecies, japonica (cv. Nipponbare) and indica (cv. 93–11). The ISPs were designed in a way that the PCR using a cDNA template will yield 60 to 100 base pair size amplicon ideal for the quantitative PCR analysis. Whereas, PCR using genomic DNA will amplify the introns, which are more prone to sequence variation. The sequence variation in the intron serves as an excellent marker resource. The application of ISPs was demonstrated by characterizing 12 diverse rice cultivars. A total of eight out of ten ISPs were found to be polymorphic. The resource will be helpful for the rice molecular biologist and breeder community. Top Keywords Gene-specific marker, gene expression analysis, informative marker, rice genome, sequence variation. Top |